Abstract：
:Amino acid sequences of 2 giant non-structural polyproteins (F1 and F2) of infectious bronchitis virus (IBV), a member of Coronaviridae, were compared, by computer-assisted methods, to sequences of a number of other positive strand RNA viral and cellular proteins. By this approach, juxtaposed putative RNA-dependent RNA polymerase, nucleic acid binding ("finger"-like) and RNA helicase domains were identified in F2. Together, these domains might constitute the core of the protein complex involved in the primer-dependent transcription, replication and recombination of coronaviruses. In F1, two cysteine protease-like domains and a growth factor-like one were revealed. One of the putative proteases of IBV is similar to 3C proteases of picornaviruses and related enzymes of como- nepo- and potyviruses. Search of IBV F1 and F2 sequences for sites similar to those cleaved by the latter proteases and intercomparison of the surrounding sequence stretches revealed 13 dipeptides Q/S(G) which are probably cleaved by the coronavirus 3C-like protease. Based on these observations, a partial tentative scheme for the functional organization and expression strategy of the non-structural polyproteins of IBV was proposed. It implies that, despite the general similarity to other positive strand RNA viruses, and particularly to potyviruses, coronaviruses possess a number of unique structural and functional features.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Gorbalenya AE,Koonin EV,Donchenko AP,Blinov VMdoi
10.1093/nar/17.12.4847subject
Has Abstractpub_date
1989-06-26 00:00:00pages
4847-61issue
12eissn
0305-1048issn
1362-4962journal_volume
17pub_type
杂志文章abstract：:The nucleolus is a unique structural component of interphase nuclei where the ribosomal genes, trans-cribed by RNA polymerase I (RNA pol I), are organized. In the present study, the repair of UV-induced photolesions was investigated in the ribosomal DNA (rDNA) in relation to RNA pol I transcription. We used hamster ce...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.12.2511
更新日期：1999-06-15 00:00:00
abstract：:The TransTerm database of termination codon contexts has been extended to include sense codon usage, and initiation codon contexts. The database was constructed from 23,721 coding sequences from 93 organisms. The database contains: a) the sequence around the termination codon (-10, +10); b) the sequence around the ini...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.17.3620
更新日期：1994-09-01 00:00:00
abstract：:The complete mitochondrial (mt) genome of Crossostoma lacustre, a freshwater loach from mountain stream of Taiwan, has been cloned and sequenced. This fish mt genome, consisting of 16558 base-pairs, encodes genes for 13 proteins, two rRNAs, and 22 tRNAs, in addition to a regulatory sequence for replication and transcr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.18.4853
更新日期：1992-09-25 00:00:00
abstract：:Many infectious diseases are caused by viral infections, and in particular by RNA viruses such as MERS, Ebola and Zika. To understand viral disease, detection and identification of these viruses are essential. Although PCR is widely used for rapid virus identification due to its low cost and high sensitivity and speci...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1095
更新日期：2017-01-04 00:00:00
abstract：:MAGIA(2) (http://gencomp.bio.unipd.it/magia2) is an update, extension and evolution of the MAGIA web tool. It is dedicated to the integrated analysis of in silico target prediction, microRNA (miRNA) and gene expression data for the reconstruction of post-transcriptional regulatory networks. miRNAs are fundamental post...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks460
更新日期：2012-07-01 00:00:00
abstract：:Several proteins that have substantially diverged during evolution retain similar three-dimensional structures and biological function inspite of poor sequence identity. The database on Genomic Distribution of protein structural domain Superfamilies (GenDiS) provides record for the distribution of 4001 protein domains...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki087
更新日期：2005-01-01 00:00:00
abstract：:Diadenosine 5',5'"-P1,P4-tetraphosphate (Ap4A) has been detected in cysts and developing embryos of the brine shrimp Artemia in amounts 10(4)-10(6) times lower than that of the guanine analogue, Gp4G. The unexpectedly high level of Ap4A in dormant cysts of 2.37 pmol/10(6) cells can be reduced to 0.03 pmol/10(6) cells ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.3.1609
更新日期：1984-02-10 00:00:00
abstract：:Peptidome similarity analysis enables researchers to gain insights into differential peptide profiles, providing a robust tool to discriminate strain-specific peptides, true intra-species differences among biological replicates or even microorganism-phenotype variations. However, no in silico peptide fingerprinting so...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx389
更新日期：2017-07-03 00:00:00
abstract：:Mature chicken erythrocyte polynucleosomes which are soluble at physiological ionic strength are enriched in beta-globin DNA sequences. Vitellogenin chromatin, which is not expressed in this tissue, is found in aggregation prone, salt insoluble chromatin. There is a direct correlation between the size of soluble fragm...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.3.1081
更新日期：1987-02-11 00:00:00
abstract：:To facilitate transcript mapping and to investigate alterations in genomic structure and gene expression in a defined genomic target, we developed a novel microarray-based method to detect transcriptional activity of the human chromosome 4q22-24 region. Loss of heterozygosity of human 4q22-24 is frequently observed in...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnh025
更新日期：2004-02-11 00:00:00
abstract：:This paper examines theoretically the effects that restraints on the tertiary structure of a superhelical DNA domain exert on the energetics of linking and the onset of conformational transitions. The most important tertiary constraint arises from the nucleosomal winding of genomic DNA in vivo. Conformational transiti...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/15.23.9985
更新日期：1987-12-10 00:00:00
abstract：:Competition binding and UV melting studies of a DNA model system consisting of three, four or five mutually complementary oligonucleotides demonstrate that unpaired bases at the branch point stabilize three- and five-way junction loops but destabilize four-way junctions. The inclusion of unpaired nucleotides permits t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.12.2212
更新日期：1995-06-25 00:00:00
abstract：:Chewie Nomenclature Server (chewie-NS, https://chewbbaca.online/) allows users to share genome-based gene-by-gene typing schemas and to maintain a common nomenclature, simplifying the comparison of results. The combination between local analyses and a public repository of allelic data strikes a balance between potenti...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa889
更新日期：2021-01-08 00:00:00
abstract：:In DNA of the dinoflagellate Crypthecodinium cohnii, 38% of the thymine is replaced by the modified base 5-hydroxymethyluracil, and approximately 3% of the cytosine is replaced by 5-methylcytosine. Both of the modified bases are non-randomly distributed in the DNA. Determinations of 3' nearest neighbors show that HOMe...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.20.4709
更新日期：1980-10-24 00:00:00
abstract：:The NONCODE database is an integrated knowledge database designed for the analysis of non-coding RNAs (ncRNAs). Since NONCODE was first released 3 years ago, the number of known ncRNAs has grown rapidly, and there is growing recognition that ncRNAs play important regulatory roles in most organisms. In the updated vers...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm1011
更新日期：2008-01-01 00:00:00
abstract：:For high-throughput in vitro protein selection using genotype (mRNA)-phenotype (protein) fusion formation and C-terminal protein labeling as a post-selection analysis, it is important to improve the stability and efficiency of mRNA templates for both technologies. Here we describe an efficient single-strand ligation (...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gng078
更新日期：2003-08-01 00:00:00
abstract：:The archaeal exosome is a phosphorolytic 3'-5' exoribonuclease complex. In a reverse reaction it synthesizes A-rich RNA tails. Its RNA-binding cap comprises the eukaryotic orthologs Rrp4 and Csl4, and an archaea-specific subunit annotated as DnaG. In Sulfolobus solfataricus DnaG and Rrp4 but not Csl4 show preference f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku969
更新日期：2014-11-10 00:00:00
abstract：:Synthesis of 8-phosphorus substituted isosteres of purine [pyrimidino (4,5-d)-1,3,2-diazaphosphole], 1-deazapurine [pyridino (2,3-d)-1,3,2-diazaphosphole] and 3-deazapurine [pyridino (4,5-d)-1,3,2-diazaphosphole] has been achieved by the reaction of equimolar amounts of triphenylphosphite and 4,5-diaminopyrimidine, 2,...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/7.1.251
更新日期：1979-09-11 00:00:00
abstract：:Cell differentiation is a central process in development and in cancer growth and dissemination. OCT4 (POU5F1) and NANOG are essential for cell stemness and pluripotency; yet, the mechanisms that regulate their expression remain largely unknown. Repetitive elements account for almost half of the Human Genome; still, t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw095
更新日期：2016-06-02 00:00:00
abstract：:Codon usage data has been compiled for 110 yeast genes. Cluster analysis on relative synonymous codon usage revealed two distinct groups of genes. One group corresponds to highly expressed genes, and has much more extreme synonymous codon preference. The pattern of codon usage observed is consistent with that expected...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.13.5125
更新日期：1986-07-11 00:00:00
abstract：:PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. In the past two years, PubChem made substantial improvements. Data from more than 100 new data sources were added to PubChem...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa971
更新日期：2021-01-08 00:00:00
abstract：:Multiple physiopathological and clinical conditions trigger skeletal muscle atrophy through the induction of a group of proteins (atrogenes) that includes components of the ubiquitin-proteasome and autophagy-lysosomal systems. Atrogenes are induced by FOXO transcription factors, but their regulation is still not fully...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky835
更新日期：2018-11-16 00:00:00
abstract：:Transcriptional regulatory networks specify regulatory proteins controlling the context-specific expression levels of genes. Inference of genome-wide regulatory networks is central to understanding gene regulation, but remains an open challenge. Expression-based network inference is among the most popular methods to i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw963
更新日期：2017-02-28 00:00:00
abstract：:Organisms exposed to reactive oxygen species, generated endogenously during respiration or by environmental conditions, undergo oxidative stress. Stress response can either repair the damage or activate one of the programmed cell death (PCD) mechanisms, for example apoptosis, and finally end in cell death. One strikin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm1100
更新日期：2008-05-01 00:00:00
abstract：:The beta-globin gene of a patient with mRNA-deficient beta o-thalassemia has been sequenced. We find a single nucleotide deletion in amino acid codon 44 that produces a UGA terminator at codon 60. We have previously shown that the beta-globin mRNA of this patient is correctly spliced and polyadenylated, but rapidly tu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.18.5421
更新日期：1982-09-25 00:00:00
abstract：:Using synthetic oligodeoxyribonucleotides to prime the transcription of interferon mRNA and cDNA, we recently determined the mRNA sequence coding for the 47 amino-terminal amino acids of mature human fibroblast interferon (1). From this sequence, we have now synthesised an oligodeoxyribonucleotide that is homologous w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.13.2885
更新日期：1980-07-11 00:00:00
abstract：:Topoisomerase II, purified from chicken erythrocytes, was reacted with a large number of different DNA fragments and cleavages were catalogued in the presence and absence of drugs that stabilize the cleavage intermediate. Cleavages were sequenced to derive a consensus for topoisomerase II that predicts catalytic sites...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.12.5533
更新日期：1988-06-24 00:00:00
abstract：:Oligoribonucleotides with 2'-5' linkages have been synthesized on solid support. UV melting and CD experiments indicate complementary strands associate to give complexes with melting temperatures 30 to 40 degrees C lower than for duplexes formed by 3'-5' oligoribonucleotides with the same sequence. UV melting and imin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.7.1685
更新日期：1992-04-11 00:00:00
abstract：:DNA circuit is a versatile and highly-programmable toolbox which can potentially be used for the autonomous sensing of dynamic events, such as biomolecular interactions. However, the experimental implementation of in silico circuit designs has been hindered by the problem of circuit leakage. Here, we systematically an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw447
更新日期：2016-08-19 00:00:00
abstract：:Methionyl-tRNA synthetase belongs to the class I aminoacyl-tRNA synthetase family characterized both by a catalytic center built around a Rossmann Fold and by the presence of the two peptidic marker sequences HIGH and KMSKS. In this study, the role of the 21HLGH24 motif of Escherichia coli methionyl-tRNA synthetase wa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.23.4793
更新日期：1995-12-11 00:00:00
