Rhizobial root attachment and rhizosphere colonization.
I am a post doc in Prof. Philip Poole’s group. I am interested in studying how rhizobia attach and colonize legume roots, a key step in rhizobia-legume symbiosis.
During doctoral research, I used microarray-based transcriptomics to study the changes in gene expression of Rhizobium leguminosarum bv viciae 3841 (Rlv3841) during pea root colonization. This study was further extended to delineate the pea-specific genes from the general plant adaptation genes, by comparing the differential gene expression of Rlv3841 during colonization of different plant roots; alfalfa (legume) and sugar beet (non-legume). This led to a detailed metabolic and transportome map of Rlv3841 gene expression during root colonization, suggesting the key components of pea root exudate and high-lighting the active metabolic pathways of Rlv3841 during colonization. In addition, a pea rhizosphere-specific plasmid was also identified, which is enriched with genes that are specifically induced in the pea rhizosphere (1).
From rhizosphere transcriptomics studies, a three-gene operon encoding lipoprotein (LppE), extra-cytoplasmic sigma factor (EcfE) and anti-EcfE (AsfE) was identified as highly and specifically transcribed during root colonization but only weakly in lab culture (and requiring phenylalanine addition). My current work is to characterize transcriptional regulation of these genes and elucidate their roles in root attachment and colonization. To do this I will employ cutting-edge luminescence assays, confocal imaging, RNA-Seq and ChIP-Seq.
The primary transcriptome of Salmonella enterica Serovar Typhimurium and its dependence on ppGpp during late stationary phase. Ramachandran VK, Shearer N, Thompson
A PloS one. 2014;9(3):e92690
The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression. Ramachandran VK, Shearer N, Jacob JJ, Sharma CM, Thompson
A BMC genomics. 2012;13:25
Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics. Ramachandran VK, East AK, Karunakaran R, Downie JA, Poole PS
Genome biology. 2011;12(10):R106
An incomplete TCA cycle increases survival of Salmonella Typhimurium during infection of resting and activated murine macrophages. Bowden SD, Ramachandran VK, Knudsen GM, Hinton JC, Thompson
A PloS one. 2010;5(11):e13871
Transcriptomic analysis of Rhizobium leguminosarum biovarviciae in symbiosis with host plants Pisumsativum and Viciacracca. Karunakaran R, Ramachandran VK, Seaman JC, East AK, Moushine B, Mauchline TH, Prell J, Skeffington A, Poole PS
Journal of bacteriology. 2009 Jun;191(12):4002-14