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  • 1. Abdurahman, Samir
    et al.
    Höglund, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry, Biochemistry.
    Höglund, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry, Biochemistry.
    Vahlne, Anders
    Mutation in the loop C-terminal to the cyclophilin A binding site of HIV-1 capsid protein disrupts proper virus assembly and infectivity2007In: Retrovirology, ISSN 1742-4690, E-ISSN 1742-4690, Vol. 4, p. 19-Article in journal (Refereed)
    Abstract [en]

    We have studied the effects associated with two single amino acid substitution mutations in HIV-1 capsid (CA), the E98A and E187G. Both amino acids are well conserved among all major HIV-1 subtypes. HIV-1 infectivity is critically dependent on proper CA cone formation and mutations in CA are lethal when they inhibit CA assembly by destabilizing the intra and/or inter molecular CA contacts, which ultimately abrogate viral replication. Glu98, which is located on a surface of a flexible cyclophilin A binding loop is not involved in any intra-molecular contacts with other CA residues. In contrast, Glu187 has extensive intra-molecular contacts with eight other CA residues. Additionally, Glu187 has been shown to form a salt-bridge with Arg18 of another N-terminal CA monomer in a N-C dimer. However, despite proper virus release, glycoprotein incorporation and Gag processing, electron microscopy analysis revealed that, in contrast to the E187G mutant, only the E98A particles had aberrant core morphology that resulted in loss of infectivity.

  • 2. Abdurahman, Samir
    et al.
    Vegvari, Akos
    Levi, Michael
    Höglund, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry.
    Högberg, Marita
    Tong, Weimin
    Romero, Ivan
    Balzarini, Jan
    Vahlne, Anders
    Isolation and characterization of a small antiretroviral molecule affecting HIV-1 capsid morphology2009In: Retrovirology, ISSN 1742-4690, E-ISSN 1742-4690, Vol. 6, p. 34-Article in journal (Refereed)
    Abstract [en]

    Background: Formation of an HIV-1 particle with a conical core structure is a prerequisite for the subsequent infectivity of the virus particle. We have previously described that glycineamide (G-NH2) when added to the culture medium of infected cells induces non-infectious HIV-1 particles with aberrant core structures. Results: Here we demonstrate that it is not G-NH2 itself but a metabolite thereof that displays antiviral activity. We show that conversion of G-NH2 to its antiviral metabolite is catalyzed by an enzyme present in bovine and porcine but surprisingly not in human serum. Structure determination by NMR suggested that the active G-NH2 metabolite was alpha-hydroxy-glycineamide (alpha-HGA). Chemically synthesized alpha-HGA inhibited HIV-1 replication to the same degree as G-NH2, unlike a number of other synthesized analogues of G-NH2 which had no effect on HIV-1 replication. Comparisons by capillary electrophoresis and HPLC of the metabolite with the chemically synthesized alpha-HGA further confirmed that the antiviral G-NH2-metabolite indeed was alpha-HGA. Conclusion: alpha-HGA has an unusually simple structure and a novel mechanism of antiviral action. Thus, alpha-HGA could be a lead for new antiviral substances belonging to a new class of anti-HIV drugs, i.e. capsid assembly inhibitors.

  • 3. Abdurahman, Samir
    et al.
    Youssefi, Masoud
    Höglund, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry.
    Vahlne, Anders
    Characterization of the invariable residue 51 mutations of human immunodeficiency virus type 1 capsid protein on in vitro CA assembly and infectivity2007In: Retrovirology, ISSN 1742-4690, E-ISSN 1742-4690, Vol. 4, p. 69-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The mature HIV-1 conical core formation proceeds through highly regulated protease cleavage of the Gag precursor, which ultimately leads to substantial rearrangements of the capsid (CAp24) molecule involving both inter- and intra-molecular contacts of the CAp24 molecules. In this aspect, Asp51 which is located in the N-terminal domain of HIV-1 CAp24 plays an important role by forming a salt-bridge with the free imino terminus Pro1 following proteolytic cleavage and liberation of the CAp24 protein from the Pr55Gag precursor. Thus, previous substitution mutation of Asp51 to alanine (D51A) has shown to be lethal and that this invariable residue was found essential for tube formation in vitro, virus replication and virus capsid formation. RESULTS: We extended the above investigation by introducing three different D51 substitution mutations (D51N, D51E, and D51Q) into both prokaryotic and eukaryotic expression systems and studied their effects on in vitro capsid assembly and virus infectivity. Two substitution mutations (D51E and D51N) had no substantial effect on in vitro capsid assembly, yet they impaired viral infectivity and particle production. In contrast, the D51Q mutant was defective both for in vitro capsid assembly and for virus replication in cell culture. CONCLUSION: These results show that substitutions of D51 with glutamate, glutamine, or asparagine, three amino acid residues that are structurally related to aspartate, could partially rescue both in vitro capsid assembly and intra-cellular CAp24 production but not replication of the virus in cultured cells.

  • 4. Cadeddu, Marta
    et al.
    Vargiu, Laura
    Rodriguez-Tome, Patricia
    Sperber, Göran O.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology.
    Blomberg, Jonas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Virology.
    Tramontano, Enzo
    Identification and analysis of HML2 sequences in human genome assembly GRCh37/hg192013In: Retrovirology, ISSN 1742-4690, E-ISSN 1742-4690, Vol. 10, no S1, p. P9-Article in journal (Other academic)
  • 5.
    Gifford, Robert J.
    et al.
    Univ Glasgow, MRC, Ctr Virus Res, Glasgow, Lanark, Scotland.
    Blomberg, Jonas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology.
    Coffin, John M.
    Tufts Univ, Dept Mol Biol & Microbiol, Boston, MA 02111 USA.
    Fan, Hung
    Univ Calif Irvine, Dept Mol Biol & Biochem, Irvine, CA 92697 USA;Univ Calif Irvine, Canc Res Inst, Irvine, CA 92697 USA.
    Heidmann, Thierry
    Inst Gustave Roussy, CNRS UMR 9196, Dept Mol Physiol & Pathol Infect & Endogenous Ret, F-94805 Villejuif, France.
    Mayer, Jens
    Univ Saarland, Med Fac, Dept Human Genet, Ctr Human & Mol Biol, Homburg, Germany.
    Stoye, Jonathan
    Francis Crick Inst, Mill Hill Lab, Mill Hill, London, England.
    Tristem, Michael
    Imperial Coll London, Silwood Pk Campus,Buckhurst Rd, Ascot SL5 7PY, Berks, England.
    Johnson, Welkin E.
    Boston Coll, Dept Biol, Chestnut Hill, MA 02467 USA.
    Nomenclature for endogenous retrovirus (ERV) loci2018In: Retrovirology, ISSN 1742-4690, E-ISSN 1742-4690, Vol. 15, article id 59Article, review/survey (Refereed)
    Abstract [en]

    Retroviral integration into germline DNA can result in the formation of a vertically inherited proviral sequence called an endogenous retrovirus (ERV). Over the course of their evolution, vertebrate genomes have accumulated many thousands of ERV loci. These sequences provide useful retrospective information about ancient retroviruses, and have also played an important role in shaping the evolution of vertebrate genomes. There is an immediate need for a unified system of nomenclature for ERV loci, not only to assist genome annotation, but also to facilitate research on ERVs and their impact on genome biology and evolution. In this review, we examine how ERV nomenclatures have developed, and consider the possibilities for the implementation of a systematic approach for naming ERV loci. We propose that such a nomenclature should not only provide unique identifiers for individual loci, but also denote orthologous relationships between ERVs in different species. In addition, we propose that-where possible-mnemonic links to previous, well-established names for ERV loci and groups should be retained. We show how this approach can be applied and integrated into existing taxonomic and nomenclature schemes for retroviruses, ERVs and transposable elements.

  • 6.
    Grandi, Nicole
    et al.
    Univ Cagliari, Dept Life & Environm Sci, Cittadella Univ Monserrato SS554, I-09042 Cagliari, Italy..
    Cadeddu, Marta
    Univ Cagliari, Dept Life & Environm Sci, Cittadella Univ Monserrato SS554, I-09042 Cagliari, Italy..
    Blomberg, Jonas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Tramontano, Enzo
    Univ Cagliari, Dept Life & Environm Sci, Cittadella Univ Monserrato SS554, I-09042 Cagliari, Italy.;CNR, Ist Ric Genet & Biomed, Cagliari, Italy..
    Contribution of type W human endogenous retroviruses to the human genome: characterization of HERV-W proviral insertions and processed pseudogenes2016In: Retrovirology, ISSN 1742-4690, E-ISSN 1742-4690, Vol. 13, article id 67Article in journal (Refereed)
    Abstract [en]

    Background: Human endogenous retroviruses (HERVs) are ancient sequences integrated in the germ line cells and vertically transmitted through the offspring constituting about 8 % of our genome. In time, HERVs accumulated mutations that compromised their coding capacity. A prominent exception is HERV-W locus 7q21.2, producing a functional Env protein (Syncytin-1) coopted for placental syncytiotrophoblast formation. While expression of HERV-W sequences has been investigated for their correlation to disease, an exhaustive description of the group composition and characteristics is still not available and current HERV-W group information derive from studies published a few years ago that, of course, used the rough assemblies of the human genome available at that time. This hampers the comparison and correlation with current human genome assemblies. Results: In the present work we identified and described in detail the distribution and genetic composition of 213 HERV-W elements. The bioinformatics analysis led to the characterization of several previously unreported features and provided a phylogenetic classification of two main subgroups with different age and structural characteristics. New facts on HERV-W genomic context of insertion and co-localization with sequences putatively involved in disease development are also reported. Conclusions: The present work is a detailed overview of the HERV-W contribution to the human genome and provides a robust genetic background useful to clarify HERV-W role in pathologies with poorly understood etiology, representing, to our knowledge, the most complete and exhaustive HERV-W dataset up to date.

  • 7. Jejcic, Alenka
    et al.
    Höglund, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry.
    Vahlne, Anders
    GPG-NH2 acts via the metabolite alpha HGA to target HIV-1 Env to the ER-associated protein degradation pathway2010In: Retrovirology, ISSN 1742-4690, E-ISSN 1742-4690, Vol. 7, p. 20-Article in journal (Refereed)
    Abstract [en]

    Background: The synthetic peptide glycyl-prolyl-glycine amide (GPG-NH2) was previously shown to abolish the ability of HIV-1 particles to fuse with the target cells, by reducing the content of the viral envelope glycoprotein (Env) in progeny HIV-1 particles. The loss of Env was found to result from GPG-NH2 targeting the Env precursor protein gp160 to the ER-associated protein degradation (ERAD) pathway during its maturation. However, the antiviral effect of GPG-NH2 has been shown to be mediated by its metabolite alpha-hydroxy-glycineamide (alpha HGA), which is produced in the presence of fetal bovine serum, but not human serum. In accordance, we wanted to investigate whether the targeting of gp160 to the ERAD pathway by GPG-NH2 was attributed to its metabolite alpha HGA. Results: In the presence of fetal bovine serum, GPG-NH2, its intermediary metabolite glycine amide (G-NH2), and final metabolite alpha HGA all induced the degradation of gp160 through the ERAD pathway. However, when fetal bovine serum was replaced with human serum only aHGA showed an effect on gp160, and this activity was further shown to be completely independent of serum. This indicated that GPG-NH2 acts as a pro-drug, which was supported by the observation that it had to be added earlier to the cell cultures than alpha HGA to induce the degradation of gp160. Furthermore, the substantial reduction of Env incorporation into HIV-1 particles that occurs during GPG-NH2 treatment was also achieved by treating HIV-1 infected cells with alpha HGA. Conclusions: The previously observed specificity of GPG-NH2 towards gp160 in HIV-1 infected cells, resulting in the production of Env (gp120/gp41) deficient fusion incompetent HIV-1 particles, was most probably due to the action of the GPG-NH2 metabolite alpha HGA.

  • 8.
    Ka, Sojeong
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Neuroscience.
    Kerje, Susanne
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Bomold, Lina
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Liljegren, Ulrika
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Siegel, P. B.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Hallböök, Finn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Neuroscience.
    Proviral integrations and expression of endogenous Avian leucosis virus during long term selection for high and low body weight in two chicken lines2009In: Retrovirology, ISSN 1742-4690, E-ISSN 1742-4690, Vol. 6, p. 68-Article in journal (Refereed)
    Abstract [en]

    Background:

    Long-term selection (> 45 generations) for low or high   juvenile body weight from a common founder population of White Plymouth   Rock chickens has generated two extremely divergent lines, the LWS and   HWS lines. In addition to a > 9-fold difference between lines for the   selected trait, large behavioural and metabolic differences between the   two lines evolved during the course of the selection. We recently   compared gene expression in brain tissue from birds representing these   lines using a global cDNA array analysis and the results showed multiple but small expression differences in protein coding genes. The   main differentially expressed transcripts were endogenous retroviral   sequences identified as avian leucosis virus subgroup-E (ALVE).  

    Results:

    In this work we confirm the differential ALVE expression and   analysed expression and number of proviral integrations in the two   parental lines as well as in F-9 individuals from an advanced   intercross of the lines. Correlation analysis between expression,   proviral integrations and body weight showed that high ALVE levels in   the LWS line were inherited and that more ALVE integrations were   detected in LWS than HWS birds.

    Conclusion:

    We conclude that only a few of the integrations contribute   to the high expression levels seen in the LWS line and that high ALVE   expression was significantly correlated with lower body weights for the   females but not males. The conserved correlation between high   expression and low body weight in females after 9 generations of   intercrosses, indicated that ALVE loci conferring high expression directly affects growth or are very closely linked to loci regulating growth.

  • 9.
    Vargiu, Laura
    et al.
    Univ Cagliari, Dept Life & Environm Sci, Cagliari, Italy.;CRS4, Ctr Adv Studies Res & Dev Sardinia, Pula, Italy.;Nurideas Srl, Cagliari, Italy..
    Rodriguez-Tome, Patricia
    CRS4, Ctr Adv Studies Res & Dev Sardinia, Pula, Italy.;Nurideas Srl, Cagliari, Italy..
    Sperber, Göran O.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology.
    Cadeddu, Marta
    Univ Cagliari, Dept Life & Environm Sci, Cagliari, Italy..
    Grandi, Nicole
    Univ Cagliari, Dept Life & Environm Sci, Cagliari, Italy..
    Blikstad, Vidar
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Tramontano, Enzo
    Univ Cagliari, Dept Life & Environm Sci, Cagliari, Italy..
    Blomberg, Jonas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Classification and characterization of human endogenous retroviruses: mosaic forms are common2016In: Retrovirology, ISSN 1742-4690, E-ISSN 1742-4690, Vol. 13, article id 7Article in journal (Refereed)
    Abstract [en]

    Background: Human endogenous retroviruses (HERVs) represent the inheritance of ancient germ-line cell infections by exogenous retroviruses and the subsequent transmission of the integrated proviruses to the descendants. ERVs have the same internal structure as exogenous retroviruses. While no replication-competent HERVs have been recognized, some retain up to three of four intact ORFs. HERVs have been classified before, with varying scope and depth, notably in the RepBase/RepeatMasker system. However, existing classifications are bewildering. There is a need for a systematic, unifying and simple classification. We strived for a classification which is traceable to previous classifications and which encompasses HERV variation within a limited number of clades. Results: The human genome assembly GRCh 37/hg19 was analyzed with RetroTector, which primarily detects relatively complete Class I and II proviruses. A total of 3173 HERV sequences were identified. The structure of and relations between these proviruses was resolved through a multi-step classification procedure that involved a novel type of similarity image analysis ("Simage") which allowed discrimination of heterogeneous (noncanonical) from homogeneous (canonical) HERVs. Of the 3173 HERVs, 1214 were canonical and segregated into 39 canonical clades (groups), belonging to class I (Gamma-and Epsilon-like), II (Beta-like) and III (Spuma-like). The groups were chosen based on (1) sequence (nucleotide and Pol amino acid), similarity, (2) degree of fit to previously published clades, often from RepBase, and (3) taxonomic markers. The groups fell into 11 supergroups. The 1959 noncanonical HERVs contained 31 additional, less well-defined groups. Simage analysis revealed several types of mosaicism, notably recombination and secondary integration. By comparing flanking sequences, LTRs and completeness of gene structure, we deduced that some noncanonical HERVs proliferated after the recombination event. Groups were further divided into envelope subgroups (altogether 94) based on sequence similarity and characteristic "immunosuppressive domain" motifs. Intra and inter(super) group, as well as intraclass, recombination involving envelope genes ("env snatching") was a common event. LTR divergence indicated that HERV-K(HML2) and HERVFC had the most recent integrations, HERVL and HUERSP3 the oldest. Conclusions: A comprehensive HERV classification and characterization approach was undertaken. It should be applicable for classification of all ERVs. Recombination was common among HERV ancestors.

  • 10. Vargiu, Luana
    et al.
    Rodriguez-Tome, Patricia
    Sperber, Göran O.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology.
    Tramontano, Enzo
    Blomberg, Jonas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Virology.
    Overview of human endogenous retroviruses found in human genome assembly GRCh37/hg192013In: Retrovirology, ISSN 1742-4690, E-ISSN 1742-4690, Vol. 10, no S1, p. P6-Article in journal (Other academic)
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