This chapter reviews what is known about the mechanism of precursor tRNA splicing: (i) the tRNA substrates for the splicing reaction, (ii) the enzymes involved in removing the introns to form the mature tRNA, (iii) interactions between these enzymes and their tRNA substrates and cofactors, (iv) the organization of tRNA splicing in the nucleus, (v) the identity of splicing mutants that affect the enzymatic machinery, (vi) current knowledge about the differences and similarities of tRNA splicing in systems of various organisms, and (vii) the possible function of tRNA introns.
One unique example of RNA processing is non-conventional splicing of RNAs, which is an essential step during transfer RNA (tRNA) maturation. tRNAs are transcribed as precursor transcripts (pre-tRNA) and are subjected to multiple posttranscriptional processing events before they can fulfil their function. Intron-containing pre-tRNAs undergo non-conventional splicing-a cytosolic, enzyme-catalysed processing reaction. The splicing of pre-tRNAs occurs in two steps: The intron is first excised by a splicing endonuclease and the resulting tRNA exon halves are ligated by tRNA ligase to form a fully matured functional tRNA. Because eukaryotic tRNA introns disrupt the anticodon stem-loop structure, the removal of these introns is an essential process ...
ID VULDI_1_PE807 STANDARD; PRT; 366 AA. AC VULDI_1_PE807; E1QP51; DT 00-JAN-0000 (Rel. 1, Created) DT 00-JAN-0000 (Rel. 2, Last sequence update) DT 00-JAN-0000 (Rel. 3, Last annotation update) DE SubName: Full=Translation initiation factor, aIF-2BI family; EC=5.3.1 23; DE (VULDI_1.PE807). GN OrderedLocusNames=Vdis_0830; OS VULCANISAETA DISTRIBUTA DSM 14429. OC Archaea; Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae; OC Vulcanisaeta. OX NCBI_TaxID=572478; RN [0] RP -.; RG -.; RL -.; CC -!- SEQ. DATA ORIGIN: Translated from the HOGENOM CDS VULDI_1.PE807. CC Vulcanisaeta distributa DSM 14429 chromosome, complete genome. CC annotated by Ensembl Genomes CC -!- ANNOTATIONS ORIGIN:E1QP51_VULDI CC -!- SIMILARITY: Belongs to the eIF-2B alpha/beta/delta subunits CC family. CC -!- GENE_FAMILY: HOG000224730 [ FAMILY / ALN / TREE ] DR UniProtKB/Swiss-Prot; E1QP51; -. DR EMBL; CP002100; ADN50222.1; -; Genomic_DNA. DR RefSeq; YP_003901273.1; NC_014537.1. DR GeneID; 9751759; -. DR GenomeReviews; ...
Este grupo comprende as ordes Thermoproteales, Sulfolobales, Desulfurococcales e Caldisphaerales (pero propuxéronse cambios), e inclúe as especies coas temperaturas de crecemento máis altas de calquera organismo coñecido. O crecemento óptimo realízase entre 75 e 105 °C, e a temperatura máxima de crecemento para Pyrolobus chega a 113 °C. A maioría destas especies non poden crecer por debaixo de 70 °C, aínda que poden sobrevivir por períodos longos a baixas temperaturas. Algunhas especies son acidófilas cun pH óptimo entre 1,5 e 4 e morren a pH 7, e outras son neutrófilas ou lixeiramente acidófilas, crecendo optimamente a un pH de 5,5-7,5. Encóntranse en hábitats volcánicos tales como mananciais quentes continentais e en fontes hidrotermais do fondo oceánico, a pouca ou moita profundidade. Os tipos de metabolismo que presentan son diversos, desde quimioorganótrofos a quimiolitótrofos. Os quimiolitótrofos aerobios obteñen enerxía da oxidación de varios compostos ...
ID CALMQ_1_PE388 STANDARD; PRT; 370 AA. AC CALMQ_1_PE388; A8MBP9; DT 00-JAN-0000 (Rel. 1, Created) DT 00-JAN-0000 (Rel. 2, Last sequence update) DT 00-JAN-0000 (Rel. 3, Last annotation update) DE SubName: Full=eIF-2B alpha/beta/delta-related uncharacterized protein; DE EC=5.3.1 23; (CALMQ_1.PE388). GN OrderedLocusNames=Cmaq_0396; OS CALDIVIRGA MAQUILINGENSIS IC-167. OC Archaea; Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae; OC Caldivirga. OX NCBI_TaxID=397948; RN [0] RP -.; RG -.; RL -.; CC -!- SEQ. DATA ORIGIN: Translated from the HOGENOM CDS CALMQ_1.PE388. CC Caldivirga maquilingensis IC-167 chromosome, complete genome. CC sequence. CC -!- ANNOTATIONS ORIGIN:A8MBP9_CALMQ CC -!- SIMILARITY: Belongs to the eIF-2B alpha/beta/delta subunits CC family. CC -!- GENE_FAMILY: HOG000224730 [ FAMILY / ALN / TREE ] DR UniProtKB/Swiss-Prot; A8MBP9; -. DR EMBL; CP000852; ABW01242.1; -; Genomic_DNA. DR RefSeq; YP_001540232.1; NC_009954.1. DR ProteinModelPortal; A8MBP9; -. DR STRING; A8MBP9; ...
Lineage: cellular organisms; Archaea; TACK group; Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae; Pyrobaculum; Pyrobaculum ...
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2 JUDICIAL COMMISSION OF THE INTERNATIONAL COMMITTEE ON SYSTEMATICS OF PROKARYOTES: The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79. Int. J. Syst. Evol. Microbiol., 2005, 55, 517-518 ...
2 JUDICIAL COMMISSION OF THE INTERNATIONAL COMMITTEE ON SYSTEMATICS OF PROKARYOTES: The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79. Int. J. Syst. Evol. Microbiol., 2005, 55, 517-518 ...
A computer program, ARAGORN, identifies tRNA and tmRNA genes. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base-paired cloverleaf. tmRNA genes are identified using a modified version of the BRUCE program. ARAGORN achieves a detection sensitivity of 99% from a set of 1290 eubacterial, eukaryotic and archaeal tRNA genes and detects all complete tmRNA sequences in the tmRNA database, improving on the performance of the BRUCE program. Recently discovered tmRNA genes in the chloroplasts of two species from the green algae lineage are detected. The output of the program reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags.. ...
Introns may be lost or gained over evolutionary time, as shown by many comparative studies of orthologous genes. Subsequent analyses have identified thousands of examples of intron loss and gain events, and it has been proposed that the emergence of eukaryotes, or the initial stages of eukaryotic evolution, involved an intron invasion.[32] Two definitive mechanisms of intron loss, Reverse Transcriptase-Mediated Intron Loss (RTMIL) and genomic deletions, have been identified, and are known to occur.[33] The definitive mechanisms of intron gain, however, remain elusive and controversial. At least seven mechanisms of intron gain have been reported thus far: Intron Transposition, Transposon Insertion, Tandem Genomic Duplication, Intron Transfer, Intron Gain during Double-Strand Break Repair (DSBR), Insertion of a Group II Intron, and Intronization. In theory it should be easiest to deduce the origin of recently gained introns due to the lack of host-induced mutations, yet even introns gained ...
The remarkable diversity of the morphologies of viruses found in terrestrial hydrothermal environments with temperatures ,80°C is unprecedented for aquatic ecosystems. The best-studied viruses from these habitats have been assigned to novel viral families: Fuselloviridae, Lipothrixviridae and Rudiviridae. They all have double-stranded DNA genomes and infect hyperthermophilic crenarchaea of the orders Sulfolobales and Thermoproteales. Representatives of the different viral families share a few homologous ORFs (open reading frames). However, about 90% of all ORFs in the seven sequenced genomes show no significant matches to sequences in public databases. This suggests that these hyperthermophilic viruses have exceptional biochemical solutions for biological functions. Specific features of genome organization, as well as strategies for DNA replication, suggest that phylogenetic relationships exist between crenarchaeal rudiviruses and the large eukaryal DNA viruses: poxviruses, the African swine ...
The use of dilution culture techniques to cultivate saccharolytic bacteria present in the anoxic soil of flooded rice microcosms allowed the isolation of three new strains of bacteria, typified by their small cell sizes, with culturable numbers estimated at between 1.2 x 10(5) and 7.3 x 10(5) cells per g of dry soil. The average cell volumes of all three strains were 0.03 to 0.04 microns3, and therefore they can be termed ultramicrobacteria or dwarf cells. The small cell size is a stable characteristic, even when the organisms grow at high substrate concentrations, and thus is not a starvation response. All three strains have genomic DNA with a mol% G+C ratio of about 63, are gram negative, and are motile by means of a single flagellum. The three new isolates utilized only sugars and some sugar polymers as substrates for growth. The metabolism is strictly fermentative, but the new strains are oxygen tolerant. Sugars are metabolized to acetate, propionate, and succinate. Hydrogen production was ...
p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.,/p> ,p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.,/p> ,p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).,/p> ,p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x,sup>64,/sup> + x,sup>4,/sup> + x,sup>3,/sup> + x + 1. The algorithm is described in the ISO 3309 standard. ,/p> ,p class=publication>Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.,br /> ,strong>Cyclic redundancy and other checksums,/strong>,br /> ,a href=http://www.nrbook.com/b/bookcpdf.php>Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993),/a>),/p> Checksum:i ...
Zhang, E. and Y.-Y. Chen, 2006. Revised diagnosis of the genus Bangana Hamilton, 1822 (Pisces: Cyprinidae), with taxonomic and nomenclatural notes on the Chinese species. Zootaxa (1281):41-54. (Ref. 72360 ...
nomenclatural synonym:Poaceae trib. Arundineae Dumort. Observ. Gramin. Belg. 82. 1824 [Jul-Sep 1824] Id: 1167508-2 Version: 1.2 View Record history. View this record in TCS-RDF format. ...
ISOTOMA LONGIFLORA PDF - display_name: Isotoma longiflora (L.) C. Presl nomenclatural_code: ICZN remark: Imported from ITIS 6 Feb scientific_name: Isotoma longiflora. Isotoma
nomenclatural synonym:Poaceae Oryza clandestina f. inclusa Wiesb. Deutsche Bot. Monatsschr. 15: 19. 1897 Id: 137036-2 Version: 1.2 View Record history. View this record in TCS-RDF format. ...
CAVIA COBAYA PDF - match type not available. display_name: Cavia cobaya nomenclatural_code: ICZN scientific_name: Cavia cobaya source_authority: UCMP taxon_status: valid.
center>,big>,big>,big>Cyanobacteria - Blue-Green Algae,/big>,/big>,/big>,/center> ,br> [[Image:Anabaena sperica.jpg,thumb,200px,center,Anabaena sperica, a filamentous cyanobacterium ([[Phycobacteria]], [[Nostocales]], [[Nostocaceae]])]] ,br> ,table border=1 cellpadding=3 cellspacing=1 width=100% > ,tr>,th bgcolor=#CCCCCC colspan=2>Cyanobacteria,/th>,/tr> ,tr> ,td align=center width=200 valign=top >Linnaean Hierarchy,/td> ,td align=center width=400 valign=top >Local Cladogram,/td> ,/tr> ,tr> ,td align=justify valign=top > [[Domain]]: [[Eubacteria]],br> [[Division]]: Cyanobacteria,br> [[Order]]s: * [[Chroococcales]] * [[Prochlorales]] * [[Pleurocapsales]] * [[Oscillatoriales]] * [[Nostocales]] * [[Stigonematales]] ,/td> ,td align=justify valign=top> [[LUCA]] ,--[[Eubacteria]] (note) , ,--[[Clostridea]] , `--[[Cyanobacteria]] , see [[#Phylogeny,phylogeny section]] (below) for subgroups `--[[Neomura]] ,--[[Archaea]] ...
The Global Ocean Sampling database contains half as many 4-hydroxybutyryl-CoA dehydratase sequences as compared with those found for another key photosynthetic CO2-fixing enzyme, ribulose-1,5-bisphosphate carboxylase-oxygenase, indicating the importance of this enzyme in global carbon cycling. The assimilation of carbon dioxide (CO2) into organic material is quantitatively the most important biosynthetic process. We discovered that an autotrophic member of the archaeal order Sulfolobales, Metallosphaera sedula, fixed CO2 with acetyl-coenzyme A (acetyl-CoA)/propionyl-CoA carboxylase as the key carboxylating enzyme. In this system, one acetyl-CoA and two bicarbonate molecules were reductively converted via 3-hydroxypropionate to succinyl-CoA. This intermediate was reduced to 4-hydroxybutyrate and converted into two acetyl-CoA molecules via 4-hydroxybutyryl-CoA dehydratase. The key genes of this pathway were found not only in Metallosphaera but also in Sulfolobus, Archaeoglobus, and Cenarchaeum species.
Cavenderia amphispora (Cavender, Vadell, J.C. Landolt & S.L. Stephenson) S. Baldauf, S. Sheikh & Thulin, in Sheikh et al., Protist 169(1):19 (2018) [see pdf] ...
Cavenderia medusoides (Vadell, M.T. Holmes & Cavender) S. Baldauf, S. Sheikh & Thulin, in Sheikh et al., Protist 169(1):19 (2018) [see pdf] ...
Name: [Bacteria, not assigned to phylum]. Category: Phylum. Proposed as: LPSN placeholder (potentially permanent). Nomenclatural status: artificial parent node of taxa incertae sedis ...