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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

Proposed PHA synthesis and degradation pathways forP. putidaLS46. Metabolic pathways involved carbon metabolism, fatty acid synthesis and degradation, and PHA synthesis are summarized. PHA can be synthesized from glucose, glycerol, or fatty acids via the PHA synthesis pathway.
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Figure 6: Proposed PHA synthesis and degradation pathways forP. putidaLS46. Metabolic pathways involved carbon metabolism, fatty acid synthesis and degradation, and PHA synthesis are summarized. PHA can be synthesized from glucose, glycerol, or fatty acids via the PHA synthesis pathway.

Mentions: P. putida LS46 shares a number of metabolic features with P. putida KT2440, P. putida F1, P. putida BIRD1, and P. putida GB-1, such as metabolism of aromatic compounds, manganese oxidation, root colonization, and PHAs production. All P. putida genomes have the ability to synthesize PHA irrespective of their applications, either as biocontrol agents or bioremediation agents. P. putida LS46 differs from other P. putida strains in number of dioxygenase genes, TonB dependent receptors, transferases, hydrolases, dehydrogenases and transferases. P. putida LS46, like other P. putida strains metabolize glucose, glycerol, and fatty acid by glycolysis, the tricarboxylic acid cycle, the pentose pathway, and β oxidation (Figure 6). At least three different metabolic pathways provide the precursors for the synthesis of PHAs. (i) Fatty acid de novo biosynthesis is the main route during growth on carbon sources that are metabolized to acetyl-CoA, like glucose, gluconate, glycerol etc. (ii) β-oxidation is the main pathway for PHAs production when fatty acids are used as carbon source, (iii) chain elongation reactions in which acetyl-CoA moieties are condensed to 3-hydroxyacyl-CoA is involved in the PHA synthesis when small chain length fatty acids like C6 and C7 are used. Intermediates of fatty acid de novo synthesis (3 hydroxylacyl-ACP) as well as fatty acid degradation pathways (3-hydroxylacyl-CoA) are used as precursors for PHAs production. Rehm et al. ([1998]) identified a link between fatty acid degradation and fatty acid synthesis by confirming the PHAs biosynthesis in β-oxidation defection mutants (fadB). This enzyme converts 3hydroxyacyl-ACP to 3-hydroxyacyl-CoA, which is a substrate for polymerization to PHAs. Glucose and glycerol are transported and metabolized to acetyl-CoA, which is further used for production of various fatty acids using fatty acid biosynthesis (fab) genes. Fatty acids or waste fryer oil containing long chain fatty acids (C16 and C18) are utilized by β-oxidation and intermediates are used for PHAs production (Wang et al. [2012]). Manipulation of fatty acid synthesis and degradation genes is known to improve PHAs production with altered monomer composition (Fiedler et al. [2002]). PHAs production in P.putida is a part of central metabolic pathway and it was evident from high level of identity among PHAs production proteins and proteins of feeding pathways like fatty acid biosynthesis and degradation.


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)

Proposed PHA synthesis and degradation pathways forP. putidaLS46. Metabolic pathways involved carbon metabolism, fatty acid synthesis and degradation, and PHA synthesis are summarized. PHA can be synthesized from glucose, glycerol, or fatty acids via the PHA synthesis pathway.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Proposed PHA synthesis and degradation pathways forP. putidaLS46. Metabolic pathways involved carbon metabolism, fatty acid synthesis and degradation, and PHA synthesis are summarized. PHA can be synthesized from glucose, glycerol, or fatty acids via the PHA synthesis pathway.
Mentions: P. putida LS46 shares a number of metabolic features with P. putida KT2440, P. putida F1, P. putida BIRD1, and P. putida GB-1, such as metabolism of aromatic compounds, manganese oxidation, root colonization, and PHAs production. All P. putida genomes have the ability to synthesize PHA irrespective of their applications, either as biocontrol agents or bioremediation agents. P. putida LS46 differs from other P. putida strains in number of dioxygenase genes, TonB dependent receptors, transferases, hydrolases, dehydrogenases and transferases. P. putida LS46, like other P. putida strains metabolize glucose, glycerol, and fatty acid by glycolysis, the tricarboxylic acid cycle, the pentose pathway, and β oxidation (Figure 6). At least three different metabolic pathways provide the precursors for the synthesis of PHAs. (i) Fatty acid de novo biosynthesis is the main route during growth on carbon sources that are metabolized to acetyl-CoA, like glucose, gluconate, glycerol etc. (ii) β-oxidation is the main pathway for PHAs production when fatty acids are used as carbon source, (iii) chain elongation reactions in which acetyl-CoA moieties are condensed to 3-hydroxyacyl-CoA is involved in the PHA synthesis when small chain length fatty acids like C6 and C7 are used. Intermediates of fatty acid de novo synthesis (3 hydroxylacyl-ACP) as well as fatty acid degradation pathways (3-hydroxylacyl-CoA) are used as precursors for PHAs production. Rehm et al. ([1998]) identified a link between fatty acid degradation and fatty acid synthesis by confirming the PHAs biosynthesis in β-oxidation defection mutants (fadB). This enzyme converts 3hydroxyacyl-ACP to 3-hydroxyacyl-CoA, which is a substrate for polymerization to PHAs. Glucose and glycerol are transported and metabolized to acetyl-CoA, which is further used for production of various fatty acids using fatty acid biosynthesis (fab) genes. Fatty acids or waste fryer oil containing long chain fatty acids (C16 and C18) are utilized by β-oxidation and intermediates are used for PHAs production (Wang et al. [2012]). Manipulation of fatty acid synthesis and degradation genes is known to improve PHAs production with altered monomer composition (Fiedler et al. [2002]). PHAs production in P.putida is a part of central metabolic pathway and it was evident from high level of identity among PHAs production proteins and proteins of feeding pathways like fatty acid biosynthesis and degradation.

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