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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

Occurrence of genomic islands inP.putidaLS46 genomes. Genomic islands were identified using IslandViewer programme using Genomic island predictions were calculated for using Integrated method of IslandPick, IslandPath-DIMOB, and SIGI-HMM (Langille and Brinkman ([2009])).
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Figure 2: Occurrence of genomic islands inP.putidaLS46 genomes. Genomic islands were identified using IslandViewer programme using Genomic island predictions were calculated for using Integrated method of IslandPick, IslandPath-DIMOB, and SIGI-HMM (Langille and Brinkman ([2009])).

Mentions: Genomic island finder using integrated method identified 22 genomic islands (GIs) in P.putida LS46 (Figure 2). The size of smallest genomic island was 4505 bp while largest was 78290 bp (Figure 2, Additional file 1: Table S3). Genomic island 3 was 26639 bp in size and it showed 96% homology to P.putida H8234 genome (Molina et al. [2013]). This GI carried a transposon Tn4652 along with heavy metal resistance genes. P. putida H8234, a clinical isolate from France, showed low pathogenic potential compared with P. aeruginosa and was resistant to commonly used antibiotics. P.putida LS46 was also resistant to ampicillin, choloramphenicol, gentamycin and tetracycline. GI 18 contains M.XmaI and R.XmaI genes, which are component of XmaI restriction system. Two unique genes PPUTLS46_017749, which encodes an N-4 cytosine-specific methyltransferase, and PPUTLS46_017754, which encode a Type II restriction enzyme, encoded this system. This restriction system is isoschizomer of XcyI of Xanthomonas campestris pv cynopsidis. The XcyI restriction-modification system recognizes the sequence, CCCGGG, and cleaves after C1 and (Withers et al. [1992]). These genes are present on the plasmid AG1 of Xanthomonas axonopodis pv glycine as well as on the plasmid pRA2 of Pseudomonsa alcaligenes NCIB 9867. This plasmid carried two mobile elements, Tn5563 and IS1633 along with Pac25I (XcyI) restriction-modification system (Kwong et al. [2000]). This restriction system did not affect the pRA2 plasmid stability in heterologous Pseudomonas hosts. The other GIs carried a number hypothetical protein.


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)

Occurrence of genomic islands inP.putidaLS46 genomes. Genomic islands were identified using IslandViewer programme using Genomic island predictions were calculated for using Integrated method of IslandPick, IslandPath-DIMOB, and SIGI-HMM (Langille and Brinkman ([2009])).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Occurrence of genomic islands inP.putidaLS46 genomes. Genomic islands were identified using IslandViewer programme using Genomic island predictions were calculated for using Integrated method of IslandPick, IslandPath-DIMOB, and SIGI-HMM (Langille and Brinkman ([2009])).
Mentions: Genomic island finder using integrated method identified 22 genomic islands (GIs) in P.putida LS46 (Figure 2). The size of smallest genomic island was 4505 bp while largest was 78290 bp (Figure 2, Additional file 1: Table S3). Genomic island 3 was 26639 bp in size and it showed 96% homology to P.putida H8234 genome (Molina et al. [2013]). This GI carried a transposon Tn4652 along with heavy metal resistance genes. P. putida H8234, a clinical isolate from France, showed low pathogenic potential compared with P. aeruginosa and was resistant to commonly used antibiotics. P.putida LS46 was also resistant to ampicillin, choloramphenicol, gentamycin and tetracycline. GI 18 contains M.XmaI and R.XmaI genes, which are component of XmaI restriction system. Two unique genes PPUTLS46_017749, which encodes an N-4 cytosine-specific methyltransferase, and PPUTLS46_017754, which encode a Type II restriction enzyme, encoded this system. This restriction system is isoschizomer of XcyI of Xanthomonas campestris pv cynopsidis. The XcyI restriction-modification system recognizes the sequence, CCCGGG, and cleaves after C1 and (Withers et al. [1992]). These genes are present on the plasmid AG1 of Xanthomonas axonopodis pv glycine as well as on the plasmid pRA2 of Pseudomonsa alcaligenes NCIB 9867. This plasmid carried two mobile elements, Tn5563 and IS1633 along with Pac25I (XcyI) restriction-modification system (Kwong et al. [2000]). This restriction system did not affect the pRA2 plasmid stability in heterologous Pseudomonas hosts. The other GIs carried a number hypothetical protein.

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