Complete Genome Sequence of 3-Chlorobenzoate-Degrading Bacterium Cupriavidus necator NH9 and Reclassification of the Strains of the Genera Cupriavidus and Ralstonia Based on Phylogenetic and Whole-Genome Sequence Analyses

Frontiers in Microbiology
Ryota MoriuchiNaoto Ogawa

Abstract

Cupriavidus necator NH9, a 3-chlorobenzoate (3-CB)-degrading bacterium, was isolated from soil in Japan. In this study, the complete genome sequence of NH9 was obtained via PacBio long-read sequencing to better understand the genetic components contributing to the strain's ability to degrade aromatic compounds, including 3-CB. The genome of NH9 comprised two circular chromosomes (4.3 and 3.4 Mb) and two circular plasmids (427 and 77 kb) containing 7,290 coding sequences, 15 rRNA and 68 tRNA genes. Kyoto Encyclopedia of Genes and Genomes pathway analysis of the protein-coding sequences in NH9 revealed a capacity to completely degrade benzoate, 2-, 3-, or 4-hydroxybenzoate, 2,3-, 2,5-, or 3,4-dihydroxybenzoate, benzoylformate, and benzonitrile. To validate the identification of NH9, phylogenetic analyses (16S rRNA sequence-based tree and multilocus sequence analysis) and whole-genome sequence analyses (average nucleotide identity, percentage of conserved proteins, and tetra-nucleotide analyses) were performed, confirming that NH9 is a C. necator strain. Over the course of our investigation, we noticed inconsistencies in the classification of several strains that were supposed to belong to the two closely-related genera Cupriavidu...Continue Reading

References

Jan 1, 1988·Annual Review of Microbiology·W Reineke, H J Knackmuss
Jul 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·B Frantz, A M Chakrabarty
Jul 21, 1995·The Journal of Biological Chemistry·S Schaper, W Messer
Jan 1, 1996·Annual Review of Microbiology·C S Harwood, R E Parales
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Mar 24, 2000·Essays in Biochemistry·J B Broderick
Nov 17, 2004·International Journal of Systematic and Evolutionary Microbiology·Peter Vandamme, Tom Coenye
Sep 12, 2006·Nature Biotechnology·Anne PohlmannBotho Bowien
Oct 27, 2006·FEMS Microbiology Reviews·Raphaël LeplaeAriane Toussaint
Dec 26, 2006·Applied and Environmental Microbiology·José A Castillo, Jean T Greenberg
Jan 16, 2007·International Journal of Systematic and Evolutionary Microbiology·Johan GorisJames M Tiedje
Sep 28, 2007·Journal of Applied Microbiology·M P RyanC C Adley
Jan 1, 1991·Annual Review of Phytopathology·A C Hayward
May 21, 2008·Genome Research·Claire AmadouCatherine Masson-Boivin
Sep 17, 2008·BMC Bioinformatics·Yoshiyuki OhtsuboMasataka Tsuda
May 15, 2009·International Journal of Environmental Research and Public Health·Jong-Su SeoQing X Li
Jun 9, 2009·Bioscience, Biotechnology, and Biochemistry·Yasunori OhmiyaTetsuya Kimura
Oct 27, 2009·Proceedings of the National Academy of Sciences of the United States of America·Michael Richter, Ramon Rosselló-Móra
Jul 12, 2011·Journal of Bacteriology·Anja PoehleinBotho Bowien
Oct 27, 2011·Environmental Microbiology·Danilo Pérez-PantojaBernardo González
Apr 21, 2012·Briefings in Bioinformatics·Helga ThorvaldsdóttirJill P Mesirov
May 7, 2013·Nature Methods·Chen-Shan ChinJonas Korlach
Sep 24, 2013·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·M P Ryan, C C Adley
Jan 24, 2014·Bioinformatics·Philip JonesSarah Hunter
Feb 8, 2014·International Journal of Systematic and Evolutionary Microbiology·Mincheol KimJongsik Chun
Mar 20, 2014·Bioinformatics·Torsten Seemann
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Apr 8, 2014·Journal of Bacteriology·Qi-Long QinYu-Zhong Zhang

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Citations

May 28, 2020·Microorganisms·Daniel Garrido-SanzRafael Rivilla
May 15, 2020·Molecular Biology Reports·Gorkhmaz AbbaszadeErika Tóth
Mar 16, 2021·Bioscience, Biotechnology, and Biochemistry·Ryota MoriuchiNaoto Ogawa
Jun 5, 2021·Current Microbiology·Yoshiaki MaejimaMasaki Shintani
Jul 14, 2020·Computers in Biology and Medicine·Bobby PaulK Satyamoorthy
Jan 6, 2022·Microbiology Spectrum·Jiro F Mori, Robert A Kanaly

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Datasets Mentioned

BETA
CP017758
CP017760
KF708
C

Methods Mentioned

BETA
Genome Sequencing
Illumina sequencing
PCA

Software Mentioned

ClustalW
Prokka
BWA
MLSA
POCP
RS HGAP Assembly
MEM
BLASTN
SMRT Analysis
Geneious

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