Landscape of RNA polyadenylation inE. coli

Abstract

Polyadenylation is thought to be involved in the degradation and quality control of bacterial RNAs but relatively few examples have been investigated. We used a combination of 5΄-tagRACE and RNA-seq to analyze the total RNA content from a wild-type strain and from a poly(A)polymerase deleted mutant. A total of 178 transcripts were either up- or down-regulated in the mutant when compared to the wild-type strain. Poly(A)polymerase up-regulates the expression of all genes related to the FliA regulon and several previously unknown transcripts, including numerous transporters. Notable down-regulation of genes in the expression of antigen 43 and components of the type 1 fimbriae was detected. The major consequence of the absence of poly(A)polymerase was the accumulation of numerous sRNAs, antisense transcripts, REP sequences and RNA fragments resulting from the processing of entire transcripts. A new algorithm to analyze the position and composition of post-transcriptional modifications based on the sequence of unencoded 3΄-ends, was developed to identify polyadenylated molecules. Overall our results shed new light on the broad spectrum of action of polyadenylation on gene expression and demonstrate the importance of poly(A) dependent degradation to remove structured RNA fragments.

RNA polyadenylation and its consequences in prokaryotes

“…Namely, in contrast to the well-known examples, in which the addition of poly(A) tails to the 3 0 end of prokaryotic RNAs or their decay intermediates promotes RNA turnover and reduces the level of functional RNA, the presence of an active poly(A) polymerase in certain cases can enhance the steady-state transcript level (e.g. those expressed from the E. coli flagellar operon [76] and others [39]). The mechanisms, direct or indirect, by which polyadenylation can increase RNA levels and whether this also enhances gene expression are poorly understood and warrant further analysis.…”

“…These properties may explain why Cs are occasionally incorporated in poly(A) tails [35]. In vivo poly(A) tails were detected at the 3 0 ends of many (but not all) RNA, including primary transcripts, processed RNAs and intermediate products of exonucleolytic degradation [36][37][38][39]. However, folding predictions and searches for conserved motifs potentially present in polyadenylated RNA could not reveal any consensus sequence or structure that could serve as a signal for PAP I to begin poly(A) addition [37].…”

“…B 373: 20180166 expression. The regulatory function of polyadenylation can affect the steady-state levels of mRNAs available for translation either positively or negatively (figure 3 and table 1) [37,39,[74][75][76][77]. Besides its apparently direct role in the regulation of mRNA abundance, polyadenylation can also indirectly influence gene expression controlled by numerous cis-and trans-encoded small RNAs.…”

“…Previous studies have shown that the addition of poly(A) tails has a destabilizing effect on several cis-encoded antisense RNAs known for their role in the control of plasmid replication (e.g. RNAI [17,56] and CopA [78] controlling the copy number of ColE1-type and R1 plasmids, respectively), bacteriophage lambda development (Oop RNA [79]), bacteriophage P4 immunity (CI RNA [80]) and expression of Type I toxin-antitoxin systems (Sok, [81], and others [39]).…”

“…Table 1. Role of polyadenylation in global RNA turnover [39]. Indicated are the numbers of genes that were up-or downregulated in the pcnB mutant when compared with the wild-type (wt) strain.…”