The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader

University of Hyderabad, India
PLoS ONE (Impact Factor: 3.53). 03/2010; 5(3):e9729. DOI: 10.1371/journal.pone.0009729
Source: PubMed

ABSTRACT 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.
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.
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.

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Available from: Thomas Ledger, Aug 23, 2015
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    • "In addition, several transcriptomic studies have recently been reported (Peplinski et al., 2010; Brigham et al., 2012), and the genome sequences for a number of other Cupriavidus spp. are also now available (Amadou et al., 2008; Pérez-Pantoja et al., 2008; Janssen et al., 2010; Lykidis et al., 2010; Poehlein et al., 2011; Cserhati et al., 2012; Hong et al., 2012; Van Houdt et al., 2012; Li et al., 2013). This information will facilitate future comparative genomics and systems biology studies to develop C. necator H16 as a robust and metabolically diverse hydrocarbon-intermediate production strain. "
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    • "Strain DR1 (YP_003732082-YP_003732085) (Jung et al. 2010), Polaromonas naphthalenivorans strain CJ2 (YP_983363– YP_983366) (Yagi et al. 2009), Azoarcus sp. strain BH72 (YP_933924–YP_933927) (Krause et al. 2006), and Cupriavidus necator JMP134 (YP_300048–YP_300051) (Lykidis et al. 2010), further supporting the functional association of these genes. "
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