Limits...
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.

Show MeSH

Related in: MedlinePlus

A) Multiple sequence alignments oflinAB)linBgene sequences in the strains showing variation. Amino acid sequences of linA and linB genes from the strains were aligned using BioEdit to depict the substitutions at the respective sites.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig7: A) Multiple sequence alignments oflinAB)linBgene sequences in the strains showing variation. Amino acid sequences of linA and linB genes from the strains were aligned using BioEdit to depict the substitutions at the respective sites.

Mentions: The highest level of divergence in the upper HCH degradation pathway lin genes was reported for the linA gene encoding for HCH dehydrochlorinase in B90A [36]. The two previously characterized linA variants observed in B90A differed by 10% of their amino acid sequence, and were named linA1 and linA2. The functional aspects of these variants have been well characterized, as they show enantioselectivity in (±) α-HCH degradation, with LinA1 selective for the (+) and LinA2 for the (-) α HCH [37]. Also, the degradation ability of LinA1 was found to be lower than that of LinA2 [36]. Among all the lin genes of the upper pathway, linA in the present study was found to be most diverged in HDIPO4, in which it appeared to be a hybrid of the two variants (linA1 and linA2) with 94.8% sequence similarity to linA1 and 92.9 to linA2. Near to the catalytic dyad D25 and H73 critical for its enzymatic activity, the HDIPO4 linA was found to be identical with linA1[38]. However, the C-terminal region corresponded to linA2 (Figure 7A). This hybrid copy, now marked as linA3, requires further experimentation, but might be responsible for the comparatively better dehydrochlorination activity of HDIPO4 against α- and γ-HCH, as reported earlier [14].Figure 7


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)

A) Multiple sequence alignments oflinAB)linBgene sequences in the strains showing variation. Amino acid sequences of linA and linB genes from the strains were aligned using BioEdit to depict the substitutions at the respective sites.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig7: A) Multiple sequence alignments oflinAB)linBgene sequences in the strains showing variation. Amino acid sequences of linA and linB genes from the strains were aligned using BioEdit to depict the substitutions at the respective sites.
Mentions: The highest level of divergence in the upper HCH degradation pathway lin genes was reported for the linA gene encoding for HCH dehydrochlorinase in B90A [36]. The two previously characterized linA variants observed in B90A differed by 10% of their amino acid sequence, and were named linA1 and linA2. The functional aspects of these variants have been well characterized, as they show enantioselectivity in (±) α-HCH degradation, with LinA1 selective for the (+) and LinA2 for the (-) α HCH [37]. Also, the degradation ability of LinA1 was found to be lower than that of LinA2 [36]. Among all the lin genes of the upper pathway, linA in the present study was found to be most diverged in HDIPO4, in which it appeared to be a hybrid of the two variants (linA1 and linA2) with 94.8% sequence similarity to linA1 and 92.9 to linA2. Near to the catalytic dyad D25 and H73 critical for its enzymatic activity, the HDIPO4 linA was found to be identical with linA1[38]. However, the C-terminal region corresponded to linA2 (Figure 7A). This hybrid copy, now marked as linA3, requires further experimentation, but might be responsible for the comparatively better dehydrochlorination activity of HDIPO4 against α- and γ-HCH, as reported earlier [14].Figure 7

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