Identification of Hfq-binding RNAs in Caulobacter crescentus

Nadine G Assis; Rodolfo A Ribeiro; Larissa G da Silva; Alexandre M Vicente; Isabelle Hug; Marilis V Marques

doi:10.1080/15476286.2019.1593091

Identification of Hfq-binding RNAs in Caulobacter crescentus

RNA Biol. 2019 Jun;16(6):719-726. doi: 10.1080/15476286.2019.1593091. Epub 2019 Mar 26.

Authors

Nadine G Assis¹, Rodolfo A Ribeiro¹, Larissa G da Silva¹, Alexandre M Vicente¹, Isabelle Hug², Marilis V Marques¹

Affiliations

¹ a Departamento de Microbiologia, Instituto de Ciências Biomédicas , Universidade de São Paulo , São Paulo , Brazil.
² b Biozentrum , University of Basel , Basel , Switzerland.

Abstract

Small RNAs are important for post-transcriptional regulation of gene expression, affecting stability and activity of their target mRNAs. The bacterial Sm-like protein Hfq is required to promote pairing between both RNAs when their sequence complementarity is limited. To provide a first global view on the post-transcriptional landscape of the α-proteobacterium Caulobacter crescentus, we have identified the Hfq-binding RNAs employing High-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP). A total of 261 RNAs, including 3 unannotated RNAs, were successfully identified and classified according to putative function. Moreover, possible interactions between the identified sRNAs with mRNA targets were postulated through computational target predictions.

Keywords: Hfq; RNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Caulobacter crescentus / genetics*
High-Throughput Nucleotide Sequencing
Host Factor 1 Protein / metabolism*
RNA, Messenger / metabolism*
RNA, Small Untranslated / chemistry
RNA, Small Untranslated / metabolism*
Sequence Analysis, RNA

Substances

Host Factor 1 Protein
RNA, Messenger
RNA, Small Untranslated

Grants and funding

This work was supported by São Paulo Research Foundation [FAPESP, grant 2014/04046–8] and Conselho Nacional de Desenvolvimento Científico e Tecnológico [CNPq-Brasil, grants 306558/2013–0 and 307974/2017–0]. During the course of this work, NGA was supported by Undergraduate fellowship from FAPESP [grant 2015/21025–7]; AMV and RAR were supported by Masters fellowship from FAPESP [grants 2014/13552–4 and 2016/06378–3, respectively]; LGS by a postdoctoral fellowship [grant 2015/1461678] from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and MVM was partially supported by CNPq-Brasil.