Peck SC, Denger K, Burrichter A, Irwin SM, Balskus EP, Schleheck D. A glycyl radical enzyme enables hydrogen sulfide production by the human intestinal bacterium Bilophila wadsworthia. Proc Natl Acad Sci USA. 2019;116:3171.
PubMed
PubMed Central
CAS
Google Scholar
Laue H, Denger K, Cook AM. Taurine reduction in anaerobic respiration of Bilophila wadsworthia RZATAU. Appl Environ Microbiol. 1997;63:2016–21.
PubMed
PubMed Central
CAS
Google Scholar
Levine J, Ellis CJ, Furne JK, Springfield J, Levitt MD. Fecal hydrogen sulfide production in ulcerative colitis. Am J Gastroenterol. 1998;93:83–7.
PubMed
CAS
Google Scholar
Roediger WE, Moore J, Babidge W. Colonic sulfide in pathogenesis and treatment of ulcerative colitis. Digestive Dis Sci. 1997;42:1571–9.
CAS
Google Scholar
Wallace JL. Physiological and pathophysiological roles of hydrogen sulfide in the gastrointestinal tract. Antioxidants Redox Signaling. 2010;12:1125–33.
PubMed
CAS
Google Scholar
Carbonero F, Benefiel AC, Alizadeh-Ghamsari AH, Gaskins HR. Microbial pathways in colonic sulfur metabolism and links with health and disease. Front Physiol. 2012;3:448.
PubMed
PubMed Central
CAS
Google Scholar
Ijssennagger N, Belzer C, Hooiveld GJ, Dekker J, van Mil SW, Muller M, Kleerebezem M, van der Meer R. Gut microbiota facilitates dietary heme-induced epithelial hyperproliferation by opening the mucus barrier in colon. Proc Natl Acad Sci USA. 2015;112:10038–43.
PubMed
PubMed Central
CAS
Google Scholar
Ijssennagger N, van der Meer R, van Mil SWC. Sulfide as a mucus barrier-breaker in inflammatory bowel disease? Trends Mol Med. 2016;22:190–9.
PubMed
CAS
Google Scholar
Attene-Ramos MS, Wagner ED, Gaskins HR, Plewa MJ. Hydrogen sulfide induces direct radical-associated DNA damage. Mol Cancer Res. 2007;5:455–9.
PubMed
CAS
Google Scholar
Attene-Ramos MS, Wagner ED, Plewa MJ, Gaskins HR. Evidence that hydrogen sulfide is a genotoxic agent. Mol Cancer Res. 2006;4:9.
PubMed
CAS
Google Scholar
Hanson BT, Dimitri Kits K, Löffler J, Burrichter AG, Fiedler A, Denger K, Frommeyer B, Herbold CW, Rattei T, Karcher N, Segata N, Schleheck D, Loy A. Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut. ISME J. 2021. https://doi.org/10.1038/s41396-021-00968-0.
Article
PubMed
PubMed Central
Google Scholar
Olson KR, Straub KD. 2016. The Role of Hydrogen Sulfide in Evolution and the Evolution of Hydrogen Sulfide in Metabolism and Signaling. Physiology (Bethesda) 31:60–72.
CAS
Google Scholar
Banerjee R. 2011. Hydrogen sulfide: redox metabolism and signaling. Antioxid Redox Signal 15:339–41.
PubMed
PubMed Central
CAS
Google Scholar
Huxtable RJ. Physiological actions of taurine. Physiol Reviews. 1992;72:101–63.
CAS
Google Scholar
Ripps H, Shen W. 2012. Review: Taurine: A “very essential” amino acid. Molecular Vision 18:2673–2686.
PubMed
PubMed Central
CAS
Google Scholar
Farag AS, Klikarova J, Ceslova L, Vytras K, Sys M. 2019. Voltammetric determination of taurine in energy drinks after o-phthalaldehyde-ethanethiol derivatization. Talanta 202:486–493.
PubMed
CAS
Google Scholar
Holst PB, Nielsen SE, Anthoni U, Bisht KS, Christophersen C, Gupta S, Parmar VS, Nielsen PH, Sahoo DB, Singh A. Isethionate in certain red algae. J Appl Phycol. 1994;6:443–6.
CAS
Google Scholar
Koechlin BA. The isolation and identification of the major anion fraction of the axoplasm of squid qiant nerve fibers. Proc Natl Acad Sci USA. 1954;40:60–2.
PubMed
PubMed Central
CAS
Google Scholar
Spaeth DG, Schneider DL. Taurine synthesis, concentration, and bile salt conjugation in rat, guinea pig, and rabbit. Proc Soc Experiment Biol Med. 1974;147:855–8.
CAS
Google Scholar
Brand HS, Jorning GG, Chamuleau RA. 1998. Changes in urinary taurine and hypotaurine excretion after two-thirds hepatectomy in the rat. Amino Acids 15:373–83.
PubMed
CAS
Google Scholar
Ridlon JM, Wolf PG, Gaskins HR. 2016. Taurocholic acid metabolism by gut microbes and colon cancer. Gut Microbes 7:201–215.
PubMed
PubMed Central
CAS
Google Scholar
Devkota S, Wang Y, Musch MW, Leone V, Fehlner-Peach H, Nadimpalli A, Antonopoulos DA, Jabri B, Chang EB. 2012. Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice. Nature 487:104–108.
PubMed
PubMed Central
CAS
Google Scholar
Xing M, Wei Y, Zhou Y, Zhang J, Lin L, Hu Y, Hua G, Nanjaraj Urs N, Liu A, Wang D, Guo F, Tong C, Li Y, Liu M, Ang Y, Zhao EL, Yuchi H, Zhang Z. Radical-mediated C-S bond cleavage in C2-sulfonate degradation by anaerobic bacteria. Nature Commun. 2019;10:1609.
Google Scholar
Kappler U, Enemark JH. Sulfite-oxidizing enzymes. JBIC J Biol Inorganic Chem. 2015;20:253–64.
CAS
Google Scholar
Tan YJC, Zhao C, Nasreen M, O’Rourke L, Dhouib R, Roberts L, Wan Y, Beatson SA, Kappler U. Control of bacterial sulfite detoxification by conserved and species-specific regulatory circuits. Front Microbiol. 2019;10.
Laue H, Cook AM. Biochemical and molecular characterization of taurine:pyruvate aminotransferase from the anaerobe Bilophila wadsworthia. Eur J Biochem. 2000;267:6841–8.
PubMed
CAS
Google Scholar
Laue H, Cook AM. Purification, properties and primary structure of alanine dehydrogenase involved in taurine metabolism in the anaerobe Bilophila wadsworthia. Arch Microbiol. 2000;174:162–7.
PubMed
CAS
Google Scholar
Kofoid E, Rappleye C, Stojiljkovic I, Roth J. The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. J Bacteriol. 1999;181:5317–29.
PubMed
PubMed Central
CAS
Google Scholar
Tanaka S, Kerfeld CA, Sawaya MR, Cai F, Heinhorst S, Cannon GC, Yeates TO. 2008. Atomic-level models of the bacterial carboxysome shell. Science 319:1083.
PubMed
CAS
Google Scholar
Moore TC, Escalante-Semerena JC. The EutQ and EutP proteins are novel acetate kinases involved in ethanolamine catabolism: physiological implications for the function of the ethanolamine metabolosome in Salmonella enterica. Mol Microbiol. 2016;99:497–511.
PubMed
CAS
Google Scholar
Crowley CS, Cascio D, Sawaya MR, Kopstein JS, Bobik TA, Yeates TO. Structural insight into the mechanisms of transport across the Salmonella enterica Pdu microcompartment shell. J Biol Chem. 2010;285:37838–46.
PubMed
PubMed Central
CAS
Google Scholar
Pang A, Warren MJ, Pickersgill RW. 2011. Structure of PduT, a trimeric bacterial microcompartment protein with a 4Fe-4S cluster-binding site. Acta Crystallographica Section D Biological Crystallography 67:91–6.
CAS
PubMed
Google Scholar
Parsons JB, Dinesh SD, Deery E, Leech HK, Brindley AA, Heldt D, Frank S, Smales CM, Lunsdorf H, Rambach A, Gass MH, Bleloch A, McClean KJ, Munro AW, Rigby SE, Warren MJ, Prentice MB. Biochemical and structural insights into bacterial organelle form and biogenesis. J Biol Chem. 2008;283:14366–75.
PubMed
CAS
Google Scholar
da Silva SM, Venceslau S, Fernandes CLV, Valente F, Cardoso Pereira I. 2008. Hydrogen as an energy source for the human pathogen Bilophila wadsworthia. Antonie Van Leeuwenhoek 93:381–90.
PubMed
CAS
Google Scholar
Kerfeld CA, Aussignargues C, Zarzycki J, Cai F, Sutter M. Bacterial microcompartments. Nature Reviews Microbiol. 2018;16:277–90.
CAS
Google Scholar
Erbilgin O, McDonald KL, Kerfeld CA. Characterization of a planctomycetal organelle: a novel bacterial microcompartment for the aerobic degradation of plant saccharides. Appl Environ Microbiol. 2014;80:2193–205.
PubMed
PubMed Central
Google Scholar
Liberton M, Austin JR, Berg RH, Pakrasi HB. Unique thylakoid membrane architecture of a unicellular N2-fixing cyanobacterium revealed by electron tomography. Plant Physiol. 2011;155:1656.
PubMed
CAS
Google Scholar
Cannon GC, Bradburne CE, Aldrich HC, Baker SH, Heinhorst S, Shively JM. Microcompartments in prokaryotes: carboxysomes and related polyhedra. Appl Environ Microbiol. 2001;67:5351–61.
PubMed
PubMed Central
CAS
Google Scholar
Codd GA, Marsden WJN. 1984. The carboxysomes (polyhedral bodies) of autotrophic prokaryotes. Biological Reviews 59:389–422.
CAS
Google Scholar
Tabita FR. 1999. Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: A different perspective. Photosynthesis Research 60:1–28.
CAS
Google Scholar
Shively JM, Ball F, Brown DH, Saunders RE. 1973. Functional organelles in prokaryotes: polyhedral inclusions (carboxysomes) of Thiobacillus neapolitanus. Science 182:584–6.
PubMed
CAS
Google Scholar
Brinsmade SR, Paldon T, Escalante-Semerena JC. Minimal functions and physiological conditions required for growth of Salmonella enterica on ethanolamine in the absence of the metabolosome. J Bacteriol. 2005;187:8039–46.
PubMed
PubMed Central
CAS
Google Scholar
Stojiljkovic I, Bäumler AJ, Heffron F. Ethanolamine utilization in Salmonella typhimurium: nucleotide sequence, protein expression, and mutational analysis of the cchA cchB eutE eutJ eutG eutH gene cluster. J Bacteriol. 1995;177:1357.
PubMed
PubMed Central
CAS
Google Scholar
Bobik TA, Havemann GD, Busch RJ, Williams DS, Aldrich HC. The propanediol utilization (pdu) operon of Salmonella enterica serovar Typhimurium LT2 includes genes necessary for formation of polyhedral organelles involved in coenzyme B12-dependent 1,2-propanediol degradation. J Bacteriol. 1999;181:5967–75.
PubMed
PubMed Central
CAS
Google Scholar
Kerfeld CA, Heinhorst S, Cannon GC. Bacterial microcompartments. Ann Review Microbiol. 2010;64:391–408.
CAS
Google Scholar
Chowdhury C, Sinha S, Chun S, Yeates TO, Bobik TA. Diverse bacterial microcompartment organelles. Microbiol Mol Biol Reviews. 2014;78:438–68.
Google Scholar
Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA, Savage DF. 2012. Modularity of a carbon-fixing protein organelle. Proc Natl Acad Sci U S A 109:478–83.
PubMed
CAS
Google Scholar
Baumgart M, Huber I, Abdollahzadeh I, Gensch T, Frunzke J. 2017. Heterologous expression of the Halothiobacillus neapolitanus carboxysomal gene cluster in Corynebacterium glutamicum. J Biotechnol 258:126–135.
PubMed
CAS
Google Scholar
Lin MT, Occhialini A, Andralojc PJ, Devonshire J, Hines KM, Parry MA, Hanson MR. 2014. β-Carboxysomal proteins assemble into highly organized structures in Nicotiana chloroplasts. Plant J 79:1–12.
Lin MT, Occhialini A, Andralojc PJ, Parry MA, Hanson MR. 2014. A faster Rubisco with potential to increase photosynthesis in crops. Nature 513:547–50.
Lawrence AD, Frank S, Newnham S, Lee MJ, Brown IR, Xue WF, Rowe ML, Mulvihill DP, Prentice MB, Howard MJ, Warren MJ. 2014. Solution structure of a bacterial microcompartment targeting peptide and its application in the construction of an ethanol bioreactor. ACS Synthetic Biology 3:454–465.
PubMed
PubMed Central
CAS
Google Scholar
Liang M, Frank S, Lünsdorf H, Warren MJ, Prentice MB. Bacterial microcompartment-directed polyphosphate kinase promotes stable polyphosphate accumulation in E. coli. Biotechnol J. 2017;12:1600415.
Google Scholar
Craciun S, Balskus EP. Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme. Proc Natl Acad Sci USA. 2012;109:21307–12.
PubMed
PubMed Central
CAS
Google Scholar
Herring TI, Harris TN, Chowdhury C, Mohanty SK, Bobik TA. A bacterial microcompartment is used for choline fermentation by Escherichia coli 536. J Bacteriol. 2018;200:e00764-17.
PubMed
PubMed Central
Google Scholar
Petit E, LaTouf WG, Coppi MV, Warnick TA, Currie D, Romashko I, Deshpande S, Haas K, Alvelo-Maurosa JG, Wardman C, Schnell DJ, Leschine SB, Blanchard JL. 2013. Involvement of a bacterial microcompartment in the metabolism of fucose and rhamnose by Clostridium phytofermentans. PloS ONE 8:e54337-e54337.
Google Scholar
O’Brien JR, Raynaud C, Croux C, Girbal L, Soucaille P, Lanzilotta WN. 2004. Insight into the mechanism of the B12-independent glycerol dehydratase from Clostridium butyricum: preliminary biochemical and structural characterization. Biochemistry 43:4635–45.
PubMed
Google Scholar
Raynaud C, Sarçabal P, Meynial-Salles I, Croux C, Soucaille P. Molecular characterization of the 1,3-propanediol (1,3-PD) operon of Clostridium butyricum. Proc Natl Acad Sci USA. 2003;100:5010–5.
PubMed
PubMed Central
CAS
Google Scholar
Schindel HS, Karty JA, McKinlay JB, Bauer CE. Characterization of a glycyl-radical enzyme bacterial microcompartment pathway in Rhodobacter capsulatus. J Bacteriol. 2018. https://doi.org/10.1128/JB.00343-18:JB.00343-18.
Article
Google Scholar
Zarzycki J, Erbilgin O, Kerfeld CA. Bioinformatic characterization of glycyl radical enzyme-associated bacterial microcompartments. Appl Environ Microbiol. 2015;81:8315–29.
PubMed
PubMed Central
CAS
Google Scholar
Axen SD, Erbilgin O, Kerfeld CA. A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. PLoS Computational Biol. 2014;10:e1003898.
Google Scholar
Craciun S, Marks JA, Balskus EP. Characterization of choline trimethylamine-lyase expands the chemistry of glycyl radical enzymes. ACS Chem Biol. 2014;9:1408–13.
PubMed
CAS
Google Scholar
Rein U, Gueta R, Denger K, Ruff J, Hollemeyer K, Cook AM. 2005. Dissimilation of cysteate via 3-sulfolactate sulfo-lyase and a sulfate exporter in Paracoccus pantotrophus NKNCYSA. Microbiology 151:737–47.
PubMed
CAS
Google Scholar
Burrichter A, Denger K, Franchini P, Huhn T, Müller N, Spiteller D, Schleheck D. Anaerobic degradation of the plant sugar sulfoquinovose concomitant with H2S production: Escherichia coli K-12 and Desulfovibrio sp. strain DF1 as co-culture model. Front Microbiol. 2018; 9.
Kuehl JV, Price MN, Ray J, Wetmore KM, Esquivel Z, Kazakov AE, Nguyen M, Kuehn R, Davis RW, Hazen TC, Arkin AP, Deutschbauer A. 2014. Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20. mBio 5:e01041-14.
Liu J, Wei Y, Lin L, Teng L, Yin J, Lu Q, Chen J, Zheng Y, Li Y, Xu R, Zhai W, Liu Y, Liu Y, Cao P, Ang EL, Zhao H, Yuchi Z, Zhang Y. 2020. Two radical-dependent mechanisms for anaerobic degradation of the globally abundant organosulfur compound dihydroxypropanesulfonate. Proc Natl Acad Sci U S A 117:15599–15608.
PubMed
PubMed Central
CAS
Google Scholar
Huseby DL, Roth JR. 2013. Evidence that a metabolic microcompartment contains and recycles private cofactor pools. Journal of Bacteriology 195:2864.
PubMed
PubMed Central
CAS
Google Scholar
Cheng S, Fan C, Sinha S, Bobik TA. 2012. The PduQ enzyme is an alcohol dehydrogenase used to recycle NAD+ internally within the Pdu microcompartment of Salmonella enterica. PloS ONE 7:e47144.
PubMed
PubMed Central
CAS
Google Scholar
Ferlez B, Sutter M, Kerfeld CA. Glycyl radical enzyme-associated microcompartments: Redox-replete bacterial organelles. Mol Biol Physiol. 2019;10:e02327-18.
Google Scholar
Cheng S, Bobik TA. Characterization of the PduS cobalamin reductase of Salmonella enterica and its role in the Pdu microcompartment. J Bacteriol. 2010;192:5071–80.
PubMed
PubMed Central
CAS
Google Scholar
Parsons JB, Lawrence AD, McLean KJ, Munro AW, Rigby SEJ, Warren MJ. 2010. Characterisation of PduS, the pdu metabolosome corrin reductase, and evidence of substructural organisation within the bacterial microcompartment. PloS ONE 5:e14009-e14009.
Google Scholar
Zeng Z, Boeren S, Bhandula V, Light SH, Smid EJ, Notebaart RA, Abee T, Laar TAV. 2021. Bacterial Microcompartments Coupled with Extracellular Electron Transfer Drive the Anaerobic Utilization of Ethanolamine in Listeria monocytogenes. mSystems 6:e01349-20.
PubMed
PubMed Central
Google Scholar
Bianchi V, Eliasson R, Fontecave M, Mulliez E, Hoover DM, Matthews RG, Reichard P. Flavodoxin is required for the activation of the anaerobic ribonucleotide reductase. Biochem Biophysica Res Commun. 1993;197:792–7.
CAS
Google Scholar
Backman LRF, Funk MA, Dawson CD, Drennan CL. 2017. New tricks for the glycyl radical enzyme family. Critical Reviews in Biochemistry and Molecular Biology 52:674–695.
PubMed
PubMed Central
CAS
Google Scholar
Shisler KA, Broderick JB. 2014. Glycyl radical activating enzymes: Structure, mechanism, and substrate interactions. Archives of Biochemistry and Biophysics 546:64–71.
PubMed
PubMed Central
CAS
Google Scholar
Klumpp J, Fuchs TM. 2007. Identification of novel genes in genomic islands that contribute to Salmonella typhimurium replication in macrophages. Microbiology (Reading) 153:1207–1220.
CAS
Google Scholar
Harvey PC, Watson M, Hulme S, Jones MA, Lovell M, Berchieri A, Jr., Young J, Bumstead N, Barrow P. 2011. Salmonella enterica serovar typhimurium colonizing the lumen of the chicken intestine grows slowly and upregulates a unique set of virulence and metabolism genes. Infect Immun 79:4105–21.
PubMed
PubMed Central
CAS
Google Scholar
Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120.
PubMed
PubMed Central
CAS
Google Scholar
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357–359.
PubMed
PubMed Central
CAS
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–9.
PubMed
PubMed Central
Google Scholar
Pertea M, Pertea GM, Antonescu CM, Chang T-C, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnol. 2015;33:290.
CAS
Google Scholar
Huber I. 2017. Establishment of bacterial microcompartments in the industrial production strain Corynebacterium glutamicumHeinrich-Heine-Universität Düsseldorf; Forschungszentrum Jülich, Jülich.
Google Scholar
Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Analytical Biochem. 1976;72:248–54.
CAS
Google Scholar
Venable JH, Coggeshall R. A simplified lead citrate stain for use in electron microscopy. J Cell Biol. 1965;25:407.
PubMed
PubMed Central
CAS
Google Scholar
Frey J, Schneider F, Schink B, Huhn T. Synthesis of short-chain hydroxyaldehydes and their 2,4-dinitrophenylhydrazone derivatives, and separation of their isomers by high-performance liquid chromatography. J Chromatography A. 2018;1531:143–50.
CAS
Google Scholar
Akasaka K, Matsuda H, Ohrui H, Meguro H, Suzuki T. Fluorometric determination of sulfite in wine by N-(9-acridinyl)maleimide. Agricultural Biol Chem. 1990;54:501–4.
CAS
Google Scholar
Hensgens CM, Hagen WR, Hansen TA. Purification and characterization of a benzylviologen-linked, tungsten-containing aldehyde oxidoreductase from Desulfovibrio gigas. J Bacteriol. 1995;177:6195–200.
PubMed
PubMed Central
CAS
Google Scholar
Müller N, Griffin BM, Stingl U, Schink B. Dominant sugar utilizers in sediment of Lake Constance depend on syntrophic cooperation with methanogenic partner organisms. Environ Microbiol. 2008;10:1501–11.
PubMed
Google Scholar
Bergmeyer HU. 1970. Methoden der enzymatischen Analyse. Bd 2. Vlg. Chemie.
Nishimura JS, Griffith MJ. Acetate kinase from Veillonella alcalescens: EC 2.7.2.1 ATP:acetate phosphotransferase. Methods Enzymol. 1981;71: 11–316. Academic Press.