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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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Related in: MedlinePlus

Functional profiling of theSphingobiumgenomes. Heat map showing the normalized relative abundance of the top 50 subsystems enriched in the nine Sphingobium genomes. The strains and enriched pathways were clustered using Pearson correlation with a 0.8% minimum abundance. The color scale represents the relative abundance of gene content for each pathway, normalized by sample mean.
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Fig4: Functional profiling of theSphingobiumgenomes. Heat map showing the normalized relative abundance of the top 50 subsystems enriched in the nine Sphingobium genomes. The strains and enriched pathways were clustered using Pearson correlation with a 0.8% minimum abundance. The color scale represents the relative abundance of gene content for each pathway, normalized by sample mean.

Mentions: Core genome analysis identified 322 orthologs conserved between the nine genomes. The majority of these genes were involved in housekeeping functions such as the synthesis of ribosomal proteins, DNA replication, transcription & translation machinery, amino acid metabolism and membrane transporters. Core genome analysis for the eight strains that were either isolated from an HCH dumpsite or showed HCH degradation potential (i.e. all except SYK6) predicted 880 orthologs (Figure 2), which suggests a significant increase in genomic conservation (~2.7 times) resulting from the selective pressure of HCH exposure. This conservation is also seen in the degradation potential for other aromatic compounds such as benzoate, 1,4-dichlorobenzene, 1,2-methylnapthalene, caprolactam, toluene and xylene, trinitrotoluene, biphenyl and styrene degradation (Figure 4). Genes involved in the degradation of p-hydroxybenzoate, benzoate, quinate, gentisare, and catechol were also identified in the nine Sphingobium genomes (Additional file 1: Table S1). The presence of degradation pathways for phenol/toluene, chlorophenol, anthranilate, and homogentisate are identified in UT26S [19]. These pathways were observed in at least two of the newly sequenced strains (Additional file 1: Table S1). This suggests that these Sphingobium spp. possess broad aromatic compound degradation potential, although we did not observe the presence of these compounds at the HCH dumpsite [20]. The link between these aromatic degradation pathways and the HCH degradation pathway requires further investigation.Figure 4


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)

Functional profiling of theSphingobiumgenomes. Heat map showing the normalized relative abundance of the top 50 subsystems enriched in the nine Sphingobium genomes. The strains and enriched pathways were clustered using Pearson correlation with a 0.8% minimum abundance. The color scale represents the relative abundance of gene content for each pathway, normalized by sample mean.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Functional profiling of theSphingobiumgenomes. Heat map showing the normalized relative abundance of the top 50 subsystems enriched in the nine Sphingobium genomes. The strains and enriched pathways were clustered using Pearson correlation with a 0.8% minimum abundance. The color scale represents the relative abundance of gene content for each pathway, normalized by sample mean.
Mentions: Core genome analysis identified 322 orthologs conserved between the nine genomes. The majority of these genes were involved in housekeeping functions such as the synthesis of ribosomal proteins, DNA replication, transcription & translation machinery, amino acid metabolism and membrane transporters. Core genome analysis for the eight strains that were either isolated from an HCH dumpsite or showed HCH degradation potential (i.e. all except SYK6) predicted 880 orthologs (Figure 2), which suggests a significant increase in genomic conservation (~2.7 times) resulting from the selective pressure of HCH exposure. This conservation is also seen in the degradation potential for other aromatic compounds such as benzoate, 1,4-dichlorobenzene, 1,2-methylnapthalene, caprolactam, toluene and xylene, trinitrotoluene, biphenyl and styrene degradation (Figure 4). Genes involved in the degradation of p-hydroxybenzoate, benzoate, quinate, gentisare, and catechol were also identified in the nine Sphingobium genomes (Additional file 1: Table S1). The presence of degradation pathways for phenol/toluene, chlorophenol, anthranilate, and homogentisate are identified in UT26S [19]. These pathways were observed in at least two of the newly sequenced strains (Additional file 1: Table S1). This suggests that these Sphingobium spp. possess broad aromatic compound degradation potential, although we did not observe the presence of these compounds at the HCH dumpsite [20]. The link between these aromatic degradation pathways and the HCH degradation pathway requires further investigation.Figure 4

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