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PubMed1985

Subtype ayw variant of hepatitis B virus. DNA primary structure analysis.

The entire genome of human hepatitis B virus (HBV) occurring in Latvia was sequenced. This sequence, which is 3182 nucleotides long, was compared with the other previously published HBV genomes and was shown to share maximum homology with HBV subtype ayw DNA. The coordinates of 4 main open reading frames as well as hairpin structures are very well conserved in the two genomes. The distribution of nucleotide substitutions among different HBV genomes suggest that the open reading frames P and X can fulfil a coding function. On the basis of primary structure comparison for hepadnaviral DNAs several evolutionary conclusions can be drawn.

Amino Acid Sequence↗

PubMed1998

Quasispecies and the implications for virus persistence and escape.

BACKGROUND: In the 1970s Manfred Eigen and colleagues proposed a new model of molecular evolution to explain adaptability and rapid evolution of simple replicons, as those that probably populated the earth at the onset of life. This model of evolution placed emphasis on mutant generation, to the point of invalidating the concept of wild-type genomes as a defined sequence of nucleotides. In striking similarity with the proposals for such early replicons, present-day RNA viruses consist of complex distributions of nonidentical but closely related genomes termed quasispecies. OBJECTIVES: To discuss indeterminations inherent to a quasispecies structure and to the analytical procedures to define it, biological implications of quasispecies, and the need to take into account this type of population structure, in order to design effective strategies to prevent and control diseases caused by highly variable viruses. RESULTS: Quasispecies have many biological implications, extending from viral pathogenesis to the emergence of new pathogens, rapid antigenic variation, and alterations in cell tropism, virulence, host range and viral gene expression. CONCLUSIONS: Diseases caused by highly variable RNA viruses prove very difficult to control and vaccine development against such viruses are largely unsuccessful. It is important to understand quasispecies composition and dynamics, as quasispecies are an important step in the natural history of RNA viruses.

Animals↗

PubMed2002

Genes on human chromosome 19 show extreme divergence from the mouse orthologs and a high GC content.

Mutational rates are known to be variable along the mammalian genome but the extent of this non-random fluctuation and their causes are less well understood. Using 5509 human and mouse orthologous genes with known chromosome positions, it is shown here that there are extreme differences in synonymous evolutionary rates between different human chromosomes when distances are measured using maximum-likelihood techniques. In particular, the average synonymous rate of genes located in human chromosome 19 is extremely high (K(s) = 1.243 substitutions/site) compared with the average of all genes (K(s) = 0.729), and significantly different from all other human chromosomes. When genes are sorted according to mouse chromosomes no such large differences are found. Strikingly, almost all genes of human chromosome 19 have very high GC content in humans but not in the mouse orthologs. More generally, correlation analysis shows that genes with very high GC content in humans have experienced the highest synonymous divergencies from the mouse. It is likely that, in such genes, the known relaxation of the isochore structure in rodents has caused an increased accumulation of synonymous substitutions in the mouse lineage, whereas the regions with the highest GC content in the human genome are accordingly maintained by a strong selective pressure.

Animals↗

PubMed1992

Guinea pig or rabbit lung flavin-containing monooxygenases with distinct mobilities in SDS-PAGE are allelic variants that differ at only two positions.

Both guinea pig and rabbit express two variants of the 'lung' flavin-containing monooxygenase (FMO), observed as three distinct phenotypes based on mobility differences in SDS-PAGE. Samples of messenger RNA prepared from lungs of the two homozygous phenotypes of the guinea pig were used for the construction of two cDNA libraries. The libraries were screened with a cDNA encoding the rabbit lung FMO, and positive clones for each guinea pig lung FMO variant were isolated and sequenced. A full length clone from each library was found to encode a protein of 535 amino acids containing two pyrophosphate binding sites. Comparison of the sequences of the guinea pig and rabbit lung FMOs shows that their primary structures are 86% identical. The coding region sequences of the guinea pig variants differ at only two positions, and both differences result in amino acid substitutions. Sequence analysis has also been completed on a partially characterized variant of the rabbit lung FMO. As with the guinea pig, the nucleotide and amino acid sequences of the rabbit variants differ at only two positions. The cDNAs encoding the guinea pig variants were expressed in yeast. The activities of the enzymes are characteristic of the lung FMO, and the mobilities of the expressed enzymes are the same as those observed for the variants present in guinea pig pulmonary microsomal preparations. Similar to findings for the rabbit, analysis of genomic DNA indicates that the guinea pig lung FMO is associated with a single gene. The results of cDNA sequence analysis, expression in yeast, and analysis of genomic DNA indicate that the multiple lung FMOs in guinea pig and rabbit are allelic variants whose mobilities in SDS-PAGE are markedly altered by minimal changes in primary structure.

Alleles↗

PubMed2005

Gene expression profile of ewing sarcoma cell lines differing in their EWS-FLI1 fusion type.

The t(11;22)(q24;q12) translocation is present in up to 95% of Ewing tumor patients and results in the formation of an EWS-FLI-1 fusion gene that encodes a chimeric transcription factor. Many alternative forms of EWS-FLI-1 exist because of variations in the location of the EWS and FLI-1 genomic breakpoints. Previous reports have shown that the type 1 fusion is associated with a significantly better prognosis than the other fusion types. It has been suggested that the observed clinical discrepancies result from different transactivation potentials of the various EWS-FLI-1 fusion proteins. In an attempt to identify genes whose expression levels are differentially modulated by structurally different EWS-FLI-1 transcription factors, we have used microarray technology to interrogate 19,000 sequence genes to compare gene expression profile of type 1 or non-type 1 Ewing sarcoma cell lines. Data analysis showed few qualitative differences on gene expression; expression of only 41 genes (0.215% of possible sequences analyzed) differed significantly between Ewing tumor cell lines carrying EWS-FLI-1 fusion type 1 with respect to those with non-type 1 fusion.

Biomarkers, Tumor↗

PubMed2005

Group II intron retroelements: function and diversity.

Group II introns are a class of retroelements capable of carrying out both self-splicing and retromobility reactions. In recent years, the number of known group II introns has increased dramatically, particularly in bacteria, and the new information is altering our understanding of these intriguing elements. Here we review the basic properties of group II introns, and summarize the differences between the organellar and bacterial introns with regard to structures, insertion patterns and inferred behaviors. We also discuss the evolution of group II introns, as they are the putative ancestors of spliceosomal introns and possibly non-LTR retroelements, and may have played an important role in the development of eukaryote genomes.

Bacteria↗

PubMed1996

[The karyotypic variability of Chinese hamster CHLV-79 RJK cells characterized by multiple drug resistance resulting from the amplification of the mdr gene family].

Variability in karyotype structure of Chinese hamster lung V-79 RJK cells and of their six cell sublines, selected for increasing concentrations of ethidium bromide (EB), was investigated in addition to the number of mdr gene copies in cells, both EB sensitive and resistant. It is shown that EB resistant cells exhibit cross-resistance to different drugs resulting from mdr genes amplification. Southern DNA blot hybridization has shown that in Vebr-2 cells (the 1st step of selection) the number of mdr gene copies increased by 10 times, whereas in Vebr-30 cells (the 6th step of selection) the number of mdr gene copies remained the same as in Vebr-2 cells. The level of mdr genes expression in Vebr-30 cells being higher than in Vebr-2 cells. In Vebr-2 cells, homogeneously and differentially stained regions (HSRs) were detected in loci 1p31 and 1q26 of chromosome 1 material (markers Z1 and Z6, respectively). On the following selection steps (prolonged cultivation or increased drug concentration) additional HSRs appeared in chromosome 2 (locus 2qter), in derivatives of chromosome 5 (marker Z7, locus Z7pter) and chromosome X (marker Z2, locus Z2qter). In the course of prolonged cultivation, chromosome 2 and derivatives of chromosomes 1, 2, 5 and X, in which HSRs were found, participated in the formation of new markers resulting from deletions, inversions, insertions and translocations of the chromosomal material. It is supposed that mdr genes amplification in V-79 RJK cells resistant to EB may be regarded as a factor inducing subsequent genome destabilization and eventual progressive changes in the karyotype structure.

Animals↗

PubMed1997

[Genetic effects of destabilizing selection for adaptively important traits in Drosophila melanogaster lines].

Related lines of Drosophila melanogaster selected for reproductive activity for more than 750 generations were studied. Results of the long-term selection experiment support D.K. Belyaev's concept of destabilizing selection. Selection for a behavioral trait (male mating activity) affected the intrinsic structure of the organism. Flies of the low-activity line (LA) exhibited numerous morphological, biochemical, and physiological alterations. Variation rate in the selected lines was accelerated; appearing mutations were often allelic and nonrandomly distributed over chromosomes. Selection was shown to mediate novel sources of variability, e.g., induction and repression of the hobo hybrid dysgenesis. In the process of selection, a genetically determined program of hobo transpositions in the genome was formed.

Adaptation, Physiological↗

PubMed1996

cDNA sequence and genomic structure of the murine p55 (Mpp1) gene.

MPP1 is an X-linked human gene encoding a heavily palmitoylated membrane protein (p55) with homology to the Drosophila tumor suppressor gene lethal(1) discs-large. As a first step toward studying the effects of mutations in this gene in a mammalian system, the nucleotide sequence of the mouse Mpp1 cDNA has been determined along with the intron-exon boundaries. Mpp1 is ubiquitously expressed and encodes a p55 protein of 466 amino acids with 93 and 65% identity to the human and puffer fish (Fugu rubripes) p55 sequences, respectively. The genomic structure of the Mpp1 gene is likewise conserved with 12 exons. The location of the Mpp1 gene, on the X chromosome, is also conserved between the human and the mouse. Conservation of the Mpp1 gene between mouse and human gives support to the notion that construction and study of a mouse knockout model may help establish the function of the human MPP1 gene, a potential tumor suppressor gene.

Amino Acid Sequence↗

PubMed1994

Virology of measles virus.

Measles virus is the prototypic member of the Morbillivirus genus of the family Paramyxoviridae. The viral genomic RNA is single-stranded, nonsegmented, and of negative polarity and encodes six major structural proteins. The two viral transmembrane glycoproteins, the hemagglutinin and fusion proteins, are both required for virus-host cell membrane fusion, while attachment to host cells is mediated by the hemagglutinin. The human CD46 molecule has been identified as a cellular receptor for measles virus. Antibodies raised against either viral glycoprotein neutralize measles virus in vitro and protect against infection. Although measles virus remains a single serotype (monotypic), nucleotide sequence analyses have identified distinct lineages among recent wild type isolates. These genetic changes were manifested by detectable antigenic variation between vaccine and wild type viruses and at some point may influence strategies for control, elimination, and eventual eradication of measles virus.

Animals↗

PubMed1991

Sequence analysis of the putative structural genes of hepatitis C virus from Japanese and European origin.

cDNA fragments encoding the putative structural genes of the hepatitis C genome were isolated from a plasma pool of Japanese non-A, non-B hepatitis patients and from sera of individual Spanish patients. From the Japanese plasma pool a series of E1 clones was obtained that showed 88-98% homology among each other, both at the nucleotide and amino acid level. Compared to the sequences published by the Chiron Corporation and Takeuchi et al., the amino acid homology was 75-79% and 91-94%, respectively. Analysis of the core and E2/NS1 genes showed a high conservation of the core sequence and a high sequence variation in the 5' end of the E2/NS1 gene. The E1 gene of one Spanish isolate showed greater homology to the Chiron than to the Japanese sequence. Another Spanish isolate was more homologous to the Japanese sequence indicating that both hepatitis C genotypes are present in Europe. Analysis of the E1 gene of an isolate derived from a single patient with a 5-year interval revealed nine nucleotide and five amino acid changes.

Amino Acid Sequence↗

PubMed1997

The Arabidopsis thaliana genome has multiple divergent forms of phosphoinositol-specific phospholipase C1.

Highly degenerate primers to conserved regions of the eukaryotic phosphoinositol-specific phospholipase C (PLC) were used to amplify fragments of plant PLCs from Arabidopsis thaliana genomic DNA. Eight completely different fragment sequences that showed high homology to PLCs of both animals and plants were isolated. The variation between these putative PLCs was high and suggests that, like animals, plants have multiple isoforms of PLC. Using one of the PCR clones, we isolated a corresponding full-length Arabidopsis PLC gene (ATHATPLC1G), and sequence analysis indicated that it was most like a delta-type PLC. This gene is 2.5 kb and contains seven introns, all but one of which has intron/exon border sequences that conform to the Arabidopsis consensus. The structural complexity of the gene is relatively simple compared to mammalian beta-type PLCs that can be 15 kb long with up to 30 introns. The plant gene is a single copy and was mapped to four Arabidopsis YACs, one located on chromosome 2. The promoter region contained two TATA-like elements at -43 and -185 and other putative regulatory elements that suggest that this PLC is hormonally regulated. This is the first plant PLC gene and the first delta type-PLC gene from a higher organism to be sequenced.

Amino Acid Sequence↗

PubMed2003

Molecular cloning, genomic structure, and expression analysis of MUC20, a novel mucin protein, up-regulated in injured kidney.

Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulonephritis in the world. Here, we identify a cDNA encoding a novel mucin protein, shown previously to be up-regulated in IgAN patients, from a human kidney cDNA library. This protein contains a mucin tandem repeat of 19 amino acids consisting of many threonine, serine, and proline residues and likely to be extensively O-glycosylated; thus, this gene was classified in the mucin family and named MUC20. The human MUC20 gene contains at least four exons and is localized close to MUC4 on chromosome 3q29. We found variations in repeat numbers in the mucin tandem domain, suggesting polymorphism of this region. Northern blot and reverse transcription-PCR analyses revealed that human MUC20 mRNA was expressed most highly in kidney and moderately in placenta, colon, lung, prostate, and liver. Immunohistochemical analysis of human kidney revealed that MUC20 protein was localized in the proximal tubules. Immunoblotting analysis of MUC20 proteins produced in Madin-Darby canine kidney and HEK293 cells indicated the localization of MUC20 protein in a membrane fraction and extensive posttranslational modification. Immunoelectron microscopy of MUC20-producing Madin-Darby canine kidney cells demonstrated that MUC20 protein was localized on the plasma membrane. Expression of MUC20 mRNA in a human kidney cell line was up-regulated by tumor necrosis factor-alpha, phorbol 12-myristate 13-acetate, or lipopolysaccharide. Two species of MUC20 mRNA (hMUC20-L and hMUC20-S), resulting from alternative transcription, were identified in human tissue, whereas only one variant was observed in mouse tissues. Mouse MUC20 mRNA was expressed in the epithelial cells of proximal tubules, and the expression increased dramatically with the progression of lupus nephritis in the kidney of MRL/MpJ-lpr/lpr mice. Moreover, the expression of mouse MUC20 was augmented in renal tissues acutely injured by cisplatin or unilateral ureteral obstruction. These characteristics suggest that the production of MUC20 is correlated with development and progression of IgAN and other renal injuries.

Amino Acid Sequence↗

PubMed2000

The human beta-myosin heavy chain gene: sequence diversity and functional characteristics of the protein.

The beta-myosin heavy chain gene (MYH7) encodes the motor protein that drives myocardial contraction. It has been proven to be a disease gene for hypertrophic cardiomyopathy (HCM). We analyzed the DNA sequence variation of MYH7 (about 16 kb) of eight individuals: six patients with HCM and two healthy controls. The overall DNA sequence identity was up to 97.2% compared to Jaenicke and coworkers (Jaenicke et al. [1990] Genomics 8:194-206), while the corresponding amino acid sequences revealed 100% identity. In HCM patients, eleven nucleotide substitutions were identified but no causative disease mutation was found: six were detected in coding, four in intronic, and one in 5' regulatory regions. The average nucleotide diversity across this locus was 0.015% with an average of 0.02% in the coding and 0.012% in the noncoding sequence. Analysis of the kinetic behaviour of beta-MHC in the intact contractile structure of normal individuals and HCM patients revealed apparent rate constants of tension development ranging between 1.58 s(-1) and 1.48 s(-1).

Base Sequence↗

PubMed2006

Analysis of the near full length genomes of HIV-1 subtypes B, F and BF recombinant from a cohort of 14 patients in São Paulo, Brazil.

The human immune deficiency virus (HIV) exhibits strikingly tremendous amount of genetic variability. Such feature is critically important for the virus to adapt to environmental changes by escaping the host immune system and by escaping candidate vaccine. Therefore, understanding of such diversity is fundamental for the design of successful drugs or vaccine, which is urgently needed to bring the HIV/AIDS epidemic under control. In this study, we investigated the magnitude of diversity of the HIV-1 near full-length genomes from patients previously assigned as infected with non-recombinant HIV-1 subtypes B and F1 variants based on small portion of viral genome. HIV-1 proviral DNA was extracted from 14 samples previously classified in our laboratory as six subtypes B and eight subtypes F on the basis of small amplicon sequencing. Reamplifications of DNA from these samples were carried out by an overlapping PCR followed by direct sequencing. The data were phylogenetically inferred. Sequence analysis revealed that two out of six partially identified subtype B and six out of eight partially identified subtype F were in fact BF recombinants throughout their full genomes. Two pairs BF recombinants had identical genomic recombination structure and distinct from the Argentinean CRF 12_BF strains, probably represents a novel circulating recombinant forms in Brazil. Our data provided new genetic material of some of the HIV-1 subtypes currently circulating in the country and points to the widespread of BF recombinants which are expected to change the epidemic nature by approaching the level of subtype B in Brazil.

Adult↗

PubMed2003

Characterization of novel LPXTG-containing proteins of Staphylococcus aureus identified from genome sequences.

Twenty-one genes encoding surface proteins belonging to the LPXTG family have been identified by in silico analysis of six Staphylococcus aureus genome sequences. Eleven genes encode previously described proteins, while 10 have not yet been characterized. Of these, eight contain the cell-wall sorting signal LPXTG responsible for covalently anchoring proteins to the cell-wall peptidoglycan. The remaining two, SasF and SasD, harbour a single residue variation in the fourth position of the LPXTG motif (LPXAG). Western blotting of lysostaphin-solubilized S. aureus cell-wall proteins demonstrated the release of SasF in the cell-wall fraction, indicating that proteins carrying LPXAG are sorted normally. Analysis of primary sequences of the Staphylococcus aureus surface (Sas) proteins indicated that several share a similar structural organization and a common signal sequence with previously characterized LPXTG proteins of S. aureus and other Gram-positive cocci. Protein SasG has 128 residue B repeats that are almost identical at the DNA level. PCR analysis indicated that recombinants with repeat length variations are present in the bacterial population whereas they are not detectable in the B-repeat-encoding region of sdrD. The sasG and sasH genes are significantly associated with invasive disease isolates compared to nasal carriage isolates. Several IgG samples purified from patients recovering from S. aureus infections had higher titres against Sas proteins than control IgG, suggesting that expression occurred during infection in some patients.

Adult↗

PubMed2025

Genomic analysis of Dasiphora on the Qinghai-Tibet Plateau provides insights into genetic divergence and flower color variation.

The Qinghai-Tibet Plateau (QTP) harbors diverse alpine flora, including the ecologically significant shrubs Dasiphora fruticosa and D. glabra, for which taxonomic uncertainties remain and adaptive mechanisms are still poorly understood. Based on high-quality genome assembly, population resequencing, and multi-omics integration, we elucidated their evolutionary divergence and flower color genetics. Chromosome-level haplotype-resolved genomes were assembled: autotetraploid D. fruticosa (929.99 Mb) and diploid D. glabra (450.89 Mb). Phylogenetic analysis showed that the tetraploid D. fruticosa and D. glabra in this study clustered together, while the diploid D. fruticosa sequenced by previous research formed a distinct lineage clustered outside. Consistently, population structure analysis of 55 samples revealed three major clades, with D. fruticosa further subdivided into two divergent branches. Additionally, hybridization events detected by Admixture, coupled with ploidy complexity identified via flow cytometry highlight the intricate genetic relationships within this genus. Adaptive gene families expanded in antioxidant (flavonoid synthesis) and secondary metabolism pathways, adapting to ultraviolet radiation and cold stress. Natural selection analysis identified 193 candidate genes (e.g., TFB5 in the DNA repair pathway), predominantly localized to chromosome 5, which are potential candidates for high-altitude adaptation. Transcriptome and metabolome analyses showed D. fruticosa's yellow petals derive from flavonol (quercetin) accumulation, while D. glabra's white petals result from proanthocyanidin biosynthesis via high LAR/ANR expression. This study provides insights into the taxonomic revision and adaptive genetic divergence of alpine plants, and offers a foundation for horticultural improvement of Dasiphora.

Flowers↗

PubMed1983

Analysis of genetic variation in Theiler's virus during persistent infection in the mouse central nervous system.

The genetic changes occurring in the BeAn strain of Theiler's murine encephalomyelitis virus (TMEV) during persistent infection in the mouse central nervous system (CNS) were studied. RNase T1-oligonucleotide fingerprinting of the RNAs of 28 BeAn viruses isolated at various times postinfection (p.i.) demonstrated that mutation occurred throughout the infection. Although plaque-purified BeAn virus was used to inoculate mice intracerebrally, genetically different viruses were recovered from the CNS. One to three oligonucleotide changes were found up to Day 152 p.i., but all three viruses isolated at Day 180 had four to nine oligonucleotide changes. No pattern of oligonucleotide changes occurring in different virus isolates was found, yet three viruses isolated from different animals at Day 180 had the same four new oligonucleotides. Overall, the number of oligonucleotide changes represented a 0.1 to 1.2% change in the virus genome. In addition, the analytical two-dimensional gel technique of P.Z. O'Farrell, H.M. Goodman, and P.H. O'Farrell (Cell 12, 1133-1142, 1977) suggested that mutation occurred in all virus isolates. In nine isolates, one to three proteins were found to have charge changes, and in general, as many nonstructural proteins had charge changes as structural proteins. P20, a nonstructural protein probably equivalent to the protease described for encephalomyocarditis virus, was found to have shifted cathodally in six different viruses. Several virus isolates had doublet patterns, suggesting the possibility that within the CNS, subpopulations existed which had proteins of slightly different charge or that virus-specified proteins had been modified after translation. Finally, antigenic variation of neutralizing site(s) on BeAn virus isolates as a way for virus to evade immune surveillance and thereby maintain the persistent state was studied. The ability of mouse serum to neutralize persisting virus isolates was not significantly different from the ability to neutralize the infecting virus. Therefore, antigenic variation does not appear to be a factor in TMEV persistence.

Animals↗