Whitehead, N. A., Barnard, A. M., Slater, H., Simpson, N. J. & Salmond, G. P. Quorum-sensing in Gram-negative bacteria. FEMS Microbiol. Rev. 25, 365–404 (2001).
Google Scholar
Miller, M. B. & Bassler, B. L. Quorum sensing in bacteria. Annu. Rev. Microbiol. 55, 165–199 (2001).
Google Scholar
Williams, P., Winzer, K., Chan, W. C. & Cámara, M. Look who’s talking: Communication and quorum sensing in the bacterial world. Philos. Trans. R. Soc. Lond. B 362, 1119–1134 (2007).
Google Scholar
Mukherjee, S. & Bassler, B. L. Bacterial quorum sensing in complex and dynamically changing environments. Nat. Rev. Microbiol. 17, 371–382 (2019).
Google Scholar
Bassler, B. L. How bacteria talk to each other: Regulation of gene expression by quorum sensing. Curr. Opin. Microbiol. 2, 582–587 (1999).
Google Scholar
Waters, C. M. & Bassler, B. L. The Vibrio harveyi quorum-sensing system uses shared regulatory components to discriminate between multiple autoinducers. Genes Dev. 20, 2754–2767 (2006).
Google Scholar
Waters, C. M. & Bassler, B. L. Quorum sensing: Cell-to-cell communication in bacteria. Annu. Rev. Cell Dev. Biol. 21, 319–346 (2005).
Google Scholar
Chen, Y. et al. The SCIFF-derived ranthipeptides participate in quorum sensing in solventogenic clostridia. Biotechnol. J. 15, 1–8 (2020).
Feng, J. et al. RRNPP-Type quorum-sensing systems regulate solvent formation, sporulation and cell motility in Clostridium saccharoperbutylacetonicum. Biotechnol. Biofuels 13, 1–16 (2020).
Kotte, A.-K. et al. RRNPP-type quorum sensing affects solvent formation and sporulation in Clostridium acetobutylicum. Microbiology 166, 579–592 (2020).
Google Scholar
Steiner, E., Scott, J., Minton, N. P. & Winzer, K. An agr quorum sensing system that regulates granulose formation and sporulation in Clostridium acetobutylicum. Appl. Environ. Microbiol. 78, 1113–1122 (2012).
Google Scholar
Steiner, E. et al. Multiple orphan histidine kinases interact directly with Spo0A to control the initiation of endospore formation in Clostridium acetobutylicum. Mol. Microbiol. 80, 641–654 (2011).
Google Scholar
Köpke, M. et al. Clostridium ljungdahlii represents a microbial production platform based on syngas. Proc. Natl. Acad. Sci. U. S. A. 107, 13087–13092 (2010).
Google Scholar
Bengelsdorf, F. R. et al. Industrial acetogenic biocatalysts: A comparative metabolic and genomic analysis. Front. Microbiol. 7, 1–15 (2016).
Jeong, Y., Song, Y., Shin, H. S. & Cho, B.-K. Draft genome sequence of acid-tolerant Clostridium drakei SL1 T, a potential chemical producer through syngas fermentation. Genome Announc. 2, 4–5 (2014).
Huhnke, R. L., Lewis, R. S. & Tanner, R. S. Isolation and Characterization of novel Clostridial Species. Patent 38 (2008).
Abubackar, H. N., Veiga, M. C. & Kennes, C. Syngas fermentation for bioethanol and bioproducts. In Sustainable Resource Recovery and Zero Waste Approaches 207–221 (Elsevier, 2019).
Köpke, M. & Simpson, S. D. Pollution to products: Recycling of ‘above ground’ carbon by gas fermentation. Curr. Opin. Biotechnol. 65, 180–189 (2020).
Google Scholar
Dürre, P. Gas fermentation: A biotechnological solution for today’s challenges. Microb. Biotechnol. 10, 14–16 (2017).
Google Scholar
Liew, F. et al. Gas fermentation: A flexible platform for commercial scale production of low-carbon-fuels and chemicals from waste and renewable feedstocks. Front. Microbiol. 7, 694 (2016).
Google Scholar
Jin, S. et al. Synthetic biology on acetogenic bacteria for highly efficient conversion of c1 gases to biochemicals. Int. J. Mol. Sci. 21, 1–25 (2020).
Abrini, J., Naveau, H. & Nyns, E. Clostridium autoethanogenum, sp. nov., an anaerobic bacterium that produces ethanol from carbon monoxide. Arch. Microbiol. 161, 345–351 (1994).
Google Scholar
Drake, H. L., Küsel, K. & Matthies, C. Acetogenic prokaryotes. The Prokaryotes 2, 354–420 (2006).
Ragsdale, S. W. & Pierce, E. Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation. Biochim. Biophys. Acta 1784, 1873–1898 (2008).
Google Scholar
Biegel, E., Schmidt, S., González, J. M. & Müller, V. Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes. Cell. Mol. Life Sci. 68, 613–634 (2011).
Google Scholar
Tremblay, P., Zhang, T., Dar, S. A., Leang, C. & Lovley, D. R. The Rnf complex of Clostridium ljungdahlii is a proton-translocating Ferredoxin:NAD + oxidoreductase essential for autotrophic growth. MBio 4, 1–8 (2013).
Müller, V. New horizons in acetogenic conversion of one-carbon substrates and biological hydrogen storage. Trends Biotechnol. 37, 1344–1354 (2019).
Google Scholar
Müller, V. Energy conservation in acetogenic bacteria. Appl. Environ. Microbiol. 69, 6345–6353 (2003).
Google Scholar
Wood, H. G. A study of carbon dioxide fixation by mass determination of the types of C13-acetate. J. Biol. Chem. 194, 905–931 (1952).
Google Scholar
Ivey, D. M. & Ljungdahl, L. G. Purification and characterization of the F1-ATPase from Clostridium thermoaceticum. J. Bacteriol. 165, 252–257 (1986).
Google Scholar
Brown, S. D. et al. Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia. Biotechnol. Biofuels 7, 40 (2014).
Google Scholar
Utturkar, S. M. et al. Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies. Sci. Data 2, 150014 (2015).
Google Scholar
Köpke, M. et al. 2,3-Butanediol production by acetogenic bacteria, an alternative route to chemical synthesis, using industrial waste gas. Appl. Environ. Microbiol. 77, 5467–5475 (2011).
Google Scholar
Marcellin, E. et al. Low carbon fuels and commodity chemicals from waste gases: Systematic approach to understand energy metabolism in a model acetogen. Green Chem. 18, 3020–3028 (2016).
Google Scholar
Mock, J. et al. Energy conservation associated with ethanol formation from H2 and CO2 in Clostridium autoethanogenum involving electron bifurcation. J. Bacteriol. 197, 2965–2980 (2015).
Google Scholar
Humphreys, C. M. et al. Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. BMC Genom. 16, 1085 (2015).
Köpke, M. & Liew, F. Production of butanol from carbon monoxide by a recombinant microorganism (WO2012053905A1). Patent 133 (2012).
Greene, J., Daniell, J., Köpke, M., Broadbelt, L. & Tyo, K. E. J. Kinetic ensemble model of gas fermenting Clostridium autoethanogenum for improved ethanol production. Biochem. Eng. J. 148, 46–56 (2019).
Google Scholar
Norman, R. O. J. et al. Genome-scale model of C. autoethanogenum reveals optimal bioprocess conditions for high-value chemical production from carbon monoxide. Eng. Biol. 3, 32–40 (2019).
de Souza Pinto Lemgruber, R. et al. Systems-level engineering and characterisation of Clostridium autoethanogenum through heterologous production of poly-3-hydroxybutyrate (PHB). Metab. Eng. 53, 14–23 (2019).
Google Scholar
Fackler, N. et al. Transcriptional control of Clostridium autoethanogenum using CRISPRi. Synth. Biol. 6, ysaab008 (2021).
Schuchmann, K. & Müller, V. Energetics and application of heterotrophy in acetogenic bacteria. Appl. Environ. Microbiol. 82, 4056–4069 (2016).
Google Scholar
Valgepea, K. et al. H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum. Biotechnol. Biofuels 11, 55 (2018).
Google Scholar
Liew, F. et al. Insights into CO 2 fixation pathway of Clostridium autoethanogenum by targeted mutagenesis. MBio 7, 1–10 (2016).
Mahamkali, V. et al. Redox controls metabolic robustness in the gas-fermenting acetogen Clostridium autoethanogenum. Proc. Natl. Acad. Sci. U. S. A. 117, 13168–13175 (2020).
Google Scholar
Aklujkar, M., Leang, C., Shrestha, P. M., Shrestha, M. & Lovley, D. R. Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H2 and CO2 compared to organotrophic growth with fructose. Sci. Rep. 7, 1–14 (2017).
Google Scholar
Ji, G., Beavis, R. C. & Novick, R. P. Cell density control of staphylococcal virulence mediated by an octapeptide pheromone. Proc. Natl. Acad. Sci. U. S. A. 92, 12055–12059 (1995).
Google Scholar
Ji, G., Beavis, R. & Novick, R. P. Bacterial interference caused by autoinducing peptide variants. Science 276, 2027–2030 (1997).
Google Scholar
Wuster, A. & Babu, M. M. Conservation and evolutionary dynamics of the agr cell-to-cell communication system across firmicutes. J. Bacteriol. 190, 743–746 (2008).
Google Scholar
Vidal, J. E., Shak, J. R. & Canizalez-Roman, A. The CpAL quorum sensing system regulates production of hemolysins CPA and PFO to build Clostridium perfringens biofilms. Infect. Immun. 83, 2430–2442 (2015).
Google Scholar
Cooksley, C. M. et al. Regulation of neurotoxin production and sporulation by a putative agrBD signaling system in proteolytic Clostridium botulinum. Appl. Environ. Microbiol. 76, 4448–4460 (2010).
Google Scholar
Stabler, R. et al. Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. Genome Biol. 10, R102 (2009).
Google Scholar
Martin, M. J. et al. The agr locus regulates virulence and colonization genes in Clostridium difficile 027. J. Bacteriol. 195, 3672–3681 (2013).
Google Scholar
Li, J., Chen, J., Vidal, J. E. & McClane, B. A. The Agr-Like Quorum-sensing system regulates sporulation and production of enterotoxin and Beta2 toxin by Clostridium perfringens type A non-food-borne human gastrointestinal disease strain F5603. Infect. Immun. 79, 2451–2459 (2011).
Google Scholar
Zhang, L. & Ji, G. Identification of a staphylococcal AgrB1 segment(s) responsible for group-specific processing of AgrD by gene swapping. J. Bacteriol. 186, 6706–6713 (2004).
Google Scholar
Novick, R. P. Autoinduction and signal transduction in the regulation of staphylococcal virulence. Mol. Microbiol. 48, 1429–1449 (2003).
Google Scholar
Ng, Y. K. et al. Expanding the repertoire of gene tools for precise manipulation of the Clostridium difficile genome: Allelic exchange using pyrE alleles. PLoS ONE 8, e56051 (2013).
Google Scholar
Ehsaan, M. et al. Mutant generation by allelic exchange and genome resequencing of the biobutanol organism Clostridium acetobutylicum ATCC 824. Biotechnol. Biofuels 9, 4 (2016).
Google Scholar
Liew, F. et al. Metabolic engineering of Clostridium autoethanogenum for selective alcohol production. Metab. Eng. 40, 104–114 (2017).
Google Scholar
Annan, F. J. et al. Engineering of vitamin prototrophy in Clostridium ljungdahlii and Clostridium autoethanogenum. Appl. Microbiol. Biotechnol. 103, 4633–4648 (2019).
Google Scholar
Heap, J. T. et al. Integration of DNA into bacterial chromosomes from plasmids without a counter-selection marker. Nucleic Acids Res. 40, e59 (2012).
Google Scholar
Nguyen, T. K., Tran, N. P. & Cavin, J. F. Genetic and biochemical analysis of PadR-padC promoter interactions during the phenolic acid stress response in Bacillus subtilis 168. J. Bacteriol. 193, 4180–4191 (2011).
Google Scholar
Isom, C. E. et al. Crystal structure and DNA binding activity of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291. BMC Microbiol. 16, 1–12 (2016).
Garsin, D. Ethanolamine utilisation in bacterial pathogens: Roles and regulation. Nat. Rev. Microbiol. 8, 290–295 (2010).
Google Scholar
Cornforth, D. M. et al. Combinatorial quorum sensing allows bacteria to resolve their social and physical environment. Proc. Natl. Acad. Sci. U. S. A. 111, 4280–4284 (2014).
Google Scholar
Dandekar, A. A., Chugani, S. & Greenberg, E. P. Bacterial quorum sensing and metabolic incentives to cooperate. Science 338, 264–266 (2012).
Google Scholar
Stouthamer, A. H. A theoretical study on the amount of ATP required for synthesis of microbial cell material. Antonie Van Leeuwenhoek 39, 545–565 (1973).
Google Scholar
Humphreys, C. M. et al. Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. BMC Genom. 16, 1–10 (2015).
Xu, H. et al. Impact of exogenous acetate on ethanol formation and gene transcription for key enzymes in Clostridium autoethanogenum grown on CO. Biochem. Eng. J. 155, 107470 (2020).
Google Scholar
Cannon, G. C. et al. Microcompartments in Prokaryotes: Carboxysomes and related polyhedra. Appl. Environ. Microbiol. 67, 5351–5361 (2001).
Google Scholar
Heldt, D. et al. Structure of a trimeric bacterial microcompartment shell protein, EtuB, associated with ethanol utilization in Clostridium kluyveri. Biochem. J. 423, 199–207 (2009).
Google Scholar
Schuchmann, K. et al. Nonacetogenic growth of the acetogen Acetobacterium woodii on 1,2-propanediol. J. Bacteriol. 197, 382–391 (2015).
Google Scholar
Ow, S. Y. et al. iTRAQ underestimation in simple and complex mixtures: ‘The good, the bad and the ugly’. J. Proteome Res. 8, 5347–5355 (2009).
Google Scholar
Perkel, J. M. iTRAQ gets put to the test. J. Proteome Res. 8, 4885–4885 (2009).
Google Scholar
Verbeke, T. J. et al. Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum. Sci. Rep. 7, 43355 (2017).
Google Scholar
Cornforth, D. M. & Foster, K. R. Competition sensing: The social side of bacterial stress responses. Nat. Rev. Microbiol. 11, 285–293 (2013).
Google Scholar
Lee, J. et al. A cell-cell communication signal integrates quorum sensing and stress response. Nat. Chem. Biol. 9, 339–343 (2013).
Google Scholar
Heap, J. T., Pennington, O. J., Cartman, S. T. & Minton, N. P. A modular system for Clostridium shuttle plasmids. J. Microbiol. Methods 78, 79–85 (2009).
Google Scholar
Minton, N. P. et al. A roadmap for gene system development in Clostridium. Anaerobe 41, 104–112 (2016).
Google Scholar
Purdy, D. et al. Conjugative transfer of clostridial shuttle vectors from Escherichia coli to Clostridium difficile through circumvention of the restriction barrier. Mol. Microbiol. 46, 439–452 (2002).
Google Scholar
Wang, S. et al. NADP-specific electron-bifurcating [FeFe]-hydrogenase in a functional complex with formate dehydrogenase in Clostridium autoethanogenum grown on CO. J. Bacteriol. 195, 4373–4386 (2013).
Google Scholar
