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sigma-spore-phage

DOI

Analysis of sporulation-like sigma factors in phages

This repository contains several different analyses all related to the publication Phage-encoded sigma factors alter bacterial dormancy (DOI:10.1128/msphere.00297-22). A second repo containing analysis of sporulation by flow-cytometry is at https://github.com/LennonLab/sigma-spore-phage-flow

  • All the analyses were done in Rstudio. I used the "here" package throughout the repo to call files using relative paths. To start up Rstusio at the right local directory I created an empty start.R file that can be used if you have .R files associated with Rstudio.

Bioinformatic analysis of phage sigma factors

This analysis spans over three interconnected folders. Analysis was run in the following order:

  1. vogdb - Retrieval and analysis of phage-encoded sigma factors from the Virus Orthologous Groups (VOG) database. This includes genomic clustering of phages and matching phages to host.

  2. TIGR - Retrieving profiles of bacterial-encoded sigma-factor families from TIGRfams, and using these profiles to classify phage sigma factors.

  3. phylo-clust - Phylogenetic analysis of (clustered) VOG genes along with bacterial sigma factors. This folder also includes the merging of TIGR and phylogeny classifications.

Phage virulence

  • Virulence - Growth curve based assay comparing phages SP10 WT and g120 knockout

Expression with inducible sigma factors

  • RNAseq - Expression analysis following induced expression in Bacillus subtilis in exponential growth

Combining bioinformatic and functional responses

  • synthesis

Within each folder a more detailed description is given in the readme file.