In the field of molecular biology the 6S RNA is a non-coding RNA that was one of the first to be identified and sequenced. What it does in the bacterial cell was unknown until recently. In the early 2000s scientists found out the function of 6S RNA to be as a regulator of sigma 70-dependent gene transcription. All bacterial RNA polymerases have a subunit called a sigma factor. The sigma factors are important because they control how DNA promoter binding and RNA transcription start sites. Sigma 70 was the first one to be discovered in Escherichia coli.
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 asd RNA motif is a conserved RNA structure found in certain lactic acid bacteria. The asd motif was detected by bioinformatics and an individual asd RNA in Streptococcus pyogenes was detected by microarray and northern hybridization experiments as a 170-nucleotide molecule called "SR914400". The transcription start site determined for SR914400 corresponds to the 5′-end of the molecule shown in the consensus diagram.
The Bacteroidales-1 RNA motif is a conserved RNA structure identified by bioinformatics. It has been identified only in bacteria within the order (biology) Bacteroidales. Its presumed length is marked by a promoter on one end that conforms to an alternate consensus sequence that is common in the phylum Bacteroidota, and its 3′ end is indicated by predicted transcription terminators. It is often located downstream of a gene that encodes the L20 ribosomal subunit, although it is unclear whether there is a functional reason underlying this apparent association.
The c4 antisense RNA is a non-coding RNA used by certain phages that infect bacteria. It was initially identified in the P1 and P7 phages of E. coli. The identification of c4 antisense RNAs solved the mystery of the mechanism for regulation of the ant gene, which is an anti-repressor.
The SAM–SAH riboswitch is a conserved RNA structure in certain bacteria that binds S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) and is therefore presumed to be a riboswitch. SAM–SAH riboswitches do not share any apparent structural resemblance to known riboswitches that bind SAM or SAH. The binding affinities for both compounds are similar, but binding for SAH is at least somewhat stronger. SAM–SAH riboswitches are exclusively found in Rhodobacterales, an order of alphaproteobacteria. They are always found in the apparent 5' untranslated regions of metK genes, which encode the enzyme that synthesizes SAM.
The Cyano-2 RNA motif is a conserved RNA structure identified by bioinformatics. Cyano-2 RNAs are found in Cyanobacterial species classified within the genus Synechococcus. Many terminal loops in the two conserved stem-loops contain the nucleotide sequence GCGA, and these sequences might in some cases form stable GNRA tetraloops. Since the two stem-loops are somewhat distant from one another it is possible that they represent two independent non-coding RNAs that are often or always co-transcribed. The region one thousand base pairs upstream of predicted Cyano-2 RNAs is usually devoid of annotated features such as RNA or protein-coding genes. This absence of annotated genes within one thousand base pairs is relatively unusual within bacteria.
The Lnt RNA motif refers to a conserved RNA structure found in certain bacteria. Specifically, Lnt RNAs are known only in species within the phylum Chlorobiota, and are located in the possible 5' untranslated regions of genes that are annotated as encoding apolipoprotein N-acyltransferase enzymes. There is some doubt as to whether the indicated motif is transcribed as RNA, or whether its reverse complement is transcribed. If the reverse complement is transcribed it would potentially in 5' UTRs of genes encoding bacteriochlorophyll A, and would be close to the start codon of those genes.
The wcaG RNA motif is an RNA structure conserved in some bacteria that was detected by bioinformatics. wcaG RNAs are found in certain phages that infect cyanobacteria. Most known wcaG RNAs were found in sequences of DNA extracted from uncultivated marine bacteria. wcaG RNAs might function as cis-regulatory elements, in view of their consistent location in the possible 5' untranslated regions of genes. It was suggested the wcaG RNAs might further function as riboswitches.
The mraW RNA motif is a conserved, structured RNA found in certain bacteria. Specifically, it is predicted in many, though not all, species of actinobacteria, and especially within the genus Mycobacterium. Structurally, the motif consists of a hairpin with a highly conserved terminal loop sequence. mraW RNAs are consistently in the presumed 5' untranslated regions of mraW genes. These mraW genes likely form operons with immediately downstream ftsI genes, and multiple types of mur genes. These genes are associated with peptidoglycan synthesis, and it was hypothesized that the mraW RNA motif might regulate these genes.
The pan RNA motif defines a conserved RNA structure that was identified using bioinformatics. pan motif RNAs are present in three phyla: Chloroflexota, Bacillota, and Pseudomonadota, although within the latter phylum they are only known in deltaproteobacteria. A pan RNA is present in the Firmicute Bacillus subtilis, which is one of the most extensively studied bacteria.
PhotoRC RNA motifs refer to conserved RNA structures that are associated with genes acting in the photosynthetic reaction centre of photosynthetic bacteria. Two such RNA classes were identified and called the PhotoRC-I and PhotoRC-II motifs. PhotoRC-I RNAs were detected in the genomes of some cyanobacteria. Although no PhotoRC-II RNA has been detected in cyanobacteria, one is found in the genome of a purified phage that infects cyanobacteria. Both PhotoRC-I and PhotoRC-II RNAs are present in sequences derived from DNA that was extracted from uncultivated marine bacteria.
The Polynucleobacter-1 RNA motif is a conserved RNA structure that was identified by bioinformatics. The RNA structure is predominantly located in genome sequences derived from DNA extracted from uncultivated marine samples. However it was also predicted in the genome of Polynucleobacter species QLW-P1DMWA-1, a kind of betaproteobacteria. The RNAs are often located near to a conserved gene that might be homologous to a gene found in a phage that infects cyanobacteria. However, it is unknown if the RNA is used by phages.
The potC RNA motif is a conserved RNA structure discovered using bioinformatics. The RNA is detected only in genome sequences derived from DNA that was extracted from uncultivated marine bacteria. Thus, this RNA is present in environmental samples, but not yet found in any cultivated organism. potC RNAs are located in the presumed 5' untranslated regions of genes predicted to encode either membrane transport proteins or peroxiredoxins. Therefore, it was hypothesized that potC RNAs are cis-regulatory elements, but their detailed function is unknown.
The radC RNA motif is a conserved RNA structure identified by bioinformatics. The radC RNA motif is found in certain bacteria where it is consistent located in the presumed 5' untranslated regions of genes whose encoded proteins bind DNA are interact with other proteins that bind DNA. These proteins include integrases, methyltransferases that might methylate DNA, proteins that inhibit restriction enzymes and radC genes. Although radC genes were thought to encode DNA repair proteins, this conclusion was based on mutation data that was later shown to affect a different gene. However, it is still possible that radC genes play some DNA-related role. No radC RNAs have been detected in any purified phage whose sequence was available as of 2010, although integrases are often used by phages.
The SAM-Chlorobi RNA motif is a conserved RNA structure that was identified by bioinformatics. The RNAs are found only in bacteria classified as within the phylum Chlorobiota. These RNAs are always in the 5' untranslated regions of operons that contain metK and ahcY genes. metK genes encode methionine adenosyltransferase, which synthesizes S-adenosyl methionine (SAM), and ahcY genes encode S-adenosylhomocysteine hydrolase, which degrade the related metabolite S-Adenosyl-L-homocysteine (SAH). In fact all predicted metK and ahcY genes within Chlorobiota bacteria as of 2010 are preceded by predicted SAM-Chlorobi RNAs. Predicted promoter sequences are consistently found upstream of SAM-Chlorobi RNAs, and these promoter sequences imply that SAM-Chlorobi RNAs are indeed transcribed as RNAs. The promoter sequences are commonly associated with strong transcription in the phyla Chlorobiota and Bacteroidota, but are not used by most lineages of bacteria. The placement of SAM-Chlorobi RNAs suggests that they are involved in the regulation of the metK/ahcY operon through an unknown mechanism.
The Termite-leu RNA motif is a conserved RNA structure discovered by bioinformatics. It is found only in DNA sequences extracted from uncultivated bacteria living in termite hindguts, and has not yet been detected in any known cultivated organism. In many cases, Termite-leu RNAs are found in the likely 5′ untranslated regions of multive genes related to the synthesis of the amino acid leucine. However, in several cases it is not found in this type of location. Therefore, it was considered ambiguous as to whether Termite-leu RNAs constitute cis-regulatory elements.
The traJ-II RNA motif is a conserved RNA structure discovered in bacteria by using bioinformatics. traJ-II RNAs appear to be in the 5' untranslated regions of protein-coding genes called traJ, which functions in the process of bacterial conjugation. A previously identified motif known as TraJ 5' UTR is also found upstream of traJ genes functions as the target of FinP antisense RNAs, so it is possible that traJ-II RNAs play a similar role as targets of an antisense RNA. However, some sequence features within the traJ-II RNA motif suggest that the biological RNA might be transcribed from the reverse-complement strand. Thus is it unclear whether traJ-II function as cis-regulatory elements. traJ-II RNAs are found in a variety of Pseudomonadota.
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.
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.
