• This study was conducted to compare the level of conservation at the DNA level (micro-colinearity) between wheat, rice and Brachypodium within a genomic region harboring the wheat domestication gene Q. We found that the micro-colinearity of genes was more conserved between wheat and rice than between wheat and Brachypodium. (usda.gov)
  • 1990 Fortunately while the high degree of conservation seen in natural product biosynthetic genes makes the accurate assembly MK-3102 of metagenomic EDM1 gene clusters hard it also allows for a substantial amount of information pertaining to the biosynthetic pathways present in a metagenome to be gleaned through the use of a PCR-based sequence tag approach that targets these conserved genes (Udwary et al. (ecolowood.com)
  • In most eukaryotes studied, ubiquitin is encoded by two classes of genes: (i) The first comprises genes coding for a single copy of ubiquitin fused to ribosomal proteins (r-proteins), most commonly eL40 and eS31. (123dok.net)
  • It usually contains 37 genes, encoding for 2 ribosomal RNAs (rRNAs), 13 proteins, and 22 transfer RNAs (tRNAs). (biomedcentral.com)
  • To resolve their evolutionary relationships and provide a first estimate of their divergence times, we used a transcriptomic approach to build a phylogenomic dataset including all major tunicate lineages, consisting of 258 evolutionarily conserved orthologous genes from representative species. (biomedcentral.com)
  • Here, we provide the first cytogenetic information on the species based on both conventional karyotyping and chromosomal mapping of 45S and 5S ribosomal genes through fluorescence in situ hybridization (FISH). (scielo.br)
  • Both classes of ribosomal genes appeared to be spread out to multiple chromosomal locations, i.e. the 45S and 5S rDNA clusters were detected on six and seven chromosome pairs, respectively. (scielo.br)
  • A linked chromosomal organization of the major and minor ribosomal genes classes has been visualized in most of the rDNAs chromosomal locations. (scielo.br)
  • This proliferation bias can be corrected by measuring the level of expression of host cellular RNAs, such as ribosomal RNAs or housekeeping genes. (biomedcentral.com)
  • A positionally conserved ORF has been found on the complementary strand of the cox1 genes of both eukaryotic mitochondria (protist, plant, fungal and animal) and alpha-proteobacteria. (biomedcentral.com)
  • Typical triploblastic animal mtDNAs contain genes that encode the large and small subunit ribosomal RNAs, 22 transfer RNAs (tRNAs), and 13 proteins that are all components of the oxidative phosphorylation process: ATPase subunits 6 and 8 (ATP6 and 8), cytochrome b (Cyt b), cytochrome c oxidase subunits 1-3 (Cox1-3) and NADH dehydrogenase subunits 1-6 and 4L (ND1-6 and 4L). (biomedcentral.com)
  • This search has led to the observation of an unknown, positionally conserved open reading frame (ORF) on the complementary strand of eukaryotic cox1 genes. (biomedcentral.com)
  • Role of unequal crossing-over in the evolution of ribosomal genes. (cnr.it)
  • Identification of transcription and processing signals of ribosomal genes of D. melanogaster. (cnr.it)
  • Plant mitochondrial genomes contain genes for their own rRNA subunits as well as for some of the ribosomal proteins and tRNAs required for translation (Figure 1 ), but many necessary ribosomal protein and tRNA genes are located in the nuclear genome, so their gene products must be imported into the mitochondrion [ 15 ]. (biomedcentral.com)
  • Sequencing the genomes of multiple, taxonomically diverse eukaryotes enables in-depth comparative-genomic analysis which is expected to help in reconstructing ancestral eukaryotic genomes and major events in eukaryotic evolution and in making functional predictions for currently uncharacterized conserved genes. (biomedcentral.com)
  • These conserved KOGs are often essential for survival and might approximate the minimal set of essential eukaryotic genes. (biomedcentral.com)
  • The KOG analysis reveals a conserved core of largely essential eukaryotic genes as well as major diversification and innovation associated with evolution of eukaryotic genomes. (biomedcentral.com)
  • however, it is believed that the other features of EBER2, particularly its two long and highly conserved stem-loops, may also serve as binding sites for yet unknown proteins. (wikipedia.org)
  • They are among the most conserved proteins and are subject to a plethora of post-translational modifications. (huanglab.ac)
  • It is generated by proteolytic cleavage of precursor proteins in which it is fused either to itself, constituting a polyubiquitin precursor of head-to-tail monomers, or as a single N-terminal moiety to ribosomal proteins. (123dok.net)
  • Understanding the role of the ubiquitin fused to ribosomal proteins becomes relevant, as these proteins are practically invariably eS31 and eL40 in the different eukaryotes. (123dok.net)
  • Herein, we used the amenable yeast Saccharomyces cerevisiae to study whether ubiquitin facilitates the expression of the fused eL40 (Ubi1 and Ubi2 precursors) and eS31 (Ubi3 precursor) ribosomal proteins. (123dok.net)
  • We conclude that ubiquitin might serve as a cis-acting molecular chaperone that assists in the folding and synthesis of the fused eL40 and eS31 ribosomal proteins. (123dok.net)
  • Ubiquitin fusion to other r-proteins, such as P1 or P2, and even to non-ribosomal proteins such as actin, has been reported in diverse genera of rare single-celled algae as, for example, Bigelowiella [6]. (123dok.net)
  • Similarly to the studies carried out two decades ago for proteins, which gave the fundamental grounds for developing comparative protein structure prediction methods, we are now able to quantify the relationship between sequence and structure conservation in RNA. (biomedcentral.com)
  • Nonetheless, it is common knowledge that RNA 3D structure is more conserved than RNA sequence and that such principle could be used for comparative RNA structure prediction in a similar way it is done for proteins [ 11 ]. (biomedcentral.com)
  • Package C/D snoRNAs are named after a common RNA motif with this subfamily that serves as a binding site for a group of box C/D proteins including NOP56 NOP58 15.5 and the conserved proteins fibrillarin which provides the particular 2'-O-methylase activity highly. (biobender.com)
  • Despite an evolutionary distance of at least 1.5 to 2.0 billion years, the deduced Gau proteins share some conserved amino acid signatures and structure, which suggests a possible conserved function. (biomedcentral.com)
  • Cysteines are one of the most rarely used amino acids, but when conserved in proteins they often play critical roles in structure, function, or regulation. (hindawi.com)
  • Indeed, it has been demonstrated that cysteines are characterized by the most extreme conservation pattern, being highly conserved in functional positions of proteins but poorly conserved otherwise [ 5 ]. (hindawi.com)
  • As observed more broadly in angiosperms, ribosomal proteins have been especially prone to gene loss in the S. latifolia lineage. (biomedcentral.com)
  • EBER1 associates with human ribosomal protein L22 and causes this protein to move from the nucleolus to the nucleoplasm. (wikipedia.org)
  • RL11_THEMA ] This protein binds directly to 23S ribosomal RNA. (proteopedia.org)
  • We report the crystal structure of a 58 nucleotide fragment of 23S ribosomal RNA bound to ribosomal protein L11. (proteopedia.org)
  • Finding a similar 90° kink in a region of ribosomal RNA that binds factors necessary for the initiation of protein synthesis, the researchers speculate that the SARS virus may use the s2m element to hijack its host cell's protein synthesis machinery. (sciencedaily.com)
  • Phosphoprotein P0 is a highly conserved ribosomal protein that forms the central scaffold of the large ribosomal subunit's "stalk complex", which is necessary for recruiting protein elongation factors to the ribosome. (uri.edu)
  • Here we describe Rfoot, a computational pipeline that analyzes ribosomal profiling data and identifies native, nonribosomal RNA-protein complexes. (huanglab.ac)
  • Ubiquitin is a highly conserved small eukaryotic protein. (123dok.net)
  • Ubiquitin is a small eukaryotic protein of 76 amino acids whose name (i.e., it occurs ubiquitously) results from its remarkable evolutionary conservation [1]. (123dok.net)
  • Comparison of the mechanisms that govern the production of calcium carbonate (CaCO 3 ) biominerals in hexacorallians (scleractinians) and octocorallians is thus expected to shed light on the conservation of the protein toolkit used by these organisms for making their biocalcification. (biomedcentral.com)
  • 2017) Characterization of the mammalian DEAD-box protein DDX5 reveals functional conservation with S. cerevisiae ortholog Dbp2 in transcriptional control and glucose metabolism. (bellbrooklabs.com)
  • Although only a subset of lncRNAs show RNase footprints, many of these have multiple footprints, and the protected regions are evolutionarily conserved, suggestive of biological functions. (huanglab.ac)
  • For the Q gene region, micro-colinearity was more conserved between wheat and rice than between wheat and Brachpodium. (usda.gov)
  • Also, a 40S ribosomal-like gene present in T. monococcum and rice was highly degenerate in B. sylvaticum. (usda.gov)
  • Analyses of invasive group A Streptococcus dysgalactiae subspecies equisimilis and conserved genomic pepD gene insertion site of highly related exotoxin speC gene-containing prophages found within group A ST128 S. equisimilis strain. (cdc.gov)
  • Repetitive use of highly conserved biosynthetic domains and the fact that a common ground metagenome may contain 104-105 unique bacterial species make it impractical to assemble large MK-3102 numbers of total biosynthetic gene clusters from metagenomic sequence data (Pop 2009 Rappé and Giovannoni 2003 MK-3102 Torsvik et al. (ecolowood.com)
  • 2012 In this approach conserved biosynthetic domains are PCR amplified from (meta)genomic DNA and the individual next-generation sequencing reads derived from these amplicons termed natural product sequence tags or simply sequence tags are used to establish the relationship between gene clusters present within a pool of metagenomic DNA and a reference set of functionally characterized gene clusters (Figures 1 and ?and55). (ecolowood.com)
  • Consequently, established primers specifically amplifying the archaeal 16S ribosomal gene region are scarce compared to the variety of primers targeting bacterial sequences. (frontiersin.org)
  • The mitochondrial gene content is highly variable across eukaryotes. (biomedcentral.com)
  • Role of Otx1 and Otx2 in brain evolution: functional equivalence between the invertebrate Orthodenticle and the murine OTX1 and OTX2 gene products supports a conserved genetic program of brain development between insects and mammals. (cnr.it)
  • Divergence in one region of 18S rRNA appears to be the result of a gene conversion event, in which recombination with a homologous gene of chloroplast origin led to the complete replacement of a helix in this ribosomal RNA. (biomedcentral.com)
  • Gene expression also relies on extensive C-to-U (and sometimes U-to-C) RNA editing, in which substitution of specific pyrimidines in the mRNA sequence restores phylogenetically conserved codons [ 8 ]. (biomedcentral.com)
  • Conservation of KOGs through the phyletic range of eukaryotes strongly correlates with their functions and with the effect of gene knockout on the organism's viability. (biomedcentral.com)
  • snoRNAs are a family of conserved nuclear RNAs concentrated in nucleoli where they either function in the changes of ribosomal RNA (rRNA) or participate in the control of rRNA during ribosome subunit synthesis[2-5]. (biobender.com)
  • Endogenous snoRNAs are abundant nuclear RNAs that are efficiently prepared from principal transcripts highly. (biobender.com)
  • This element sits at one end of the viral genome, and, as the researchers show, its sequence is highly conserved in related coronaviruses. (sciencedaily.com)
  • Frameshifting elements are highly conserved regions of coronaviruses that are responsible for programmed ribosomal frameshifting (PRF). (growkudos.com)
  • In addition, we also investigated whether the highly conserved nature of P0 meant that it could be useful for phylogenetic and evolutionary studies. (uri.edu)
  • This database combines assay results (phenotypes) with information about sequences, structures, post-translational modifications, and evolutionary conservation. (huanglab.ac)
  • miR21 was one of the 1st miRNAs recognized in the human being genome and displays strong evolutionary conservation across a wide range of vertebrate varieties including mammalian avian and fish clades[9]. (biobender.com)
  • Furthermore, unlike the rest of the SARS genome, which changes rapidly, the s2m element is absolutely conserved in SARS variants obtained from patients during the SARS epidemic. (sciencedaily.com)
  • We have explored the possible conservation of relationships between mRNA abundances and chromosomal organization in the highly reduced genome of Buchnera aphidicola , the primary endosymbiont of the aphids, and a close relative to Escherichia coli . (biomedcentral.com)
  • The genomes of plant mitochondria, like any organelle genome, depend on highly integrated functional coordination with the nucleus. (biomedcentral.com)
  • Simple sequence repeats (SSRs) are highly variable features of all genomes. (biomedcentral.com)
  • The C domain, the central DNA-binding domain (DBD), contains two highly conserved zinc finger motifs that are characteristic of the nuclear receptor superfamily (NRs). (biomedcentral.com)
  • The higher mutation rate of mtDNA compared to nDNA [ 16 ], coupled with variable levels of conservation of mtDNA regions, can be used to delineate different types of phylogenetic relationships among species [ 18 ]. (biomedcentral.com)
  • Sequence comparison and phylogenetic analysis showed striking conservations among insect ecdysone receptors, especially between P. xylostella and other lepidopterans. (biomedcentral.com)
  • When the insert was modeled "in-context" in the presence of a previously published crystal structure of the T. thermophila ribosomal RNA, we discovered a surprising association between the insert and a highly variable portion of the rRNA, termed expansion segment 7, or ES7. (uri.edu)
  • It functions as an RNA chaperone, a transcriptional regulator, a facilitator of mRNA processing, an enabler of nonsense-mediated decay, an important player in R loop resolution, an aid in micro-RNA processing, and an instrument of ribosomal biogenesis. (bellbrooklabs.com)
  • Molecular and structural organization of the non-transcribed spacer (NTS) of ribosomal DNA of D. melanogaster. (cnr.it)
  • Given its ubiquitous nature, wide metabolic and functional impact of its inhibition, and lack of sequence conservation between prokaryotes and humans, the CoA pathway is therefore an attractive pathway for drug discovery for many different infectious diseases, including TB. (nature.com)
  • Scott and colleagues used this approach to hypothesize that the function of the s2m element involves interaction with a conserved host factor during the SARS life cycle. (sciencedaily.com)
  • Preliminary analyses confirm that mutations at highly conserved residues and modifiable residues are more likely to generate phenotypes. (huanglab.ac)
  • This strong sequence conservation indicates that the tertiary structure of s2m could be important for viral function, and when the researchers solved the three-dimensional crystal structure of the element, they found that it had a unique tertiary structure. (sciencedaily.com)
  • Finally, with the aim of characterizing RNA structure diversity, Abraham and co-workers recently studied the RNA conservation at three levels: primary, secondary, and tertiary structure. (biomedcentral.com)
  • CoA is essential for the synthesis of phospholipids, fatty acids, polyketides and non-ribosomal peptides, for the operation of the tricarboxylic acid cycle and in the degradation of lipids 3 . (nature.com)
  • Cap-dependent translation initiation begins when the 40 s ribosomal subunit encounters a start codon as it scans along the 5′UTR. (nature.com)
  • The complete sequences of the galago and rabbit beta-globin locus control regions: extended sequence and functional conservation outside the cores of DNase hypersensitive sites. (shengsci.com)
  • This highly conserved ribonucleoprotein domain is the target for the thiostrepton family of antibiotics that disrupt elongation factor function. (proteopedia.org)
  • However, the secondary structure of EBER2 is highly conserved (see Figure 1). (wikipedia.org)
  • When we investigated if this association could occur in other ciliates, we found very little data for the ES7 sequence in other species, meaning that further analysis on the conservation of this association is not possible at this time. (uri.edu)
  • However, to date no general large-scale study has systematically addressed the quantitative analysis of the relationship between sequence and structure conservation in RNA molecules. (biomedcentral.com)
  • Members of this family also possess highly conserved ATPase and helicase domains, flanked by individually distinctive N and/or C-terminal motifs. (bellbrooklabs.com)
  • A detailed view of a ribosomal active site: the structure of the L11-RNA complex. (proteopedia.org)
  • Wimberly BT, Guymon R, McCutcheon JP, White SW, Ramakrishnan V. A detailed view of a ribosomal active site: the structure of the L11-RNA complex. (proteopedia.org)
  • The E domain, referred to as the ligand binding domain (LBD), functions uniquely to NRs and is well-conserved. (biomedcentral.com)
  • Ribosomal frameshifting is important for virus propagation. (growkudos.com)
  • However, few studies have been conducted to determine the level of conservation at the DNA level (micro-colinearity) between Brachypodium and wheat. (usda.gov)
  • For example, early reports of the imaging of DNA in scanning tunneling microscopes (STMs) used highly ordered pyrolitic graphite (HOPG) substrate, and subsequent investigations showed that at least some of the features reported were not those of DNA at all but of artifacts on the HOPG surface. (nationalacademies.org)