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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

Pangenome analysis of nineP. putidastrains withP. putidaKT2440 as a reference. From inside to outside the circles. COG categories, GC content, backbone, COG in positive strand of pangenome, COG in negative strand in pangenome, P. putida KT2440, P. putida F1, P. putida GB-1, P. putida W619, P. putida S16, P. putida BIRD-1, P. putida ND6, P. putida DOT-T1E and P. putida LS46.
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Figure 4: Pangenome analysis of nineP. putidastrains withP. putidaKT2440 as a reference. From inside to outside the circles. COG categories, GC content, backbone, COG in positive strand of pangenome, COG in negative strand in pangenome, P. putida KT2440, P. putida F1, P. putida GB-1, P. putida W619, P. putida S16, P. putida BIRD-1, P. putida ND6, P. putida DOT-T1E and P. putida LS46.

Mentions: BLASTn analysis of all genes of P. putida LS46 (80% minimal identity e value 1−5) against nine genome identified 82.02- 93.75% homologous genes encoded by the P. putida strains were shared by the ten genomes. P.putida F1 shared highest number (93.7%) of genes with P.putida LS46 while P.putida ND6 (85%) and P.putida UW4 (82%) least number of genes with P.putida LS46 (Table 1). Using single gene profiler 3271 genes were identified which were present in present in all P.putida strains. A total of 8786 core and unique genes were represented the pangenome of nine P. putida strains (excluding P.putida UW4). Unique region in P. putida genomes were identified using pangenome analysis, which identified unique genes present in only one strain (Figure 4). However, all genomes showed higher functional identity (presence of COGs) reflected by high correlation coefficients among the different genomes (r2 = 0.94), although the distribution of different COGs categories among the different genomes was different and represented the functional diversity. The number and percentage of different COG categories varied greatly among ten P. putida strains. P.putida LS46 had highest number of COGs with unknown function. P.putida LS6 genome arrangement was strikingly different from P.putida DOT-T1E however both the strains shared higher percentage of genes (91.6%). Inversely P.putida LS46 and P.putida ND6 had significantly similar genome arrangement but % of shared genes between two genomes was low (85%).


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)

Pangenome analysis of nineP. putidastrains withP. putidaKT2440 as a reference. From inside to outside the circles. COG categories, GC content, backbone, COG in positive strand of pangenome, COG in negative strand in pangenome, P. putida KT2440, P. putida F1, P. putida GB-1, P. putida W619, P. putida S16, P. putida BIRD-1, P. putida ND6, P. putida DOT-T1E and P. putida LS46.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Pangenome analysis of nineP. putidastrains withP. putidaKT2440 as a reference. From inside to outside the circles. COG categories, GC content, backbone, COG in positive strand of pangenome, COG in negative strand in pangenome, P. putida KT2440, P. putida F1, P. putida GB-1, P. putida W619, P. putida S16, P. putida BIRD-1, P. putida ND6, P. putida DOT-T1E and P. putida LS46.
Mentions: BLASTn analysis of all genes of P. putida LS46 (80% minimal identity e value 1−5) against nine genome identified 82.02- 93.75% homologous genes encoded by the P. putida strains were shared by the ten genomes. P.putida F1 shared highest number (93.7%) of genes with P.putida LS46 while P.putida ND6 (85%) and P.putida UW4 (82%) least number of genes with P.putida LS46 (Table 1). Using single gene profiler 3271 genes were identified which were present in present in all P.putida strains. A total of 8786 core and unique genes were represented the pangenome of nine P. putida strains (excluding P.putida UW4). Unique region in P. putida genomes were identified using pangenome analysis, which identified unique genes present in only one strain (Figure 4). However, all genomes showed higher functional identity (presence of COGs) reflected by high correlation coefficients among the different genomes (r2 = 0.94), although the distribution of different COGs categories among the different genomes was different and represented the functional diversity. The number and percentage of different COG categories varied greatly among ten P. putida strains. P.putida LS46 had highest number of COGs with unknown function. P.putida LS6 genome arrangement was strikingly different from P.putida DOT-T1E however both the strains shared higher percentage of genes (91.6%). Inversely P.putida LS46 and P.putida ND6 had significantly similar genome arrangement but % of shared genes between two genomes was low (85%).

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