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The Lacto-3 RNA motif is a conserved RNA structure that was discovered by bioinformatics. [1] Lacto-3 motif RNAs are found in a wide variety of organisms classified under Lactobacillales. Lacto-3 RNAs likely function in trans as small RNAs, and no organism is predicted to contain more than one Lacto-3 RNA.
A nucleic acid sequence is a succession of bases within the nucleotides forming alleles within a DNA or RNA (GACU) molecule. This succession is denoted by a series of a set of five different letters that indicate the order of the nucleotides. By convention, sequences are usually presented from the 5' end to the 3' end. For DNA, with its double helix, there are two possible directions for the notated sequence; of these two, the sense strand is used. Because nucleic acids are normally linear (unbranched) polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule. For this reason, the nucleic acid sequence is also termed the primary structure.
In biology, the SECIS element is an RNA element around 60 nucleotides in length that adopts a stem-loop structure. This structural motif directs the cell to translate UGA codons as selenocysteines. SECIS elements are thus a fundamental aspect of messenger RNAs encoding selenoproteins, proteins that include one or more selenocysteine residues.
An aminoacyl-tRNA synthetase, also called tRNA-ligase, is an enzyme that attaches the appropriate amino acid onto its corresponding tRNA. It does so by catalyzing the transesterification of a specific cognate amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA. In humans, the 20 different types of aa-tRNA are made by the 20 different aminoacyl-tRNA synthetases, one for each amino acid of the genetic code.
The T-arm or T-loop is a specialized region on the tRNA molecule which acts as a special recognition site for the ribosome to form a tRNA-ribosome complex during protein biosynthesis or translation (biology).
The lacto-2 RNA motif is an RNA structure that is conserved amongst bacteria within the order Lactobacillales. The motif consists of a stem-loop whose stem is interrupted by many internal loops and bulges. Nucleotide identities in many places are conserved, and one internal loop in particular is highly conserved.
A wide variety of non-coding RNAs have been identified in various species of organisms known to science. However, RNAs have also been identified in "metagenomics" sequences derived from samples of DNA or RNA extracted from the environment, which contain unknown species. Initial work in this area detected homologs of known bacterial RNAs in such metagenome samples. Many of these RNA sequences were distinct from sequences within cultivated bacteria, and provide the potential for additional information on the RNA classes to which they belong.
The Chlorobi-1 RNA motif is a conserved RNA secondary structure identified by bioinformatics. It is predicted to be used only by Chlorobiota, a phylum of bacteria. The motif consists of two stem-loops that are followed by an apparent rho-independent transcription terminator. The motif is presumed to function as an independently transcribed non-coding RNA.
The glutamine riboswitch is a conserved RNA structure that was predicted by bioinformatics. It is present in a variety of lineages of cyanobacteria, as well as some phages that infect cyanobacteria. It is also found in DNA extracted from uncultivated bacteria living in the ocean that are presumably species of cyanobacteria.
The Lacto-rpoB RNA motif is a conserved RNA structure identified by bioinformatics. It has been detected only in lactic acid bacteria, and is always located in the presumed 5' untranslated regions of rpoB genes. These genes encode a subunit of RNA polymerase, and it is hypothesized that Lacto-rpoB RNA participate in the regulation of these genes.
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 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 Ocean-V RNA motif is a conserved RNA structure discovered using bioinformatics. Only a few Ocean-V RNA sequences have been detected, all in sequences derived from DNA that was extracted from uncultivated bacteria found in ocean water. As of 2010, no Ocean-V RNA has been detected in any known, cultivated organism.
The ARRPOF RNA motif is a conserved RNA structure that was discovered by bioinformatics.
The CyVA-1 RNA motif is a conserved RNA structure that was discovered by bioinformatics. CyVA-1 motifs are found in Cyanobacteria, Acidobacteriota, and Verrucomicrobiota. Only one example of the RNA is known in any Acidobacterial organism, and only one CyVA-1 RNA was found in any Verrucomicrobial organism. This could suggest that the RNA is not well-established in these bacterial lineages, or simply reflect the fact that relatively few genome sequences are available for organisms in these phyla. CyVA-1 RNAs likely function in trans as sRNAs, and organisms commonly have 2 or 3 separate copies of the CyVA-1 RNA motif in their genomes.
The DUF3577 RNA motif is a conserved RNA structure that was discovered by bioinformatics. DUF3577 motifs are found in the organism Cardiobacterium valvarum and metagenomic sequences from unknown organisms.
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 Lacto-phage-1 RNA motif is a conserved RNA structure that was discovered by bioinformatics. Lacto-phage-1 motif RNAs are found in Lactobacillales.
malK RNA motifs are conserved RNA structures that were discovered by bioinformatics. They are defined by being consistently located upstream of malK genes, which encode an ATPase that is used by transporters whose ligand is likely a kind of sugar. Most of these genes are annotated either as transporting maltose or glycerol-3-phosphate, however the substrate of the transporters associated with malK motif RNAs has not been experimentally determined. All known types of malK RNA motif are generally located nearby to the Shine-Dalgarno sequence of the downstream gene.
The Methylosinus-1 RNA motif is a conserved RNA structure that was discovered by bioinformatics. Methylosinus-1 motif RNAs are found, as of 2018, only in the organism Methylosinus trichosporium strain OB3b. The motif occurs in six locations in this organism. A possible homolog also occurs in Methylosinus rosea SV97.
The skipping-rope RNA motif is a conserved RNA structure that was discovered by bioinformatics. skipping-rope motif RNAs are found in multiple phyla: Bacillota, Fusobacteriota, Pseudomonadota and Spirochaetota. A skipping-rope RNA was also found in a purified phage, specifically the phage Bacillus phage SPbeta, which infects Bacillus organisms that fit into the phylum Bacillota. Therefore, skipping-rope RNAs likely function, at least sometimes, to perform a function useful to phages.
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