Online today in #MGen : How we can use transcriptomic data to reveal new temperate phage biology microbiologyresearch.org/content/journa… This started with a simple idea and became a nice proof of concept. And one of the last papers from my PhD in @jay_salsa lab !
( a thread ⤵️ ) @MicrobioSoc
( a thread ⤵️ ) @MicrobioSoc
Phages can be broadly classified into two groups: temperate and virulent (or lyosogenic and lytic if you prefer). Temperate phages are by far the most interesting of the two! (Sorry phage therapists). This is because:
temperate phages can integrate their genomes into the DNA of bacterial hosts and manipulate their biology with new genes (=accessory/moron genes). For example, so many professional bacterial pathogens rely upon prophage-encoded toxins and virulence factors.
Since the majority of a temperate phage genome is devoted to genes needed for the lytic replication (e.g. making proteins that make new viruses and lyse cells) which are highly toxic to bacterial cells, prophages need to transcriptionally repress almost all of their genes
However, in order to manipulate the biology of their hosts, any accessory genes they encode need to be expressed (along with the genes that repress everything else)
Given this, I reasoned that prophage accessory genes would have distinct transcriptional signatures to prophage lytic genes, and wondered if we could use gene expression data to find new prophage accessory genes
Luckily, in the @jay_salsa lab, we had A LOT of Salmonella RNA-seq data. First, I set a gene expression threshold and filtered out all of the highly expressed genes from 5 different Salmonella prophages. I found this was a very good way to enrich for known accessory genes
11 / 12 of the known prophage accessory genes in Salmonella were highly expressed, whereas 141 / 142 of the lytic cycle genes were not expressed (repressed). Excitingly, there were many more highly-expressed prophage genes that had no known function (hypothetical proteins)
These genes are very likely to be new prophage accessory genes, modulating the biology of Salmonella in unknown ways. E.g.look at this gene, which is specifically up-regulated in anaerobic conditions, suggesting its function in low-oxygen environments (like parts of the GI tract)
But of course, prophage accessory loci don't only contribute to pathogenesis. Many are known to mediate resistance to other infecting bacteriophages. Using our transcriptomic approach, we detected a novel prophage-encoded anti-sense RNA that functioned in phage exclusion
This particularly highlights the value of the approach, because novel non-coding RNAs can only be detected using transcriptomic data (i.e. not genome data).
We anticipate that adoption of this approach
could bring many new insights into the fundamental biology of temperate phages, and discovery of many new and exciting prophage accessory genes/ proteins
could bring many new insights into the fundamental biology of temperate phages, and discovery of many new and exciting prophage accessory genes/ proteins
Don't have any RNA-seq data? There are thousands of bacterial RNA-seq datasets sitting in the NCBI Gene Expression Omnibus (GEO) repository ncbi.nlm.nih.gov/gds/?term= that could be mined for prophage gene expression
Finally, thanks to coauthors @knalsal, @DHammarlof @KroegerLab and Nico Wenner (the wonderful postdocs who taught me everything I know)
