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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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Comparative genome map ofSphingobiumspp. Mapped (BLASTN) over Sphingobium japonicum UT26S as a reference genome in which all genetic elements of UT26S were concatenated in the order of Chr1 (3,514,822 bp), Chr2 (681,892 bp), pCHQ1 (190,974 bp), pUT1 (31,776 bp) and pUT2 (5398 bp). Genes for HCH, Phenol/Toluene, Chlorophenol, Anthranilate and Homogentisate degradation pathways are identified in the outermost region of the figure. Genetic breakpoints between UT26S and other Sphingobium spp.; from the outside in; outermost circle1: Orthologous genes, circle 2: Draft genome of S. lactosutens DS20, circle 3: Draft genome of S. baderi LL03, circle 4: Draft genome of S. quisquilarium P25, circle 5: Draft genome of S. ummariense RL3, circle 6: Draft genome of Sphingobium sp. HDIPO4, circle 7: Draft genome of S. chinhatense IP26, circle 8 (innermost circle): Draft genome of S.indicum B90A. (Higher color intensity represents higher percentage identity i.e., darker shades show higher sequence identity).
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Fig2: Comparative genome map ofSphingobiumspp. Mapped (BLASTN) over Sphingobium japonicum UT26S as a reference genome in which all genetic elements of UT26S were concatenated in the order of Chr1 (3,514,822 bp), Chr2 (681,892 bp), pCHQ1 (190,974 bp), pUT1 (31,776 bp) and pUT2 (5398 bp). Genes for HCH, Phenol/Toluene, Chlorophenol, Anthranilate and Homogentisate degradation pathways are identified in the outermost region of the figure. Genetic breakpoints between UT26S and other Sphingobium spp.; from the outside in; outermost circle1: Orthologous genes, circle 2: Draft genome of S. lactosutens DS20, circle 3: Draft genome of S. baderi LL03, circle 4: Draft genome of S. quisquilarium P25, circle 5: Draft genome of S. ummariense RL3, circle 6: Draft genome of Sphingobium sp. HDIPO4, circle 7: Draft genome of S. chinhatense IP26, circle 8 (innermost circle): Draft genome of S.indicum B90A. (Higher color intensity represents higher percentage identity i.e., darker shades show higher sequence identity).

Mentions: The genome sizes for the six newly sequenced Sphingobium spp. averaged 4.83 Mbp and ranged from 4.08 to 5.89 Mbp, with S. chinhatense IP26 maintaining the largest genome (Table 1). These sizes are consistent with existing Sphingobium spp. [15]. The variation in genome size can be partially correlated to the presence of genomic islands; IP26 maintained the largest genome and the highest genomic island content, while LL03 had the least (Table 1). This potentially reflects differential degrees of HGT and mobile genetic element acquisition among these strains. UT26S, B90A, IP26 and HDIPO4 all shared high sequence identity (>97%), whereas LL03, P25, RL3 and DS20 have accumulated more sequence variation despite being under similar selection pressures (90-70%) (Figure 2).Table 1


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)

Comparative genome map ofSphingobiumspp. Mapped (BLASTN) over Sphingobium japonicum UT26S as a reference genome in which all genetic elements of UT26S were concatenated in the order of Chr1 (3,514,822 bp), Chr2 (681,892 bp), pCHQ1 (190,974 bp), pUT1 (31,776 bp) and pUT2 (5398 bp). Genes for HCH, Phenol/Toluene, Chlorophenol, Anthranilate and Homogentisate degradation pathways are identified in the outermost region of the figure. Genetic breakpoints between UT26S and other Sphingobium spp.; from the outside in; outermost circle1: Orthologous genes, circle 2: Draft genome of S. lactosutens DS20, circle 3: Draft genome of S. baderi LL03, circle 4: Draft genome of S. quisquilarium P25, circle 5: Draft genome of S. ummariense RL3, circle 6: Draft genome of Sphingobium sp. HDIPO4, circle 7: Draft genome of S. chinhatense IP26, circle 8 (innermost circle): Draft genome of S.indicum B90A. (Higher color intensity represents higher percentage identity i.e., darker shades show higher sequence identity).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Comparative genome map ofSphingobiumspp. Mapped (BLASTN) over Sphingobium japonicum UT26S as a reference genome in which all genetic elements of UT26S were concatenated in the order of Chr1 (3,514,822 bp), Chr2 (681,892 bp), pCHQ1 (190,974 bp), pUT1 (31,776 bp) and pUT2 (5398 bp). Genes for HCH, Phenol/Toluene, Chlorophenol, Anthranilate and Homogentisate degradation pathways are identified in the outermost region of the figure. Genetic breakpoints between UT26S and other Sphingobium spp.; from the outside in; outermost circle1: Orthologous genes, circle 2: Draft genome of S. lactosutens DS20, circle 3: Draft genome of S. baderi LL03, circle 4: Draft genome of S. quisquilarium P25, circle 5: Draft genome of S. ummariense RL3, circle 6: Draft genome of Sphingobium sp. HDIPO4, circle 7: Draft genome of S. chinhatense IP26, circle 8 (innermost circle): Draft genome of S.indicum B90A. (Higher color intensity represents higher percentage identity i.e., darker shades show higher sequence identity).
Mentions: The genome sizes for the six newly sequenced Sphingobium spp. averaged 4.83 Mbp and ranged from 4.08 to 5.89 Mbp, with S. chinhatense IP26 maintaining the largest genome (Table 1). These sizes are consistent with existing Sphingobium spp. [15]. The variation in genome size can be partially correlated to the presence of genomic islands; IP26 maintained the largest genome and the highest genomic island content, while LL03 had the least (Table 1). This potentially reflects differential degrees of HGT and mobile genetic element acquisition among these strains. UT26S, B90A, IP26 and HDIPO4 all shared high sequence identity (>97%), whereas LL03, P25, RL3 and DS20 have accumulated more sequence variation despite being under similar selection pressures (90-70%) (Figure 2).Table 1

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