Open access
Announcement
22 February 2018

Complete Genome Sequence of the Facultative Methylotroph Methylobacterium extorquens TK 0001 Isolated from Soil in Poland

ABSTRACT

Methylobacterium extorquens TK 0001 (DSM 1337, ATCC 43645) is an aerobic pink-pigmented facultative methylotrophic alphaproteobacterium isolated from soil in Poland. Here, we report the whole-genome sequence and annotation of this organism, which consists of a single 5.71-Mb chromosome.

GENOME ANNOUNCEMENT

The genus Methylobacterium contains rod-shaped Gram-negative bacteria and belongs to the family Rhizobiales. The members of this group of microorganisms are able to grow on reduced C1 compounds such as methane, methanol, and methylamine as sole carbon and energy sources (1, 2). They have been isolated from diverse soil, air, and water environments (3). Methylobacterium extorquens TK 0001 was isolated from soil in Poland (4, 5).
M. extorquens TK 0001 was obtained from the DSMZ (Braunschweig, Germany) and was grown at 30°C in a minimal medium (DSMZ medium no. 1629) supplemented with 1% methanol. Genomic DNA was purified using the GenElute bacterial genomic DNA kit (Sigma). Genome sequencing was performed at Genoscope, using both Illumina and Nanopore technologies (6, 7). First, the long reads generated by the MinION device (Oxford Nanopore Technologies) were corrected using Canu software (8). The corrected reads were assembled using smartdenovo (https://github.com/ruanjue/smartdenovo), and the resulting assembly was then polished with the help of 2 × 150-bp paired-end reads generated by a MiSeq sequencer (Illumina) with a genome coverage of ~134×. The final assembly was composed of a single contig of 5.71 Mb with a GC content of 68.2%. Automatic functional annotation and comparative genome analysis were performed using the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) (9). In total, 6,251 genomic objects were identified comprising 6,160 coding sequences (CDSs), 17 miscellaneous RNAs, 59 tRNAs, and 15 rRNAs (5 5S, 5 16S, and 5 23S). The M. extorquens TK 0001 genome contains the mxa gene clusters (mxaABCD and mxaFJGIR) coding for methanol dehydrogenase and for enzymes involved in the synthesis of the periplasmic pyrroloquinoline quinone electron carrier. No methylamine dehydrogenase was found. The enzymes for the N-methylglutamate pathway, mgsABC and gmaS, are present, accounting for the growth on methylamine (10). Genes for the serine cycle and the ethylmalonyl-coenzyme A pathway implicated in C1 assimilation are specified. M. extorquens TK 0001 is a facultative methylotroph growing also on complex carbon sources. Accordingly, the Entner-Doudoroff pathway and the pentose phosphate pathway are predicted, as well as the oxidative tricarboxylic acid cycle.
A comparative genome analysis was performed between TK 0001 and M. extorquens strains AM1, PA1, CM4, and DM4 showing that these strains are strongly related. A fraction of 24.3% of the CDSs is specific to M. extorquens strain TK 0001, and 61.9% of the CDSs correspond to the core genome of this group of organisms.

Accession number(s).

This whole-genome project has been deposited in DDBJ/EMBL/GenBank under the accession no. LT962688.

ACKNOWLEDGMENTS

This work was financially supported by a CEA internal research project joining the Fundamental Research Division (DRF) and the Technological Research Division (DRT). The LABGeM (CEA/IG/Genoscope and CNRS UMR 8030) and the France Génomique national infrastructure (funded as part of Investissements d’Avenir program managed by the Agence Nationale pour la Recherche, contract ANR-10-INBS-09) are acknowledged for support within the MicroScope annotation platform and many other functionalities of the system.

REFERENCES

1.
Anthony C. 1982. The biochemistry of methylotrophs. Academic Press, New York, NY.
2.
Schrader J, Schilling M, Holtmann D, Sell D, Filho MV, Marx A, Vorholt JA. 2009. Methanol-based industrial biotechnology: current status and future perspectives of methylotrophic bacteria. Trends Biotechnol 27:107–115.
3.
Lidstrom ME. 2006. Aerobic methylotrophic prokaryotes. Springer, New York, NY.
4.
Bousfield IJ, Green PN. 1985. Reclassification of bacteria of the genus Protomonas Urakami and Komagata 1984 in the genus Methylobacterium (Patt, Cole, and Hanson) emend. Green and Bousfield 1983. Int J Syst Bacteriol 35:209–209.
5.
Urakami T, Komagata K. 1984. Protomonas, a new genus of facultatively methylotrophic bacteria. Int J Syst Bacteriol 34:188–201.
6.
Magi A, Semeraro R, Mingrino A, Giusti B, D’Aurizio R. 2017. Nanopore sequencing data analysis: state of the art, applications and challenges. Brief Bioinform.
7.
Madoui MA, Engelen S, Cruaud C, Belser C, Bertrand L, Alberti A, Lemainque A, Wincker P, Aury JM. 2015. Genome assembly using nanopore-guided long and error-free DNA reads. BMC Genomics 16:327.
8.
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736.
9.
Vallenet D, Calteau A, Cruveiller S, Gachet M, Lajus A, Josso A, Mercier J, Renaux A, Rollin J, Rouy Z, Roche D, Scarpelli C, Médigue C. 2017. MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes. Nucleic Acids Res 45:D517–D528.
10.
Nayak DD, Marx CJ. 2014. Methylamine utilization via the N-methylglutamate pathway in Methylobacterium extorquens PA1 involves a novel flow of carbon through C1 assimilation and dissimilation pathways. J Bacteriol 196:4130–4139.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 6Number 822 February 2018
eLocator: 10.1128/genomea.00018-18

History

Received: 9 January 2018
Accepted: 11 January 2018
Published online: 22 February 2018

Contributors

Authors

Sophia Belkhelfa
Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d’Évry, Université Paris-Saclay, Evry, France
Karine Labadie
Genoscope, Institut François Jacob, CEA, Evry, France
Corinne Cruaud
Genoscope, Institut François Jacob, CEA, Evry, France
Jean-Marc Aury
Genoscope, Institut François Jacob, CEA, Evry, France
David Roche
Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d’Évry, Université Paris-Saclay, Evry, France
Madeleine Bouzon
Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d’Évry, Université Paris-Saclay, Evry, France
Marcel Salanoubat
Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d’Évry, Université Paris-Saclay, Evry, France
Volker Döring
Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d’Évry, Université Paris-Saclay, Evry, France

Notes

Address correspondence to Volker Döring, [email protected].

Metrics & Citations

Metrics

Note: There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.

Citation counts come from the Crossref Cited by service.

Citations

If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. For an editable text file, please select Medlars format which will download as a .txt file. Simply select your manager software from the list below and click Download.

View Options

Figures and Media

Figures

Media

Tables

Share

Share

Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy