In genetics, a promoter is a sequence of DNA to which proteins bind to initiate transcription of a single RNA transcript from the DNA downstream of the promoter. The RNA transcript may encode a protein (mRNA), or can have a function in and of itself, such as tRNA or rRNA. Promoters are located near the transcription start sites of genes, upstream on the DNA . Promoters can be about 100–1000 base pairs long, the sequence of which is highly dependent on the gene and product of transcription, type or class of RNA polymerase recruited to the site, and species of organism.
A ρ factor is a bacterial protein involved in the termination of transcription. Rho factor binds to the transcription terminator pause site, an exposed region of single stranded RNA after the open reading frame at C-rich/G-poor sequences that lack obvious secondary structure.
fis is an E. coli gene encoding the Fis protein. The regulation of this gene is more complex than most other genes in the E. coli genome, as Fis is an important protein which regulates expression of other genes. It is supposed that fis is regulated by H-NS, IHF and CRP. It also regulates its own expression (autoregulation). Fis is one of the most abundant DNA binding proteins in Escherichia coli under nutrient-rich growth conditions.
The yybP-ykoY leader RNA element was originally discovered in E. coli during a large scale screen and was named SraF. This family was later found to exist upstream of related families of protein genes in many bacteria, including the yybP and ykoY genes in B. subtilis. The specific functions of these proteins are unknown, but this structured RNA element may be involved in their genetic regulation as a riboswitch. The yybP-ykoY element was later proposed to be manganese-responsive after another associated family of genes, YebN/MntP, was shown to encode Mn2+ efflux pumps in several bacteria. Genetic data and a crystal structure confirmed that yybp-ykoY is a manganese riboswitch that directly binds Mn2+
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 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 JUMPstart RNA motif describes a conserved RNA-based secondary structure associated with JUMPstart elements. The 39-base-pair JUMPstart sequence describes a conserved element upstream of genes that participate in polysaccharide synthesis. The JUMPstart element has been shown to function as an RNA, and is present in the 5' untranslated regions of the genes it regulates.
Ribonuclease E is a bacterial ribonuclease that participates in the processing of ribosomal RNA and the chemical degradation of bulk cellular RNA.
The COG2908 RNA motif is a conserved RNA structure that was discovered by bioinformatics. COG2908 motif RNAs are found in genomic sequences extracted from fresh water environments. They have not, as of 2018, been detected in any classified organism.
The DUF2800 RNA motif is a conserved RNA structure that was discovered by bioinformatics. DUF2800 motif RNAs are found in Bacillota. DUF2800 RNAs are also predicted in the phyla Actinomycetota and Synergistota, although these RNAs are likely the result of recent horizontal gene transfer or conceivably sequence contamination.
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 leuA-Halobacteria RNA motif is a conserved RNA structure that was discovered by bioinformatics. leuA-Halobacteria motifs are found in Halobacteriaceae, a lineage of archaea.
The osmY RNA motif is a conserved RNA structure that was discovered by bioinformatics. osmY motif RNAs are found in Enterobacteriaceae organisms, although it is not predicted to reside in Escherichia coli.
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 raiA RNA motif is a conserved RNA structure that was discovered by bioinformatics. raiA motif RNAs are found in Actinomycetota and Bacillota, and have many conserved features—including conserved nucleotide positions, conserved secondary structures and associated protein-coding genes—in both of these phyla. Some conserved features of the raiA RNA motif suggest that they function as cis-regulatory elements, but other aspects of the motif suggest otherwise.
The sbcC RNA motif is a conserved RNA structure that was discovered by bioinformatics. The sbcC motif has, as of 2018, only been detected in metagenomic sequences, and the identities of organisms that contain these RNAs is unknown.
The ssNA-helicase RNA motif is a conserved RNA structure that was discovered by bioinformatics. Although the ssNA-helicase motif was published as an RNA candidate, there is some reason to suspect that it 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.
The sul1 RNA motif is a conserved RNA structure that was discovered by bioinformatics. Energetically stable tetraloops often occur in this motif. sul1 motif RNAs are found in Alphaproteobacteria.
The uup RNA motif is a conserved RNA structure that was discovered by bioinformatics. uup motif RNAs are found in Bacillota and Gammaproteobacteria.
An RNA motif is a description of a group of RNAs that have a related structure. RNA motifs consist of a pattern of features within the primary sequence and secondary structure of related RNAs. Thus, it extends the concept of a sequence motif to include RNA secondary structure. The term "RNA motif" can refer both to the pattern and to the RNA sequences that match it.
