Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes

被引:96
作者
Sittka, Alexandra [1 ]
Sharma, Cynthia M. [1 ]
Rolle, Katarzyna [1 ]
Vogel, Joerg [1 ]
机构
[1] Max Planck Inst Infect Biol, D-10117 Berlin, Germany
关键词
Hfq; small RNA; noncoding RNA; pyrosequencing; RNA processing; ESCHERICHIA-COLI-HFQ; SM-LIKE PROTEIN; ENVELOPE STRESS-RESPONSE; SMALL NONCODING RNA; MESSENGER-RNA; CRYSTAL-STRUCTURE; EXPRESSION; RNOMICS; DOMAIN; GENES;
D O I
10.4161/rna.6.3.8332
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The bacterial Sm-like protein, Hfq, is a key factor for the stability and function of small non-coding RNAs (sRNAs) in Escherichia coli. Homologues of this protein have been predicted in many distantly related organisms yet their functional conservation as sRNA-binding proteins has not entirely been clear. TO address this, we expressed in Salmonella the Hfq proteins of two eubacteria (Neisseria meningitides, Aquifex aeolicus) and an archaeon (Methanocaldococcus jannaschii), and analyzed the associated RNA by deep sequencing. This in vivo approach identified endogenous Salmonella sRNAs as a major target of the foreign Hfq proteins. New Salmonella sRNA species were also identified, and some of these accumulated specifically in the presence of a foreign Hfq protein. In addition, we observed specific RNA processing defects, e.g., suppression of precursor processing of SraH sRNA by Methanocaldococcus Hfq, or aberrant accumulation of extracytoplasmic target mRNAs of the Salmonella GcvB, MicA or RybB sRNAs. Taken together, our study provides evidence of a conserved inherent sRNA-binding property of Hfiq, which may facilitate the lateral transmission of regulatory sRNAs among distantly related species. It also suggests that the expression of heterologous RNA-binding proteins combined with deep sequencing analysis of RNA ligands can be used as a molecular tool to dissect individual steps of RNA metabolism in vivo.
引用
收藏
页码:266 / 275
页数:10
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