GSE173854
Levels and Characteristics of mRNAs in Dormant Spores of Firmicute Species
Spores of Bacillales and Clostridiales species contain 100s of different mRNAs, and their major function in Bacillus subtilis is to provide ribonucleotides for new RNA synthesis when spores germinate.  In new work, RNA was isolated from spores of five Bacillales and one Clostridioides species and relative spore mRNA levels were determined by RNA-seq.  Determination of RNA levels in single spores allowed calculation of RNA nt/spore, and assuming mRNA is 3% of spore RNA allowed calculation that only ~6% of spore mRNAs were present at = 1/spore. Bacillus subtilis, Bacillus atrophaeus and Clostridioides difficile spores had 49, 42 and 51 mRNAs at >1/spore, respectively. Numbers of mRNAs at =1/spore were ~10 to 50% higher in Geobacillus stearothermophilus and Bacillus thuringiensis Al Hakam spores, respectively, and ~ 4-fold higher in Bacillus megaterium spores. Notably, in all species: i) many of the 60 most abundant spore mRNAs were transcribed by RNA polymerase with forespore-specific s factors; ii) some to many of the most abundant spore mRNAs encoded  orthologs of those encoded by abundant B. subtilis spore mRNAs and proteins present in dormant spores ; and iii) some spore mRNAs were likely transcribed in the mother cell compartment of the sporulating cell.  Indeed , analysis of the coverage of RNA-seq reads on mRNAs from all six species suggested that abundant spore mRNAs were at least somewhat fragmented. This observation was confirmed by RT-qPCR analysis of three abundant mRNAs each from B. subtilis and C. difficile spores.  These data add to a growing body of evidence indicating that the great majority of mRNAs in spores of Firmicutes are degradation and function as a ribonucleotide depot for new RNA synthesis when spores germinate. Overall design: RNA from spores of 5 different Bacillales and 1 Clostridiales were isolated and submitted for next generation sequencing via illumina HiSeq.