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Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways.

Verma H, Kumar R, Oldach P, Sangwan N, Khurana JP, Gilbert JA, Lal R - BMC Genomics (2014)

Bottom Line: Genes associated with nitrogen stress response and two-component systems were found to be enriched.Further, in HDIPO4, linA was found as a hybrid of two natural variants i.e., linA1 and linA2 known for their different enantioselectivity.The bacteria isolated from HCH dumpsites provide a natural testing ground to study variations in the lin system and their effects on degradation efficacy.

View Article: PubMed Central - PubMed

Affiliation: Room No, 115, Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India. ruplal@gmail.com.

ABSTRACT

Background: Sphingobium spp. are efficient degraders of a wide range of chlorinated and aromatic hydrocarbons. In particular, strains which harbour the lin pathway genes mediating the degradation of hexachlorocyclohexane (HCH) isomers are of interest due to the widespread persistence of this contaminant. Here, we examined the evolution and diversification of the lin pathway under the selective pressure of HCH, by comparing the draft genomes of six newly-sequenced Sphingobium spp. (strains LL03, DS20, IP26, HDIPO4, P25 and RL3) isolated from HCH dumpsites, with three existing genomes (S. indicum B90A, S. japonicum UT26S and Sphingobium sp. SYK6).

Results: Efficient HCH degraders phylogenetically clustered in a closely related group comprising of UT26S, B90A, HDIPO4 and IP26, where HDIPO4 and IP26 were classified as subspecies with ANI value >98%. Less than 10% of the total gene content was shared among all nine strains, but among the eight HCH-associated strains, that is all except SYK6, the shared gene content jumped to nearly 25%. Genes associated with nitrogen stress response and two-component systems were found to be enriched. The strains also housed many xenobiotic degradation pathways other than HCH, despite the absence of these xenobiotics from isolation sources. Additionally, these strains, although non-motile, but posses flagellar assembly genes. While strains HDIPO4 and IP26 contained the complete set of lin genes, DS20 was entirely devoid of lin genes (except linKLMN) whereas, LL03, P25 and RL3 were identified as lin deficient strains, as they housed incomplete lin pathways. Further, in HDIPO4, linA was found as a hybrid of two natural variants i.e., linA1 and linA2 known for their different enantioselectivity.

Conclusion: The bacteria isolated from HCH dumpsites provide a natural testing ground to study variations in the lin system and their effects on degradation efficacy. Further, the diversity in the lin gene sequences and copy number, their arrangement with respect to IS6100 and evidence for potential plasmid content elucidate possible evolutionary acquisition mechanisms for this pathway. This study further opens the horizon for selection of bacterial strains for inclusion in an HCH bioremediation consortium and suggests that HDIPO4, IP26 and B90A would be appropriate candidates for inclusion.

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dN/dS v/s dS plot of orthologs, xenobiotic degradation pathway genes and IS elements/integrases. Sequences of orthologs, xenobiotic degradation pathway genes and IS elements/Integrases were used for calculating their dN/dS. Genes having dN/dS value >1 are under positive natural selection.
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Fig10: dN/dS v/s dS plot of orthologs, xenobiotic degradation pathway genes and IS elements/integrases. Sequences of orthologs, xenobiotic degradation pathway genes and IS elements/Integrases were used for calculating their dN/dS. Genes having dN/dS value >1 are under positive natural selection.

Mentions: To identify the substitutions that have fixed along the independent lineages and their direction of evolution, dN/dS (rate of non-synonymous over synonymous substitution) analysis was performed for sets of orthologous genes, and in particular those responsible for the degradation of HCH, phenol/toluene, homogentisate, chlorophenol and transposons/integrases (Figure 10). The genes of interest found to be under diversifying selection (dN/dS > 1) includes those for Fe(II) dependent oxygenase, ABC transporters, assimilatory nitrate reductase, and general secretory pathway protein. These genes are largely associated with stress tolerance. As mentioned earlier, ABC transporters are involved in uptake of high molecular weight pharmacological agents including xenobiotic compounds [44]. Hence, these transporters and their activity are crucial for their capability of HCH degradation and other aromatic compounds and likewise, their positive selection indicates the importance of their function in the HCH-stressed environments from which these bacterial strains were isolated. Additionally, nitrate reductase catalyzes the conversion of nitrate into free nitrogen and likely would enable the Sphingobium spp. to more effectively enact a nitrogen stress response. Finally, the diversification of genes such as oxygenases, secretory pathway proteins and translocase components adds to the sphingomonads skill of degradation of a wide range of aromatic compounds. Notably, only linH has shown the dN/dS > 1, while the other lin genes did not. This clearly indicates that under strong HCH pressure, the whole lin pathway is likely to get stabilized in the population with more synonomous substitutions compared to non-synonomous ones and tends to be retained in the population.Figure 10


Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways.

Verma H, Kumar R, Oldach P, Sangwan N, Khurana JP, Gilbert JA, Lal R - BMC Genomics (2014)

dN/dS v/s dS plot of orthologs, xenobiotic degradation pathway genes and IS elements/integrases. Sequences of orthologs, xenobiotic degradation pathway genes and IS elements/Integrases were used for calculating their dN/dS. Genes having dN/dS value >1 are under positive natural selection.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4289293&req=5

Fig10: dN/dS v/s dS plot of orthologs, xenobiotic degradation pathway genes and IS elements/integrases. Sequences of orthologs, xenobiotic degradation pathway genes and IS elements/Integrases were used for calculating their dN/dS. Genes having dN/dS value >1 are under positive natural selection.
Mentions: To identify the substitutions that have fixed along the independent lineages and their direction of evolution, dN/dS (rate of non-synonymous over synonymous substitution) analysis was performed for sets of orthologous genes, and in particular those responsible for the degradation of HCH, phenol/toluene, homogentisate, chlorophenol and transposons/integrases (Figure 10). The genes of interest found to be under diversifying selection (dN/dS > 1) includes those for Fe(II) dependent oxygenase, ABC transporters, assimilatory nitrate reductase, and general secretory pathway protein. These genes are largely associated with stress tolerance. As mentioned earlier, ABC transporters are involved in uptake of high molecular weight pharmacological agents including xenobiotic compounds [44]. Hence, these transporters and their activity are crucial for their capability of HCH degradation and other aromatic compounds and likewise, their positive selection indicates the importance of their function in the HCH-stressed environments from which these bacterial strains were isolated. Additionally, nitrate reductase catalyzes the conversion of nitrate into free nitrogen and likely would enable the Sphingobium spp. to more effectively enact a nitrogen stress response. Finally, the diversification of genes such as oxygenases, secretory pathway proteins and translocase components adds to the sphingomonads skill of degradation of a wide range of aromatic compounds. Notably, only linH has shown the dN/dS > 1, while the other lin genes did not. This clearly indicates that under strong HCH pressure, the whole lin pathway is likely to get stabilized in the population with more synonomous substitutions compared to non-synonomous ones and tends to be retained in the population.Figure 10

Bottom Line: Genes associated with nitrogen stress response and two-component systems were found to be enriched.Further, in HDIPO4, linA was found as a hybrid of two natural variants i.e., linA1 and linA2 known for their different enantioselectivity.The bacteria isolated from HCH dumpsites provide a natural testing ground to study variations in the lin system and their effects on degradation efficacy.

View Article: PubMed Central - PubMed

Affiliation: Room No, 115, Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India. ruplal@gmail.com.

ABSTRACT

Background: Sphingobium spp. are efficient degraders of a wide range of chlorinated and aromatic hydrocarbons. In particular, strains which harbour the lin pathway genes mediating the degradation of hexachlorocyclohexane (HCH) isomers are of interest due to the widespread persistence of this contaminant. Here, we examined the evolution and diversification of the lin pathway under the selective pressure of HCH, by comparing the draft genomes of six newly-sequenced Sphingobium spp. (strains LL03, DS20, IP26, HDIPO4, P25 and RL3) isolated from HCH dumpsites, with three existing genomes (S. indicum B90A, S. japonicum UT26S and Sphingobium sp. SYK6).

Results: Efficient HCH degraders phylogenetically clustered in a closely related group comprising of UT26S, B90A, HDIPO4 and IP26, where HDIPO4 and IP26 were classified as subspecies with ANI value >98%. Less than 10% of the total gene content was shared among all nine strains, but among the eight HCH-associated strains, that is all except SYK6, the shared gene content jumped to nearly 25%. Genes associated with nitrogen stress response and two-component systems were found to be enriched. The strains also housed many xenobiotic degradation pathways other than HCH, despite the absence of these xenobiotics from isolation sources. Additionally, these strains, although non-motile, but posses flagellar assembly genes. While strains HDIPO4 and IP26 contained the complete set of lin genes, DS20 was entirely devoid of lin genes (except linKLMN) whereas, LL03, P25 and RL3 were identified as lin deficient strains, as they housed incomplete lin pathways. Further, in HDIPO4, linA was found as a hybrid of two natural variants i.e., linA1 and linA2 known for their different enantioselectivity.

Conclusion: The bacteria isolated from HCH dumpsites provide a natural testing ground to study variations in the lin system and their effects on degradation efficacy. Further, the diversity in the lin gene sequences and copy number, their arrangement with respect to IS6100 and evidence for potential plasmid content elucidate possible evolutionary acquisition mechanisms for this pathway. This study further opens the horizon for selection of bacterial strains for inclusion in an HCH bioremediation consortium and suggests that HDIPO4, IP26 and B90A would be appropriate candidates for inclusion.

Show MeSH
Related in: MedlinePlus