The Actino-pnp RNA motif is a conserved structure found in Actinomycetota that is apparently in the 5' untranslated regions of genes predicted to encode exoribonucleases. The RNA element's function is likely analogous to an RNA structure found upstream of polynucleotide phosphorylase genes in E. coli and related enterobacteria. In this latter system, the polynucleotide phosphorlyase gene regulates its own expression levels by a feedback mechanism that involves its activity upon the RNA structure. However, the E. coli RNA appears to be structurally unrelated to the Actino-pnp motif.
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 Bacteroides-1 RNA motif is a conserved RNA structure identified in bacteria within the genus Bacteroides. The RNAs are typically found downstream of of genes that participate in the synthesis of exopolysaccharides of unknown types. It is possible that Bacteroides-1 RNAs regulate the upstream genes, but since this mode of regulation is unusual in bacteria, it is more likely that the structure functions as a non-coding RNA.
The Chlorobi-RRM RNA motif is a conserved RNA structure identified by bioinformatics. It is found within bacteria in the phylum Chlorobiota, and is exclusively detected in the presumed 5' untranslated regions of genes that encode putative RNA-binding proteins. Since many RNA-binding proteins regulate their own expression in a feedback mechanism by binding or acting up their 5' UTR, it was proposed that the Chlorobi-RRM is a component in an analogous feedback mechanism. Structurally, the motif consists of two stem-loops, the second of which might function as a rho-independent transcription terminator.
The Downstream-peptide motif refers to a conserved RNA structure identified by bioinformatics in the cyanobacterial genera Synechococcus and Prochlorococcus and one phage that infects such bacteria. It was also detected in marine samples of DNA from uncultivated bacteria, which are presumably other species of cyanobacteria.
The L17 downstream element RNA motif is a conserved RNA structure identified in bacteria by bioinformatics. All known L17 downstream elements were detected immediately downstream of genes encoding the L17 subunit of the ribosome, and therefore might be in the 3' untranslated regions of these genes. The element is found in a variety of lactic acid bacteria and in the genus Listeria.
The Lacto-usp RNA motif is a conserved RNA structure identified in bacteria by bioinformatics. Lacto-usp RNAs are found exclusively in lactic acid bacteria, and exclusively in the possible 5′ untranslated regions of operons that contain a hypothetical gene and a usp gene. The usp gene encodes the universal stress protein. It was proposed that the Lacto-usp might correspond to the 6S RNA of the relevant species, because four of five of these species lack a predicted 6S RNA, and 6S RNAs commonly occur in 5′ UTRs of usp genes. However, given that the Lacto-usp RNA motif is much shorter than the standard 6S RNA structure, the function of Lacto-usp RNAs remains unclear.
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 Moco-II RNA motif is a conserved RNA structure identified by bioinformatics. However, only 8 examples of the RNA motif are known. The RNAs are potentially in the 5' untranslated regions of genes related to molybdenum cofactor (Moco), specifically a gene that encodes a molybdenum-binding domain and a nitrate reductase, which uses Moco as a cofactor. Thus the RNA might be involved in the regulation of genes based on Moco levels. Reliable predictions of Moco-II RNAs are restricted to deltaproteobacteria, but a Moco-II RNA might be present in a betaproteobacterial species. The Moco RNA motif is another RNA that is associated with Moco, and its complex secondary structure and genetic experiments have led to proposals that it is a riboswitch. However, the simpler structure of the Moco-II RNA motif is less typical of riboswitches. Moco-II RNAs are typically followed by a predicted rho-independent transcription terminator.
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 msiK RNA motif describes a conserved RNA structure discovered using bioinformatics. The RNA is always found in the presumed 5' untranslated regions of genes annotated as msiK, and is therefore hypothesized to be an RNA-based cis-regulatory element that regulates these genes.
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.
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 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 Pseudomon-groES RNA motif is a conserved RNA structure identified in certain bacteria using bioinformatics. It is found in most species within the family Pseudomonadaceae, and is consistently located in the 5' untranslated regions of operons that contain groES genes. RNA transcripts of the groES genes in Pseudomonas aeruginosa where shown experimentally to be initiated at one of two start sites, from promoters called "P1" and "P2". The Pseudomon-groES RNA is in the 5' UTR of transcripts initiated from the P1 site, but is truncated in P2 transcripts. groES genes are involved in the cellular response to heat shock, but it is not thought that the Pseudomonas-groES RNA motif is involved in heat shock regulation. However, it is thought that the motif might regulate groES genes in response to other stimuli.
The rmf RNA motif is a conserved RNA structure that was originally detected using bioinformatics. rmf RNAs are consistently foundwithin species classified into the genus Pseudomonas, and is located potentially in the 5′ untranslated regions of rmf genes. These genes encodes the ribosome modulation factor protein, which affects the translation of genes by modifying ribosome structure in response to stress such as starvation. This ribosome modulation is a part of the stringent response in bacteria. The likely biological role of rmf RNAs is ambiguous. Since the RNA could be in the 5′ UTRs of protein-coding genes, it was hypothesized that it functions as a cis-regulatory element. This hypothesis is bolstered by the observation that ribosome modulation factor binds ribosomal RNA, and many cis-regulatory RNAs called ribosomal protein leaders participate in a feedback regulation mechanism by binding to proteins that normally bind to ribosomal RNA. However, since rmf RNAs are not very close to the rmf genes, they might function as non-coding RNAs.
The rne-II RNA motif is a conserved RNA structure identified using bioinformatics. It is detected only in species classified within the family Pseudomonadaceae, a group of gammaproteobacteria. rne-II RNAs are consistently located in the presumed 5' untranslated regions of genes that encode Ribonuclease E. The RNase E 5' UTR element is a previously identified RNA structure that is also found in the 5' UTRs of RNase E genes. However, the latter motif is found only in enterobacteria, and the two motifs have apparently unrelated structure. In view of their differences, it was hypothesized that rne-II RNAs fulfill the same functional role as RNase E 5' UTR elements, which is to regulate the levels of RNase E proteins by acting as a substrate for RNase E. Thus, when concentrations of RNase E are high, they will degrade their own messenger RNA.
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 sucC RNA motif is a conserved RNA structure discovered using bioinformatics. sucC RNAs are found in the genus Pseudomonas. They ae consistently found in possible 5' untranslated regions of sucC genes. These genes encode Succinyl coenzyme A synthetase, and are hypothesised to be regulated by the sucC RNAs. sucC genes participate in the citric acid cycle, and another gene involved in the citric acid cycle, sucA, is also predicted to be regulated by a conserved RNA structure.
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.
