1
|
Cambridge JM, Blinkova AL, Salvador Rocha EI, Bode Hernández A, Moreno M, Ginés-Candelaria E, Goetz BM, Hunicke-Smith S, Satterwhite E, Tucker HO, Walker JR. Genomics of Clostridium taeniosporum, an organism which forms endospores with ribbon-like appendages. PLoS One 2018; 13:e0189673. [PMID: 29293521 PMCID: PMC5749712 DOI: 10.1371/journal.pone.0189673] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 11/30/2017] [Indexed: 01/21/2023] Open
Abstract
Clostridium taeniosporum, a non-pathogenic anaerobe closely related to the C. botulinum Group II members, was isolated from Crimean lake silt about 60 years ago. Its endospores are surrounded by an encasement layer which forms a trunk at one spore pole to which about 12–14 large, ribbon-like appendages are attached. The genome consists of one 3,264,813 bp, circular chromosome (with 26.6% GC) and three plasmids. The chromosome contains 2,892 potential protein coding sequences: 2,124 have specific functions, 147 have general functions, 228 are conserved but without known function and 393 are hypothetical based on the fact that no statistically significant orthologs were found. The chromosome also contains 101 genes for stable RNAs, including 7 rRNA clusters. Over 84% of the protein coding sequences and 96% of the stable RNA coding regions are oriented in the same direction as replication. The three known appendage genes are located within a single cluster with five other genes, the protein products of which are closely related, in terms of sequence, to the known appendage proteins. The relatedness of the deduced protein products suggests that all or some of the closely related genes might code for minor appendage proteins or assembly factors. The appendage genes might be unique among the known clostridia; no statistically significant orthologs were found within other clostridial genomes for which sequence data are available. The C. taeniosporum chromosome contains two functional prophages, one Siphoviridae and one Myoviridae, and one defective prophage. Three plasmids of 5.9, 69.7 and 163.1 Kbp are present. These data are expected to contribute to future studies of developmental, structural and evolutionary biology and to potential industrial applications of this organism.
Collapse
Affiliation(s)
- Joshua M. Cambridge
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas, Austin, TX, United States of America
| | - Alexandra L. Blinkova
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas, Austin, TX, United States of America
| | - Erick I. Salvador Rocha
- Department of Natural Sciences, Health & Wellness, Miami Dade College-Wolfson Campus, Miami, FL, United States of America
| | - Addys Bode Hernández
- Department of Natural Sciences, Health & Wellness, Miami Dade College-Wolfson Campus, Miami, FL, United States of America
| | - Maday Moreno
- Department of Natural Sciences, Health & Wellness, Miami Dade College-Wolfson Campus, Miami, FL, United States of America
| | - Edwin Ginés-Candelaria
- Department of Natural Sciences, Health & Wellness, Miami Dade College-Wolfson Campus, Miami, FL, United States of America
| | - Benjamin M. Goetz
- Center for Computational Biology and Bioinformatics, University of Texas, Austin, TX, United States of America
| | - Scott Hunicke-Smith
- Genomic Sequencing and Analysis Facility, Institute for Cell and Molecular Biology, University of Texas, Austin, TX, United States of America
| | - Ed Satterwhite
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas, Austin, TX, United States of America
| | - Haley O. Tucker
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas, Austin, TX, United States of America
| | - James R. Walker
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas, Austin, TX, United States of America
- * E-mail:
| |
Collapse
|
2
|
Douriet-Gámez NR, Maldonado-Mendoza IE, Ibarra-Laclette E, Blom J, Calderón-Vázquez CL. Genomic Analysis of Bacillus sp. Strain B25, a Biocontrol Agent of Maize Pathogen Fusarium verticillioides. Curr Microbiol 2017; 75:247-255. [DOI: 10.1007/s00284-017-1372-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 10/10/2017] [Indexed: 11/24/2022]
|
3
|
Kubiak X, Duval R, Pluvinage B, Chaffotte AF, Dupret JM, Rodrigues-Lima F. Xenobiotic-metabolizing enzymes in Bacillus anthracis: molecular and functional analysis of a truncated arylamine N-acetyltransferase isozyme. Br J Pharmacol 2016; 174:2174-2182. [PMID: 27846346 DOI: 10.1111/bph.13647] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 09/01/2016] [Accepted: 09/26/2016] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND AND PURPOSE The arylamine N-acetyltransferases (NATs) are xenobiotic-metabolizing enzymes that play an important role in the detoxification and/or bioactivation of arylamine drugs and xenobiotics. In bacteria, NATs may contribute to the resistance against antibiotics such as isoniazid or sulfamides through their acetylation, which makes this enzyme family a possible drug target. Bacillus anthracis, a bacterial species of clinical significance, expresses three NAT isozymes with distinct structural and enzymatic properties, including an inactive isozyme ((BACAN)NAT3). (BACAN)NAT3 features both a non-canonical Glu residue in its catalytic triad and a truncated C-terminus domain. However, the role these unusual characteristics play in the lack of activity of the (BACAN)NAT3 isozyme remains unclear. EXPERIMENTAL APPROACH Protein engineering, recombinant expression, enzymatic analyses with aromatic amine substrates and phylogenetic analysis approaches were conducted. KEY RESULTS The deletion of guanine 580 (G580) in the nat3 gene was shown to be responsible for the expression of a truncated (BACAN)NAT3 isozyme. Artificial re-introduction of G580 in the nat3 gene led to a functional enzyme able to acetylate several arylamine drugs displaying structural characteristics comparable with its functional Bacillus cereus homologue ((BACCR)NAT3). Phylogenetic analysis of the nat3 gene in the B. cereus group further indicated that nat3 may constitute a pseudogene of the B. anthracis species. CONCLUSION AND IMPLICATIONS The existence of NATs with distinct properties and evolution in Bacillus species may account for their adaptation to their diverse chemical environments. A better understanding of these isozymes is of importance for their possible use as drug targets. LINKED ARTICLES This article is part of a themed section on Drug Metabolism and Antibiotic Resistance in Micro-organisms. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.14/issuetoc.
Collapse
Affiliation(s)
- Xavier Kubiak
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Romain Duval
- Sorbonne Paris Cité, Univ Paris Diderot, Unité BFA, CNRS UMR 8251, Paris, France
| | - Benjamin Pluvinage
- Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Alain F Chaffotte
- Unité de Résonance Magnétique Nucléaire des Biomolécules, Institut Pasteur, Paris, France
| | - Jean-Marie Dupret
- Sorbonne Paris Cité, Univ Paris Diderot, Unité BFA, CNRS UMR 8251, Paris, France
| | | |
Collapse
|
4
|
Tourasse NJ, Stabell FB, Kolstø AB. Survey of chimeric IStron elements in bacterial genomes: multiple molecular symbioses between group I intron ribozymes and DNA transposons. Nucleic Acids Res 2014; 42:12333-51. [PMID: 25324310 PMCID: PMC4227781 DOI: 10.1093/nar/gku939] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
IStrons are chimeric genetic elements composed of a group I intron associated with an insertion sequence (IS). The group I intron is a catalytic RNA providing the IStron with self-splicing ability, which renders IStron insertions harmless to the host genome. The IS element is a DNA transposon conferring mobility, and thus allowing the IStron to spread in genomes. IStrons are therefore a striking example of a molecular symbiosis between unrelated genetic elements endowed with different functions. In this study, we have conducted the first comprehensive survey of IStrons in sequenced genomes that provides insights into the distribution, diversity, origin and evolution of IStrons. We show that IStrons have a restricted phylogenetic distribution limited to two bacterial phyla, the Firmicutes and the Fusobacteria. Nevertheless, diverse IStrons representing two major groups targeting different insertion site motifs were identified. This taken with the finding that while the intron components of all IStrons belong to the same structural class, they are fused to different IS families, indicates that multiple intron–IS symbioses have occurred during evolution. In addition, introns and IS elements related to those that were at the origin of IStrons were also identified.
Collapse
Affiliation(s)
- Nicolas J Tourasse
- Laboratory for Microbial Dynamics (LaMDa), Department of Pharmaceutical Biosciences, University of Oslo, Oslo, Norway Institut de Biologie Physico-Chimique, UMR CNRS 7141, Université Pierre et Marie Curie, Paris, France
| | - Fredrik B Stabell
- Laboratory for Microbial Dynamics (LaMDa), Department of Pharmaceutical Biosciences, University of Oslo, Oslo, Norway
| | - Anne-Brit Kolstø
- Laboratory for Microbial Dynamics (LaMDa), Department of Pharmaceutical Biosciences, University of Oslo, Oslo, Norway
| |
Collapse
|
5
|
Abhyankar W, Hossain AH, Djajasaputra A, Permpoonpattana P, Ter Beek A, Dekker HL, Cutting SM, Brul S, de Koning LJ, de Koster CG. In Pursuit of Protein Targets: Proteomic Characterization of Bacterial Spore Outer Layers. J Proteome Res 2013; 12:4507-21. [DOI: 10.1021/pr4005629] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - Patima Permpoonpattana
- School
of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, United Kingdom
| | | | | | - Simon M. Cutting
- School
of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, United Kingdom
| | | | | | | |
Collapse
|