Transcriptome analysis of Variovorax strains under different growth conditions
Poster Number
2C
Format
Poster Presentation
Faculty Mentor Name
Paul Orwin
Faculty Mentor Department
Biological Sciences
Abstract/Artist Statement
Variovorax paradoxus and related species are gram-negative beta proteobacteria thought to be important in the formation of the rhizosphere community, as well as sources of biotechnologically relevant enzymatic activities. Isolates from this phylogentic group have been shown to promote plant growth while exhibiting diverse morphological, physiological, and metabolic characteristics under varied conditions. Previous studies in the Orwin lab have mapped the complete multipartite genomes of several Variovorax isolates and identified potential target genes for biofilm formation in a preliminary analysis of the static biofilm transcriptome of V. paradoxus EPS. In this study we use a similar approach to identify important genes differentially regulated in biofilms of related Variovorax strains. Our hypothesis is that there will be some degree of common genetic programming responsible for biofilm formation in Variovorax. We are also interested in comparing gene regulation across the different replicons using a comparative transcriptomic analysis, with an emphasis on toxin-antitoxin (TA) gene pairs. Triplicate biological samples from log phase planktonic and static biofilm cultures were imaged and tracked for growth for seven V. paradoxus strains (4MfCol3.1, 110B, MF350, NFACC26, ATCC 17713(NBRC 15149), EPS, and VAI-C) in 2.5 g/L YE media. RNA was extracted from each sample and 20-30 million paired end reads (2x150bp) were acquired from each. A secondary species-specific rRNA depletion was performed before genome alignment. Prokka annotations were used to identify the genes within the replicons. Based on PCoA clustering, we observed substantial variation between the alternative conditions and a large set of genes with altered expression.
Location
Information Commons, William Knox Holt Memorial Library and Learning Center
Start Date
29-4-2023 10:00 AM
End Date
29-4-2023 1:00 PM
Transcriptome analysis of Variovorax strains under different growth conditions
Information Commons, William Knox Holt Memorial Library and Learning Center
Variovorax paradoxus and related species are gram-negative beta proteobacteria thought to be important in the formation of the rhizosphere community, as well as sources of biotechnologically relevant enzymatic activities. Isolates from this phylogentic group have been shown to promote plant growth while exhibiting diverse morphological, physiological, and metabolic characteristics under varied conditions. Previous studies in the Orwin lab have mapped the complete multipartite genomes of several Variovorax isolates and identified potential target genes for biofilm formation in a preliminary analysis of the static biofilm transcriptome of V. paradoxus EPS. In this study we use a similar approach to identify important genes differentially regulated in biofilms of related Variovorax strains. Our hypothesis is that there will be some degree of common genetic programming responsible for biofilm formation in Variovorax. We are also interested in comparing gene regulation across the different replicons using a comparative transcriptomic analysis, with an emphasis on toxin-antitoxin (TA) gene pairs. Triplicate biological samples from log phase planktonic and static biofilm cultures were imaged and tracked for growth for seven V. paradoxus strains (4MfCol3.1, 110B, MF350, NFACC26, ATCC 17713(NBRC 15149), EPS, and VAI-C) in 2.5 g/L YE media. RNA was extracted from each sample and 20-30 million paired end reads (2x150bp) were acquired from each. A secondary species-specific rRNA depletion was performed before genome alignment. Prokka annotations were used to identify the genes within the replicons. Based on PCoA clustering, we observed substantial variation between the alternative conditions and a large set of genes with altered expression.