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

Sharma PK, Fu J, Zhang X, Fristensky B, Sparling R, Levin DB - AMB Express (2014)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biosystems Engineering, University of Manitoba, Winnipeg R3T 2N2, MB, Canada.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree depicting the relationship amongPseudomonasspecies. The tree is based on cpn60 gene sequences, which were aligned by ClustalW and a neighbor-joining tree was generated using MEGA5 program. Bootstrap values are mentioned at the node.
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Figure 1: Phylogenetic tree depicting the relationship amongPseudomonasspecies. The tree is based on cpn60 gene sequences, which were aligned by ClustalW and a neighbor-joining tree was generated using MEGA5 program. Bootstrap values are mentioned at the node.

Mentions: A polyhydroxyalkanoate producing bacterium was isolated from wastewater and was identified as a strain of Pseudomonas putida on the basis of 16S rRNA gene sequence. The16S rRNA gene sequence analysis revealed more than 99% nucleotide sequence identity to other P. putida strains. Protein-encoding genes are known to provide higher levels of taxonomic resolution than non-protein-encoding genes like 16S rRNA gene. Therefore, a protein coding gene cpn60 (Hsp60 or GroEL) was used for phylogenetic analysis of Pseudomonas species and strains. Neighbor joining trees based on cpn60 genes divided the Pseudomonas species into two clades, one containing P. putida, P. entomophila, P. mendocina, P. fulva P. aeruginosa and P. stutzeri. The other clade included P. fluorescens and P. syringae strains. Although P.putida strains were clustered in one subclade yet minor differences in cpn60 gene sequence separated these strains from each other. Pseudomonas putida LS46 was closely related to P. putida strains ND6, F1, DOT-T1E, BIRD1, KT2440 and clustered with these strains forming a sub-clade (FigureĀ 1). Pseudomonas putida strains LS46 was more distantly related to P.putida strains GB1, S16 and W619. Pseudomonas putida UW4 was not related to any other P. putida strains and clustered with P. fluorescens.


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

Sharma PK, Fu J, Zhang X, Fristensky B, Sparling R, Levin DB - AMB Express (2014)

Phylogenetic tree depicting the relationship amongPseudomonasspecies. The tree is based on cpn60 gene sequences, which were aligned by ClustalW and a neighbor-joining tree was generated using MEGA5 program. Bootstrap values are mentioned at the node.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230813&req=5

Figure 1: Phylogenetic tree depicting the relationship amongPseudomonasspecies. The tree is based on cpn60 gene sequences, which were aligned by ClustalW and a neighbor-joining tree was generated using MEGA5 program. Bootstrap values are mentioned at the node.
Mentions: A polyhydroxyalkanoate producing bacterium was isolated from wastewater and was identified as a strain of Pseudomonas putida on the basis of 16S rRNA gene sequence. The16S rRNA gene sequence analysis revealed more than 99% nucleotide sequence identity to other P. putida strains. Protein-encoding genes are known to provide higher levels of taxonomic resolution than non-protein-encoding genes like 16S rRNA gene. Therefore, a protein coding gene cpn60 (Hsp60 or GroEL) was used for phylogenetic analysis of Pseudomonas species and strains. Neighbor joining trees based on cpn60 genes divided the Pseudomonas species into two clades, one containing P. putida, P. entomophila, P. mendocina, P. fulva P. aeruginosa and P. stutzeri. The other clade included P. fluorescens and P. syringae strains. Although P.putida strains were clustered in one subclade yet minor differences in cpn60 gene sequence separated these strains from each other. Pseudomonas putida LS46 was closely related to P. putida strains ND6, F1, DOT-T1E, BIRD1, KT2440 and clustered with these strains forming a sub-clade (FigureĀ 1). Pseudomonas putida strains LS46 was more distantly related to P.putida strains GB1, S16 and W619. Pseudomonas putida UW4 was not related to any other P. putida strains and clustered with P. fluorescens.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biosystems Engineering, University of Manitoba, Winnipeg R3T 2N2, MB, Canada.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus