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Chlorobi-1 RNA Motif
The Chlorobi-1 RNA motif is a conserved RNA secondary structure identified by bioinformatics. It is predicted to be used only by Chlorobiota (formerly Chlorobi), 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. A number of other RNAs were identified in the same study, including: * Bacteroidales-1 RNA motif * CrcB RNA Motif * Gut-1 RNA motif *JUMPstart RNA motif *Lactis-plasmid RNA motif The ''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 ... * Lacto-usp RNA motif * MraW RNA motif * Ocean-V RNA motif * PsaA RNA motif * Pseudomon-Rho RNA motif * Rne-II RNA motif References External links * Non-coding RNA {{m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties (e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
JUMPstart RNA Motif
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. JUMPstart sequences include an ops element, which is an acronym for "operon-polarity suppressor" and has the nucleotide consensus GGCGGUAG. The ops element acts in concert with the RfaH protein to improve transcription Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including: Genetics * Transcription (biology), the copying of DNA into RNA, the fir ... of genes downstream of the ops element, especially genes far away within long operons. References External links * Cis-regulatory RNA el ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pseudomon-Rho RNA Motif
The ''Pseudomon''-Rho RNA motif refers to a conserved RNA structure that was discovered using bioinformatics. The RNAs that conform to this motif (see diagram) are found in species within the genus ''Pseudomonas'', as well as the related ''Azotobacter vinelandii''. They are consistently located in what could be the 5' untranslated regions of genes that encode the Rho factor protein, and this arrangement in bacteria suggested that ''Pseudomon''-Rho RNAs might be cis-regulatory element ''Cis''-regulatory elements (CREs) or ''Cis''-regulatory modules (CRMs) are regions of non-coding DNA which regulate the transcription of neighboring genes. CREs are vital components of genetic regulatory networks, which in turn control morphoge ...s that regulate concentrations of the Rho protein. References External links * Cis-regulatory RNA elements {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PsaA RNA Motif
The ''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 cis-regulatory elements of these genes. The ''psaAB'' genes encode proteins that form subunits in the photosystem I structure used for photosynthesis. ''psaA'' RNAs have been detected only in cyanobacteria, which is consistent with their association with photosynthesis. ''psaAB'' genes are known to be regulated in species of cyanobacteria that do not use ''psaA'' RNAs, and this system of regulation involves transcription factor proteins. In this system, the expression of ''psaAB'' genes is increased when cells are growing with limited amount of light, presumably to maximize their energy from the limited resource. On the other hand, the genes' expression is reduced when l ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ocean-V RNA Motif
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 The ocean (also the sea or the world ocean) is the body of salt water that covers approximately 70.8% of the surface of Earth and contains 97% of Earth's water. An ocean can also refer to any of the large bodies of water into which the wo ... water. As of 2010, no Ocean-V RNA has been detected in any known, cultivated organism. References External links * Non-coding RNA {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MraW RNA Motif
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 (red nucleotides in diagram at right). ''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 Peptidoglycan or murein is a unique large macromolecule, a polysaccharide, consisting of sugars and amino acids that forms a mesh-like peptidoglycan layer outside the plasma membrane, the rigid cell wall (murein sacculus) characteristic of most ... synthesis, and it was hypothesized that the ''mraW'' RNA motif might regulate these genes. References External links * Cis-re ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lacto-usp RNA Motif
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 (5′ UTRs) 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 In the field of molecular biology the 6S RNA is a non-coding RNA that was one of the first to be identified and sequenced. What it does in the bacterial cell was unknown until recently. In the early 2000s scientists found out the function of 6S ... 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. References E ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lactis-plasmid RNA Motif
The ''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 ''lactis''-plasmid RNAs participate in the control of plasmid abundance. However, many of the plasmids that carry ''lactis''-plasmid RNAs also carry ctRNA In molecular biology ctRNA (counter-transcribed RNA) is a plasmid encoded noncoding RNA that binds to the mRNA of repB and causes translation (genetics), translational inhibition. ctRNA is encoded by plasmids and functions in rolling circle repl ...-pND324 RNAs, which are involved in plasmid copy count regulation. Therefore ''lactis''-plasmid RNAs might have a different function. See also * R1162-like plasmid antisense RNA References External links * Non-coding RNA {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gut-1 RNA Motif
The Gut-1 RNA motif (also called gt-1) 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 bacteria present in samples from the human Humans (''Homo sapiens'') are the most abundant and widespread species of primate, characterized by bipedalism and exceptional cognitive skills due to a large and complex brain. This has enabled the development of advanced tools, culture, ... gut. References External links * Non-coding RNA {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chlorobiota
The green sulfur bacteria are a phylum of obligately anaerobic photoautotrophic bacteria that metabolize sulfur. Green sulfur bacteria are nonmotile (except ''Chloroherpeton thalassium'', which may glide) and capable of anoxygenic photosynthesis. They live in anaerobic aquatic environments. In contrast to plants, green sulfur bacteria mainly use sulfide ions as electron donors. They are autotrophs that utilize the reverse tricarboxylic acid cycle to perform carbon fixation. They are also mixotrophs and reduce nitrogen. Characteristics Green sulfur bacteria are gram-negative rod or spherical shaped bacteria. Some types of green sulfur bacteria have gas vacuoles that allow for movement. They are photolithoautotrophs, and use light energy and reduced sulfur compounds as the electron source. Electron donors include H2, H2S, S. The major photosynthetic pigment in these bacteria is Bacteriochlorophylls ''c'' or ''d'' in green species and ''e'' in brown species, and is located in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CrcB RNA Motif
The fluoride riboswitch (formerly called the ''crcB'' RNA motif) is a conserved RNA structure identified by bioinformatics in a wide variety of bacteria and archaea. These RNAs were later shown to function as riboswitches that sense fluoride ions. These "fluoride riboswitches" increase expression of downstream genes when fluoride levels are elevated, and the genes are proposed to help mitigate the toxic effects of very high levels of fluoride. Many genes are presumed to be regulated by these fluoride riboswitches. Two of the most common encode proteins that are proposed to function by removing fluoride from the cell. These proteins are CrcB proteins and a fluoride-specific subtype of chloride channels referred to as EriCF or ClCF. ClCF proteins have been shown to function as fluoride-specific fluoride/proton antiporters. The three-dimensional structure of a fluoride riboswitch has been solved at atomic resolution by X-ray crystallography. Fluoride riboswitches are found in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacteroidales-1 RNA Motif
The Bacteroidales-1 RNA motif is a conserved RNA structure identified by bioinformatics. It has been identified only in bacteria within the order (biology) Bacteroidales. Its presumed length is marked by a promoter on one end that conforms to an alternate consensus sequence that is common in the phylum Bacteroidota, and its 3′ end is indicated by predicted transcription terminators. It is often located downstream of a gene that encodes the L20 ribosomal subunit, although it is unclear whether there is a functional reason underlying this apparent association. Bacteroidales-1 RNA motif has been reported as a 6S RNA homologue by a report of ''Bacteroides thetaiotaomicron'' transcriptome map. The existence of small product RNAs (pRNAs) that rescue sequestered RNA polymerases In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that synthesizes RNA from a DNA template. Using t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
