The 23S methyl RNA motif is a conserved RNA structure found upstream of genes predicted to encode rRNA methyltransferases, possibly for 23S rRNA. However, in one case it is far from the rRNA methyltransferase gene. Nonetheless, it was proposed that this RNA could be a cis-regulatory element, an attractive hypothesis in view of the fact that rRNA methyltransferases can bind RNA, and therefore presumably the 23S methyl RNA. This regulatory strategy is common in bacteria to control levels of ribosomal subunits, using RNA motifs called ribosomal leaders. Additionally, 23S methyl RNAs have rho-independent transcription terminators downstream, which could be a mechanism of regulation.
The Bacillaceae-1 RNA motif is a conserved RNA structure identified by bioinformatics within bacteria in the family bacillaceae. The RNA is presumed to operate as a non-coding RNA, and is sometimes adjacent to operons containing ribosomal RNAs. The most characteristic feature is two terminal loops that have the nucleotide consensus RUCCU, where R is either A or G. The motif might be related to the Desulfotalea-1 RNA motif, as the motifs share some similarity in conserved features, and the Desulfotalea-1 RNA motif is also sometimes adjacent to ribosomal RNA operons.
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 Bacteroidetes, 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 Chlorobi-RRM RNA motif is a conserved RNA structure identified by bioinformatics. It is found within bacteria in the phylum Chlorobi, 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 Clostridiales-1 RNA motif is a conserved RNA structure identified by bioinformatics. It is a four-stem structure common in bacteria that inhabit the human gut and is also found in a variety of bacteria classified within the order Clostridiales. Its function is unknown.
The Collinsella-1 RNA motif denotes a particular conserved RNA structure discovered by bioinformatics. Of the six sequences belonging to this motif that were originally identified, five are from uncultivated bacteria residing in the human gut, while only the sixth is in a cultivated species, Collinsella aerofaciens. The evidence supporting the stem-loops designated as "P1" and "P2" is ambiguous.
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 Flavo-1 RNA motif is a conserved RNA structure that was identified by bioinformatics. The vast majority of Flavo-1 RNAs are found in Flavobacteria, but some were detected in the phylum Bacteroidetes, which contains Flavobacteria, or the phylum Spirochaetes, which is evolutionarily related to Bacteroidetes. It was presumed that Flavo-1 RNAs function as non-coding RNAs.
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 Chlorobi, 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 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-1 RNA motif is a conserved RNA identified by bioinformatics. It is used by most species whose genomes have been sequenced and that are classified within the genus Pseudomonas, and is also present in Azotobacter vinelandii, a closely related species. It is presumed to function as a non-coding RNA. Pseudomon-1 RNAs consistently have a downstream rho-independent transcription terminator.
The Pseudomon-Rho RNA motif refers to a conserved RNA structure that was discovered using bioinformatics. The RNAs that conform to this motif are found in species within the genus Pseudomonas, as well as the related Azotobacter vinelandii. They are consistently located in what could be the 5' untranslated regions of genes that encode the Rho factor protein, and this arrangement in bacteria suggested that Pseudomon-Rho RNAs might be cis-regulatory elements that regulate concentrations of the Rho protein.
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 Chlorobi. 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 Chlorobi 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 Chlorobi and Bacteroidetes, 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 Ssbp, Topoisomerase, Antirestriction, XerDC Integrase RNA motif is a conserved RNA-like structure identified using bioinformatics. STAXI RNAs are located near to genes encoding proteins that interact with DNA or are associated with such proteins. This observation raised the possibility that instances of the STAXI motif function as single-stranded DNA molecules, perhaps during DNA replication or DNA repair. On the other hand, STAXI motifs often contain terminal loops conforming to the stable UNCG tetraloop, but the DNA version of this tetraloop (TNCG) is not especially stable. The STAXI motif consists of a simple pseudoknot structure that is repeated two or more times.
The sucA-II RNA motif is a conserved RNA structure identified by bioinformatics. It is consistently found in the presumed 5' untranslated regions of sucA genes, which encode Oxoglutarate dehydrogenase enzymes that participate in the citric acid cycle. Given this arrangement, sucA-II RNAs might regulate the downstream sucA gene. This genetic arrangement is similar to the previously reported sucA RNA motif. However, sucA-II RNAs are found only in bacteria classified within the genus Pseudomonas, whereas the previously reported motif is found only in betaproteobacteria.
αr35 is a family of bacterial small non-coding RNAs with representatives in a reduced group of α-proteobacteria from the order Hyphomicrobiales. The first member of this family (Smr35B) was found in a Sinorhizobium meliloti 1021 locus located in the symbiotic plasmid B (pSymB). Further homology and structure conservation analysis have identified full-length SmrB35 homologs in other legume symbionts, as well as in the human and plant pathogens Ochrobactrum anthropi and Agrobacterium tumefaciens, respectively. αr35 RNA species are 139-142 nt long and share a common secondary structure consisting of two stem loops and a well conserved rho independent terminator. Most of the αr35 transcripts can be catalogued as trans-acting sRNAs expressed from well-defined promoter regions of independent transcription units within intergenic regions of the α-proteobacterial genomes.
The uup RNA motif is a conserved RNA structure that was discovered by bioinformatics. uup motif RNAs are found in Firmicutes and Gammaproteobacteria.
