Abstract
In this study, a wild type Methylophilus sp. strain D22 belonging to the family Methylophilus was isolated and characterized, which shows high tolerance towards methanol, as it can grow under 50 g/L of methanol. Methylophilus sp. strain D22 was isolated from the lake sludge in Nanjing Tech University, China. The assembled draft genome contains one circular chromosome with 3,004,398 bp, 49.7% of GC content, and 2107 predicted encoding proteins. Sequence-based genomic analysis demonstrates that the assimilation pathway of ribulose monophosphate (RuMP) pathway and dissimilation pathway of tetrahydromethanopterin (H4MPT) pathway are co-existing and contribute to the high methanol utilization efficiency.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Hirasawa T, Shimizu H (2016) Recent advances in amino acid production by microbial cells. Curr Opin Biotechnol 42:133–146
Irla M, Neshat A, Brautaset T, Rückert C et al (2015) Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape. BMC Genom 16:73
Hopson S, Thompson M (2016) Heterologous expression of the human polybromo-1 protein in the methylotrophic yeast Pichia pastoris. FASEB J. https://doi.org/10.1096/fasebj.30.1_supplement.579.1
Ishikanwa K, Gunji Y, Yasueda H, Asano K (2008) Improvement of L-lysine production by Methylophilus methylotrophus from methanol via the Entner-Doudoroff pathway, originating in Escherichia coli. Biosci Biotechnol Biochem 72:2535–2542
Chistoserdova L, Kalyuzhnaya MG, Lidstrom ME (2009) The expanding world of methylotrophic metabolism. Annu Rev Microbiol 63:477–499
Knief C, Frances L, Vorholt JA (2010) Competitiveness of diverse methylobacterium strains in the phyllosphere of Arabidopsis thaliana and identification of representative models, including M. extorquens PA1. Microb Ecol 60:440–452
Muller JEN, Litsanov B, Bortfeld-Miller M, Trachsel C et al (2014) Proteomic analysis of the thermophilic methylotroph Bacillus methanolicus MGA3. Proteomics 14:725–737
Doronina NV, Gogleva AA, Trotsenko YA (2012) Methylophilus glucosoxydans sp. nov., a restricted facultative methylotroph from rice rhizosphere. Int J Syst Evol Microbiol 62:196–201
Gogleva AA, Kaparullina EN, Doronina NV, Trotsenko YA (2010) Methylophilus flavus sp. nov. and Methylophilus luteus sp. nov., aerobic, methylotrophic bacteria associated with plants. Int J Syst Evol Microbiol 60:2623–2628
Ishikawa K, Toda-Murakoshi Y, Ohnishi F, Kondo K et al (2008) Medium composition suitable for L-lysine production by Methylophilus methylotrophus in Fed-Batch cultivation. J Biosci Bioeng 106:574–579
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829
Khan AL, Asaf S, Khan AR, Al-Harrasi A et al (2016) First draft genome sequencing of indole acetic acid producing and plant growth promoting fungus Preussia sp. BSL10. J Biotechnol 225:44–45
Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679
Hyatt D, Chen GL, LoCascio PF, Land ML et al (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11:119
Kugo T, Kitagawa W, Shimomura Y, Yamagishi T et al (2014) Draft genome sequence of methanol-utilizing Methylophilus sp. strain OH31, isolated from pond sediment in Hokkaido, Japan. Genome Announc. https://doi.org/10.1128/genomeA.00274-14
Xia F, Zou B, Shen C, Zhu T et al (2015) Complete genome sequence of Methylophilus sp. TWE2 isolated from methane oxidation enrichment culture of tap-water. J Biotechnol 211:121–122
Yasokawa D, Murata S, Iwahashi Y, Kitagawa E et al (2010) Toxicity of methanol and formaldehyde towards Saccharomyces cerevisiae as assessed by DNA microarray analysis. Appl Biochem Biotechnol 160:1685–1698
Acknowledgements
This work was supported by the National Key Research and Development Program of China (Grant No. 2018YFA0901500), the Jiangsu Province Natural Science Foundation for Youths (Grant Nos. BK20170993, BK20170997), the Key Science and Technology Project of Jiangsu Province (Grant No. BE2016389), the National Natural Science Foundation of China (Grant Nos. 21706125, 21727818, 21706124, 31700092), and the Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture (Grant No. XTE1840).
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
The authors have declared that there was no conflict of interest.
Additional information
Nucleotide sequence accession numbers
This Whole Genome project has been deposited into GenBank under the accession no. CP033953.1.
Rights and permissions
About this article
Cite this article
Dai, Z., Guo, F., Ma, J. et al. The Draft Genome Sequence of Methylophilus sp. D22, Capable of Growing Under High Concentration of Methanol. Curr Microbiol 76, 1520–1524 (2019). https://doi.org/10.1007/s00284-019-01765-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00284-019-01765-x