YjdF RNA motif
Encyclopedia
The yjdF RNA motif is a conserved RNA
structure identified using bioinformatics
. Most yjdF RNAs are located in bacteria
classified within the phylum
Firmicutes
. A yjdF RNA is found in the presumed 5' untranslated region (5' UTR) 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 moderately complex secondary structure
and nucleotide
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
es. One yjdF RNA is found instead in the presumed 5' UTR of genes encoding enzyme
s involved in the synthesis of nicotinamide adenine dinucleotide
(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
ligand
.
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
. The biochemical function of yjdF RNAs remains unknown.
A number of other RNAs were identified in the same study, including:
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
structure identified using bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
. Most yjdF RNAs are located in bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
classified within the phylum
Phylum
In biology, a phylum The term was coined by Georges Cuvier from Greek φῦλον phylon, "race, stock," related to φυλή phyle, "tribe, clan." is a taxonomic rank below kingdom and above class. "Phylum" is equivalent to the botanical term division....
Firmicutes
Firmicutes
The Firmicutes are a phylum of bacteria, most of which have Gram-positive cell wall structure. A few, however, such as Megasphaera, Pectinatus, Selenomonas and Zymophilus, have a porous pseudo-outer-membrane that causes them to stain Gram-negative...
. A yjdF RNA is found in the presumed 5' untranslated region (5' UTR) of the yjdF gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
in Bacillus subtilis
Bacillus subtilis
Bacillus subtilis, known also as the hay bacillus or grass bacillus, is a Gram-positive, catalase-positive bacterium commonly found in soil. A member of the genus Bacillus, B. subtilis is rod-shaped, and has the ability to form a tough, protective endospore, allowing the organism to tolerate...
, and almost all yjdF RNAs are found in the 5' UTRs of homologs
Homology (biology)
Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...
of this gene. The function of the yjdF gene is unknown, but the protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
that it is predicted to encode is classified by the Pfam
Pfam
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.- Features :For each family in Pfam one can:* Look at multiple alignments* View protein domain architectures...
Database as DUF2992.
The moderately complex secondary structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
and nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
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
Riboswitch
In molecular biology, a riboswitch is a part of an mRNA molecule that can directly bind a small target molecule, and whose binding of the target affects the gene's activity. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the...
es. One yjdF RNA is found instead in the presumed 5' UTR of genes encoding enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
s involved in the synthesis of nicotinamide adenine dinucleotide
Nicotinamide adenine dinucleotide
Nicotinamide adenine dinucleotide, abbreviated NAD, is a coenzyme found in all living cells. The compound is a dinucleotide, since it consists of two nucleotides joined through their phosphate groups. One nucleotide contains an adenine base and the other nicotinamide.In metabolism, NAD is involved...
(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
Small molecule
In the fields of pharmacology and biochemistry, a small molecule is a low molecular weight organic compound which is by definition not a polymer...
ligand
Ligand
In coordination chemistry, a ligand is an ion or molecule that binds to a central metal atom to form a coordination complex. The bonding between metal and ligand generally involves formal donation of one or more of the ligand's electron pairs. The nature of metal-ligand bonding can range from...
.
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
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
separately from the upstream manPA operon
Operon
In genetics, an operon is a functioning unit of genomic DNA containing a cluster of genes under the control of a single regulatory signal or promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo trans-splicing to create...
. The biochemical function of yjdF RNAs remains unknown.
A number of other RNAs were identified in the same study, including:
- Bacteroidales-1 RNA motifBacteroidales-1 RNA motifThe Bacteroidales-1 RNA motif is a conserved RNA structure identified by bioinformatics. It has been identified only in bacteria within the order Bacteroidales...
- CrcB RNA MotifCrcB RNA MotifThe crcB RNA motif is a conserved RNA structure identified by bioinformatics in a wide variety of bacteria and archaea. The motif exhibits the rigid or almost perfect conservation of the nucleotide identity at several positions across two domains of life...
- Chlorobi-1 RNA motifChlorobi-1 RNA motifThe Chlorobi-1 RNA motif is a conserved RNA secondary structure identified by bioinformatics. It is predicted to be used only by Chlorobi, a phylum of bacteria. The motif consists of two stem-loops that are followed by an apparent rho-independent transcription terminator...
- Gut-1 RNA motifGut-1 RNA motifThe Gut-1 RNA motif is a conserved RNA structure identified by bioinformatics. These RNAs are present in environmental sequences, and as of 2010 are not known to be present in any species that has been grown under laboratory conditions. Gut-1 RNA is exclusively found in DNA from uncultivated...
- JUMPstart RNA motifJUMPstart RNA motifThe 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...
- Lactis-plasmid RNA motifLactis-plasmid RNA motifThe lactis-plasmid RNA motif is a conserved RNA structure identified by bioinformatics. The RNAs are restricted to lactic acid bacteria, and are especially common in Lactococcus lactis. They typically lie near to repB genes, and are almost found in plasmids. This data suggested that...
- Lacto-usp RNA motifLacto-usp RNA motifThe 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...
- MraW RNA motifMraW RNA motifThe 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...
- Ocean-V RNA motifOcean-V RNA motifThe 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,...
- PotC RNA motifPotC RNA motifThe 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...
- PsaA RNA motifPsaA RNA motifThe psaA RNA motif describes a class of RNAs with a common secondary structure. psaA RNAs are exclusively found in locations that presumably correspond to the 5' untranslated regions of operons formed of psaA and psaB genes. For this reason, it was hypothesized that psaA RNAs function as...
- Pseudomon-Rho RNA motifPseudomon-Rho RNA motifThe 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...
- Rne-II RNA motifRne-II RNA motifThe rne-II RNA motif is a conserved RNA structure identified using bioinformatics. It is detected only in species classified within the family Pseudomonadaceae, a group of gammaproteobacteria. rne-II RNAs are consistently located in the presumed 5' untranslated regions of genes that encode...
- STAXI RNA motifSTAXI RNA motifThe 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...
- TwoAYGGAY RNA motifTwoAYGGAY RNA motifThe TwoAYGGAY RNA motif is a conserved RNA structure identified by bioinformatics. Its name refers to the conserved AYGGAY nucleotide sequence found in the motif's two terminal loops...
- Whalefall-1 RNA motifWhalefall-1 RNA motifThe Whalefall-1 RNA motif refers to a conserved RNA structure that was discovered using bioinformatics. Structurally, the motif consists of two stem-loops , the second of which is often terminated by a CUUG tetraloop, which is an energetically favorable RNA sequence...
- WcaG RNA motifWcaG RNA motifThe wcaG RNA motif is an RNA structure conserved in some bacteria that was detected by bioinformatics. wcaG RNAs are found in certain phages that infect cyanobacteria. Most known wcaG RNAs were found in sequences of DNA extracted from uncultivated marine bacteria...
- YkkC-yxkD leaderYkkC-yxkD leaderThe YkkC/YxkD leader is a conserved RNA structure found upstream of the ykkC and yxkD genes in Bacillus subtilis and related genes in other bacteria. The function of this family is unclear although it has been suggested that it may function to switch on efflux pumps and detoxification systems in...