scholarly journals NMR detection of intermolecular interaction sites in the dimeric 5′-leader of the HIV-1 genome

2016 ◽  
Vol 113 (46) ◽  
pp. 13033-13038 ◽  
Author(s):  
Sarah C. Keane ◽  
Verna Van ◽  
Heather M. Frank ◽  
Carly A. Sciandra ◽  
Sayo McCowin ◽  
...  
Keyword(s):  
Interface Structure ◽  
Base Pairing ◽  
Rna Dimerization ◽  
Interaction Sites ◽  
Intermolecular Contacts ◽  
Hiv Type 1 ◽  
Rna Chaperones ◽  
Genome Dimerization ◽  
Hiv 1

HIV type-1 (HIV-1) contains a pseudodiploid RNA genome that is selected for packaging and maintained in virions as a noncovalently linked dimer. Genome dimerization is mediated by conserved elements within the 5′-leader of the RNA, including a palindromic dimer initiation signal (DIS) that has been proposed to form kissing hairpin and/or extended duplex intermolecular contacts. Here, we have applied a2H-edited NMR approach to directly probe for intermolecular interactions in the full-length, dimeric HIV-1 5′-leader (688 nucleotides; 230 kDa). The interface is extensive and includes DIS:DIS base pairing in an extended duplex state as well as intermolecular pairing between elements of the upstream Unique-5′ (U5) sequence and those near thegagstart site (AUG). Other pseudopalindromic regions of the leader, including the transcription activation (TAR), polyadenylation (PolyA), and primer binding (PBS) elements, do not participate in intermolecular base pairing. Using a2H-edited one-dimensional NMR approach, we also show that the extended interface structure forms on a time scale similar to that of overall RNA dimerization. Our studies indicate that a kissing dimer-mediated structure, if formed, exists only transiently and readily converts to the extended interface structure, even in the absence of the HIV-1 nucleocapsid protein or other RNA chaperones.

scholarly journals Impact of Human Immunodeficiency Virus Type 1 RNA Dimerization on Viral Infectivity and of Stem-Loop B on RNA Dimerization and Reverse Transcription and Dissociation of Dimerization from Packaging

2000 ◽  
Vol 74 (12) ◽  
pp. 5729-5735 ◽  
Author(s):  
Ni Shen ◽  
Louis Jetté ◽  
Chen Liang ◽  
Mark A. Wainberg ◽  
Michael Laughrea
Keyword(s):  
Reverse Transcription ◽  
Viral Infectivity ◽  
Stem Loop ◽  
Rna Dimerization ◽  
Reduced Genome ◽  
Immunodeficiency Virus ◽  
Genome Dimerization ◽  
Hiv 1 ◽  
Kissing Loop

ABSTRACT The kissing-loop domain (KLD) encompasses a stem-loop, named kissing-loop or dimerization initiation site (DIS) hairpin (nucleotides [nt] 248 to 270 in the human immunodeficiency virus type 1 strains HIV-1Lai and HIV-1Hxb2), seated on top of a 12-nt stem-internal loop called stem-loop B (nt 243 to 247 and 271 to 277). Destroying stem-loop B reduced genome dimerization by ∼50% and proviral DNA synthesis by ∼85% and left unchanged the dissociation temperature of dimeric genomic RNA. The most affected step of reverse transcription was plus-strand DNA transfer, which was reduced by ∼80%. Deleting nt 241 to 256 or 200 to 256 did not reduce genome dimerization significantly more than the destruction of stem-loop B or the DIS hairpin. We conclude that the KLD is nonmodular: mutations in stem-loop B and in the DIS hairpin have similar effects on genome dimerization, reverse transcription, and encapsidation and are also “nonadditive”; i.e., a larger deletion spanning both of these structures has the same effects on genome dimerization and encapsidation as if stem-loop B strongly impacted DIS hairpin function and vice versa. A C258G transversion in the palindrome of the kissing-loop reduced genome dimerization by ∼50% and viral infectivity by ∼1.4 log. Two mutations, CGCG261→UUAA261 (creating a weaker palindrome) and a Δ241–256 suppressor mutation, were each able to reduce genome dimerization but leave genome packaging unaffected.

scholarly journals Role of Stem B, Loop B, and Nucleotides next to the Primer Binding Site and the Kissing-Loop Domain in Human Immunodeficiency Virus Type 1 Replication and Genomic-RNA Dimerization

2001 ◽  
Vol 75 (21) ◽  
pp. 10543-10549 ◽  
Author(s):  
Ni Shen ◽  
Louis Jetté ◽  
Mark A. Wainberg ◽  
Michael Laughrea
Keyword(s):  
Human Immunodeficiency Virus ◽  
Viral Replication ◽  
Base Pair ◽  
Complete Genome ◽  
Genomic Rna ◽  
Rna Dimerization ◽  
Immunodeficiency Virus ◽  
Genome Dimerization ◽  
Hiv 1

ABSTRACT Stem-loop B is a 12-nucleotide [nt]-long completely conserved sequence postulated to form a 4-bp stem and a 4-nt internal loop under the kissing-loop hairpin (klh) (nt 248 to 270) of human immunodeficiency virus type 1 (HIV-1) genomic RNA. We investigated its role in viral replication, genomic RNA dimerization, and dimerization of partial HIV-1 RNA transcripts. The putative CUCG246-CGAG277 duplex was replaced by nine alternative complementary sequences, five likely to base pair only in short RNAs and four likely to base pair in long (∼500-nt) RNAs, as assessed by the algorithm mfold. Among the five former sequences, none preserved genome dimerization and all reduced viral replication by 98 to 99.9%. Among the four latter sequences, three (MB6, -9, and -10) preserved genome dimerization, one (MB7) did not significantly inhibit it, and two (MB9 and -10) preserved viral replication. We conclude that duplex formation by stem B nucleotides is necessary for viral infectivity and complete genome dimerization. Deleting the 5′ or 3′ side of loop B or of stem B had little impact on dimerization of partial RNA transcript and no impact on klh folding (and, for loop B mutations, on stem B folding), but each deletion inhibited genome dimerization almost as much as klh destruction. This suggests that loop B is required for complete genome dimerization and that loop B and stem B stimulate dimerization only in very long RNAs and/or in the presence of unidentified viral and cellular factors. Finally, we asked if nine deletions or nucleotide substitutions within nt 200 to 242 and/or nt 282 to 335 could influence genome dimerization. These mutations had intermediate inhibitory impacts consistent with their predicted influence on stem B, loop B, and klh formation. Two exceptions were Δ200–226 and Δ236–242 genomic RNAs, which dimerized relatively poorly despite having neutral or positive influences on stem B, loop B, and klh folding.

scholarly journals Novel TRIM5 Isoforms Expressed by Macaca nemestrina

2007 ◽  
Vol 81 (22) ◽  
pp. 12210-12217 ◽  
Author(s):  
Greg Brennan ◽  
Yury Kozyrev ◽  
Toshiaki Kodama ◽  
Shiu-Lok Hu
Keyword(s):  
Coiled Coil ◽  
Macaca Nemestrina ◽  
Cdna Clones ◽  
Reading Frame ◽  
Spry Domain ◽  
Immunodeficiency Virus ◽  
Hiv Type 1 ◽  
Hiv 1

ABSTRACT The TRIM5 family of proteins contains a RING domain, one or two B boxes, and a coiled-coil domain. The TRIM5α isoform also encodes a C-terminal B30.2(SPRY) domain, differences within which define the breadth and potency of TRIM5α-mediated retroviral restriction. Because Macaca nemestrina animals are susceptible to some human immunodeficiency virus (HIV) isolates, we sought to determine if differences exist in the TRIM5 gene and transcripts of these animals. We identified a two-nucleotide deletion (Δ2) in the transcript at the 5′ terminus of exon 7 in all M. nemestrina TRIM5 cDNA clones examined. This frameshift results in a truncated protein of 300 amino acids lacking the B30.2(SPRY) domain, which we have named TRIM5θ. This deletion is likely due to a single nucleotide polymorphism that alters the 3′ splice site between intron 6 and exon 7. In some clones, a deletion of the entire 27-nucleotide exon 7 (Δexon7) resulted in the restoration of the TRIM5 open reading frame and the generation of another novel isoform, TRIM5η. There are 18 amino acid differences between M. nemestrina TRIM5η and Macaca mulatta TRIM5α, some of which are at or near locations previously shown to affect the breadth and potency of TRIM5α-mediated restriction. Infectivity assays performed on permissive CrFK cells stably transduced with TRIM5η or TRIM5θ show that these isoforms are incapable of restricting either HIV type 1 (HIV-1) or simian immunodeficiency virus infection. The expression of TRIM5 alleles incapable of restricting HIV-1 infection may contribute to the previously reported increased susceptibility of M. nemestrina to HIV-1 infection in vivo.

Neuropsychological studies of asymptomatic Human Immunodeficiency Virus-Type-1 infected individuals

1995 ◽  
Vol 1 (3) ◽  
pp. 304-315 ◽  
Author(s):  
Desirée A. White ◽  
Robert K. Heaton ◽  
Andreas U. Monsch ◽  
Keyword(s):  
Test Battery ◽  
Neuropsychological Impairment ◽  
Ongoing Debate ◽  
Immunodeficiency Virus ◽  
Type Test ◽  
Hiv Type 1 ◽  
Hiv 1 ◽  
Asymptomatic Human Immunodeficiency Virus ◽  
Asymptomatic Hiv

AbstractThe current review was conducted to address the ongoing debate regarding the presence or absence of neuropsychological impairment in asymptomatic HIV-Type 1 (HIV-1) seropositive individuals. Results were summarized from 57 studies that compared the performances of seropositive asymptomatic and seronegative individuals. Overall, the differences observed between median rates of impairment for asymptomatic (35%) and seronegative (12%) groups provided the clearest indication of deficits in asymptomatics. In addition, five variables were examined as possible contributors to inconsistencies found in the literature: mode of infection, test battery type, test battery size, sample size, and method of data analysis. Of these variables, only mode of infection and test battery size appeared to substantially influence the outcome of the studies reviewed with regard to identifying neuropsychological impairment in asymptomatics. (JINS, 1995, I, 304–315.)

scholarly journals Membrane-Anchored Peptide Inhibits Human Immunodeficiency Virus Entry

2001 ◽  
Vol 75 (6) ◽  
pp. 3038-3042 ◽  
Author(s):  
Markus Hildinger ◽  
Matthias T. Dittmar ◽  
Patricia Schult-Dietrich ◽  
Boris Fehse ◽  
Barbara S. Schnierle ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
T Helper ◽  
Immunodeficiency Virus ◽  
Retrovirus Vector ◽  
Human Immunodeficiency Virus Entry ◽  
Hiv Type 1 ◽  
Heptad Repeats ◽  
Hiv 1 ◽  
Gp41 Envelope

ABSTRACT Peptides derived from the heptad repeats of human immunodeficiency virus (HIV) gp41 envelope glycoprotein, such as T20, can efficiently inhibit HIV type 1 (HIV-1) entry. In this study, replication of HIV-1 was inhibited more than 100-fold in a T-helper cell line transduced with a retrovirus vector expressing membrane-anchored T20 on the cell surface. Inhibition was independent of coreceptor usage.

scholarly journals Effect of Human Immunodeficiency Virus (HIV) Type 1 Viral Genotype on Mother‐to‐Child Transmission of HIV‐1

2000 ◽  
Vol 181 (2) ◽  
pp. 746-749 ◽  
Author(s):  
Melanie C. M. Murray ◽  
Joanne E. Embree ◽  
Sue G. Ramdahin ◽  
Aggrey O. Anzala ◽  
Simon Njenga ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Mother To Child Transmission ◽  
Viral Genotype ◽  
Child Transmission ◽  
Immunodeficiency Virus ◽  
Hiv Type 1 ◽  
Mother To Child ◽  
Hiv 1

Cell-Mediated Immune Response to Human Immunodeficiency Virus (HIV) Type 1 in Seronegative Homosexual Men with Recent Sexual Exposure to HIV-1

1992 ◽  
Vol 165 (6) ◽  
pp. 1012-1019 ◽  
Author(s):  
Mario Clerici ◽  
Janis V. Giorgi ◽  
Chen-Cheng Chou ◽  
Vaheideh K. Gudeman ◽  
Jerome A. Zack ◽  
...  
Keyword(s):  
Immune Response ◽  
Human Immunodeficiency Virus ◽  
Homosexual Men ◽  
Cell Mediated Immune Response ◽  
Immunodeficiency Virus ◽  
Hiv Type 1 ◽  
Hiv 1

scholarly journals Persistence of Human Immunodeficiency Virus (HIV) Type 1 DNA in Peripheral Blood Despite Prolonged Suppression of Plasma HIV‐1 RNA in Children

2002 ◽  
Vol 185 (10) ◽  
pp. 1409-1416 ◽  
Author(s):  
Akihiko Saitoh ◽  
Karen Hsia ◽  
Terence Fenton ◽  
Christine A. Powell ◽  
Cindy Christopherson ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Peripheral Blood ◽  
Immunodeficiency Virus ◽  
Hiv Type 1 ◽  
Hiv 1
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