Abundance of 4Feâ4S motifs in the genomes of methanogens and other prokaryotes

Major, Tiffany A.; Burd, Henry; Whitman, William B.

doi:10.1016/j.femsle.2004.08.027

Cited by 55Metalloenzymes and iron-sulfur proteinsAnaerobic Digestion and Biogas ProductionGenomics and Phylogenetic Studies

Abundance of 4Feâ4S motifs in the genomes of methanogens and other prokaryotes

Major, Tiffany A., Burd, Henry, Whitman, William B.·2004·FEMS Microbiology Letters

DOI 10.1016/j.femsle.2004.08.027

Open this paper in CoChat — free account

Abstract

The abundance of 4Fe-4S motifs of the form CX2CX2CX3C was analyzed in the open reading frames (ORFs) of 120 prokaryotic genomes. The abundance of ORFs containing the CX2CX2CX3C motif or isORFs correlated (r=0.82) with methanogenesis (p=0.0001), archaea (p=0.0173), anaerobiosis (p<0.0001) and genome size (p<0.0001). Optimal growth temperature (hyperthermophily) did not correlate with the number of isORFs (p=0.6283). Large numbers of CX2CX2CX3C motifs may be associated with unique physiologies: methanogenic archaea contained the greatest number of CX2CX2CX3C motifs found among the prokaryotic groups; however, only about 15% of the motifs were in genes directly involved in methanogenesis. Large numbers of CX2CX2CX3C motifs may also be associated with generalists such as Desulfitobacterium hafniense, which is an anaerobic bacterium containing multiple reductases.

Integrity signals

Registry

Crossref · 10.1016/j.femsle.2004.08.027

Cites

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

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?

Among the 120 genomes sampled by Major et al., methanogens had by far the highest frequency of FeS proteins.
“Major et al. [165] found that among the 120 genomes sampled then, the methanogens had by far the highest frequency of FeS proteins.”
From Early bioenergetic evolution (2013) · cites this paper as [165]

Sorted by citations

Superoxide dismutases and superoxide reductases
Sheng, Y., Abreu, I. A., Cabelli, D. E., Maroney, M. J., Miller, A.-F., Teixeira, M., & Valentine, J. S. (2014) · Chemical Reviews · doi:10.1021/cr4005296 · Cited by 1,081 · see citing works
How did LUCA make a living? Chemiosmosis in the origin of life
Lane, N., Allen, J. F., & Martin, W. (2010) · BioEssays · doi:10.1002/bies.200900131 · Cited by 377 · see citing works
The Origin of Life in Alkaline Hydrothermal Vents
Sojo, V., Herschy, B., Whicher, A., Camprubí, E., & Lane, N. (2016) · Astrobiology · doi:10.1089/ast.2015.1406 · Cited by 341 · see citing works
“…a large proportion of the enzymes involved depend on simple Fe(Ni)S cofactors, with structures similar to minerals such as greigite (Cody, 2004; Major et al. , 2004; Russell and Martin, 2004; Bender et al. , 2011; Kim et al. , 2013; Harel et al. , 2014) offering a plausible route to get from…”
Early bioenergetic evolution
Sousa, F. L., Thiergart, T., Landan, G., Nelson-Sathi, S., Pereira, I. A. C., Allen, J. F., Lane, N., & Martin, W. F. (2013) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2013.0088 · Cited by 286 · see citing works
Iron-sulfur clusters: ever-expanding roles
Fontecave, M. (2006) · Nature Chemical Biology · doi:10.1038/nchembio0406-171 · Cited by 225 · see citing works
Feasibility analysis of anaerobic digestion of excess sludge enhanced by iron: A review
Wei, J.-H., Hao, X., van Loosdrecht, M., & Li, J. (2018) · Renewable & Sustainable Energy Reviews · doi:10.1016/j.rser.2018.02.042 · Cited by 209 · see citing works
An origin-of-life reactor to simulate alkaline hydrothermal vents
Herschy, B., Whicher, A., Camprubi, E., Watson, C., Dartnell, L., Ward, J., Evans, J. R. G., & Lane, N. (2014) · Journal of Molecular Evolution · doi:10.1007/s00239-014-9658-4 · Cited by 194 · see citing works
“It is replete with Fe(Ni)S proteins, in which the inorganic cofactors that actually catalyse the key reactions in proteins such as ferredoxin and hydrogenases have structures essentially identical to FeS minerals such as greigite and mackinawite (Eck and Dayhoff 1966; Russell and Martin 2004; Ragsdale and Kumar 1996;…”
Background
From one amino acid to another: tRNA-dependent amino acid biosynthesis
Sheppard, K., Yuan, J., Hohn, M. J., Jester, B. C., Devine, K. M., & Söll, D. G. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn015 · Cited by 177 · see citing works
“Methanogens encode an unusually high number of Fe-S cluster proteins (98).”
Background
Methanogens: a window into ancient sulfur metabolism
Liu, Y., Beer, L. L., & Whitman, W. B. (2012) · Trends in Microbiology · doi:10.1016/j.tim.2012.02.002 · Cited by 113 · see citing works
Self-citation
Cysteine Is Not the Sulfur Source for Iron-Sulfur Cluster and Methionine Biosynthesis in the Methanogenic Archaeon Methanococcus maripaludis*
Liu, Y., Sieprawska-Lupa, M., Whitman, W., & White, R. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.152447 · Cited by 111 · see citing works
Self-citation
Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments
Lyu, Z., & Lu, Y. (2017) · The ISME Journal · doi:10.1038/ismej.2017.173 · Cited by 127 · see citing works
“The presence of [4Fe-4S] clusters in methanogenesis redox enzymes was summarized from various experimental sources and verified via examining conserved [4Fe-4S] binding motifs for all strains by sequence alignments (Major et al., 2004).”
The cellular machinery of Ferroplasma acidiphilum is iron-protein-dominated
Ferrer, M., Golyshina, O., Beloqui, A., Golyshin, P., & Timmis, K. (2007) · Nature · doi:10.1038/nature05362 · Cited by 101 · see citing works
Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism
Sousa, F. L., & Martin, W. F. (2014) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/j.bbabio.2014.02.001 · Cited by 100 · see citing works
“[110] in the proteins they use in the acetyl-CoA pathway, which is also clearly ancient [16,61], serpentinization generates methane abiotically from H2 and CO2 [121] and serpentinization is clearly ancient [8], methanogens use H2S instead of cysteine as precursor of iron–sulfur centers [106], and contain 21 times more…”
Background
The long goodbye: the rise and fall of flavodoxin during plant evolution.
Karlusich, J. P. P., Lodeyro, A. F., & Carrillo, N. (2014) · Journal of Experimental Botany · doi:10.1093/jxb/eru273 · Cited by 79 · see citing works
The evolutionary history of Cys-tRNA Cys formation
O’Donoghue, P., Sethi, A., Woese, C. R., & Luthey-Schulten, Z. A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0509617102 · Cited by 76 · see citing works
Insights into the Mode of Action of Benzyl Isothiocyanate on Campylobacter jejuni
Dufour, V., Stahl, M., Rosenfeld, E., Stintzi, A., & Baysse, C. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.01967-13 · Cited by 54 · see citing works
“The oxygen requirement and oxygen sensitivity influence the number of enzymes with CXXC/CXXS/CXXT motifs; these motifs are found significantly more frequently in the proteins of microaerobes and anaerobes than in aerobic bacteria (80, 81).”
Background
Iron sulfur cluster proteins and microbial regulation: implications for understanding tuberculosis
Saini, V., Farhana, A., Glasgow, J. N., & Steyn, A. J. C. (2012) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2012.03.004 · Cited by 53 · see citing works
Bioenergetic constraints on the origin of autotrophic metabolism
Boyd, E. S., Amenabar, M. J., Poudel, S., & Templeton, A. S. (2020) · Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences · doi:10.1098/rsta.2019.0151 · Cited by 46 · see citing works
“This is particularly true for the genomes of strictly anaerobic, hydrogenotrophic methanogens [6], a group of organisms often advocated as having the most primitive of extant metabolisms [8,9].”
BackgroundResult
Redundant Synthesis of Cysteinyl-tRNACys in Methanosarcina mazei
Hauenstein, S. I., & Perona, J. J. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m801839200 · Cited by 46 · see citing works
Reductive dissolution of pyrite by methanogenic archaea
Payne, D., Spietz, R. L., & Boyd, E. S. (2021) · The ISME Journal · doi:10.1038/s41396-021-01028-3 · Cited by 50 · see citing works
Variation among species in proteomic sulphur content is related to environmental conditions
Bragg, J., Thomas, D., & Baudouin‐Cornu, P. (2006) · Proceedings of the Royal Society of London. Biological Sciences · doi:10.1098/rspb.2005.3441 · Cited by 39 · see citing works
“Our observation that anaerobic prokaryotes tend to have higher proteomic sulphur content than non-anaerobes is consistent with the tendency of anaerobes to have elevated use of cysteine-containing motifs (Major et al. 2004).”
Background
On the evolution of coenzyme biosynthesis
Kirschning, A. (2022) · Natural Product Reports · doi:10.1039/d2np00037g · Cited by 37 · see citing works
The emerging role of gasotransmitters in the pathogenesis of tuberculosis
Chinta, K. C., Saini, V., Glasgow, J. N., Mazorodze, J. H., Rahman, M. A., Reddy, D., Lancaster, J. R., & Steyn, A. J. C. (2016) · Nitric Oxide · doi:10.1016/j.niox.2016.06.009 · Cited by 39 · see citing works
Amino acid modifications on tRNA †
Yuan, J., Sheppard, K., & Söll, D. G. (2008) · Acta Biochimica et Biophysica Sinica · doi:10.1111/j.1745-7270.2008.00435.x · Cited by 35 · see citing works
Pathways of Iron and Sulfur Acquisition, Cofactor Assembly, Destination, and Storage in Diverse Archaeal Methanogens and Alkanotrophs
Johnson, C., England, A. M., Munro-Ehrlich, M., Colman, D., DuBois, J., & Boyd, E. (2021) · Journal of Bacteriology · doi:10.1128/jb.00117-21 · Cited by 30 · see citing works
Investigating Abiotic and Biotic Mechanisms of Pyrite Reduction
Spietz, R. L., Payne, D., Kulkarni, G., Metcalf, W. W., Roden, E., & Boyd, E. S. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.878387 · Cited by 33 · see citing works
An integrative computational model for large-scale identification of metalloproteins in microbial genomes: a focus on iron-sulfur cluster proteins.
Estellon, J., Ollagnier-de-Choudens, S., Smadja, M., Fontecave, M., & Vandenbrouck, Y. (2014) · Metallomics · doi:10.1039/c4mt00156g · Cited by 28
Reductive biomining of pyrite by methanogens
Spietz, R. L., Payne, D., Szilagyi, R. K., & Boyd, E. S. (2022) · Trends in Microbiology · doi:10.1016/j.tim.2022.05.005 · Cited by 33 · see citing works
Presence of tRNA-dependent pathways correlates with high cysteine content in methanogenic Archaea.
Klipcan, L., Frenkel-Morgenstern, M., & Safro, M. (2008) · Trends in Genetics · doi:10.1016/j.tig.2007.11.007 · Cited by 26 · see citing works
Examining Pathways of Iron and Sulfur Acquisition, Trafficking, Deployment, and Storage in Mineral-Grown Methanogen Cells
Payne, D., Shepard, E. M., Spietz, R. L., Steward, K. F., Brumfield, S., Young, M., Bothner, B. B., Broderick, W. E., Broderick, J. B., & Boyd, E. S. (2021) · Journal of Bacteriology · doi:10.1128/jb.00146-21 · Cited by 27 · see citing works
The Archaeon Methanosarcina acetivorans Contains a Protein Disulfide Reductase with an Iron-Sulfur Cluster
Lessner, D., & Ferry, J. (2007) · Journal of Bacteriology · doi:10.1128/jb.00891-07 · Cited by 22 · see citing works
“Thus, it is important to note that methanoarchaea appear to contain the greatest number of Fe-S proteins, as estimated by the abundance of the CX2CX2CX3C motif in proteins encoded in methanoarchaeon genomes (47).”
Background
Subunit D of RNA Polymerase from Methanosarcina acetivorans Contains Two Oxygen-labile [4Fe-4S] Clusters
Lessner, F. H., Jennings, M. E., Hirata, A., Duin, E. C., & Lessner, D. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.331199 · Cited by 19 · see citing works
“Methanogens are predicted to contain the largest number of [4Fe-4S] proteins, many of which are oxygen-labile (39).”
Background
The Fur iron regulator-like protein is cryptic in the hyperthermophilic archaeonThermococcus kodakaraensis
Louvel, H. ̈., Kanai, T., Atomi, H., & Reeve, J. N. (2009) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2009.01594.x · Cited by 17 · see citing works
Tuning Gene Expression by Phosphate in the Methanogenic Archaeon Methanococcus maripaludis.
Akinyemi, T. S., Shao, N.-N., Lyu, Z., Drake, I., Liu, Y., & Whitman, W. (2021) · ACS Synthetic Biology · doi:10.1021/acssynbio.1c00322 · Cited by 18 · see citing works
Self-citation
An ancient family of SelB elongation factor-like proteins with a broad but disjunct distribution across archaea
Atkinson, G. C., Hauryliuk, V., & Tenson, T. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-22 · Cited by 15 · see citing works
“Cysteine is overrepresented in methanogenic archaea, which contain many iron sulfur cluster proteins, coordinating iron via cysteine-rich motifs [35].”
Background
Identification of disulfide reductases in Campylobacterales: a bioinformatics investigation
Kaakoush, N., Sterzenbach, T., Miller, W., Suerbaum, S., & Mendz, G. (2007) · Antonie van Leeuwenhoek · doi:10.1007/s10482-007-9171-5 · Cited by 16
“This distribution was similar to that of CXXCXXCXXXC motifs (4Fe–4S clusters) found in 120 bacterial and archeal genomes (Major et al. 2004).”
MethodResultInfluential
Methanosarcina acetivorans contains a functional ISC system for iron-sulfur cluster biogenesis
Deere, T. M., Prakash, D., Lessner, F. H., Duin, E. C., & Lessner, D. J. (2020) · BMC Microbiology · doi:10.1186/s12866-020-02014-z · Cited by 12 · see citing works
Experimental Approaches for Testing the Hypothesis of the Emergence of Life at Submarine Alkaline Vents
Altair, T., Borges, L. G. F., Galante, D., & Varela, H. (2021) · Life · doi:10.3390/life11080777 · Cited by 33 · see citing works
“Iron–sulfur shows its importance due to its prevalence in active centers of metalloenzymes [54,96].”
Background
Coacervates Forming Coexisting Phases on a Mineral Surface
Chen, J., Bai, Q., Li, Y., Liu, Z., Li, Y., & Liang, D. (2023) · Langmuir · doi:10.1021/acs.langmuir.3c00101 · Cited by 14 · see citing works
Sulfur Assimilation and Trafficking in Methanogens
Perona, J., Rauch, B. J., & Driggers, C. M. (2018) · doi:10.1007/978-3-319-69078-0_14 · Cited by 7
The [4Fe‐4S] clusters of Rpo3 are key determinants in the post Rpo3/Rpo11 heterodimer formation of RNA polymerase in Methanosarcina acetivorans
Jennings, M. E., Lessner, F. H., Karr, E. A., & Lessner, D. J. (2016) · MicrobiologyOpen · doi:10.1002/mbo3.399 · Cited by 4 · see citing works
A shift between mineral and nonmineral sources of iron and sulfur causes proteome-wide changes in Methanosarcina barkeri
Fausset, H., Spietz, R. L., Cox, S., Cooper, G., Spurzem, S., Tokmina-Lukaszewska, M., DuBois, J. L., Broderick, J., Shepard, E., Boyd, E. S., et al. (2024) · Microbiology spectrum · doi:10.1128/spectrum.00418-23 · Cited by 3
Development of molecular cluster models to probe pyrite surface reactivity
Kour, M., Táborosi, A., Boyd, E., & Szilágyi, R. (2023) · Journal of Computational Chemistry · doi:10.1002/jcc.27213 · Cited by 3
Purine salvage in Methanocaldococcus jannaschii: Elucidating the role of a conserved cysteine in adenine deaminase
Miller, D. V., Brown, A. M., Xu, H.-M., Bevan, D., & White, R. (2016) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.25033 · Cited by 3
Feedback regulation of iron-sulfur cluster biogenesis
Stuteley, S. M., Chen, J.-H., Wang, J., Dawes, S., Baker, E. N., Squire, C. J., Pandelia, M., & Bashiri, G. (2025) · bioRxiv · doi:10.1101/2025.06.15.659787 · Cited by 2
Impact of mineral and non-mineral sources of iron and sulfur on the metalloproteome of Methanosarcina barkeri
Larson, J., Tokmina-Lukaszewska, M., Payne, D., Spietz, R. L., Fausset, H., Alam, M., Brekke, B. K., Pauley, J., Hasenoehrl, E. J., Shepard, E., et al. (2024) · Applied and Environmental Microbiology · doi:10.1128/aem.00516-24 · Cited by 2
Biochemical and genetic studies define the functions of methylthiotransferases in methanogenic and methanotrophic archaea
Boswinkle, K., Dinh, T.-A., & Allen, K. D. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1304671 · Cited by 2
“They are found in a wide range of anaerobic environments including marine and freshwater ecosystems, anoxic soils, anaerobic sewage digesters, and as important components of animal microbiomes (Lyu et al., 2018; Moissl-Eichinger et al., 2018; Borrel et al., 2020).”
Environmental controls on the kinetics of iron-sulfur cluster nucleation and nanoparticle formation
Kour, M., Callaway, H. M., & Boyd, E. S. (2025) · Journal of Nanoparticle Research · doi:10.1007/s11051-025-06445-5 · Cited by 1 · see citing works
“…Fe(II), HS − , and FeS aq are commonly detected in marine hydrothermal environment emissions [68], potentially consistent with the prevalence of anaerobes, including methanogens and sulfate reducers in these environments (as reviewed in [69]), that have a high demand for iron-sulfur cofactors [70].”
Metabolic adaptation of a methanogen to a ferruginous environment associated with intracellular Fe- and S-rich nanoparticles
Zhang, Y., Zhang, D., 盛翊智, Chen, H., Li, G., & Dong, H. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1967823
“…of 22.2 4Fe-4S motif-containing open reading frames (ORFs) per 1,000 total ORFs, far exceeding the values observed in obligate anaerobes Desulfitobacterium hafniense (~16.0), facultative anaerobe E. coli K-12 (~9.1), and aerobic archaeon Sulfolobus solfataricus (~6.4) (Major et al., 2004).”
Influential
Protein Thioether Crosslinks Installed by a SPASM-Containing Radical SAM Enzyme from Methanogenic Archaea
Dieter, E. M., Woodard, A., Green, J., Xiong, J., Guo, Y.-S., Broderick, W., Mitchell, D. A., & Broderick, J. (2026) · ACS Bio & Med Chem Au · doi:10.1021/acsbiomedchemau.6c00133
Développements méthodologiques pour l'identification in silico des métalloprotéines dans les protéomes bactériens : le cas des protéines à centre Fer-Soufre
Estellon, J. (2012) · doi:10.70675/ae93d28fz1d57z42bez8dbbze9558434cd7b

Authors: Major, T. A., Burd, H., & Whitman, W. B.
Affiliations: University of Georgia (US)
Igenbio (United States) (US)
Corresponding author: Whitman, William B.
ORCID: Whitman, William B.
Venue: FEMS Microbiology Letters
Publisher: Oxford University Press (OUP)
Published: 2004-10
Volume: 239
Issue: 1
Pages: 117-123
ISSN: 0378-1097 (ISSN-L)
1574-6968
DOI: 10.1016/j.femsle.2004.08.027
OpenAlex: W2056437023
Cited by: 55
References: 0
Citations by year: 2026: 3 · 2025: 2 · 2024: 2 · 2023: 3 · 2022: 4 · 2021: 5 · 2020: 3 · 2018: 2 · 2017: 1 · 2016: 4 · 2014: 5 · 2013: 2 · 2012: 3
FWCI: 1.83
Type: journal article
Language: en
Open access: closed
Locations: FEMS Microbiology Letters (publishedVersion)
PubMed (publishedVersion)
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
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: methanogenic archaea, methanogenesis, archaea, anaerobic bacteria, open reading frames, genome size, Desulfitobacterium hafniense, reductase
MeSH terms: Anaerobiosis, Archaea, Bacteria, Hot Temperature, Iron-Sulfur Proteins, Methane, Phylogeny, Genome, Bacterial, Genome, Archaeal, Amino Acid Motifs, Genomics

About these checks

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.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review