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PotC RNA Motif
The ''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. Thus, this RNA is present in environmental samples, but not yet found in any cultivated organism. ''potC'' RNAs are located in the presumed 5' untranslated regions of genes predicted to encode either membrane transport proteins or peroxiredoxins. Therefore, it was hypothesized that ''potC'' RNAs are cis-regulatory elements, but their detailed function is unknown. A number of other RNAs were identified in the same study, including: *Lacto-usp RNA motif *mraW RNA motif *Ocean-V RNA motif *psaA RNA motif *Pseudomon-Rho RNA motif *rne-II RNA motif *STAXI RNA motif *TwoAYGGAY RNA motif *Whalefall-1 RNA motif *wcaG RNA motif *ykkC-yxkD leader The ykkC/yxkD leader is a conserved sequence, conserved Cis-regulatory element, RNA structure found Upstream and downstream (DNA), upstream ... [...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] |
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] |
WcaG RNA Motif
The ''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. ''wcaG'' RNAs might function as cis-regulatory elements, in view of their consistent location in the possible 5' untranslated regions of genes. It was suggested the ''wcaG'' RNAs might further function as riboswitches. The genes hypothesized to be regulated by ''wcaG'' RNAs function in the synthesis of exopolysaccharides, or are induced by high amounts of light. These latter genes presumably related to cyanobacterial photosynthesis Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored i .... The detected ''wcaG ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Whalefall-1 RNA Motif
The Whalefall-1 RNA motif (also called wf-1) refers to a conserved RNA structure that was discovered using bioinformatics. Structurally, the motif consists of two stem-loops (see diagram), the second of which is often terminated by a CUUG tetraloop, which is an energetically favorable RNA sequence. Whalefall-1 RNAs are found only in DNA extracted from uncultivated bacteria found on whale fall, i.e., a whale carcass. As of 2010, Whalefall-1 RNAs have not been detected in any known, cultivated species of bacteria, and are thus one of several RNAs present in environmental samples A wide variety of non-coding RNAs have been identified in various species of organisms known to science. However, RNAs have also been identified in "metagenomics" sequences derived from samples of DNA or RNA extracted from the environment, which .... References External links * Non-coding RNA {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
TwoAYGGAY RNA Motif
The TwoAYGGAY RNA motif is a conserved RNA structure identified by bioinformatics. Its name refers to the conserved AYGGAY nucleotide sequence (Y refers to either a C or U nucleotide) found in the motif's two terminal loops (see diagram). The RNAs are found in sequences derived from DNA extracted from uncultivated bacteria present in the human gut, as well as some bacteria in the classes Clostridia and Gammaproteobacteria Gammaproteobacteria is a class of bacteria in the phylum Pseudomonadota (synonym Proteobacteria). It contains about 250 genera, which makes it the most genera-rich taxon of the Prokaryotes. Several medically, ecologically, and scientifically imp .... References External links * Non-coding RNA {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
STAXI RNA Motif
The Ssbp, Topoisomerase, Antirestriction, XerDC Integrase RNA motif (STAXI RNA motif) is a conserved RNA-like structure identified using bioinformatics. STAXI RNAs are located near to genes encoding proteins that interact with DNA ( Ssbp, topoisomerase, XerDC integrase) or are associated with such proteins ( antirestriction proteins, which inhibit restriction enzymes). This observation raised the possibility that instances of the STAXI motif function as single-stranded DNA molecules, perhaps during DNA replication or DNA repair. On the other hand, STAXI motifs often contain terminal loops conforming to the stable UNCG tetraloop, but the DNA version of this tetraloop (TNCG) is not especially stable. The STAXI motif consists of a simple pseudoknot structure that is repeated two or more times (see diagram). A number of other RNAs were identified in the same study, including: * Bacteroidales-1 RNA motif * Chlorobi-1 RNA motif * JUMPstart RNA motif * Lactis-plasmid RNA motif *Ocea ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rne-II RNA Motif
The ''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 (5' UTRs) of genes that encode Ribonuclease E (RNase E). The RNase E 5' UTR element is a previously identified RNA structure that is also found in the 5' UTRs of RNase E genes. However, the latter motif is found only in enterobacteria, and the two motifs have apparently unrelated structure. In view of their differences, it was hypothesized that ''rne''-II RNAs fulfill the same functional role as RNase E 5' UTR elements, which is to regulate the levels of RNase E proteins by acting as a substrate for RNase E. Thus, when concentrations of RNase E are high, they will degrade their own messenger RNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that cor ... [...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] |
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] |
Genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences (see non-coding DNA), and often a substantial fraction of 'junk' DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome. Algae and plants also contain chloroplasts with a chloroplast genome. The study of the genome is called genomics. The genomes of many organisms have been sequenced and various regions have been annotated. The International Human Genome Project reported the sequence of the genome for ''Homo sapiens'' in 200The Human Genome Project although the initial "finished" sequence was missing 8% of the genome consisting mostly of repetitive sequences. With advancements in technology that could handle sequenci ... [...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] |
