Journal of Proteomics & Bioinformatics
Open Access
ISSN: 0974-276X
+44 1223 790975
ISSN: 0974-276X
+44 1223 790975
Gauri Garg Dhingra, Verma H and Lal R
University of Delhi, India
Posters & Accepted Abstracts: J Proteomics Bioinform
A HCH tolerant strain, R11HT was isolated from the soil sample of HCH dumpsite located at Ummari village, Lucknow, Uttar Pradesh, India. On the basis of 16S rRNA gene similarity, the strain was identified as the member of genus Sphingopyxis with highest identity with Sphingopyxis indica DS15T (97.85 %). In addition, three more strains were identified with similarity >97%. The pairwise DDH analysis revealed that the strain R11HT belongs to a separate species. Further biochemical and chemotaxonomic studies confirmed the novelty of the strain and thus designated as Sphingopyxis flava R11HT. Due to the HCH tolerance ability, strain R11HT was selected for genome sequencing using Illumina Hiseq technology. It has a genome size of 4.15 Mbp, with G+C content of 63.75% and 90.40% coding potential. The strain was found to code for 4185 protein coding sequences. The total number of RNA coded by the strain is equal to 58 with a single copy of 5S, 16S and 23S rRNA and 46 tRNAs. The pfam analysis revealed 3219 protein sequences engaged in variety of metabolic functions, dominated by amino acid transport and metabolism, energy production and conversion, lipid transport and metabolism, replication, transcription and translation. The strain was also found to harbor five biosynthetic gene clusters including terpene and ectoine. The KEGG pathway genes include degradation pathways for number of compounds including amino-benzoate, benzoate, bisphenol, caprolactlam, chloroalkene, chlorohexane but lin genes which are known for HCH degradation were not annotated in the genome. It will be interesting to further analyze the probable metabolic pathways of strain R11HT which helps the strain to withstand in such high concentration of HCH. Recent Publications â�?¢ Verma H, Bajaj A, Kumar R, Kaur J, Anand S, Nayyar N, Puri A, Singh Y, Khurana JP, Lal R (2017) Genome organization of Sphingobium indicum B90A: an archetypal hexachlorocyclohexane (HCH) degrading genotype. Genome Biol Evol. DOI: 1093/gbe/evx133. â�?¢ Mahato NK, Gupta V, Singh P, Kumari R, Verma H, Tripathi C, Rani P, Sharma A, Singhvi N, Sood U, Hira P, Kohli P, Nayyar N, Puri A, Bajaj A, Kumar R, Negi V, Talwar C, Khurana H, Nagar S, Sharma M, Mishra H, Singh AK, Dhingra G, Negi RK, Shakarad M, Singh Y, Lal R (2017) Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques. Antonie Van Leeuwenhoek. doi: 10.1007/s10482-017-0928-1. â�?¢ Kumar R, Verma H, Haider S, Bajaj A, Sood U, Ponnusamy K, Nagar S, Shakarad M, Negi R, Singh Y, Khurana J, Gilbert J, Lal R (2017) Comparative genomic analysis reveals habitat specific genes and regulatory hubs within the genus Novosphingobium. mSystems. 10.1128/mSystems.00020-17. â�?¢ Verma H, Rani P, Singh AK, Kumar R, Dwivedi V and Lal R (2015) Sphingopyxis flava sp. nov., isolated from an hexachlorocyclohexane (HCH) contaminated soil, India. Int. J. Syst. Evol. Microbiol. 65: 3720-3726. â�?¢ Verma H, Kumar R, Oldach P, Sangwan N, Khurana J P, Gilbert J A, Lal R (2014) Comparative genomic analysis of nine Sphingobium strains: Insights into their evolution and Hexachlorocyclohexane (HCH) degradation pathway. BMC Genomics, 15:1014.
Gauri Garg Dhingra is an Assistant Professor of Zoology at the University of Delhi, Kirori Mal College - Department of Zoology and has been involved in undergraduate teaching since past 13 years. She completed her PhD under supervision of Prof. Rup Lal, Department of Zoology in 2005 on Manipulations of Rifamycin Biosynthetic Gene Clusters in Amycolatopsis mediterranei. Presently she is working with Rup Lal’s group focusing on metagenomic diversity of pesticide contaminated sites.