Abstract
Backgrounds
The genus Methylobacterium is composed of a variety of pink-pigmented and facultatively methylotrophic bacteria. Most of the species of these genera have been shown to be either gamma radiation resistant or UV radiation resistant or both. Strain Methylobacterium sp. 17Sr1-43 was isolated from a gamma- irradiated soil sample collected at Seoul Women’s University, South Korea.
Methods
The complete genome of strain Methylobacterium sp. 17Sr1-43 was sequenced and assembled using Pacific Biosciences RS II system. The genome sequence was annotated using JGI GenePRIMP, Prodigal, and Genomes-Expert Review (IMG-ER) platform. The protein-coding genes were identified using Pfam and COG databases implemented in the IMG and NCBI systems.
Results
The complete genome of strain Methylobacterium sp. 17Sr1-43 was found to comprise a complete circular chromosome of 5,539,695 bp, with 5,103 coding sequences (CDs) and 5,186 genes. Many identified genes involved either in DNA repair or the cellular response to ionization radiation. However, contributions by genes involved in cell wall structure/function, cell division, and intermediary metabolism were also evident. Some identified genes were previously have been associated with IR resistance or recovery from IR exposure, including the RecBCD pathway and UmuCD system.
Conclusion
The new strains of Methylobacterium sp. 17Sr1-43 showed both gamma and UV-C irradiation resistance, and their complete genome sequence annotation features correspondingly showed the presence of the genes involved in the radiation-resistance.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Ul Hussain Shah, A. M. et al. A Mur regulator protein in the extremophilic bacterium Deinococcus radiodurans. PloS One 9, e106341 (2014).
Ortiz de Orue Lucana, D., Wedderhoff, I. & Groves, M. R. ROS–Mediated Signalling in Bacteria: Zinc–Containing Cys–X–X–Cys Redox Centres and Iron–Based Oxidative Stress. J Signal Transduct Article ID 605905, 9 pages (2012).
Waldeck, W. et al. ROS–mediated killing efficiency with visible light of bacteria carrying different red fluorochrome proteins. J Photochem Photobiol B 109, 28–33 (2012).
Yu, S.–L. & Lee, S.–K. Ultraviolet radiation: DNA damage, repair, and human disorders. Mol Cell Toxicol 13, 21–28 (2017).
Kim, M. K. et al. Complete genome sequence of Hymenobacter sp. DG25B, a novel bacterium with gamma–radiation resistance isolated from soil in South Korea. J Biotech 217, 98–99 (2016).
Kim, M. K. et al. Complete genome sequence of Deinococcus swuensis, a bacterium resistant to radiation toxicity. Mol Cell Toxicol 11, 315–321 (2015).
Kim, M. K., Back, C. G., Jung, H. Y. & Srinivasan, S. Complete genome sequence of Spirosoma radiotolerans, a gamma–radiation–resistant bacterium isolated from rice field in South Korea. J Biotech 208, 11–12 (2015).
Kim, M. K. et al. Complete genome sequence of Hymenobacter sedentarius DG5BT, a bacterium resistant to gamma radiation. Mol Cell Toxicol 13, 199–205 (2017).
Srinivasan, S., Lee, S.–Y., Kim, M. K. & Jung, H.–Y. Complete genome sequence of Hymenobacter sp. DG25A, a gamma radiation–resistant bacterium isolated from soil. Mol Cell Toxicol 13, 65–72 (2017).
Srinivasan, S. et al. Deinococcus radioresistens sp. nov., a UV and gamma radiation–resistant bacterium isolated from mountain soil. Antonie van Leeuwenhoek 107, 539–545 (2015).
Cha, S., Srinivasan, S., Seo, T. & Kim, M. K. Deinococcus soli sp. nov., a gamma–radiation–resistant bacterium isolated from rice field soil. Curr Microbiol 68, 777–783 (2014).
Srinivasan, S., Lee, J. J., Lim, S., Joe, M. & Kim, M. K. Deinococcus humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 62, 2844–2850 (2012).
Srinivasan, S., Kim, M. K., Lim, S., Joe, M. & Lee, M. Deinococcus daejeonensis sp. nov., isolated from sludge in a sewage disposal plant. Int J Syst Evol Microbiol 62, 1265–1270 (2012).
Field, D. et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 26, 541–547 (2008).
Markowitz, V. M. et al. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25, 2271–2278 (2009).
Lowe, T. M. & Eddy, S. R. tRNAscan–SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25, 955–964 (1997).
Lagesen, K. et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35, 3100–3108 (2007).
Nawrocki, E. P., Kolbe, D. L. & Eddy, S. R. Infernal 1.0: inference of RNA alignments. Bioinformatics 25, 1335–1337 (2009).
Tatusov, R. L. et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41 (2003).
Dillingham, M. S. & Kowalczykowski, S. C. RecBCD Enzyme and the Repair of Double–Stranded DNA Breaks. Microbiol Mol Biol Rev 72, 642–671 (2008).
BATTISTA, J. R. & COX, M. M. in Radiation Risk Estimates in Normal and Emergency Situations (eds Arrigo A. Cigna & Marco Durante) 341–359 (Springer Netherlands, 2006).
Jia, H. et al. Rotations of the 2B sub–domain of E. coli UvrD helicase/translocase coupled to nucleotide and DNA binding. J Mol Biol 411, 633–648 (2011).
Wilkinson, M., Chaban, Y. & Wigley, D. B. Mechanism for nuclease regulation in RecBCD. eLife 5, e18227 (2016).
Leung, W. Y., Chung, L. H., Kava, H. W. & Murray, V. RecBCD (Exonuclease V) is inhibited by DNA adducts produced by cisplatin and ultraviolet light. Biochem Biophys Res Commun 495, 666–671 (2018).
Yang, L. et al. Alteration of chi recognition by RecBCD reveals a regulated molecular latch and suggests a channel–bypass mechanism for biological control. Proc Natl Acad Sci U S A 109, 8907–8912 (2012).
Wigley, D. B. Bacterial DNA repair: recent insights into the mechanism of RecBCD, AddAB and AdnAB. Nat Rev Microbiol 11, 9–13 (2013).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Kang, MS., Srinivasan, S. Complete genome sequence of Methylobacterium sp. 17Sr1-43, a radiation-resistant bacterium. Mol. Cell. Toxicol. 14, 453–457 (2018). https://doi.org/10.1007/s13273-018-0050-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13273-018-0050-0