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PubMed1997

Five new or recently discovered (GBV-A) virus species are indigenous to New World monkeys and may constitute a separate genus of the Flaviviridae.

In previous studies, human hepatitis viruses have been experimentally transmitted to New World monkeys of the genus Saguinus (tamarins). Recently, two Flaviviridae-like agents (GBV-A and GBV-B) were identified in tamarins that developed hepatitis following inoculation with serum of the 11th tamarin passage of a potentially new human hepatitis agent. However, it was not shown that these viruses originated from the initial inoculum. We here report the discovery of indigenous species-specific viruses related to GBV-A in several species of New World monkeys and suggest that GBV-A virus was fortuitously acquired during passage in tamarins. Sera or plasma from 98 wild-caught New World monkeys representing 10 different species was tested by RT-PCR with conserved degenerate primers to the 5' noncoding region of the genome. Viral sequences were identified in 33 animals and sequence analysis was performed on the amplicons. In addition, the genomic region corresponding to the putative NS3 RNA helicase of GBV-A was amplified from most positive animals and sequenced. We detected GBV-A-like viruses in 13 (35%) of 37 S. mystax, 7 (78%) of 9 S. nigricollis, 3 (25%) of 12 S. labiatus, 2 (50%) of 4 S. oedipus, 2 (100%) of 2 Callithrix jacchus, and 6 (50%) of 12 Aotus trivirgatus monkeys. Each positive animal was infected with a unique strain of the GBV-A-like viruses. Analysis of the 5' NC and NS3 helicase sequences revealed that these viruses could be classified into 5 major genetic groups with genetic distances equivalent to or greater than those found among major genetic groups of hepatitis C virus. Species-specific GBV-A-like viruses were found in S. mystax, S. nigricollis, S. oedipus, C. jacchus, and A. trivirgatus species. The viruses specific for S. nigricollis were closely related to GBV-A, suggesting that GBV-A was acquired by passage through this species during the initial transmission studies. The natural history of the GBV-A-like viruses was studied in serial serum samples from 9 S. mystax and 2 A. trivirgatus monkeys. Each animal was chronically infected and the viral strain did not vary during 9-27 months of follow-up. Finally, we demonstrated that four S. mystax were positive upon arrival to the United States from the country of origin. No apparent disease was associated with chronic infection of the GBV-A-like viruses. In conclusion, many New World monkeys are persistently infected with indigenous species-specific viruses that may represent a new genus within the virus family Flaviviridae.

Animals↗

PubMed2025

Quantitative Real-Time PCR for Circular RNA Detection and Analysis.

In eukaryotes, nearly 2% of the genome represented by the coding proteins. However, emerging evidence suggest more than 75% of the human genome referred to as noncoding part also plays a crucial role in governing major regulatory pathways. Noncoding RNAs can be categorized into several groups, such as microRNAs (miRNAs), small nuclear RNA (snRNAs), small nucleolar RNA (snoRNAs), transfer RNA (tRNA), and circular RNA (circRNAs), which contribute to this regulatory landscape. Circular RNAs (circRNAs) are identified as a new class of regulatory noncoding RNAs with gene regulatory roles by acting as miRNA or RNA binding protein sponges or interacting with proteins. Researchers employ quantitative real-time PCR methods to examine circular RNA expression utilizing divergent primers for identification and quantification.

RNA, Circular↗

PubMed2004

Emergence and virulence of encephalitogenic arboviruses.

Each arbovirus that causes encephalitis is geographically restricted by the availability of appropriate vectors and reservoir hosts. These viruses evolve regionally by recombination, reassortment and point mutation and can "emerge" as causes of human encephalitis through extension to new geographic regions or by selection of more virulent or more efficiently transmitted virus variants. The properties of arboviruses that result in encephalitis involve efficient replication in peripheral tissues after initiation of infection, production of a viremia, entry into the central nervous system and efficient replication in neurons with spread to additional populations of neurons. Many of these steps are determined by properties of the envelope glycoproteins responsible for cellular attachment, but changes in noncoding regions of the genome, as well as in other structural and nonstructural proteins, also contribute to neurovirulence.

Animals↗

PubMedDate not supplied

Pattern of nucleotide substitution and the extent of purifying selection in retroviruses.

The patterns of point mutation and nucleotide substitution are inferred from nucleotide differences in three coding and two noncoding regions of retroviral genomes. Evidence is presented in favor of the view that the majority of mutations accumulate at the reverse transcription stage. Purifying selection is apparently very weak at the amino acid level, and almost nonexistent between synonymous codons. The pattern of purifying selection obeys the rules previously established in vertebrates [Gojobori T, Li W-H, Graur D (1982) J Mol Evol 18:360-369]; i.e., the magnitude of purifying selection at the amino acid level is negatively correlated with Grantham's [Grantham R (1974) Science 185: 862-864] chemical distances between the amino acids interchanged. We refute Modiano et al.'s [Modiano G, Battistuzzi G, Motulsky AG (1981) Proc Natl Acad Sci USA 78:1110-1114] hypothesis, according to which the pattern of mutation is preadapted to buffer against deleterious mutations. On the contrary, the pattern of mutation reduces the level of conservativeness from that imposed on the amino acid substitution pattern by the structure of the genetic code. The extraordinarily high rate of nucleotide substitution in retroviruses in comparison with that in other organisms is apparently caused by an extremely high rate of mutation coupled with a lack of stringent purifying selection at both the codon and the amino acid levels.

Animals↗

PubMed1989

Evolution of chromosome bands: molecular ecology of noncoding DNA.

Giemsa dark bands, G-bands, are a derived chromatin character that evolved along the chromosomes of early chordates. They are facultative heterochromatin reflecting acquisition of a late replication mechanism to repress tissue-specific genes. Subsequently, R-bands, the primitive chromatin state, became directionally GC rich as evidenced by Q-banding of mammalian and avian chromosomes. Contrary to predictions from the neutral mutation theory, noncoding DNA is positionally constrained along the banding pattern with short interspersed repeats in R-bands and long interspersed repeats in G-bands. Chromosomes seem dynamically stable: the banding pattern and gene arrangement along several human and murine autosomes has remained constant for 100 million years, whereas much of the noncoding DNA, especially retroposons, has changed. Several coding sequence attributes and probably mutation rates are determined more by where a gene lives than by what it does. R-band exons in homeotherms but not G-band exons have directionally acquired GC-rich wobble bases and the corresponding codon usage: CpG islands in mammals are specific to R-band exons, exons not facultatively heterochromatinized, and are independent of the tissue expression pattern of the gene. The dynamic organization of noncoding DNA suggests a feedback loop that could influence codon usage and stabilize the chromosome's chromatin pattern: DNA sequences determine affinities of----proteins that together form----a chromatin that modulates----rate constants for DNA modification that determine----DNA sequences. Theories of hierarchical selection and molecular ecology show how selection can act on Darwinian units of noncoding DNA at the genome level thus creating positionally constrained DNA and contributing minimal genetic load at the individual level.

Base Sequence↗

PubMed1993

Detection of HCV RNA using reverse transcription and nested polymerase chain reaction in chronic non-A, non-B liver diseases in Korea.

To investigate the interrelationship between the anti-HCV prevalence and the HCV RNA positivity in chronic non-A, non-B (NANB) liver diseases in Korea (n = 137), we performed RT-nested PCR using 4 primers in the 5'-noncoding region of HCV genome. The overall HCV RNA positive rates were 62.8%; 87.7% (57/65) of anti-HCV positive cases and 40.3% (29/72) of anti-HCV negative cases. Four patterns according to the combination of anti-HCV and HCV RNA assays could be observed; 41.6% in [anti-HCV+/HCV RNA+], 5.8% in [anti-HCV+/HCV RNA], 21.2% in [anti-HCV+/HCV RNA], and 31.4% in [anti-HCV+/HCV RNA]. Our results suggested that HCV may be still related to chronic NANB liver diseases negative for anti-HCV, and other unknown agents, so-called non-B non-C, might be accounted for patients negative for both, although a low concentration of HCV RNA, or the presence of HCV RNA or HBV DNA in liver tissue should be excluded.

Hepacivirus↗

PubMed2000

Divergence of noncoding sequences and of insertions encoding nonglobular domains at a genomic region well conserved in plasmodia.

To identify conserved features in the rapidly diverging portions of a well-conserved locus, completely sequenced in Plasmodium falciparum and Plasmodium berghei, a computational method based on recurrence analysis was exploited. At the level of the genomic sequence, in both species, introns and intergenic sequences-though subject to rapid diversification-do not drift without constraints, but rather coevolve, in the sense that they maintain not only an AT-rich base composition, but also a consistent use of recurring (AT)(n) tracts. One of the two genes present in the conserved locus encodes a protein that exhibits blocks of high similarity to the first enzyme in glutathione biosynthesis (gamma-glutamylcysteine synthetase) but bears long low-complexity insertions, absent in other organisms. From an analysis of the aminoacid sequence, different constraints appear to act on the borders and on the central part of the insertions. Albeit maintaining a strong bias toward hydrophilic residues, central portions diverge more rapidly than borders, through point mutation and differential presence of entire tracts.

Amino Acid Sequence↗

PubMed1987

Characterization of a mutant polyoma that expresses in F9 embryonal carcinoma cells: morphology, tumorigenicity, and restriction enzyme analysis.

A mutant polyoma virus (TT340), which replicates in F9 embryonal carcinoma (EC) cells and contains 2500 base pairs (bp) of additional DNA located in the early noncoding region of the genome, was analyzed to determined the DNA origin of the mutant insertion. Two fragments, representing repeated units of the 2500-bp insert, were isolated from TT340, labeled, and hybridized to the parental wild-type viral DNA. A BglI 500-bp unit, of which there are approximately five copies within the 2500-bp insert, contains sequences homologous to regions on the early and late side of the viral origin of replication. A HpaII 400-bp repeated fragment shows homology to sequences on the early side with little hybridization to the late side. Removal of the 2500-bp insert results in the loss of infectivity on F9 EC cells but not on 3T6 or mouse embryo fibroblasts. Insertion of the BglI 500-bp repeat element into wild-type DNA at the BglI site allows replication of the constructed virus in F9 cells. The mutant virions were tumorigenic in newborn Syrian hamsters and the morphology of the virus was that of wild-type as assayed by electron microscopy.

Animals↗

PubMed1987

Partial nucleotide sequence of St. Louis encephalitis virus RNA: structural proteins, NS1, ns2a, and ns2b.

cDNA clones of the St. Louis encephalitis (SLE) virus genome have been obtained and the nucleotide sequence of 4.7 kb corresponding to the 5' terminal half of the genome determined. The genome contains a 5' noncoding region of 98 nucleotides followed by a single continuous open reading frame that encodes three structural proteins in the order capsid (C), membrane precursor (prM)-membrane (M), and envelope (E). Immediately following the C-terminus of E are located nonstructural proteins NS1 through NS3. The SLE amino acid sequence homology with yellow fever (YF), Murray Valley encephalitis (MVE), West Nile (WN), and dengue-2 (DEN) viruses over the sequenced region is 39, 66, 64, and 43%, respectively. The start of each SLE protein has been assigned on the basis of N-terminal sequence data and potential proteolytic cleavage sites homologous with YF and MVE viruses. Flaviviruses have conserved glycosylation sites in prM and NS1 proteins, although only one of the two glycosylation sites in the SLE E protein is conserved in MVE and DEN viruses. An evolutionary tree showing relationships of SLE, MVE, WN, YF, and DEN-2 flaviviruses is proposed on the basis of the amino acid sequences of the C proteins.

Base Sequence↗

PubMed1984

Maintenance of multicopy plasmid Clo DF13 in E. coli cells: evidence for site-specific recombination at parB.

Certain derivatives of copy-control mutants of plasmid Clo DF13 are not stably inherited in E. coli. These plasmids, predominantly present as multimeric DNA molecules, lack a specific region, designated parB. Here we present the nucleotide sequence of this parB region spanning 328 bp between 46% and 49% on the plasmid genome. parB is a noncoding region with extensive internal symmetry. A recA-independent, site-specific resolution process occurs between two intramolecular parB sites present in direct orientation relative to each other. A gene located in the direct vicinity of parB, gene L, is not essential for parB functioning. However, our genetic data indicate that transcription from the gene L-containing operon into parB is required. We conclude that the efficient maintenance of Clo DF13 cop derivatives containing parB is provided by resolution of mutimeric molecules. Because Clo DF13 wt and cop derivatives have a different response to the deletion of parB we postulate that two different recombination systems, a parB-dependent and a parB-independent system, operate in the efficient maintenance of Clo DF13 plasmids.

Bacterial Proteins↗

PubMed1994

Structure of human rhinovirus 3C protease reveals a trypsin-like polypeptide fold, RNA-binding site, and means for cleaving precursor polyprotein.

The structure of human rhinovirus-14 3C protease (3Cpro) has been determined at 2.3 A resolution and refined to an R factor of 0.22. This cysteine protease folds into two topologically equivalent six-stranded beta barrels and in this sense is similar to trypsin-like serine proteases. However, there are differences in the lengths and positioning of individual beta strands as well as in loops connecting elements of secondary structure. The catalytic residues Cys-146, His-40, and Glu-71 are positioned as in serine proteases, but the oxyanion hole is moved 1-1.2 A away. Residues that bind to the 5' noncoding region of rhinovirus genomic RNA are located on the opposite side of the molecule from the active site. Interactions between individual 3Cpro molecules in the crystal lattice suggest a model for intermolecular proteolytic cleavage of the 3CD polyprotein.

3C Viral Proteases↗

PubMed1991

A characterization of the nonstructural protein from which the virus-specified tubules in epizootic haemorrhagic disease virus-infected cells are composed.

The complete nucleotide sequence of segment 6 of epizootic haemorrhagic disease virus serotype 2 (Alberta) which encodes nonstructural protein NS1 was determined from a cDNA clone containing a full-length copy of the gene. The gene was found to be 1806 bp in length, constituted by one open reading frame of 1656 bp which is flanked by 5' and 3' noncoding regions of 32 and 118 bp, respectively. The conserved 5' and 3' terminal hexanucleotide sequences were identical to those of BTV-10. The 5' noncoding nucleotide sequences of cognate genome segments 4, 6 and 8 were found to be highly conserved in EHDV-2 and BTV-10. The 3' noncoding regions are less conserved but share common characteristics. The predicted EHDV-2 NS1 gene product, a 552 amino acid polypeptide, is predominantly hydrophobic and has a net charge of +5 at neutral pH. Comparison to its BTV-10 counterpart revealed a high degree of homology. Regions of high amino acid similarity were shown to correlate with hydrophobic domains on the proteins whilst regions of lower amino acid similarity corresponded with the hydrophilic domains. Thirteen conserved cysteine residues of which the majority occurred in hydrophobic regions with more than 80% amino acid similarity were identified.

Amino Acid Sequence↗

PubMed1985

Sequence organization of the mitochondrial genome of yeast--a review.

We have compiled the available primary structural data for the mitochondrial genome of Saccharomyces cerevisiae and have estimated the size of the remaining gaps, which represent 12-13% of the genome. The lengths of sequenced regions and of gaps lead to a new assessment of genome sizes; these range (in round figures) from 85 000 bp for the long genomes, to 78 000 bp for the short genomes, to 74 000 bp for the supershort genome of Saccharomyces carlsbergensis. These values are 8-11% higher than those previously estimated from restriction fragments. Interstrain differences concern not only facultative intervening sequences (introns) and mini-inserts, but also insertions/deletions in intergenic sequences. The primary structure appears to be extremely conserved in genes and ori sequences, and highly conserved in intergenic sequences. Since coding sequences represent at most 33-35% of the genome, at least two thirds of the genome are formed by noncoding and yet highly conserved sequences. The G + C level of genes or exon is 25%, and that of intronic open reading frames (ORFs) 22%; increasingly lower values are shown by intronic closed reading frames (CRFs), 20%, ori sequences, 19%, intergenic ORFs, 17.5% and intergenic sequences, 15%.

Base Sequence↗

PubMed1997

Enteroviral RNA and virus-like particles in the skeletal muscle of patients with idiopathic dilated cardiomyopathy.

The role of chronic viral infection in the etiopathogenesis of idiopathic dilated cardiomyopathy (IDC) has generated considerable research. Enteroviruses were the favorite candidates as etiologic agents of IDC. However, enteroviruses were rarely demonstrated in affected hearts. We investigated whether enteroviral infection persists in the heart and in extracardiac sites, particularly in skeletal muscle, in patients with IDC. Blood and myocardial and skeletal muscle samples were collected at cardiac transplantation from 31 IDC patients, 24 non-IDC heart disease patients, and 3 heart donors. Samples underwent ultrastructural studies and ribonucleic acid (RNA) extraction. RNA was reverse-transcribed, and 2 nested fragments (bps 179 and 126) were amplified in the highly conserved 5' noncoding region of enteroviral genomic RNA. Enteroviral RNA was found in the skeletal muscle of 12 cases, whereas only 4 hearts (2 of which with positive skeletal muscle) were positive. Of the 24 controls, 2 were positive (1 muscle and heart, 1 muscle only). Automated sequencing confirmed the enteroviral nature of the amplified products. Ultrastructural study showed enterovirus-like particles in 4 of the enterovirus-positive muscles, and myopathic changes in all enterovirus-positive cases. Skeletal muscle hosts chronic enteroviral infection in more than one third of patients with sporadic IDC. Two hypotheses may explain this link. Myocardial damage may derive directly from recurrent subclinical heart infections caused by enteroviruses harbored in skeletal muscle. Alternatively, enterovirus-related myopathy may trigger an autoimmune response to antigens shared by muscle and myocardium. Further studies are needed to assess the importance of these, non-mutually exclusive mechanisms in IDC pathogenesis.

Adult↗

PubMed1999

Breeding systems in Echinococcus granulosus (Cestoda; Taeniidae): selfing or outcrossing?

We used the PCR-SSCP method followed by sequencing in order to assess the genetic variability of coding and noncoding parts of the genome of Echinococcus granulosus (Cestoda; Taeniidae) and to test whether or not the parasite populations are mainly self-fertilizing. For this, we analysed a sample of 110 E. granulosus metacestode isolates collected from different geographical regions (Southern Brazil, Europe and Australia) and from different intermediate hosts (ovine, bovine, human, macropod, swine and equine). Using appropriate controls, we were able to identify 4 strains in that sample (sheep, cattle, pig and horse strains). The high degree of genetic differentiation between strains, but not within, and the monomorphism found in most loci (EgAg4, EgActII, EgHbx2 and EgAg6-non-coding-EgAgB/1 and EgND1-coding) indicated that they are largely selfed. On the other hand, outcrossing was also shown to occur, since 5 potential hybrid genotypes between cattle and sheep strains were found in populations of Southern Brazil, but absent in other geographical areas. We suggest that both processes are adaptive. The article also reports, for the first time, the occurrence of the E. granulosus cattle strain in South America.

Animals↗

PubMed2026

Increased PRSS56 expression is a causal factor and therapeutic target for human axial high myopia.

High myopia (HM), characterized by significant ocular axial length elongation, affects hundreds of millions of people and is often inherited, particularly in cases that develop during childhood or adolescence. Although numerous myopia loci (MYP) have been identified, most causative genes remain undefined. Here, we analyzed two large HM pedigrees and refined the critical region through haplotype linkage analysis to a 3.9-Mb interval on 2q37.1, which was previously reported as MYP12 with an unknown pathogenic gene. Whole-genome sequencing identified the noncoding promoter variants c.-187G>T and c.-187G>C in PRSS56, encoding a trypsin-like serine protease, which exclusively co-segregated with all affected members in both pedigrees. Compared with matched controls, increased PRSS56 expression was observed in both patient-derived iPSCs carrying c.-187G>T and knock-in mice (c.-155G>T, corresponding to human c.-187G>T) that faithfully recapitulate myopia phenotypes. Noncoding PRSS56 variants promote self-expression via enhanced binding to the transcription factor EGR1, as confirmed by dual-luciferase assays. Notably, we demonstrated that higher PRSS56 levels directly increase ocular axial length in a dose- and activity-dependent manner in multiple transgenic mouse models. Guinea pig myopia models consistently exhibited high Prss56 expression, and short-wave light exposure reduced Prss56 mRNA levels and attenuated further axial elongation. Mechanistically, higher PRSS56 expression was associated with reduced abundance of myosin-4 in the sclera and with molecular signatures of scleral remodeling, which were in turn correlated with axial elongation. In conclusion, our findings provide strong genetic and functional evidence for the pathogenic role of noncoding PRSS56 variants in HM and highlight PRSS56 as a promising therapeutic target for juvenile HM.

Humans↗

PubMed2003

Cell size as a link between noncoding DNA and metabolic rate scaling.

Accumulation of noncoding DNA and therefore genome size (C-value) may be under strong selection toward increase of body size accompanied by low metabolic costs. C-value directly affects cell size and specific metabolic rate indirectly. Body size can enlarge through increase of cell size and/or cell number, with small cells having higher metabolic rates. We argue that scaling exponents of interspecific allometries of metabolic rates are by-products of evolutionary diversification of C-values within narrow taxonomic groups, which underlines the participation of cell size and cell number in body size optimization. This optimization leads to an inverse relation between slopes of interspecific allometries of metabolic rates and C-value. To test this prediction we extracted literature data on basal metabolic rate (BMR), body mass, and C-value of mammals and birds representing six and eight orders, respectively. Analysis of covariance revealed significant heterogeneity of the allometric slopes of BMR and C-value in both mammals and birds. As we predicted, the correlation between allometric exponents of BMR and C-value was negative and statistically significant among mammalian and avian orders.

Animals↗

PubMed1991

A determinant of disease symptom severity is located in the 3'-terminal noncoding region of the RNA of a plant virus.

Inoculation of Nicotiana tabacum plants with RNA transcribed in vitro from a variant (pXBS8) of a cloned full-length DNA copy of tobacco vein mottling virus (TVMV) RNA resulted in attenuation of the vein mottling and blotching symptoms typically produced by transcripts of cloned wild-type cDNA (pXBS7). Similar amounts of virus were detected by ELISA (using anti-TVMV coat protein serum) in systemically infected leaves of plants inoculated with pXBS7 or pXBS8 transcripts. pXBS8 was shown to contain a 58-nucleotide segment in the sequence corresponding to the 3'-terminal untranslated region of TVMV RNA that was not present in pXBS7. This segment resulted in the appearance in pXBS8 transcripts of four adjacent direct repeats of a 14-nucleotide sequence, AUAAUUAUAUAUAU, that is present in the 3'-untranslated region of TVMV RNA, with two additional nucleotides (AU) between the first and second repeats. Insertion of restriction fragments containing the segment into pXBS7 and inoculation of plants with transcripts of the chimeric construct (pXBS78) resulted in the attenuated-symptom phenotype and was not accompanied by a reduced accumulation of virus in the plant as determined by ELISA and Northern blot analysis. When the extra nucleotides were removed from the variant clone, symptoms induced by transcripts of the cDNA (pXBS87) resembled those induced by wild-type transcripts. The results indicate that a noncoding region of the genome can have a direct effect on the induction of disease symptoms by an RNA virus.

Base Sequence↗