Most RNAs regulating ribosomal protein biosynthesis in Escherichia coli are narrowly distributed to Gammaproteobacteria

Fu, Yang; Deiorio-Haggar, Kaila; Anthony, Jon; Meyer, Michelle M.

doi:10.1093/nar/gkt055

Cited by 83 publications

(108 citation statements)

References 101 publications

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“…3). The similar phylogenetic distribution has been previously found for the 5 ′ UTRs of the S10 (Allen et al 1999) and rpsA operons (Boni et al 2001;Tchufistova et al 2003), while the rpsB-tsf regulatory RNA showed more wide conservation including Psedomonadaceae (Aseev et al 2009;Fu et al 2013). The found phylogenetic similarity implies that the predicted folding of the rplY 5 ′ UTR might have biological relevance (Fig.…”

Section: Resultssupporting

confidence: 84%

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Regulation of the rplY gene encoding 5S rRNA binding protein L25 in Escherichia coli and related bacteria

Aseev

Bylinkina

Boni

2015

RNA

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Ribosomal protein (r-protein) L25 is one of the three r-proteins (L25, L5, L18) that interact with 5S rRNA in eubacteria. Specific binding of L25 with a certain domain of 5S r-RNA, a so-called loop E, has been studied in detail, but information about regulation of L25 synthesis has remained totally lacking. In contrast to the rplE (L5) and rplR (L18) genes that belong to the polycistronic spc-operon and are regulated at the translation level by r-protein S8, the rplY (L25) gene forms an independent transcription unit. The main goal of this work was to study the regulation of the rplY expression in vivo. We show that the rplY promoter is down-regulated by ppGpp and its cofactor DksA in response to amino acid starvation. At the level of translation, the rplY expression is subjected to the negative feedback control. The 5 ′ -untranslated region of the rplY mRNA comprises specific sequence/structure features, including an atypical SD-like sequence, which are highly conserved in a subset of gammaproteobacterial families. Despite the lack of a canonical SD element, the rplY'-'lacZ single-copy reporter showed unusually high translation efficiency. Expression of the rplY gene in trans decreased the translation yield, indicating the mechanism of autogenous repression. Site-directed mutagenesis of the rplY 5 ′ UTR revealed an important role of the conserved elements in the translation control. Thus, the rplY expression regulation represents one more example of regulatory pathways that control ribosome biogenesis in Escherichia coli and related bacteria.

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Section: Resultssupporting

confidence: 84%

“…Regulation of ribosomal protein L25 synthesis www.rnajournal.org 853 bacterial phyla has been found in a few cases (Fu et al 2013).…”

Section: Resultsmentioning

confidence: 99%

Regulation of the rplY gene encoding 5S rRNA binding protein L25 in Escherichia coli and related bacteria

Aseev

Bylinkina

Boni

2015

RNA

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“…According to the recent study on RNA motifs regulating r-protein biosynthesis (Fu et al 2013), such universal occurrence puts the S6S18CBM motif among most widespread cis-regulatory motifs in bacterial r-protein operon leaders.…”

Section: Thementioning

confidence: 99%

“…This interaction inhibits translation initiation by occlusion of a ribosome binding site or ribosome entrapment, permitting maintenance of the balance of r-protein and rRNA levels. In Escherichia coli, there are 12 known distinct mRNA regulatory elements that control 11 r-protein operons, i.e., α, spc, S10, str, rpsT, rpsB-tsf, rspA, rpmI-rplT, rpsO, rplK-rplA, and rplJ-rplL (Fu et al 2013). …”

Section: Introductionmentioning

confidence: 99%

“…Numerous studies have shown that the similarity between these two types of binding sites is detectable at the structural level (Serganov et al 2003;Merianos et al 2004;Nevskaya et al 2005), and sometimes they also share common sequence patterns (Olins and Nomura 1981;Iben and Draper 2008). The regulatory sites can be conserved in closely related bacteria (Robert and Brakier-Gingras 2001;Aseev et al 2008), between different bacterial phyla (Fu et al 2013), or even between domains of life (Kraft et al 1999), but in many cases they appear to have originated independently in the individual taxonomic groups (Allen et al 1999;Springer and Portier 2003).…”

Section: Introductionmentioning

confidence: 99%

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S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA

Matelska

Purta

Panek

et al. 2013

RNA

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Prokaryotic ribosomal protein genes are typically grouped within highly conserved operons. In many cases, one or more of the encoded proteins not only bind to a specific site in the ribosomal RNA, but also to a motif localized within their own mRNA, and thereby regulate expression of the operon. In this study, we computationally predicted an RNA motif present in many bacterial phyla within the 5 ′ untranslated region of operons encoding ribosomal proteins S6 and S18. We demonstrated that the S6:S18 complex binds to this motif, which we hereafter refer to as the S6:S18 complex-binding motif (S6S18CBM). This motif is a conserved CCG sequence presented in a bulge flanked by a stem and a hairpin structure. A similar structure containing a CCG trinucleotide forms the S6:S18 complex binding site in 16S ribosomal RNA. We have constructed a 3D structural model of a S6:S18 complex with S6S18CBM, which suggests that the CCG trinucleotide in a specific structural context may be specifically recognized by the S18 protein. This prediction was supported by site-directed mutagenesis of both RNA and protein components. These results provide a molecular basis for understanding protein-RNA recognition and suggest that the S6S18CBM is involved in an auto-regulatory mechanism.

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Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families

Barquist

Burge

Gardner

2016

CP in Bioinformatics

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Emerging high-throughput technologies have led to a deluge of putative non-coding RNA (ncRNA) sequences identified in a wide variety of organisms. Systematic characterization of these transcripts will be a tremendous challenge. Homology detection is critical to making maximal use of functional information gathered about ncRNAs: identifying homologous sequence allows us to transfer information gathered in one organism to another quickly and with a high degree of confidence. ncRNA presents a challenge for homology detection, as the primary sequence is often poorly conserved and de novo secondary structure prediction and search remains difficult. This protocol introduces methods developed by the Rfam database for identifying "families" of homologous ncRNAs starting from single "seed" sequences using manually curated sequence alignments to build powerful statistical models of sequence and structure conservation known as covariance models (CMs), implemented in the Infernal software package. We provide a step-bystep iterative protocol for identifying ncRNA homologs, then constructing an alignment and corresponding CM. We also work through an example for the bacterial small RNA MicA, discovering a previously unreported family of divergent MicA homologs in genus Xenorhabdus in the process.

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Most RNAs regulating ribosomal protein biosynthesis in Escherichia coli are narrowly distributed to Gammaproteobacteria

Cited by 83 publications

References 101 publications

Regulation of the rplY gene encoding 5S rRNA binding protein L25 in Escherichia coli and related bacteria

Regulation of the rplY gene encoding 5S rRNA binding protein L25 in Escherichia coli and related bacteria

S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA

Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families

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