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Tetrahydrofolate Riboswitch
Tetrahydrofolate riboswitches are a class of homologous RNAs in certain bacteria that bind tetrahydrofolate (THF). It is almost exclusively located in the probable 5' untranslated regions of protein-coding genes, and most of these genes are known to encode either folate transporters or enzymes involved in folate metabolism. For these reasons it was inferred that the RNAs function as riboswitches. THF riboswitches are found in a variety of Bacillota, specifically the orders Clostridiales and Lactobacillales, and more rarely in other lineages of bacteria. The THF riboswitch was one of many conserved RNA structures found in a project based on comparative genomics. The 3-d structure of the tetrahydrofolate riboswitch has been solved by separate groups using X-ray crystallography. These structures were deposited into the Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and ... [...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] |
Membrane Transport Protein
A membrane transport protein (or simply transporter) is a membrane protein involved in the movement of ions, small molecules, and macromolecules, such as another protein, across a biological membrane. Transport proteins are integral transmembrane proteins; that is they exist permanently within and span the membrane across which they transport substances. The proteins may assist in the movement of substances by facilitated diffusion or active transport. The two main types of proteins involved in such transport are broadly categorized as either ''channels'' or ''carriers''. The solute carriers and atypical SLCs are secondary active or facilitative transporters in humans. Collectively membrane transporters and channels are known as the transportome. Transportomes govern cellular influx and efflux of not only ions and nutrients but drugs as well. Difference between channels and carriers A carrier is not open simultaneously to both the extracellular and intracellular environments. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, RCSB, and BMRB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB. The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB. For example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. History Two force ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Comparative Genomics
Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural landmarks. In this branch of genomics, whole or large parts of genomes resulting from genome projects are compared to study basic biological similarities and differences as well as evolutionary relationships between organisms. The major principle of comparative genomics is that common features of two organisms will often be encoded within the DNA that is evolutionarily conserved between them. Therefore, comparative genomic approaches start with making some form of alignment of genome sequences and looking for orthologous sequences (sequences that share a common ancestry) in the aligned genomes and checking to what extent those sequences are conserved. Based on these, genome and molecular evolution are inferred and this may in turn be put in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Order (biology)
Order ( la, wikt:ordo#Latin, ordo) is one of the eight major hierarchical taxonomic ranks in Linnaean taxonomy. It is classified between Family_(biology), family and Class_(biology), class. In biological classification, the order is a taxonomic rank used in the classification of organisms and recognized by the nomenclature codes. An immediately higher rank, superorder, is sometimes added directly above order, with suborder directly beneath order. An order can also be defined as a group of related families. What does and does not belong to each order is determined by a taxonomist, as is whether a particular order should be recognized at all. Often there is no exact agreement, with different taxonomists each taking a different position. There are no hard rules that a taxonomist needs to follow in describing or recognizing an order. Some taxa are accepted almost universally, while others are recognized only rarely. The name of an order is usually written with a capital letter. Fo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacillota
The Bacillota (synonym Firmicutes) are a phylum of bacteria, most of which have gram-positive cell wall structure. The renaming of phyla such as Firmicutes in 2021 remains controversial among microbiologists, many of whom continue to use the earlier names of long standing in the literature. The name "Firmicutes" was derived from the Latin words for "tough skin," referring to the thick cell wall typical of bacteria in this phylum. Scientists once classified the Firmicutes to include all gram-positive bacteria, but have recently defined them to be of a core group of related forms called the low- G+C group, in contrast to the Actinomycetota. They have round cells, called cocci (singular coccus), or rod-like forms (bacillus). A few Firmicutes, such as ''Megasphaera'', ''Pectinatus'', ''Selenomonas'' and ''Zymophilus'', have a porous pseudo-outer membrane that causes them to stain gram-negative. Many Bacillota (Firmicutes) produce endospores, which are resistant to desiccation and can ... [...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] |
Metabolism
Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cellular processes; the conversion of food to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of metabolic wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to the sum of all chemical reactions that occur in living organisms, including digestion and the transportation of substances into and between different cells, in which case the above described set of reactions within the cells is called intermediary (or intermediate) metabolism. Metabolic reactions may be categorized as ''catabolic'' – the ''breaking down'' of compounds (for example, of glucose to pyruvate by ce ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Enzyme
Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. Almost all metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called ''enzymology'' and the field of pseudoenzyme analysis recognizes that during evolution, some enzymes have lost the ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties. Enzymes are known to catalyze more than 5,000 biochemical reaction types. Other biocatalysts are catalytic RNA molecules, called ribozymes. Enzymes' specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the reaction ra ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Folate
Folate, also known as vitamin B9 and folacin, is one of the B vitamins. Manufactured folic acid, which is converted into folate by the body, is used as a dietary supplement and in food fortification as it is more stable during processing and storage. Folate is required for the body to make DNA and RNA and metabolise amino acids necessary for cell division. As humans cannot make folate, it is required in the diet, making it an essential nutrient. It occurs naturally in many foods. The recommended adult daily intake of folate in the U.S. is 400 micrograms from foods or dietary supplements. Folate in the form of folic acid is used to treat anemia caused by folate deficiency. Folic acid is also used as a supplement by women during pregnancy to reduce the risk of neural tube defects (NTDs) in the baby. Low levels in early pregnancy are believed to be the cause of more than half of babies born with NTDs. More than 80 countries use either mandatory or voluntary fortification of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Clostridiales
The Eubacteriales are an order of bacteria placed within the class Clostridia. Families Eubacteriales comprises the following families: * " Betainaceae" Jones et al. 2019 * " Bianqueaceae" Liu et al. 2021 * " Borkfalkiaceae" Hildebrand, Pallen & Bork 2020 * Caldicoprobacteraceae Yokoyama et al. 2010 * Christensenellaceae Morotomi, Nagai & Watanabe 2012 * Clostridiaceae Pribram 1933 * Defluviitaleaceae Jabari et al. 2012 * Eubacteriaceae Ludwig et al. 2010 * " Feifaniaceae" Liu et al. 2021 * " Galloscillospiraceae" Gilroy et al. 2021 * Gottschalkiaceae Poehlein et al. 2017c * Hungateiclostridiaceae Zhang et al. 2018b * Lachnospiraceae Rainey 2010 * " Mageeibacillaceae" Hildebrand, Pallen & Bork 2020 * " Mogibacteriaceae" Wylensek et al. 2020 * Oscillospiraceae Peshkoff 1940 * Peptoniphilaceae Johnson et al. 2014 * Peptostreptococcaceae Ezaki 2010 * Ruminococcaceae Rainey 2010 * " Pumilibacteraceae" Afrizal et al. 2021 * Thermohalobacteraceae Spring 2021 * Tissierellaceae W ... [...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] |
