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YkoK Leader
The Ykok leader or M-box is a Mg2+-sensing RNA structure that controls the expression of Magnesium ion transport proteins in bacteria. It is a distinct structure to the Magnesium responsive RNA element. The Ykok leader was originally described as a conserved sequence with potential riboswitch function found upstream of the ''B. subtilis'' ykoK gene and genes with related functions in other bacteria. Examples of the conserved M-box RNA structure occur upstream of each of the three major families of Mg2+ transporters (CorA, MgtE and MgtA/MgtB) in various bacterial species. The molecular structure of the M-box example upstream of the ''B. subtilis'' ykoK gene includes six bound Mg2+ ions. Biochemical studies indicate that this M-Box RNA compacts in the presence of Mg2+ and other divalent ions. This folding process appears to disrupt an antiterminator structure, and thereby allow a transcription terminator structure to form. As expected from this model, ''B. subtilis'' cells r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Secondary Structure
Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein protein folding, folds into its three dimensional protein tertiary structure, tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the Amine, amino hydrogen and carboxyl oxygen atoms in the peptide backbone chain, backbone. Secondary structure may alternatively be defined based on the regular pattern of backbone Dihedral angle#Dihedral angles of proteins, dihedral angles in a particular region of the Ramachandran plot regardless of whether it has the correct hydrogen bonds. The concept of secondary structure was first introduced by Kaj Ulrik ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Conservation
In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids ( DNA and RNA) or proteins across species ( orthologous sequences), or within a genome ( paralogous sequences), or between donor and receptor taxa ( xenologous sequences). Conservation indicates that a sequence has been maintained by natural selection. A highly conserved sequence is one that has remained relatively unchanged far back up the phylogenetic tree, and hence far back in geological time. Examples of highly conserved sequences include the RNA components of ribosomes present in all domains of life, the homeobox sequences widespread amongst Eukaryotes, and the tmRNA in Bacteria. The study of sequence conservation overlaps with the fields of genomics, proteomics, evolutionary biology, phylogenetics, bioinformatics and mathematics. History The discovery of the role of DNA in heredity, and observations by Frederick Sanger of variation between animal insulins in 1949, promp ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 morphogenesis, the development of anatomy, and other aspects of embryonic development, studied in evolutionary developmental biology. CREs are found in the vicinity of the genes that they regulate. CREs typically regulate gene transcription by binding to transcription factors. A single transcription factor may bind to many CREs, and hence control the expression of many genes ( pleiotropy). The Latin prefix ''cis'' means "on this side", i.e. on the same molecule of DNA as the gene(s) to be transcribed. CRMs are stretches of DNA, usually 100–1000 DNA base pairs in length, where a number of transcription factors can bind and regulate expression of nearby genes and regulate their transcription rates. They are labeled as ''cis'' because they are ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, and the deep biosphere of Earth's crust. Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of dead bodies; bacteria are responsible for the putrefaction stage in this process. In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Bacteria also live in symbiotic and parasitic relationsh ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene Expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. These products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) and small nuclear RNA (snRNA), the product is a functional non-coding RNA. Gene expression is summarized in the central dogma of molecular biology first formulated by Francis Crick in 1958, further developed in his 1970 article, and expanded by the subsequent discoveries of reverse transcription and RNA replication. The process of gene expression is used by all known life—eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea), and utilized by viruses—to generate the macromolecular machinery for life. In genetics, gene expression is the most fundamental level at which the genotype gives rise to the phenotype, '' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Magnesium Transporter
Magnesium transporters are proteins that transport magnesium across the cell membrane. All forms of life require magnesium, yet the molecular mechanisms of Mg2+ uptake from the environment and the distribution of this vital element within the organism are only slowly being elucidated. The ATPase function of MgtA is highly cardiolipin dependent and has been shown to detect free magnesium in the μM range In bacteria, Mg2+ is probably mainly supplied by the CorA protein and, where the CorA protein is absent, by the MgtE protein. In yeast the initial uptake is via the Alr1p and Alr2p proteins, but at this stage the only internal Mg2+ distributing protein identified is Mrs2p. Within the protozoa only one Mg2+ transporter (XntAp) has been identified. In metazoa, Mrs2p and MgtE homologues have been identified, along with two novel Mg2+ transport systems TRPM6/TRPM7 and PCLN-1. Finally, in plants, a family of Mrs2p homologues has been identified along with another novel protein, AtMHX. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Magnesium Responsive RNA Element
The Magnesium responsive RNA element, not to be confused with the completely distinct M-box riboswitch, is a cis-regulatory element that regulates the expression of the magnesium transporter protein MgtA. It is located in the 5' UTR of this gene. The mechanism for the potential magnesium-sensing capacity of this RNA is still unclear, though a recent report suggests that the RNA element targets the mgtA transcript for degradation by RNase E when cells are grown in high Mg2+ environments. Background The term riboswitches refer to a collective group of cis-regulatory elements which are mostly located in the untranslated regions of messenger RNAs. The purpose of these molecules is that they have the ability to regulate gene expression through the association with different metabolites, and as such, do not require assistance from various protein factors. These specific types of RNA can have individualized structures and functions, but for the most part, have certain features and fu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Conserved Sequence
In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids ( DNA and RNA) or proteins across species ( orthologous sequences), or within a genome ( paralogous sequences), or between donor and receptor taxa ( xenologous sequences). Conservation indicates that a sequence has been maintained by natural selection. A highly conserved sequence is one that has remained relatively unchanged far back up the phylogenetic tree, and hence far back in geological time. Examples of highly conserved sequences include the RNA components of ribosomes present in all domains of life, the homeobox sequences widespread amongst Eukaryotes, and the tmRNA in Bacteria. The study of sequence conservation overlaps with the fields of genomics, proteomics, evolutionary biology, phylogenetics, bioinformatics and mathematics. History The discovery of the role of DNA in heredity, and observations by Frederick Sanger of variation between animal insulins in 1949, prompt ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 production of the proteins encoded by the mRNA. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the concentrations of its effector molecule. The discovery that modern organisms use RNA to bind small molecules, and discriminate against closely related analogs, expanded the known natural capabilities of RNA beyond its ability to code for proteins, catalyze reactions, or to bind other RNA or protein macromolecules. The original definition of the term "riboswitch" specified that they directly sense small-molecule metabolite concentrations. Although this definition remains in common use, some biologists have used a broader definition that includes other cis-regulatory RNAs. However, this article will discuss only metabolite-binding riboswitches. Most known riboswitches occur in bac ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Upstream And Downstream (DNA)
In molecular biology and genetics, upstream and downstream both refer to relative positions of genetic code in DNA or RNA. Each strand of DNA or RNA has a 5' end and a 3' end, so named for the carbon position on the deoxyribose (or ribose) ring. By convention, upstream and downstream relate to the 5' to 3' direction respectively in which RNA transcription takes place. Upstream is toward the 5' end of the RNA molecule and downstream is toward the 3' end. When considering double-stranded DNA, upstream is toward the 5' end of the coding strand for the gene in question and downstream is toward the 3' end. Due to the anti-parallel nature of DNA, this means the 3' end of the template strand is upstream of the gene and the 5' end is downstream. Some genes on the same DNA molecule may be transcribed in opposite directions. This means the upstream and downstream areas of the molecule may change depending on which gene is used as the reference. See also *Upstream and downstream (transdu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Divalent
In chemistry, the valence (US spelling) or valency (British spelling) of an element is the measure of its combining capacity with other atoms when it forms chemical compounds or molecules. Description The combining capacity, or affinity of an atom of a given element is determined by the number of hydrogen atoms that it combines with. In methane, carbon has a valence of 4; in ammonia, nitrogen has a valence of 3; in water, oxygen has a valence of 2; and in hydrogen chloride, chlorine has a valence of 1. Chlorine, as it has a valence of one, can be substituted for hydrogen. Phosphorus has a valence of 5 in phosphorus pentachloride, . Valence diagrams of a compound represent the connectivity of the elements, with lines drawn between two elements, sometimes called bonds, representing a saturated valency for each element. The two tables below show some examples of different compounds, their valence diagrams, and the valences for each element of the compound. Modern definitions ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rho-independent Transcription Termination
Intrinsic, or rho-independent termination, is a process in prokaryotes to signal the end of transcription and release the newly constructed RNA molecule. In prokaryotes such as E. coli, transcription is terminated either by a rho-dependent process or rho-independent process. In the Rho-dependent process, the rho-protein locates and binds the signal sequence in the mRNA and signals for cleavage. Contrarily, intrinsic termination does not require a special protein to signal for termination and is controlled by the specific sequences of RNA. When the termination process begins, the transcribed mRNA forms a stable secondary structure hairpin loop, also known as a Stem-loop. This RNA hairpin is followed by multiple uracil nucleotides. The bonds between uracil and adenine are very weak. A protein bound to RNA polymerase (nusA) binds to the stem-loop structure tightly enough to cause the polymerase to temporarily stall. This pausing of the polymerase coincides with transcription of the po ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
