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PubMed2006

[Retroviruses-derived sequences in the human genome. Human endogenous retroviruses (HERVs)].

Retroviruses-derived elements in the human genome constitute 90% of non-coding mobile sequences. Reverse transcriptase (RT) plays an essential role in their transposition as do long terminal repeats (LTRs), which contain promotors, enhancers, and regulatory sequences. Some retroelements (pseudogens and retrogenes, e.g. SINE) are non-autonomic and do not possess their own RT. These elements are dependent on autonomic elements (retroposons, e.g. LINE, retrotransposons, exo- and endogenous retroviruses). The genome of retroviruses is composed of gag, pol, and env genes flanked by long terminal repeats. Endogenous retroviruses are probably the remnants of ancient germ cell infection by exogenous retroviruses and are transmissible to the next generation in a Mendelian way. Most of them are defective (because of mutation accumulation), but some are still active and their expression is regulated by different factors (UV radiation, inflammatory cytokines, steroid hormones, and exogenous virus products). Retroelements as well as their gene products exert influence on the organism's functions. They influence the plasticity and evolution of genomes, are a source of promotors and regulatory sequences, but they also supply additional signals of transcription initiation, mRNA splicing, and STOP codons. One of the positive aspects of human endogenous retroviruses (HERVs) is the participation of their products in normal syncytiotrophoblast formation. They also block exogenous retrovirus replication by receptor interference or antisense mRNA. Their presence is considered to be connected with a number of autoimmunological diseases (multiple sclerosis, insulin-dependent diabetes mellitus, systemic lupus erythematosus), cancer, or even psychiatric disorders (schizophrenia). There are also other problems connected with the potential role of ERVs in genomic therapy (with retroviruses vectors) and transplantology (xenotransplantation).

Autoimmune Diseases↗

PubMed1998

Insertional inactivation of the tomato polygalacturonase gene.

The site-selected insertion (SSI) procedure was used to generate insertional knockout mutations in the gene for tomato polygalacturonase (PG), a critical enzyme in fruit ripening. Previously, it had been shown that the Dissociation (Ds) elements in a select group of tomato plants frequently inserted into PG, at least in somatic tissues. DNA isolated from pollen produced by progeny of these plants was screened by SSI to identify plants likely to transmit the insertions in PG to progeny. These results identified one family as likely candidate for yielding germinally transmitted insertions. Four thousand progeny were screened and five were found containing germinally transmitted Ds insertions in PG, one of which contained two Ds insertions in PG. The Ds elements were stabilized by genetically removing the transposase and four of the five insertions were recovered as homozygous in the next generation. Enzymatic analysis of fruit from these individuals demonstrated that there was at least a 1000-fold reduction in polygalacturonase levels in those plants bearing Ds insertions in PG exons. Individuals with modified PG sequences due to the sequence footprint, resulting from excision of the element, were identified using the single-strand conformational polymorphism (SSCP) method. Enzymatic analysis of fruit from a plant homozygous for one such excision allele showed a significant reduction in polygalacturonase activity. Since there is no transgenic material left in PG, this demonstrates the ability to modify a gene of commercial value in planta and subsequently removing all transgenic material.

Alleles↗

PubMed2025

Transposable elements create distinct genomic niches for effector evolution among Magnaporthe oryzae lineages.

BACKGROUND: Plant-pathogen interactions are characterized by evolutionary arms races. At the molecular level, fungal effectors can target important plant functions, while plants evolve to improve effector recognition. Rapid evolution in genes encoding effectors can be facilitated by transposable elements (TEs). In Magnaporthe oryzae, the causal agent of blast disease in several cereals and grasses, TEs play important roles in chromosomal evolution as well as the gain or loss of effector genes in host specialized lineages. However, a global understanding of TE dynamics driving effector evolution at population scale and across lineages is lacking. RESULTS: Here, we focus on 16 AVR effector loci assessed across a global sampling of 11 reference genomes and 447 newly generated draft genome assemblies from publicly available short-read sequencing data across all major M. oryzae lineages and outgroups. We classified each effector based on evidence for duplication, deletion and translocation processes among lineages. Next, we determined AVR gain and loss dynamics across lineages allowing for a broad categorization of effector dynamics. Each AVR was integrated in a distinct genomic niche determined by the TE activity profile contributing to the diversification at the locus. We quantified TE contributions to effector niches and found that TE identity helped diversify AVR loci. We used the large genomic dataset to recapitulate the evolution of the rice blast AVR1-CO39 locus. CONCLUSIONS: Taken together, our work demonstrates how TE dynamics are an integral component of M. oryzae effector evolution, likely facilitating escape from host recognition. In-depth tracking of effector loci is a valuable tool to predict the durability of host resistance.

Ascomycota↗

PubMed2005

Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis.

A fundamental tenet of classical mendelian genetics is that allelic information is stably inherited from one generation to the next, resulting in predictable segregation patterns of differing alleles. Although several exceptions to this principle are known, all represent specialized cases that are mechanistically restricted to either a limited set of specific genes (for example mating type conversion in yeast) or specific types of alleles (for example alleles containing transposons or repeated sequences). Here we show that Arabidopsis plants homozygous for recessive mutant alleles of the organ fusion gene HOTHEAD (HTH) can inherit allele-specific DNA sequence information that was not present in the chromosomal genome of their parents but was present in previous generations. This previously undescribed process is shown to occur at all DNA sequence polymorphisms examined and therefore seems to be a general mechanism for extra-genomic inheritance of DNA sequence information. We postulate that these genetic restoration events are the result of a template-directed process that makes use of an ancestral RNA-sequence cache.

Alleles↗

PubMed1996

Lobster shal: comparison with Drosophila shal and native potassium currents in identified neurons.

The transient potassium (K+) current, or A-current (IA), plays an essential role in shaping the firing properties of identified neurons in the 14-cell pyloric network in the stomatogastric ganglion of the spiny lobster, Panulirus interruptus. The different cells in the pyloric network have distinct IAs. To begin to understand the molecular basis for IA heterogeneity, we examined the relationship between the Panulirus shal current, the IAs in the lateral pyloric (LP) and pyloric dilator (PY) cells, and the Drosophila shal current. After isolating a complete open reading frame for lobster shal 1, which shows significant sequence homology to the fly, mouse, and rat shal homologs, we used a single-cell reverse transcription polymerase chain reaction method to demonstrate that the shal 1 gene was expressed in the LP and PY cells. Next, we compared the lobster shal 1 current generated in a Xenopus oocyte expression system to the IAs in the LP and PY neurons as well as to the Drosophila shal current in Xenopus oocytes. While the transient K+ lobster shal 1 current was similar to the IAs in pyloric neurons, a detailed comparison shows that they are not identical and differ in kinetic and voltage-dependent parameters. The highly homologous lobster and fly shal genes also produce currents with some significant similarities and differences in an oocyte expression system.

Amino Acid Sequence↗

PubMedDate not supplied

Construction of a chimaeric type 1/type 2 poliovirus by genetic recombination.

A chimaeric poliovirus carrying a type-2-specific neutralization epitope on a type 1 capsid was created by site-directed mutagenesis of the Mahoney strain of poliovirus type 1. An EcoRV and a HindIII restriction sites were first constructed in the cDNA of poliovirus type 1 at nucleotide positions 2756 and 2786, respectively, i.e. on either side of the sequence encoding neutralization epitope C3 (VP1 amino acids 93-103), which is part of neutralization site NImI. The cDNA sequence framed by the two sites was next taken out and replaced by custom-made oligonucleotides encoding the equivalent region of VP1 from the Lansing strain of poliovirus type 2. The DNA from the plasmid carrying such a hybrid construct was transfected onto CV1 cells generating a chimaeric virus, v510. Neutralization of v510 with a panel of monoclonal antibodies showed that v510 has lost the poliovirus type 1 C3 epitope but acquired a new, poliovirus type-2-specific neutralization epitope. Preliminary results indicate that v510 also shows neurovirulence for mice, which is a specific trait of the Lansing strain of poliovirus type 2.

Antibodies, Monoclonal↗

PubMed1981

Parathyroid hormone: chemistry and structure-activity relations.

Peptide synthesis and the application of a wide range of biological assays have permitted intensive and detailed study of structure-activity relations for parathyroid hormone. Within the structure of the hormone molecule reside largely distinct domains critical for receptor binding or activation of adenylate cyclase in addition to receptor binding. Subtle modifications of hormonal structure can cause striking changes in hormone potency or in the nature of the biological properties displayed by such analogs. For parathyroid hormone, structure-activity studies have identified several discrete regions of the molecule that are responsible for independent biological functions. It was determined that these separate functions are displayed in an almost linear fashion along the primary sequence of the hormone--a conceptual framework that has greatly facilitated synthesis of parathyroid hormone analogs. The amino-terminal region of the initially biosynthesized precursor form of parathyroid hormone, pre-proparathyroid hormone, - 31 through - 7, contains a leader or signal sequence. Despite differences in sequence of the parathyroid hormone signal region and other precursor-specific sequences, this region of the molecule possesses biological properties related to intracellular transport and metabolism that appear to be universal for precursor forms of many, if not all, peptide hormones and other secreted proteins. In contrast, the amino-terminal portion of the secreted form of the molecule, sequence region 1-34, has an amino acid sequence that is homologous to that of several peptide hormones, including ACTH, alpha-MSH, beta-MSH, and beta-lipotropin. Yet the biological "message" conveyed by this peptide sequence appears unique to parathyroid hormone. Directions have now been established for the design of hormone inhibitors and for analogs of enhanced biological activity and perhaps even analogs possessing an altered spectrum of biological properties. The rapid advances that are occurring in techniques for peptide synthesis, purification, and analysis; in the variety, sensitivity, and specificity of the increasing number of bioassays; and in the elucidation of peptide and protein conformation may provide further important new directions for analog design. Extension of these investigations of structure and function over the next several years should yield a more sophisticated understanding of the mode of hormone action. In such studies lies the promise of generating highly refined and perhaps clinically useful analogs of parathyroid hormone.

Adenylyl Cyclases↗

PubMed1996

Structure and expression of the ATFa gene.

The human ATFa proteins belong to the ATF/CREB family of transcription factors. We have previously shown that they mediate the transcriptional activation by the largest E1a protein and can heterodimerize with members of the Jun/Fos family. ATFa proteins have also been found tightly associated with JNK2, a stress-activated kinase. We now report on the structure of the ATFa gene, which mapped to chromosome 12 (band 12q13). Sequence analysis revealed that ATFa isoforms are generated by alternative splice donor site usage. A minimal promoter region of approximately 200 base pairs was identified that retained nearly full transcriptional activity. Binding sites for potential transcription factors were delineated within a GC-rich segment by DNase I footprinting. Expression studies revealed that ATFa accumulates in the nuclei of transfected cells, and the nuclear localization signal was defined next to the leucine zipper domain. As revealed by hybridization with mouse ATFa sequences, low levels of ATFa mRNAs were ubiquitously distributed in fetal or adult mice, with enhanced expression in particular tissues, like squamous epithelia and specific brain cell layers. The possible significance of coexpression of ATFa, ATF-2, and Jun at similar sites in the brain is discussed.

Activating Transcription Factors↗

PubMed2004

Specification of polarity of teloblastogenesis in the oligochaete annelid Tubifex: cellular basis for bilateral symmetry in the ectoderm.

Ectodermal teloblastogenesis in the oligochaete annelid Tubifex is a spatiotemporally regulated process that gives rise to four bilateral pairs of ectoteloblasts (N, O, P, and Q) that assume distinct fates. Ectoteloblasts on either side of the embryo arise from an invariable sequence of asymmetric cell divisions of a proteloblast, NOPQ, which occur with a defined orientation with respect to the embryonic axes: the N teloblast is generated first and located ventralmost, and the Q teloblast, which is generated next, is located dorsalmost; finally, the O and P teloblasts are generated by almost equal division of their precursor cell, OP. Polarity of teloblastogenesis on one side of the embryo is a mirror image of the other; this mirror symmetry of ectoteloblasts about the embryo's midline gives rise to the bilaterally symmetric organization of the ectoderm. In this study, we examined whether cellular interactions are involved in specification of polarity of asymmetric cell divisions in NOPQ cells. A set of cell transplantation experiments demonstrated that NOPQ cells are initially uncommitted in terms of division pattern and cell fates: If a left NOPQ cell is transplanted to the right side of a host embryo, it exhibits a polarity comparable to that of right NOPQ cells. The results of another set of cell transplantation experiments suggest that contact between NOPQ cells serves as an external cue for their polarization, irrespective of their position in the embryo, and that in the absence of host NOPQ cells, transplanted NOPQ cells can be polarized according to positional information residing in the host embryo. The competence of NOPQ cells to respond to external cues tapers down before their division into N and OPQ. A set of cell ablation experiments demonstrated that neighboring cells such as posteriorly located M teloblasts and anterolaterally located micromeres play a role in controlling spatial aspects of NOPQ's behavior that gives rise to their division along the dorsoventral axis. These results suggest that NOPQ cells, which do not initially have a rigidly fixed polarity, become polarized through external cues. Possible sources of signals for this polarizing induction are discussed in the light of the present results.

Animals↗

PubMed1997

Human cytomegalovirus open reading frame UL11 encodes a highly polymorphic protein expressed on the infected cell surface.

Human cytomegalovirus (HCMV) open reading frame (ORF) UL11 locates within a polymorphic region of the viral genome identified previously by a restriction-fragment-length-polymorphism. We report here that ORF UL11 encodes a polymorphic protein expressed on the surface of HCMV-infected cells. First, we determined the nucleotide sequence of ORF UL11 from ten strains and compared it among the strains. Out of 205 amino acids consisting of the predicted N-terminal region beside the putative transmembrane stretch in strain AD169, 88 residues were divergent on more than one strain. In contrast, the predicted C-terminal side including the putative transmembrane domain was identical at the amino acid sequence level. In addition, the number and location of predicted cysteine residues were also conserved. Next, we screened a cDNA library from HCMV-infected cells and obtained a cDNA clone containing the full-length ORF UL11. Finally, we identified the gene product of UL11 on the surface of HCMV-infected cells by FACS analysis with polyclonal antibodies generated against a glutathione S-transferase/UL11 fusion protein. The fusion protein contained a region within the N-terminal side next to the predicted transmembrane stretch. These results indicate that the N-terminal side of UL11 protein containing variable amino acid residues protrudes from the infected cell surface.

Amino Acid Sequence↗

PubMed2000

Interaction of platelet activating factor, reactive oxygen species generated by xanthine oxidase, and leukocytes in the generation of hepatic injury after shock/resuscitation.

OBJECTIVE: To evaluate the putative relation of platelet activating factor (PAF), xanthine oxidase, reactive oxidants, and leukocytes in the pathogenesis of hepatic injury after shock/resuscitation (S/R) in vivo. BACKGROUND: Reactive oxygen metabolites generated by xanthine oxidase at reperfusion have been found to trigger postischemic injury in many organs, including the liver. However, the precise linear sequence of the mechanism of consequent hepatic injury after S/R remains to be characterized. METHODS: Unheparinized male rats were bled to a mean blood pressure of 45 +/- 3 mmHg. After 2 hours of shock, they were resuscitated by reinfusion of shed blood (anticoagulated with citrate-phosphate-dextrose) and crystalloid and observed for the next 6 or 24 hours. RESULTS: S/R caused the oxidation of hepatic glutathione and generated centrolobular leukocyte accumulation at 6 hours, followed by predominantly centrolobular hepatocellular injury at 24 hours. Each of these components was attenuated by PAF inhibition with WEB 2170, xanthine oxidase inhibition with allopurinol, antioxidant treatment with N-acetylcysteine, or severe leukopenia induced by vinblastine. In each case, the degree of leukocyte accumulation at 6 hours correlated with the hepatocellular injury seen at 24 hours. However, xanthine oxidase inhibition with allopurinol failed to attenuate further the small level of residual hepatocellular injury seen in leukopenic rats. CONCLUSION: These findings suggest that reactive oxidants generated by xanthine oxidase at reperfusion, stimulated by PAF, mediate hepatocellular injury by triggering leukocyte accumulation, primarily within the centrolobular sinusoids.

Animals↗

PubMed2006

Mouse homologue of skin-specific retroviral-like aspartic protease involved in wrinkle formation.

Retroviral proteases are encoded in the retroviral genome and are responsible for maturation and assembly of infectious virus particles. A number of retroviral protease sequences with retroviral elements are integrated in every eukaryotic genome as endogenous retroviruses. Recently, retroviral-like aspartic proteases that were not embedded within endogenous retroviral elements were identified throughout the eukaryotic and prokaryotic genomes. However, the physiological role of this novel protease family, especially in mammals, is not known. During the high throughput in situ hybridization screening of mouse epidermis, as a granular layer-expressing clone, we identified a mouse homologue of SASPase (Skin ASpartic Protease), a recently identified retroviral-like aspartic protease. We detected and purified the endogenous 32-kDa (mSASP32) and 15-kDa (mSASP15) forms of mSASP from mouse stratum corneum extracts and determined their amino acid sequences. Next, we bacterially produced recombinant mSASP15 via autoprocessing of GST-mSASP32. Purified recombinant mSASP15 cleaved a quenched fluorogenic peptide substrate, designed from the autoprocessing site for mSASP32 maximally at pH 5.77, which is close to the pH of the epidermal surface. Finally, we generated mSASP-deficient mice that at 5 weeks of age showed fine wrinkles that ran parallel on the lateral trunk without apparent epidermal differentiation defects. These results indicate that the retroviral-like aspartic protease, SASPase, is involved in prevention of fine wrinkle formation via activation in a weakly acidic stratum corneum environment. This study provides the first evidence that retroviral-like aspartic protease is functionally important in mammalian tissue organization.

Amino Acid Sequence↗

PubMed1995

Telomere and LINE-like elements at the termini of the Chlorella chromosome I.

The telomeres of Chlorella chromosomes consisted of 5'-TTTAGGG repeats, which are exactly the same as those of higher plants. This sequence was reiterated approximately 70 times at both termini of chromosome I. Subtelomeric sequences next to the telomeres were totally different between the right and left arms. On the left-side subtelomeric region, polyA associated LINE (long interspersed element)-like elements were found tandemly repeated just next to the telomeric repeats. It is very interesting to compare this unique structure with telomeres of Drosophila, where a transposable element play a major role in forming telomerase-generated repeats. We propose a mechanism of transposon-mediated healing of a broken chromosomal end that would operate in the unicellular green alga Chlorella.

Animals↗

PubMed2001

QSAR: hydropathic analysis of inhibitors of the p53-mdm2 interaction.

To date, a number of p53-derived peptides have been evaluated in vitro for their ability to inhibit the carcinogenic p53-mdm2 interaction. Design of second-generation nonpeptidic compounds requires the reduction of large peptide structures down to small molecules maintaining the proper spatial arrangement of key functional groups. Molecular modeling software exists that can predict and rank intermolecular interactions from the p53-mdm2 complex crystal structure. Such analyses can yield a pharmacophore model suitable as a search query for a 3D chemical database to generate new lead compounds. As preliminary validation of this methodology, the Hydropathic INTeractions (HINT) program has been used to generate noncovalent interaction measurements between reported peptide inhibitors and mdm2. Quantitative structure-activity relationships were developed expressing peptide activity as a linear combination of hydropathic descriptors. In general, HINT measurements accurately modeled the effects of even single-atom alterations of the p53-peptide structure on activity, accounting for 70-90% of variation in experimental inhibition constants. These results surpassed those of a recently described molecular dynamics-based approach and required significantly less computation time. In conclusion, the HINT program can be integrated into the drug design cycle for next-generation p53-mdm2 complex inhibitors with confidence in its ability to simulate this noteworthy protein-protein interaction.

Amino Acid Sequence↗

PubMed2005

Intraordinal phylogenetics of treeshrews (Mammalia: Scandentia) based on evidence from the mitochondrial 12S rRNA gene.

Despite their traditional and continuing prominence in studies of interordinal mammalian phylogenetics, treeshrews (order Scandentia) remain relatively unstudied with respect to their intraordinal relationships. At the same time, significant morphological variation among living treeshrews has been shown to have direct relevance to higher-level interpretations of character state change as reconstructed in traditional interordinal studies, which have often included only a single species of treeshrew. Therefore, the importance of resolving relationships among treeshrews extends well beyond a better understanding of patterns of diversification within the order. A recent review highlighted several shortcomings in published studies of treeshrew phylogenetics based on morphology. Here we present the first investigation of treeshrew phylogenetics based on DNA sequences, utilizing previously published sequences from the mitochondrial 12S rRNA gene and combining them with newly generated sequence data from 15 species. Parsimony, likelihood, and Bayesian analyses all strongly support a sister relationship between Ptilocercus and the remaining species, further substantiating its recent elevation to familial status. Dendrogale is consistently recovered as the next taxon to diverge, but relationships among the remaining taxa are poorly supported by these data. We provide evidence for a relatively rapid radiation within the genera Tupaia and Urogale, but limited resolution precludes more than a cursory interpretation of biogeographic patterns.

Animals↗

PubMed1999

Chromosome healing in mouse embryonic stem cells.

The addition of new telomeres to the ends of broken chromosomes, termed chromosome healing, has been extensively studied in unicellular organisms; however, its role in the mammalian cell response to double-strand breaks is unknown. A system for analysis of chromosome healing, which involves the integration of plasmid sequences immediately adjacent to a telomere, has been established in mouse embryonic stem cells. This "marked" telomere contains a neo gene for positive selection in G418, an I-SceI endonuclease recognition sequence for introducing double-strand breaks, and a herpes simplex virus thymidine kinase gene for negative selection with ganciclovir for cells that have lost the telomere. Transient expression of the I-SceI endonuclease results in terminal deletions involving telomeric repeat sequences added directly onto the end of the broken chromosome. The sites of addition of the new telomeres contain short regions of complementarity to telomeric repeat sequences. The most common site of addition is the last A of the ATAA 3' overhang generated by the I-SceI endonuclease, without the loss of a single nucleotide from the end of the chromosome. The next most frequent site involved 5 bp of complementarity, which occurred after the loss of four nucleotides from the end of the chromosome. The new telomeres are generally much shorter than in the parental cell line, and most increase in size with time in culture. These results demonstrate that chromosome healing is a mechanism for repair of chromosome breaks in mammalian cells.

Animals↗

PubMed1984

An RNA folding rule.

The folding of single-stranded RNA into its secondary structure is postulated to be equivalent to the simple rule that the next double-helical region (stem) to form is the one with the largest equilibrium constant. The rule is tested and shown to give results consistent with the enzyme cleavage data of several sequences. Computational time complexity is of order NxN for a sequence of N bases. A modification of the rule provides for the probabilistic choice of the next stem among those having an equilibrium constant within a specified range of the largest. Populations of competing structures are thus generated for detecting common characteristics and for assessing the applicability of the simple rule.

Hydrogen Bonding↗

PubMed1988

Organization of the Ly-5 gene.

A single Ly-5 gene is known to generate a variety of transmembrane glycoprotein isoforms that distinguish various cell lineages and stages of differentiation within the hematopoietic developmental compartment of the mouse. Systems homologous to Ly-5 are known in rats and in humans. The complete exon-intron organization of the Ly-5 gene is described in this report. The Ly-5 gene occupies about 120 kilobases of chromosome 1 and comprises 34 exons, of which 32 (Ex-3 to Ex-34) are protein coding. Ex-1, Ex-2, and parts of Ex-3 and Ex-34 are untranslated. In all cDNA clones examined, either Ex-1 or Ex-2 was represented, but not both, implying that Ex-1 and Ex-2 in Ly-5 mRNA may be mutually exclusive. Primer extension and S1 nuclease protection mapping were used to identify initiation (cap) sites for transcription. The finding of putative cap sites for Ex-1 and Ex-2, and of corresponding TATA-like sequences, suggests the presence of two promoters. In both Ex-1+ and Ex-2+ cDNA clones the next exon is Ex-3, which has a translation-initiating codon. The intron between Ex-3 and Ex-4 is unusually long, about 50 kilobases. Evidence is given that Ex-5, like Ex-6 and Ex-7 (studied previously), is another alternative exon that is selectively programmed, alone or together with Ex-6 or Ex-7 or both, to generate actual or potential Ly-5 isoforms by alternative splicing.

Animals↗