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YkkC-yxkD Leader
The ykkC/yxkD leader is a conserved sequence, conserved Cis-regulatory element, RNA structure found Upstream and downstream (DNA), upstream of the ykkC and yxkD genes in ''Bacillus subtilis'' and related genes in other bacteria. The function of this family is unclear for many years although it has been suggested that it may function to switch on Efflux (microbiology)#Bacterial efflux pumps, efflux pumps and detoxification systems in response to harmful environmental molecules. The ''Thermoanaerobacter tengcongensis'' sequencAE013027overlaps with that of purine riboswitch suggesting that the two riboswitches may work in conjunction to regulate the upstream gene which codes for TTE058(Q8RC62) a member of the permease family. Nelson et al. showed that this riboswitch senses and responds to guanidine and it was renamed Guanidine-I riboswitch. Furthermore, they demonstrated that bacteria are capable of endogenously producing guanidine and the riboswitch controls genes whose products a ... [...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] |
Purine Riboswitch
A purine riboswitch is a sequence of ribonucleotides in certain messenger RNA (mRNA) that selectively binds to purine ligands via a natural aptamer domain. This binding causes a conformational change in the mRNA that can affect translation by revealing an expression platform for a downstream gene, or by forming a translation-terminating stem-loop. The ultimate effects of such translational regulation often take action to manage an abundance of the instigating purine, and might produce proteins that facilitate purine metabolism or purine membrane uptake. Binding properties Purine riboswitches bind to their purine ligands via interactions at a three-way junction formed by junctional helix P1 and hairpin helices P2 and P3. Associations that a purine makes when it is within this ''binding pocket'' stabilize the three-way junction, and support the ligand-bound conformation of the mRNA molecule. The purine riboswitch can become saturated at concentrations as low as 5 nM, which reflect ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleotide
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are obtained in the diet and are also synthesized from common nutrients by the liver. Nucleotides are composed of three subunit molecules: a nucleobase, a five-carbon sugar (ribose or deoxyribose), and a phosphate group consisting of one to three phosphates. The four nucleobases in DNA are guanine, adenine, cytosine and thymine; in RNA, uracil is used in place of thymine. Nucleotides also play a central role in metabolism at a fundamental, cellular level. They provide chemical energy—in the form of the nucleoside triphosphates, adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP) and uridine triphosphate (UTP)—throughout the cell for the many cellular func ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a basic unit of heredity and 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: protein-coding genes and noncoding genes. During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic traits. These genes make up different DNA sequences called genotypes. Genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes (many different genes) as well as gen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mini-ykkC RNA Motif
The mini-ykkC RNA motif (later renamed Guanidine-II riboswitch) was discovered as a putative RNA structure that is conserved in bacteria. The motif consists of two conserved stem-loops whose terminal loops contain the RNA sequence ACGR, where R represents either A or G. Mini-ykkC RNAs are widespread in Pseudomonadota, but some are predicted in other phyla of bacteria. It was expected that the RNAs are cis-regulatory elements, because they are typically located upstream of protein-coding genes. The genes that are apparently controlled by mini-ykkC RNAs bear a resemblance to the genes controlled by ykkC-yxkD leader The ykkC/yxkD leader is a conserved sequence, conserved Cis-regulatory element, RNA structure found Upstream and downstream (DNA), upstream of the ykkC and yxkD genes in ''Bacillus subtilis'' and related genes in other bacteria. The function of t ... (guanidine-I), and nine gene families are common to both. Therefore, it was proposed that these two RNA classes have ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Guanidine
Guanidine is the compound with the formula HNC(NH2)2. It is a colourless solid that dissolves in polar solvents. It is a strong base that is used in the production of plastics and explosives. It is found in urine predominantly in patients experiencing renal failure. A guanidine moiety also appears in larger organic molecules, including on the side chain of arginine. Structure Guanidine can be thought of as a nitrogenous analogue of carbonic acid. That is, the C=O group in carbonic acid is replaced by a C=NH group, and each OH is replaced by a group. Isobutene can be seen as the carbon analogue in much the same way. A detailed crystallographic analysis of guanidine was elucidated 148 years after its first synthesis, despite the simplicity of the molecule. In 2013, the positions of the hydrogen atoms and their displacement parameters were accurately determined using single-crystal neutron diffraction. Production Guanidine can be obtained from natural sources, being first isolat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Permease
The permeases are membrane transport proteins, a class of multipass transmembrane proteins that allow the diffusion of a specific molecule in or out of the cell in the direction of a concentration gradient, a form of facilitated diffusion. The permease binding is first step of translocation. LacY protein from Escherichia coli is an example of a permease. See also * Lactose permease * Beta-galactoside permease It was originally discovered in the 1930s by Joy Adames. It is a transporter protein that helps in various aspects of cellular life including DNA replication, translation of RNA, and diffusion. * Amino acid permease Amino acid permeases are membrane permeases involved in the transport of amino acids into the cell. A number of such proteins have been found to be evolutionary related. These proteins contain 12 transmembrane segments. See also *Amino acid tra ... A permease (porter) is a protein or protein complex that catalyzes a vectorial reaction, irrespective of whether ... [...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] |
Thermoanaerobacter Tengcongensis
''Thermoanaerobacter'' is a genus in the phylum Bacillota (Bacteria). Members of this genus are thermophilic and anaerobic, several of them were previously described as ''Clostridium'' species and members of the now obsolete genera ''Acetogenium'' and ''Thermobacteroides'' Etymology The name ''Thermoanaerobacter'' derives from:Greek adjective ''thermos (θερμός)'', hot; Greek prefix ''an (ἄν)'', not; Greek noun ''aer, aeros (ἀήρ, ἀέρος)'', air; New Latin masculine gender noun, '' bacter'', nominally meaning "a rod", but in effect meaning a bacterium, rod; New Latin masculine gender noun ''Thermoanaerobacter'', rod which grows in the absence of air at elevated temperatures. Species The genus contains 15 species, namely * '' T. acetoethylicus'' (Ben-Bassat and Zeikus 1983) Rainey and Stackebrandt 1993 (Latin noun ''acetum'', vinegar; New Latin adjective ''ethylicus'', pertaining to ethyl alcohol; New Latin masculine gender adjective ''acetoethylicus'', intended ... [...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] |
Efflux (microbiology)
In microbiology, efflux is the moving of a variety of different compounds out of cells, such as antibiotics, heavy metals, organic pollutants, plant-produced compounds, quorum sensing signals, bacterial metabolites and neurotransmitters. All microorganisms, with a few exceptions, have highly conserved DNA sequences in their genome that are transcribed and translated to efflux pumps. Efflux pumps actively move substances out of a microorganism, in a process known as active efflux, which is a vital part of xenobiotic metabolism. This active efflux mechanism is responsible for various types of resistance to bacterial pathogens within bacterial species - the most concerning being antibiotic resistance because microorganisms can have adapted efflux pumps to divert toxins out of the cytoplasm and into extracellular media. Efflux systems function via an energy-dependent mechanism (active transport) to pump out unwanted toxic substances through specific efflux pumps. Some efflux systems ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 ''Bacillus'', ''B. subtilis'' is rod-shaped, and can form a tough, protective endospore, allowing it to tolerate extreme environmental conditions. ''B. subtilis'' has historically been classified as an obligate aerobe, though evidence exists that it is a facultative anaerobe. ''B. subtilis'' is considered the best studied Gram-positive bacterium and a model organism to study bacterial chromosome replication and cell differentiation. It is one of the bacterial champions in secreted enzyme production and used on an industrial scale by biotechnology companies. Description ''Bacillus subtilis'' is a Gram-positive bacterium, rod-shaped and catalase-positive. It was originally named ''Vibrio subtilis'' by Christian Gottfried Ehrenberg, and renamed ''B ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
