Male celebrity weight. Why a genomic approach?
In the tonsils and adenoids of HIV-infected patients, macrophages fuse into multinucleated giant cells that produce huge amounts of virus. Author Contributions. Spreadsheets with in-depth annotation of genome features and coordinates are available: In-depth Annotation Resources. The molecular mechanisms behind this are not yet fully understood. This raises the possibility that new categories of RNA structure-mediated regulation remain to be identified. For HIV, as well as for viruses in general, successful infection depends on overcoming host defensive strategies that often include production of genenpme reactive oxygen species. SHAPE reactivities are genfnome sensitive to local nucleotide flexibility and disorder, but are insensitive to solvent accessibility Fig. Perspectives in Medical Virology. Hvi Hiv genenome represent nucleotide building blocks, and different colors correspond to varying degrees of flexibility. Bibcode : Hiv genenome
This work, and the scientist responsible, have been widely condemned.
- Research has shown for both same-sex and opposite-sex couples that HIV is untransmissable through condomless sexual intercourse if the HIV-positive partner has a consistently undetectable viral load.
- Open reading frames are shown as rectangles.
- Single-stranded RNA viruses encompass broad classes of infectious agents and cause the common cold, cancer, AIDS, and other serious health threats.
- August 31,
- This an excellent non-technical website on explaining scientific aspects HIV and immunology.
The integrated form of HIV-1, also known as the provirus, is approximately 9. The first part of this chapter reviews the individual viral proteins and their functions.
The second part discusses factors regulating the transcription and processing of viral mRNA. The gag gene gives rise to the kilodalton kD Gag precursor protein, also called p55, which is expressed from the unspliced viral mRNA.
During translation, the N terminus of p55 is myristoylated, 3 triggering its association with the cytoplasmic aspect of cell membranes. The membrane-associated Gag polyprotein recruits two copies of the viral genomic RNA along with other viral and cellular proteins that triggers the budding of the viral particle from the surface of an infected cell.
After budding, p55 is cleaved by the virally encoded protease 4 a product of the pol gene during the process of viral maturation into four smaller proteins designated MA matrix [p17] , CA capsid [p24] , NC nucleocapsid [p9] , and p6. The MA polypeptide is derived from the N-terminal, myristoylated end of p Most MA molecules remain attached to the inner surface of the virion lipid bilayer, stabilizing the particle. A subset of MA is recruited inside the deeper layers of the virion where it becomes part of the complex which escorts the viral DNA to the nucleus.
This phenomenon allows HIV to infect nondividing cells, an unusual property for a retrovirus. The p24 CA protein forms the conical core of viral particles. Cyclophilin A has been demonstrated to interact with the p24 region of p55 leading to its incorporation into HIV particles. NC also facilitates reverse transcription. The p6 polypeptide region mediates interactions between p55 Gag and the accessory protein Vpr, leading to the incorporation of Vpr into assembling virions.
The frequency of ribosomal frameshifting explains why the Gag and the Gag-Pol precursor are produced at a ratio of approximately During viral maturation, the virally encoded protease cleaves the Pol polypeptide away from Gag and further digests it to separate the protease p10 , RT p50 , RNase H p15 , and integrase p31 activities.
The HIV-1 protease is an aspartyl protease 16 that acts as a dimer. Protease activity is required for cleavage of the Gag and Gag-Pol polyprotein precursors during virion maturation as described previously. The three-dimensional structure of the protease dimer has been determined. These antiviral compounds have greatly improved treatment for HIV-infected individuals. The pol gene encodes reverse transcriptase.
During the process of reverse transcription, the polymerase makes a double-stranded DNA copy of the dimer of single-stranded genomic RNA present in the virion. Viral DNA can be completely synthesized within 6 hours after viral entry, although the DNA may remain unintegrated for prolonged periods. For example, the TAR element, a small RNA stem-loop structure located at the 5' end of viral RNAs and containing the binding site for Tat, is required for the initiation of reverse transcription.
All of the pol gene products can be found within the capsid of free HIV-1 virions. Because the polymerase does not contain a proof-reading activity, replication is error-prone and introduces several point mutations into each new copy of the viral genome. This process is mediated by three distinct functions of IN. Then, a double-stranded endonuclease activity cleaves the host DNA at the integration site.
Finally, a ligase activity generates a single covalent linkage at each end of the proviral DNA. It is believed that cellular enzymes then repair the integration site. No exogenous energy source, such as ATP, is required for this reaction.
The accessibility of the chromosomal DNA within chromatin, rather than specific DNA sequences, seems to influence the choice of integration sites.
Viral genes are not efficiently expressed from nonintegrated proviral DNA. First synthesized in the endoplasmic reticulum, Env migrates through the Golgi complex where it undergoes glycosylation with the addition of 25 to 30 complex N-linked carbohydrate side chains that are added at asparagine residues.
Env glycosylation is required for infectivity. The gp41 moeity contains the transmembrane domain of Env, while gp is located on the surface of the infected cell and of the virion through noncovalent interactions with gp Env exists as a trimer on the surface of infected cells and virions. Interactions between HIV and the virion receptor, CD4, are mediated through specific domains of gp Also present in gp are five hypervariable regions, designated V1 through V5, whose amino acid sequences can vary greatly among HIV-1 isolates.
One such region, called the V3 loop, is not involved in CD4 binding, but is rather an important determinant of the preferential tropism of HIV-1 for either T lymphoid cell lines or primary macrophages. The gp41 moiety contains an N-terminal fusogenic domain that mediates the fusion of the viral and cellular membranes, thereby allowing the delivery of the virions inner components into the cytoplasm of the newly infected cell.
Tat is a transcriptional transactivator that is essential for HIV-1 replication. Both forms function as transcriptional activators and are found within the nuclei and nucleoli of infected cells. Tat binding occurs in conjunction with cellular proteins that contribute to the effects of Tat. The mechanism of Tat function has recently been elucidated. Tat acts principally to promote the elongation phase of HIV-1 transcription, so that full-length transcripts can be produced. Stimulation of polymerase elongation is accomplished by the recruitment of a serine kinase which phosphorylates the carboxylterminal domain CTD of RNA polymerase II.
This kinase, which is known as CDK9, is part of a complex which binds directly to Tat. Tat has been shown to activate the expression of a number of cellular genes including tumor necrosis factor beta 44 and transforming growth factor beta, 45 and to downregulate the expression of other cellular genes including bcl-2 46 and the chemokine, MIP-1 alpha.
Rev is a kD sequence-specific RNA binding protein. The binding of Rev to the RRE facilitates the export of unspliced and incompletely spliced viral RNAs from the nucleus to the cytoplasm. High levels of Rev expression can lead to the export of so much intron containing viral RNA that the amount of RNA available for complete splicing is decreased, which, in turn, reduces the levels of Rev expression.
Therefore, this ability of Rev to decrease the rate of splicing of viral RNA generates a negative feedback loop whereby Rev expression levels are tightly regulated. Rev has been shown to contain at least three functional domains. A multimerization domain is required for Rev to function. NES mutants of Rev are dominant negative. In addition to the gag , pol , and env genes contained in all retroviruses, and the tat and rev regulatory genes, HIV-1 contains four additional genes: nef , vif , vpr and vpu , encoding the so-called accessory proteins.
HIV-2 does not contain vpu , but instead harbors another gene, vpx. The accessory proteins are not absolutely required for viral replication in all in vitro systems, but represent critical virulence factors in vivo. Nef is expressed from a multiply spliced mRNA and is therefore Rev independent.
Most of the small accessory proteins of HIV have multiple functions as described below. Nef an acronym for negative factor is a kD myristoylated protein that is encoded by a single exon that extends into the 3' LTR. Nef, an early gene of HIV, is the first viral protein to accumulate to detectable levels in a cell following HIV-1 infection.
It is no longer believed, however, that Nef has a direct effect on HIV gene expression. Nef has been shown to have multiple activities, including the downregulation of the cell surface expression of CD4, the perturbation of T cell activation, and the stimulation of HIV infectivity.
Nef acts post-translationally to decrease the cell-surface expression of CD4, the primary receptor for HIV. Nef perturbs T cell activation. Studies in the Jurkat T cell line indicated that Nef expression has a negative effect on induction of the transcription factor NF-kappa B and on IL-2 expression. When the CD8-Nef chimera was expressed at high levels on the cell surface, however, spontaneous activation followed by apoptosis was detected.
Together, these observations suggest that Nef can exert pleiomorphic effects on T cell activation depending on the context of expression. Consistent with this model, Nef has been found to associate with several different cellular kinases that are present in helper T lymphocytes.
Nef also stimulates the infectivity of HIV virions. Nef is packaged into virions, where it is cleaved by the viral protease during virion maturation. Virions produced in the absence of Nef are less efficient for proviral DNA synthesis, although Nef does not appear to influence directly the process of reverse transcription. There is compelling genetic evidence that the Nef protein of simian immunodeficiency virus is absolutely required for high-titer growth and the typical development of disease in adult animals.
The Vpr protein is incorporated into viral particles. Approximately copies of Vpr are associated with each virion.
Vpr plays a role in the ability of HIV to infect nondividing cells by facilitating the nuclear localization of the preintegration complex PIC. However, rather than tethering additional nuclear localization signals to the PIC, Vpr may act as a nucleocytoplasmic transport factor by directly tethering the viral genome to the nuclear pore. Consistent with this model, Vpr expressed in cells is found associated with the nuclear pore and can be biochemically demonstrated to bind to components of the nuclear pore complex.
Another enzyme involved with the modification of deoxyuracil dUTP , deoxyuracil phosphatase dUTPase , is expressed by two lentiviruses that do not contain a vpr gene: equine infectious anemia virus and feline immunodeficiency virus.
The kD Vpu polypeptide is an integral membrane phosphoprotein that is primarily localized in the internal membranes of the cell. Vpu is translated from this mRNA at levels tenfold lower than that of Env because the Vpu translation initiation codon is not efficient. In HIV-infected cells, complexes form between the viral receptor, CD4, and the viral envelope protein in the endoplasmic reticulum causing the trapping of both proteins to within this compartment.
The formation of intracellular Env-CD4 complexes thus interferes with virion assembly. Vpu liberates the viral envelope by triggering the ubiquitin-mediated degradation of CD4 molecules complexed with Env. Vpu also increases the release of HIV from the surface of an infected cell. In the absence of Vpu, large numbers of virions can be seen attached to the surface of infected cells.
Vif is a kD polypeptide that is essential for the replication of HIV in peripheral blood lymphocytes, macrophages, and certain cell lines. These cell lines are called permissive for Vif mutants of HIV. Virions generated in permissive cells can infect nonpermissive cells but the virus subsequently produced is noninfectious.
Complementation studies indicate that it is possible to restore the infectivity of HIV Vif mutants by expression of Vif in producer cells but not in target cells. Vif is incorporated into virions of HIV. This observation suggests that cellular factors, rather than viral components, are the target of Vif action. Vif mutant virions have improperly packed nucleoprotein cores as revealed by electron microscopic analyses.
The regulation of HIV gene expression is accomplished by a combination of both cellular and viral factors. HIV gene expression is regulated at both the transcriptional and post-transcriptional levels. The HIV genes can be divided into the early genes and the late genes.
An alternative view—unsupported by evidence—holds that unsafe medical practices in Africa during years following World War II, such as unsterile reuse of single-use syringes during mass vaccination, antibiotic, and anti-malaria treatment campaigns, were the initial vector that allowed the virus to adapt to humans and spread. Bibcode : Sci Methods Enzymol. Protein Feature Accent. Clinical Laboratory Methods. The maximum distance allowed between any two paired positions was nucleotides.
Hiv genenome. Associated Data
Architecture and secondary structure of an entire HIV-1 RNA genome | Nature
Viral replication is regulated at many levels, including the use of conserved genomic RNA structures. Most potential regulatory elements in viral RNA genomes are uncharacterized. The genome encodes protein structure at two levels. In addition to the correspondence between RNA and protein primary sequences, a correlation exists between high levels of RNA structure and sequences that encode inter-domain loops in HIV proteins.
This correlation suggests that RNA structure modulates ribosome elongation to promote native protein folding. Some simple genome elements previously shown to be important, including the ribosomal gag-pol frameshift stem-loop, are components of larger RNA motifs. We also identify organizational principles for unstructured RNA regions, including splice site acceptors and hypervariable regions. These results emphasize that the HIV-1 genome and, potentially, many coding RNAs are punctuated by previously unrecognized regulatory motifs and that extensive RNA structure constitutes an important component of the genetic code.
Cann, A. Principles of Molecular Virology Ch. Coffin, J. Frankel, A. Damgaard, C. Goff, S. Host factors exploited by retroviruses. Nature Rev. Wilkinson, K. PLoS Biol. Levin, J. Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: critical role in reverse transcription and molecular mechanism. Nucleic Acid Res. Paillart, J. Merino, E. Mortimer, S. Vasa, S. ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis.
RNA 14 , — Gherghe, C. Pedersen, J. A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res. Leitner, T. Purcell, D. Alternative splicing of human immunodeficiency virus type 1 mRNA modulates viral protein expression, replication, and infectivity. Kwong, P. Structure of an HIV gp envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody.
Nature , — Komar, A. A pause for thought along the co-translational folding pathway. Trends Biochem. Farabaugh, P. Programmed translational frameshifting. Wen, J. Following translation by single ribosomes one codon at a time. Nackley, A. Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science , — Hartz, D. Extension inhibition analysis of translation initiation complexes.
Methods Enzymol. Mathews, D. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Natl Acad. USA , — Deigan, K.
USA , 97— Kim, D. Nature Biotechnol. Stein, B. Intracellular processing of the gp HIV-1 envelope precursor. Endoproteolytic cleavage occurs in a cis or medial compartment of the Golgi complex. Wilson, W. HIV expression strategies: ribosomal frameshifting is directed by a short sequence in both mammalian and yeast systems.
Cell 55 , — Giedroc, D. Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting. Biswas, P. The human immunodeficiency virus type 1 ribosomal frameshifting site is an invariant sequence determinant and an important target for antiviral therapy.
Means, R. Ability of the V3 loop of simian immunodeficiency virus to serve as a target for antibody-mediated neutralization: correlation of neutralization sensitivity, growth in macrophages, and decreased dependence on CD4. Graham, F. A new technique for the assay of infectivity of human adenovirus 5 DNA. Virology 52 , — Adachi, A.
Production of acquired immunodeficiency syndrome-associated retrovirus in human and nonhuman cells transfected with an infectious molecular clone. Chertova, E. Ott, D. Analysis and localization of cyclophilin A found in the virions of human immunodeficiency virus type 1 MN strain. AIDS Res. Retroviruses 11 , — Thomas, J. Human immunodeficiency virus type 1 nucleocapsid zinc-finger mutations cause defects in reverse transcription and integration.
Virology , 41—51 Cline, A. Highly sensitive SIV plasma viral load assay: practical considerations, realistic performance expectations, and application to reverse engineering of vaccines for AIDS. Buckman, J. Nature Protocols 1 , — Badorrek, C. Architecture of a gamma retroviral genomic RNA dimer. Biochemistry 45 , — Dowell, R.