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Global analysis of mRNA decay intermediates in B acillus subtilis wild‐type and polynucleotide phosphorylase‐deletion strains
Author(s) -
Liu Bo,
Deikus Gintaras,
Bree Anna,
Durand Sylvain,
Kearns Daniel B.,
Bechhofer David H.
Publication year - 2014
Publication title -
molecular microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.857
H-Index - 247
eISSN - 1365-2958
pISSN - 0950-382X
DOI - 10.1111/mmi.12748
Subject(s) - polynucleotide phosphorylase , biology , exoribonuclease , exonuclease , messenger rna , rna , mutant , microbiology and biotechnology , exosome complex , degradosome , rnase p , biochemistry , purine nucleoside phosphorylase , enzyme , gene , polymerase , purine
Summary Messenger RNA decay in B acillus subtilis is accomplished by a combination of exoribonucleases and endoribonucleases. Intermediates in the decay process have not been readily detectable, and previous studies on mRNA decay have used a handful of highly expressed transcripts as models. Here, we use RNA ‐Seq analysis to probe mRNA turnover globally. A significant fraction of messages showed differential accumulation of RNA fragments that mapped near the 5′ or 3′ end of the coding sequence, consistent with initiation of decay from either the 5′ end or from an internal cleavage site. Patterns of mRNA decay in the wild type were compared with patterns in a mutant strain lacking polynucleotide phosphorylase ( PNPase ), which is considered the major 3′ exonuclease activity in mRNA decay and which is one of four known 3′ exonucleases in B . subtilis . The results showed a striking dependence on PNPase for mRNA turnover in many cases, suggesting specificity in the ability of 3′ exonucleases to degrade from 3′‐hydroxyl termini. RNA ‐Seq data demonstrated a sharp decrease in expression of Sigma D in the PNPase ‐deletion strain. Reduction in sigD regulon expression explained the chain growth phenotype of the PNPase mutant and also predicted a defect in swarming motility.