Draft Genome Sequence of Medium-Chain-Length Polyhydroxyalkanoate-Producing Pseudomonas putida Strain LS46

Sharma, Parveen; Fu, Jilagamazhi; Zhang, Xiangli; Fristensky, Brian; Davenport, Karen W.; Chain, Patrick; Sparling, Richard; Levin, David B.

doi:10.1128/genomea.00151-13

Cited by 6 publications

(1 citation statement)

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“…The P. putida LS46 genome was sequenced by the Genome Canada sequencing facility at McGill University, Montreal, Quebec, using a combination of Illumina Gaii (Bennett [ 2002 ]) and 454 pyro-sequencing technology (Margulies et al [ 2005 ]). The draft genome sequence of P.putida LS46 was deposited in the NCBI GenBank database with Accession number ALPV02000000 (Sharma et al [ 2013 ]). The complete genomes of nine P. putida strains KT2440 (NC002947), F1 (NC009512), BIRD1 (NC017530), GB-1 (NC010322) S16 (CP003734), ND6 (CP_003589), DOT-T1E (NC_018222), UW4 (CP_003890) and W619 (NC010501) were obtained from the Joint Genome Institute database ( http://img.jgi.doe.gov ) and compared with the newly sequenced P. putida LS46.…”

Section: Methodsmentioning

confidence: 99%

Genome features of Pseudomonas putida LS46, a novel polyhydroxyalkanoate producer and its comparison with other P. putida strains

Sharma

Zhang

et al. 2014

AMB Expr

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A novel strain of Pseudomonas putida LS46 was isolated from wastewater on the basis of its ability to synthesize medium chain-length polyhydroxyalkanoates (mcl-PHAs). P.putida LS46 was differentiated from other P.putida strains on the basis of cpn60 (UT). The complete genome of P.putida LS46 was sequenced and annotated. Its chromosome is 5,86,2556 bp in size with GC ratio of 61.69. It is encoding 5316 genes, including 7 rRNA genes and 76 tRNA genes. Nucleotide sequence data of the complete P. putida LS46 genome was compared with nine other P. putida strains (KT2440, F1, BIRD-1, S16, ND6, DOT-T1E, UW4, W619 and GB-1) identified either as biocontrol agents or as bioremediation agents and isolated from different geographical region and different environment. BLASTn analysis of whole genome sequences of the ten P. putida strains revealed nucleotide sequence identities of 86.54 to 97.52%. P.putida genome arrangement was LS46 highly similar to P.putida BIRD1 and P.putida ND6 but was markedly different than P.putida DOT-T1E, P.putida UW4 and P.putida W619. Fatty acid biosynthesis (fab), fatty acid degradation (fad) and PHA synthesis genes were highly conserved among biocontrol and bioremediation P.putida strains. Six genes in pha operon of P. putida LS46 showed >98% homology at gene and proteins level. It appears that polyhydroxyalkanoate (PHA) synthesis is an intrinsic property of P. putida and was not affected by its geographic origin. However, all strains, including P. putida LS46, were different from one another on the basis of house keeping genes, and presence of plasmid, prophages, insertion sequence elements and genomic islands. While P. putida LS46 was not selected for plant growth promotion or bioremediation capacity, its genome also encoded genes for root colonization, pyoverdine synthesis, oxidative stress (present in other soil isolates), degradation of aromatic compounds, heavy metal resistance and nicotinic acid degradation, manganese (Mn II) oxidation. Genes for toluene or naphthalene degradation found in the genomes of P. putida F1, DOT-T1E, and ND6 were absent in the P. putida LS46 genome. Heavy metal resistant genes encoded by the P. putida W619 genome were also not present in the P. putida LS46 genome. Despite the overall similarity among genome of P.putida strains isolated for different applications and from different geographical location a number of differences were observed in genome arrangement, occurrence of transposon, genomic islands and prophage. It appears that P.putida strains had a common ancestor and by acquiring some specific genes by horizontal gene transfer it differed from other related strains.

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Section: Methodsmentioning

confidence: 99%