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

Verma, Helianthous; Kumar, Roshan; Oldach, Phoebe; Sangwan, Naseer; Khurana, Jitendra P.; Gilbert, Jack A.; Lal, Rup

doi:10.1186/1471-2164-15-1014

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

Journal Article · Sun Nov 23 04:00:00 UTC 2014 · BMC Genomics

DOI: https://doi.org/10.1186/1471-2164-15-1014 · OSTI ID:1223126

Verma, Helianthous ^[1]; Kumar, Roshan ^[1]; Oldach, Phoebe ^[1]; Sangwan, Naseer ^[1]; Khurana, Jitendra P. ^[2]; Gilbert, Jack A. ^[3]; Lal, Rup ^[1]

Univ. of Delhi, Delhi (India)
Univ. of Delhi, South Campus, New Delhi (India)
Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Chicago, Chicago, IL (United States)

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. In addition, 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. In 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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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1223126

Journal Information:: BMC Genomics, Journal Name: BMC Genomics Journal Issue: 1 Vol. 15; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

References (124)

Sphingomonas and Related Genera Balkwill, David L.; Fredrickson, J. K.; Romine, M. F. The Prokaryotes https://doi.org/10.1007/0-387-30747-8_23	book	January 2006
Degradation of β-hexachlorocyclohexane by haloalkane dehalogenase LinB from γ-hexachlorocyclohexane-utilizing bacterium Sphingobium sp. MI1205 Ito, Michihiro; Prokop, Zbyňek; Klvaňa, Martin Archives of Microbiology, Vol. 188, Issue 4 https://doi.org/10.1007/s00203-007-0251-8	journal	May 2007
A gene linB2 responsible for the conversion of β-HCH and 2,3,4,5,6-pentachlorocyclohexanol in Sphingomonas sp. BHC-A Wu, Jun; Hong, Qing; Han, Peng Applied Microbiology and Biotechnology, Vol. 73, Issue 5 https://doi.org/10.1007/s00253-006-0579-z	journal	January 2007
Aerobic degradation of lindane (γ-hexachlorocyclohexane) in bacteria and its biochemical and molecular basis Nagata, Yuji; Endo, Ryo; Ito, Michihiro Applied Microbiology and Biotechnology, Vol. 76, Issue 4 https://doi.org/10.1007/s00253-007-1066-x	journal	July 2007
Localization of HCH catabolic genes (lin genes) in Sphingobium indicum B90A Malhotra, Shweta; Sharma, Pooja; Kumari, Hansi Indian Journal of Microbiology, Vol. 47, Issue 3 https://doi.org/10.1007/s12088-007-0050-6	journal	September 2007
Genomic organization and genomic structural rearrangements of Sphingobium japonicum UT26, an archetypal γ-hexachlorocyclohexane-degrading bacterium Nagata, Yuji; Natsui, Shunsuke; Endo, Ryo Enzyme and Microbial Technology, Vol. 49, Issue 6-7 https://doi.org/10.1016/j.enzmictec.2011.10.005	journal	December 2011
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/s0022-2836(05)80360-2	journal	October 1990
Targeted A-to-G base editing of chloroplast DNA in plants Mok, Young Geun; Hong, Sunghyun; Bae, Su-Ji Nature Plants, Vol. 8, Issue 12 https://doi.org/10.1038/s41477-022-01279-8	journal	December 2022
Patterns and Rates of Plastid rps12 Gene Evolution Inferred in a Phylogenetic Context using Plastomic Data of Ferns Liu, Shanshan; Wang, Zhen; Wang, Hui Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-66219-y	journal	June 2020
Complete analysis of genes and enzymes for ?-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26 Nagata, Y.; Miyauchi, K.; Takagi, M. Journal of Industrial Microbiology and Biotechnology, Vol. 23, Issue 4-5 https://doi.org/10.1038/sj.jim.2900736	journal	October 1999
Genomic insights that advance the species definition for prokaryotes Konstantinidis, K. T.; Tiedje, J. M. Proceedings of the National Academy of Sciences, Vol. 102, Issue 7 https://doi.org/10.1073/pnas.0409727102	journal	February 2005
Crosstalk between bacterial chemotaxis signal transduction proteins and regulators of transcription of the Ntr regulon: evidence that nitrogen assimilation and chemotaxis are controlled by a common phosphotransfer mechanism. Ninfa, A. J.; Ninfa, E. G.; Lupas, A. N. Proceedings of the National Academy of Sciences, Vol. 85, Issue 15 https://doi.org/10.1073/pnas.85.15.5492	journal	August 1988
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Li, W.; Godzik, A. Bioinformatics, Vol. 22, Issue 13 https://doi.org/10.1093/bioinformatics/btl158	journal	May 2006
Clustal W and Clustal X version 2.0 Larkin, M. A.; Blackshields, G.; Brown, N. P. Bioinformatics, Vol. 23, Issue 21, p. 2947-2948 https://doi.org/10.1093/bioinformatics/btm404	journal	September 2007
IslandViewer: an integrated interface for computational identification and visualization of genomic islands Langille, M. G. I.; Brinkman, F. S. L. Bioinformatics, Vol. 25, Issue 5 https://doi.org/10.1093/bioinformatics/btp030	journal	January 2009
Fast and accurate short read alignment with Burrows-Wheeler transform Li, H.; Durbin, R. Bioinformatics, Vol. 25, Issue 14 https://doi.org/10.1093/bioinformatics/btp324	journal	May 2009
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0 Tamura, K.; Dudley, J.; Nei, M. Molecular Biology and Evolution, Vol. 24, Issue 8 https://doi.org/10.1093/molbev/msm092	journal	April 2007
KAAS: an automatic genome annotation and pathway reconstruction server Moriya, Y.; Itoh, M.; Okuda, S. Nucleic Acids Research, Vol. 35, Issue S2, p. W182-W185 https://doi.org/10.1093/nar/gkm321	journal	May 2007
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats Grissa, I.; Vergnaud, G.; Pourcel, C. Nucleic Acids Research, Vol. 35, Issue Web Server https://doi.org/10.1093/nar/gkm360	journal	May 2007
MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data Vallenet, David; Belda, Eugeni; Calteau, Alexandra Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1194	journal	November 2012
Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Takeuchi, M.; Hamana, K.; Hiraishi, A. International Journal of Systematic and Evolutionary Microbiology, Vol. 51, Issue 4 https://doi.org/10.1099/00207713-51-4-1405	journal	July 2001
Sphingobium lactosutens sp. nov., isolated from a hexachlorocyclohexane dump site and Sphingobium abikonense sp. nov., isolated from oil-contaminated soil Kumari, H.; Gupta, S. K.; Jindal, S. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 9 https://doi.org/10.1099/ijs.0.004739-0	journal	July 2009
Sphingobium chinhatense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite Dadhwal, M.; Jit, S.; Kumari, H. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 12 https://doi.org/10.1099/ijs.0.005553-0	journal	July 2009
Sphingobium quisquiliarum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH-contaminated soil Bala, K.; Sharma, P.; Lal, R. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 2 https://doi.org/10.1099/ijs.0.010868-0	journal	August 2009
Sphingobium baderi sp. nov., isolated from a hexachlorocyclohexane dump site Kaur, J.; Moskalikova, H.; Niharika, N. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 2 https://doi.org/10.1099/ijs.0.039834-0	journal	April 2012
Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov. Pal, R. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 55, Issue 5 https://doi.org/10.1099/ijs.0.63201-0	journal	September 2005
Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium Maruyama, T. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 56, Issue 1 https://doi.org/10.1099/ijs.0.63789-0	journal	January 2006
Proposal of biostimulation for hexachlorocyclohexane (HCH)-decontamination and characterization of culturable bacterial community from high-dose point HCH-contaminated soils Dadhwal, M.; Singh, A.; Prakash, O. Journal of Applied Microbiology, Vol. 106, Issue 2 https://doi.org/10.1111/j.1365-2672.2008.03982.x	journal	February 2009
Distribution and phylogeny of hexachlorocyclohexane-degrading bacteria in soils from Spain Mohn, William W.; Mertens, Birgit; Neufeld, Josh D. Environmental Microbiology, Vol. 8, Issue 1 https://doi.org/10.1111/j.1462-2920.2005.00865.x	journal	January 2006
16S rDNA phylogeny and distribution of lin genes in novel hexachlorocyclohexane-degrading Sphingomonas strains Boltner, Dietmar; Moreno-Morillas, Silvia; Ramos, Juan-Luis Environmental Microbiology, Vol. 7, Issue 9 https://doi.org/10.1111/j.1462-5822.2005.00820.x	journal	September 2005
Plasmid-encoded Î³-hexachlorocyclohexane degradation genes and insertion sequences in Sphingobium francense (ex- Sphingomonas paucimobilis Sp+) CÃ©rÃ©monie, HÃ©lÃ¨ne; Boubakri, Hasna; Mavingui, Patrick FEMS Microbiology Letters, Vol. 257, Issue 2 https://doi.org/10.1111/j.1574-6968.2006.00188.x	journal	April 2006
Comparison of 26 Sphingomonad Genomes Reveals Diverse Environmental Adaptations and Biodegradative Capabilities Aylward, Frank O.; McDonald, Bradon R.; Adams, Sandra M. Applied and Environmental Microbiology, Vol. 79, Issue 12 https://doi.org/10.1128/aem.00518-13	journal	April 2013
Cloning and Characterization of lin Genes Responsible for the Degradation of Hexachlorocyclohexane Isomers by Sphingomonas paucimobilis Strain B90 Kumari, R.; Subudhi, S.; Suar, M. Applied and Environmental Microbiology, Vol. 68, Issue 12 https://doi.org/10.1128/aem.68.12.6021-6028.2002	journal	December 2002
Dynamics of Multiple lin Gene Expression in Sphingomonas paucimobilis B90A in Response to Different Hexachlorocyclohexane Isomers Suar, M.; van der Meer, J. R.; Lawlor, K. Applied and Environmental Microbiology, Vol. 70, Issue 11 https://doi.org/10.1128/aem.70.11.6650-6656.2004	journal	November 2004
Complete Genome Sequence of the γ-Hexachlorocyclohexane-Degrading Bacterium Sphingomonas sp. Strain MM-1 Tabata, M.; Ohtsubo, Y.; Ohhata, S. Genome Announcements, Vol. 1, Issue 3 https://doi.org/10.1128/genomea.00247-13	journal	June 2013
Draft Genome Sequence of a Hexachlorocyclohexane-Degrading Bacterium, Sphingobium baderi Strain LL03 ^T Kaur, Jasvinder; Verma, Helianthous; Tripathi, Charu Genome Announcements, Vol. 1, Issue 5 https://doi.org/10.1128/genomea.00751-13	journal	October 2013
Genome Sequence of Sphingobium indicum B90A, a Hexachlorocyclohexane-Degrading Bacterium Anand, S.; Sangwan, N.; Lata, P. Journal of Bacteriology, Vol. 194, Issue 16 https://doi.org/10.1128/jb.00901-12	journal	July 2012
Identification and Characterization of Genes Encoding a Putative ABC-Type Transporter Essential for Utilization of -Hexachlorocyclohexane in Sphingobium japonicum UT26 Endo, R.; Ohtsubo, Y.; Tsuda, M. Journal of Bacteriology, Vol. 189, Issue 10 https://doi.org/10.1128/jb.01883-06	journal	March 2007
Genome Sequence of Sphingobium yanoikuyae XLDN2-5, an Efficient Carbazole-Degrading Strain Gai, Zhonghui; Wang, Xiaoyu; Tang, Hongzhi Journal of Bacteriology, Vol. 193, Issue 22 https://doi.org/10.1128/jb.06050-11	journal	October 2011
Complete Genome Sequence of Sphingobium sp. Strain SYK-6, a Degrader of Lignin-Derived Biaryls and Monoaryls Masai, E.; Kamimura, N.; Kasai, D. Journal of Bacteriology, Vol. 194, Issue 2 https://doi.org/10.1128/jb.06254-11	journal	December 2011
Organization of lin Genes and IS6100 among Different Strains of Hexachlorocyclohexane-Degrading Sphingomonas paucimobilis: Evidence for Horizontal Gene Transfer Dogra, C.; Raina, V.; Pal, R. Journal of Bacteriology, Vol. 186, Issue 8 https://doi.org/10.1128/jb.186.8.2225-2235.2004	journal	April 2004
CRISPR-Mediated Adaptive Immune Systems in Bacteria and Archaea Sorek, Rotem; Lawrence, C. Martin; Wiedenheft, Blake Annual Review of Biochemistry, Vol. 82, Issue 1 https://doi.org/10.1146/annurev-biochem-072911-172315	journal	June 2013
CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation Bhaya, Devaki; Davison, Michelle; Barrangou, Rodolphe Annual Review of Genetics, Vol. 45, Issue 1, p. 273-297 https://doi.org/10.1146/annurev-genet-110410-132430	journal	December 2011
The RAST Server: Rapid Annotations using Subsystems Technology Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A. BMC Genomics, Vol. 9, Issue 1, Article No. 75 https://doi.org/10.1186/1471-2164-9-75	journal	January 2008
Purification and Characterization of γ -Hexachlorocyclohexane ( γ -HCH) Dehydrochlorinase (LinA) from Pseudomonas paucimobilis Nagata, Yuji; Hatta, Takashi; Imai, Ryozo Bioscience, Biotechnology, and Biochemistry, Vol. 57, Issue 9 https://doi.org/10.1271/bbb.57.1582	journal	January 1993
A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes Ye, Yuzhen; Doak, Thomas G. PLoS Computational Biology, Vol. 5, Issue 8 https://doi.org/10.1371/journal.pcbi.1000465	journal	August 2009
Kinetic and Sequence-Structure-Function Analysis of Known LinA Variants with Different Hexachlorocyclohexane Isomers Sharma, Pooja; Pandey, Rinku; Kumari, Kirti PLoS ONE, Vol. 6, Issue 9 https://doi.org/10.1371/journal.pone.0025128	journal	September 2011
Comparative Metagenomic Analysis of Soil Microbial Communities across Three Hexachlorocyclohexane Contamination Levels Sangwan, Naseer; Lata, Pushp; Dwivedi, Vatsala PLoS ONE, Vol. 7, Issue 9 https://doi.org/10.1371/journal.pone.0046219	journal	September 2012
TM4: A Free, Open-Source System for Microarray Data Management and Analysis Saeed, A. I.; Sharov, V.; White, J. BioTechniques, Vol. 34, Issue 2 https://doi.org/10.2144/03342mt01	journal	February 2003
Data from: Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways Verma, Helianthous; Kumar, Roshan; Oldach, Phoebe Dryad https://doi.org/10.5061/dryad.g7t27	dataset	January 2015
Data from: Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and Hexachlorocyclohexane (HCH) degradation pathways Verma, Helianthous; Kumar, Roshan; Oldach, Phoebe Dryad-Supplementary information for journal article at DOI: 10.1186/1471-2164-15-1014, 11 files https://doi.org/10.5061/dryad.t4624	dataset	December 2014
Identification of protein fold and catalytic residues of γ-hexachlorocyclohexane dehydrochlorinase LinA: Structure and Catalytic Residues of LinA Nagata, Yuji; Mori, Katsuki; Takagi, Masamichi Proteins: Structure, Function, and Bioinformatics, Vol. 45, Issue 4 https://doi.org/10.1002/prot.10007	journal	October 2001
Sphingomonas and Related Genera Balkwill, David L.; Fredrickson, J. K.; Romine, M. F. The Prokaryotes https://doi.org/10.1007/0-387-30747-8_23	book	January 2006
ggplot2 Wickham, Hadley Springer New York, NY https://doi.org/10.1007/978-0-387-98141-3	book	January 2009
Degradation of β-hexachlorocyclohexane by haloalkane dehalogenase LinB from γ-hexachlorocyclohexane-utilizing bacterium Sphingobium sp. MI1205 Ito, Michihiro; Prokop, Zbyňek; Klvaňa, Martin Archives of Microbiology, Vol. 188, Issue 4 https://doi.org/10.1007/s00203-007-0251-8	journal	May 2007
Potential application in amoxicillin removal of Alcaligenes sp. MMA and enzymatic studies through molecular docking Sodhi, Kushneet Kaur; Kumar, Mohit; Singh, Dileep Kumar Archives of Microbiology, Vol. 202, Issue 6 https://doi.org/10.1007/s00203-020-01868-1	journal	March 2020
A gene linB2 responsible for the conversion of β-HCH and 2,3,4,5,6-pentachlorocyclohexanol in Sphingomonas sp. BHC-A Wu, Jun; Hong, Qing; Han, Peng Applied Microbiology and Biotechnology, Vol. 73, Issue 5 https://doi.org/10.1007/s00253-006-0579-z	journal	January 2007
Aerobic degradation of lindane (γ-hexachlorocyclohexane) in bacteria and its biochemical and molecular basis Nagata, Yuji; Endo, Ryo; Ito, Michihiro Applied Microbiology and Biotechnology, Vol. 76, Issue 4 https://doi.org/10.1007/s00253-007-1066-x	journal	July 2007
Functional screening of enzymes and bacteria for the dechlorination of hexachlorocyclohexane by a high-throughput colorimetric assay Sharma, Pooja; Jindal, Swati; Bala, Kiran Biodegradation, Vol. 25, Issue 2 https://doi.org/10.1007/s10532-013-9650-5	journal	June 2013
Evaluation of hexachlorocyclohexane contamination from the last lindane production plant operating in India Jit, Simran; Dadhwal, Mandeep; Kumari, Hansi Environmental Science and Pollution Research, Vol. 18, Issue 4 https://doi.org/10.1007/s11356-010-0401-4	journal	October 2010
Localization of HCH catabolic genes (lin genes) in Sphingobium indicum B90A Malhotra, Shweta; Sharma, Pooja; Kumari, Hansi Indian Journal of Microbiology, Vol. 47, Issue 3 https://doi.org/10.1007/s12088-007-0050-6	journal	September 2007
Evolution of Protein Molecules Jukes, Thomas H.; Cantor, Charles R. Mammalian Protein Metabolism, p. 21-132 https://doi.org/10.1016/B978-1-4832-3211-9.50009-7	book	January 1969
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
Global technical hexachlorocyclohexane usage and its contamination consequences in the environment: from 1948 to 1997 Li, Y. F. Science of The Total Environment, Vol. 232, Issue 3 https://doi.org/10.1016/S0048-9697(99)00114-X	journal	August 1999
Genomic organization and genomic structural rearrangements of Sphingobium japonicum UT26, an archetypal γ-hexachlorocyclohexane-degrading bacterium Nagata, Yuji; Natsui, Shunsuke; Endo, Ryo Enzyme and Microbial Technology, Vol. 49, Issue 6-7 https://doi.org/10.1016/j.enzmictec.2011.10.005	journal	December 2011
Global technical hexachlorocyclohexane usage and its contamination consequences in the environment: from 1948 to 1997 Li, Y. F. Science of The Total Environment, Vol. 232, Issue 3 https://doi.org/10.1016/s0048-9697(99)00114-x	journal	August 1999
Complete analysis of genes and enzymes for ?-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26 Nagata, Y.; Miyauchi, K.; Takagi, M. Journal of Industrial Microbiology and Biotechnology, Vol. 23, Issue 4-5 https://doi.org/10.1038/sj.jim.2900736	journal	October 1999
Genomic insights that advance the species definition for prokaryotes Konstantinidis, K. T.; Tiedje, J. M. Proceedings of the National Academy of Sciences, Vol. 102, Issue 7 https://doi.org/10.1073/pnas.0409727102	journal	February 2005
Covalent modification of the glnG product, NRI, by the glnL product, NRII, regulates the transcription of the glnALG operon in Escherichia coli. Ninfa, A. J.; Magasanik, B. Proceedings of the National Academy of Sciences, Vol. 83, Issue 16 https://doi.org/10.1073/pnas.83.16.5909	journal	August 1986
Crosstalk between bacterial chemotaxis signal transduction proteins and regulators of transcription of the Ntr regulon: evidence that nitrogen assimilation and chemotaxis are controlled by a common phosphotransfer mechanism. Ninfa, A. J.; Ninfa, E. G.; Lupas, A. N. Proceedings of the National Academy of Sciences, Vol. 85, Issue 15 https://doi.org/10.1073/pnas.85.15.5492	journal	August 1988
HyPhy: hypothesis testing using phylogenies Pond, S. L. K.; Frost, S. D. W.; Muse, S. V. Bioinformatics, Vol. 21, Issue 5 https://doi.org/10.1093/bioinformatics/bti079	journal	October 2004
ACT: the Artemis comparison tool Carver, T. J.; Rutherford, K. M.; Berriman, M. Bioinformatics, Vol. 21, Issue 16 https://doi.org/10.1093/bioinformatics/bti553	journal	June 2005
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Li, W.; Godzik, A. Bioinformatics, Vol. 22, Issue 13 https://doi.org/10.1093/bioinformatics/btl158	journal	May 2006
Identifying bacterial genes and endosymbiont DNA with Glimmer Delcher, Arthur L.; Bratke, Kirsten A.; Powers, Edwin C. Bioinformatics, Vol. 23, Issue 6 https://doi.org/10.1093/bioinformatics/btm009	journal	January 2007
Clustal W and Clustal X version 2.0 Larkin, M. A.; Blackshields, G.; Brown, N. P. Bioinformatics, Vol. 23, Issue 21, p. 2947-2948 https://doi.org/10.1093/bioinformatics/btm404	journal	September 2007
IslandViewer: an integrated interface for computational identification and visualization of genomic islands Langille, M. G. I.; Brinkman, F. S. L. Bioinformatics, Vol. 25, Issue 5 https://doi.org/10.1093/bioinformatics/btp030	journal	January 2009
Fast and accurate short read alignment with Burrows-Wheeler transform Li, H.; Durbin, R. Bioinformatics, Vol. 25, Issue 14 https://doi.org/10.1093/bioinformatics/btp324	journal	May 2009
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0 Tamura, K.; Dudley, J.; Nei, M. Molecular Biology and Evolution, Vol. 24, Issue 8 https://doi.org/10.1093/molbev/msm092	journal	April 2007
KAAS: an automatic genome annotation and pathway reconstruction server Moriya, Y.; Itoh, M.; Okuda, S. Nucleic Acids Research, Vol. 35, Issue S2, p. W182-W185 https://doi.org/10.1093/nar/gkm321	journal	May 2007
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats Grissa, I.; Vergnaud, G.; Pourcel, C. Nucleic Acids Research, Vol. 35, Issue Web Server https://doi.org/10.1093/nar/gkm360	journal	May 2007
MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data Vallenet, David; Belda, Eugeni; Calteau, Alexandra Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1194	journal	November 2012
Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Takeuchi, M.; Hamana, K.; Hiraishi, A. International Journal of Systematic and Evolutionary Microbiology, Vol. 51, Issue 4 https://doi.org/10.1099/00207713-51-4-1405	journal	July 2001
Sphingobium lactosutens sp. nov., isolated from a hexachlorocyclohexane dump site and Sphingobium abikonense sp. nov., isolated from oil-contaminated soil Kumari, H.; Gupta, S. K.; Jindal, S. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 9 https://doi.org/10.1099/ijs.0.004739-0	journal	July 2009
Sphingobium chinhatense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite Dadhwal, M.; Jit, S.; Kumari, H. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 12 https://doi.org/10.1099/ijs.0.005553-0	journal	July 2009
Sphingobium quisquiliarum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH-contaminated soil Bala, K.; Sharma, P.; Lal, R. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 2 https://doi.org/10.1099/ijs.0.010868-0	journal	August 2009
Sphingobium baderi sp. nov., isolated from a hexachlorocyclohexane dump site Kaur, J.; Moskalikova, H.; Niharika, N. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 2 https://doi.org/10.1099/ijs.0.039834-0	journal	April 2012
Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov. Pal, R. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 55, Issue 5 https://doi.org/10.1099/ijs.0.63201-0	journal	September 2005
Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium Maruyama, T. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 56, Issue 1 https://doi.org/10.1099/ijs.0.63789-0	journal	January 2006
Sphingobium ummariense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium, isolated from HCH-contaminated soil Singh, A.; Lal, R. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 1 https://doi.org/10.1099/ijs.0.65712-0	journal	January 2009
ABySS: A parallel assembler for short read sequence data Simpson, J. T.; Wong, K.; Jackman, S. D. Genome Research, Vol. 19, Issue 6 https://doi.org/10.1101/gr.089532.108	journal	February 2009
Metabolomics of hexachlorocyclohexane (HCH) transformation: ratio of LinA to LinB determines metabolic fate of HCH isomers: Metabolomics of HCH transformation Geueke, Birgit; Garg, Nidhi; Ghosh, Sneha Environmental Microbiology, Vol. 15, Issue 4 https://doi.org/10.1111/1462-2920.12009	journal	November 2012
Proposal of biostimulation for hexachlorocyclohexane (HCH)-decontamination and characterization of culturable bacterial community from high-dose point HCH-contaminated soils Dadhwal, M.; Singh, A.; Prakash, O. Journal of Applied Microbiology, Vol. 106, Issue 2 https://doi.org/10.1111/j.1365-2672.2008.03982.x	journal	February 2009
Distribution and phylogeny of hexachlorocyclohexane-degrading bacteria in soils from Spain Mohn, William W.; Mertens, Birgit; Neufeld, Josh D. Environmental Microbiology, Vol. 8, Issue 1 https://doi.org/10.1111/j.1462-2920.2005.00865.x	journal	January 2006
16S rDNA phylogeny and distribution of lin genes in novel hexachlorocyclohexane-degrading Sphingomonas strains Boltner, Dietmar; Moreno-Morillas, Silvia; Ramos, Juan-Luis Environmental Microbiology, Vol. 7, Issue 9 https://doi.org/10.1111/j.1462-5822.2005.00820.x	journal	September 2005
Plasmid-encoded Î³-hexachlorocyclohexane degradation genes and insertion sequences in Sphingobium francense (ex- Sphingomonas paucimobilis Sp+) CÃ©rÃ©monie, HÃ©lÃ¨ne; Boubakri, Hasna; Mavingui, Patrick FEMS Microbiology Letters, Vol. 257, Issue 2 https://doi.org/10.1111/j.1574-6968.2006.00188.x	journal	April 2006
Comparison of 26 Sphingomonad Genomes Reveals Diverse Environmental Adaptations and Biodegradative Capabilities Aylward, Frank O.; McDonald, Bradon R.; Adams, Sandra M. Applied and Environmental Microbiology, Vol. 79, Issue 12 https://doi.org/10.1128/AEM.00518-13	journal	April 2013
Cloning and Characterization of lin Genes Responsible for the Degradation of Hexachlorocyclohexane Isomers by Sphingomonas paucimobilis Strain B90 Kumari, R.; Subudhi, S.; Suar, M. Applied and Environmental Microbiology, Vol. 68, Issue 12 https://doi.org/10.1128/AEM.68.12.6021-6028.2002	journal	December 2002
Dynamics of Multiple lin Gene Expression in Sphingomonas paucimobilis B90A in Response to Different Hexachlorocyclohexane Isomers Suar, M.; van der Meer, J. R.; Lawlor, K. Applied and Environmental Microbiology, Vol. 70, Issue 11 https://doi.org/10.1128/AEM.70.11.6650-6656.2004	journal	November 2004
Genome Sequence of Sphingobium indicum B90A, a Hexachlorocyclohexane-Degrading Bacterium Anand, S.; Sangwan, N.; Lata, P. Journal of Bacteriology, Vol. 194, Issue 16 https://doi.org/10.1128/JB.00901-12	journal	July 2012
Complete Genome Sequence of the Representative -Hexachlorocyclohexane-Degrading Bacterium Sphingobium japonicum UT26 Nagata, Y.; Ohtsubo, Y.; Endo, R. Journal of Bacteriology, Vol. 192, Issue 21 https://doi.org/10.1128/JB.00961-10	journal	September 2010
Identification and Characterization of Genes Encoding a Putative ABC-Type Transporter Essential for Utilization of -Hexachlorocyclohexane in Sphingobium japonicum UT26 Endo, R.; Ohtsubo, Y.; Tsuda, M. Journal of Bacteriology, Vol. 189, Issue 10 https://doi.org/10.1128/JB.01883-06	journal	March 2007
Genome Sequence of Sphingobium yanoikuyae XLDN2-5, an Efficient Carbazole-Degrading Strain Gai, Zhonghui; Wang, Xiaoyu; Tang, Hongzhi Journal of Bacteriology, Vol. 193, Issue 22 https://doi.org/10.1128/JB.06050-11	journal	October 2011
Complete Genome Sequence of Sphingobium sp. Strain SYK-6, a Degrader of Lignin-Derived Biaryls and Monoaryls Masai, E.; Kamimura, N.; Kasai, D. Journal of Bacteriology, Vol. 194, Issue 2 https://doi.org/10.1128/JB.06254-11	journal	December 2011
Organization of lin Genes and IS6100 among Different Strains of Hexachlorocyclohexane-Degrading Sphingomonas paucimobilis: Evidence for Horizontal Gene Transfer Dogra, C.; Raina, V.; Pal, R. Journal of Bacteriology, Vol. 186, Issue 8 https://doi.org/10.1128/JB.186.8.2225-2235.2004	journal	April 2004
Biochemistry of Microbial Degradation of Hexachlorocyclohexane and Prospects for Bioremediation Lal, R.; Pandey, G.; Sharma, P. Microbiology and Molecular Biology Reviews, Vol. 74, Issue 1 https://doi.org/10.1128/MMBR.00029-09	journal	March 2010
Complete Genome Sequence of the γ-Hexachlorocyclohexane-Degrading Bacterium Sphingomonas sp. Strain MM-1 Tabata, M.; Ohtsubo, Y.; Ohhata, S. Genome Announcements, Vol. 1, Issue 3 https://doi.org/10.1128/genomeA.00247-13	journal	June 2013
Draft Genome Sequence of Sphingobium chinhatense Strain IP26 ^T , Isolated from a Hexachlorocyclohexane Dumpsite Niharika, Neha; Sangwan, Naseer; Ahmad, Salar Genome Announcements, Vol. 1, Issue 4 https://doi.org/10.1128/genomeA.00680-13	journal	August 2013
Draft Genome Sequence of Sphingobium sp. Strain HDIPO4, an Avid Degrader of Hexachlorocyclohexane Mukherjee, U.; Kumar, R.; Mahato, N. K. Genome Announcements, Vol. 1, Issue 5 https://doi.org/10.1128/genomeA.00749-13	journal	August 2013
Draft Genome Sequence of a Hexachlorocyclohexane-Degrading Bacterium, Sphingobium baderi Strain LL03 ^T Kaur, Jasvinder; Verma, Helianthous; Tripathi, Charu Genome Announcements, Vol. 1, Issue 5 https://doi.org/10.1128/genomeA.00751-13	journal	October 2013
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TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences Teeling, Hanno; Waldmann, Jost; Lombardot, Thierry BMC Bioinformatics, Vol. 5, Issue 1 https://doi.org/10.1186/1471-2105-5-163	journal	October 2004
The RAST Server: Rapid Annotations using Subsystems Technology Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A. BMC Genomics, Vol. 9, Issue 1, Article No. 75 https://doi.org/10.1186/1471-2164-9-75	journal	January 2008
Versatile and open software for comparing large genomes Kurtz, Stefan; Phillippy, Adam; Delcher, Arthur L. Genome Biology, Vol. 5, Issue 2, R12 https://doi.org/10.1186/gb-2004-5-2-r12	journal	January 2004
Purification and Characterization of γ -Hexachlorocyclohexane ( γ -HCH) Dehydrochlorinase (LinA) from Pseudomonas paucimobilis Nagata, Yuji; Hatta, Takashi; Imai, Ryozo Bioscience, Biotechnology, and Biochemistry, Vol. 57, Issue 9 https://doi.org/10.1271/bbb.57.1582	journal	January 1993
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Kinetic and Sequence-Structure-Function Analysis of Known LinA Variants with Different Hexachlorocyclohexane Isomers Sharma, Pooja; Pandey, Rinku; Kumari, Kirti PLoS ONE, Vol. 6, Issue 9 https://doi.org/10.1371/journal.pone.0025128	journal	September 2011
Comparative Metagenomic Analysis of Soil Microbial Communities across Three Hexachlorocyclohexane Contamination Levels Sangwan, Naseer; Lata, Pushp; Dwivedi, Vatsala PLoS ONE, Vol. 7, Issue 9 https://doi.org/10.1371/journal.pone.0046219	journal	September 2012
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TM4: A Free, Open-Source System for Microarray Data Management and Analysis Saeed, A. I.; Sharov, V.; White, J. BioTechniques, Vol. 34, Issue 2 https://doi.org/10.2144/03342mt01	journal	February 2003
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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
lin genes
Sphingobium
Hexachlorocyclohexane (HCH)
Xenobiotic compounds