Landscape of RNA polyadenylation in E. coli

Alexandre Maes, Céline Gracia, Nicolas Innocenti, Kaiyang Zhang, Erik Aurell, Eliane Hajnsdorf*

*Corresponding author for this work

Research output: Contribution to journalArticleScientificpeer-review

7 Citations (Scopus)
207 Downloads (Pure)

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 froma poly(A)polymerase deletedmutant. 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.

Original languageEnglish
Pages (from-to)2746-2756
Number of pages11
JournalNucleic Acids Research
Volume45
Issue number5
DOIs
Publication statusPublished - 17 Mar 2017
MoE publication typeA1 Journal article-refereed

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    Maes, A., Gracia, C., Innocenti, N., Zhang, K., Aurell, E., & Hajnsdorf, E. (2017). Landscape of RNA polyadenylation in E. coli. Nucleic Acids Research, 45(5), 2746-2756. https://doi.org/10.1093/nar/gkw894