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Highlighted
Publications Real-Time
Traffic Report: How HIV-1 Travels from Cell to Cell
Although person-to-person
transmission of HIV has been well undersood for years, researchers are still trying
to figure out how the virus moves from one cell to another. To shed light
on this matter, Eric
O. Freed, Ph.D., and Karine Gousset, Ph.D., both of the HIV Drug
Resistance Program in the Center for Cancer Research (CCR), conducted a study
with collaborators from the University of Michigan and NCI's AIDS Vaccine and
Advanced Technology programs at SAIC-Frederick, Inc. The results of their
work were selected as the CCR Science Advance of the year in HIV/AIDS research.
To visualize trafficking of Gag proteins in real time, Freed and colleagues inserted
a small molecular tag—tetracysteine (TC)—into the HIV-1 Gag protein.
A cellular stain that becomes fluorescent upon binding to the TC tag was applied
so that Gag's position could be tracked by fluorescence microscopy. It was
determined that Gag accumulates at the cell membrane and in compartments in the
interior of infected macrophages. Remarkably, when uninfected macrophages
or T cells were added, the researchers were able to observe migration of fluorescent
Gag to the points of cell-cell contact, so-called "virological synapses."
Electron microscopy analysis demonstrated budding of viral particles at the synapse.
This study demonstrates that HIV-1 particles are retained in internal
reservoirs from which they can be rapidly released at opportune times, such as
when contact is established with uninfected cells. The TC system provides
an efficient way of observing Gag trafficking in living cells without disrupting
the normal virus assembly and release and is likely to become an important tool
in identifying molecular clues for HIV-1 trafficking within and between cells.
The results of this study may set the groundwork for the development of new HIV
treatments based on interruption of intracellular viral trafficking. [Excerpted
from the CCR In the Journals article "Revealing the Gag Itinerary:
How HIV Is Transmitted One Cell at a Time." To read more, click
here (PDF - 104 K).] Gousset, K., Ablan, S.D., Coren, L.V.,
Ono, A., Soheilian, F., Nagashima, K., Ott, D.E., and, Freed,
E.O. (2008) Real-time
visualization of HIV-1 Gag trafficking in infected macrophages (PDF - 667
K). PLoS Pathog. 4: e1000015. Retroviral
Gymnastics: Slip Sliding Away HIV
reverse transcriptase (RT) catalyzes a series of intricate reactions through which
it converts single-stranded viral RNA of the invading virus into integration-competent
double-stranded DNA. This process requires a variety of enzymatic activities
encoded within its p66 subunit, including DNA synthesis, RNase H-mediated cleavage
of the RNA/DNA replication intermediate, strand transfer, and strand displacement
synthesis. Using single-molecule fluorescence resonance energy transfer
(FRET), we have probed interactions between HIV-1 RT and nucleic acid substrates
in real time. RT was observed to slide on nucleic acid duplexes, rapidly
shuttling between opposite termini of the duplex. Upon reaching the DNA
3' terminus, the enzyme can spontaneously “flip” into a polymerization orientation.
Sliding kinetics were also regulated by cognate nucleotides and anti-HIV drugs,
which stabilized and destabilized the polymerization mode, respectively.
These long-range translocation activities facilitate multiple stages of the reverse
transcription pathway and possibly provide insights into a unique mechanism of
action of nonnucleoside RT inhibitors. To read more, click
here (PDF - 470 K). Liu, S., Abbondanzieri, E., Rausch,
J.W., Le
Grice, S.F.J., and Zhuang, X. (2008) Slide
into action: Dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates
(PDF - 470 K). Science 322: 1092-1097.
Science
online supporting material related to this article (PDF - 2432 K)
Science
Perspectives feature related to this article: Sarafianos, S.G., and Arnold,
E. (2008) Biochemistry:
RT Slides Home… (PDF - 280 K). Science 322: 1059-1060.
HHMS
News November 2008 feature about this article: An
HIV enzyme with a flair for the acrobatic. See also the related article
by Abbondanzieri et al.: Abbondanzieri, E.A., Bokinsky, G., Rausch, J.W.,
Zhang, J.X., Le
Grice, S.F.J., and Zhuang, X. (2008) Dynamic
binding orientations direct activity of HIV reverse transcriptase (PDF - 546
K). Nature 453: 184-189. Drug
Resistance in HIV: The SHAPE of Things to Come Nuclear export
of certain HIV-1 mRNAs requires an interaction between the retroviral Rev protein
and the Rev response element (RRE), a structured element located in the Env region
of its RNA genome. Disrupting this interaction has been an attractive target
for drug design and gene therapy, exemplified by RevM10, a transdominant negative
protein that, when introduced into host cells, disrupts viral mRNA export and
inhibits virus replication. However, two silent G->A mutations in the RRE
(designated RRE61) conferred RevM10 resistance. This observation prompted
Legiewicz et al. to examine RRE evolution at the structural level using SHAPE
(Selective 2'-Hydroxyl Acylation analyzed by Primer
Extension) chemistry, a novel footprinting approach that interrogates the
base pairing status of all RNA nucleotides in a single reaction. Structural
variations in region III/IV/V of mutant RNAs suggest a stepwise rearrangement
of the RRE to RevM10 resistance. Using high-resolution mass spectrometry,
these authors could also demonstrate that the stoichiometry of Rev "loading" onto
RRE61 is unaffected by these structural changes, while chemical footprinting highlighted
subtle differences between wild-type and mutant Rev and the RRE variants.
To read more, click
here (PDF - 958 K). Legiewicz, M., Badorrek, C.S., Turner,
K.B., Fabris, D., Hamm, T.E., Rekosh, D., Hammarskjold, M.-L., and Le
Grice, S.F.J. (2008) Resistance
to RevM10 inhibition reflects a conformational switch in the HIV-1 Rev response
element (PDF - 958 K). Proc. Natl. Acad. Sci. USA 105: 14365-14370.
Dirt
Under the Thumbs: Allosteric Inhibition of HIV-1 RNase H by Vinylogous Ureas
High-throughput screening of NCI libraries of synthetic and natural compounds,
totaling ~230,000, has identified the vinylogous ureas 2-amino-5,6,7,8-tetrahydro-4H- cyclohepta[b]thiophene-3-carboxamide
(NSC727447) and N-[3-(aminocarbonyl)-4,5-dimethyl-2-thienyl]-2-furancarboxamide
(NSC727448) as inhibitors of the ribonuclease H (RNase H) activity of HIV-1 and
HIV-2 reverse transcriptase (RT). Synergy studies demonstrated that NSC727447
and the active site hydroxytropolone RNase H inhibitor b-thujaplicinol
were mutually exclusive in their interaction with the RNase H domain of RT.
Mass spectrometric protein footprinting of the NSC727447 binding site indicated
that residues Cys280 and Lys281 in helix I of the p51 thumb subdomain were affected
by inhibitor binding. Although DNA polymerase and pyrophosphorolysis activities
of HIV-1 RT were less sensitive to inhibition by NSC727447, protein footprinting
indicated that NSC727447 occupied the equivalent region of the p66 thumb.
Site-directed mutagenesis using reconstituted p66/p51 heterodimers substituted
with natural or non-natural amino acids indicates that altering the p66 RNase
H primer grip significantly affects inhibitor sensitivity. The study by
Wendeler et al. shows that NSC727447 represents a novel class of allosteric RNase
H antagonists with a mechanism of action differing from active site, divalent
metal-chelating inhibitors that have been reported. To read more, click
here (PDF - 1450 K). Wendeler, M., Lee, H.-F., Bermingham,
A., Miller, J.T., Chertov, O., Bona, M.K., Baichoo, N.S., Ehteshami, M., Beutler,
J., O'Keefe, B.R., Götte, M., Kvaratskhelia, M., and Le
Grice, S. (2008) Vinylogous
ureas as a novel class of inhibitors of reverse transcriptase-associated ribonuclease
H activity (PDF - 1450 K). ACS Chem. Biol. 3: 635-644.
ACS
Chemical Biology online supporting material related to this article (PDF -
336 K)
ACS Chemical Biology feature about Michaela Wendeler: Introducing
our Authors. Chem. Biol. 3: 593.
ACS Chemical Biology podcast
featuring Stuart Le Grice: October
2008 ACS Chemical Biology Podcast. HIV
and Drug Resistance: Hitting a Moving Target
HIV can take many roads to evade the effects of drug therapy. Investigators
at CCR [the National Cancer Institute's Center for Cancer Research] and Rutgers
University recently identified a novel mechanism by which HIV can circumvent the
antiviral activity of a compound called amphotericin B methyl ester (AME), providing
new insights into how the virus replicates and evolves into more resistant strains.
Prior research revealed how HIV-1 makes its destructive entry into the target
cell by fusing together the cholesterol-rich lipid bilayer of the viral envelope—made
with key glycoproteins gp120 and gp41—and the host cell's plasma membrane.
Cell-viral interactions begin with the binding of gp120 to the CD4 receptor molecule
on the target cell, followed by gp120 binding to coreceptors. These coreceptors
likely reside in structures called lipid rafts—areas in the cell plasma
membrane that are rich in cholesterol, saturated fatty acids, and certain proteins—that
facilitate the entry of viruses into host cells. Finally, sequences in gp41
trigger the fusion of the viral and cellular lipid bilayers. The lipid rafts
are then involved in the production of new viral particles.
Drugs that
hone in on the close interaction between cell and virus by disrupting lipid rafts
would likely slow the virus's spread because they would hinder its ability to
enter and leave host cells. AME is such an agent; it acts by binding to
cholesterol in the viral membrane, which itself is lipid raft like, potently blocking
the virus’s entry into immune cells. Eric
O. Freed, Ph.D., and first author Abdul A. Waheed, Ph.D., both of
CCR's HIV Drug Resistance Program, along with other researchers at CCR and Rutgers
University, used AME in experimental systems to learn more about how HIV attaches
to and infects cells. They found that continual HIV exposure to low levels
of AME induced the virus to mutate and become resistant to AME. [Excerpted
from the CCR In the Journals article "HIV and Drug Resistance: Hitting
a Moving Target." To read more, click
here (PDF - 284 K).] Waheed, A.A., Ablan, S.D., Roser, J.D.,
Sowder, R.C., Schaffner, C.P., Chertova, E., and Freed,
E.O. (2007) HIV-1
escape from the entry-inhibiting effects of a cholesterol-binding compound via
cleavage of gp41 by the viral protease (PDF - 284 K). Proc. Natl. Acad.
Sci. USA 104: 8467–8471.
Probing
the Building Block of HIV-1 and Other Retroviruses
A single viral
protein, termed "Gag," is sufficient for efficient assembly and release of retrovirus-like
particles from mammalian cells. Furthermore, purified HIV-1 Gag protein
can be induced to assemble into virus-like particles in a defined system in
vitro by the addition of nucleic acid. Thus, the Gag protein is the
fundamental building block of retrovirus particles. As reported in a pair
of recent publications, research conducted principally in Alan
Rein's laboratory has studied the properties of assembly-competent
HIV-1 Gag in solution; this is the first published analysis of this type for any
retroviral Gag protein. In order to more fully characterize this key building
block, they have analyzed both its conformation in solution and its intermolecular
interactions. This approach to probing the intricacies of Gag should advance
the understanding of molecular mechanisms involved in formation of infectious
retrovirus particles, and could ultimately reveal new clinical approaches to inhibiting
the replication of viruses such as HIV-1. To read more, click on the titles
shown below. Datta, S.A.K., Zhao, Z., Clark, P.K., Tarasov, S., Alexandratos,
J.N., Campbell, S.J., Kvaratskhelia, M., Lebowitz, J., and Rein,
A. (2007) Interactions
between HIV-1 Gag molecules in solution: An inositol phosphate-mediated switch
(PDF - 726 K). J. Mol. Biol. 365: 799-811. Datta, S.A.K., Curtis,
J.E., Ratcliff, W., Clark, P.K., Crist, R.M., Lebowitz, J., Krueger, S., and Rein,
A. (2007) Conformation
of the HIV-1 Gag protein in solution (PDF - 1376 K). J. Mol. Biol. 365:
812-824. A
New "Connection" Between HIV-1 Drug Resistance and RNase H Activity
Reverse
transcriptase (RT), a key enzyme in the life cycle of HIV-1, possesses DNA polymerase
and RNase H activities. Because RT is essential for viral replication, it
has been one of the attractive targets for antiretroviral drugs. However,
drug resistance remains a major obstacle to the effective management of HIV-1
infection and AIDS, as drug-resistance mutations arise very quickly in response
to treatment. A greater understanding of the molecular mechanisms that mediate
HIV-1 drug resistance is therefore critical for developing more effective antiretroviral
agents and successful therapy. New insights into drug-resistance mechanisms
have been provided by Nikolenko et al., whose recently published study revealed
that mutations in the C-terminal domains of HIV-1 RT that are selected in response
to antiviral therapy play a critical role in resistance to nucleoside RT inhibitors
(NRTIs), a major class of clinically available antiretroviral drugs. The
authors propose that an increase in resistance to AZT (one of the NRTIs) is dependent
on the balance between the RNase H activity of RT and the rate of removal of AZT
from terminated DNA. Because only the N-terminal portions of RT from clinical
samples are included in standard genotypic and phenotypic drug-resistance testing,
this study highlights the importance of analyzing the whole RT sequence for more
effective control of HIV-1 infection and development of improved antiviral strategies.
To read more, click
here (PDF - 898 K). Nikolenko, G.N., Delviks-Frankenberry,
K.A., Palmer, S., Maldarelli, F., Fivash, M.J., Jr., Coffin, J.M., and Pathak,
V.K. (2007) Mutations
in the connection domain of HIV-1 reverse transcriptase increase 3'-azido-3'-deoxythymidine
resistance (PDF - 898 K). Proc. Natl. Acad. Sci. USA 104: 317-322.
Recent
HIV DRP Publications (November 2008–February 2009)
Crist,
R.M., Datta, S.A.K., Stephen, A.G., Soheilian, F., Mirro, J., Fisher, R.J., Nagashima,
K., and Rein,
A. (2009) Assembly properties of HIV-1 Gag-leucine zipper
chimeras: Implications for retroviral assembly. J. Virol., in press (Dec
10 Epub ahead of print). [Abstract] [Full-text
PDF
article] Dash,
C., Scarth, B.J., Badorrek, C., Götte, M., and Le
Grice, S.F.J. (2008) Examining the ribonuclease H primer
grip of HIV-1 reverse transcriptase by charge neutralization of RNA/DNA hybrids.
Nucleic Acids Res. 36: 6363-6371. [Abstract] [Full-text
PDF
article - 8700 K] Datta,
S.A.K., and Rein,
A. (2009) Preparation of recombinant HIV-1 Gag protein
and assembly of virus-like particles in vitro. In Prasad, V.R.,
and Kalpana, G.V. (eds.), HIV Protocols, 2nd Ed., Methods in Molecular Biology,
Vol. 485, Humana Press, pp. 197-208. [Abstract] Gorelick,
R.J., Thomas, J.A., Coren, L.V., Bosche, W.J., Gagliardi, T.D., Shulenin, S.,
and Oroszlan,
S. (2009) Characterization of human immunodeficiency
virus type 1 (HIV-1) nucleocapsid protein mutants with alterations at a putative
HIV-1 protease cleavage site. Virology, in press. Greene,
W.C., Debyser, Z., Ikeda, Y., Freed,
E.O., Stephens, E., Yonemoto, W., Buckheit, R.W., Este, J.A., and
Cihlar, T. (2008) Novel targets for HIV therapy. Antiviral Res.
80: 251-265. [Abstract] [Full-text
PDF
article - 1737 K] Joshi,
A., Munshi, U., Ablan, S.D., Nagashima, K., and Freed,
E.O. (2008) Functional replacement of a retroviral late
domain by ubiquitin fusion. Traffic 9: 1972-1983. [Abstract] [Full-text
PDF
article - 796 K] Kearney,
M., Maldarelli,
F., Shao, W., Margolick, J.B., Daar, E.S., Mellors, J.W., Rao, V.,
Coffin,
J.M., and Palmer, S. (2009) HIV-1 population genetics
and adaptation in newly infected individuals. J. Virol. , in press (Dec
30 Epub ahead of print). [Abstract] [Full-text
PDF
article - 293 K] Kvaratskhelia,
M., and Le
Grice, S.F.J. (2008) Structural analysis of protein-RNA
interactions with mass spectrometry. In Lin, R.J. (ed.), RNA-Protein
Interaction Protocols, Methods in Molecular Biology, Vol. 488, Humana Press, Totowa,
NJ, pp. 213-220. LaRue,
R.S., Andrésdóttir, V., Blanchard, Y., Conticello, S.G., Derse,
D., Emerman, M., Greene, W.C., Jónsson, S.R., Landau, N.R., Löchelt,
M., Malik, H.S., Malim, M.H., Münk, C., O'Brien, S.J., Pathak,
V.K., Strebel, K., Wain-Hobson, S., Yu, X.F., Yuhki, N., and Harris,
R.S. (2009) Guidelines for naming nonprimate APOBEC3 genes and proteins.
J. Virol. 83: 494-497. [PubMed
citation] [Full-text PDF
article - 148 K] Liu,
S., Abbondanzieri, E., Rausch, J.W., Le
Grice, S.F.J., and Zhuang, X. (2008) Slide into action:
Dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates.
Science 322: 1092-1097. [Abstract] [Full-text
PDF
article - 470 K] [Science
online supporting material - 2432 K PDF] [HHMI
News: An HIV Enzyme with a Flair for the Acrobatic] [Science
Perspectives feature: Biochemistry: RT Slides Home… (PDF - 470 K)]
Mbisa,
J., K.A. Delviks-Frankenberry, J.A. Thomas, R.J. Gorelick, and Pathak,
V.K. (2009) Real-time PCR analysis of HIV-1 replication
post-entry events. In Prasad, V.R., and Kalpana, G.V. (eds.), HIV
Protocols, 2nd Ed., Methods in Molecular Biology, Vol. 485, Humana Press, pp.
55-72. [Abstract]
Michel, N., Goffinet, C., Ganter, K., Allespach, I., KewalRamani,
V.N.,Saifuddin, M., Littman, D.R., Greene, W.C., Goldsmith, M.A., and Keppler, O.T. (2009) Human cyclin T1 expression ameliorates a T-cell-specific transcriptional limitation for HIV in transgenic rats, but is not sufficient for a spreading infection of prototypic R5 HIV-1 strains ex vivo. Retrovirology 6:2. [Abstract] [Full-text
PDF
article - 856 K]
Migueles,
S.A., Osborne, C.M., Royce, C., Compton, A.A., Joshi, R.P., Weeks, K.A., Rood,
J.E., Berkley, A.M., Sacha ,J.B., Cogliano-Shutta, N.A., Lloyd, M., Roby, G.,
Kwan, R., McLaughlin, M., Stallings, S., Rehm, C., O'Shea, M.A., Mican, J., Packard,
B.Z., Komoriya, A., Palmer, S., Wiegand, A.P., Maldarelli,
F., Coffin,
J.M., Mellors, J.W., Hallahan, C.W., Follman, D.A., and Connors,
M. (2008) Lytic granule loading of CD8+ T cells is required for HIV-infected
cell elimination associated with immune control. Immunity 29: 1009-1021. [Abstract] [Full-text
PDF
article - 1649 K] Moore,
M.D., and Hu,
W.-S. (2009) HIV-1 RNA dimerization: It takes two to
tango. AIDS Rev., in press. Moore,
M.D., Chin, M.P.S., and Hu,
W.-S. (2009) HIV-1 recombination: An experimental assay
and a phylogenetic approach. In Prasad, V.R., and Kalpana, G.V.
(eds.), HIV Protocols, 2nd Ed., Methods in Molecular Biology, Vol. 485, Humana
Press, pp. 87-105. [Abstract] Morse,
C., and Maldarelli,
F. (2009) HIV infection. In Strober, W.,
and Gottesman, S. (eds.), Immunology, Clinical Case Studies and Disease Pathophysiology,
John Wiley & Sons, in press. Oh,
J., Chang, K.W., and Hughes,
S.H. (2008) Integration of Rous sarcoma virus DNA: A
CA dinucleotide is not required for the integration of the U3 end of viral DNA.
J. Virol. 82: 11480-11483. [Abstract] [Full-text
PDF
article - 276 K]
Perkovic, M., Schmidt, S., Marino, D., Russell, R.A., Stauch, B., Hofmann, H.,
Kopietz, F., Kloke, B.P., Zielonka, J., Ströver, H., Hermle, J., Lindemann, D.,
Pathak,
V.K., Schneider, G., Löchelt, M., Cichutek, K., and Münk, C.
(2009) Species-specific inhibition of APOBEC3C by the prototype foamy virus
protein Bet. J. Biol. Chem., in press (Dec 12 Epub ahead of print). [Abstract] [Full-text
PDF
article - 881 K] Porter,
B.O., Anthony, K.B., Shen, J., Hahn, B., Keh, C.E., Maldarelli,
F., Blackwelder, W.C., Lane, H.C., Kovacs, J.A., Davey, R.T., and
Sereti, I. (2009) Inferiority of IL-2 alone versus IL-2 with HAART
in maintaining CD4 T cell counts during HAART interruption: A randomized controlled
trial. AIDS 23: 203-212. [Abstract] [Full-text
PDF
article - 252 K] Ramanathan,
R., Pau, A.K., Busse, K.H., Zemskova, M., Nieman, L., Kwan, R., Hammer, J.H.,
Mican, J.M., and Maldarelli,
F. (2008) Iatrogenic Cushing syndrome after epidural
triamcinolone injections in an HIV type 1-infected patient receiving therapy with
ritonavir-lopinavir. Clin. Infect. Dis. 47: e97-99. [Abstract] [Full-text
PDF
article - 109 K] Rausch,
J.W., Chelico, L., Goodman, M.F., and Le
Grice, S. (2009) Dissecting APOBEC3G substrate specificity
by nucleoside analog interference. J. Biol. Chem., in press (Jan 9 Epub
ahead of print). [Abstract] [Full-text
PDF
article - 1058 K] Robertson,
S.M., Maldarelli,
F., Natarajan, V., Formentini, E., Alfaro, R.M., and Penzak, S.R.
(2009) Efavirenz induces CYP2B6-mediated hydroxylation of bupropion in healthy
subjects. J. Acquir. Immune Defic. Syndr., in press (Nov 4 Epub ahead of
print). [Abstract] [Full-text
PDF
article - 119 K] Russell,
R.A., Smith, J., Barr, R., Bhattacharyya, D., and Pathak,
V.K. (2009) Distinct domains within APOBEC3G and APOBEC3F
interact with separate regions of human immunodeficiency virus type 1 Vif.
J. Virol. 83: 1992-2003. [Abstract] [Full-text
PDF
article - 1351 K] Sarafianos,
S.G., Marchand, B., Das, K., Himmel, D.M., Parniak, M.A., Hughes,
S.H., and Arnold, E. (2009) Structure and function of
HIV-1 reverse transcriptase: Molecular mechanisms of polymerization and inhibition.
J. Mol. Biol. 385: 693-713. [Abstract] [Full-text
PDF
article - 1561 K] Waheed,
A.A., and Freed,
E.O. (2008) Peptide inhibitors of HIV-1 egress.
ACS Chem. Biol. 3: 745-747. [Abstract] [Full-text
PDF
article - 183 K] Waheed,
A.A., Ono, A., and Freed,
E.O. (2009) Methods for the study of HIV-1 assembly.
In Prasad, V.R., and Kalpana, G.V. (eds.), HIV Protocols, 2nd Ed., Methods
in Molecular Biology, Vol. 485, Humana Press, pp. 163-184. [Abstract] Wendeler,
M., Beilhartz, G.L., Beutler, J.A., Götte, M., and Le
Grice, S.F.J. (2009) HIV ribonuclease H: Continuing the
search for small molecule antagonists. HIV Ther. 3: 39-53. [Full-text
PDF
article - 3282 K] Wendeler,
M., and Le
Grice, S.F.J. (2009) HIV-1 reverse transcriptase.
In Gotte, M., Cameron, C.E., and Raney, K. (eds.), Viral Genome Replication,
Springer Publications Company, New York, NY. Wilkinson,
T.A., Januszyk, K., Phillips, M.L., Tekeste, S.S., Zhang, M., Miller, J.T., Le
Grice, S.F.J., Clubb, R.T., and Chow, S.A. (2009) Identifying
and characterizing a functional HIV-1 reverse transcriptase-binding site on integrase.
J. Biol. Chem., in press (Jan 16 Epub ahead of print). [Abstract] [Full-text
PDF
article - 1603 K] Last
modified: 30 January 2009 | ... |