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Defining global in vivo RNA interactions in Streptococcal species

Principal Supervisor: Emma Denham - WMS

Co-supervisor: Chrystala Constantinidou and Andrew Millard

PhD project title: Defining global in vivo RNA interactions in Streptococcal species

University of Registration: University of Warwick

Project outline:

Streptococci are significant pathogens of man, animals, aquatic mammals and fish. Some show a high degree of host and disease specificity whilst others are able to cause a wide array of different pathologies in distinct host targets. Many streptococcal species (including pathogens) are also able to co-exist in an asymptomatic carriage state with their host; while others originally considered benign commensals, have now been associated with issues such as endocarditis and colon cancer in humans. Streptococcal species are amongst those where antibiotic resistance is rising and an increased understanding of their fundamental biology may enable development of new strategies to combat this.

Efficient pre and post-transcriptional regulation of gene expression is essential for bacterial survival. Regulatory RNAs have been identified in all species where they have been looked for and they bring the central dogma of molecular biology in to question. These RNA molecules can be divided into different classes and include, untranslated regions at the 5’ and 3’ ends of transcripts, sRNAs and antisense RNAs. Many of these RNAs are thought to play roles in the response of bacterial cells to changes in environmental conditions including regulation of growth phase1, nutrient availability, survival during stress and iron starvation2,3.

Understanding the role regulatory RNAs play in the biology of Gram-positive organisms is lagging behind that of their Gram-negative counterparts. Many of the proteins and tools that have aided study of Gram-negative organisms are not available in Gram-positive species. For example the RNA binding protein Hfq does not appear to play a central role for sRNA-mRNA interaction as it does in the model Gram-negative E. coli. Therefore new strategies are required to understand the role these important molecules play in the biology of these organisms. We are currently using in vivo RNA-RNA interaction studies to define how the model Gram-positive bacteria Bacillus subtilis uses RNA to maintain homeostasis and remodel the cell when under perturbation. This allows us to take a global snapshot at any time of RNA interactions occurring in the cell.

This project will analyse in vivo RNA-RNA interactions in a number of Streptococcus species (such as Streptococcus agalactiae) under standard growth conditions and under environmental perturbations such oxidative stress. We will identify the regulatory RNAs that are expressed under these conditions and how these interact with other RNAs in the cell. Using a comparative approach with several different Streptococcus species we will identify similarities and differences, and try and understand regulatory networks. Do regulatory RNAs have regulons and are these the same in all streptococcal species studied?

References:

  1. Mars et al., Small regulatory RNA-induced growth rate heterogeneity of Bacillus subtilis PLoS Genetics 2015 19;11(3):e1005046
  2. A. Gaballa et al., The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins. Proceedings of the National Academy of Sciences of the United States of America 105, 11927 (Aug 19, 2008).
  3. S. Brantl, R. Bruckner, Small regulatory RNAs from low-GC Gram-positive bacteria. RNA biology 11, 443 (May, 2014).

BBSRC Strategic Research Priority: Molecules, cells and systems

Techniques that will be undertaken during the project:

  • Molecular and Microbiology
  • RNA-seq
  • Bioinformatics
  • In vivo analysis of RNA-RNA interactions
  • Comparative genomics and transcriptomics

Contact: Dr Emma Denham, University of Warwick