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.
RNA-dependent RNA polymerase (RdRp) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template. Specifically, it catalyzes synthesis of the RNA strand complementary to a given RNA template. This is in contrast to typical DNA-dependent RNA polymerases, which all organisms use to catalyze the transcription of RNA from a DNA template.
In molecular biology, U3 snoRNA is a non-coding RNA found predominantly in the nucleolus. U3 has C/D box motifs that technically make it a member of the box C/D class of snoRNAs; however, unlike other C/D box snoRNAs, it has not been shown to direct 2'-O-methylation of other RNAs. Rather, U3 is thought to guide site-specific cleavage of ribosomal RNA (rRNA) during pre-rRNA processing.
The sucA RNA motif is a conserved RNA structure found in bacteria of the order Burkholderiales. RNAs within this motif are always found in the presumed 5' UTR of sucA genes. sucA encodes a subunit of an enzyme that participates in the citric acid cycle by synthesizing succinyl-CoA from 2-oxoglutarate. A part of the conserved structure overlaps predicted Shine-Dalgarno sequences of the downstream sucA genes. Because of the RNA motif's consistent gene association and a possible mechanism for sequestering the ribosome binding site, it was proposed that the sucA RNA motif corresponds to a cis-regulatory element. Its relatively complex secondary structure could indicate that it is a riboswitch. However, the function of this RNA motif remains unknown.
The anti-hemB RNA motif is a conserved RNA structure that was found in all known bacteria in the genus Burkholderia, and in a variety of other betaproteobacteria. The anti-hemB RNA motif consists primarily of two stem-loops, followed by a predicted rho-independent transcription termination stem-loop. As anti-hemB RNAs are generally not located in a 5' UTR, the RNAs are presumed to be non-coding RNAs. The terminator stem-loop implies that anti-hemB RNAs are transcribed as independent molecules.
The TD-1 RNA motif is a conserved RNA structure found only in the species Treponema denticola, at least among bacteria whose genomes were sequenced in 2007 when the RNA motif was identified. The T. denticola genome contains 28 predicted TD-1 RNAs, and all but two of these are positioned such that they are likely to be in the 5' UTR of the downstream gene. This arrangement suggests that TD-1 RNAs likely correspond to cis-regulatory elements. However, due to the variety of genes apparently regulated by TD-1 RNAs, no specific hypothesis as to its function was suggested.
Nucleic acid tertiary structure is the three-dimensional shape of a nucleic acid polymer. RNA and DNA molecules are capable of diverse functions ranging from molecular recognition to catalysis. Such functions require a precise three-dimensional structure. While such structures are diverse and seemingly complex, they are composed of recurring, easily recognizable tertiary structural motifs that serve as molecular building blocks. Some of the most common motifs for RNA and DNA tertiary structure are described below, but this information is based on a limited number of solved structures. Many more tertiary structural motifs will be revealed as new RNA and DNA molecules are structurally characterized.
The Bacteroid-trp RNA motif is a conserved RNA element detected by bioinformatics. It is found in the phylum Bacteroidota in the apparent 5' untranslated regions of genes that encode enzymes used in the synthesis of the amino acid tryptophan. A short open reading frame is found within the motif that encodes at least two tryptophan codons. Similar motifs have been identified regulating tryptophan genes in Pseudomonadota, but not in Bacteroidota. However, the Bacteroid-trp RNA motif likely operates via the same mechanism of attenuation.
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 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.
The Bacteroidales-2 RNA motif is a conserved RNA structure that was discovered by bioinformatics. Bacteroidales-2 motifs are found in Bacteroidales. Bacteroidales-2 RNAs likely function in trans as sRNAs.
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 drum RNA motif is a conserved RNA structure that was discovered by bioinformatics. Drum motifs are found in Bacillota, Bacteroidota, Pseudomonadota, and Spirochaetota, and exhibit multiple highly conserved nucleotide positions, despite their widespread distribution.
The DUF805 RNA motif is a conserved RNA structure that was discovered by bioinformatics. The motif is subdivided into the DUF805 motif and the DUF805b motif, which have similar, but distinct secondary structures. Together, these motifs are found in Bacteroidota, Chlorobiota, and Pseudomonadota.
The Extended-Gap, in Firmicutes and One Actiobacterium RNA motif is a conserved RNA structure that was discovered by bioinformatics. EGFOA motifs are found in Bacillota and one example was detected in Actinomycetota. The EGFOA-assoc-1 and EGFOA-assoc-2 RNA motifs are conserved RNA structures that are often located nearby to EGFOA RNAs, and presumably functions in some related mechanism.
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 pemK RNA motif is a conserved RNA structure that was discovered by bioinformatics. pemK motif RNAs are found in organisms within the phylum Bacillota, and is very widespread in this phylum.
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.
