The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader.

<h4>Background</h4>Cupriavidus necator JMP134 is a Gram-negative beta-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source.<h4>Methodology/principal findings</h4>Its genome consists of four replicons (two chro...

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Autores principales:	Athanasios Lykidis, Danilo Pérez-Pantoja, Thomas Ledger, Kostantinos Mavromatis, Iain J Anderson, Natalia N Ivanova, Sean D Hooper, Alla Lapidus, Susan Lucas, Bernardo González, Nikos C Kyrpides
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0dad813d0d644d2eb50401698a2e07f7
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spelling	oai:doaj.org-article:0dad813d0d644d2eb50401698a2e07f72021-11-25T06:25:15ZThe complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader.1932-620310.1371/journal.pone.0009729https://doaj.org/article/0dad813d0d644d2eb50401698a2e07f72010-03-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20339589/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Cupriavidus necator JMP134 is a Gram-negative beta-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source.<h4>Methodology/principal findings</h4>Its genome consists of four replicons (two chromosomes and two plasmids) containing a total of 6631 protein coding genes. Comparative analysis identified 1910 core genes common to the four genomes compared (C. necator JMP134, C. necator H16, C. metallidurans CH34, R. solanacearum GMI1000). Although secondary chromosomes found in the Cupriavidus, Ralstonia, and Burkholderia lineages are all derived from plasmids, analyses of the plasmid partition proteins located on those chromosomes indicate that different plasmids gave rise to the secondary chromosomes in each lineage. The C. necator JMP134 genome contains 300 genes putatively involved in the catabolism of aromatic compounds and encodes most of the central ring-cleavage pathways. This strain also shows additional metabolic capabilities towards alicyclic compounds and the potential for catabolism of almost all proteinogenic amino acids. This remarkable catabolic potential seems to be sustained by a high degree of genetic redundancy, most probably enabling this catabolically versatile bacterium with different levels of metabolic responses and alternative regulation necessary to cope with a challenging environment. From the comparison of Cupriavidus genomes, it is possible to state that a broad metabolic capability is a general trait for Cupriavidus genus, however certain specialization towards a nutritional niche (xenobiotics degradation, chemolithoautotrophy or symbiotic nitrogen fixation) seems to be shaped mostly by the acquisition of "specialized" plasmids.<h4>Conclusions/significance</h4>The availability of the complete genome sequence for C. necator JMP134 provides the groundwork for further elucidation of the mechanisms and regulation of chloroaromatic compound biodegradation.Athanasios LykidisDanilo Pérez-PantojaThomas LedgerKostantinos MavromatisIain J AndersonNatalia N IvanovaSean D HooperAlla LapidusSusan LucasBernardo GonzálezNikos C KyrpidesPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 3, p e9729 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Athanasios Lykidis Danilo Pérez-Pantoja Thomas Ledger Kostantinos Mavromatis Iain J Anderson Natalia N Ivanova Sean D Hooper Alla Lapidus Susan Lucas Bernardo González Nikos C Kyrpides The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader.
description	<h4>Background</h4>Cupriavidus necator JMP134 is a Gram-negative beta-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source.<h4>Methodology/principal findings</h4>Its genome consists of four replicons (two chromosomes and two plasmids) containing a total of 6631 protein coding genes. Comparative analysis identified 1910 core genes common to the four genomes compared (C. necator JMP134, C. necator H16, C. metallidurans CH34, R. solanacearum GMI1000). Although secondary chromosomes found in the Cupriavidus, Ralstonia, and Burkholderia lineages are all derived from plasmids, analyses of the plasmid partition proteins located on those chromosomes indicate that different plasmids gave rise to the secondary chromosomes in each lineage. The C. necator JMP134 genome contains 300 genes putatively involved in the catabolism of aromatic compounds and encodes most of the central ring-cleavage pathways. This strain also shows additional metabolic capabilities towards alicyclic compounds and the potential for catabolism of almost all proteinogenic amino acids. This remarkable catabolic potential seems to be sustained by a high degree of genetic redundancy, most probably enabling this catabolically versatile bacterium with different levels of metabolic responses and alternative regulation necessary to cope with a challenging environment. From the comparison of Cupriavidus genomes, it is possible to state that a broad metabolic capability is a general trait for Cupriavidus genus, however certain specialization towards a nutritional niche (xenobiotics degradation, chemolithoautotrophy or symbiotic nitrogen fixation) seems to be shaped mostly by the acquisition of "specialized" plasmids.<h4>Conclusions/significance</h4>The availability of the complete genome sequence for C. necator JMP134 provides the groundwork for further elucidation of the mechanisms and regulation of chloroaromatic compound biodegradation.
format	article
author	Athanasios Lykidis Danilo Pérez-Pantoja Thomas Ledger Kostantinos Mavromatis Iain J Anderson Natalia N Ivanova Sean D Hooper Alla Lapidus Susan Lucas Bernardo González Nikos C Kyrpides
author_facet	Athanasios Lykidis Danilo Pérez-Pantoja Thomas Ledger Kostantinos Mavromatis Iain J Anderson Natalia N Ivanova Sean D Hooper Alla Lapidus Susan Lucas Bernardo González Nikos C Kyrpides
author_sort	Athanasios Lykidis
title	The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader.
title_short	The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader.
title_full	The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader.
title_fullStr	The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader.
title_full_unstemmed	The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader.
title_sort	complete multipartite genome sequence of cupriavidus necator jmp134, a versatile pollutant degrader.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/0dad813d0d644d2eb50401698a2e07f7
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The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader.

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