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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

Comparative Synteny Dot plot ofP.putidastrains showing orthologous relationship ofP. putidaLS46 with nineP.putidastrains. The analysis was carried out using the Dot plot from Integrated Microbial Genome (IMG) website.
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Figure 3: Comparative Synteny Dot plot ofP.putidastrains showing orthologous relationship ofP. putidaLS46 with nineP.putidastrains. The analysis was carried out using the Dot plot from Integrated Microbial Genome (IMG) website.

Mentions: Genome arrangement of P.putida LS46 was compared with 9 other P.putida strains using Dot plot analysis (Figure 3). Dot plot analysis of P.putida LS46 with other P.putida genomes indicated the similarities in genome arrangement at the nucleotide level. The diagonal line showed the co-linearity DNA strands. The blue block on the left hand indicated the translocation and inversions in the genomes. The red blocks represented translocations in anti parallel strands of the genome. The high degrees of genome similarity as well as differences in the arrangement were apparent among P.putida genomes. The genome wide distribution of conserved region of P. putida strains varied from strain to strain. Organization of the P. putida LS46 genome was clearly different than other strains and a number of inversions and translocations were observed the genome in comparison to other P.putida genomes (Figure 3). On the basis of genome arrangement P.putida strains could be divided into two groups. In first group P.putida strains LS46, ND6, F1, KT2440, GB-1, S16 and BIRD1 can be placed which had significantly similarity to P.putida LS46 genome arrangement while in second group comprises of P.putida W619, DOT-T1E and UW4 which had low similarity to P.putida LS46. P.putida LS46 genome arrangement was markedly different from P.putida DOT-T1E, W619 and UW4 with large number translocations and inversions. Pseudomonas putida LS46 genome showed large conserved blocks that are also present in P. putida BIRD1, F1, and ND6 strains, while P. putida DOT-T1E had a large number of small conserved blocks. In comparison to P. putida LS46, the genomes of P.putida KT2440 and S16 genomes had more inversions.


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)

Comparative Synteny Dot plot ofP.putidastrains showing orthologous relationship ofP. putidaLS46 with nineP.putidastrains. The analysis was carried out using the Dot plot from Integrated Microbial Genome (IMG) website.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Comparative Synteny Dot plot ofP.putidastrains showing orthologous relationship ofP. putidaLS46 with nineP.putidastrains. The analysis was carried out using the Dot plot from Integrated Microbial Genome (IMG) website.
Mentions: Genome arrangement of P.putida LS46 was compared with 9 other P.putida strains using Dot plot analysis (Figure 3). Dot plot analysis of P.putida LS46 with other P.putida genomes indicated the similarities in genome arrangement at the nucleotide level. The diagonal line showed the co-linearity DNA strands. The blue block on the left hand indicated the translocation and inversions in the genomes. The red blocks represented translocations in anti parallel strands of the genome. The high degrees of genome similarity as well as differences in the arrangement were apparent among P.putida genomes. The genome wide distribution of conserved region of P. putida strains varied from strain to strain. Organization of the P. putida LS46 genome was clearly different than other strains and a number of inversions and translocations were observed the genome in comparison to other P.putida genomes (Figure 3). On the basis of genome arrangement P.putida strains could be divided into two groups. In first group P.putida strains LS46, ND6, F1, KT2440, GB-1, S16 and BIRD1 can be placed which had significantly similarity to P.putida LS46 genome arrangement while in second group comprises of P.putida W619, DOT-T1E and UW4 which had low similarity to P.putida LS46. P.putida LS46 genome arrangement was markedly different from P.putida DOT-T1E, W619 and UW4 with large number translocations and inversions. Pseudomonas putida LS46 genome showed large conserved blocks that are also present in P. putida BIRD1, F1, and ND6 strains, while P. putida DOT-T1E had a large number of small conserved blocks. In comparison to P. putida LS46, the genomes of P.putida KT2440 and S16 genomes had more inversions.

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