[논문]Complete Genome of Bacillus subtilis subsp. subtilis KCTC 3135T and Variation in Cell Wall Genes of B. subtilis Strains

Ahn, Seonjoo; Jun, Sangmi; Ro, Hyun-Joo; Kim, Ju Han; Kim, Seil

doi:10.4014/jmb.1712.12006

Complete Genome of Bacillus subtilis subsp. subtilis KCTC 3135T and Variation in Cell Wall Genes of B. subtilis Strains 원문보기

Journal of microbiology and biotechnology, v.28 no.10, 2018년, pp.1760 - 1768

Ahn, Seonjoo (Department of Biomedical Sciences, Seoul National University College of Medicine) , Jun, Sangmi (Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology) , Ro, Hyun-Joo (Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology) , Kim, Ju Han (Department of Biomedical Sciences, Seoul National University College of Medicine) , Kim, Seil (Division of Chemical and Medical Metrology, Center for Bioanalysis, Korea Research Institute of Standards and Science)

Abstract ▼ AI-Helper

The type strain Bacillus subtilis subsp. subtilis KCTC $3135^T$ was deeply sequenced and annotated, replacing a previous draft genome in this study. The tar and tag genes were involved in synthesizing wall teichoic acids (WTAs), and these genes and their products were previously regarded as the distinguishing difference between B. s. subtilis and B. s. spizizenii. However, a comparative genomic analysis of B. subtilis spp. revealed that both B. s. subtilis and B. s. spizizenii had various types of cell walls. These tar and tag operons were mutually exclusive and the tar genes from B. s. spizizenii were very similar to the genes from non-Bacillus bacteria, unlike the tag genes from B. s. subtilis. The results and previous studies suggest that the tar genes and the tag genes are not inherited after subspecies speciation. The phylogenetic tree based on whole genome sequences showed that each subspecies clearly formed a monophyletic group, while the tree based on tar genes showed that monophyletic groups were formed according to the cell wall type rather than the subspecies. These findings indicate that the tar genes and the presence of ribitol as a cell-wall constituent were not the distinguishing difference between the subspecies of B. subtilis and that the description of subspecies B. s. spizizenii should be updated.

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subtilis subsp. subtilis strains were selected. Five complete and nine incomplete genomes of B.

이론/모형

Among the retrieved genes, tarABD genes and/or the conserved genes were sequentially concatenated and used for a multi-locus sequence analysis (MLSA) [32]. The alignment was carried out using MUSCLE [33] and Neighborjoining (NJ) tree was constructed using the Maximum Composite Likelihood method [34]. The Tar proteins from B.
Among the 60 genomes, 25 unique genomes were selected t˚Construct concise phylogenetic trees and a heatmap. The phylogenetic trees were constructed using the neighbor-joining (NJ) algorithm [35] with MEGA 7 [36]. The distance matrix was generated based on the whole genome similarity by OrthoANI [37] (Fig.

성능/효과

Each B. subtilis subspecies was clearly distinguished and formed separate groups in OrthoANI trees and MLSA trees with conservative genes (Figs. 1, S2, and S4). This is als˚Clearly congruent with previous study [44].
In conclusion, the overall genomic structures of B. s. subtilis KCTC 3135^T and B.
However, the tarABD MLSA NJ tree and combined MLSA tree did not coincide with the OrthoANI tree. The MLSA trees showed that each subspecies had multiple cell wall types, also indicating that the B. subtilis subspecies cannot be distinguished by thepresence of ribitol as a cell-wall constituent. It also indicated that tar genes were not inherited after the speciation of B.
Among these strains, strain VV2 had tarIJKL genes. These indicated that tag operons can be substituted with tar operons or vice versa in the genome of B. subtilis strains regardless of subspecies, showing the presence of ribitol is not a distinguishing characteristic of specific subspecies.

참고문헌 (56)

Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, et al. 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390: 249-256.

상세보기
Nazina TN, Tourova TP, Poltaraus AB, Novikova EV, Grigoryan AA, Ivanova AE, et al. 2001. Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermoglucosidasius and Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. thermocatenulatus, G. thermoleovorans, G. kaustophilus, G. thermoglucosidasius and G. thermodenitrificans. Int. J. Syst. Evol. Microbiol. 51: 433-446.

상세보기
Porwal S, Lal S, Cheema S, Kalia VC. 2009. Phylogeny in aid of the present and novel microbial lineages: diversity in Bacillus. PLoS One 4: e4438.

상세보기
Harwood CR. 1992. Bacillus subtilis and its relatives: molecular biological and industrial workhorses. Trends Biotechnol. 10: 247-256.

상세보기
Earl AM, Losick R, Kolter R. 2008. Ecology and genomics of Bacillus subtilis. Trends Microbiol. 16: 269-275.

상세보기
Schallmey M, Singh A, Ward OP. 2004. Developments in the use of Bacillus species for industrial production. Can. J. Microbiol. 50: 1-17.

상세보기
Jin P, Zhang L, Yuan P, Kang Z, Du G, Chen J. 2016. Efficient biosynthesis of polysaccharides chondroitin and heparosan by metabolically engineered Bacillus subtilis. Carbohydr. Polym. 140: 424-432.

상세보기
Deshmukh AN, Nipanikar-Gokhale P, Jain R. 2016. Engineering of Bacillus subtilis for the Production of 2,3-Butanediol from Sugarcane Molasses. Appl. Biochem. Biotechnol. 179: 321-331.

상세보기
Nakamura LK, Roberts MS, Cohan FM. 1999. Relationship of Bacillus subtilis clades associated with strains 168 and W23: a proposal for Bacillus subtilis subsp. subtilis subsp. nov. and Bacillus subtilis subsp. spizizenii subsp. nov. Int. J. Syst. Bacteriol. 49: 1211-1215.

상세보기
Rooney AP, Price NP, Ehrhardt C, Swezey JL, Bannan JD. 2009. Phylogeny and molecular taxonomy of the Bacillus subtilis species complex and description of Bacillus subtilis subsp. inaquosorum subsp. nov. Int. J. Syst. Evol. Microbiol. 59: 2429-2436.

상세보기
Swoboda JG, Campbell J, Meredith TC, Walker S. 2010. Wall teichoic acid function, biosynthesis, and inhibition. ChemBioChem. 11: 35-45.

상세보기
Brown S, Santa Maria JP Jr, Walker S. 2013. Wall teichoic acids of gram-positive bacteria. Annu. Rev. Microbiol. 67: 313-336.

상세보기
Lazarevic V, Abellan FX, Moller SB, Karamata D, Mauel C. 2002. Comparison of ribitol and glycerol teichoic acid genes in Bacillus subtilis W23 and 168: identical function, similar divergent organization, but different regulation. Microbiology 148: 815-824.

상세보기
Mauel C, Young M, Karamata D. 1991. Genes concerned with synthesis of poly(glycerol phosphate), the essential teichoic acid in Bacillus subtilis strain 168, are organized in two divergent transcription units. J. Gen. Microbiol. 137: 929-941.

상세보기
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. 2012. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19: 455-477.

상세보기
Nawrocki EP, Eddy SR. 2013. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29: 2933-2935.

상세보기
Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, et al. 2015. Rfam 12.0: updates to the RNA families database. Nucleic Acids Res. 43: D130-D137.

상세보기
Edgar RC. 2007. PILER-CR: Fast and accurate identification of CRISPR repeats. BMC Bioinformatics 8: 18.

상세보기
Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, et al. 2007. CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 8: 209.

상세보기
Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.

상세보기
Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. 2014. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42: D199-D205.

상세보기
Chen C, Huang H, Wu CH. 2017. Protein bioinformatics databases and resources. Methods Mol. Biol. 1558: 3-39.

상세보기
Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, et al. 2014. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res. 42: D231-D239.

상세보기
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, et al. 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33: 5691-5702.

상세보기
Mistry J, Finn RD, Eddy SR, Bateman A, Punta M. 2013. Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Res. 41: e121-e121.

상세보기
Gibson MK, Forsberg KJ, Dantas G. 2015. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME J. 9: 207-216.

상세보기
Caspi R, Billington R, Ferrer L, Foerster H, Fulcher CA, Keseler IM, et al. 2016. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 44: D471-480.

상세보기
Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, et al. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67: 1613-1617.

상세보기
Zhu Q, Kosoy M, Dittmar K. 2014. HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers. BMC Genomics 15: 717.

상세보기
Jolley KA, Maiden MC. 2010. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11: 595.

상세보기
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10: 421.

상세보기
Maiden MCJ, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, et al. 1998. Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95: 3140-3145.

상세보기
Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797.

상세보기
Tamura K, Nei M, Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl. Acad. Sci. USA 101: 11030-11035.

상세보기
Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.

상세보기
Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33: 1870-1874.

상세보기
Lee I, Kim YO, Park SC, Chun J. 2016. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int. J. Syst. Evol. Microbiol. 66: 1100-1103.

상세보기
Kim S, Gong G, Woo HM, Kim Y, Um Y. 2016. Burkholderia jirisanensis sp. nov., isolated from forest soil. Int. J. Syst. Evol. Microbiol. 66: 1260-1267.

상세보기
Yun SH, Lee SY, Choi CW, Lee H, Ro HJ, Jun S, et al. 2017. Proteomic characterization of the outer membrane vesicle of the halophilic marine bacterium Novosphingobium pentaromativorans US6-1. J. Microbiol. 55: 56-62.

상세보기
Garcia-Vallve S, Romeu A, Palau J. 2000. Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res. 10: 1719-1725.

상세보기
Zuniga M, Comas I, Linaje R, Monedero V, Yebra MJ, Esteban CD, et al. 2005. Horizontal gene transfer in the molecular evolution of mannose PTS transporters. Mol. Biol. Evol. 22: 1673-1685.

상세보기
Comas I, Gonzalez-Candelas F, Zuniga M. 2008. Unraveling the evolutionary history of the phosphoryl-transfer chain of the phosphoenolpyruvate: phosphotransferase system through phylogenetic analyses and genome context. BMC Evol. Biol. 8: 147.

상세보기
Young M, Mauel C, Margot P, Karamata D. 1989. Pseudo-allelic relationship between non-homologous genes concerned with biosynthesis of polyglycerol phosphate and polyglycerol phosphate teichoic acids in Bacillus subtilis strains 168 and W23. Mol. Microbiol. 3: 1805-1812.

상세보기
Yi H, Chun J, Cha CJ. 2014. Genomic insights into the taxonomic status of the three subspecies of Bacillus subtilis. Syst. Appl. Microbiol. 37: 95-99.

상세보기
Halling SM, Burtis K, Doi R. 1977. Reconstitution studies show that rifampicin resistance is determined by the largest polypeptide of Bacillus subtilis RNA polymerase. J. Biol. Chem. 252: 9024-9031.
Goldstein BP. 2014. Resistance to rifampicin: a review. J. Antibiot. 67: 625.

상세보기
Sigle S, Steblau N, Wohlleben W, Muth G. 2016. Polydiglycosylphosphate transferase PdtA (SCO2578) of Streptomyces coelicolor A3 (2) is crucial for proper sporulation and apical tip extension under stress conditions. Appl. Environ. Microbiol. 82: 5661-5672.

상세보기
Sharma D, Cukras AR, Rogers EJ, Southworth DR, Green R. 2007. Mutational analysis of S12 protein and implications for the accuracy of decoding by the ribosome. J. Mol. Biol. 374: 1065-1076.

상세보기
Nguyen-Disteche M, Leyh-Bouille M, Ghuysen J-M. 1982. Isolation of the membrane-bound 26 000-Mr penicillin-binding protein of Streptomyces strain K15 in the form of a penicillin-sensitive D-alanyl-D-alanine-cleaving transpeptidase. Biochem. J. 207: 109-115.

상세보기
Gordon E, Mouz N, Duee E, Dideberg O. 2000. The crystal structure of the penicillin-binding protein 2x from Streptococcus pneumoniae and its acyl-enzyme form: implication in drug resistance. J. Mol. Biol. 299: 477-485.

상세보기
Lowy FD. 2003. Antimicrobial resistance: the example of Staphylococcus aureus. J. Clin. Invest. 111: 1265-1273.

상세보기
Drawz SM, Bonomo RA. 2010. Three decades of $\beta$ -lactamase inhibitors. Clin. Microbiol. Rev. 23: 160-201.

상세보기
Farha MA, Leung A, Sewell EW, D'Elia MA, Allison SE, Ejim L, et al. 2012. Inhibition of WTA synthesis blocks the cooperative action of PBPs and sensitizes MRSA to $\beta$ -lactams. ACS Chem. Biol. 8: 226-233.
Roberts MC. 2005. Update on acquired tetracycline resistance genes. FEMS Microbiol. Lett. 245: 195-203.

상세보기
Bhavsar AP, Beveridge TJ, Brown ED. 2001. Precise deletion of tagD and controlled depletion of its product, glycerol 3-phosphate cytidylyltransferase, leads to irregular morphology and lysis of Bacillus subtilis grown at physiological temperature. J. Bacteriol. 183: 6688-6693.

상세보기
D'Elia MA, Millar KE, Beveridge TJ, Brown ED. 2006. Wall teichoic acid polymers are dispensable for cell viability in Bacillus subtilis. J. Bacteriol. 188: 8313-8316.

상세보기

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