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The whole genome sequence of Sphingobium chlorophenolicum L-1: insights into the evolution of the pentachlorophenol degradation pathway.

Copley SD, Rokicki J, Turner P, Daligault H, Nolan M, Land M - Genome Biol Evol (2011)

Bottom Line: The genes responsible for degradation of PCP are found on chromosome 2.We have compared the genomes of S. chlorophenolicum Strain L-1 and Sphingobium japonicum, a closely related Sphingomonad that degrades lindane.Our analysis suggests that the genes encoding the first three enzymes in the PCP degradation pathway were acquired via two different horizontal gene transfer events, and the genes encoding the final two enzymes in the pathway were acquired from the most recent common ancestor of these two bacteria.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, CO, USA. shelley.copley@colorado.edu

ABSTRACT
Sphingobium chlorophenolicum Strain L-1 can mineralize the toxic pesticide pentachlorophenol (PCP). We have sequenced the genome of S. chlorophenolicum Strain L-1. The genome consists of a primary chromosome that encodes most of the genes for core processes, a secondary chromosome that encodes primarily genes that appear to be involved in environmental adaptation, and a small plasmid. The genes responsible for degradation of PCP are found on chromosome 2. We have compared the genomes of S. chlorophenolicum Strain L-1 and Sphingobium japonicum, a closely related Sphingomonad that degrades lindane. Our analysis suggests that the genes encoding the first three enzymes in the PCP degradation pathway were acquired via two different horizontal gene transfer events, and the genes encoding the final two enzymes in the pathway were acquired from the most recent common ancestor of these two bacteria.

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Related in: MedlinePlus

Relationships between proteins encoded by (a) chromosome 1, (b) chromosome 2, and (c) the plasmid of Sphingobium chlorophenolicum and the best hits in the Sphingobium japonicum genome found by a Blast search using each S. chlorophenolicum protein as a query sequence. The number of pairs is plotted as a function of % identity and % coverage of the query sequence for each replicon. (Only pairs for which E < 0.0001 are shown.)
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fig4: Relationships between proteins encoded by (a) chromosome 1, (b) chromosome 2, and (c) the plasmid of Sphingobium chlorophenolicum and the best hits in the Sphingobium japonicum genome found by a Blast search using each S. chlorophenolicum protein as a query sequence. The number of pairs is plotted as a function of % identity and % coverage of the query sequence for each replicon. (Only pairs for which E < 0.0001 are shown.)

Mentions: A more detailed analysis of the relationships between proteins found in both S. chlorophenolicum and S. japonicum is shown in figure 4, which shows plots of sequence identity versus coverage for the top hit in the S. japonicum genome for each S. chlorophenolicum protein. (Coverage is defined as the length of the S. chlorophenolicum query sequence that is aligned to a sequence in S. japonicum divided by the total length of the query sequence. The data were filtered to remove pairs for which the e value was >0.0001.) On this plot, homologs cluster in three regions: 1) close homologs that share high sequence identity over most of the query sequence; 2) more distant homologs that share moderate sequence identity over most of the query sequence; and 3) homologs that share sequence identity only over part of the query sequence. Notably, chromosome 1 is highly enriched in close homologs, and chromosome 2 is modestly enriched in distant homologs. Together with the observation that most of the genes for core metabolic processes are present on chromosome 1, this observation suggests that chromosome 2 may preferentially collect horizontally transferred genes.


The whole genome sequence of Sphingobium chlorophenolicum L-1: insights into the evolution of the pentachlorophenol degradation pathway.

Copley SD, Rokicki J, Turner P, Daligault H, Nolan M, Land M - Genome Biol Evol (2011)

Relationships between proteins encoded by (a) chromosome 1, (b) chromosome 2, and (c) the plasmid of Sphingobium chlorophenolicum and the best hits in the Sphingobium japonicum genome found by a Blast search using each S. chlorophenolicum protein as a query sequence. The number of pairs is plotted as a function of % identity and % coverage of the query sequence for each replicon. (Only pairs for which E < 0.0001 are shown.)
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3318906&req=5

fig4: Relationships between proteins encoded by (a) chromosome 1, (b) chromosome 2, and (c) the plasmid of Sphingobium chlorophenolicum and the best hits in the Sphingobium japonicum genome found by a Blast search using each S. chlorophenolicum protein as a query sequence. The number of pairs is plotted as a function of % identity and % coverage of the query sequence for each replicon. (Only pairs for which E < 0.0001 are shown.)
Mentions: A more detailed analysis of the relationships between proteins found in both S. chlorophenolicum and S. japonicum is shown in figure 4, which shows plots of sequence identity versus coverage for the top hit in the S. japonicum genome for each S. chlorophenolicum protein. (Coverage is defined as the length of the S. chlorophenolicum query sequence that is aligned to a sequence in S. japonicum divided by the total length of the query sequence. The data were filtered to remove pairs for which the e value was >0.0001.) On this plot, homologs cluster in three regions: 1) close homologs that share high sequence identity over most of the query sequence; 2) more distant homologs that share moderate sequence identity over most of the query sequence; and 3) homologs that share sequence identity only over part of the query sequence. Notably, chromosome 1 is highly enriched in close homologs, and chromosome 2 is modestly enriched in distant homologs. Together with the observation that most of the genes for core metabolic processes are present on chromosome 1, this observation suggests that chromosome 2 may preferentially collect horizontally transferred genes.

Bottom Line: The genes responsible for degradation of PCP are found on chromosome 2.We have compared the genomes of S. chlorophenolicum Strain L-1 and Sphingobium japonicum, a closely related Sphingomonad that degrades lindane.Our analysis suggests that the genes encoding the first three enzymes in the PCP degradation pathway were acquired via two different horizontal gene transfer events, and the genes encoding the final two enzymes in the pathway were acquired from the most recent common ancestor of these two bacteria.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, CO, USA. shelley.copley@colorado.edu

ABSTRACT
Sphingobium chlorophenolicum Strain L-1 can mineralize the toxic pesticide pentachlorophenol (PCP). We have sequenced the genome of S. chlorophenolicum Strain L-1. The genome consists of a primary chromosome that encodes most of the genes for core processes, a secondary chromosome that encodes primarily genes that appear to be involved in environmental adaptation, and a small plasmid. The genes responsible for degradation of PCP are found on chromosome 2. We have compared the genomes of S. chlorophenolicum Strain L-1 and Sphingobium japonicum, a closely related Sphingomonad that degrades lindane. Our analysis suggests that the genes encoding the first three enzymes in the PCP degradation pathway were acquired via two different horizontal gene transfer events, and the genes encoding the final two enzymes in the pathway were acquired from the most recent common ancestor of these two bacteria.

Show MeSH
Related in: MedlinePlus