YjdF RNA Motif
   HOME

TheInfoList



OR:

The ''yjdF'' RNA motif is a conserved
RNA Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...
structure identified using
bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...
. Most ''yjdF'' RNAs are located in
bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
classified within the
phylum In biology, a phylum (; : phyla) is a level of classification, or taxonomic rank, that is below Kingdom (biology), kingdom and above Class (biology), class. Traditionally, in botany the term division (taxonomy), division has been used instead ...
Bacillota The Bacillota (synonym Firmicutes) are a phylum of bacteria, most of which have Gram-positive cell wall structure. They have round cells, called cocci (singular coccus), or rod-like forms (bacillus). A few Bacillota, such as '' Megasphaera'', ...
. A ''yjdF'' RNA is found in the presumed
5' untranslated region The 5′ untranslated region (also known as 5′ UTR, leader sequence, transcript leader, or leader RNA) is the region of a messenger RNA (mRNA) that is directly upstream from the initiation codon. This region is important for the regulation of ...
(5' UTR) of the ''yjdF''
gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
in ''
Bacillus subtilis ''Bacillus subtilis'' (), known also as the hay bacillus or grass bacillus, is a gram-positive, catalase-positive bacterium, found in soil and the gastrointestinal tract of ruminants, humans and marine sponges. As a member of the genus ''Bacill ...
'', and almost all ''yjdF'' RNAs are found in the 5' UTRs of
homologs Homologous chromosomes or homologs are a set of one maternal and one paternal chromosome that pair up with each other inside a cell during meiosis. Homologs have the same genes in the same loci, where they provide points along each chromosome th ...
of this gene. The function of the ''yjdF'' gene is unknown, but the
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
that it is predicted to encode is classified by the
Pfam Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The latest version of Pfam, 37.0, was released in June 2024 and contains 21,979 families. It is cur ...
Database as DUF2992. The moderately complex
secondary structure Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...
and
nucleotide Nucleotides are Organic compound, organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both o ...
positions conserved in the ''yjdF'' RNA motif and the fact that it is likely to be present in 5' UTRs led to the hypothesis that ''yjdF'' RNAs function as
riboswitch In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in Translation (biology), production of the proteins encoded by the mRNA. Thus, an mRNA that contains a ribo ...
es. One ''yjdF'' RNA is found instead in the presumed 5' UTR of genes encoding
enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...
s involved in the synthesis of
nicotinamide adenine dinucleotide Nicotinamide adenine dinucleotide (NAD) is a Cofactor (biochemistry), coenzyme central to metabolism. Found in all living cell (biology), cells, NAD is called a dinucleotide because it consists of two nucleotides joined through their phosphat ...
(NAD). These RNAs lack a region of the otherwise conserved ''yjdF'' RNA motif and might be non-functional, or conform to a distinct structure that achieves the same function. If ''yjdF'' RNAs are riboswitches, this other RNA might bind a distinct
small molecule In molecular biology and pharmacology, a small molecule or micromolecule is a low molecular weight (≤ 1000 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm. Many drugs are small molecules; ...
ligand In coordination chemistry, a ligand is an ion or molecule with a functional group that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's el ...
. Experiments support the conclusion that the ''yjdF'' RNA in ''B. subtilis'' is indeed in the 5' UTR of the ''yjdF'' gene, and that the ''yjdF'' genes are transcribed separately from the upstream ''manPA''
operon In genetics, an operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo splic ...
. The biochemical function of ''yjdF'' RNAs remains unknown. ''yjdF'' RNAs appear to function as riboswitches that sense azaaromatic compounds, although the precise compound or set of compounds that is sensed by this riboswitch in the cell remains unclear.


References


External links

{{Rfam, id=RF01764, name=yjdF RNA Cis-regulatory RNA elements