The Hangry Behavior of Myxobacteria: Transcriptome Analyses of Starving Cells
Disciplines
Bioinformatics | Genetics and Genomics | Microbiology
Abstract (300 words maximum)
Myxobacteria exhibit social behavior by coordinating cellular response through cell signaling, making them perfect models to study these mechanisms. They are commonly found in soil. One example of their social behavior is the ability to coordinate multicellular spore formation (sporulation) during starvation and their predatory nature toward other bacteria and yeasts. The gene csgA codes for C-Signal production, which indicates close cell proximity—an important prerequisite for the starvation response, which in turn activates transcription factor FruA. FruA coordinates with MrpC, a starvation-induced transcription factor, and upregulates expression of thousands of genes essential for sporulation, while shutting down unneeded metabolic processes. In this project, I used R to preform various bioinformatics tests to analyze which genes were upregulated or down regulated in deletion mutant strains of csgA, fruA, and mrpC compared to the wild type (DK1622) strain of Myxococcus xanthus. Out of the hundreds of genes downregulated in the mutant strains, we selected around 50 candidates for further analysis. Some of them are predicted to code for proteins involved in peptidoglycan synthesis and remodeling, such as penicillin-binding proteins, carboxypeptidases, and the Fts cell division proteins. Others interesting candidates are CRISPR-Cas genes which are typically involved in mediating bacterial immunity to phage attack. I will do GO enrichment analysis on the list of differentially expressed gene get a functional profile and to identify those that are over or under represented. This analysis provides rich insights into gene regulation and cell signaling mechanisms with potential applications in industry and medicine.
Academic department under which the project should be listed
CSM - Molecular and Cellular Biology
Primary Investigator (PI) Name
Ramya Rajagopalan
The Hangry Behavior of Myxobacteria: Transcriptome Analyses of Starving Cells
Myxobacteria exhibit social behavior by coordinating cellular response through cell signaling, making them perfect models to study these mechanisms. They are commonly found in soil. One example of their social behavior is the ability to coordinate multicellular spore formation (sporulation) during starvation and their predatory nature toward other bacteria and yeasts. The gene csgA codes for C-Signal production, which indicates close cell proximity—an important prerequisite for the starvation response, which in turn activates transcription factor FruA. FruA coordinates with MrpC, a starvation-induced transcription factor, and upregulates expression of thousands of genes essential for sporulation, while shutting down unneeded metabolic processes. In this project, I used R to preform various bioinformatics tests to analyze which genes were upregulated or down regulated in deletion mutant strains of csgA, fruA, and mrpC compared to the wild type (DK1622) strain of Myxococcus xanthus. Out of the hundreds of genes downregulated in the mutant strains, we selected around 50 candidates for further analysis. Some of them are predicted to code for proteins involved in peptidoglycan synthesis and remodeling, such as penicillin-binding proteins, carboxypeptidases, and the Fts cell division proteins. Others interesting candidates are CRISPR-Cas genes which are typically involved in mediating bacterial immunity to phage attack. I will do GO enrichment analysis on the list of differentially expressed gene get a functional profile and to identify those that are over or under represented. This analysis provides rich insights into gene regulation and cell signaling mechanisms with potential applications in industry and medicine.