crossmark
Draft Genome Sequence of an Industrially Important Bacillus sp. from Mandarmani Coastal Waters in Midnapur District, West Bengal, India Shaon Ray Chaudhuria,b Department of Microbiology, Tripura University, Suryamaninagar, Tripura West, Indiaa; Centre of Excellence in Environmental Technology and Management, Maulana Abul Kalam Azad University of Technology, West Bengal, Kolkata, Indiab
Reported here is the draft genome sequence of an amylase-, protease-, DNase-, oxidase-, gelatinase-, and catalaseproducing, Gram-positive diplobacillus (Bacillus sp. SM1 strain MCC2138), which was isolated from marine coastal waters and has the ability to degum raw silk fabric as well as Ramie fiber. The genome comprises 1.76 Mb with a GC content of 34.5%. Received 25 June 2016 Accepted 27 June 2016 Published 18 August 2016 Citation Ray Chaudhuri S. 2016. Draft genome sequence of an industrially important Bacillus sp. from Mandarmani coastal waters in Midnapur District, West Bengal, India. Genome Announc 4(4):e00867-16. doi:10.1128/genomeA.00867-16. Copyright © 2016 Ray Chaudhuri. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to [email protected].
T
he marine environment is rich in microbial diversity with an expected population of about 3.67 ⫻ 1028 microorganisms (1). This environment shows striking differences in terms of pressure, salinity, temperature, and light from other water bodies and is expected to harbor diverse microbial populations belonging to aerobic, anoxygenic, and phototrophic groups simultaneously. These populations demonstrate adaptability to maintain intracellular sodium ion concentrations and hence avoid osmotic shock (2). They are a promising source for natural products of the future due to the incredible diversity of chemical compounds that have been isolated from them (3). Proteases account for 60% of the world enzyme market, while 40% are of microbial origin (4–6). In lieu of the wide applications of proteases, this biofilm-forming Gram-positive diplobacillus, with optimum temperature of 37°C and pH of 7, was isolated from Mandarmani coastal waters in milk media. The strain (MCC2138) was closest to Bacillus thuringensis at the 16SrDNA (FJ377720) sequence level. It could accumulate Pb, Cr, Ni, Cu, and Co (7). Its extracellular enzyme was efficient in degumming of raw silk fabric (8) as well as Ramie fiber (9). SOAPdenovo version 2.04-r240 was used to assemble the raw reads (29 contigs) with a 2.0⫻ coverage generated on an Illumina platform, totaling 17,69,494 bp, with a largest contig length of 5,01,909 bp and N50 and L50 values of 216,057 bp and 3 bp, respectively. The contigs submitted to the RAST server (10) revealed 5,580 genes, of which only 27% fall under the subsystem category. The maximum similarity was with Bacillus cereus followed by Bacillus sp. and Bacillus thuringiensis, as per RAST analysis. The functional annotation using Blast2GOPro version 2.8 revealed 3,380 genes responsible for biological processes, 2,210 for cellular components, and 3,205 for molecular functions. A total of 2,059 genes were annotated for metabolic pathways. The important genes contained in the different contigs are as follows: ABC transporter ATP binding protein; redox-sensitive transcriptional regulator (AT-rich DNA binding protein); heat
July/August 2016 Volume 4 Issue 4 e00867-16
shock protein 60 family cochaperone GroES/GroEL; ATP pyrophosphatase subunit (EC 6.3.5.2); phosphate regulon transcriptional regulatory protein PhoB (SphR) (accession no. LXJX01000001.1); oligopeptide ABC transporter, periplasmic oligopeptide-binding protein OppA/B/C/D/F (TC3.A.1.5.1); hydrolase, tRNA; glycerate kinase (EC2.7.1.31); arginase (EC3.5.3.1); diadenylate cyclase spyDAC; bacterial checkpoint controller DisA with nucleotide-binding domain; phosphoglucosamine mutase (EC 5.4.2.10; accession no. NZ_LXJX01000003.1); programmed cell death toxin YdcE and YdcD; outer membrane lipoprotein receptor; Holo (acyl carrier protein) synthase (EC2.7.8.7); UV endonuclease UvdE family; DEAD box ATPdependent RNA helicase CshA (EC3.6.4.13); t-RNA (accession no. NZ_LXJX01000007.1); ABC transporter permease protein YvcS; ABC transporter ATP-binding protein YvcR; betalactamase class A; secreted and spore coat–associated protein 1; chitinase (EC 3.2.1.14); cell-division protein FtsW; microbial collagenase (EC 3.4.24.3); transcriptional regulator, TetR family (accession no. NZ_LXJX01000017.1); cysteine synthase (EC 2.5.1.47); chaperonin (heat shock protein 33); tRNA (Ile) lysidine synthetase (EC 6.3.4.19); AbrB family transcriptional regulator (SpoVT); transcription repair coupling factor; Fin, required for the switch from sigma F to sigma G during sporulation; peptidyl-tRNA hydrolase (EC 3.1.1.29) (accession no. NZ_LXJX01000019.1). Accession number(s). This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number LXJX00000000. The version described in this paper is the first version, LXJX01000000. ACKNOWLEDGMENTS This work was supported by a grant from the Ministry of Human Resource Development, Government of India, under the FAST scheme. I also thank Sourav Ghosh for sequence submission and Sumana Das for strain isolation.
Genome Announcements
genomea.asm.org 1
Ray Chaudhuri
FUNDING INFORMATION This work was funded by Ministry of Human Resource Development (MHRD), Government of India (sanction letter no. 5-5/2014-TS.VII [4 September 2014]).
6. 7.
The research is funded by the Ministry of Human Resource Development, Government of India, under the FAST scheme. 8.
REFERENCES 1. Whitman WB, Coleman DC, Wiebe WJ. 1998. Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95:6578 – 6583. http://dx.doi.org/ 10.1073/pnas.95.12.6578. 2. Das S, Lyla PS, Khan SA. 2006. Marine microbial diversity and ecology: importance and future perspectives. Curr Sci 90:1325–1335. 3. Burkholder PR, Pfister RM, Leitz FH. 1966. Production of a pyrrole antibiotic by a marine bacterium. Appl Microbiol 14:649 – 653. 4. Gupta R, Beg QK, Lorenz P. 2002. Bacterial alkaline proteases: molecular approaches and industrial applications. Appl Microbiol Biotechnol 59: 15–32. http://dx.doi.org/10.1007/s00253-002-0975-y. 5. Rao MB, Tanksale AM, Ghatge MS, Deshpande VV. 1998. Molecular
2 genomea.asm.org
9. 10.
and biotechnological aspects of microbial proteases. Microbiol Mol Biol Rev 62:597– 635. Godfrey T, West S. 1996. Industrial enzymology. Macmillan, New York, NY. Das S, Mukherjee I, Sudarshan M, Sinha TP, Thakur AR, Ray Chaudhuri S. 2012. Bacterial isolates of marine coast as commercial producer of protease. OnLine J Biol Sci 12:96 –107. http://dx.doi.org/10.3844/ ojbsci.2012.96.107 Sumana D, Sudarshan M, Thakur AR, Ray Chaudhuri S. 2013. Degumming of raw silk fabric with help of marine extracellular protease. Am J Biochem Biotechnol 9:12–18. http://dx.doi.org/10.3844/ ajbbsp.2013.12.18. Gupta M, Roy A, Banerjee S, Kapoor R, Adhikari B, Thakur AR, Ray Chaudhuri S. 2015. Bacillus sp. MCC2138: a potential candidate for microbial degumming of ramie. Int J Fiber Text Res 5:39 – 43. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. http://dx.doi.org/10.1186/ 1471-2164-9-75.
Genome Announcements
July/August 2016 Volume 4 Issue 4 e00867-16
Draft Genome Sequence of an Industrially Important Bacillus sp. from Mandarmani Coastal Waters in Midnapur District, West Bengal, India Shaon Ray Chaudhuria,b Department of Microbiology, Tripura University, Suryamaninagar, Tripura West, Indiaa; Centre of Excellence in Environmental Technology and Management, Maulana Abul Kalam Azad University of Technology, West Bengal, Kolkata, Indiab
Reported here is the draft genome sequence of an amylase-, protease-, DNase-, oxidase-, gelatinase-, and catalaseproducing, Gram-positive diplobacillus (Bacillus sp. SM1 strain MCC2138), which was isolated from marine coastal waters and has the ability to degum raw silk fabric as well as Ramie fiber. The genome comprises 1.76 Mb with a GC content of 34.5%. Received 25 June 2016 Accepted 27 June 2016 Published 18 August 2016 Citation Ray Chaudhuri S. 2016. Draft genome sequence of an industrially important Bacillus sp. from Mandarmani coastal waters in Midnapur District, West Bengal, India. Genome Announc 4(4):e00867-16. doi:10.1128/genomeA.00867-16. Copyright © 2016 Ray Chaudhuri. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to [email protected].
T
he marine environment is rich in microbial diversity with an expected population of about 3.67 ⫻ 1028 microorganisms (1). This environment shows striking differences in terms of pressure, salinity, temperature, and light from other water bodies and is expected to harbor diverse microbial populations belonging to aerobic, anoxygenic, and phototrophic groups simultaneously. These populations demonstrate adaptability to maintain intracellular sodium ion concentrations and hence avoid osmotic shock (2). They are a promising source for natural products of the future due to the incredible diversity of chemical compounds that have been isolated from them (3). Proteases account for 60% of the world enzyme market, while 40% are of microbial origin (4–6). In lieu of the wide applications of proteases, this biofilm-forming Gram-positive diplobacillus, with optimum temperature of 37°C and pH of 7, was isolated from Mandarmani coastal waters in milk media. The strain (MCC2138) was closest to Bacillus thuringensis at the 16SrDNA (FJ377720) sequence level. It could accumulate Pb, Cr, Ni, Cu, and Co (7). Its extracellular enzyme was efficient in degumming of raw silk fabric (8) as well as Ramie fiber (9). SOAPdenovo version 2.04-r240 was used to assemble the raw reads (29 contigs) with a 2.0⫻ coverage generated on an Illumina platform, totaling 17,69,494 bp, with a largest contig length of 5,01,909 bp and N50 and L50 values of 216,057 bp and 3 bp, respectively. The contigs submitted to the RAST server (10) revealed 5,580 genes, of which only 27% fall under the subsystem category. The maximum similarity was with Bacillus cereus followed by Bacillus sp. and Bacillus thuringiensis, as per RAST analysis. The functional annotation using Blast2GOPro version 2.8 revealed 3,380 genes responsible for biological processes, 2,210 for cellular components, and 3,205 for molecular functions. A total of 2,059 genes were annotated for metabolic pathways. The important genes contained in the different contigs are as follows: ABC transporter ATP binding protein; redox-sensitive transcriptional regulator (AT-rich DNA binding protein); heat
July/August 2016 Volume 4 Issue 4 e00867-16
shock protein 60 family cochaperone GroES/GroEL; ATP pyrophosphatase subunit (EC 6.3.5.2); phosphate regulon transcriptional regulatory protein PhoB (SphR) (accession no. LXJX01000001.1); oligopeptide ABC transporter, periplasmic oligopeptide-binding protein OppA/B/C/D/F (TC3.A.1.5.1); hydrolase, tRNA; glycerate kinase (EC2.7.1.31); arginase (EC3.5.3.1); diadenylate cyclase spyDAC; bacterial checkpoint controller DisA with nucleotide-binding domain; phosphoglucosamine mutase (EC 5.4.2.10; accession no. NZ_LXJX01000003.1); programmed cell death toxin YdcE and YdcD; outer membrane lipoprotein receptor; Holo (acyl carrier protein) synthase (EC2.7.8.7); UV endonuclease UvdE family; DEAD box ATPdependent RNA helicase CshA (EC3.6.4.13); t-RNA (accession no. NZ_LXJX01000007.1); ABC transporter permease protein YvcS; ABC transporter ATP-binding protein YvcR; betalactamase class A; secreted and spore coat–associated protein 1; chitinase (EC 3.2.1.14); cell-division protein FtsW; microbial collagenase (EC 3.4.24.3); transcriptional regulator, TetR family (accession no. NZ_LXJX01000017.1); cysteine synthase (EC 2.5.1.47); chaperonin (heat shock protein 33); tRNA (Ile) lysidine synthetase (EC 6.3.4.19); AbrB family transcriptional regulator (SpoVT); transcription repair coupling factor; Fin, required for the switch from sigma F to sigma G during sporulation; peptidyl-tRNA hydrolase (EC 3.1.1.29) (accession no. NZ_LXJX01000019.1). Accession number(s). This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number LXJX00000000. The version described in this paper is the first version, LXJX01000000. ACKNOWLEDGMENTS This work was supported by a grant from the Ministry of Human Resource Development, Government of India, under the FAST scheme. I also thank Sourav Ghosh for sequence submission and Sumana Das for strain isolation.
Genome Announcements
genomea.asm.org 1
Ray Chaudhuri
FUNDING INFORMATION This work was funded by Ministry of Human Resource Development (MHRD), Government of India (sanction letter no. 5-5/2014-TS.VII [4 September 2014]).
6. 7.
The research is funded by the Ministry of Human Resource Development, Government of India, under the FAST scheme. 8.
REFERENCES 1. Whitman WB, Coleman DC, Wiebe WJ. 1998. Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95:6578 – 6583. http://dx.doi.org/ 10.1073/pnas.95.12.6578. 2. Das S, Lyla PS, Khan SA. 2006. Marine microbial diversity and ecology: importance and future perspectives. Curr Sci 90:1325–1335. 3. Burkholder PR, Pfister RM, Leitz FH. 1966. Production of a pyrrole antibiotic by a marine bacterium. Appl Microbiol 14:649 – 653. 4. Gupta R, Beg QK, Lorenz P. 2002. Bacterial alkaline proteases: molecular approaches and industrial applications. Appl Microbiol Biotechnol 59: 15–32. http://dx.doi.org/10.1007/s00253-002-0975-y. 5. Rao MB, Tanksale AM, Ghatge MS, Deshpande VV. 1998. Molecular
2 genomea.asm.org
9. 10.
and biotechnological aspects of microbial proteases. Microbiol Mol Biol Rev 62:597– 635. Godfrey T, West S. 1996. Industrial enzymology. Macmillan, New York, NY. Das S, Mukherjee I, Sudarshan M, Sinha TP, Thakur AR, Ray Chaudhuri S. 2012. Bacterial isolates of marine coast as commercial producer of protease. OnLine J Biol Sci 12:96 –107. http://dx.doi.org/10.3844/ ojbsci.2012.96.107 Sumana D, Sudarshan M, Thakur AR, Ray Chaudhuri S. 2013. Degumming of raw silk fabric with help of marine extracellular protease. Am J Biochem Biotechnol 9:12–18. http://dx.doi.org/10.3844/ ajbbsp.2013.12.18. Gupta M, Roy A, Banerjee S, Kapoor R, Adhikari B, Thakur AR, Ray Chaudhuri S. 2015. Bacillus sp. MCC2138: a potential candidate for microbial degumming of ramie. Int J Fiber Text Res 5:39 – 43. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. http://dx.doi.org/10.1186/ 1471-2164-9-75.
Genome Announcements
July/August 2016 Volume 4 Issue 4 e00867-16
