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The longitudinal and cross-sectional heterogeneity of the intestinal microbiota. Curr Opin Microbiol 2021; 63:221-230. [PMID: 34428628 DOI: 10.1016/j.mib.2021.08.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/04/2021] [Indexed: 02/07/2023]
Abstract
A central goal of microbiome research is to understand the factors that balance gut-associated microbial communities, thereby creating longitudinal and cross-sectional heterogeneity in their composition and density. Whereas the diet dictates taxa dominance, microbial communities are linked intimately to host physiology through digestive and absorptive functions that generate longitudinal heterogeneity in nutrient availability. Additionally, the host differentially controls the access to electron acceptors along the longitudinal axis of the intestine to drive the development of microbial communities that are dominated by facultatively anaerobic bacteria in the small intestine or obligately anaerobic bacteria in the large intestine. By secreting mucus and antimicrobials, the host further constructs microhabitats that generate cross-sectional heterogeneity in the colonic microbiota composition. Here we will review how understanding the host factors involved in generating longitudinal and cross-sectional microbiota heterogeneity helps define physiological states that are characteristic of or appropriate to a homeostatic microbiome.
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Buckel W, Thauer RK. Flavin-Based Electron Bifurcation, Ferredoxin, Flavodoxin, and Anaerobic Respiration With Protons (Ech) or NAD + (Rnf) as Electron Acceptors: A Historical Review. Front Microbiol 2018; 9:401. [PMID: 29593673 PMCID: PMC5861303 DOI: 10.3389/fmicb.2018.00401] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 02/21/2018] [Indexed: 12/19/2022] Open
Abstract
Flavin-based electron bifurcation is a newly discovered mechanism, by which a hydride electron pair from NAD(P)H, coenzyme F420H2, H2, or formate is split by flavoproteins into one-electron with a more negative reduction potential and one with a more positive reduction potential than that of the electron pair. Via this mechanism microorganisms generate low- potential electrons for the reduction of ferredoxins (Fd) and flavodoxins (Fld). The first example was described in 2008 when it was found that the butyryl-CoA dehydrogenase-electron-transferring flavoprotein complex (Bcd-EtfAB) of Clostridium kluyveri couples the endergonic reduction of ferredoxin (E0′ = −420 mV) with NADH (−320 mV) to the exergonic reduction of crotonyl-CoA to butyryl-CoA (−10 mV) with NADH. The discovery was followed by the finding of an electron-bifurcating Fd- and NAD-dependent [FeFe]-hydrogenase (HydABC) in Thermotoga maritima (2009), Fd-dependent transhydrogenase (NfnAB) in various bacteria and archaea (2010), Fd- and H2-dependent heterodisulfide reductase (MvhADG-HdrABC) in methanogenic archaea (2011), Fd- and NADH-dependent caffeyl-CoA reductase (CarCDE) in Acetobacterium woodii (2013), Fd- and NAD-dependent formate dehydrogenase (HylABC-FdhF2) in Clostridium acidi-urici (2013), Fd- and NADP-dependent [FeFe]-hydrogenase (HytA-E) in Clostridium autoethanogrenum (2013), Fd(?)- and NADH-dependent methylene-tetrahydrofolate reductase (MetFV-HdrABC-MvhD) in Moorella thermoacetica (2014), Fd- and NAD-dependent lactate dehydrogenase (LctBCD) in A. woodii (2015), Fd- and F420H2-dependent heterodisulfide reductase (HdrA2B2C2) in Methanosarcina acetivorans (2017), and Fd- and NADH-dependent ubiquinol reductase (FixABCX) in Azotobacter vinelandii (2017). The electron-bifurcating flavoprotein complexes known to date fall into four groups that have evolved independently, namely those containing EtfAB (CarED, LctCB, FixBA) with bound FAD, a NuoF homolog (HydB, HytB, or HylB) harboring FMN, NfnB with bound FAD, or HdrA harboring FAD. All these flavoproteins are cytoplasmic except for the membrane-associated protein FixABCX. The organisms—in which they have been found—are strictly anaerobic microorganisms except for the aerobe A. vinelandii. The electron-bifurcating complexes are involved in a variety of processes such as butyric acid fermentation, methanogenesis, acetogenesis, anaerobic lactate oxidation, dissimilatory sulfate reduction, anaerobic- dearomatization, nitrogen fixation, and CO2 fixation. They contribute to energy conservation via the energy-converting ferredoxin: NAD+ reductase complex Rnf or the energy-converting ferredoxin-dependent hydrogenase complex Ech. This Review describes how this mechanism was discovered.
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Affiliation(s)
- Wolfgang Buckel
- Laboratory for Microbiology, Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Netz DJA, Pierik AJ, Stümpfig M, Mühlenhoff U, Lill R. The Cfd1–Nbp35 complex acts as a scaffold for iron-sulfur protein assembly in the yeast cytosol. Nat Chem Biol 2007; 3:278-86. [PMID: 17401378 DOI: 10.1038/nchembio872] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2006] [Accepted: 03/08/2007] [Indexed: 11/08/2022]
Abstract
Biogenesis of iron-sulfur ([Fe-S]) proteins in eukaryotes requires the function of complex proteinaceous machineries in both mitochondria and cytosol. In contrast to the mitochondrial pathway, little is known about [Fe-S] protein assembly in the cytosol. So far, four highly conserved proteins (Cfd1, Nbp35, Nar1 and Cia1) have been identified as members of the cytosolic [Fe-S] protein assembly machinery, but their molecular function is unresolved. Using in vivo and in vitro approaches, we found that the soluble P-loop NTPases Cfd1 and Nbp35 form a complex and bind up to three [4Fe-4S] clusters, one at the N terminus of Nbp35 and one each at a new C-terminal cysteine-rich motif present in both proteins. These labile [Fe-S] clusters can be rapidly transferred and incorporated into target [Fe-S] apoproteins in a Nar1- and Cia1-dependent fashion. Our data suggest that the Cfd1-Nbp35 complex functions as a novel scaffold for [Fe-S] cluster assembly in the eukaryotic cytosol.
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Affiliation(s)
- Daili J A Netz
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, D-35033 Marburg, Germany
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Sparling R, Islam R, Cicek N, Carere C, Chow H, Levin DB. Formate synthesis by Clostridium thermocellum during anaerobic fermentation. Can J Microbiol 2006; 52:681-8. [PMID: 16917525 DOI: 10.1139/w06-021] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have detected formate synthesis by Clostridium thermocellum 27405 cultured in both cellobiose and alpha-cellulose. While formate synthesis has been reported for one strain of C. thermocellum (strain I-1-B), numerous studies of C. thermocellum 27405 fermentation, conducted under different growth conditions, failed to detect the presence of formate. Thus, the status of formate synthesis as a fermentation end product by C. thermocellum has been uncertain. Formate synthesis competes with the synthesis of hydrogen (H2) as a fermentation end product, and thus would negatively impact H2 yields in processes designed to generate H2 from biomass. Understanding the mechanism of formate synthesis is the first step in devising means of mitigating its production. Transcription of putative pfl, fnr, and adhE genes, encoding pyruvate formate-lyase (PFL), PFL-activating enzyme (PFL-AE), and alcohol dehydrogenase E (ADH-E) enzymes, respectively, were detected by reverse transcriptase polymerase chain reactions using total RNA extracted from stationary phase C. thermocellum cultured on cellobiose. The PCR products observed correspond to the expected amplicon sizes. Nucleotide sequence analysis of the cloned PCR products followed by BLAST analyses confirmed their identity. Formate production was detected throughout growth, and PFL enzyme activity was detected in late log and stationary phase (OD600 = 0.7 and 0.9, respectively) in extracts of C. thermocellum cultured on cellobiose. BLAST analyses revealed that C. thermocellum PFL and PFL-AE have greater amino acid sequence identity with equivalent enzymes from Bacillus and Thermocynechococcus species than with other Clostridium species, but C. thermocellum ADH-E has greater amino acid sequence identity with Clostridium species.
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Watrous MM, Clark S, Kutty R, Huang S, Rudolph FB, Hughes JB, Bennett GN. 2,4,6-trinitrotoluene reduction by an Fe-only hydrogenase in Clostridium acetobutylicum. Appl Environ Microbiol 2003; 69:1542-7. [PMID: 12620841 PMCID: PMC150091 DOI: 10.1128/aem.69.3.1542-1547.2003] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2002] [Accepted: 12/23/2002] [Indexed: 11/20/2022] Open
Abstract
The role of hydrogenase on the reduction of 2,4,6-trinitrotoluene (TNT) in Clostridium acetobutylicum was evaluated. An Fe-only hydrogenase was isolated and identified by using TNT reduction activity as the selection basis. The formation of hydroxylamino intermediates by the purified enzyme corresponded to expected products for this reaction, and saturation kinetics were determined with a K(m) of 152 micro M. Comparisons between the wild type and a mutant strain lacking the region encoding an alternative Fe-Ni hydrogenase determined that Fe-Ni hydrogenase activity did not significantly contribute to TNT reduction. Hydrogenase expression levels were altered in various strains, allowing study of the role of the enzyme in TNT reduction rates. The level of hydrogenase activity in a cell system correlated (R(2) = 0.89) with the organism's ability to reduce TNT. A strain that overexpressed the hydrogenase activity resulted in maintained TNT reduction during late growth phases, which it is not typically observed in wild type strains. Strains exhibiting underexpression of hydrogenase produced slower TNT rates of reduction correlating with the determined level of expression. The isolated Fe-only hydrogenase is the primary catalyst for reducing TNT nitro substituents to the corresponding hydroxylamines in C. acetobutylicum in whole-cell systems. A mechanism for the reaction is proposed. Due to the prevalence of hydrogenase in soil microbes, this research may enhance the understanding of nitroaromatic compound transformation by common microbial communities.
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Affiliation(s)
- Mary M Watrous
- Civil and Environmental Engineering, Rice University, Houston, TX 77005-1892, USA
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Girbal L, Vasconcelos I, Saint-Amans S, Soucaille P. How neutral red modified carbon and electron flow inClostridium acetobutylicumgrown in chemostat culture at neutral pH. FEMS Microbiol Rev 1995. [DOI: 10.1111/j.1574-6976.1995.tb00163.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Tanisho S, Kamiya N, Wakao N. Hydrogen evolution of Enterobacter aerogenes depending on culture pH: mechanism of hydrogen evolution from NADH by means of membrane-bound hydrogenase. BIOCHIMICA ET BIOPHYSICA ACTA 1989; 973:1-6. [PMID: 2643990 DOI: 10.1016/s0005-2728(89)80393-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The pH dependency of cell mass productivity, the hydrogen evolution rate and the yield of hydrogen from glucose was measured by controlling the pH of the culture automatically. The cell mass productivity of Enterobacter aerogenes increased in a linear fashion up to a pH value of approx. 7.0. In contrast, both the evolution rate and the yield of hydrogen showed convex relationships up to a pH value of 7.0, both having maximum values at a pH of approx. 5.8. The maximum evolution rate was approx. 11.3 mmol H2 per g dry cell per h at 38 degrees C. A hypothetical mechanism for hydrogen evolution was proposed by taking our results and other research work into consideration. The proposed mechanism of hydrogen evolution was that NADH was oxidized on the inside surface of the cell membrane and protons were reduced on the outside surface by means of membrane-bound hydrogenase. This mechanism explains in a thermodynamic context the relation between the activity of the hydrogen evolution and the pH of the culture.
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Affiliation(s)
- S Tanisho
- Department of Materials Science and Chemical Engineering, Yokohama National University, Japan
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Thauer RK, Jungermann K, Decker K. Energy conservation in chemotrophic anaerobic bacteria. BACTERIOLOGICAL REVIEWS 1977; 41:100-80. [PMID: 860983 PMCID: PMC413997 DOI: 10.1128/br.41.1.100-180.1977] [Citation(s) in RCA: 1326] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Jungermann K, Kirchniawy H, Katz N, Thauer RK. NADH, a physiological electron donor in clostridial nitrogen fixation. FEBS Lett 1974; 43:203-6. [PMID: 4368970 DOI: 10.1016/0014-5793(74)81000-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Jungermann K, Thauer RK, Leimenstoll G, Decker K. Function of reduced pyridine nucleotide-ferredoxin oxidoreductases in saccharolytic Clostridia. BIOCHIMICA ET BIOPHYSICA ACTA 1973; 305:268-80. [PMID: 4147457 DOI: 10.1016/0005-2728(73)90175-8] [Citation(s) in RCA: 146] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Schön G, Biedermann M. Growth and adaptive hydrogen production of Rhodospirillum rubrum (F 1 ) in anaerobic dark cultures. BIOCHIMICA ET BIOPHYSICA ACTA 1973; 304:65-75. [PMID: 4633594 DOI: 10.1016/0304-4165(73)90115-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Thauer RK, Kirchniawy FH, Jungermann KA. Properties and function of the pyruvate-formate-lyase reaction in clostridiae. EUROPEAN JOURNAL OF BIOCHEMISTRY 1972; 27:282-90. [PMID: 4340563 DOI: 10.1111/j.1432-1033.1972.tb01837.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Benemann JR, Yoch DC, Valentine RC, Arnon DI. The electron transport system in nitrogen fixation by azotobacter. 3. Requirements for NADPH-supported nitrogenase activity. BIOCHIMICA ET BIOPHYSICA ACTA 1971; 226:205-12. [PMID: 4396856 DOI: 10.1016/0005-2728(71)90087-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Jungermann K, Rupprecht E, Ohrloff C, Thauer R, Decker K. Regulation of the Reduced Nicotinamide Adenine Dinucleotide-Ferredoxin Reductase System in Clostridium kluyveri. J Biol Chem 1971. [DOI: 10.1016/s0021-9258(18)62417-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Thauer RK, Rupprecht E, Ohrloff C, Jungermann K, Decker K. Regulation of the Reduced Nicotinamide Adenine Dinucleotide Phosphate-Ferredoxin Reductase System in Clostridium kluyveri. J Biol Chem 1971. [DOI: 10.1016/s0021-9258(18)62416-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Jungermann KA, Schmidt W, Kirchniawy FH, Rupprecht EH, Thauer RK. Glycine formation via threonine and serine aldolase. Its interrelation with the pyruvate formate lyase pathway of one-carbon unit synthesis in Clostridium kluyveri. EUROPEAN JOURNAL OF BIOCHEMISTRY 1970; 16:424-9. [PMID: 5477287 DOI: 10.1111/j.1432-1033.1970.tb01097.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Thauer RK, Rupprecht E, Jungermann K. Glyoxylate inhibition of clostridial pyruvate synthase. FEBS Lett 1970; 9:271-273. [PMID: 11947689 DOI: 10.1016/0014-5793(70)80374-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- R K. Thauer
- Biochemisches Institut, Albert Ludwigs Universität, 78, Freiburg, Germany
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Thauer RK, Rupprecht E, Jungermann K. The synthesis of one-carbon units from CO(2) via a new ferredoxin dependent monocarboxylic acid cycle. FEBS Lett 1970; 8:304-307. [PMID: 11947600 DOI: 10.1016/0014-5793(70)80293-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- R K. Thauer
- Biochemisches Institut, Albert Ludwigs Universität, 78, Freiburg, Germany
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Thauer RK, Jungermann K, Rupprecht E, Decker K. Hydrogen formation from NADH in cell-free extracts of Clostridium kluyveri. Acetyl coenzyme A requirement and ferredoxin dependence. FEBS Lett 1969; 4:108-112. [PMID: 11947158 DOI: 10.1016/0014-5793(69)80208-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- R K. Thauer
- Biochemisches Institut, Albert Ludwigs Universität, 78, Freiburg im Breisgau, Germany
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