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Pramod P. Wangikar, Ph.D.: Operonic structure of key metabolic pathways in cyanobacteria

Abstract

Genes involved in a common metabolic pathway are often organized in the form of an operon, which are transcribed into a single poly-cistronic mRNA. Analysis of the operonic structure of a genome can be a useful tool in obtaining pathway level annotation for hypothetical genes.  In this work we have used a comparative genomics based approach for the prediction of cyanobacterial operons using intergenic distance and gene neighborhood conservation as features.  The predicted operons were then mapped to KEGG metabolic pathways to identify operons whose genes map to a common metabolic pathway. We identified a total of 39 pathways in cyanobacteria which correspond to at least one operon.  These included operons unique to cyanobacteria such as those involved in photosynthesis.  We detected a significant rearrangement in the operonic structure of genes in metabolic pathways across different cyanobacteria.  To exemplify, the phycobilisome five-gene operon in photosynthesis pathway of Synechocystis sp. PCC 6803 was found to be rearranged and extended in the form of a ten-gene operon containing new phycocyanobilin lyase subunits and additional phycobilisome linker proteins in Anabaena species.  Further, a total of 317 genes were annotated at the pathway level using our analysis. The results provide a vast resource for biologists working on cyanobacteria for further experimental validation.

Biography

Professor Wangikar received his Bachelor’s degree in chemical engineering from UDCT and a PhD in chemical and biochemical engineering from the University of Iowa.  After working in a biotechnology company in the US, he joined IIT Bombay in 1997 in the department of chemical engineering.  His research interests are in the area of structural bioinformatics and metabolic modeling.  He has published over 35 research papers in international journals, which together have received over 500 citations.  He is the recipient of several awards including the 2006 National Bioscience Award for Career Development, INAE Young Engineer Award and DAE Young Scientist Award.  He is on the editorial board of Biotechnology and Bioegineering.