Small RNAs making a small protein

Morita, Teppei; Aiba, Hirofumi

doi:10.1073/pnas.0710634105

Cited by 12 publications

(8 citation statements)

References 16 publications

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“…Certain genomic loci express a bifunctional RNA that exert biological activity as both an RNA molecule and a small peptide (10). One such bifunctional RNA is a 227-nt long RNA called SgrS (sugar-transport related small RNA) that plays an important role responding to metabolic stress in E. coli (11, 12). A clear demonstration that the biological activity of a lncRNA is driven by the RNA molecule itself should be the gold standard for the characterization of bona fide functional lncRNAs (discussed in greater detail below).…”

Section: Introductionmentioning

confidence: 99%

Immunobiology of Long Noncoding RNAs

Atianand

Caffrey

Fitzgerald

2017

Annu. Rev. Immunol.

399

359

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The discovery of long noncoding RNAs (lncRNA) has provided a new perspective on gene regulation in diverse biological contexts. lncRNAs are remarkably versatile molecules that interact with RNA, DNA, or proteins to promote or restrain the expression of protein-coding genes. Activation of immune cells is associated with dynamic changes in expression of genes, the products of which combat infectious microorganisms, initiate repair, and resolve inflammatory responses in cells and tissues. Recent evidence indicates that lncRNAs play important roles in directing the development of diverse immune cells and controlling the dynamic transcriptional programs that are a hallmark of immune cell activation. The importance of these molecules is underscored by their newly recognized roles in inflammatory diseases. In this review, we discuss the contribution of lncRNAs in the development and activation of immune cells and their roles in immune-related diseases. We also discuss challenges faced in identifying biological functions for this large and complex class of genes

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Section: Introductionmentioning

confidence: 99%

Immunobiology of Long Noncoding RNAs

Atianand

Caffrey

Fitzgerald

2017

Annu. Rev. Immunol.

399

359

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“…At least seven different proteins are involved in the transcriptional control (reviewed in [ 7 ]). Moreover, several research groups have identified and characterized the function of the sgrRST -system, which creates a sophisticated posttranscriptional feedback regulation mechanism of glucose transport during intracellular Glc6-P or Fru6-P accumulation [ 23 , 24 , 26 , 27 , 34 , 35 ]. Whereas the small regulatory RNA SgrS destabilizes ptsG m-RNA, the function of the small regulatory peptide SgrT, which is simultaneously encoded by the sgrS gene, has not been very well characterized thus far.…”

Section: Resultsmentioning

confidence: 99%

Characterization of the Interaction Between the Small Regulatory Peptide SgrT and the EIICBGlc of the Glucose-Phosphotransferase System of E. coli K-12

Kosfeld

Jahreis

2012

Metabolites

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Escherichia coli is a widely used microorganism in biotechnological processes. An obvious goal for current scientific and technical research in this field is the search for new tools to optimize productivity. Usually glucose is the preferred carbon source in biotechnological applications. In E. coli, glucose is taken up by the phosphoenolpyruvate-dependent glucose phosphotransferase system (PTS). The regulation of the ptsG gene for the glucose transporter is very complex and involves several regulatory proteins. Recently, a novel posttranscriptional regulation system has been identified which consists of a small regulatory RNA SgrS and a small regulatory polypeptide called SgrT. During the accumulation of glucose-6-phosphate or fructose-6-phosphate, SgrS is involved in downregulation of ptsG mRNA stability, whereas SgrT inhibits glucose transport activity by a yet unknown mechanism. The function of SgrS has been studied intensively. In contrast, the knowledge about the function of SgrT is still limited. Therefore, in this paper, we focused our interest on the regulation of glucose transport activity by SgrT. We identified the SgrT target sequence within the glucose transporter and characterized the interaction in great detail. Finally, we suggest a novel experimental approach to regulate artificially carbohydrate uptake in E. coli to minimize metabolic overflow in biotechnological applications.

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“…However, the significance of sRNAs is still elusive. Recently, Morita and Aiba [21] suggested that sRNA not only act through base-pairing mechanism but also serve as an mRNA template for small functional proteins to deal with metabolic stress. Nevertheless, many such ’RNA within RNA‘ (sRNAs) molecules warrant further investigations in order to understand their cryptic functions.…”

Section: Discussionmentioning

confidence: 99%

Regulatory elements in the 5’region of 16SrRNA gene of Bacillus sp. strain SJ-101

Singh¹,

Al-Khedhairy²,

Alarifi³

et al. 2009

Bioinformation

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Advancement in bioinformatics with the development of computational tools has enabled the insilico prediction and identification of transcription regulatory factors and other genetic elements with great ease. In this study, computational analysis of sequence homology of 546 bp 5’ region of 16SrRNA gene of Bacillus sp. strain SJ101 resulted in identification of promoterlike sequences within the rrn gene. Using BPROM tool, the regulatory motifs like -35 and -10 boxes were mapped at 392 and 411 positions, respectively. Furthermore, the cis-acting elements as the binding sites for transcription factors (TF) cpxR and argR were identified at positions 413 and 416 at the upstream of an open reading frame (ORF). The probable functions of the putative TFs were predicted through the UniProt/SwissProt protein database. Search for the ShineDalgarno sequence (SD) found the presence of highly conserved SD sequence (AATACC), and a short 42 bp coding sequence/ORF bounded with characteristic transcription start site (AAC) and a stop codon (TGA) at positions 426 and 465 downstream to the promoter elements. A 13 amino acid long translation product of a short ORF has exhibited 100% homology with protein sequences of Bacillus spp., while showing some degree of polymorphism with other reference strains. The comparative homology of the small protein exhibited maximum similarity with Prolyl4 hydroxylase of Chlamydomonas reinhardtii with 4.11 ZSCORE. The highly conserved regulatory elements and the putative ORF predicted within the 16SrRNA gene may help understand the role of relatively unexplored short ORFs within rrn operon, and their functional products in genetic regulatory mechanisms in eubacteria.

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Small RNAs making a small protein

Cited by 12 publications

References 16 publications

Immunobiology of Long Noncoding RNAs

Immunobiology of Long Noncoding RNAs

Characterization of the Interaction Between the Small Regulatory Peptide SgrT and the EIICBGlc of the Glucose-Phosphotransferase System of E. coli K-12

Regulatory elements in the 5’region of 16SrRNA gene of Bacillus sp. strain SJ-101

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