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Pyrobaculum AsR3 Small RNA
asR3 is an archeal small RNA identified in seven ''Pyrobaculum ''Pyrobaculum'' is a genus of the Thermoproteaceae. Description and significance As its Latin name ''Pyrobaculum'' (the "fire stick") suggests, the archaeon is rod-shaped and isolated from locations with high temperatures. It is Gram-negative ...'' species. The genus-specific nature can indicate this could be recent, stable adaptation. asR3 binds to the 3′-end of the ''tpi'' gene ( triose-phosphate-isomerse). The tpi mRNA has a conserved structural element located close to the stop codon. Binding of the asR3 may be able to compete against the formation of the tpi element structure and this may modulate the function of this highly conserved element. References See also Other archaeal sRNAs: * Archaeal H/ACA sRNA * Methanosarcina sRNA162 Non-coding RNA {{molecular-cell-biology-stub ... [...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] |
Archaea
Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), but this term has fallen out of use. Archaeal cells have unique properties separating them from the other two domains, Bacteria and Eukaryota. Archaea are further divided into multiple recognized phyla. Classification is difficult because most have not been isolated in a laboratory and have been detected only by their gene sequences in environmental samples. Archaea and bacteria are generally similar in size and shape, although a few archaea have very different shapes, such as the flat, square cells of ''Haloquadratum walsbyi''. Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Small RNA
Small RNA (sRNA) are polymeric RNA molecules that are less than 200 nucleotides in length, and are usually non-coding Non-coding DNA (ncDNA) sequences are components of an organism's DNA that do not encode protein sequences. Some non-coding DNA is transcribed into functional non-coding RNA molecules (e.g. transfer RNA, microRNA, piRNA, ribosomal RNA, and regula .... RNA silencing is often a function of these molecules, with the most common and well-studied example being RNA interference (RNAi), in which endogenously expressed microRNA (miRNA) or exogenously derived small interfering RNA (siRNA) induces the degradation of complementarity (molecular biology), complementary messenger RNA. Other classes of small RNA have been identified, including piwi-interacting RNA (piRNA) and its subspecies rasiRNA, repeat associated small interfering RNA (rasiRNA). Small RNA "is unable to induce RNAi alone, and to accomplish the task it must form the core of the RNA–protein complex termed the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pyrobaculum
''Pyrobaculum'' is a genus of the Thermoproteaceae. Description and significance As its Latin name ''Pyrobaculum'' (the "fire stick") suggests, the archaeon is rod-shaped and isolated from locations with high temperatures. It is Gram-negative and its cells are surrounded by an S-layer of protein subunits. ''P. aerophilum'' is a hyperthermophilic and metabolically versatile organism. Different from other hyperthermophiles, it can live in the presence of oxygen and grows efficiently in microaerobic conditions. ''Pyrobaculum yellowstonensis'' strain WP30 was obtained from an elemental sulfur sediment (Joseph's Coat Hot Spring CHS 80 °C, pH 6.1, 135 μM As) in Yellowstone National Park (YNP), USA and is a chemoorganoheterotroph and requires elemental sulfur and/or arsenate as an electron acceptor. Growth in the presence of elemental sulfur and arsenate resulted in the formation of thioarsenates and polysulfides. The complete genome of this organism was sequenced (1.99 Mb, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Triosephosphate Isomerase
Triose-phosphate isomerase (TPI or TIM) is an enzyme () that catalyzes the reversible interconversion of the triose phosphate isomers dihydroxyacetone phosphate and D-glyceraldehyde 3-phosphate. TPI plays an important role in glycolysis and is essential for efficient energy production. TPI has been found in nearly every organism searched for the enzyme, including animals such as mammals and insects as well as in fungi, plants, and bacteria. However, some bacteria that do not perform glycolysis, like ureaplasmas, lack TPI. In humans, deficiencies in TPI are associated with a progressive, severe neurological disorder called triose phosphate isomerase deficiency. Triose phosphate isomerase deficiency is characterized by chronic hemolytic anemia. While there are various mutations that cause this disease, most include the replacement of glutamic acid at position 104 with an aspartic acid. Triose phosphate isomerase is a highly efficient enzyme, performing the reaction billion ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Archaeal H/ACA SRNA
In archaea like in eukaryotes, uridines in various RNAs are converted to pseudouridines by ribonucleoprotein complexes ( RNPs) containing H/ACA sRNA. Because of their conserved function, these sRNAs are also called small "nucleolar" RNAs (snoRNA) like in eukaryotes, despite no nucleus is present in prokaryotes. By using various computational and experimental approaches in three ''Pyrococcus'' genomes seven H/ACA sRNAs and 15 pseudouridine (Ψ) resides on rRNA were identified. One H/ACA motif was shown to guide up to three distinct pseudouridylations. Atypical pseudouridine guide RNA features were identified in ''Pyrobaculum'' species. Lack of the conserved 3'-terminal ACA sequence and sometimes lack of 5' portion of the pseudouridylation pocket feature in few conserved ''Pyrobaculum'' H/ACA-like sRNAs. A study by Toffano-Nioche ''et al.'' proposes an unified structure/function model based on the common structural components in "Euryarchaeota" and Thermoproteota (formerly C ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Methanosarcina SRNA162
sRNA162, sRNA154, sRNA41 are small non-coding RNA (sRNA) identified together with 248 other sRNA candidates by RNA sequencing in methanogenic archaeon ''Methanosarcina mazei'' Gö1. These sRNAs were further characterised. It was shown that sRNA162 can interact with both, a '' cis-'' and a ''trans''-encoded mRNAs using two distinct domains. The sRNA overlaps the 5′UTR of the MM2442 mRNA and acts as a cis-encoded antisense RNA, and it also regulates MM2441 expression as a trans-encoded sRNA. It exhibits a regulatory role in the metabolic switch between methanol and trimethylamine as carbon and energy source. sRNA154, exclusively expressed under nitrogen deficiency, has a central regulatory role in nitrogen metabolism affecting nitrogenase and glutamine synthetase by masking the ribosome binding site or positively affecting transcript stability. sRNA41, highly expressed during nitrogen sufficiency, is capable to bind several ribosome binding sites independently within a polycist ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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