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Cited by 367Metalloenzymes and iron-sulfur proteinsAnaerobic Digestion and Biogas ProductionAlgal biology and biofuel production

Cyanobacterial hydrogenases: diversity, regulation and applications

Open access
Tamagnini, Paula, Leitão, Elsa, Oliveira, Paulo, Ferreira, Daniela, Pinto, Filipe, Harris, David James, Heidorn, Thorsten, Lindblad, Peter·2007·FEMS Microbiology Reviews
DOI 10.1111/j.1574-6976.2007.00085.x
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Abstract

Cyanobacteria may possess two distinct nickel-iron (NiFe)-hydrogenases: an uptake enzyme found in N(2)-fixing strains, and a bidirectional one present in both non-N(2)-fixing and N(2)-fixing strains. The uptake hydrogenase (encoded by hupSL) catalyzes the consumption of the H(2) produced during N(2) fixation, while the bidirectional enzyme (hoxEFUYH) probably plays a role in fermentation and/or acts as an electron valve during photosynthesis. hupSL constitute a transcriptional unit, and are essentially transcribed under N(2)-fixing conditions. The bidirectional hydrogenase consists of a hydrogenase and a diaphorase part, and the corresponding five hox genes are not always clustered or cotranscribed. The biosynthesis/maturation of NiFe-hydrogenases is highly complex, requiring several core proteins. In cyanobacteria, the genes that are thought to affect hydrogenases pleiotropically (hyp), as well as the genes presumably encoding the hydrogenase-specific endopeptidases (hupW and hoxW) have been identified and characterized. Furthermore, NtcA and LexA have been implicated in the transcriptional regulation of the uptake and the bidirectional enzyme respectively. Recently, the phylogenetic origin of cyanobacterial and algal hydrogenases was analyzed, and it was proposed that the current distribution in cyanobacteria reflects a differential loss of genes according to their ecological needs or constraints. In addition, the possibilities and challenges of cyanobacterial-based H(2) production are addressed.

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Crossref · 10.1111/j.1574-6976.2007.00085.x

Cites

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Claims the paper makes

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  • Findingcitation

    Analysis of available genomes revealed ORFs whose products could potentially anchor the HupSL heterodimer to the membrane.

    “In fact, analysis of the available genomes revealed the presence of ORFs whose products could potentially fulfill this anchoring role (Lindberg, 2003).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Lindberg, 2003

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  • Findingown data

    HupL generally has 531 aa.

    “while HupL generally has 531 aa”
    Quote in the paperNot a substantial claim
  • Findingown data

    In HupS, the number of residues is constant at 320 aa in all known cyanobacteria.

    “analysis of the predicted proteins demonstrates that in HupS the number of residues in all known cyanobacteria is constant (320 aa)”
    Quote in the paperNot a substantial claim
  • Findingnone given

    In all cyanobacterial genomes sequenced to date and in the Chloroflexus genome, the hup and hox operons are widely separated on the chromosome, making simultaneous gene transfer unlikely.

    “In all cyanobacterial genomes sequenced to date, and in the genome of Chloroflexus, the two hydrogenase operons -hup and hox -are widely separated on the chromosome, rendering simultaneous gene transfer unlikely.”
    Quote in the paperSubstantial claim
  • Findingown data

    Both analyses gave widely congruent estimates of phylogeny.

    “Both analyses gave widely congruent estimates of phylogeny (Fig. 6).”
    Quote in the paperNot a substantial claim
  • May combine two claims. 129
  • Classified as probably not a substantial claim. 51

  • May combine two claims.

    Findingown data

    Analysis of available cyanobacterial genomic sequences showed that the position and orientation of hoxW in the chromosome varies, but in most cases hoxW lies downstream of hoxH.

    “Similar to what happens for hupW, analysis of the available cyanobacterial genomic sequences revealed that the position and orientation of hoxW in the chromosome is also variable but, in most of the cases, hoxW is downstream of hoxH, one of the bidirectional hydrogenase structural genes (Fig. 2).”
    Quote in the paperNot a substantial claim

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    Findingown data

    The three heterocystous strains form a clade with 100% support, separated from the nonheterocystous strains by 16-21% divergence.

    “The three heterocystous strains form a clade with 100% support, separated from the nonheterocystous strains by between 16% and 21% divergence.”
    Quote in the paperNot a substantial claim

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    Findingown data

    Within the nonheterocystous strains, two pairs of taxa-Cyanothece with Crocosphaera and the two Lyngbya species-are well supported.

    “Within the nonheterocystous strains, two pairs of taxa -Cyanothece with Crocosphaera and the two Lyngbya species are well supported.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    Not all amino acid sequences of hydrogenase accessory proteins are available for all species analyzed for the uptake hydrogenase structural genes.

    “Further, not all of the amino acid sequences of hydrogenase accessory proteins are available for all the species analyzed for the uptake hydrogenase structural genes.”
    Quote in the paperNot a substantial claim

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    Interpretationnone given

    The bidirectional hydrogenase encoded by hoxEFUYH probably functions in fermentation and/or as an electron valve during photosynthesis.

    “the bidirectional enzyme (hoxEFUYH) probably plays a role in fermentation and/or acts as an electron valve during photosynthesis”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Cyanobacteria can contain two different NiFe hydrogenases: an uptake enzyme in N2-fixing strains and a bidirectional enzyme in both non-N2-fixing and N2-fixing strains.

    “Cyanobacteria may possess two distinct nickel-iron (NiFe)-hydrogenases: an uptake enzyme found in N 2 -fixing strains, and a bidirectional one present in both non-N 2 -fixing and N 2 -fixing strains.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Tamagnini et al., 2002

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    • cites Tamagnini et al., 2005

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisenone given

    Both cyanobacterial hydrogenases are NiFe enzymes.

    “Both cyanobacterial hydrogenases are NiFe enzymes, which are the most common hydrogenases found in bacteria and Archaea.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    Cyanobacteria and green algae are the only organisms known so far that can perform both oxygenic photosynthesis and hydrogen production.

    “Cyanobacteria and green algae are the only organisms known so far that are capable of both oxygenic photosynthesis and hydrogen production.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    The biosynthesis and maturation of NiFe hydrogenases is highly complex and requires several core proteins.

    “The biosynthesis/ maturation of NiFe-hydrogenases is highly complex, requiring several core proteins.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The core NiFe hydrogenase is an ab heterodimer; the large subunit contains the bimetallic active site and the small subunit contains FeS clusters for electron transfer.

    “The core enzyme consists of an ab heterodimer with the large/a subunit hosting the bimetallic active site, and the small/b-subunit containing the FeS clusters, which function as electron transfer domains between the electron acceptors/donors and the catalytic center of the enzyme (Fig. 1).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Vignais et al., 2001

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    • cites Vignais & Colbeau, 2004

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisenone given

    In cyanobacteria, hyp genes and genes presumably encoding hydrogenase-specific endopeptidases hupW and hoxW have been identified and characterized.

    “In cyanobacteria, the genes that are thought to affect hydrogenases pleiotropically (hyp), as well as the genes presumably encoding the hydrogenasespecific endopeptidases (hupW and hoxW) have been identified and characterized.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    The H2 produced by nitrogenase is rapidly consumed by an uptake hydrogenase, which is found in almost all N2-fixing cyanobacteria examined, with one reported exception, Synechococcus sp. BG 043511.

    “The H 2 produced by the nitrogenase is rapidly consumed by an uptake hydrogenase, an enzyme that has been found in almost all the N 2 -fixing cyanobacteria examined so far, with one reported exception -Synechococcus sp.BG 043511 (Ludwig et al., 2006).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Ludwig et al., 2006

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    Interpretationcitation

    Physiological and biochemical data indicate the uptake hydrogenase is membrane-bound, and hydropathy profiles of HupL and HupS show no transmembrane domains, suggesting an anchoring polypeptide.

    “Because the physiological and biochemical data point to a membrane-bound enzyme (Houchins & Burris, 1981b;Houchins, 1984;Lindblad & Sellstedt, 1990;Rai et al., 1992), and the hydropathy profiles of the HupL and the HupS proteins do not indicate any transmembrane domains (Tamagnini et al., 2005), the existence of a polypeptide that anchors the HupSL heterodimer to the membrane seems likely.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Houchins & Burris, 1981b

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    • cites Houchins, 1984

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    • cites Lindblad & Sellstedt, 1990

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  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    NiFe hydrogenases are divided into four groups; cyanobacterial uptake hydrogenases cluster with group 2 cytoplasmic H2 sensors, and bidirectional enzymes belong to group 3.

    “In general, the NiFe hydrogenases are divided into four groups, with the cyanobacterial uptake hydrogenases clustering together with the cytoplasmic H 2 sensors of group 2, and the bidirectional enzymes belonging to group 3 comprising the bidirectional heteromultimeric cytoplasmic hydrogenases”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Vignais et al., 2001

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    • cites Vignais & Colbeau, 2004

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  • May combine two claims.

    Premisenone given

    The cyanobacterial uptake hydrogenase is found exclusively in N2-fixing strains, is encoded by hup genes, and is at least a heterodimer with HupL about 60 kDa containing the active site and HupS about 35 kDa involved in electron transfer.

    “The cyanobacterial uptake hydrogenase, found exclusively in N 2 -fixing strains and encoded by the hup -hydrogen uptake -genes, is at least a heterodimeric enzyme with a large subunit of about 60 kDa containing the active site (HupL) and a small subunit of c. 35 kDa playing a role in electron transfer (HupS)”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    NtcA and LexA have been implicated in transcriptional regulation of the uptake and bidirectional hydrogenases, respectively.

    “NtcA and LexA have been implicated in the transcriptional regulation of the uptake and the bidirectional enzyme respectively.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Lindberg, 2003

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    • cites Oliveira et al., 2004

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    • cites Leita ˜o et al., 2005

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  • May combine two claims.

    Premisereasoning

    In heterocystous cyanobacteria grown in air without combined nitrogen, uptake hydrogenase activity is mainly confined to heterocysts, where it is protected from oxygen inactivation.

    “In heterocystous cyanobacteria grown in air and without combined nitrogen, the uptake hydrogenase activity is mainly confined to heterocysts, where it is protected from oxygen inactivation”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    In Anabaena/Nostoc sp. PCC 7120, hupL undergoes rearrangement allowing expression only in heterocysts, and this rearrangement does not occur in N. punctiforme.

    “in this strain the hupL gene undergoes a rearrangement, allowing its expression in the heterocysts only, and that this process does not occur in N. punctiforme”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Oxelfelt et al., 1998

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  • May combine two claims.

    Interpretationcitation

    No definitive proof of the anchoring polypeptide exists, and a soluble and a membrane-bound form of the enzyme cannot be excluded.

    “However, to date no definitive proof was obtained, and the existence of both a soluble and a membrane-bound form of the enzyme cannot be excluded”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    In Gloeothece sp. ATCC 27152 and Trichodesmium erythraeum IMS 101, hupW is immediately downstream of hupL, and in Gloeothece it is cotranscribed with hupSL.

    “In the unicellular Gloeothece sp.ATCC 27152 and in the filamentous Trichodesmium erythraeum IMS 101 hupW -the gene encoding for the putative uptake hydrogenase-specific endopeptidase -is the ORF located immediately downstream of hupL, and was shown to be cotranscribed with hupSL in Gloeothece sp.ATCC 27152”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Oliveira et al., 2004

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  • May combine two claims.

    Premisecitation

    In other strains, the position of hupW relative to hupSL varies considerably, and they are transcribed independently.

    “In other strains, the position of hupW related to the hupSL varies considerably, and in the strains examined they are transcribed independently”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Wünschiers et al., 2003

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  • May combine two claims.

    Premiseown data

    HupS has 320 amino acids in all cyanobacteria investigated; HupL generally has 531 amino acids, except L. aestuarii and L. majuscula have six extra and T. erythraeum has three extra.

    “whereas HupS has the same number of amino acid residues in all the cyanobacteria investigated [320 amino acids (aa)], HupL generally has 531 aa with the exception of the filamentous nonheterocystous L. aestuarii CCY 9616 (six extra), L. majuscula (six extra), and T. erythraeum (three extra).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisenone given

    HupL contains a C-terminal region presumably cleaved off by a specific endopeptidase during maturation.

    “HupL contains the C-terminal region that is presumably cleaved off, by a specific endopeptidase, as the last step of the maturation of the large subunit.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    In NiFe hydrogenases, the large subunit harbors the active center buried near the subunit interface, and the small subunit contains FeS clusters that conduct electrons.

    “In the NiFe hydrogenases, the large subunit harbors the active center that is deeply buried inside the protein, close to the large interface between the two subunits, and the small subunit contains the FeS clusters that conduct electrons between the active center and the physiological electron acceptor/donor”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Vignais et al., 2001

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    • cites Vignais & Colbeau, 2004

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  • May combine two claims.

    Premisecitation

    Cyanobacterial HupL sequences contain four conserved cysteine residues coordinating the bimetallic NiFe center; HupS contains eight cysteine residues for FeS clusters and a ninth cysteine slightly shifted.

    “the cyanobacterial HupL sequences contain the four conserved cysteine residues that are involved in the coordination of the bimetallic NiFe center of the active site, and HupS contains eight cysteine residues clearly corresponding to those involved in the formation of the FeS clusters, and a ninth cysteine slightly shifted compared with other bacteria”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Tamagnini et al., 2002

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  • May combine two claims.

    Premisecitation

    The bidirectional hydrogenase is not ubiquitous among heterocystous cyanobacteria, and no correlation was established between its presence or absence and hupL rearrangement.

    “the presence of the bidirectional hydrogenase is not ubiquitous among heterocystous cyanobacteria, although they could not establish a correlation between the presence/absence of the bidirectional enzyme and hupL rearrangement.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Tamagnini et al., 2000

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  • May combine two claims.

    Premisecitation

    STRR sequences are frequent in heterocyst-forming cyanobacteria and less frequent in unicellular strains.

    “STRR sequences have previously been shown to be frequent in heterocyst-forming cyanobacteria and relatively less frequent in unicellular strains”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Asayama et al., 1996

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  • May combine two claims.

    Premisecitation

    Inactivation of xisC blocks hupL rearrangement, and XisC alone is sufficient to catalyze the site-specific recombination in Nostoc sp. PCC 7120.

    “it has been unequivocally demonstrated that the inactivation of xisC blocks the hupL rearrangement and that XisC alone is sufficient to catalyze the hupL element site-specific recom-bination in Nostoc sp.PCC 7120”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Carrasco et al., 2005

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  • May combine two claims.

    Premisecitation

    The hupL element is absent from A. variabilis and N. punctiforme.

    “Despite the hupL element being absent from the two other heterocystous strains for which genome sequences are available, A. variabilis and N. punctiforme”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Oxelfelt et al., 1998

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    • cites Happe et al., 2000

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  • May combine two claims.

    Premisecitation

    In L. majuscula, about 10% of the hupSL intergenic region is nonrepetitive, with two distinct sets of LRR sequences.

    “in the filamentous nonheterocystous L. majuscula only about 10% of the intergenic region consists of nonrepetitive nucleotides, with two distinct sets of Long Repeated Repetitive (LRR) sequences clearly identified”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Leita ˜o et al., 2005

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  • May combine two claims.

    Premisecitation

    The xisC mutant forms heterocysts without obvious developmental defects and, under N2-fixing conditions, is defective for hydrogen uptake activity but evolves H2.

    “It was also shown that the xisC-mutant forms heterocysts without any obvious developmental defects and that the mutant grown under N 2 -fixing conditions (BG11 0 ) was not only defective for hydrogen uptake activity but evolves H 2”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Lindblad et al., 2002

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    • cites Carrasco et al., 2005

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    Premisecitation

    Analysis upstream of the tsp revealed a -10 and a -35 box in L. majuscula and N. punctiforme, while only a -10 box was clearly discerned in Gloeothece sp. ATCC 27152 and A. variabilis.

    “The analysis of the regions upstream the transcriptional start point (tsp) revealed the presence of a À 10 and a À 35 box in both L. majuscula and N. punctiforme, while in Gloeothece sp.ATCC 27152 and A. variabilis only a À 10 box could be clearly discerned.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Happe et al., 2000

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    • cites Lindberg et al., 2000

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    • cites Oliveira et al., 2004

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  • May combine two claims.

    Interpretationcitation

    Sequestration of the hupL ribosome-binding site may be effective in N. punctiforme, where the hairpin folds the entire hupSL intergenic region, but it does not occur in all predicted hupSL intergenic hairpin structures.

    “although the sequestration of the hupL RBS may be effective in N. punctiforme in which the hairpin folds the entire hupSL intergenic region (Lindberg et al., 2000), it does not occur in all hupSL intergenic hairpin structures predicted.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Lindberg et al., 2000

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  • May combine two claims.

    Premiseown data

    A putative NtcA binding site was found in Gloeothece sp. ATCC 27152, L. majuscula, and N. punctiforme, with its position relative to the tsp varying by strain.

    “A putative binding site for NtcA (a protein that operates global nitrogen control in cyanobacteria) could be found in Gloeothece sp.ATCC 27152, L. majuscula and N. punctiforme, although its relative position to the tsp varied depending on the strain.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Lindberg, 2003

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    • cites Oliveira et al., 2004

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    • cites Leita ˜o et al., 2005

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  • May combine two claims.

    Premisecitation

    Transcriptional start sites of hup operons are localized 238, 59, 103, and 259 bp upstream from the hupS start codon for Gloeothece sp. ATCC 27152, L. majuscula, A. variabilis, and N. punctiforme, respectively.

    “The transcriptional start sites of the hup operons are localized 238, 59, 103 and 259 bp upstream from the hupS start codon for the unicellular Gloeothece sp.ATCC 27152, the filamentous L. majuscula and the filamentous heterocystous A. variabilis and N. punctiforme, respectively”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Happe et al., 2000

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    • cites Lindberg et al., 2000

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    • cites Oliveira et al., 2004

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  • May combine two claims.

    Interpretationreasoning

    The transcription of uptake hydrogenase structural genes is under control of NtcA, reinforcing the correlation between uptake hydrogenase activity and N2 fixation.

    “The fact that the transcription of the uptake hydrogenase structural genes is under the control of the transcriptional regulator that operates global nitrogen control in cyanobacteria reinforces the correlation observed between the activity of the uptake hydrogenase and N 2 fixation”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Houchins, 1984

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    • cites Wolk et al., 1994

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    • cites Oxelfelt et al., 1995

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  • May combine two claims.

    Premisecitation

    Band shift assays indicate specific binding of NtcA to DNA sequences upstream of hupS in Gloeothece sp. ATCC 27152, L. majuscula, and N. punctiforme, suggesting NtcA involvement in transcription regulation of the uptake hydrogenase gene cluster.

    “These experiments indicate a specific binding of NtcA to DNA sequences upstream of hupS in the three cyanobacterial strains tested (Gloeothece sp.ATCC 27152, L. majuscula and N. punctiforme), suggesting, indeed, the involvement of NtcA in the transcription regulation of the uptake hydrogenase gene cluster”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Lindberg, 2003

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    • cites Oliveira et al., 2004

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    • cites Leita ˜o et al., 2005

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  • May combine two claims.

    Premisecitation

    In A. variabilis, although there is no rearrangement of hupL, hupSL are expressed only in heterocysts.

    “In A. variabilis, although there is no rearrangement of the hupL gene, hupSL are expressed in heterocysts only.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Happe et al., 2000

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  • May combine two claims.

    Premisecitation

    In L. majuscula and N. punctiforme, NtcA-binding sites are centered at -233.5 and -258.5, respectively, resembling class I CAP-dependent promoters.

    “In L. majuscula and N. punctiforme, the NtcA-binding sites were found to be centered at positions À 233.5 and À 258.5, respectively, resembling class I CAPdependent promoters”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Busby & Ebright, 1999

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    • cites Herrero et al., 2001

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    • cites Herrero et al., 2004

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  • May combine two claims.

    Premisecitation

    Both Gloeothece sp. ATCC 27152 and L. majuscula exhibit higher hydrogen-uptake activities during the dark period.

    “both organisms exhibit higher hydrogenuptake activities during the dark period”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Reade et al., 1999

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    • cites Lundgren et al., 2003

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  • May combine two claims.

    Premisecitation

    Transfer of N. muscorum from non-N2-fixing to N2-fixing conditions induced a transcript after about 24 h, and relative transcript amounts increased in parallel with H2-uptake activity.

    “the transfer of N. muscorum cells from non-N 2 -fixing (ammonia) to N 2 -fixing conditions induced the appearance of a transcript (after c. 24 h), and the relative amounts of transcript increased in parallel with the H 2 -uptake activity”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Axelsson et al., 1999

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  • May combine two claims.

    Premisecitation

    In Gloeothece sp. ATCC 27152 and L. majuscula grown under nitrogen-fixing conditions and 12 h light/12 h dark cycles, hupSL(W) transcript levels are highest during the light phase or at the light-to-dark transition, respectively.

    “in the nonheterocystous Gloeothece sp.ATCC 27152 (unicellular) and L. majuscula (filamentous), grown under nitrogenfixing conditions and 12 h light/12 h dark cycles, there is an evident light/dark regulation with the highest levels of hupSL(W) transcripts detected during the light phase or in the transition between the light and dark phase, respectively”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Oliveira et al., 2004

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    • cites Leita ˜o et al., 2005

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  • May combine two claims.

    Premisecitation

    hupSL transcripts were missing in A. variabilis and N. punctiforme grown with ammonia, and in A. variabilis with nitrate, but present under N2-fixing conditions.

    “hupSL transcripts were missing in A. variabilis and in N. punctiforme cells grown with ammonia (and in A. variabilis cells grown with nitrate), but were present in both organisms grown under N 2 -fixing conditions.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Happe et al., 2000

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    • cites Hansel et al., 2001

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  • May combine two claims.

    Interpretationcitation

    In L. majuscula, protein turnover occurs, with degradation during the light period and de novo synthesis during the dark phase.

    “These results suggest that in L. majuscula, a protein turnover occurs, with degradation taking place during the light period and de novo synthesis taking place during the dark phase.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Leita ˜o et al., 2005

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  • May combine two claims.

    Premisecitation

    The activity of the cyanobacterial uptake hydrogenase depends on nickel availability, and adding external nickel to the growth medium increases uptake hydrogenase activity in several strains.

    “the activity of the cyanobacterial uptake enzyme was shown to be dependent on nickel availability, and the addition of external nickel to the growth medium (up to a certain concentration) increased the uptake hydrogenase activity in several strains”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Xiankong et al., 1984

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    • cites Daday et al., 1985

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    • cites Kumar & Polasa, 1991

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  • May combine two claims.

    Premisecitation

    N. muscorum and N. punctiforme transferred from aerobic to anaerobic conditions show increased hupL transcription and hydrogen uptake activity.

    “Nostoc muscorum and N. punctiforme cultures transferred from aerobic to anaerobic conditions showed an increase in both the transcription of hupL and hydrogen uptake activity”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Axelsson & Lindblad, 2002

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  • May combine two claims.

    Premisecitation

    In the presence of combined nitrogen, hupSLW transcription is totally repressed in Gloeothece sp. ATCC 27152, while in L. majuscula hupSL transcription and expression are significantly reduced but a pattern similar to N2-fixing conditions can be discerned.

    “In the presence of combined nitrogen, hupSLW transcription is totally repressed in Gloeothece sp.ATCC 27152, while in L. majuscula the levels of hupSL transcription and expression are significantly reduced but it is possible to discern a pattern similar to the one observed in cells grown under N 2 -fixing conditions”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Oliveira et al., 2004

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    • cites Leita ˜o et al., 2005

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    • cites Ferreira et al., 2007

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    The results for L. majuscula under non-N2-fixing conditions could be explained by its mode of growth, in which inner cells probably have different access to combined nitrogen.

    “The results obtained for L. majuscula under non-N 2 -fixing conditions could be explained by the mode of growth of this cyanobacterium, in which the inner cells are probably not in the same conditions notably in terms of access to the combined nitrogen.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    At the beginning of the light phase in L. majuscula, no hupSL transcription is detectable, and levels of both polypeptides and H2 uptake activity begin to decline.

    “In the beginning of the light phase, no hupSL transcription is detectable, and the levels of both polypeptides and H 2 uptake activity begin to decline”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Leita ˜o et al., 2005

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Addition of exogenous hydrogen induces hupSL transcription and hydrogen uptake activity in N. muscorum and N. punctiforme, and hydrogen uptake activity in Nostoc sp. PCC 7120.

    “the addition of exogenous hydrogen was shown to induce hupSL transcription and hydrogen uptake activity in N. muscorum and N. punctiforme (Oxelfelt et al., 1995;Axelsson & Lindblad, 2002), as well as hydrogen uptake activity in Nostoc sp.PCC 7120”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Oxelfelt et al., 1995

      Not checked in the free run.

    • cites Axelsson & Lindblad, 2002

      Not checked in the free run.

    • cites Houchins & Burris, 1981b

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    The cyanobacterial bidirectional hydrogenase is considered a heteropentameric enzyme encoded by hoxEFUYH, with HoxE belonging to the diaphorase part.

    “the cyanobacterial bidirectional hydrogenase is considered to be a heteropentameric enzyme encoded by hoxEFUYH, HoxE belonging to the diaphorase part”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Schmitz et al., 2002

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    The effect of carbon substrates on cyanobacterial uptake hydrogenase activity is difficult to assess, and apparently contradictory results are reported.

    “However, the effect of carbon substrates on the cyanobacterial uptake hydrogenase activity is difficult to assess, and apparently contradictory results are reported in the literature”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Houchins, 1984

      Not checked in the free run.

    • cites Kumar et al., 1986

      Not checked in the free run.

    • cites Chen et al., 1989

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Bidirectional hydrogenases with more than four subunits have been identified in other bacteria, including heteropentameric cyanobacterial-type enzymes in Thiocapsa roseopersicina and Allochromatium vinosum, and Ralstonia eutropha with two HoxI subunits besides HoxFUYH.

    “Bidirectional hydrogenases with more than four subunits have also been identified in other bacteria, such as the photosynthetic purple sulfur bacteria Thiocapsa roseopersicina and Allochromatium vinosum which contain heteropentameric cyanobacterial-type bidirectional hydrogenases (Rákhely et al., 2004;Long et al., 2007), and Ralstonia eutropha, which possess two HoxI subunits besides HoxFUYH”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Rákhely et al., 2004

      Not checked in the free run.

    • cites Long et al., 2007

      Not checked in the free run.

    • cites Burgdorf et al., 2005

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Dark H2 evolution is increased by added glucose and arises from oxidation of NAD(P)H generated by fermentation.

    “This dark H 2 evolution was enhanced by exogenously added glucose and resulted from the oxidation of NAD(P)H produced by fermentation reactions.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Cournac et al., 2004

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    hoxU mutants in Synechococcus PCC 6301 and hoxEF mutants in Synechocystis PCC 6803 retain respiratory O2 uptake but are affected in H2 evolution.

    “mutants of hoxU in Synechococcus sp.PCC 6301 (former Anacystis nidulans) (Boison et al., 1998) and hoxEF in Synechocystis sp.PCC 6803 (Howitt & Vermaas, 1999) showed nonimpaired respiratory O 2 uptake while being affected in H 2 evolution.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Boison et al., 1998

      Not checked in the free run.

    • cites Howitt & Vermaas, 1999

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    In Synechocystis PCC 6803, hoxH mutants show impaired PSI oxidation, elevated PSII fluorescence, and altered transcript levels of psbA, psaA, and petB relative to wild type.

    “hoxH À mutants are impaired in the oxidation of PSI, have higher fluorescence of PSII and have different transcript levels of the photosynthetic genes psbA, psaA and petB when compared with the wild type (Appel et al., 2000).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Appel et al., 2000

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    The bidirectional hydrogenase of Synechocystis PCC 6803 is light-insensitive, reversibly inactivated by O2, and rapidly reactivated by NADH or NADPH.

    “the bidirectional hydrogenase in Synechocystis sp.PCC 6803 is insensitive to light, reversibly inactivated by O 2 and can be quickly reactivated by NADH or NADPH.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Cournac et al., 2004

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    In A. variabilis and Synechocystis PCC 6803, the bidirectional hydrogenase has been proposed to associate with the thylakoid membrane, while in Synechococcus PCC 6301 immunological evidence suggests cytoplasmic membrane association.

    “in A. variabilis and Synechocystis sp.PCC 6803, an association with the thylakoid membrane was proposed (Serebriakova et al., 1994;Appel et al., 2000), while in Synechococcus sp.PCC 6301 immunological data implied an association with the cytoplasmic membrane (Kentemich et al., 1989(Kentemich et al., , 1991)).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Serebriakova et al., 1994

      Not checked in the free run.

    • cites Appel et al., 2000

      Not checked in the free run.

    • cites Kentemich et al., 1989

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    In Nostoc PCC 7120, the bidirectional hydrogenase is recovered in the soluble fraction after cell disruption and has therefore been regarded as soluble.

    “in Nostoc sp.PCC 7120 appears in the soluble fraction after cell disruption, and consequently has been considered to be a soluble enzyme (Houchins & Burris, 1981b).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Houchins & Burris, 1981b

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Under anoxia or microaerobiosis with H2 present, H2 uptake reaches the same magnitude as photosynthetic activity and may contribute substantially to CO2 fixation.

    “in anoxia (or microaerobiosis) and in the presence of H 2 , H 2 uptake was of the same magnitude as photosynthetic activity and could therefore contribute significantly to CO 2 fixation.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Cournac et al., 2004

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Illumination causes a brief H2 burst lasting under about 30 seconds, then rapid H2 uptake and a fall in CO2 concentration, both tied to thylakoid photosynthetic electron transport.

    “Upon illumination, a short (o 30 s) burst of H 2 output was observed, followed by rapid H 2 uptake, and a concomitant decrease in CO 2 concentration in the cyanobacterial cell suspension, which were both linked to photosynthetic electron transport in the thylakoids (Cournac et al., 2004).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Cournac et al., 2004

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    Although the Synechocystis PCC 6803 hydrogenase and the homologous NAD+-dependent hydrogenase of R. eutropha share sequence homology, their properties differ, suggesting the enzyme may have somewhat different functions in different organisms.

    “despite sequence homologies between the two enzymes, their characteristics are not identical, which might indicate that this enzyme might have slightly different functions in different organisms (Cournac et al., 2004).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Cournac et al., 2004

      Not checked in the free run.

  • May combine two claims.

    Premisenone given

    In other cyanobacteria, the hox genes are split into two clusters separated by several kilobases, about 333 kb in Synechococcus PCC 6301 and 8.8 kb in Nostoc PCC 7120.

    “In other cases, the hox genes are found in two different clusters separated by several kilobase (c.333 and 8.8 kb in Synechococcus sp.PCC 6301 and Nostoc sp.PCC 7120, respectively).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    In the ndhB mutant M55, which lacks NDH-1 and produces little O2 in light, H2 uptake is negligible during dark-to-light transitions, permitting several minutes of continuous H2 production.

    “In the ndhB mutant M55, which is defective in the type I NADPHdehydrogenase complex (NDH-1) and produces only low amounts of O 2 in the light, H 2 uptake was negligible during dark-to-light transitions, allowing several minutes of continuous H 2 production.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Cournac et al., 2004

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    In M55, H2 production receives electrons through two routes: water photolysis at photosystem II and carbohydrate-dependent reduction of the plastoquinone pool.

    “two pathways of electron supply for H 2 production operate in M55, namely photolysis of water at the level of photosystem II and carbohydrate-mediated reduction of the plastoquinone pool.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Cournac et al., 2004

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    In Synechocystis PCC 6803, the hox genes are transcribed as one operon, with the transcription start point 168 bp upstream of the hoxE start codon.

    “the hox genes in Synechocystis sp.PCC 6803 are transcribed as a single operon (Gutekunst et al., 2005;Oliveira & Lindblad, 2005;Antal et al., 2006) with the transcription start point located 168-bp upstream of the hoxE start codon (Gutekunst et al., 2005;Oliveira & Lindblad, 2005).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Gutekunst et al., 2005

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    • cites Oliveira & Lindblad, 2005

      Not checked in the free run.

    • cites Antal et al., 2006

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationnone given

    HoxE may serve as a bridging subunit that attaches the enzyme to membranes.

    “HoxE may be involved as a bridging subunit in membrane attachment.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    The native bidirectional hydrogenase has a molecular mass of 375 kDa, indicating a dimeric Hox(EFUYH)2 assembly.

    “The molecular weight of the native protein (375 kDa) indicates a dimeric assembly of the enzyme complex, Hox(EFUYH) 2 (Schmitz et al., 2002).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Schmitz et al., 2002

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Iron is liganded by two cyanide ions and one carbon monoxide, while nickel is coordinated by two additional cysteines.

    “The iron has two cyanide ions and one carbon monoxide as ligands, whereas the nickel ion is coordinated by two additional cysteines (Volbeda et al., 1995).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Volbeda et al., 1995

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    In A. variabilis, bidirectional hydrogenase transcripts occur in NH4+-grown filaments and in both vegetative cells and heterocysts under nitrogen-fixing conditions.

    “transcripts of the bidirectional hydrogenase have been shown to be present in NH 4 1 -grown filaments, and in both vegetative cells and heterocysts under nitrogenfixing conditions in A. variabilis (Boison et al., 2000).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Boison et al., 2000

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Synechocystis PCC 6803 LexA has been detected in proteomic studies and its transcript in microarray experiments.

    “Synechocystis sp.PCC 6803 LexA has been detected in different proteomic studies (Wang et al., 2000;Gan et al., 2005;Srivastava et al., 2005;Fulda et al., 2006;Kurian et al., 2006;Slabas et al., 2006), and its transcript has also been identified in microarray experiments (Hihara et al., 2001;Kamei et al., 2001;Li et al., 2004;Singh et al., 2004;Tu et al., 2004;Shapiguzov et al., 2005).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Wang et al., 2000

      Not checked in the free run.

    • cites Hihara et al., 2001

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    A LexA-depleted mutant has lower hydrogenase activity than wild type, suggesting LexA activates hox gene transcription in Synechocystis PCC 6803.

    “a LexA-depleted mutant showed a reduced hydrogenase activity compared with the wild-type, suggesting that LexA works as a transcription activator of the hox genes in Synechocystis sp.PCC 6803 (Gutekunst et al., 2005).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Gutekunst et al., 2005

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Some proteomic studies place LexA in thylakoid membrane fractions, an unexpected location for a transcription regulator.

    “in some proteomic studies, LexA has been identified in association with thylakoid membrane fractions (Wang et al., 2000;Srivastava et al., 2005), which represents an unexpected location for a transcription regulator.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Wang et al., 2000

      Not checked in the free run.

    • cites Srivastava et al., 2005

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    lexA and crhR are divergently expressed, and their transcripts accumulate differently under oxidizing versus reducing conditions, suggesting LexA represses crhR transcription.

    “Transcript analysis indicated that lexA and crhR are divergently expressed, with the respective transcripts accumulating differently under conditions, which, respectively, oxidize and reduce the electron transport chain, suggesting that LexA works as a repressor of the crhR transcription (Patterson-Fortin et al., 2006).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Patterson-Fortin et al., 2006

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    In aerobically grown Nostoc PCC 7120 filaments, the bidirectional hydrogenase is active in both vegetative cells and heterocysts, with heterocysts showing several-fold higher activity.

    “The bidirectional hydrogenase in Nostoc sp.PCC 7120 is active in both vegetative cells and in heterocysts in aerobically grown filaments, with heterocysts having several fold more activity than vegetative cells.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Houchins & Burris, 1981a

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    In Synechococcus PCC 6301, hoxEF are cotranscribed and the second transcript contains hoxUYH plus hoxW, hypA, and hypB; in PCC 7942, the second transcript contains only hoxUYHW.

    “While hoxEF are cotranscribed in both strains, the second transcript is constituted by hoxUYH together with hoxW, hypA and hypB in Synechococcus sp.PCC 6301 (Boison et al., 2000), and by hoxUYHW only in Synechococcus sp.PCC 7942 (Schmitz et al., 2001).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Boison et al., 2000

      Not checked in the free run.

    • cites Schmitz et al., 2001

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    In A. variabilis, transfer to low oxygen induces both enzyme activity and the relative amount of hoxH.

    “a transfer to a low level of oxygen in A. variabilis induced both the enzyme activity as well as the relative amount of hoxH (Sheremetieva et al., 2002).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Sheremetieva et al., 2002

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    In Synechocystis PCC 6803 under combined nitrogen limitation, hox gene transcription increases, followed by increased enzyme activity.

    “Northern blot analyses of the hox genes expression in Synechocystis sp.PCC 6803 under combined nitrogen-limiting growth conditions demonstrated an increase in transcription (Antal et al., 2006), followed by an increase in enzyme activity (T.K. Antal, P. Oliveira & P. Lindblad, unpublished data).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Antal et al., 2006

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    The hox genes show circadian clock expression, and this has also been demonstrated for hoxE in Synechocystis PCC 6803.

    “it was demonstrated that the hox genes have a circadian clock expression (Schmitz et al., 2001), a fact that has also been demonstrated for hoxE in Synechocystis sp.PCC 6803 (Kucho et al., 2005).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Schmitz et al., 2001

      Not checked in the free run.

    • cites Kucho et al., 2005

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  • May combine two claims.

    Premisecitation

    When Nostoc PCC 7120 filaments are moved to anaerobic conditions, bidirectional hydrogenase activity rises by about two orders of magnitude, with similar levels in both cell types.

    “When the filaments were transferred to anaerobic conditions, the activity of the bidirectional hydrogenase increased by about two orders of magnitude with approximately the same activity levels in both types of cells (Houchins & Burris, 1981a).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Houchins & Burris, 1981a

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    In G. alpicola under combined nitrogen limitation, hoxY and hoxH transcription analysis shows increased enzyme activity but no transcript-level regulation.

    “Analysis of the transcription of hoxY and hoxH in G. alpicola, under combined nitrogen-limiting growth conditions, demonstrated an increase in the enzyme activity, but no regulation at the transcript level (Sheremetieva et al., 2002).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Sheremetieva et al., 2002

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Chroococcidiopsis thermalis CALU 758 has a bidirectional hydrogenase whose catalytic properties resemble an uptake hydrogenase, as it is not induced by anaerobic or nitrate-starving conditions.

    “the unicellular strain Chroococcidiopsis thermalis CALU 758 contains a bidirectional hydrogenase with some catalytic properties more related to an uptake hydrogenase, i.e. not inducible under anaerobic conditions or under nitrate-starving conditions (Serebryakova et al., 2000).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Serebryakova et al., 2000

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationcitation

    The rise in hox gene transcription during iron starvation may be a feedback response that compensates for the shortage of active enzyme.

    “The increase in transcription of the hox genes, when the cells undergo iron starvation, might be a feedback mechanism to compensate for the lack of functionally active enzyme (Gutekunst et al., 2006).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Gutekunst et al., 2006

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    Homologues of the hyp genes occur in all organisms able to form NiFe hydrogenases.

    “Homologues of the hyp genes are present in all organisms capable of forming NiFe hydrogenases.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    In Synechocystis PCC 6803, hypA2 and hypB2 are clustered but do not appear to be key for maturation of the bidirectional hydrogenase.

    “in this organism the homologs hypA2 and hypB2 are clustered (Kaneko et al., 1996), but these two do not seem to play a key role in the maturation of the bidirectional hydrogenase (Hoffmann et al., 2006).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Kaneko et al., 1996

      Not checked in the free run.

    • cites Hoffmann et al., 2006

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  • May combine two claims.

    Premisecitation

    In Synechococcus elongatus PCC 6301, PCC 7942, and Synechococcus PCC 7002, hypABFC are together downstream of hox genes, while hypD and hypE are separate in the first two organisms.

    “In three Synechococcus, closely related strains (Synechococcus elongatus PCC 6301, Synechococcus elongatus PCC 7942 and Synechococcus sp.PCC 7002) hypABFC are together and downstream of hox genes, while hypD and hypE are apart in the two first organisms (Boison et al., 1996).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Boison et al., 1996

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    hupW and hoxW encode putative hydrogenase C-terminal endopeptidases and appear specific for cyanobacterial uptake and bidirectional hydrogenase, respectively.

    “the genes encoding for the putative hydrogenase C-terminal endopeptidases -hupW and hoxW -were identified and seem to be specific for the cyanobacterial uptake and the bidirectional hydrogenase, respectively, resembling the situation in other organisms (Wünschiers et al., 2003;Oliveira et al., 2004;Leita ˜o et al., 2006).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Wünschiers et al., 2003

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    • cites Oliveira et al., 2004

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    • cites Leitao et al., 2006

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  • May combine two claims.

    Premisecitation

    Cyanobacterial hyp genes are often clustered near the structural genes of one hydrogenase, except in Synechocystis PCC 6803 where hypABCDEF are scattered.

    “The hyp genes in cyanobacteria are frequently clustered and in the vicinity of the structural genes of one of the hydrogenases (Fig. 2), with a well-known exception -the unicellular non-N 2 -fixing Synechocystis sp.PCC 6803 -in which the hypABCDEF genes are scattered throughout the genome.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Kaneko et al., 1996

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Hydrogenase maturation genes were first characterized in E. coli; most Hyp proteins act pleiotropically, while each hydrogenase large subunit is processed by a specific endopeptidase.

    “The genes encoding the proteins involved in the maturation of hydrogenases were firstly characterized for E. coli, and while most of the Hyp proteins affect hydrogenases pleiotropically, the large subunit of each hydrogenase is proteolytically processed by a specific endopeptidase (Lutz et al., 1991;Jacobi et al., 1992;Menon et al., 1994;Rossmann et al., 1995;Theodoratou et al., 2005;Böck et al.,”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Lutz et al., 1991

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    • cites Jacobi et al., 1992

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    • cites Menon et al., 1994

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisenone given

    Fe is thought to be the first of the two active-center metal ions incorporated into a NiFe hydrogenase.

    “It is believed that from the two metal ions present in the active center of a NiFe hydrogenase, Fe is the first to be incorporated into the enzyme.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    In N. punctiforme, Nostoc PCC 7120, A. variabilis, and L. majuscula, hyp genes form a cluster with all genes in the same direction, relatively close to uptake hydrogenase structural genes but opposite in orientation.

    “In the heterocystous strains, N. punctiforme, Nostoc sp.PCC 7120 and A. variabilis and in the N 2 -fixing but nonheterocystous L. majuscula, the hyp genes are located in a cluster with all genes orientd in the same direction, and relatively close to the uptake hydrogenase structural genes, although in the opposite direction (Gubili & Borthakur, 1998;Hansel et al., 2001;Leita ˜o et al., 2006).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Gubili & Borthakur, 1998

      Not checked in the free run.

    • cites Hansel et al., 2001

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    • cites Leitao et al., 2006

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  • May combine two claims.

    Premisecitation

    HypF uses carbamoyl phosphate as a substrate, catalyzes CP-dependent ATP hydrolysis to AMP and inorganic phosphate, and forms an adenylated CP derivative.

    “HypF accepts carbamoyl phosphate (CP) as a substrate, catalyzes a CP-dependent hydrolysis of ATP into AMP and inorganic phosphate (PPi) and forms an adenylated CP derivative.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Paschos et al., 2002

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    • cites Reissmann et al., 2003

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  • May combine two claims.

    Interpretationcitation

    Putative cyanobacterial Hyp proteins contain conserved motifs and may carry out functions similar to their counterparts in other organisms.

    “The putative cyanobacterial Hyp proteins possess conserved motifs and may fulfill functions similar to the corresponding proteins in other organisms (Tamagnini et al., 2002;Vignais & Colbeau, 2004;Hoffmann et al., 2006;Leita ˜o et al., 2006).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Tamagnini et al., 2002

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    • cites Vignais & Colbeau, 2004

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    • cites Hoffmann et al., 2006

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  • May combine two claims.

    Premisecitation

    The liganded Fe is transferred to the large-subunit precursor, and HypC remains attached, keeping the subunit open for nickel insertion.

    “Subsequently, the liganded Fe is transferred to the precursor of the hydrogenase large subunit (Blokesch & Böck, 2006), and HypC remains attached to the large subunit, maintaining it in an open conformation, allowing the insertion of nickel.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Blokesch & Böck, 2006

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    HypC is a small chaperone-like protein that forms a complex with HypD and interacts with the hydrogenase large subunit.

    “HypC is a small chaperone-like protein that was shown to form a complex with HypD (Blokesch & Bock, 2002) and to interact with the large subunit of the hydrogenase (Magalon”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Blokesch & Bock, 2002

      Not checked in the free run.

    • cites Magalon & Bock, 2000a

      Not checked in the free run.

    • cites Casalot & Rousset, 2001

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    Iron liganding probably occurs at the HypC-HypD complex, and interaction between HypC and the large-subunit precursor releases HypD.

    “Probably, the liganding of the iron takes place at the HypC-HypD complex (Blokesch et al., 2002(Blokesch et al., , 2004a)), and the interaction between HypC and the precursor of the large subunit leads to the liberation of HypD (Blokesch et al., 2004a;Blokesch & Böck, 2006).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Blokesch et al., 2002

      Not checked in the free run.

    • cites Blokesch et al., 2004a

      Not checked in the free run.

    • cites Blokesch & Böck, 2006

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    HypA is a zinc-containing nickel-binding protein, and HypB is a GTPase probably involved in both nickel storage and insertion.

    “HypA is a zinc-containing protein that binds nickel (Mehta et al., 2003;Blokesch et al., 2004b), and HypB is a GTPase that probably plays a dual function: nickel storage and nickel insertation (Maier et al., 1993(Maier et al., , 1995)).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Mehta et al., 2003

      Not checked in the free run.

    • cites Blokesch et al., 2004b

      Not checked in the free run.

    • cites Maier et al., 1993

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    HypA is thought to act as a nickel chaperone, while HypB regulates donation of the metal to the apoprotein or release of the nickel-free chaperone.

    “It is thought that HypA functions as a nickel chaperone and that HypB acts as a regulator, controlling the donation of the metal to the apoprotein or the release of the nickel-free chaperone (Blokesch et al., 2004b).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Blokesch et al., 2004b

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    NtcA and LexA bind to the promoter regions of hup and hox genes, suggesting they regulate the uptake and bidirectional hydrogenases, respectively.

    “The transcriptional regulators NtcA and LexA were shown to bind to the promoter regions of the hup and the hox genes, suggesting their involvement in the regulation of the uptake and bidirectional hydrogenase, respectively (see above, Lindberg, 2003;Oliveira et al., 2004;Gutekunst et al., 2005;Leita ˜o et al., 2005;Oliveira & Lindblad, 2005).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Lindberg, 2003

      Not checked in the free run.

    • cites Oliveira et al., 2004

      Not checked in the free run.

    • cites Gutekunst et al., 2005

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Interpretationnone given

    Maturation of the small subunit occurs in parallel with and independently of large-subunit maturation.

    “Maturation of the small subunit should occur in parallel, and independently from the large subunit maturation.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    In L. majuscula, the corresponding hyp promoter region has a -10 box and two putative NtcA-binding sites; a clear -35 box is absent, but its sequence is highly variable.

    “in the corresponding region of L. majuscula the presence of a À 10 box, and two putative NtcA-binding sites could be identified.In this organism, a clear À 35 box is not present, but it should be taken into account that its sequence is highly variable.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Leitao et al., 2006

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    The hyp cluster promoter region of N. punctiforme contains -10 and -35 elements and putative NtcA binding sites.

    “Analysis of the hyp cluster promoter region of N. punctiforme revealed the presence of À 10 and À 35 elements, and putative binding sites for NtcA (Hansel et al., 2001; Fig. 4).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Hansel et al., 2001

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Once both metals are coordinated to the large-subunit precursor, the C-terminal extension becomes accessible and can be removed by the specific endopeptidase.

    “After both metals have been coordinated to the precursor of the large subunit, the C-terminal extension is accessible and can be removed by the specific endopeptidase.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Theodoratou et al., 2005

      Not checked in the free run.

    • cites Böck et al., 2006

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Deletion of hypA2 and hypB2 does not affect bidirectional hydrogenase activity even though they are transcribed in wild type, showing their products are not actively involved in maturation.

    “the deletion of the homologues hypA2 and hypB2 had no effect on the bidirectional hydrogenase activity even though they are transcribed in the wild type, demonstrating that the products of these genes are not actively involved in the maturation process of the bidirectional hydrogenase (Hoffmann et al., 2006).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Hoffmann et al., 2006

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    N. punctiforme has only the uptake hydrogenase, and both hupL transcription and H2 uptake activity are repressed when combined nitrogen is present.

    “N. punctiforme contains only one hydrogenase (the uptake enzyme), and that in this organism both the transcription of hupL and the H 2 uptake activity are repressed when combined nitrogen is present in the growth medium (Oxelfelt et al., 1995;Hansel et al., 2001).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Oxelfelt et al., 1995

      Not checked in the free run.

    • cites Hansel et al., 2001

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The endopeptidase is postulated to recognize the nickel-containing hydrogenase precursor at least partly through the metal coordinated by three thiolates and to bind the exposed C-terminal domain.

    “It has been postulated that the endopeptidase recognizes its substrate, the nickel-containing hydrogenase precursor, at least in part via the metal that is coordinated by three thiolates, and binds to the exposed C-terminal domain (Theodoratou et al., 2000a(Theodoratou et al., , b, 2005 and Fig. 5).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Theodoratou et al., 2000a

      Not checked in the free run.

    • cites Theodoratou et al., 2000b

      Not checked in the free run.

    • cites Theodoratou et al., 2005

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    The cutting-site motif is completely conserved for each cyanobacterial hydrogenase large subunit: HoxH has DPCLSCSTH and HupL has DSCLVCTVH.

    “The sequence of the cutting site motif is totally conserved for each of the cyanobacterial hydrogenases large subunits: HoxH (bidirectional hydrogenase) -DPCLSCSTH; HupL (uptake hydrogenase) -DSCLVCTVH (see Wünschiers et al., 2003 and Fig. 5).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Wünschiers et al., 2003

      Not checked in the free run.

  • May combine two claims.

    Premisenone given

    The chromosomal position of hupW and hoxW is variable, but in several cases hupW lies near hupSL and in the same direction.

    “The position of hupW and hoxW in the cyanobacterial chromosome is rather variable; however, in several cases hupW is in the vicinity and in the same direction of hupSL (uptake hydrogenase structural genes).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    In A. variabilis, Nostoc PCC 7120, and N. punctiforme, hupW is not part of any known hydrogenase cluster, and in the latter two strains it is transcribed under both N2-fixing and non-N2-fixing conditions.

    “in the heterocystous strains A. variabilis, Nostoc sp.PCC 7120 and N. punctiforme, hupW is not part of any known hydrogenase cluster (Fig. 2), and it was shown to be transcribed under N 2 -and non-N 2 -fixing conditions in the last two strains (Wünschiers et al., 2003).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Wünschiers et al., 2003

      Not checked in the free run.

  • May combine two claims.

    Premiseown data

    In cyanobacterial hydrogenase large subunits, the C-terminal motif [DPCxxCxx(H/R)] occurs in all deduced sequences, but in HupL the proline at position 2 is replaced by serine.

    “In cyanobacteria hydrogenase large subunits, the Cterminal consensus motif [DPCxxCxx(H/R)] was found in all the deduced amino acid sequences; however, in the uptake hydrogenase large subunits (HupL) the neutral proline (P) at position 2 of the cutting site motif is exchanged for an uncharged polar serine (S).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    In Synechococcus sp. PCC 7942, hoxW forms a unit with hoxUYH but is mainly expressed from its own promoter.

    “while in Synechococcus sp.PCC 7942 it was demonstrated that although hoxW constitute a unit together with hoxUYH, it is mainly expressed by its own promoter (Schmitz et al., 2001).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Schmitz et al., 2001

      Not checked in the free run.

  • May combine two claims.

    Premiseown data

    The putative cleaved C-terminal polypeptide varies in length (25-32 aa) and sequence (10-96% similarity) for HoxH, whereas for HupL it is always 16 aa and highly conserved.

    “The putative cleaved C-terminal polypeptide varies in length (25-32 aa residues) and sequence (10-96% similarity) for HoxH, while for HupL the polypeptide always has the same length (16 aa residues) and is highly conserved for all the deduced sequences [AHDAKTG(E/K)ELARFRT(A/ N/S)].”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    In Gloeothece sp. ATCC 27152 and T. erythraeum, hupW is immediately downstream of hupL, and in Gloeothece it is cotranscribed with hupSL.

    “In the nonheterocystous Gloeothece sp.ATCC 27152 and T. erythraeum, hupW is even the ORF located immediately downstream of hupL, and was shown to be cotranscribed with hupSL in Gloeothece sp.ATCC 27152 (Oliveira et al., 2004).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Oliveira et al., 2004

      Not checked in the free run.

  • May combine two claims.

    Premisenone given

    After proteolytic cleavage, the mature large subunit assembles with the small subunit and the enzyme eventually becomes active.

    “After the proteolytic cleavage, the mature large hydrogenase subunit assembles with the small subunit and eventually the enzyme becomes active.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Ludwig et al. (2006) clearly demonstrated the monophyly of cyanobacteria and their relationship with other photosynthetic bacteria, but relationships within cyanobacteria were poorly resolved using HupL sequences.

    “Although the phylogenetic analysis of Ludwig et al. (2006) clearly demonstrated the monophyly of cyanobacteria, and their relationship with other photosynthetic bacteria, relationships within the cyanobacteria were poorly resolved using HupL sequences.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Ludwig et al., 2006

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    HycI and HybD are monomeric proteins of about 17 kDa and lack metal or other cofactors.

    “Both are monomeric proteins of a molecular mass of c. 17 kDa, and they are devoid of metal or other cofactors.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Chloroflexus is probably the closest ancestor of cyanobacteria.

    “Recently, the phylogenetic origin of cyanobacterial and algal hydrogenases was analyzed (Ludwig et al., 2006), leading to the conclusion that Chloroflexus is probably the closest ancestor of cyanobacteria.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Ludwig et al., 2006

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Two hydrogenase-specific endopeptidases, HycI and HybD from E. coli, have been purified and studied.

    “To date, two different hydrogenase specific-endopeptidases have been purified and studied, namely HycI and HybD from E. coli (Rossmann et al., 1995;Fritsche et al., 1999).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Rossmann et al., 1995

      Not checked in the free run.

    • cites Fritsche et al., 1999

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Interpretationreasoning

    The overall theoretical energy conversion efficiency from solar energy to H2 may be the highest possible.

    “and the overall theoretical energy conversion efficiency (from solar energy sun to H 2 ) may be the highest possible.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Cyanobacteria can use sunlight as an energy source, water as an electron source, and air as a carbon (CO2) and nitrogen (N2) source.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    T. erythraeum may be sister taxa to the remaining sampled cyanobacteria.

    “although T. erythraeum may be sister taxa to the remaining sampled cyanobacteria (Ludwig et al., 2006).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Ludwig et al., 2006

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    In Ludwig et al. (2006), the only well-supported node within cyanobacteria is that of the three heterocystous strains.

    “in which the only wellsupported node within cyanobacteria is that of the three heterocystous strains.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Ludwig et al., 2006

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    These results are not in conflict with those suggested by Ludwig et al. (2006).

    “These results are not in conflict with those suggested by Ludwig et al. (2006)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Ludwig et al., 2006

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    In cyanobacteria, two natural pathways for H2 production can be used.

    “In cyanobacteria, two natural pathways for H 2 production can be used.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisereasoning

    Under molybdenum-deprived conditions, the conventional molybdenum-nitrogenase is replaced by an alternative vanadium-nitrogenase, and if vanadium is also limited, some N2-fixing microorganisms can synthesize an alternative iron-nitrogenase.

    “Under molybdenum-deprived conditions, the conventional molybdenum-nitrogenase is replaced by an alternative vanadium-nitrogenase, and if vanadium is also limited, some N 2 -fixing microorganisms are able to synthesize an alternative iron-nitrogenase.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisenone given

    With sufficient molybdenum available, the active site harbors molybdenum and iron.

    “With sufficient amounts of molybdenum available, the active site harbors molybdenum and iron.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisenone given

    It has been reported that n is 1 for molybdenum-containing enzymes, 3 for vanadium-nitrogenases, and 7.5 for iron-only nitrogenases.

    “It has been reported that n is 1 for the molybdenumcontaining enzymes, 3 for the vanadium-nitrogenases and 7.5 for the iron-only nitrogenases, respectively.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    Alternative nitrogenases may be better H2 producers compared with the more conventional molybdenum-nitrogenases, although little is known in cyanobacteria.

    “As a consequence, the alternative nitrogenases, although still very little is known in cyanobacteria, may be better H 2 producers compared with the more conventional molybdenum-nitrogenases.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    This was first achieved by chemical mutagenesis and later by targeted knock-out of structural or accessory genes of the uptake hydrogenase.

    “This was first achieved by chemical mutagenesis (Kumar & Kumar, 1991;Mikheeva et al., 1995), and later, since the molecular biology tools for genetic engineering were established, by targeted knock-out of structural or accessory genes of the uptake hydrogenase.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Kumar & Kumar, 1991

      Not checked in the free run.

    • cites Mikheeva et al., 1995

      Not checked in the free run.

  • Classified as probably not a substantial claim. May combine two claims.

    Premisenone given

    To achieve sustainable, renewable cyanobacterial-based H2 production, seven challenges must be addressed: efficient H2 uptake by cells; low energy efficiency and turnover of nitrogenase and/or hydrogenase; limiting amounts of active H2-evolving enzymes; high oxygen sensitivity of nitrogenase and/or hydrogenase; electron flow inhibition by ATP accumulation in a hydrogenase-driven system; low量子效率due

    “In summary, to achieve a sustainable, renewable cyanobacterial-based H 2 production, the following challenges have to be addressed: (1) efficient H 2 uptake by the cells, (2) low energy efficiency and turnover of the nitrogenase and/or the hydrogenase, (3) limiting amounts of active H 2 -evolving enzymes, (4) high oxygen sensitivity of the nitrogenase and/or the hydrogenase, (5) electron flow”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    The turnover of the nitrogenase enzyme is not very high (less than 10 s−1).

    “The turnover of the nitrogenase enzyme is not very high (o 10 s À1 )”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisereasoning

    There are additional unsolved issues for photoautotrophic H2 production in general.

    “Besides the specific challenges for H 2 production connected to the H 2 -evolving enzymes, there are additional unsolved issues for photoautotrophical H 2 production in general.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Cyanobacterial nitrogenases contain molybdenum, vanadium, or iron in the active site, with different genes and gene products making up the different nitrogenases.

    “Cyanobacterial nitrogenases contain molybdenum (Mo), vanadium (V) or iron (Fe) in the active site, with different genes and gene products making up the different nitrogenases (Eady, 1996;Zhao et al., 2006).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Eady, 1996

      Not checked in the free run.

    • cites Zhao et al., 2006

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    Because the bidirectional hydrogenase reaction is not dependent on ATP, it is energetically more efficient and favorable for H2 production, with a much higher turnover (1 million turnovers per second) compared with nitrogenase-based H2 production.

    “Because this reaction is not dependent on ATP, it is energetically more efficient and favorable for H 2 production, with a much higher turnover (1 million turnovers per second) compared with the nitrogenase-based H 2 production.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisenone given

    The bidirectional hydrogenase is not specifically located in an oxygen-protected environment, and the reaction reverses to H2 uptake above a certain H2 partial pressure.

    “At the same time, the enzyme is not specifically located in an oxygen-protected environment, and the reaction turns into the opposite direction (H 2 uptake) above a certain H 2 partial pressure.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisenone given

    In recent years, attempts have been made to overcome these barriers and problems, mainly by targeted genetic engineering of cyanobacterial strains.

    “In recent years, there have been attempts to overcome these barriers and problems, mainly by targeted genetic engineering of cyanobacterial strains:”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisereasoning

    These additional issues are related to low quantum efficiency due to naturally large antenna systems of the photosystems and to electron-consuming pathways directly competing with nitrogenases and hydrogenases.

    “These are related to the low quantum efficiency, due to the naturally large antenna systems of the photosystems, and to electron consuming pathways directly competing with e.g.nitrogenases and hydrogenases.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    All these strains, with the exception of N. punctiforme, also possess a bidirectional hydrogenase.

    “One should bear in mind that all these strains, with the exception of N. punctiforme, also possess a bidirectional hydrogenase.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    In the wild type, H2 produced by nitrogenase is quickly reoxidized by uptake hydrogenase, whereas in an uptake hydrogenase-deficient mutant the H2 produced leaves the cells.

    “In general, the H 2 produced by a nitrogenase in the wild type will be quickly reoxidized by the uptake hydrogenase, whereas in an uptake hydrogenase-deficient mutant the H 2 produced will leave the cells.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    A Nostoc sp. PCC 7120 mutant deficient in both hydrogenases (ΔhupL/ΔhoxH) showed the same increase in H2 evolution as the uptake hydrogenase-deficient mutant (ΔhupL), whereas the bidirectional hydrogenase-deficient mutant (ΔhoxH) produced less H2 compared with the wild type.

    “A Nostoc sp.PCC 7120 mutant deficient in both hydrogenases (DhupL/DhoxH) showed the same increase in H 2 evolution as the uptake hydrogenase-deficient mutant (DhupL), whereas the bidirectional hydrogenase-deficient mutant (DhoxH) produced less H 2 compared with the wild type.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisenone given

    Fe-hydrogenases are irreversibly inactivated by oxygen and are present in fermentative bacteria and green algae but not in cyanobacteria.

    “These enzymes are irreversibly inactivated by oxygen, and are present in e.g.fermentative bacteria (e.g.Clostridium) and green algae (e.g.Chlamydomonas) but not in cyanobacteria.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    To the authors' knowledge, heterologous expression of a more oxygen-tolerant hydrogenase in any cyanobacterium remains to be shown.

    “However, to the authors' knowledge, the heterologous expression of a more oxygen-tolerant hydrogenase in any cyanobacterium remains to be shown.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisenone given

    In heterocystous cyanobacteria grown under N2-fixing conditions, about 5-10% of vegetative cells differentiate into heterocysts.

    “In heterocystous cyanobacteria grown under N 2 -fixing conditions, c. 5-10% of the vegetative cells differentiate into heterocysts.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Premisenone given

    In addition to electron flow in the photosynthetic electron transport chain, a transmembrane potential is built up that is used for generating ATP through an ATP synthase.

    “In addition to the electron flow in the photosynthetic electron transport chain, a transmembrane potential is built up that is used for generating ATP through an ATP synthase.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Heterocyst frequency can be increased, for example, by overexpression of hetR or by inactivation of patS or hetN.

    “Interestingly, it has been shown that the heterocyst frequency can be increased, e.g. by overexpression of hetR or by inactivation of patS, or hetN (Buikema & Haselkorn, 2001;Golden & Yoon, 2003;Borthakur et al., 2005).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Buikema & Haselkorn, 2001

      Not checked in the free run.

    • cites Golden & Yoon, 2003

      Not checked in the free run.

    • cites Borthakur et al., 2005

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    The in vivo half-life of this hydrogenase is 21 h in air and 6 h in air when the protein is partially purified.

    “The in vivo half-life of this hydrogenase is 21 h in air and 6 h in air when the protein is partially purified (Ghirardi et al., 2005).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Ghirardi et al., 2005

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S1 (asserted), S3 (load-bearing).

    Premisecitation

    At the Craig Venter Institute, work is being carried out aiming at transferring the O2-tolerant NiFe-hydrogenase of T. roseopersicina into a Synechococcus strain.

    “At the Craig Venter Institute (US), work is being carried out aiming at transferring the O 2 -tolerant NiFehydrogenase of the purple-sulfur photosynthetic bacterium T. roseopersicina (Kovacs et al., 2005) into a Synechococcus strain.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Kovacs et al., 2005

      Not checked in the free run.

  • May combine two claims.

    Premisereasoning

    Heterocysts are compartments with reduced O2 pressure and are thus suitable for H2 production, either via nitrogenase or via an introduced hydrogenase.

    “These specialized cells are compartments with reduced O 2 pressure, and thus suitable for H 2 production, either via nitrogenase or via an introduced hydrogenase.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisenone given

    In a nitrogenase-based system, ATP is clearly needed for N2 fixation.

    “In a nitrogenase-based system, the ATP is clearly needed for N 2 fixation.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationcitation

    It may be possible to link an introduced iron-hydrogenase to an existing electron transfer pathway within the cyanobacterial cell.

    “it may be possible to link the introduced iron-hydrogenase to an existing electron transfer pathway within the cyanobacterial cell.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationcitation

    In the hydrogenase-catalyzed reaction no ATP is consumed, and electron flow could be inhibited by the accumulated transmembrane potential across the thylakoid membrane.

    “However, in the hydrogenase-catalyzed reaction no ATP is consumed and the electron flow could, in a photosynthetic microorganism, be inhibited by the accumulated transmembrane potential across the thylakoid membrane (Lee & Greenbaum, 2003).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Lee & Greenbaum, 2003

      Not checked in the free run.

  • May combine two claims.

    Premisereasoning

    One main obstacle in H2 production using photosynthetic microorganisms is the high sensitivity of the H2-evolving enzymes, and some attempts have been made to introduce less oxygen-sensitive hydrogenases into cyanobacteria.

    “One main obstacle in H 2 production using photosynthetic microorganisms is the high sensitivity of the H 2 -evolving enzymes, and some attempts have been made to introduce less oxygen sensitive hydrogenases into cyanobacteria.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S4 (based).

    Premisenone given

    The H2-evolving enzymes (nitrogenases and/or bidirectional hydrogenases) are strictly regulated at several levels: transcription, translation, and maturation.

    “Because the H 2 -evolving enzymes (nitrogenase(s) and/or bidirectional hydrogenases) are strictly regulated on several different levels (transcription, translation and maturation)”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    One possible way to enhance H2 production may be overexpression of these enzymes.

    “one possible way to enhance the production of H 2 may be the overexpression of these enzymes.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The genes encoding the more O2-tolerant NiFe hydrogenase of Rubrivivax gelatinosus CBS and its accessory proteins are being introduced into Synechocystis.

    “Also in the US, the genes encoding the more O 2 -tolerant NiFe hydrogenase of the purple nonsulfur photosynthetic bacterium Rubrivivax gelatinosus CBS (Ghirardi et al., 2005), and its accessory proteins, are being introduced into Synechocystis.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Ghirardi et al., 2005

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.

    Premisenone given

    The primary electron donors for the H2-producing enzymes are ferredoxin (for nitrogenase and Fe-hydrogenases) and NADH/NADPH (for NiFe-hydrogenases).

    “The primary electron donors for the H 2 -producing enzymes are ferredoxin (nitrogenase, Fe-hydrogenases) and NADH/ NADPH (NiFe-hydrogenases).”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Premisenone given

    For H2 production through an active nitrogenase or hydrogenase, electrons are required to combine with protons to form H2.

    “For the production of H 2 through the action of an active nitrogenase or hydrogenase electrons are required to combine with protons to form H 2 .”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Antenna-deficient green algal mutants, created by chemical mutagenesis or genetic engineering, showed remarkably greater solar conversion efficiencies and higher photosynthetic productivity than the respective wild type under mass culture conditions.

    “Antenna-deficient green algal mutants, created by chemical mutagenesis (Lee et al., 2002) or genetic engineering (Polle et al., 2003;Tetali et al., 2007), also showed remarkably greater solar conversion efficiencies and a higher photosynthetic productivity than the respective wild type under mass culture conditions.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Lee et al., 2002

      Not checked in the free run.

    • cites Polle et al., 2003

      Not checked in the free run.

    • cites Tetali et al., 2007

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationcitation

    A proton channel may be expressed under H2-producing (anaerobic) conditions to dissipate the proton gradient across the thylakoid membrane.

    “The proton channel may be expressed under H 2 -producing (anaerobic) conditions, to dissipate the proton gradient across the thylakoids membrane.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Premisenone given

    In nature, phototrophic organisms have evolved large antenna systems to handle and compete during very low light intensities.

    “In nature, phototrophic organisms have developed to handle and compete during very low light intensities, and, therefore, large antenna systems have been evolved.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Experiments with the ndhB mutant M55 of Synechocystis PCC 6803, defective in the type I NADPH dehydrogenase complex (NDH-1), showed that this mutant produces only low amounts of O2 in the light, has a poor capacity to fix CO2, and evolves H2 for several minutes during dark-to-light transitions, while H2 uptake was negligible.

    “Experiments with the ndhB mutant M55 of Synechocystis PCC 6803, which is defective in the type I NADPHdehydrogenase complex (NDH-1) (Cournac et al., 2004), showed that this mutant produces only low amounts of O 2 in the light, has a poor capacity to fix CO 2 and evolves H 2 for several minutes during dark-to-light transitions, while the H 2 uptake was negligible.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Cournac et al., 2004

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Reduction of antenna size has been proposed to overcome this problem.

    “To overcome this problem, a reduction of the antenna size has been proposed (Melis et al., 1998;Nakajima & Ueda, 1999;Lee et al., 2002).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Melis et al., 1998

      Not checked in the free run.

    • cites Nakajima & Ueda, 1999

      Not checked in the free run.

    • cites Lee et al., 2002

      Not checked in the free run.

  • May combine two claims.

    Premiseown data

    The electrons used to produce H2 in this mutant were mainly coming from water splitting in PSII and from carbohydrate-mediated reduction of the PQ pool.

    “The electrons used to produce H 2 were mainly coming from water splitting in PSII and from the carbohydrate-mediated reduction of the PQ pool.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S4 (based).

    Premisenone given

    Significant progress is being made in understanding the molecular regulation of the genes encoding both the enzymes and the accessory proteins needed for correct assembly of an active hydrogenase.

    “At the same time, significant progress is being made in the understanding of the molecular regulation of the genes encoding both the enzymes as well as the accessory proteins needed for the correct assembly of an active hydrogenase.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    The activity of the hydrogenase-PsaE fusion protein was only 16% of that of the wild-type hydrogenase protein and was totally suppressed by adding ferredoxin and ferredoxin-NADP+ reductase, leading the authors to conclude that the linker between hydrogenase and PsaE has to be optimized.

    “However, as the activity of the hydrogenase-PsaE fusion protein was only 16% of that of the wild-type hydrogenase protein and was totally suppressed by adding ferredoxin (Fd) and ferredoxin-NADP 1 -reductase (FNR), the authors concluded that the linker between the hydrogenase and PsaE has to be optimized.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Ihara et al. (2006b) fused the membrane-bound NiFe hydrogenase from Ralstonia eutropha H16 to the peripheral PSI subunit PsaE of Thermosynechococcus elongatus (Hyd-PsaE) and used a PsaE-free PSI extract from a PsaE-deficient mutant of Synechocystis sp. PCC 6803.

    “Ihara et al. (2006b) fused the membrane-bound NiFe hydrogenase from Ralstonia eutropha H16 to the peripheral PSI subunit PsaE of the cyanobacterium Thermosynechococcus elongatus (Hyd-PsaE), and used a PsaE-free PSI (PSI Ã ) extract from a PsaE-deficient mutant of Synechocystis sp.PCC 6803.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Ihara et al., 2006b

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisenone given

    Both in the US and in Europe, the first attempts have been initiated to use synthetic biology to design reusable, standardized molecular building blocks that will produce a photosynthetic bacterium containing engineered chemical pathways for competitive, clean, and sustainable H2 production.

    “Both in the US (e.g. the Craig Venter Institute) and in Europe (e.g. the EU/NEST project 'BioModularH 2 '), the first attempts have been initiated to use this new concept aiming at designing reusable, standardized molecular building blocks that will produce a photosynthetic bacterium containing engineered chemical pathways for competitive, clean and sustainable H 2 production.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    NADPH production by this complex coupled with Fd and FNR decreased to about 10% of the original activity, whereas H2 production by the cytc3/PSI complex coupled with hydrogenase from Desulfovibrio vulgaris was enhanced sevenfold.

    “The NADPH production by this complex coupled with Fd and FNR decreased to c. 10% of the original activity, whereas the H 2 production by the cytc3/PSI complex coupled with hydrogenase from Desulfovibrio vulgaris was enhanced sevenfold.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Interpretationcitation

    Because the cyanobacterial bidirectional hydrogenase evolves H2 at a relatively high level of reduced NAD(P), constructing mutants with blocked electron transfer in selected key pathways to increase the relative level of reduced NAD(P) may be a promising strategy to increase H2 production capacity.

    “As the cyanobacterial bidirectional hydrogenase evolves H 2 at a relatively high level of reduced NAD(P), the construction of mutants with blocked electron transfer in selected key pathways, increasing the relative level of reduced NAD(P), may be a promising strategy to increase the H 2 production capacity.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based).

    Premisenone given

    The fundamental aspects of cyanobacterial hydrogenases and their applied potential use as future producers of renewable H2 from sun and water are receiving increased international attention.

    “The fundamental aspects of cyanobacterial hydrogenases, and their more applied potential use as future producers of renewable H 2 from sun and water, are receiving increased international attention.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    In the last few years, the transcription factors directly involved in the regulation of cyanobacterial hydrogenases have been identified.

    “In the last few years, the transcription factors directly involved in the regulation of cyanobacterial hydrogenases have been identified.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S4 (based).

    Premisenone given

    The first steps to use isolated components from cyanobacteria and other microorganisms to create a functional H2-producing unit are being taken.

    “Moreover, the first steps to use isolated components from cyanobacteria and other microorganisms in order to create a functional H 2 -producing unit are being taken.”
    Quote in the paperNot a substantial claim
171 of 171

  • The paper relies on this without support.

    Cyanobacteria can use sunlight as an energy source, water as an electron source, and air as a carbon (CO2) and nitrogen (N2) source.

    “As the main advantages, cyanobacteria can use sunlight as an energy source, water as an electron source and air as a carbon (CO 2 ) and a nitrogen (N 2 ) source.”
1 of 1

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Hyd1 resembles Group 2a uptake hydrogenases from cyanobacteria, which indicates that Hyd1 oxidizes H2.

    “Hyd1 aligns closely with Group 2a uptake hydrogenases of the cyanobacteria such as Nostoc, indicating it oxidises H2 (51).”

    From Energetics of Respiration and Oxidative Phosphorylation in Mycobacteria (2014) · cites this paper as [51]

    The Introduction (page not available) places cyanobacterial uptake hydrogenases in group 2, and the H₂-production section says these enzymes oxidize H₂. The paper does not identify Hyd1 or report its alignment with cyanobacterial hydrogenases, so it does not establish that Hyd1 itself oxidizes H₂. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • Accessory proteins encoded by the hypABCDEF gene cluster are required for maturation of the active site within the catalytic cluster of the hydrogenase subunit.

    “Accessory proteins (encoded by the hypABCDEF gene cluster) are required for the maturation of the active site within the catalytic cluster of the hydrogenase subunit 3.”

    From The Draft Genome of a Hydrogen-producing Cyanobacterium, <i>Arthrospira platensis</i> NIES-46 (2019) · cites this paper as [3]

    The ‘Maturation of cyanobacterial hydrogenases’ section (page unavailable) says NiFe-hydrogenase maturation requires core proteins to incorporate the metals and ligands of the active center. The ‘Physical organization of hyp genes and the corresponding proteins’ section describes roles for HypA–F in that process. However, it treats their corresponding functions in cyanobacteria as putative and notes that hypABCDEF genes are scattered rather than clustered in some strains, so the claim is more categorical than the source. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • The bidirectional [NiFe]-hydrogenase is composed of five subunits encoded by the hox gene cluster (hoxEFUHY).

    “This enzyme is composed of five subunits encoded by the hox gene cluster (hoxEFUHY).”

    From The Draft Genome of a Hydrogen-producing Cyanobacterium, <i>Arthrospira platensis</i> NIES-46 (2019) · cites this paper as [3]

    The Bidirectional hydrogenase section describes a five-subunit enzyme encoded by hoxEFUYH. However, the Physical organization of hox genes section says these genes form one cluster in some cyanobacterial strains but occur in two separate clusters in others, so calling them a single gene cluster without qualification overstates the source. (LLM, conf=0.87)

    Experimental — accuracy not yet measured

  • Several cyanobacterial genomes possess the hox and hyp gene clusters.

    “Several cyanobacterial genomes possess the hox and hyp gene clusters 3.”

    From The Draft Genome of a Hydrogen-producing Cyanobacterium, <i>Arthrospira platensis</i> NIES-46 (2019) · cites this paper as [3]

  • Arthrospira can produce hydrogen via a bidirectional [NiFe]-hydrogenase.

    “Arthrospira can produce hydrogen via a bidirectional [NiFe]-hydrogenase”

    From The Draft Genome of a Hydrogen-producing Cyanobacterium, <i>Arthrospira platensis</i> NIES-46 (2019) · cites this paper as [3]

Cites

Flagged first, then by citations

Research works printed but not linked: 2

  1. Smith GD (1990) Hydrogen metabolism in cyanobacteria. Phycotalk ( Kumar EHD , ed), pp. 131–143. Rastogi & Co, Meerut, India.
  2. Xu Q Yooseph S Smith HO Venter JC (2005) Development of a novel recombinant cyanobacterial system for hydrogen production from water. DOE Genomics: GTL Contractor-Grantee Workshop III 63.

Cited by

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Related

Authors
Tamagnini, P., Leitão, E., Oliveira, P., Ferreira, D., Pinto, F., Harris, D. J., Heidorn, T., & Lindblad, P.
Affiliations
  • Universidade do Porto (PT)
  • Uppsala University (SE)
Corresponding author
Tamagnini, Paula
ORCID
Venue
FEMS Microbiology Reviews
Publisher
Oxford University Press (OUP)
Published
2007-11
Volume
31
Issue
6
Pages
692-720
ISSN
  • 0168-6445 (ISSN-L)
  • 1574-6976
DOI
10.1111/j.1574-6976.2007.00085.x
OpenAlex
W1992990770
Cited by
367
References
192
Citations by year
2026: 8 · 2025: 13 · 2024: 6 · 2023: 15 · 2022: 10 · 2021: 8 · 2020: 21 · 2019: 16 · 2018: 21 · 2017: 17 · 2016: 20 · 2015: 21 · 2014: 32 · 2013: 29 · 2012: 28
FWCI
0.84
Type
journal article
Language
en
Open access
Locations
  • FEMS Microbiology Reviews (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • Federation of European Microbiological Societies
  • Vetenskapsrådet
  • Energimyndigheten
  • Nordic Energy Research
  • Fundação para a Ciência e a Tecnologia (SFRH/BD/16954/2004, SFRH/BD/4912/2001)
  • European Social Fund
Topics
  • Physical Sciences › Energy › Renewable Energy, Sustainability and the Environment › Metalloenzymes and iron-sulfur proteins
  • Physical Sciences › Engineering › Building and Construction › Anaerobic Digestion and Biogas Production
  • Physical Sciences › Energy › Renewable Energy, Sustainability and the Environment › Algal biology and biofuel production
Keywords
[NiFe] hydrogenase, uptake hydrogenase, bidirectional hydrogenase, nitrogen fixation, Hox genes, diaphorase, endopeptidase, NtcA, LexA, transcriptional regulation, hydrogen production, cyanobacteria
MeSH terms
Cyanobacteria, Bacterial Proteins, Hydrogen, Hydrogenase, Nitrogen Fixation, Promoter Regions, Genetic, Transcription, Genetic, Protein Engineering

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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-05.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-05.

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