Half-lives mRNA analysis of Stenotrophomonas maltophilia D457 and rng-deficient mutant

We calculated half-life values of mRNAs quantified by RNA-Seq by a suitable method of normalization. We determined the half-lives of more than 2200 mRNAs in the Stenotrophomonas maltophilia D457 wild-type strain and in an isogenic RNase G deficient mutant. Median half-lives were 2,74 and 3 min in the wild-type and the rng-deficient mutant respectively. We found an overall enhancement of half-life times of mRNAs when the gene encoding RNase G is lacking, showing that many RNAs are targets of RNase G in S. maltophilia. For achieving such goal, we propose a method for the normalization of RNA-Seq based studies on global bacterial mRNA decay. A RNA run-out experiment was carry out adding rifampicin to S. maltophilia D457 and rng-interrupted mutant growing at exponential phase. RNA was sequenced by RNASeq Illumina and quantified to calculated RNA half-lives.