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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 ofphaC1andphaC2genes amongPseudomonasspecies. The phaC gene sequences 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 5: Phylogenetic tree depicting the relationship ofphaC1andphaC2genes amongPseudomonasspecies. The phaC gene sequences were aligned by ClustalW and a neighbor-joining tree was generated using MEGA5 program. Bootstrap values are mentioned at the node.

Mentions: The phaC1 and phaC2 of different Pseudomonas species formed different clusters in neighbor joining tree. The phaC1 and phaC2 in P.putida strains were highly conserved but were different phaC1 and phaC2 from other Pseudomonas species. The phaC1 and phaC2 genes of P. putida, P.aeruginosa, P.fluorescens, P.stutzeri. P.entomophila and P.mendocina formed different cluster in neighbor joining tree (FigureĀ 5). Further fatty acid biosynthesis and fatty acid degradation proteins were highly conserved among P.putida strains. Fatty acid biosynthesis (fab) and fatty acid degradation (fad) gene products provide the precursor for PHAs synthesis. Most of the fatty acid synthesis and degradation proteins of P.putida LS46 had multiple genes coding isozymes i.e. FadB had 4 isologs, FadA had 5 isologs and FadD had 7 isologs for short and long chain fatty acids. Likewise FadE (acyl-CoA dehydrogenase) had six isologs specific for small, medium and long chain fatty acids. Fab and Fad proteins of P.putida LS46 showed high homology to Fab and Fad proteins of other P.putida strains. P.putida LS46 can utilize fatty acids (C5-C18) for PHAs production. Two fatty acid transporters (FadL), one for short chain fatty acid (PPUTLS46_007654) and other for long fatty acid (PPUTLS46_015009) were present in P.putida LS46. However, it preferentially used long chain fatty acids (C6-C18) than short chain fatty acid C3-C5) for PHAs synthesis. The specificity of FadD and FadL these proteins are not known but transfer of FadD from E.coli and FadL from P.putida into Aeromonas hydrophila improved its ability to utilize C6 and C8 fatty acids. (Jian et al. [2010]). The intermediate 3hydroxyacyl-ACP of de novo fatty acid synthesis is converted to 3hydroxyacyl-CoA for polymerization to PHAs with help of (R)-3-hydroxyacyl-ACP:CoA transacylase enzyme PhaG. PhaG was present in all P.putida strains. The absence of PhaG in PHB producers limits their ability to produce mcl-PHAs. Transfer and expression of phaG of P.putida in Ralstonia eutropha or Aeromonas hydrophila producer may confer mcl-PHAs production ability into PHB producers.Recently, a PHAs granule-associated acyl-CoA-synthetase (Acs1) has been identified which is highly conserved among P.putida strains. It directs the carbon flux of these central metabolites towards PHA accumulation and converts 3hydroxyalkanoic acids to 3 hydroxyacyl-CoA thioesters (Ruth et al. [2008]).


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 ofphaC1andphaC2genes amongPseudomonasspecies. The phaC gene sequences 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 5: Phylogenetic tree depicting the relationship ofphaC1andphaC2genes amongPseudomonasspecies. The phaC gene sequences were aligned by ClustalW and a neighbor-joining tree was generated using MEGA5 program. Bootstrap values are mentioned at the node.
Mentions: The phaC1 and phaC2 of different Pseudomonas species formed different clusters in neighbor joining tree. The phaC1 and phaC2 in P.putida strains were highly conserved but were different phaC1 and phaC2 from other Pseudomonas species. The phaC1 and phaC2 genes of P. putida, P.aeruginosa, P.fluorescens, P.stutzeri. P.entomophila and P.mendocina formed different cluster in neighbor joining tree (FigureĀ 5). Further fatty acid biosynthesis and fatty acid degradation proteins were highly conserved among P.putida strains. Fatty acid biosynthesis (fab) and fatty acid degradation (fad) gene products provide the precursor for PHAs synthesis. Most of the fatty acid synthesis and degradation proteins of P.putida LS46 had multiple genes coding isozymes i.e. FadB had 4 isologs, FadA had 5 isologs and FadD had 7 isologs for short and long chain fatty acids. Likewise FadE (acyl-CoA dehydrogenase) had six isologs specific for small, medium and long chain fatty acids. Fab and Fad proteins of P.putida LS46 showed high homology to Fab and Fad proteins of other P.putida strains. P.putida LS46 can utilize fatty acids (C5-C18) for PHAs production. Two fatty acid transporters (FadL), one for short chain fatty acid (PPUTLS46_007654) and other for long fatty acid (PPUTLS46_015009) were present in P.putida LS46. However, it preferentially used long chain fatty acids (C6-C18) than short chain fatty acid C3-C5) for PHAs synthesis. The specificity of FadD and FadL these proteins are not known but transfer of FadD from E.coli and FadL from P.putida into Aeromonas hydrophila improved its ability to utilize C6 and C8 fatty acids. (Jian et al. [2010]). The intermediate 3hydroxyacyl-ACP of de novo fatty acid synthesis is converted to 3hydroxyacyl-CoA for polymerization to PHAs with help of (R)-3-hydroxyacyl-ACP:CoA transacylase enzyme PhaG. PhaG was present in all P.putida strains. The absence of PhaG in PHB producers limits their ability to produce mcl-PHAs. Transfer and expression of phaG of P.putida in Ralstonia eutropha or Aeromonas hydrophila producer may confer mcl-PHAs production ability into PHB producers.Recently, a PHAs granule-associated acyl-CoA-synthetase (Acs1) has been identified which is highly conserved among P.putida strains. It directs the carbon flux of these central metabolites towards PHA accumulation and converts 3hydroxyalkanoic acids to 3 hydroxyacyl-CoA thioesters (Ruth et al. [2008]).

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