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PubMed2004

Analysis of the RNA of Potato yellow vein virus: evidence for a tripartite genome and conserved 3'-terminal structures among members of the genus Crinivirus.

Double-stranded RNA preparations produced from potato plants graft-inoculated with a Peruvian isolate of Potato yellow vein virus (PYVV; genus Crinivirus, family Closteroviridae) contain five RNA species denoted RNA 1, RNA 2, RNA 3, x and y of approximately 8, 5.3, 3.8, 2.0 and 1.8 kbp, respectively. The complete nucleotide sequences of PYVV RNAs 1, 2 and 3 and Northern hybridization analysis showed that PYVV RNA 1 contained the replication module and an additional open reading frame (p7), while two distinct species, RNAs 2 and 3, contain the Closteroviridae hallmark gene array. Pairwise comparisons and phylogeny of genome-encoded proteins showed that PYVV shares significant homology with other criniviruses but is most closely related to the Trialeurodes vaporariorum-vectored Cucumber yellows virus. Secondary structure prediction of the 3'-untranslated regions of all three PYVV RNAs revealed four conserved stem-loop structures and a 3'-terminal pseudoknot structure, also predicted for all fully characterized members of the genus Crinivirus and some members of the genera Closterovirus and Ampelovirus.

3' Untranslated Regions↗
PubMed2000

Amphidiploid Brassica juncea contains conserved progenitor genomes.

To perform a detailed study of genome evolution in the natural Brassica amphidiploid B. juncea, we have constructed two linkage maps based on RFLP (restriction fragment length polymorphism) markers; one generated from a cross between a resynthesized B. juncea (a chromosome doubled interspecific B. rapa x B. nigra hybrid) and a natural B. juncea cultivar, the other from a cross between two B. juncea cultivars. By using a common cultivar in both crosses, the two maps could be unambiguously integrated. All loci exhibited disomic inheritance of parental alleles in the natural x resynthesized cross, showing that B. rapa chromosomes paired exclusively with their A-genome homologues in B. juncea and that B. nigra chromosomes likewise paired with their B-genome homologues. The maps derived from the two crosses were also perfectly collinear. Furthermore, these maps were collinear with maps of the diploid progenitor species (B. nigra and B. rapa) produced using the same set of RFLP probes. These data indicate that the genome of B. juncea has remained essentially unchanged since polyploid formation. Our observations appear to refute the suggestion that the formation of polyploid genomes is accompanied by rapid change in genome structure.

Brassica↗
PubMed1996

Analysis of the murine Dtk gene identifies conservation of genomic structure within a new receptor tyrosine kinase subfamily.

The receptor tyrosine kinase Dtk/Tyro 3/Sky/rse/brt/tif is a member of a new subfamily of receptors that also includes Axl/Ufo/Ark and Eyk/Mer. These receptors are characterized by the presence of two immunoglobulin-like loops and two fibronectin type III repeats in their extracellular domains. The structure of the murine Dtk gene has been determined. The gene consists of 21 exons that are distributed over 21 kb of genomic DNA. An isoform of Dtk is generated by differential splicing of exons from the 5' region of the gene. The overall genomic structure of Dtk is virtually identical to that determined for the human UFO gene. This particular genomic organization is likely to have been duplicated and closely maintained throughout evolution.

Alternative Splicing↗
PubMed1984

Variant dsRNAs associated with transmission-defective isolates of wound tumor virus represent terminally conserved remnants of genome segments.

Variant double-stranded RNAs are often associated with the genome of transmission-defective isolates of wound tumor virus. These RNAs are replicated and packaged into virus particles in systemically infected plants and are transcribed in vitro by the virion-associated transcriptase. Direct physical evidence that the variant RNAs are remnants of particular WTV genome segments was provided by molecular hybridization studies. Subsequently, ribonuclease T1 digestion products of 3'-end-labeled genome and remnant RNAs were analyzed by one- and two-dimensional electrophoretic techniques. One-dimensional partial and complete digestion patterns were indistinguishable, indicating that the guanosine positions relative to the 3' terminus of the corresponding strands of a particular genome segment and its remnant RNA are the same for at least 40 nucleotides from each end. Fingerprints of the 3' terminal ribonuclease T1-resistant fragments were identical, showing that the nucleotide composition of the 3' terminal ends of the corresponding strands of a particular genome segment and its remnant RNA are also identical. These results indicate that variant RNAs associated with transmission-defective WTV isolates are formed by deletion of an internal portion (as much as 85%) of genomic RNA segments yielding terminally conserved genomic remnants that are functional with respect to transcription, replication, and packaging.

Animals↗
PubMed2005

DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

The identification and study of evolutionarily conserved genomic sequences that surround disease-related genes is a valuable tool to gain insight into the functional role of these genes and to better elucidate the pathogenetic mechanisms of disease. We created the DG-CST (Disease Gene Conserved Sequence Tags) database for the identification and detailed annotation of human-mouse conserved genomic sequences that are localized within or in the vicinity of human disease-related genes. CSTs are defined as sequences that show at least 70% identity between human and mouse over a length of at least 100 bp. The database contains CST data relative to over 1088 genes responsible for monogenetic human genetic diseases or involved in the susceptibility to multifactorial/polygenic diseases. DG-CST is accessible via the internet at http://dgcst.ceinge.unina.it/ and may be searched using both simple and complex queries. A graphic browser allows direct visualization of the CSTs and related annotations within the context of the relative gene and its transcripts.

Animals↗
PubMed1994

Evolutionary conservation and genomic organization of XAP-4, an Xq28 located gene coding for a human rab GDP-dissociation inhibitor (GDI).

After the development of efficient methods for the construction of transcription maps of defined genomic regions, the rate-limiting step in the analysis of the coding potentials of these regions is the elucidation of function of the novel genes and the examination of their possible involvement in hereditary diseases localized to the region. This can be greatly facilitated by the detection of sequence homology to a gene of known function. XAP-4 is one of the genes identified in the G6PD region of the human Xq28 by direct cDNA selection. The rapid assembly of this gene and the determination of its function was possible because of its sequence homology with the bovine smg p25A/rab3A GDP dissociation inhibitor (GDI). Sequence comparison with other GDIs in the databases has revealed that XAP-4 belongs to one of at least two distinct classes of mammalian rab GDIs. The rab GDIs, which play an important role in the regulation of cellular transport, are highly evolutionarily conserved, as are several other genes identified in the neighborhood of XAP-4. This genomic region is very gene dense, and all the cDNA clones from the approximately 2.5-kb-long transcript of XAP-4 map to a single 7.5-kb genomic EcoRI fragment. The genomic organization of XAP-4 has been examined to determine the distribution of the exonic sequences within this short segment of genomic DNA. It was found that, similar to several other genes from the region, XAP-4 is split into exons of average size, which are interrupted by very short introns.

Amino Acid Sequence↗
PubMed1997

The major histocompatability complex (MHC) contains conserved polymorphic genomic sequences that are shuffled by recombination to form ethnic-specific haplotypes.

The major histocompatibility complex (MHC) consists of polymorphic frozen blocks (PFBs) that are linked to form megabase haplotypes. These blocks consist of polymorphic sequences and define regions where recombination appears to be inhibited. We have been able to show, using a highly polymorphic sequence centromeric of HLA-B (within the beta block), that PFBs are conserved and contain specific insertions/deletions and substitutions that are the same for individuals with the same MHC haplotype but that differ between at least most different haplotypes. A sequence comparison between ethnic-specific haplotypes shows that these sequences have remained stable and predate the formation of these haplotypes. To determine whether the same conserved block has been involved in the generation of multiple haplotypes, we compared the block typing profiles of different ethnic specific haplotypes. Block typing profiles have previously been shown to be identical in individuals with the same MHC haplotype but, generally, to differ between different haplotypes. It was found that some PFBs are common to more than one haplotype, implying a common ancestry. Subsequently, haplotypes have been generated by the shuffling and exchange of these PFBs. The regions between these PFBs appear to permit the recombination sites and therefore could be expected to exhibit either low polymorphism or a localized "hotspot."

Asian People↗
PubMed1993

Structural analysis of the CD11b gene and phylogenetic analysis of the alpha-integrin gene family demonstrate remarkable conservation of genomic organization and suggest early diversification during evolution.

CD11b is a member of the beta 2 subfamily of the human leukocyte integrins. Its expression is limited to mature myeloid and NK cells and is up-regulated during the course of granulocytic and monocytic differentiation. The CD11b/CD18 (Mo1) heterodimer promotes adhesion of granulocytes and monocytes to C3bi-coated bacteria and endothelial cells. In an attempt to relate the exon structure to the known functional domains, as well as to identify and study cis-acting elements that are involved in its tissue-specific expression, we have isolated genomic clones encoding CD11b, deduced the exon/intron organization, and determined the transcriptional start site. The CD11b gene spans 55 kb and is encoded by 30 exons. Its structure closely resembles that of CD11c, another of the three leukocyte integrin alpha-chains, and suggests that these two genes arose by a gene duplication event. Furthermore, comparison of the CD11b gene structure with that of platelet glycoprotein IIb and Drosophila PS2 suggest how the human leukocyte integrins evolved and dispersed during the course of evolution.

Amino Acid Sequence↗
PubMed2002

Viral RNA mutations are region specific and increased by ribavirin in a full-length hepatitis C virus replication system.

High rates of genetic variation ensure the survival of RNA viruses. Although this variation is thought to result from error-prone replication, RNA viruses must also maintain highly conserved genomic segments. A balance between conserved and variable viral elements is especially important in order for viruses to avoid "error catastrophe." Ribavirin has been shown to induce error catastrophe in other RNA viruses. We therefore used a novel hepatitis C virus (HCV) replication system to determine relative mutation frequencies in variable and conserved regions of the HCV genome, and we further evaluated these frequencies in response to ribavirin. We sequenced the 5' untranslated region (5' UTR) and the core, E2 HVR-1, NS5A, and NS5B regions of replicating HCV RNA isolated from cells transfected with a T7 polymerase-driven full-length HCV cDNA plasmid containing a cis-acting hepatitis delta virus ribozyme to control 3' cleavage. We found quasispecies in the E2 HVR-1 and NS5B regions of untreated replicating viral RNAs but not in conserved 5' UTR, core, or NS5A regions, demonstrating that important cis elements regulate mutation rates within specific viral segments. Neither T7-driven replication nor sequencing artifacts produced these nucleotide substitutions in control experiments. Ribavirin broadly increased error generation, especially in otherwise invariant regions, indicating that it acts as an HCV RNA mutagen in vivo. Similar results were obtained in hepatocyte-derived cell lines. These results demonstrate the potential utility of our system for the study of intrinsic factors regulating genetic variation in HCV. Our results further suggest that ribavirin acts clinically by promoting nonviable HCV RNA mutation rates. Finally, the latter result suggests that our replication model may be useful for identifying agents capable of driving replicating virus into error catastrophe.

Amino Acid Sequence↗
PubMed2026

Evolutionary history of Aotearoa New Zealand's extinct mātuhituhi | bush wren.

The reconstruction of ecosystem responses to past climate change has historically focused on large vertebrates. In contrast, small vertebrates with potentially stricter habitat preferences have been neglected in ancient DNA studies despite their potential utility as proxies for inferring geographic and temporal changes in habitat. Aotearoa New Zealand's acanthisittid wrens are a speciose group of tiny perching birds, including the mātuhituhi | bush wren (Xenicus longipes ssp.). Despite its relatively recent extinction in the 1970s, very little is known about this enigmatic bird. Here we sequence mitochondrial genomes and nuclear ultra conserved genomic elements from 32 historical bush wren specimens to reconstruct their evolutionary history. We also genetically sex specimens and reanalyse their plumage to reconstruct aspects of bush wren plumage variation. Our analyses suggest North and South Island bush wren populations diverged 2.6 million years ago when narrowing and closure of Plio-Pleistocene seaways allowed colonisation of new habitats, followed by rapid glaciation-driven diversification of South Island populations 470,000-94,000 years ago. Genetic sexing allowed an accurate reconstruction of ontogenetic, sexual, and geographic variation in plumage. Our multidisciplinary data supports recognition of North and South Island populations as separate species, and the description of a new subspecies X. longipes perditus subsp. nov. This research shows how ecosystems can buffer against the impacts of climate change up to an ecological tipping point, which has important lessons for conservation management in a fast-changing world.

Acanthisittidae↗
PubMed1997

Clinical similarities and close genetic relationship of human and animal Borna disease virus.

Borna disease virus (BDV) is the prototype genus of a new family, Bornaviridae, within the order Mononegavirales. BDV naturally infects animals and man. The symptomatology in animals ranges from subclinical infection to rare cases of encephalitis. Asymptomatic infection seemed more frequent than expected, based on antibody data from 100 healthy horses derived from different stables with a history of diseased cases (30-40% carriers). Likewise, phasic episodes of a neurobehavioral syndrome followed by recovery were much more common than fatal neurologic disease. They were paralleled by expression of BDV antigens (N-protein p40, P-protein p24) and RNA transcripts in peripheral blood mononuclear cells, indicating viral activation. Representative longitudinal studies showed that episodes of depressive illness in humans as well as apathetic phases in infected horses were accompanied by antigen expression and followed a similar clinical course. After recovery, BDV antigen disappeared. This temporal congruence, together with the recent isolation of infectious BDV from such patients, points to a contributory role of this virus in human affective disorders. Successful amelioration of BDV-induced neurobehavioral disease in horses with antidepressants applied in psychiatry, supported a common viral pathomechanism, involving reversible disturbances of the neurotransmitter network in the limbic system. Sequences of genetic material amplified from infected animal tissue and human PBMCs revealed a close interspecies relationship and high sequence conservation of the BDV genome. In human BDV isolates, however, single unique mutations were prominent in four genes. This finding supports the hypothesis that despite of high genomic conservation, species-specific genotypes may be definable, provided the sequences are derived from RNA of infectious virus.

Aged↗
PubMed1993

Evolutionary conservation of genomic sequences related to the GGP1 gene encoding a yeast GPI-anchored glycoprotein.

The GGP1 gene encodes the only GPI-anchored glycoprotein (gp115) that has been purified to-date in the budding yeast Saccharomyces cerevisiae. It is a single-copy gene whose deduced amino-acid sequence shares no significant homology to any other known protein. In this paper we report a Southern hybridization analysis of genomic DNA from different eukaryotic organisms to identify homologues of the GGP1 gene. We have analyzed DNA prepared from a unicellular green alga (Chlamydomonas eugametos), from two distantly related yeast species (Candida cylindracea and Schizosaccharomyces pombe), and from the common bean Phasoleus vulgaris. The moderate stringency of the experimental conditions and the high specificity of the probes used indicate that a single-copy of GGP1-related sequences exists in all these eukaryotic organisms. The chromosomal localization of the GGP1 gene in S. cerevisiae has also been determined.

Animals↗
PubMed1985

Conservation of genome form but not sequence in the transcription antitermination determinants of bacteriophages lambda, phi 21 and P22.

Comparisons are made among DNA sequences upstream from terminators in both leftwards and rightwards early operons of related coliphages lambda, phi 21 and P22. These sequences include both left and right determinants of response to phage-coded antitermination proteins, "N", as well as the N structural genes themselves. Despite almost total disparity of DNA sequence, the three genomes can be discerned to include the same elements in the same order and spacing: downstream from the early left promoter are sequentially a site of recognition for host nusA protein, a dyad symmetry "nut" essential for N function in lambda, overlapping sites for processing of the transcript by RNAase III and then the N structural genes; downstream from the cro gene on the right are sites of nusA recognition and nut dyad symmetries homologous to those on the left. Because the N proteins of lambda, phi 21 and P22 do not for the most part complement each other, a specific site of N recognition has been postulated for each N-responding operon. The nut dyad symmetry qualifies as such a site, since the loop of the left dyad in lambda is marked by mutations that block N function leftwards, and since DNA sequences here show close homology between the loops of left and right dyads for each phage, but less if not little homology for different phages.

Adult↗
PubMed1994

Genome organization of the DNA-binding protein gene region of Cryptophlebia leucotreta granulosis virus is closely related to that of nuclear polyhedrosis viruses.

The nucleotide sequence and genomic organization of a conserved genome region within the EcoRI G fragment of cryptophlebia leucotreta granulosis virus (ClGV) is presented. Five open reading frames (ORFs) were identified which were homologous to those of Autographa californica nuclear polyhedrosis virus (AcMNPV), located upstream of the helicase gene (p143) at 63.6 to 65.6 map units. The ORFs of ClGV and AcMNPV share nucleotide sequence homologies of about 47 to 53% and are very similarly arranged. One of the ClGV ORFs potentially encodes a basic DNA-binding protein with an M(r) of about 7.3 K. Its predicted amino acid sequence mainly consists of multiple arginine and serine residues and shows a 52 to 55% identity to the DNA-binding proteins of AcMNPV and other nuclear polyhedrosis viruses. Its amino acid composition conforms to that of the DNA-binding proteins of Plodia interpunctella granulosis virus and Spodoptera litura granulosis virus.

Amino Acid Sequence↗
PubMed1989

Conservation of genomic sequences among isolates of Mycobacterium leprae.

Restriction fragment length polymorphism analysis has been used to assess relatedness among the genomes of four isolates of Mycobacterium leprae, the causative agent of leprosy. The M. leprae isolates were from human patients from India, a Mangabey monkey from West Africa, and an armadillo from Louisiana. A total of 16 probes were used; these were insert fragments of M. leprae DNA from plasmid recombinant libraries, 5 of which had genes with identifiable functions and 11 of which were randomly chosen recombinant molecules. In spite of the widely diverse origins of the isolates, restriction fragment length polymorphism analysis demonstrated that less than 0.3% of the nucleotides differ among the genomes.

Animals↗
PubMed1984

Conservation of genome organization in two multicapsid nuclear polyhedrosis viruses.

The genome of the multicapsid nuclear polyhedrosis virus of Orgyia pseudotsugata was mapped by examining overlapping HindIII fragments from cosmid clones which had been constructed from partial HindIII digests of viral DNA. Five OpMNPV cosmid clones containing fragments encompassing the entire OpMNPV genome were hydridized to blots of DNA from the multicapsid nuclear polyhedrosis virus of Autographa californica. The hybridization pattern indicated that the genomes of these viruses are similarly organized.

Base Sequence↗