In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production of the proteins encoded by the mRNA. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the concentrations of its effector molecule. The discovery that modern organisms use RNA to bind small molecules, and discriminate against closely related analogs, expanded the known natural capabilities of RNA beyond its ability to code for proteins, catalyze reactions, or to bind other RNA or protein macromolecules.
In molecular biology, small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs. There are two main classes of snoRNA, the C/D box snoRNAs, which are associated with methylation, and the H/ACA box snoRNAs, which are associated with pseudouridylation. SnoRNAs are commonly referred to as guide RNAs but should not be confused with the guide RNAs that direct RNA editing in trypanosomes or the guide RNAs (gRNAs) used by Cas9 for CRISPR gene editing.
Eukaryotic translation termination factor1 (eRF1), also referred to as TB3-1 or SUP45L1, is a protein that is encoded by the ERF1 gene. In Eukaryotes, eRF1 is an essential protein involved in stop codon recognition in translation, termination of translation, and nonsense mediated mRNA decay via the SURF complex.
Cobalamin riboswitch is a cis-regulatory element which is widely distributed in 5' untranslated regions of vitamin B12 (Cobalamin) related genes in bacteria.
The ykkC/yxkD leader is a conserved RNA structure found upstream of the ykkC and yxkD genes in Bacillus subtilis and related genes in other bacteria. The function of this family is unclear for many years although it has been suggested that it may function to switch on efflux pumps and detoxification systems in response to harmful environmental molecules. The Thermoanaerobacter tengcongensis sequence AE013027 overlaps with that of purine riboswitch suggesting that the two riboswitches may work in conjunction to regulate the upstream gene which codes for TTE0584 (Q8RC62), a member of the permease family.
The fluoride riboswitch is a conserved RNA structure identified by bioinformatics in a wide variety of bacteria and archaea. These RNAs were later shown to function as riboswitches that sense fluoride ions. These "fluoride riboswitches" increase expression of downstream genes when fluoride levels are elevated, and the genes are proposed to help mitigate the toxic effects of very high levels of fluoride.
The pfl RNA motif refers to a conserved RNA structure present in some bacteria and originally discovered using bioinformatics. pfl RNAs are consistently present in genomic locations that likely correspond to the 5' untranslated regions of protein-coding genes. This arrangement in bacteria is commonly associated with cis-regulatory elements. Moreover, they are in presumed 5' UTRs of multiple non-homologous genes, suggesting that they function only in these locations. Additional evidence of cis-regulatory function came from the observation that predicted rho-independent transcription terminators overlap pfl RNAs. This overlap suggests that the alternate secondary structures of pfl RNA and the transcription terminator stem-loops compete with each other, and this is a common mechanism for cis gene control in bacteria.
The psaA RNA motif describes a class of RNAs with a common secondary structure. psaA RNAs are exclusively found in locations that presumably correspond to the 5' untranslated regions of operons formed of psaA and psaB genes. For this reason, it was hypothesized that psaA RNAs function as cis-regulatory elements of these genes. The psaAB genes encode proteins that form subunits in the photosystem I structure used for photosynthesis. psaA RNAs have been detected only in cyanobacteria, which is consistent with their association with photosynthesis.
The yjdF RNA motif is a conserved RNA structure identified using bioinformatics. Most yjdF RNAs are located in bacteria classified within the phylum Bacillota. A yjdF RNA is found in the presumed 5' untranslated region of the yjdF gene in Bacillus subtilis, and almost all yjdF RNAs are found in the 5' UTRs of homologs of this gene. The function of the yjdF gene is unknown, but the protein that it is predicted to encode is classified by the Pfam Database as DUF2992.
Yfr2 is a family of non-coding RNAs. Members of the Yrf2 family have been identified in almost all studied species of cyanobacteria. The family was identified through a bioinformatics screen of published cyanobacterial genomes, having previously been grouped in a family of Yfr2–5.
αr14 is a family of bacterial small non-coding RNAs with representatives in a broad group of α-proteobacteria. The first member of this family (Smr14C2) was found in a Sinorhizobium meliloti 1021 locus located in the chromosome (C). It was later renamed NfeR1 and shown to be highly expressed in salt stress and during the symbiotic interaction on legume roots. Further homology and structure conservation analysis identified 2 other chromosomal copies and 3 plasmidic ones. Moreover, full-length Smr14C homologs have been identified in several nitrogen-fixing symbiotic rhizobia, in the plant pathogens belonging to Agrobacterium species as well as in a broad spectrum of Brucella species. αr14C RNA species are 115-125 nt long and share a well defined common secondary structure. Most of the αr14 transcripts can be catalogued as trans-acting sRNAs expressed from well-defined promoter regions of independent transcription units within intergenic regions (IGRs) of the α-proteobacterial genomes.
αr15 is a family of bacterial small non-coding RNAs with representatives in a broad group of α-proteobacteria from the order Rhizobiales. The first members of this family were found tandemly arranged in the same intergenic region (IGR) of the Sinorhizobium meliloti 1021 chromosome (C). Further homology and structure conservation analysis have identified full-length Smr15C1 and Smr15C2 homologs in several nitrogen-fixing symbiotic rhizobia, in the plant pathogens belonging to Agrobacterium species as well as in a broad spectrum of Brucella species. The Smr15C1 and Smr15C2 homologs are also encoded in tandem within the same IGR region of Rhizobium and Agrobacterium species, whereas in Brucella species the αr15C loci are spread in the IGRs of Chromosome I. Moreover, this analysis also identified a third αr15 loci in extrachromosomal replicons of the mentioned nitrogen-fixing α-proteobacteria and in the Chromosome II of Brucella species. αr15 RNA species are 99-121 nt long and share a well defined common secondary structure consisting of three stem loops. The transcripts of the αr15 family can be catalogued as trans-acting sRNAs encoded by independent transcription units with recognizable promoter and transcription termination signatures within intergenic regions (IGRs) of the α-proteobacterial genomes.
The DUF1646 RNA motif is a conserved RNA structure that was discovered by bioinformatics. One of the two DUF1646 RNAs in Enterococcus faecalis was independently detected by term-seq. Data from both discoveries suggest that DUF1646 RNAs are cis-regulatory RNAss, and that at least some DUF1646 RNAs use Rho-independent transcription terminators as their mechanism to regulate gene expression.
Non-coding RNAs have been discovered using both experimental and bioinformatic approaches. Bioinformatic approaches can be divided into three main categories. The first involves homology search, although these techniques are by definition unable to find new classes of ncRNAs. The second category includes algorithms designed to discover specific types of ncRNAs that have similar properties. Finally, some discovery methods are based on very general properties of RNA, and are thus able to discover entirely new kinds of ncRNAs.
The Fibro-purF RNA motif is a conserved RNA structure that was discovered by bioinformatics. Fibro-purF motif RNAs are found in Fibrobacterota, a group of bacteria that are common in cow rumen. Additionally, the RNAs are found in metagenomic sequences of DNA isolated from cow rumen.
IS605-orfB RNA motifs refer to conserved RNA or DNA structures that were discovered by bioinformatics. Although such motifs were published as a RNA candidates, there is some reason to suspect that they might function as a single-stranded DNA. In terms of secondary structure, RNA and DNA are difficult to distinguish when only sequence information is available. If the motifs function as RNA, they likely are small RNAs, that are independently transcribed.
The terC RNA motif is a conserved RNA structure that was discovered by bioinformatics. terC motif RNAs are found in Pseudomonadota, within the sub-lineages Alphaproteobacteria and Pseudomonadales.
The uup RNA motif is a conserved RNA structure that was discovered by bioinformatics. uup motif RNAs are found in Bacillota and Gammaproteobacteria.
The Zeta-pan RNA motif is a conserved RNA structure that was discovered by bioinformatics. Zeta-pan motif RNAs are found in Zetaproteobacteria.
An RNA motif is a description of a group of RNAs that have a related structure. RNA motifs consist of a pattern of features within the primary sequence and secondary structure of related RNAs. Thus, it extends the concept of a sequence motif to include RNA secondary structure. The term "RNA motif" can refer both to the pattern and to the RNA sequences that match it.
