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Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains.

Pearce SL, Oakeshott JG, Pandey G - G3 (Bethesda) (2015)

Bottom Line: To further elucidate the evolution of the lin pathway, we have biochemically and genetically characterized three HCH-degrading strains from the Czech Republic and compared the genomes of these and seven other HCH-degrading bacterial strains.Variable assembly of the pathway is a common feature across the 10 genomes, eight of which (including all three Czech strains) were either missing key lin genes or containing duplicate copies of upstream lin genes (linA-F).This study identifies a number of strains that are in the early stages of lin pathway acquisition and shows that the state of the pathway can explain the degradation patterns observed.

View Article: PubMed Central - PubMed

Affiliation: CSIRO Ecosystem Sciences, Acton, ACT-2601, Australia.

No MeSH data available.


Related in: MedlinePlus

Degradation assays for HCH isomers. Degradation of α-HCH, β-HCH, γ-HCH, and δ-HCH (left-hand axis) by UT26, LL01, LL02, and LL03 and relative quantification of metabolites by peak area (right-hand axis). Time postinoculation is shown on the bottom axis and the timescale for the γ-HCH assay has been adjusted to observe both the very fast (less than 1 hr) and very slow (96 hr) degradation of γ-HCH by different strains. Values are the mean of three biological replicates, with standard deviations. Identity of metabolites was confirmed by comparison to authentic standards or to metabolites produced with purified UT26 LinA or LinB enzymes. HCH, hexachlorocyclohexane; PCCH, pentachlorocyclohexene; PCHL, pentachlorocyclohexanol; TCB, trichlorobenzene.
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fig1: Degradation assays for HCH isomers. Degradation of α-HCH, β-HCH, γ-HCH, and δ-HCH (left-hand axis) by UT26, LL01, LL02, and LL03 and relative quantification of metabolites by peak area (right-hand axis). Time postinoculation is shown on the bottom axis and the timescale for the γ-HCH assay has been adjusted to observe both the very fast (less than 1 hr) and very slow (96 hr) degradation of γ-HCH by different strains. Values are the mean of three biological replicates, with standard deviations. Identity of metabolites was confirmed by comparison to authentic standards or to metabolites produced with purified UT26 LinA or LinB enzymes. HCH, hexachlorocyclohexane; PCCH, pentachlorocyclohexene; PCHL, pentachlorocyclohexanol; TCB, trichlorobenzene.

Mentions: Growth assays with four HCH isomers allowed us to compare the abilities of LL01, LL02, and LL03 to degrade the various HCH isomers with those of the well characterized strain UT26 (Figure 1). We were able to confirm the ability of LL01 to degrade all four isomers tested (relative rates: α = γ > δ >> β), and of LL03 to degrade α-, γ-, and δ-HCH (α > γ >> δ) (Kaur et al. 2013; Niharika et al. 2013a). LL02 was found to degrade only α-, γ-, and δ-HCH (δ > α >> γ). Compared with UT26, LL01 exhibited a similar degradation pattern for each isomer, whereas LL03 was much slower than UT26 for the three isomers it could degrade. LL02 had a novel degradation pattern, with slower γ-HCH and faster δ-HCH degradation than the other strains. Although LinA variants are known to affect the α-HCH enantiomer specificity or the α/γ isomer preference (Sharma et al. 2011; Suar et al. 2005), this is the first strain reported to degrade δ-HCH faster than all other isomers.


Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains.

Pearce SL, Oakeshott JG, Pandey G - G3 (Bethesda) (2015)

Degradation assays for HCH isomers. Degradation of α-HCH, β-HCH, γ-HCH, and δ-HCH (left-hand axis) by UT26, LL01, LL02, and LL03 and relative quantification of metabolites by peak area (right-hand axis). Time postinoculation is shown on the bottom axis and the timescale for the γ-HCH assay has been adjusted to observe both the very fast (less than 1 hr) and very slow (96 hr) degradation of γ-HCH by different strains. Values are the mean of three biological replicates, with standard deviations. Identity of metabolites was confirmed by comparison to authentic standards or to metabolites produced with purified UT26 LinA or LinB enzymes. HCH, hexachlorocyclohexane; PCCH, pentachlorocyclohexene; PCHL, pentachlorocyclohexanol; TCB, trichlorobenzene.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4478539&req=5

fig1: Degradation assays for HCH isomers. Degradation of α-HCH, β-HCH, γ-HCH, and δ-HCH (left-hand axis) by UT26, LL01, LL02, and LL03 and relative quantification of metabolites by peak area (right-hand axis). Time postinoculation is shown on the bottom axis and the timescale for the γ-HCH assay has been adjusted to observe both the very fast (less than 1 hr) and very slow (96 hr) degradation of γ-HCH by different strains. Values are the mean of three biological replicates, with standard deviations. Identity of metabolites was confirmed by comparison to authentic standards or to metabolites produced with purified UT26 LinA or LinB enzymes. HCH, hexachlorocyclohexane; PCCH, pentachlorocyclohexene; PCHL, pentachlorocyclohexanol; TCB, trichlorobenzene.
Mentions: Growth assays with four HCH isomers allowed us to compare the abilities of LL01, LL02, and LL03 to degrade the various HCH isomers with those of the well characterized strain UT26 (Figure 1). We were able to confirm the ability of LL01 to degrade all four isomers tested (relative rates: α = γ > δ >> β), and of LL03 to degrade α-, γ-, and δ-HCH (α > γ >> δ) (Kaur et al. 2013; Niharika et al. 2013a). LL02 was found to degrade only α-, γ-, and δ-HCH (δ > α >> γ). Compared with UT26, LL01 exhibited a similar degradation pattern for each isomer, whereas LL03 was much slower than UT26 for the three isomers it could degrade. LL02 had a novel degradation pattern, with slower γ-HCH and faster δ-HCH degradation than the other strains. Although LinA variants are known to affect the α-HCH enantiomer specificity or the α/γ isomer preference (Sharma et al. 2011; Suar et al. 2005), this is the first strain reported to degrade δ-HCH faster than all other isomers.

Bottom Line: To further elucidate the evolution of the lin pathway, we have biochemically and genetically characterized three HCH-degrading strains from the Czech Republic and compared the genomes of these and seven other HCH-degrading bacterial strains.Variable assembly of the pathway is a common feature across the 10 genomes, eight of which (including all three Czech strains) were either missing key lin genes or containing duplicate copies of upstream lin genes (linA-F).This study identifies a number of strains that are in the early stages of lin pathway acquisition and shows that the state of the pathway can explain the degradation patterns observed.

View Article: PubMed Central - PubMed

Affiliation: CSIRO Ecosystem Sciences, Acton, ACT-2601, Australia.

No MeSH data available.


Related in: MedlinePlus