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Genome Organization of Sphingobium indicum B90A: An Archetypal Hexachlorocyclohexane (HCH) Degrading Genotype

Among sphingomonads, Sphingobium indicum B90A is widely investigated for its ability to degrade a manmade pesticide, γ-hexachlorocyclohexane (γ-HCH) and its isomers (α-, β-, δ-, and ε-HCH). In this study, complete genome of strain B90A was constructed using Single Molecule Real Time Sequencing (SMRT...

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Autores principales: Verma, Helianthous, Bajaj, Abhay, Kumar, Roshan, Kaur, Jasvinder, Anand, Shailly, Nayyar, Namita, Puri, Akshita, Singh, Yogendra, Khurana, Jitendra P., Lal, Rup
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737386/
https://www.ncbi.nlm.nih.gov/pubmed/28922869
http://dx.doi.org/10.1093/gbe/evx133
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author Verma, Helianthous
Bajaj, Abhay
Kumar, Roshan
Kaur, Jasvinder
Anand, Shailly
Nayyar, Namita
Puri, Akshita
Singh, Yogendra
Khurana, Jitendra P.
Lal, Rup
author_facet Verma, Helianthous
Bajaj, Abhay
Kumar, Roshan
Kaur, Jasvinder
Anand, Shailly
Nayyar, Namita
Puri, Akshita
Singh, Yogendra
Khurana, Jitendra P.
Lal, Rup
author_sort Verma, Helianthous
collection PubMed
description Among sphingomonads, Sphingobium indicum B90A is widely investigated for its ability to degrade a manmade pesticide, γ-hexachlorocyclohexane (γ-HCH) and its isomers (α-, β-, δ-, and ε-HCH). In this study, complete genome of strain B90A was constructed using Single Molecule Real Time Sequencing (SMRT) and Illumina platform. The complete genome revealed that strain B90A harbors four replicons: one chromosome (3,654,322 bp) and three plasmids designated as pSRL1 (139,218 bp), pSRL2 (108,430 bp) and pSRL3 (43,761 bp). The study determined the precise location of lin genes (genes associated with the degradation of HCH isomers), for example, linA2, linB, linDER, linF, linGHIJ, and linKLMN on the chromosome; linA1, linC, and linF on pSRL1 and linDEbR on pSRL3. Strain B90A contained 26 copies of IS6100 element and most of them (15 copies) was found to be associated with lin genes. Duplication of several lin genes including linA, linDER, linGHIJ, and linF along with two variants of linE, that is, linEa (hydroquinone 1,2-dioxygenase) and linEb (chlorohydroquinone/hydroquinone 1,2-dioxygenase) were identified. This suggests that strain B90A not only possess efficient machinery for upper and lower HCH degradation pathways but it can also act on both hydroquinone and chlorohydroquinone metabolites produced during γ-HCH degradation. Synteny analysis revealed the duplication and transposition of linA gene (HCH dehydrochlorinase) between the chromosome and pSRL1, possibly through homologous recombination between adjacent IS6100 elements. Further, in silico analysis and laboratory experiments revealed that incomplete tyrosine metabolism was responsible for the production of extracellular brown pigment which distinguished strain B90A from other HCH degrading sphingomonads. The precise localization of lin genes, and transposable elements (IS6100) on different replicons now opens up several experimental avenues to elucidate the functions and regulatory mechanism of lin genes acquisition and transfer that were not completely known among the bacterial population inhabiting the HCH contaminated environment.
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spelling pubmed-57373862018-01-08 Genome Organization of Sphingobium indicum B90A: An Archetypal Hexachlorocyclohexane (HCH) Degrading Genotype Verma, Helianthous Bajaj, Abhay Kumar, Roshan Kaur, Jasvinder Anand, Shailly Nayyar, Namita Puri, Akshita Singh, Yogendra Khurana, Jitendra P. Lal, Rup Genome Biol Evol Genome Report Among sphingomonads, Sphingobium indicum B90A is widely investigated for its ability to degrade a manmade pesticide, γ-hexachlorocyclohexane (γ-HCH) and its isomers (α-, β-, δ-, and ε-HCH). In this study, complete genome of strain B90A was constructed using Single Molecule Real Time Sequencing (SMRT) and Illumina platform. The complete genome revealed that strain B90A harbors four replicons: one chromosome (3,654,322 bp) and three plasmids designated as pSRL1 (139,218 bp), pSRL2 (108,430 bp) and pSRL3 (43,761 bp). The study determined the precise location of lin genes (genes associated with the degradation of HCH isomers), for example, linA2, linB, linDER, linF, linGHIJ, and linKLMN on the chromosome; linA1, linC, and linF on pSRL1 and linDEbR on pSRL3. Strain B90A contained 26 copies of IS6100 element and most of them (15 copies) was found to be associated with lin genes. Duplication of several lin genes including linA, linDER, linGHIJ, and linF along with two variants of linE, that is, linEa (hydroquinone 1,2-dioxygenase) and linEb (chlorohydroquinone/hydroquinone 1,2-dioxygenase) were identified. This suggests that strain B90A not only possess efficient machinery for upper and lower HCH degradation pathways but it can also act on both hydroquinone and chlorohydroquinone metabolites produced during γ-HCH degradation. Synteny analysis revealed the duplication and transposition of linA gene (HCH dehydrochlorinase) between the chromosome and pSRL1, possibly through homologous recombination between adjacent IS6100 elements. Further, in silico analysis and laboratory experiments revealed that incomplete tyrosine metabolism was responsible for the production of extracellular brown pigment which distinguished strain B90A from other HCH degrading sphingomonads. The precise localization of lin genes, and transposable elements (IS6100) on different replicons now opens up several experimental avenues to elucidate the functions and regulatory mechanism of lin genes acquisition and transfer that were not completely known among the bacterial population inhabiting the HCH contaminated environment. Oxford University Press 2017-07-21 /pmc/articles/PMC5737386/ /pubmed/28922869 http://dx.doi.org/10.1093/gbe/evx133 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Genome Report
Verma, Helianthous
Bajaj, Abhay
Kumar, Roshan
Kaur, Jasvinder
Anand, Shailly
Nayyar, Namita
Puri, Akshita
Singh, Yogendra
Khurana, Jitendra P.
Lal, Rup
Genome Organization of Sphingobium indicum B90A: An Archetypal Hexachlorocyclohexane (HCH) Degrading Genotype
title Genome Organization of Sphingobium indicum B90A: An Archetypal Hexachlorocyclohexane (HCH) Degrading Genotype
title_full Genome Organization of Sphingobium indicum B90A: An Archetypal Hexachlorocyclohexane (HCH) Degrading Genotype
title_fullStr Genome Organization of Sphingobium indicum B90A: An Archetypal Hexachlorocyclohexane (HCH) Degrading Genotype
title_full_unstemmed Genome Organization of Sphingobium indicum B90A: An Archetypal Hexachlorocyclohexane (HCH) Degrading Genotype
title_short Genome Organization of Sphingobium indicum B90A: An Archetypal Hexachlorocyclohexane (HCH) Degrading Genotype
title_sort genome organization of sphingobium indicum b90a: an archetypal hexachlorocyclohexane (hch) degrading genotype
topic Genome Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737386/
https://www.ncbi.nlm.nih.gov/pubmed/28922869
http://dx.doi.org/10.1093/gbe/evx133
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