Skip to main content
  • Submit
  • About
    • Editorial Board
    • PNAS Staff
    • FAQ
    • Rights and Permissions
    • Site Map
  • Contact
  • Journal Club
  • Subscribe
    • Subscription Rates
    • Subscriptions FAQ
    • Open Access
    • Recommend PNAS to Your Librarian
  • Log in
  • My Cart

Main menu

  • Home
  • Articles
    • Current
    • Latest Articles
    • Special Features
    • Colloquia
    • Collected Articles
    • PNAS Classics
    • Archive
  • Front Matter
  • News
    • For the Press
    • Highlights from Latest Articles
    • PNAS in the News
  • Podcasts
  • Authors
    • Information for Authors
    • Purpose and Scope
    • Editorial and Journal Policies
    • Submission Procedures
    • For Reviewers
    • Author FAQ
  • Submit
  • About
    • Editorial Board
    • PNAS Staff
    • FAQ
    • Rights and Permissions
    • Site Map
  • Contact
  • Journal Club
  • Subscribe
    • Subscription Rates
    • Subscriptions FAQ
    • Open Access
    • Recommend PNAS to Your Librarian

User menu

  • Log in
  • My Cart

Search

  • Advanced search
Home
Home

Advanced Search

  • Home
  • Articles
    • Current
    • Latest Articles
    • Special Features
    • Colloquia
    • Collected Articles
    • PNAS Classics
    • Archive
  • Front Matter
  • News
    • For the Press
    • Highlights from Latest Articles
    • PNAS in the News
  • Podcasts
  • Authors
    • Information for Authors
    • Purpose and Scope
    • Editorial and Journal Policies
    • Submission Procedures
    • For Reviewers
    • Author FAQ

New Research In

Physical Sciences

Featured Portals

  • Physics
  • Chemistry
  • Sustainability Science

Articles by Topic

  • Applied Mathematics
  • Applied Physical Sciences
  • Astronomy
  • Computer Sciences
  • Earth, Atmospheric, and Planetary Sciences
  • Engineering
  • Environmental Sciences
  • Mathematics
  • Statistics

Social Sciences

Featured Portals

  • Anthropology
  • Sustainability Science

Articles by Topic

  • Economic Sciences
  • Environmental Sciences
  • Political Sciences
  • Psychological and Cognitive Sciences
  • Social Sciences

Biological Sciences

Featured Portals

  • Sustainability Science

Articles by Topic

  • Agricultural Sciences
  • Anthropology
  • Applied Biological Sciences
  • Biochemistry
  • Biophysics and Computational Biology
  • Cell Biology
  • Developmental Biology
  • Ecology
  • Environmental Sciences
  • Evolution
  • Genetics
  • Immunology and Inflammation
  • Medical Sciences
  • Microbiology
  • Neuroscience
  • Pharmacology
  • Physiology
  • Plant Biology
  • Population Biology
  • Psychological and Cognitive Sciences
  • Sustainability Science
  • Systems Biology

Discovery and analysis of the first endogenous lentivirus

Aris Katzourakis, Michael Tristem, Oliver G. Pybus, and Robert J. Gifford
PNAS April 10, 2007 104 (15) 6261-6265; https://doi.org/10.1073/pnas.0700471104
Aris Katzourakis
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Michael Tristem
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Oliver G. Pybus
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Robert J. Gifford
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  1. Edited by John M. Coffin, Tufts University School of Medicine, Boston, MA, and approved February 13, 2007 (received for review January 17, 2007)

  • Article
  • Figures & SI
  • Info & Metrics
  • PDF
Loading

Article Figures & SI

Figures

  • Fig. 1.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 1.

    Lentiviral genome organizations. The genome organization of the consensus RELIK provirus is shown in comparison to representative genome organizations of other lentiviral subgroups: equine (equine infectious anemia virus, EIAV), feline (feline immunodeficiency virus, FIV), bovine (bovine immunodeficiency virus, BIV), caprine/ovine (caprine arthritis–encephalitis virus, CAEV; ovine maedi–visna virus, OMVV), and primate lineages. Most primate lineages lack a vpu gene.

  • Fig. 2.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 2.

    Alignment of the putative RELIK Tat protein with the Tat proteins of other lentiviruses. Numbers refer to the relative positions aligned. Boxes denote identical amino acid residues, and bold type indicates residues with similar properties. Lentiviral Rev proteins share little sequence similarity, but we did identify putative nuclear localization and nuclear export signals (34), which are underlined in SI Fig. 5.

  • Fig. 3.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 3.

    Phylogenetic relationships of RELIK to other retroviruses. (a) Phylogeny of RELIK and other lentiviruses together with a sample of nonlentiviral exogenous retroviruses, rooted on BLV, HTLV1, and HTLV2. Support for the ML trees was assessed via 1,000 nonparametric bootstrap replicates, and posterior clade probabilities were assessed for the Bayesian phylogeny. Both support indices are indicated as values out of 100, with posterior clade probabilities indicated above the branches and bootstrap scores below. Branches with posterior probabilities <95% were collapsed. The RELIK sequences are indicated by their accession numbers. (b) Unrooted phylogeny showing the relationships of the lentiviruses. Bootstrap scores and Bayesian posterior probabilities are indicated to the left and right of the forward slash, respectively, and nodes with only 100 indicated showed maximal support under both measures.

  • Fig. 4.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 4.

    Schematic of the three segmental duplications used for dating RELIK insertions. Open boxes show RELIK LTRs and the location of the single short interspersed nuclear element insertion, and flanking sequences are indicated by thinner lines. Indels between the sequences are represented by solid triangles, with the number of inserted/deleted bases involved below. Thirty bases of flanking sequences are shown for each segmentally duplicated pair. Percentage divergence was calculated by using the GTR model with all parameters estimated from the data.

Data supplements

  • Katzourakis et al. 10.1073/pnas.0700471104.

    Supporting Information

    Files in this Data Supplement:

    SI Figure 5
    SI Figure 6
    SI Figure 7
    SI Figure 8




    SI Figure 5

    Fig. 5. The RELIK consensus sequence. The inverted repeats at the ends of both LTRs are highlighted in light gray with the putative promoter and polyadenylation signals indicated in bold type. Regions of nucleic acid secondary structure, the slippery sequence at the 5' end of pol, and the PPT and P.B.S. are highlighted in dark gray. The locations of the proteins encoded by the gag, pol and env genes were determined by homology to the HIV-1 reference sequence HXB2 (1), by searches against the pFAM database(2), or from alignments of retroviral envelope sequences (3). The identities of the two accessory genes were determined using the pFAM database (Tat) or from Pollard and Malim (4) (Rev). Some lentiviruses contain short Rev and Tat domains toward the 5' and 3' ends of the env gene respectively (see Fig. 1). The general lack of sequence similarity of these regions within the lentiviruses meant that it was not possible to determine whether or not RELIK encodes such domains. The consensus sequence contained one in-frame TGA stop-codon at position 2555 that has been removed from the figure. Analysis of the proviruses from which the RELIK consensus was derived indicated that some had CGA codons in this position. Thus this stop-codon most likely arose from independent, host-mediated mutation of a CG nucleotide hotspot (i.e., CGA-TGA) in many of the sequences.

    1. Petropoulos C (1997) in Retroviruses, eds Coffin JM, Hughes SH, Varmus HE (Cold Spring Harbor Lab Press, Cold Spring Harbor , NY), pp 757-805.

    2. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, et al. (2006) Nucleic Acids Res 34:D247-D251.

    3. Bénit L, Dessen P, Heidmann T (2001) J Virol 75:11709-11719.

    4. Pollard VW, Malim MH (1998) Annu Rev Microbiol 52:491-532.





    SI Figure 6

    Fig. 6. Secondary structure motifs within the RELIK sequence. Secondary structures were predicted using the MFOLD thermodynamic folding algorithm (1), and assessed by comparison to well-characterized examples in other lentiviruses. (a) The putative TAR (transactivation responsive region) downstream of the viral promoter is a well-defined and consistently predicted two-finger structure similar to the TAR found in HIV-2 (2). (b) The putative RRE (Rev responsive element) contains a consistently predicted three-finger structure. The precise boundaries of the RRE are uncertain. (c) The predicted ribosomal frameshift site at the gag-pol junction comprises a simple 8bp stem loop downstream of a heptameric slippery sequence.

    1. Zuker M, Mathews DH, Turner DH (1999) in RNA Biochemistry and Biotechnology, eds Barciszewski J, Clark BFC (Kluwer Academic).

    2. Rabson AB, Graves BJ (1997) in Retroviruses, eds Coffin JM, Hughes SH, Varmus HE (Cold Spring Harbor Lab Press, Cold Spring Harbor , NY), p 226.





    SI Figure 7

    Fig. 7. Nucleotide compositional bias across the first 6,000 bp of the coding regions of the consensus RELIK genome (Top), and the genomes of two other representative lentiviruses, EIAV (Middle) and FIV (Bottom). Biases were calculated using a sliding window of 500 nt and a step size of 100 nt.





    SI Figure 8

    Fig. 8. Alignment of the 5' 2500bp of the upper segmental duplication shown in Fig. 4. Flanking sequences are indicated in dark gray, LTRs in light gray and the SINE insertion in green. Transitions and transversions are shown in blue and red, respectively.

PreviousNext
Back to top
Article Alerts
Email Article

Thank you for your interest in spreading the word on PNAS.

NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.

Enter multiple addresses on separate lines or separate them with commas.
Discovery and analysis of the first endogenous lentivirus
(Your Name) has sent you a message from PNAS
(Your Name) thought you would like to see the PNAS web site.
Citation Tools
Discovery and analysis of the first endogenous lentivirus
Aris Katzourakis, Michael Tristem, Oliver G. Pybus, Robert J. Gifford
Proceedings of the National Academy of Sciences Apr 2007, 104 (15) 6261-6265; DOI: 10.1073/pnas.0700471104

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Request Permissions
Share
Discovery and analysis of the first endogenous lentivirus
Aris Katzourakis, Michael Tristem, Oliver G. Pybus, Robert J. Gifford
Proceedings of the National Academy of Sciences Apr 2007, 104 (15) 6261-6265; DOI: 10.1073/pnas.0700471104
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Tweet Widget
  • Facebook Like
  • Mendeley logo Mendeley
Proceedings of the National Academy of Sciences: 116 (8)
Current Issue

Submit

Sign up for Article Alerts

Jump to section

  • Article
    • Abstract
    • Results
    • Discussion
    • Materials and Methods
    • Acknowledgments
    • Footnotes
    • References
  • Figures & SI
  • Info & Metrics
  • PDF

You May Also be Interested in

News Feature: Cities serve as testbeds for evolutionary change
Urban living can pressure flora and fauna to adapt in intriguing ways. Biologists are starting to take advantage of this convenient laboratory of evolution.
Image credit: Kristin Winchell (Washington University in St. Louis, St. Louis).
Several aspects of the proposal, which aims to expand open access, require serious discussion and, in some cases, a rethink.
Opinion: “Plan S” falls short for society publishers—and for the researchers they serve
Several aspects of the proposal, which aims to expand open access, require serious discussion and, in some cases, a rethink.
Image credit: Dave Cutler (artist).
Featured Profile
PNAS Profile of NAS member and biochemist Hao Wu
 Nonmonogamous strawberry poison frog (Oophaga pumilio).  Image courtesy of Yusan Yang (University of Pittsburgh, Pittsburgh).
Putative signature of monogamy
A study suggests a putative gene-expression hallmark common to monogamous male vertebrates of some species, namely cichlid fishes, dendrobatid frogs, passeroid songbirds, common voles, and deer mice, and identifies 24 candidate genes potentially associated with monogamy.
Image courtesy of Yusan Yang (University of Pittsburgh, Pittsburgh).
Active lifestyles. Image courtesy of Pixabay/MabelAmber.
Meaningful life tied to healthy aging
Physical and social well-being in old age are linked to self-assessments of life worth, and a spectrum of behavioral, economic, health, and social variables may influence whether aging individuals believe they are leading meaningful lives.
Image courtesy of Pixabay/MabelAmber.

More Articles of This Classification

Biological Sciences

  • Major histocompatibility complex class I diversity limits the repertoire of T cell receptors
  • LINC00116 codes for a mitochondrial peptide linking respiration and lipid metabolism
  • Unnatural verticilide enantiomer inhibits type 2 ryanodine receptor-mediated calcium leak and is antiarrhythmic
Show more

Evolution

  • Major histocompatibility complex class I diversity limits the repertoire of T cell receptors
  • Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores
  • Symbiotic organs shaped by distinct modes of genome evolution in cephalopods
Show more

Related Content

  • Ancient lentiviruses leave their mark
  • Scopus
  • PubMed
  • Google Scholar

Cited by...

  • Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations
  • Pan-vertebrate comparative genomics unmasks retrovirus macroevolution
  • Our Viral Inheritance
  • Betaretroviral Envelope Subunits Are Noncovalently Associated and Restricted to the Mammalian Class
  • The First Full-Length Endogenous Hepadnaviruses: Identification and Analysis
  • Discovery of Retroviral Homologs in Bats: Implications for the Origin of Mammalian Gammaretroviruses
  • Host Genes Important to HIV Replication and Evolution
  • Endogenous Lentiviruses in the Ferret Genome
  • Productive Replication and Evolution of HIV-1 in Ferret Cells
  • Origins of HIV and the AIDS Pandemic
  • Unique Spectrum of Activity of Prosimian TRIM5{alpha} against Exogenous and Endogenous Retroviruses
  • Hare TRIM5{alpha} Restricts Divergent Retroviruses and Exhibits Significant Sequence Variation from Closely Related Lagomorpha TRIM5 Genes
  • Widespread Horizontal Gene Transfer from Double-Stranded RNA Viruses to Eukaryotic Nuclear Genomes
  • Lentiviral Vif Degrades the APOBEC3Z3/APOBEC3H Protein of Its Mammalian Host and Is Capable of Cross-Species Activity
  • Vif of Feline Immunodeficiency Virus from Domestic Cats Protects against APOBEC3 Restriction Factors from Many Felids
  • A novel active endogenous retrovirus family contributes to genome variability in rat inbred strains
  • Restriction of Equine Infectious Anemia Virus by Equine APOBEC3 Cytidine Deaminases
  • Sharing of Endogenous Lentiviral Gene Fragments among Leporid Lineages Separated for More than 12 Million Years
  • A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution
  • A proviral puzzle with a prosimian twist
  • Conserved Footprints of APOBEC3G on Hypermutated Human Immunodeficiency Virus Type 1 and Human Endogenous Retrovirus HERV-K(HML2) Sequences
  • Rhesus Macaque TRIM5 Alleles Have Divergent Antiretroviral Specificities
  • Human RNA "Rumor" Viruses: the Search for Novel Human Retroviruses in Chronic Disease
  • An Active TRIM5 Protein in Rabbits Indicates a Common Antiviral Ancestor for Mammalian TRIM5 Proteins
  • Ancient lentiviruses leave their mark
  • Scopus (137)
  • Google Scholar

Similar Articles

Site Logo
Powered by HighWire
  • Submit Manuscript
  • Twitter
  • Facebook
  • RSS Feeds
  • Email Alerts

Articles

  • Current Issue
  • Latest Articles
  • Archive

PNAS Portals

  • Classics
  • Front Matter
  • Teaching Resources
  • Anthropology
  • Chemistry
  • Physics
  • Sustainability Science

Information

  • Authors
  • Editorial Board
  • Reviewers
  • Press
  • Site Map

Feedback    Privacy/Legal

Copyright © 2019 National Academy of Sciences. Online ISSN 1091-6490