Energetics of Respiration and Oxidative Phosphorylation in Mycobacteria

May combine two claims.

In M. tuberculosis, the bc1-aa3 pathway is essential for growth, suggesting that this bacterium cannot adapt in the way M. smegmatis does.

“In M. tuberculosis, the bc1-aa3 pathway is essential for growth suggesting an inability of this bacterium to adapt in a manner analogous to M. smegmatis (70).”

• cites [70] sourceDisputed

  The Discussion describes the pathway’s essentiality in M. tuberculosis as apparent, based on failure to recover mutants under the conditions tested. Although it considers inability to adapt as a possibility, it concludes that respiratory adaptation probably does occur in M. tuberculosis; the mutants may instead grow too poorly to be detected. (LLM, conf=0.88)

  Checked by a reasoning model — may be wrong.

  Experimental — accuracy not yet measured

May combine two claims.

nuo is down-regulated in M. tuberculosis during mouse lung infection, survival in macrophages, NRP-1 and NRP-2, and starvation in vitro.

“Several studies have reported that nuo is down-regulated in M. tuberculosis during mouse lung infection (18), survival in macrophages (19), in both non-replicating persistence (NRP)-1 (1% oxygen saturation) and NRP-2 (0.06% oxygen saturation) relative to aerated mid-log growth (18), and upon starvation in vitro (20).”

• cites [18] sourceSupported
• cites [19] sourceSupported
• cites [20] sourceSupported

May combine two claims.

Proline dehydrogenase is upregulated under both energy-limiting conditions and hypoxia.

“Proline dehydrogenase is upregulated under both energy-limiting conditions and hypoxia (7, 16)”

• cites [7] sourceNot checked — no full text of the source
• cites [16] sourcePartly supported

  The Results (Energy Metabolism; page unavailable) identify proline dehydrogenase as upregulated during energy-limited slow growth. The same section says that nearly all dehydrogenases upregulated during slow growth had very low mRNA levels under hypoxia, with hydrogenases the only exceptions. It therefore does not support the claim that proline dehydrogenase was also upregulated under hypoxia. (LLM, conf=0.90)

  Experimental — accuracy not yet measured

May combine two claims.

Gene expression studies suggest that Hyd1 and Hyd2 serve as alternative electron sources during nutrient starvation, whereas Hyd3 and the membrane-bound hydrogenase more likely dispose electrons under anaerobic conditions.

“Gene expression studies suggest that Hyd1 and Hyd2 are used during nutrient starvation as an alternative electron source (Figure 2) while Hyd3 and the membrane-bound hydrogenase are more likely to have a function in disposing electrons under anaerobic conditions (16) (Figure 3).”

• cites [16] sourcePartly supported

  The Results (Energy Metabolism; page unavailable) show that Hyd3 is upregulated under low oxygen, and the Discussion (Adaptation to Hypoxia; page unavailable) proposes hydrogen production as a redox sink under hypoxia. But the paper predicts all three hydrogenases to be soluble, not membrane-bound, and does not establish electron disposal as Hyd3’s specific function. (LLM, conf=0.88)

  Experimental — accuracy not yet measured

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

Hyd2 appears to be a founding member of the Group 5 high-affinity hydrogenases.

“Hyd2 appears to be a founding member of the Group 5 high-affinity hydrogenases (52, 53).”

• cites [52] sourceCould not verify

  The Discussion (p. 6) defines group 5 as a distinct group of putative high-affinity [NiFe]-hydrogenases. Searches for “Hyd2,” “hydrogenase 2,” and a founding member found no passage identifying Hyd2 or placing it in that group, so our copy does not establish the claim about Hyd2. (LLM, conf=0.72)

  Experimental — accuracy not yet measured
• cites [53] sourceNot checked — no full text of the source

May combine two claims.

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).”

• cites [51] sourcePartly supported

  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

May combine two claims.

A more recent study suggests the glyoxylate shunt, not the reverse TCA cycle, is used to metabolize glycolytic and fatty acid carbon sources in response to oxygen limitation, producing succinate.

“A more recent study suggests that the glyoxylate shunt, and not the reverse TCA, is used to metabolize both glycolytic and fatty acid carbon sources in response to oxygen limitation and this route also produces succinate as its metabolic end product (43).”

• cites [43] sourceSupported

May combine two claims.

NDH-2 has not been reported in mammalian mitochondria, leading to the proposal that it may be a drug target.

“NDH-2 has not been reported in mammalian mitochondria leading to the proposal that these enzymes may represent a potential drug target for the treatment of human pathogens (6, 12, 27, 30, 31) and intracellular parasites (32).”

• cites [6] sourceNot checked — no full text of the source
• cites [12] sourceSupported
• cites [27] sourceSupported

May combine two claims.

NDH-2 is non-proton translocating, does not conserve energy, and is present in two copies in M. tuberculosis.

“The second class is NDH-2, a non-proton translocating type II NADH dehydrogenase that does not conserve energy and is present in two copies (Ndh and NdhA) in M. tuberculosis (12) (Table 1).”

• cites [12] sourceSupported

May combine two claims.

During oxygen limitation, large amounts of succinate are produced by this pathway and used to sustain membrane potential, ATP synthesis, and TCA cycle precursors.

“The authors propose that during oxygen limitation large amounts of succinate are produced by this pathway that are used to sustain the membrane potential, ATP synthesis and TCA cycle precursors akin to a “metabolic battery” (43).”

• cites [43] sourceSupported

May combine two claims.

M. smegmatis can grow on proline as the sole carbon and energy source, and PRODH is an important electron donor under energy-limiting conditions and hypoxia.

“It has been shown that M. smegmatis can grow on proline as the sole carbon and energy source and also that PRODH is an important electron donor, under both energy-limiting conditions and hypoxia (7, 16).”

• cites [7] sourceNot checked — no full text of the source
• cites [16] sourcePartly supported

  The Results > Energy Metabolism section (page unavailable) reports that proline dehydrogenase was among the proposed electron donors upregulated during slow growth under energy limitation. It does not establish that M. smegmatis grows on proline as its sole carbon and energy source or that PRODH is an important electron donor under hypoxia; the same section says nearly all dehydrogenases upregulated during slow growth had very low mRNA levels under hypoxia, except hydrogenases. (LLM, conf=0.87)

  Experimental — accuracy not yet measured

May combine two claims.

SDH1 and SDH2 are differentially expressed under energy- or oxygen-limiting conditions in M. smegmatis: under energy limitation SDH1 is upregulated 4-fold and SDH2 downregulated 3-fold; under oxygen limitation SDH1 is downregulated 30-fold and SDH2 upregulated 2-fold.

“In fact, SDH1 and SDH2 have been shown to be differentially expressed under energy- or oxygen-limiting conditions in M. smegmatis (16). Under energy-limiting conditions SDH1 was upregulated 4-fold while SDH2 was downregulated 3-fold. Under oxygen-limiting conditions, SDH1 was downregulated 30-fold while SDH2 was upregulated 2-fold.”

• cites [16] sourcePartly supported

  Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  Experimental — accuracy not yet measured

May combine two claims.

The M. tuberculosis genome encodes NDH-1 (nuo operon) and NDH-2 (two copies, Ndh and NdhA).

“Weinstein et al. identified genes for two classes of NADH:menaquinone oxidoreductases in the genome of M. tuberculosis (12) (Table 1).”

• cites [12] sourceSupported

May combine two claims.

M. smegmatis can oxidize molecular hydrogen in the presence of carbon monoxide, which implies that it expresses a functional hydrogenase.

“It has been shown that M. smegmatis, among other mycobacterial species, can oxidize molecular hydrogen in the presence of carbon monoxide (CO), implying that M. smegmatis expresses a functional hydrogenase (54).”

• cites [54] sourcePartly supported

  The Results report H₂ uptake by M. smegmatis, supporting the inference that it has a functional hydrogen-oxidizing enzyme. They report CO uptake separately, however, and do not establish that H₂ oxidation occurred in the presence of CO; the paper does not directly identify a hydrogenase. (LLM, conf=0.84)

  Experimental — accuracy not yet measured

May combine two claims.

Membrane-associated malate quinone oxidoreductase oxidizes malate to oxaloacetate and transfers reducing equivalents to menaquinone.

“The membrane-associated malate quinone oxidoreductase (MQO) oxidizes malate to oxaloacetate and transfers the reducing equivalents to menaquinone (MK) (59, 60) (Figure 3).”

• cites [59] sourceNot checked — no full text of the source
• cites [60] sourcePartly supported

  The introductory passage and the L-malate oxidation section state that Mqo oxidizes malate to oxaloacetate and donates electrons at the quinone pool; the latter section demonstrates reduction of ubiquinone-1. The paper does not establish menaquinone specifically as the electron acceptor: it says the natural direct acceptor is most likely a quinone, while menaquinone-4 did not stimulate activity in the reported assay. No page number is available in our copy. (LLM, conf=0.86)

  Experimental — accuracy not yet measured

May combine two claims.

TMC207 is bactericidal against most mycobacterial species but only bacteriostatic against M. avium and M. smegmatis.

“TMC207 is bactericidal towards most species of mycobacteria (109), but is only bacteriostatic against M. avium (118) and M. smegmatis (Berney and Cook, unpublished data).”

• cites [109] sourcePartly supported

  The Chemistry and in vitro anti-mycobacterial activity section reports bactericidal activity against M. tuberculosis and low MICs for several other mycobacterial species. Low MICs do not establish that the drug is bactericidal against most species. The M. avium and M. smegmatis clauses cite different sources, so they are not judged against this paper; page numbers are unavailable in our copy. (LLM, conf=0.88)

  Experimental — accuracy not yet measured
• cites [118] sourceNot checked — no full text of the source

May combine two claims.

The nirA gene is misannotated and is actually sirA, a sulfite reductase essential for growth on sulfate or sulfite as the sole sulfur source.

“However, a subsequent study has reported that the nirA gene is misannotated and is in fact sirA, a sulfite reductase shown to be essential for growth on sulfate or sulfite as the sole sulfur source (93) (Table 1).”

• cites [93] sourceSupported

May combine two claims.

The clinically most promising diarylquinolines target F1Fo-ATP synthase and inhibit ATP synthesis.

“The most promising compounds clinically, the diarylquinolines, have been shown to target the F1Fo-ATP synthase and inhibit ATP synthesis (109, 111, 112).”

• cites [109] sourcePartly supported

  The Chemistry and in vitro anti-mycobacterial activity section identifies the F0 subunit of ATP synthase as the target of the diarylquinoline R207910 and says the drug inhibits its proton pump. The Discussion says ATP synthase inhibition may lead to ATP depletion, but does not establish direct inhibition of ATP synthesis; nor does the paper rank diarylquinolines as the most promising compounds clinically. Page numbers are unavailable in our copy. (LLM, conf=0.84)

  Experimental — accuracy not yet measured
• cites [111] sourceNot checked — no full text of the source
• cites [112] sourceSupported

May combine two claims.

In M. tuberculosis, cytochrome bd is upregulated in early NRP-1, in NRP-2, and in response to nitric oxide.

“In M. tuberculosis, cytochrome bd is upregulated in the early stages of NRP-1 (i.e. decreasing oxygen) (68), in NRP-2 (18) and in response to nitric oxide (NO) (18).”

• cites [68] sourceNot checked — no full text of the source
• cites [18] sourceSupported

May combine two claims.

Exogenous nitrate did not affect long-term persistence during gradual oxygen depletion but was important during rapid adaptation to hypoxia lasting less than 18 h.

“Sohaskey (91) has reported that exogenously supplied nitrate has no effect on long-term persistence during gradual oxygen depletion, but played an important role during rapid adaptation to hypoxia (< 18 h).”

• cites [91] sourcePartly supported

  The Results report that nitrate had no effect on survival during gradual oxygen depletion and improved survival after sudden anaerobiosis. However, the <18 h threshold describes how quickly anaerobic conditions were created, not how long hypoxia lasted; survival was tracked for 26 days. (LLM, conf=0.85)

  Experimental — accuracy not yet measured

May combine two claims.

Under the same macrophage conditions, fumarate reductase, nitrate reductase, and NDH-2 are upregulated.

“In contrast, fumarate reductase, nitrate reductase and NDH-2 are all upregulated under these conditions (19).”

• cites [19] sourceSupported

May combine two claims.

In M. tuberculosis, the atp operon is downregulated during growth in macrophages, in mouse lung, and in cells exposed to NO or hypoxia.

“In M. tuberculosis, the atp operon is downregulated during growth in macrophages (19), the mouse lung and in cells exposed to NO or hypoxia (18).”

• cites [19] sourceSupported
• cites [18] sourcePartly supported

  The Results and Discussion report decreased atpA and atpD expression during chronic mouse-lung infection. The section on in vitro respiratory flexibility reports that both transcripts decreased under oxygen depletion, but its discussion of NO-treated cells does not establish downregulation of the atp genes. The macrophage portion is cited to a different source (19), not this paper (18). (LLM, conf=0.84)

  Experimental — accuracy not yet measured

May combine two claims.

Hyd2 oxidizes hydrogen at very low concentrations, consistent with its proposed role as a high-affinity hydrogenase.

“These data suggest that Hyd2 oxidizes hydrogen at very low concentrations, which fits with its purported role as a high-affinity hydrogenase (52).”

• cites [52] sourcePartly supported

  The Results (p. 3) identify a putative high-affinity [NiFe]-hydrogenase in S. avermitilis, and the Discussion (p. 6) describes high-affinity H₂ oxidation in Streptomyces isolates possessing the relevant genes. These passages support the proposed role of that hydrogenase group, but the paper does not identify Hyd2 or establish that Hyd2 itself oxidizes H₂ at very low concentrations. (LLM, conf=0.78)

  Experimental — accuracy not yet measured

May combine two claims.

In E. coli, cytochrome bo has a micromolar oxygen Km and cytochrome bd has a nanomolar oxygen Km, and both are coordinately regulated by ArcBA and FNR.

“For example, in E. coli, cytochrome bo (Km for oxygen in the micromolar range) and cytochrome bd (Km for oxygen in the nanomolar range) (63, 64) are coordinately regulated by the ArcBA system and transcriptional regulator FNR (65).”

• cites [63] sourceNot checked — no full text of the source
• cites [64] sourceNot checked — no full text of the source
• cites [65] sourcePartly supported

  The Abstract and Introduction (page not available) state that ArcA/ArcB and Fnr regulate the cytochrome bd (cydAB) operon. The paper contrasts cytochrome bo and bd expression as oxygen becomes limiting, but its substantive passages do not establish that both oxidases are coordinately regulated by both regulators. The oxygen-Km values are attached to other citations in the citing sentence, not to this paper. (LLM, conf=0.79)

  Experimental — accuracy not yet measured

May combine two claims.

M. smegmatis lacks an MDH homologue, and MQO gene expression increased fourfold in response to low oxygen.

“M. smegmatis lacks an MDH homologue and it was shown that MQO responded to low oxygen concentration with 4-fold increase in gene expression (16).”

• cites [16] sourceSupported

May combine two claims.

Slow-growing M. smegmatis cells with low atp operon expression upregulate the atp operon threefold when exposed to 0.6% oxygen saturation, suggesting an important role in hypoxia adaptation.

“When slow growing cells of M. smegmatis (70 h doubling time), with low levels of atp operon expression, are exposed to hypoxia (0.6% oxygen saturation), the atp operon is upregulated 3-fold suggesting an important role for this enzyme during adaptation to hypoxia (16).”

• cites [16] sourcePartly supported

  The Results (Energy Metabolism; page not available) report that the F1Fo-ATP synthase gene cluster was downregulated during slow growth at 50% oxygen saturation, supporting the claim of low expression. The paper also studies slow-growing cells at 0.6% oxygen saturation, but its account of the hypoxic response does not report threefold upregulation of the atp operon or assign that operon an important role in hypoxia adaptation; it instead highlights oxidases and hydrogenases. (LLM, conf=0.84)

  Experimental — accuracy not yet measured

May combine two claims.

Induction of the enduring hypoxic response is independent of DosR, suggesting that other sensory and regulatory mechanisms signal prolonged hypoxia.

“Induction of EHR was independent of DosR, suggesting that other sensory and regulatory mechanisms must exist to signal prolonged exposure to hypoxia.”

• cites [125] sourceSupported
  Experimental — accuracy not yet measured

May combine two claims.

A set of 230 genes is significantly upregulated at four and seven days of hypoxia but not initially, and this set is called the enduring hypoxic response.

“In contrast, a set of 230 genes was significantly up-regulated at four and seven days of hypoxia, but not initially, and were termed the enduring hypoxic response (EHR) (125).”

• cites [125] sourceSupported

May combine two claims.

The fourth putative hydrogenase is found only in pathogenic mycobacteria, including the M. tuberculosis complex, and appears restricted to slow-growing species.

“However, the fourth putative hydrogenase is only found in pathogenic mycobacteria (including M. tuberculosis complex) and seems to be restricted to slow-growers (Table 1).”

• cites Table 1Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

May combine two claims.

A proC mutant of M. tuberculosis was avirulent in immunocompetent mice, but this was not due to inability to proliferate intracellularly because bacterial loads increased in mouse lungs after 20 days.

“Interestingly, a proC mutant of M. tuberculosis was avirulent in immunocompetent mice, however this was not due to its inability to proliferate intracellulary because bacterial loads increased in the mouse lungs after 20 days post infection (49).”

• cites [49] sourceNot checked — no full text of the source

May combine two claims.

TMC207, an inhibitor of F1FO-ATP synthase, is bactericidal against hypoxic non-replicating M. tuberculosis but has no effect on ΔΨ.

“The addition of TMC207, a specific inhibitor of the F1FO-ATP synthase, was bactericidal against hypoxic, non-replicating M. tuberculosis, but had no effect on the ΔΨ (6).”

• cites [6] sourceNot checked — no full text of the source

May combine two claims.

M. tuberculosis H37Rv grown in infected mouse lungs had high endogenous respiration not stimulated by exogenous substrates, while in vitro grown cells respired these substrates at high rates.

“Early studies on respiration demonstrated that Mycobacterium tuberculosis H37Rv, grown in the lungs of infected mice, had high rates of endogenous respiration that were not stimulated by exogenous substrates (e.g. acetate, pyruvate, glucose, glycerol, lactate) (1). In contrast, cells grown in vitro respired these substrates at high rates.”

• cites [1] sourceNot checked — no full text of the source

May combine two claims.

Mutations in ndh of M. smegmatis cause temperature sensitivity, amino acid auxotrophy, and resistance to INH and ETH.

“Mutations in the ndh gene of M. smegmatis result in a pleitropic effect: temperature sensitivity, amino acid auxotrophy and resistance to the first-line anti-TB drug isoniazid (INH) and its analog and second-line anti-TB drug ethionamide (ETH) (14, 15).”

• cites [14] sourceNot checked — no full text of the source
• cites [15] sourceNot checked — no full text of the source

May combine two claims.

Measured P/O ratios for mycobacteria oxidizing NADH or succinate are 0.52 and 0.36, respectively.

“Measured experimental values for mycobacteria oxidizing NADH or succinate yield P/O ratios of 0.52, and 0.36, respectively (5).”

• cites [5]Not checked — no full text of the source

May combine two claims.

Hypoxic, non-replicating M. tuberculosis generate a total PMF of −113 mV, with −73 mV electrical potential and −41 mV ZΔpH.

“Rao et al. (6) have reported that hypoxic, non-replicating M. tuberculosis generate a total PMF of −113 mV, −73 mV of electrical potential (ΔΨ) and −41 mV of ZΔpH.”

• cites [6] sourceNot checked — no full text of the source

May combine two claims.

Mycobacteria possess two terminal respiratory oxidases: an aa3-type cytochrome c oxidase encoded by ctaBCDE and a cytochrome bd-type menaquinol oxidase encoded by cydABCD.

“only two terminal respiratory oxidases present in mycobacteria, an aa3-type cytochrome c oxidase (encoded by ctaBCDE) belonging to the heme-copper respiratory oxidase family and cytochrome bd-type menaquinol oxidase (cydABCD) (Figure 1).”

May combine two claims.

Growth of mycobacteria is sensitive to compounds that dissipate the membrane potential, and these compounds are bactericidal towards growing and non-growing cells.

“Growth of mycobacteria is sensitive to compounds that dissipate the membrane potential (e.g. protonophores and valinomycin) and these compounds are bactericidal towards growing and non-growing (aerobic or hypoxic) cells”

• cites [4] sourceNot checked — no full text of the source
• cites [6] sourceNot checked — no full text of the source

May combine two claims.

Thioridazine, which targets NDH-2, dissipates the ΔΨ and causes significant cell death in hypoxic non-replicating M. tuberculosis, suggesting NADH is an important electron donor for ΔΨ generation under hypoxia.

“The addition of thioridazine, a compound that targets NDH−2, results in dissipation of the ΔΨ and significant cell death suggesting that NADH is an important electron donor for the generation of the ΔΨ under hypoxic conditions.”

• cites [6] sourceNot checked — no full text of the source

May combine two claims.

Proline can be utilized as an electron donor as well as a carbon and nitrogen source.

“Proline can be utilized as an electron donor as well as a carbon and nitrogen source (Figure 2).”

May combine two claims.

The PMF-generating machinery comprises three energy-conserving steps: complex I (4H+/2e−), complex III (4H+/2e−), and complex IV (2H+/2e−), giving an overall stoichiometry of 10H+/2e− from NADH to oxygen.

“The PMF-generating machinery in mycobacteria comprises three energy-conserving steps: complex I (4H+/2e−), complex III (menaquinol-cytochrome c oxidoreductase, 4H+/2e−) and complex IV (2H+/2e−) suggesting that the overall proton translocation stoichiometry for the transfer of 2e− from NADH to oxygen is 10H+/2e−.”

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

ATP synthesis is obligatorily coupled to the electron transport chain and F1Fo-ATP synthase irrespective of oxygen concentration or PMF.

“Irrespective of the oxygen concentration or the protonmotive force (PMF), ATP synthesis is obligatorily coupled to the electron transport chain and the F1Fo-ATP synthase”

May combine two claims.

Fatty acids stimulated respiration of in vivo grown M. tuberculosis, suggesting M. tuberculosis switches to different energy sources in host tissues.

“Fatty acids, however, stimulated the respiration of in vivo grown M. tuberculosis, suggesting for the first time that M. tuberculosis switches to different energy sources in host tissues to fuel respiration.”

• cites [1] sourceNot checked — no full text of the source

May combine two claims.

These expression patterns indicate that SDH1 is the dedicated succinate dehydrogenase and SDH2 catalyses fumarate reductase activity important for survival under hypoxia.

“This indicates that SDH1 could be the dedicated succinate dehydrogenase and SDH2 catalyses fumarate reductase activity, which is important for survival under hypoxia.”

May combine two claims.

NDH-1 transfers electrons to menaquinone and conserves energy by translocating protons to generate a PMF.

“NDH-1 is encoded by the nuoABCDEFGHIJKLMN operon and transfers electrons to menaquinone, conserving energy by translocating protons across the membrane to generate a PMF (Figure 2).”

May combine two claims.

M. tuberculosis encodes a third complex (frdABCD) annotated as a fumarate reductase, absent in other pathogenic strains.

“As an exception among mycobacteria, M. tuberculosis encodes a third complex (frdABCD) that is annotated as a fumarate reductase (Table 1) and is absent in all other pathogenic strains like Mycobacterium avium paratuberculosis, Mycobacterium marinum, Mycobacterium ulcerans and M. leprae.”

May combine two claims.

Succinate dehydrogenase forms complex II of the respiratory chain and couples oxidative phosphorylation to central carbon metabolism.

“Succinate dehydrogenase forms complex II of the respiratory chain and couples oxidative phosphorylation to central carbon metabolism by being an integral part of the TCA cycle (Figure 2).”

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

In bacteria, three types of respiratory NADH dehydrogenases exist: NDH-1, NDH-2, and NQR.

“In bacteria three different types of respiratory NADH dehydrogenases have been identified and characterized on the basis of reaction mechanism, subunit composition and protein architecture (11). These include the proton-pumping type I NADH dehydrogenase (NDH-1, complex I), non-proton pumping type II NADH dehydrogenase (NDH-2) and sodium-pumping NADH dehydrogenase (NQR).”

• cites [11] sourceNot checked — no full text of the source

May combine two claims.

Mycobacteria generally grow at neutral pH and generate a PMF of approximately −180 mV.

“Mycobacteria generally grow at neutral pH and under these conditions generate a PMF of approximately −180 mV (4).”

• cites [4] sourceNot checked — no full text of the source

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

In the absence of oxygen, mycobacterial growth is inhibited even if alternative electron acceptors such as nitrate or fumarate are present.

“In the absence of oxygen, mycobacterial growth is inhibited, even if alternative electron acceptors are present (e.g. nitrate, fumarate).”

Classified as probably not a substantial claim.

Fumarate may be an important endogenous electron acceptor for energy production and redox balance in hypoxic non-replicating mycobacteria.

“In fact, it has been proposed that fumarate may be an important endogenous electron acceptor for energy production and maintenance of redox balance (oxidation of NADH to NAD+) in hypoxic non-replicating mycobacteria (6).”

• cites [6] sourceNot checked — no full text of the source

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

Hydrogenases catalyze reversible oxidation of molecular hydrogen and are central to energy metabolism in bacteria, archaea, and eukarya.

“Hydrogenases catalyze the reversible oxidation of molecular hydrogen: 2H+ + 2e−→ H2 and play a central role in energy metabolism of bacteria, archaea and eukarya (50).”

• cites [50]Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

May combine two claims.

These results suggest SDH2 has a pivotal role in the transition of M. tuberculosis from aerobic to hypoxic conditions and supports the hypothesis that it is a fumarate reductase.

“These results suggest that SDH2 has a pivotal role in the transition of M. tuberculosis from aerobic to hypoxic conditions and supports the hypothesis of it being a fumarate reductase.”

May combine two claims.

The cytochrome bd branch is bioenergetically less efficient because it does not translocate protons, and it is synthesized at low oxygen tensions in mycobacteria.

“The cytochrome bd branch is bioenergetically less efficient (non-proton translocating) and is synthesized at low oxygen tensions in mycobacteria (67).”

• cites [67] sourceNot checked — no full text of the source

May combine two claims.

Ehr enzymes lack the cysteine residues needed to ligate a [NiFe] center, and M. tuberculosis lacks maturation factors for these centers.

“Ehr enzymes lack the cysteine residues needed to ligate a [NiFe] center, which is the catalytic center of hydrogenases. Additionally, no maturation factors to synthesize these complex centers are present in M. tuberculosis.”

May combine two claims.

M. tuberculosis H37Ra has CO-DH activity and can grow on CO as a sole carbon and energy source.

“It has been shown that M. tuberculosis H37Ra, which possesses CO-DH activity, can grow on CO as a sole source of carbon and fuel for energy generation (56) (Figure 2).”

• cites [56] sourceNot checked — no full text of the source

May combine two claims.

M. tuberculosis narK2 complemented an E. coli double mutant, supporting a role for NarK2 in nitrate reduction by transporting nitrate into and nitrite out of the cell.

“The M. tuberculosis narK2 was shown to complement this E. coli double mutant, supporting a role for narK2 in nitrate reduction by coding for a transporter of nitrate into and nitrite out of the cell (85).”

• cites [85] sourceNot checked — no full text of the source

May combine two claims.

M. smegmatis does not appear to exploit the strategy of losing ATP synthase on fermentable substrates; the enzyme is essential for growth even on fermentable substrates, suggesting that substrate-level ATP production alone may be insufficient.

“This strategy does not appear to be exploited by M. smegmatis: the F1Fo-ATP synthase is essential for growth even on fermentable substrates, suggesting that ATP production from substrate level phosphorylation alone, despite increased glycolytic flux, may be insufficient to sustain growth of these bacteria (103).”

• cites [103] sourceNot checked — no full text of the source

May combine two claims.

Nitrite produced by nitrate reductase is not converted to ammonium but is exported from the cell by NarK2.

“These data support the proposal that nitrite produced by nitrate reductase is not converted to ammonium, but instead is exported from the cell by NarK2.”

• AssumptionRests on an assumption: M. tuberculosis cannot reduce nitrite.

May combine two claims.

In carboxydobacteria, carbon monoxide dehydrogenase oxidizes CO to CO2, and these bacteria can grow on CO as their sole carbon and energy source.

“Carbon monoxide dehydrogenase (CO-DH) is responsible for the oxidation of CO to carbon dioxide (CO2) in carboxydobacteria, which grow on CO as a sole source of carbon and energy (55).”

• cites [55] sourceNot checked — no full text of the source

May combine two claims.

Overexpression of recombinant M. tuberculosis nitrate reductase in M. tuberculosis or M. smegmatis did not allow anaerobic growth with nitrate, even though whole-cell nitrate reductase activity increased.

“Sohaskey and Wayne demonstrate that overexpression of recombinant M. tuberculosis nitrate reductase in either M. tuberculosis or M. smegmatis (low nitrate reductase activity) does not confer the ability of these cells to grow anaerobically i.e. no growth of either species is observed with nitrate anaerobically even though the nitrate reductase activity of whole cells increases (85).”

• cites [85] sourceNot checked — no full text of the source

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

Anaerobic bacteria commonly evolve H2 to recycle reducing equivalents obtained from anaerobic degradation of organic substrates.

“The evolution of H2 is a mechanism commonly employed by anaerobic bacteria to recycle reducing equivalents obtained from anaerobic degradation of organic substrates.”

May combine two claims.

An M. smegmatis cydA mutant had a reduced growth rate at 0.5-1% air saturation and a tenfold CFU difference after 140 h with cyanide at 21% air saturation when co-cultured with wild-type.

“The M. smegmatis cydA mutant showed a reduced growth rate at 0.5–1 % air saturation and also a 10-fold difference in CFU after 140 h of growth in the presence of cyanide at 21% air saturation when co-cultured with wild-type M. smegmatis (67).”

• cites [67] sourceNot checked — no full text of the source

May combine two claims.

Although no function has been proposed for Ehr enzymes, their homology to hydrogenases and proton-pumping type I NADH dehydrogenases suggests a role in energy metabolism.

“No function has yet been proposed for Ehr enzymes, but its homology to hydrogenases and to proton-pumping type I NADH dehydrogenases points to a role in energy metabolism.”

May combine two claims.

M. tuberculosis contains a copy of MQO and a cytoplasmic NAD+-dependent malate dehydrogenase.

“M. tuberculosis harbors a copy of MQO and a cytoplasmic NAD+-dependent malate dehydrogenase (MDH) (61, 62).”

• cites [61]Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

• cites [62] sourceNot checked — no full text of the source

May combine two claims.

The mycobacterial nitrate reductase does not support anaerobic growth, leaving its physiological role unclear.

“Based on these observations, it is apparent that this enzyme does not support anaerobic growth of mycobacteria and therefore the role of this enzyme in the physiology of mycobacteria is unclear.”

May combine two claims.

WhiB3 contains a 4Fe-4S cluster that binds NO.

“Singh and colleagues report that WhiB3 contains a 4Fe-4S cluster, which binds NO (121).”

• cites [121] sourceNot checked — no full text of the source

May combine two claims.

NarK2 is proposed to sense cellular redox state, possibly by monitoring electron flow to cytochrome oxidase, and to transport nitrate under reducing but not oxidizing conditions.

“It is proposed that NarK2 senses the redox state of the cell, possibly by monitoring the flow of electrons to cytochrome oxidase, and adjusts its activity so that nitrate is transported under reducing, but not under oxidizing conditions (86).”

• cites [86] sourceNot checked — no full text of the source

May combine two claims.

Without oxygen, alternative electron acceptors such as nitrate and fumarate are available to mycobacteria, but none has been shown to support growth of mycobacterial species.

“In the absence of oxygen, alternative electron acceptors (e.g. nitrate and fumarate) are available for mycobacterial metabolism, but none of these electron acceptors have been shown to support growth of mycobacterial species.”

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

During aerobic respiration, energy is conserved by generating a proton motive force across a proton-impermeable membrane.

“During aerobic respiration, energy is conserved by the generation of a PMF across a proton-impermeable membrane.”

May combine two claims.

Neither the Dos system nor WhiB3 controls any component of the electron transport machinery in M. tuberculosis.

“A striking observation is that neither Dos nor WhiB3 controls any component of the electron transport machinery in M. tuberculosis.”