1
|
Roe JM, Seely K, Bussard CJ, Eischen Martin E, Mouw EG, Bayles KW, Hollingsworth MA, Brooks AE, Dailey KM. Hacking the Immune Response to Solid Tumors: Harnessing the Anti-Cancer Capacities of Oncolytic Bacteria. Pharmaceutics 2023; 15:2004. [PMID: 37514190 PMCID: PMC10384176 DOI: 10.3390/pharmaceutics15072004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Oncolytic bacteria are a classification of bacteria with a natural ability to specifically target solid tumors and, in the process, stimulate a potent immune response. Currently, these include species of Klebsiella, Listeria, Mycobacteria, Streptococcus/Serratia (Coley's Toxin), Proteus, Salmonella, and Clostridium. Advancements in techniques and methodology, including genetic engineering, create opportunities to "hijack" typical host-pathogen interactions and subsequently harness oncolytic capacities. Engineering, sometimes termed "domestication", of oncolytic bacterial species is especially beneficial when solid tumors are inaccessible or metastasize early in development. This review examines reported oncolytic bacteria-host immune interactions and details the known mechanisms of these interactions to the protein level. A synopsis of the presented membrane surface molecules that elicit particularly promising oncolytic capacities is paired with the stimulated localized and systemic immunogenic effects. In addition, oncolytic bacterial progression toward clinical translation through engineering efforts are discussed, with thorough attention given to strains that have accomplished Phase III clinical trial initiation. In addition to therapeutic mitigation after the tumor has formed, some bacterial species, referred to as "prophylactic", may even be able to prevent or "derail" tumor formation through anti-inflammatory capabilities. These promising species and their particularly favorable characteristics are summarized as well. A complete understanding of the bacteria-host interaction will likely be necessary to assess anti-cancer capacities and unlock the full cancer therapeutic potential of oncolytic bacteria.
Collapse
Affiliation(s)
- Jason M Roe
- College of Osteopathic Medicine, Rocky Vista University, Ivins, UT 84738, USA
| | - Kevin Seely
- College of Osteopathic Medicine, Rocky Vista University, Ivins, UT 84738, USA
| | - Caleb J Bussard
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80130, USA
| | | | - Elizabeth G Mouw
- College of Osteopathic Medicine, Rocky Vista University, Ivins, UT 84738, USA
| | - Kenneth W Bayles
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Michael A Hollingsworth
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Amanda E Brooks
- College of Osteopathic Medicine, Rocky Vista University, Ivins, UT 84738, USA
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80130, USA
- Office of Research & Scholarly Activity, Rocky Vista University, Ivins, UT 84738, USA
| | - Kaitlin M Dailey
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68198, USA
| |
Collapse
|
2
|
Bouché L, Panico M, Hitchen P, Binet D, Sastre F, Faulds-Pain A, Valiente E, Vinogradov E, Aubry A, Fulton K, Twine S, Logan SM, Wren BW, Dell A, Morris HR. The Type B Flagellin of Hypervirulent Clostridium difficile Is Modified with Novel Sulfonated Peptidylamido-glycans. J Biol Chem 2016; 291:25439-25449. [PMID: 27758867 PMCID: PMC5207245 DOI: 10.1074/jbc.m116.749481] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/12/2016] [Indexed: 01/15/2023] Open
Abstract
Glycosylation of flagellins is a well recognized property of many bacterial species. In this study, we describe the structural characterization of novel flagellar glycans from a number of hypervirulent strains of C. difficile. We used mass spectrometry (nano-LC-MS and MS/MS analysis) to identify a number of putative glycopeptides that carried a variety of glycoform substitutions, each of which was linked through an initial N-acetylhexosamine residue to Ser or Thr. Detailed analysis of a LLDGSSTEIR glycopeptide released by tryptic digestion, which carried two variant structures, revealed that the glycopeptide contained, in addition to carbohydrate moieties, a novel structural entity. A variety of electrospray-MS strategies using Q-TOF technology were used to define this entity, including positive and negative ion collisionally activated decomposition MS/MS, which produced unique fragmentation patterns, and high resolution accurate mass measurement to allow derivation of atomic compositions, leading to the suggestion of a taurine-containing peptidylamido-glycan structure. Finally, NMR analysis of flagellin glycopeptides provided complementary information. The glycan portion of the modification was assigned as α-Fuc3N-(1→3)-α-Rha-(1→2)-α-Rha3OMe-(1→3)-β-GlcNAc-(1→)Ser, and the novel capping moiety was shown to be comprised of taurine, alanine, and glycine. This is the first report of a novel O-linked sulfonated peptidylamido-glycan moiety decorating a flagellin protein.
Collapse
Affiliation(s)
- Laura Bouché
- From the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Maria Panico
- From the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Paul Hitchen
- From the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Daniel Binet
- BioPharmaSpec, Suite 3.1 Lido Medical Centre, St. Saviours Road, Jersey JE2 7LA, United Kingdom
| | - Federico Sastre
- From the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Alexandra Faulds-Pain
- the Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Esmeralda Valiente
- the Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Evgeny Vinogradov
- the Vaccine Program, Human Health Therapeutics Portfolio, National Research Council, Ottawa, Ontario K1A 0R6, Canada, and
| | - Annie Aubry
- the Vaccine Program, Human Health Therapeutics Portfolio, National Research Council, Ottawa, Ontario K1A 0R6, Canada, and
| | - Kelly Fulton
- the Vaccine Program, Human Health Therapeutics Portfolio, National Research Council, Ottawa, Ontario K1A 0R6, Canada, and
| | - Susan Twine
- the Vaccine Program, Human Health Therapeutics Portfolio, National Research Council, Ottawa, Ontario K1A 0R6, Canada, and
| | - Susan M Logan
- the Vaccine Program, Human Health Therapeutics Portfolio, National Research Council, Ottawa, Ontario K1A 0R6, Canada, and
| | - Brendan W Wren
- the Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Anne Dell
- From the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom,
| | - Howard R Morris
- From the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom.,BioPharmaSpec, Suite 3.1 Lido Medical Centre, St. Saviours Road, Jersey JE2 7LA, United Kingdom
| |
Collapse
|
3
|
Raut MP, Couto N, Pham TK, Evans C, Noirel J, Wright PC. Quantitative proteomic analysis of the influence of lignin on biofuel production by Clostridium acetobutylicum ATCC 824. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:113. [PMID: 27247624 PMCID: PMC4886415 DOI: 10.1186/s13068-016-0523-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 05/09/2016] [Indexed: 05/30/2023]
Abstract
BACKGROUND Clostridium acetobutylicum has been a focus of research because of its ability to produce high-value compounds that can be used as biofuels. Lignocellulose is a promising feedstock, but the lignin-cellulose-hemicellulose biomass complex requires chemical pre-treatment to yield fermentable saccharides, including cellulose-derived cellobiose, prior to bioproduction of acetone-butanol-ethanol (ABE) and hydrogen. Fermentation capability is limited by lignin and thus process optimization requires knowledge of lignin inhibition. The effects of lignin on cellular metabolism were evaluated for C. acetobutylicum grown on medium containing either cellobiose only or cellobiose plus lignin. Microscopy, gas chromatography and 8-plex iTRAQ-based quantitative proteomic technologies were applied to interrogate the effect of lignin on cellular morphology, fermentation and the proteome. RESULTS Our results demonstrate that C. acetobutylicum has reduced performance for solvent production when lignin is present in the medium. Medium supplemented with 1 g L(-1) of lignin led to delay and decreased solvents production (ethanol; 0.47 g L(-1) for cellobiose and 0.27 g L(-1) for cellobiose plus lignin and butanol; 0.13 g L(-1) for cellobiose and 0.04 g L(-1) for cellobiose plus lignin) at 20 and 48 h, respectively, resulting in the accumulation of acetic acid and butyric acid. Of 583 identified proteins (FDR < 1 %), 328 proteins were quantified with at least two unique peptides. Up- or down-regulation of protein expression was determined by comparison of exponential and stationary phases of cellobiose in the presence and absence of lignin. Of relevance, glycolysis and fermentative pathways were mostly down-regulated, during exponential and stationary growth phases in presence of lignin. Moreover, proteins involved in DNA repair, transcription/translation and GTP/ATP-dependent activities were also significantly affected and these changes were associated with altered cell morphology. CONCLUSIONS This is the first comprehensive analysis of the cellular responses of C. acetobutylicum to lignin at metabolic and physiological levels. These data will enable targeted metabolic engineering strategies to optimize biofuel production from biomass by overcoming limitations imposed by the presence of lignin.
Collapse
Affiliation(s)
- Mahendra P. Raut
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
| | - Narciso Couto
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
| | - Trong K. Pham
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
| | - Caroline Evans
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
| | - Josselin Noirel
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
- />Chaire de Bioinformatique, LGBA, Conservatoire National Des Arts Et Métiers, 75003 Paris, France
| | - Phillip C. Wright
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
- />School of Chemical Engineering and Advanced Materials, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| |
Collapse
|
4
|
Janesch B, Schirmeister F, Maresch D, Altmann F, Messner P, Kolarich D, Schäffer C. Flagellin glycosylation in Paenibacillus alvei CCM 2051T. Glycobiology 2015; 26:74-87. [PMID: 26405108 DOI: 10.1093/glycob/cwv087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 09/21/2015] [Indexed: 12/21/2022] Open
Abstract
Flagellin glycosylation impacts, in several documented cases, the functionality of bacterial flagella. The basis of flagellin glycosylation has been studied for various Gram-negative bacteria, but less is known about flagellin glycans of Gram-positive bacteria including Paenibacillus alvei, a secondary invader of honeybee colonies diseased with European foulbrood. Paenibacillus alvei CCM 2051(T) swarms vigorously on solidified culture medium, with swarming relying on functional flagella as evidenced by abolished biofilm formation of a non-motile P. alvei mutant defective in the flagellin protein Hag. Here, the glycobiology of the polar P. alvei flagella was investigated. Analysis on purified flagellin demonstrated that the 30-kDa Hag protein (PAV_2c01710) is modified with an O-linked trisaccharide comprised of one hexose and two N-acetyl-hexosamine residues, at three sites of glycosylation. Downstream of the hag gene on the bacterial chromosome, two open reading frames (PAV_2c01630, PAV_2c01640) encoding putative glycosyltransferases were shown to constitute a flagellin glycosylation island. Mutants defective in these genes exhibited altered migration in sodium dodecyl sulfate polyacrylamide gel electrophoresis as well as loss of extracellular flagella production and bacterial motility. This study reveals that flagellin glycosylation in P. alvei is pivotal to flagella formation and bacterial motility in vivo, and simultaneously identifies flagella glycosylation as a second protein O-glycosylation system in this bacterium, in addition to the well-investigated S-layer tyrosine O-glycosylation pathway.
Collapse
Affiliation(s)
- Bettina Janesch
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, Muthgasse 11, Vienna A-1190, Austria
| | - Falko Schirmeister
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam 14424, Germany Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, Berlin 14195, Germany
| | - Daniel Maresch
- Department of Chemistry, Division of Biochemistry, Universität für Bodenkultur Wien, Muthgasse 18, Vienna A-1190, Austria
| | - Friedrich Altmann
- Department of Chemistry, Division of Biochemistry, Universität für Bodenkultur Wien, Muthgasse 18, Vienna A-1190, Austria
| | - Paul Messner
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, Muthgasse 11, Vienna A-1190, Austria
| | - Daniel Kolarich
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam 14424, Germany
| | - Christina Schäffer
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, Muthgasse 11, Vienna A-1190, Austria
| |
Collapse
|
5
|
The sweet tooth of bacteria: common themes in bacterial glycoconjugates. Microbiol Mol Biol Rev 2015; 78:372-417. [PMID: 25184559 DOI: 10.1128/mmbr.00007-14] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Humans have been increasingly recognized as being superorganisms, living in close contact with a microbiota on all their mucosal surfaces. However, most studies on the human microbiota have focused on gaining comprehensive insights into the composition of the microbiota under different health conditions (e.g., enterotypes), while there is also a need for detailed knowledge of the different molecules that mediate interactions with the host. Glycoconjugates are an interesting class of molecules for detailed studies, as they form a strain-specific barcode on the surface of bacteria, mediating specific interactions with the host. Strikingly, most glycoconjugates are synthesized by similar biosynthesis mechanisms. Bacteria can produce their major glycoconjugates by using a sequential or an en bloc mechanism, with both mechanistic options coexisting in many species for different macromolecules. In this review, these common themes are conceptualized and illustrated for all major classes of known bacterial glycoconjugates, with a special focus on the rather recently emergent field of glycosylated proteins. We describe the biosynthesis and importance of glycoconjugates in both pathogenic and beneficial bacteria and in both Gram-positive and -negative organisms. The focus lies on microorganisms important for human physiology. In addition, the potential for a better knowledge of bacterial glycoconjugates in the emerging field of glycoengineering and other perspectives is discussed.
Collapse
|
6
|
Comparative shotgun proteomic analysis of Clostridium acetobutylicum from butanol fermentation using glucose and xylose. Proteome Sci 2011; 9:66. [PMID: 22008648 PMCID: PMC3212805 DOI: 10.1186/1477-5956-9-66] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 10/18/2011] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Butanol is a second generation biofuel produced by Clostridium acetobutylicum through acetone-butanol-ethanol (ABE) fermentation process. Shotgun proteomics provides a direct approach to study the whole proteome of an organism in depth. This paper focuses on shotgun proteomic profiling of C. acetobutylicum from ABE fermentation using glucose and xylose to understand the functional mechanisms of C. acetobutylicum proteins involved in butanol production. RESULTS We identified 894 different proteins in C. acetobutylicum from ABE fermentation process by two dimensional - liquid chromatography - tandem mass spectrometry (2D-LC-MS/MS) method. This includes 717 proteins from glucose and 826 proteins from the xylose substrate. A total of 649 proteins were found to be common and 22 significantly differentially expressed proteins were identified between glucose and xylose substrates. CONCLUSION Our results demonstrate that flagellar proteins are highly up-regulated with glucose compared to xylose substrate during ABE fermentation. Chemotactic activity was also found to be lost with the xylose substrate due to the absence of CheW and CheV proteins. This is the first report on the shotgun proteomic analysis of C. acetobutylicum ATCC 824 in ABE fermentation between glucose and xylose substrate from a single time data point and the number of proteins identified here is more than any other study performed on this organism up to this report.
Collapse
|
7
|
Mao S, Luo Y, Bao G, Zhang Y, Li Y, Ma Y. Comparative analysis on the membrane proteome of Clostridium acetobutylicum wild type strain and its butanol-tolerant mutant. MOLECULAR BIOSYSTEMS 2011; 7:1660-77. [DOI: 10.1039/c0mb00330a] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
8
|
Janssen H, Döring C, Ehrenreich A, Voigt B, Hecker M, Bahl H, Fischer RJ. A proteomic and transcriptional view of acidogenic and solventogenic steady-state cells of Clostridium acetobutylicum in a chemostat culture. Appl Microbiol Biotechnol 2010; 87:2209-26. [PMID: 20617312 PMCID: PMC3227527 DOI: 10.1007/s00253-010-2741-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 06/15/2010] [Accepted: 06/15/2010] [Indexed: 12/02/2022]
Abstract
The complex changes in the life cycle of Clostridium acetobutylicum, a promising biofuel producer, are not well understood. During exponential growth, sugars are fermented to acetate and butyrate, and in the transition phase, the metabolism switches to the production of the solvents acetone and butanol accompanied by the initiation of endospore formation. Using phosphate-limited chemostat cultures at pH 5.7, C. acetobutylicum was kept at a steady state of acidogenic metabolism, whereas at pH 4.5, the cells showed stable solvent production without sporulation. Novel proteome reference maps of cytosolic proteins from both acidogenesis and solventogenesis with a high degree of reproducibility were generated. Yielding a 21% coverage, 15 protein spots were specifically assigned to the acidogenic phase, and 29 protein spots exhibited a significantly higher abundance in the solventogenic phase. Besides well-known metabolic proteins, unexpected proteins were also identified. Among these, the two proteins CAP0036 and CAP0037 of unknown function were found as major striking indicator proteins in acidogenic cells. Proteome data were confirmed by genome-wide DNA microarray analyses of the identical cultures. Thus, a first systematic study of acidogenic and solventogenic chemostat cultures is presented, and similarities as well as differences to previous studies of batch cultures are discussed.
Collapse
Affiliation(s)
- Holger Janssen
- Abteilung Mikrobiologie, Institut für Biowissenschaften, Universität Rostock, Albert-Einstein-Str. 3, 18051 Rostock, Germany
| | - Christina Döring
- Abteilung Allgemeine Mikrobiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Armin Ehrenreich
- Abteilung Allgemeine Mikrobiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
- Lehrstuhl für Mikrobiologie, Technische Universität München, Am Hochanger 4, 85350 Freising, Germany
| | - Birgit Voigt
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße 15, 17487 Greifswald, Germany
| | - Michael Hecker
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße 15, 17487 Greifswald, Germany
| | - Hubert Bahl
- Abteilung Mikrobiologie, Institut für Biowissenschaften, Universität Rostock, Albert-Einstein-Str. 3, 18051 Rostock, Germany
| | - Ralf-Jörg Fischer
- Abteilung Mikrobiologie, Institut für Biowissenschaften, Universität Rostock, Albert-Einstein-Str. 3, 18051 Rostock, Germany
| |
Collapse
|
9
|
Twine SM, Paul CJ, Vinogradov E, McNally DJ, Brisson JR, Mullen JA, McMullin DR, Jarrell HC, Austin JW, Kelly JF, Logan SM. Flagellar glycosylation in Clostridium botulinum. FEBS J 2008; 275:4428-44. [DOI: 10.1111/j.1742-4658.2008.06589.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
10
|
Sebaihia M, Peck MW, Minton NP, Thomson NR, Holden MT, Mitchell WJ, Carter AT, Bentley SD, Mason DR, Crossman L, Paul CJ, Ivens A, Wells-Bennik MH, Davis IJ, Cerdeño-Tárraga AM, Churcher C, Quail MA, Chillingworth T, Feltwell T, Fraser A, Goodhead I, Hance Z, Jagels K, Larke N, Maddison M, Moule S, Mungall K, Norbertczak H, Rabbinowitsch E, Sanders M, Simmonds M, White B, Whithead S, Parkhill J. Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes. Genome Res 2007; 17:1082-92. [PMID: 17519437 PMCID: PMC1899119 DOI: 10.1101/gr.6282807] [Citation(s) in RCA: 210] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Clostridium botulinum is a heterogeneous Gram-positive species that comprises four genetically and physiologically distinct groups of bacteria that share the ability to produce botulinum neurotoxin, the most poisonous toxin known to man, and the causative agent of botulism, a severe disease of humans and animals. We report here the complete genome sequence of a representative of Group I (proteolytic) C. botulinum (strain Hall A, ATCC 3502). The genome consists of a chromosome (3,886,916 bp) and a plasmid (16,344 bp), which carry 3650 and 19 predicted genes, respectively. Consistent with the proteolytic phenotype of this strain, the genome harbors a large number of genes encoding secreted proteases and enzymes involved in uptake and metabolism of amino acids. The genome also reveals a hitherto unknown ability of C. botulinum to degrade chitin. There is a significant lack of recently acquired DNA, indicating a stable genomic content, in strong contrast to the fluid genome of Clostridium difficile, which can form longer-term relationships with its host. Overall, the genome indicates that C. botulinum is adapted to a saprophytic lifestyle both in soil and aquatic environments. This pathogen relies on its toxin to rapidly kill a wide range of prey species, and to gain access to nutrient sources, it releases a large number of extracellular enzymes to soften and destroy rotting or decayed tissues.
Collapse
Affiliation(s)
- Mohammed Sebaihia
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Michael W. Peck
- Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, United Kingdom
| | - Nigel P. Minton
- Centre for Biomolecular Sciences, Institute of Infection, Immunity and Inflammation, School of Molecular Medical Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Nicholas R. Thomson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Matthew T.G. Holden
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Wilfrid J. Mitchell
- School of Life Sciences, Heriot-Watt University, Riccarton, Edinburgh EH14 4AS, United Kingdom
| | - Andrew T. Carter
- Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, United Kingdom
| | - Stephen D. Bentley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - David R. Mason
- Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, United Kingdom
| | - Lisa Crossman
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Catherine J. Paul
- Bureau of Microbial Hazards, Health Canada, Ottawa, Ontario, K1A 0L2, Canada
| | - Alasdair Ivens
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | | | - Ian J. Davis
- Centre for Biomolecular Sciences, Institute of Infection, Immunity and Inflammation, School of Molecular Medical Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Ana M. Cerdeño-Tárraga
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Carol Churcher
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Michael A. Quail
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Tracey Chillingworth
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Theresa Feltwell
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Audrey Fraser
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Ian Goodhead
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Zahra Hance
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Kay Jagels
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Natasha Larke
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Mark Maddison
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Sharon Moule
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Karen Mungall
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Halina Norbertczak
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Ester Rabbinowitsch
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Mandy Sanders
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Mark Simmonds
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Brian White
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Sally Whithead
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
- Corresponding author.E-mail ; fax 44-1223-494919
| |
Collapse
|
11
|
Paul CJ, Twine SM, Tam KJ, Mullen JA, Kelly JF, Austin JW, Logan SM. Flagellin diversity in Clostridium botulinum groups I and II: a new strategy for strain identification. Appl Environ Microbiol 2007; 73:2963-75. [PMID: 17351097 PMCID: PMC1892883 DOI: 10.1128/aem.02623-06] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Strains of Clostridium botulinum are traditionally identified by botulinum neurotoxin type; however, identification of an additional target for typing would improve differentiation. Isolation of flagellar filaments and analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) showed that C. botulinum produced multiple flagellin proteins. Nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS) analysis of in-gel tryptic digests identified peptides in all flagellin bands that matched two homologous tandem flagellin genes identified in the C. botulinum Hall A genome. Designated flaA1 and flaA2, these open reading frames encode the major structural flagellins of C. botulinum. Colony PCR and sequencing of flaA1/A2 variable regions classified 80 environmental and clinical strains into group I or group II and clustered isolates into 12 flagellar types. Flagellar type was distinct from neurotoxin type, and epidemiologically related isolates clustered together. Sequencing a larger PCR product, obtained during amplification of flaA1/A2 from type E strain Bennett identified a second flagellin gene, flaB. LC-MS analysis confirmed that flaB encoded a large type E-specific flagellin protein, and the predicted molecular mass for FlaB matched that observed by SDS-PAGE. In contrast, the molecular mass of FlaA was 2 to 12 kDa larger than the mass predicted by the flaA1/A2 sequence of a given strain, suggesting that FlaA is posttranslationally modified. While identification of FlaB, and the observation by SDS-PAGE of different masses of the FlaA proteins, showed the flagellin proteins of C. botulinum to be diverse, the presence of the flaA1/A2 gene in all strains examined facilitates single locus sequence typing of C. botulinum using the flagellin variable region.
Collapse
Affiliation(s)
- Catherine J Paul
- Bureau of Microbial Hazards, HFPB, Health Canada, Sir Frederick G. Banting Research Centre, Ottawa, Ontario, Canada
| | | | | | | | | | | | | |
Collapse
|
12
|
Logan SM. Flagellar glycosylation - a new component of the motility repertoire? MICROBIOLOGY-SGM 2006; 152:1249-1262. [PMID: 16622043 DOI: 10.1099/mic.0.28735-0] [Citation(s) in RCA: 178] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The biosynthesis, assembly and regulation of the flagellar apparatus has been the subject of extensive studies over many decades, with considerable attention devoted to the peritrichous flagella of Escherichia coli and Salmonella enterica. The characterization of flagellar systems from many other bacterial species has revealed subtle yet distinct differences in composition, regulation and mode of assembly of this important subcellular structure. Glycosylation of the major structural protein, the flagellin, has been shown most recently to be an important component of numerous flagellar systems in both Archaea and Bacteria, playing either an integral role in assembly or for a number of bacterial pathogens a role in virulence. This review focuses on the structural diversity in flagellar glycosylation systems and demonstrates that as a consequence of the unique assembly processes, the type of glycosidic linkage found on archaeal and bacterial flagellins is distinctive.
Collapse
Affiliation(s)
- Susan M Logan
- Institute for Biological Sciences, National Research Council, Ottawa, Ontario K1A OR6, Canada
| |
Collapse
|
13
|
Paredes CJ, Alsaker KV, Papoutsakis ET. A comparative genomic view of clostridial sporulation and physiology. Nat Rev Microbiol 2005; 3:969-78. [PMID: 16261177 DOI: 10.1038/nrmicro1288] [Citation(s) in RCA: 265] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Clostridia are anaerobic, endospore-forming prokaryotes that include strains of importance to human and animal health and physiology, cellulose degradation, solvent production and bioremediation. Their differentiation and related developmental programmes are not well understood at the molecular level. Recent genome sequencing and transcriptional-profiling studies have offered a glimpse of their inner workings and indicate that a better understanding of the orchestration of the molecular events that underlie their unique physiology, capabilities and diversity will pay major dividends.
Collapse
Affiliation(s)
- Carlos J Paredes
- Department of Chemical & Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | | | | |
Collapse
|
14
|
Sullivan L, Bennett GN. Proteome analysis and comparison of Clostridium acetobutylicum ATCC 824 and Spo0A strain variants. J Ind Microbiol Biotechnol 2005; 33:298-308. [PMID: 16308714 DOI: 10.1007/s10295-005-0050-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Accepted: 10/01/2005] [Indexed: 11/24/2022]
Abstract
The proteomic profiles of several Clostridium acetobutylicum strains were compared by two-dimensional gel electrophoresis and mass spectroscopy. The proteomic profile of C. acetobutylicum wild type strain ATCC 824 with and without a commonly used control plasmid and with a spo0A overexpression plasmid pMSPOA was compared. A total of 2,081 protein spots were analyzed; 23 proteins were chosen to be identified of which 18 were unique and 5 were proteins located in more than one location. The proteins identified were classified into heat shock stress response, acid and solvent formation, and transcription and translation proteins. Spo0A was identified and its protein expression was confirmed to be absent in the spo0A knockout SKO1 strain as expected, as was the protein Adc, which is known to be regulated by Spo0A. The expression of six proteins was not detected in strain SKO1 indicating these proteins require Spo0A. Spo0A overexpression affected the abundance of proteins involved in glycolysis, translation, heat shock stress response, and energy production. Two features were identified: five of the 23 proteins identified were located in more than one position and clusters of protein spots resembled fingers of a straightened hand. Normally a protein localizes to only one spot on the gel; localization of a protein to more than one spot is indicative of post-translational modifications, suggesting that such modification of proteins may be a more prevalent mechanism in C. acetobutylicum than previously thought. The clusters of protein spots resembling fingers of a straightened hand were in the acidic high molecular weight areas. Two such protein spots were identified as variants of the same protein, GroEL.
Collapse
Affiliation(s)
- Leighann Sullivan
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA
| | | |
Collapse
|
15
|
Desvaux M, Khan A, Scott-Tucker A, Chaudhuri RR, Pallen MJ, Henderson IR. Genomic analysis of the protein secretion systems in Clostridium acetobutylicum ATCC 824. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1745:223-53. [PMID: 15950297 DOI: 10.1016/j.bbamcr.2005.04.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2005] [Revised: 04/20/2005] [Accepted: 04/20/2005] [Indexed: 12/21/2022]
Abstract
Consistent information about protein secretion in Gram-positive bacteria is essentially restricted to the model organism Bacillus subtilis. Among genome-sequenced clostridia, Clostridium acetobutylicum has been the most extensively studied from a physiological point of view and is the organism for which the largest variety of molecular biology tools have been developed. Following in silico analyses, both secreted proteins and protein secretion systems were identified. The Tat (Twin arginine translocation; TC #2.A.64) pathway and ABC (ATP binding cassette) protein exporters (TC #3.A.1.) could not be identified, but the Sec (secretion) pathway (TC #3.A.5) appears to be used prevalently. Similarly, a flagella export apparatus (FEA; TC #3.A.6.), holins (TC #1.E.), and an ESAT-6/WXG100 (early secreted antigen target of 6 kDa/proteins with a WXG motif of approximately 100 residues) secretion system were identified. Here, we report for the first time the identification of a fimbrilin protein exporter (FPE; TC #3.A.14) and a Tad (tight adherence) export apparatus in C. acetobutylicum. This investigation highlights the potential use of this saprophytic bacterium in biotechnological and biomedical applications as well as a model organism for studying protein secretion in pathogenic Gram-positive bacteria.
Collapse
Affiliation(s)
- Mickaël Desvaux
- The Institute for Biomedical Research (IBR), The University of Birmingham-The Medical School, Division of Immunity and Infection, Bacterial Pathogenesis and Genomics Unit, Edgbaston, Birmingham B15 2TT, UK.
| | | | | | | | | | | |
Collapse
|
16
|
Tomas CA, Alsaker KV, Bonarius HPJ, Hendriksen WT, Yang H, Beamish JA, Paredes CJ, Papoutsakis ET. DNA array-based transcriptional analysis of asporogenous, nonsolventogenic Clostridium acetobutylicum strains SKO1 and M5. J Bacteriol 2003; 185:4539-47. [PMID: 12867463 PMCID: PMC165787 DOI: 10.1128/jb.185.15.4539-4547.2003] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The large-scale transcriptional program of two Clostridium acetobutylicum strains (SKO1 and M5) relative to that of the parent strain (wild type [WT]) was examined by using DNA microarrays. Glass DNA arrays containing a selected set of 1,019 genes (including all 178 pSOL1 genes) covering more than 25% of the whole genome were designed, constructed, and validated for data reliability. Strain SKO1, with an inactivated spo0A gene, displays an asporogenous, filamentous, and largely deficient solventogenic phenotype. SKO1 displays downregulation of all solvent formation genes, sigF, and carbohydrate metabolism genes (similar to genes expressed as part of the stationary-phase response in Bacillus subtilis) but also several electron transport genes. A major cluster of genes upregulated in SKO1 includes abrB, the genes from the major chemotaxis and motility operons, and glycosylation genes. Strain M5 displays an asporogenous and nonsolventogenic phenotype due to loss of the megaplasmid pSOL1, which contains all genes necessary for solvent formation. Therefore, M5 displays downregulation of all pSOL1 genes expressed in the WT. Notable among other genes expressed more highly in WT than in M5 were sigF, several two-component histidine kinases, spo0A, cheA, cheC, many stress response genes, fts family genes, DNA topoisomerase genes, and central-carbon metabolism genes. Genes expressed more highly in M5 include electron transport genes (but different from those downregulated in SKO1) and several motility and chemotaxis genes. Most of these expression patterns were consistent with phenotypic characteristics. Several of these expression patterns are new or different from what is known in B. subtilis and can be used to test a number of functional-genomic hypotheses.
Collapse
Affiliation(s)
- Christopher A Tomas
- Department of Chemical Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | | | | | | | | | | | | | | |
Collapse
|