| description |
Clostridium phytofermentans is a model for gram-positive soil and intestinal bacteria that ferment diverse polysaccharides in lignocellulosic biomass. Here we explored the transcription architecture enabling C. phytofermentans to metabolize plant substrates by profiling nearly 10,000 transcriptional start sites (TSS) using Capp-Switch sequencing. This approach combines capture of synthetically capped 5' mRNA fragments with template-switching reverse transcription to reproducibly quantify expression at TSS with single base resolution. We observed pervasive use of alternative promoters, especially by genes for cellulases and other biomass-degrading enzymes. Antisense transcription is much rarer in C. phytofermentans than other bacteria, but it is associated with genes controlling processes including sporulation and sugar transport. TSS also revealed non-coding RNA including riboswitches and other novel transcription units, one of which has the most highly expressed TSS during growth on biomass. We integrated TSS identification with RNA-seq, proteomics, and an updated genome annotation to discover new genes and evidence for widespread mRNA processing. We discuss how Capp-Switch is a general approach to profile transcription initiation in model bacteria and mixed communities. |