Landau Lab - Microbiology

 

NedPicNathaniel Landau, Ph.D.
Professor, Department of Microbiology

Member of the Microbial Pathogenesis Program
in the Joan and Joel Smilow Research Center

Joan and Joel Smilow Research Center
10th Floor
522 First Avenue, New York, NY 10016
Direct Line: (212) 263-9197
Fax: (212) 263-9180
Email: Nathaniel Landau

KEY INTERESTS:

Dr. Landau's research focuses on HIV replication and AIDS.

 

BIOGRAPHICAL DETAILS:

Graduate Education:

1986: Ph.D. in Biology from the Massachusetts Institute of Technology

Postdoctoral Training:

1987: University of California, San Francisco

Academic Appointments:

1991: Staff investigator at the Aaron Diamond AIDS Research Center
1999: Associate professor in the Infectious Disease Laboratory, The Salk Institute for Biological Studies
2004: Professor in the Infectious Disease Laboratory, The Salk Institute for Biological Studies.
2006: Professor in the Department of Microbiology, NYUSoM

RESEARCH INTERESTS:

Innate Immunity to HIV-1 and Mechanisms of Virus Escape

Mammalian cells resist viruses through a collection of mechanisms termed innate or intrinsic immunity.  These mechanisms differ from the classical adaptive immune response in which specialized B, T helper and cytolytic T cells recognize foreign antigens and clonally expand upon engagement of their antigen receptor.  Intrinsic and innate mechanisms are more generalized.  They are active in many different cell types; some are constitutively active and others are induced by type-I interferons.  Some innate immune mechanisms are activated by toll-like receptors or related proteins that warn the cell of the presence of a foreign invader by sensing the viral RNA or DNA in the cytoplasm of the cell.  Viruses have responded over the course of evolution by developing remarkable and diverse ways to escape the adaptive and innate responses.  A major focus of our research is to understand how innate immune mechanisms restrict retroviruses and how the viruses counteract them.

I.  The APOBEC3 family of cytidine deaminases.

APOBEC3G: a potent host restriction factor that is counteracted by the lentivirus Vif accessory protein.  The APOBEC3 gene family which, in humans, includes APOBEC3A, B, C, D/E, F, G and H, are antiviral cytidine deaminases.  These enzymes act as DNA mutators that target the genome of viruses by deaminating cytosine nucleotides to uracil. APOBEC3G (and to a lesser extent, APOBEC3F) is of particular importance because it specifically restricts HIV-1.  APOBEC3G is expressed in the CD4+ T cells and monocytes that are the target of the virus.  HIV-1 is able to productively replicate in such cells by virtue of the Vif accessory protein, which binds to APOBEC3G and causes its degradation.  Infection of a cell with vif HIV-1 that cannot encode a functional Vif results in an abortive infection.  Virions are produced by the vif HIV-1-infected cell, but these are noninfectious.  The virions contain APOBEC3G molecules, packaged in the particles, that attack the viral genome as it is copied from RNA into DNA in the next round of replication.  In a sort of evolutionary biological warfare, the virus developed Vif to bind APOBEC3G before it is packaged and then shunt it to the proteasome for degradation.  Vif contains a zinc binding motif and a conserved SOCS box that interacts with a Cul5-based E3 ubiquitin ligase that ubiquitinates APOBEC3G, flagging it for proteasomal degradation.  We are addressing several aspects of how this system operates.  These include defining the interaction domains of Vif, APOBEC3 and the E3 ubiquitin ligase; developing small molecule inhibitors of the interaction; and understanding how the APOBEC3 genes are transcrptionally regulated.

Figure 2. Vif, Vpr/Vpx and Vpu counteract cellular restriction factors.  Vif, Vpr/Vpx and Vpu associate with E3 ubiquitin ligases to induce the proteasomal degradation of restriction factors. Vpx overcomes a post-entry block to reverse transcription by targeting SAMHD1.  The target of Vpr is not known.  Vif induces the degradation of APOBEC3G to prevent its packaging into the virion and the subsequent C®U deamination of the reverse transcribed viral DNA.  Vpu antagonizes tetherin which hold the virus onto the cell surface.

 

Physiological role of APOBEC3 in the mouse.  In contrast to the human, the mouse genome contains only one APOBEC3 gene.  Although mice are not subject to lentivirus infection, the mouse APOBEC3 protein (mu-APOBEC3) is a potent inhibitor of HIV-1 when introduced into human cells in culture.  Interestingly, mu-APOBEC3 is not recognized by HIV-1 Vif, and as a result, the murine enzyme restricts the replication of wild-type HIV-1.  The presence of only a single gene in the mouse is convenient because APOBEC3 knock-out mice are then completely deficient.  We have generated such mice and, consistent with the findings of other groups, there is no obvious phenotype.  As shown by others, APOBEC3 knock-out mice are more susceptible to murine retroviruses such as mouse mammary tumor virus and Friend murine leukemia virus.  We are currently using the knock-out mouse to study the mechanisms by which APOBEC3 protects against these viruses.  Interestingly, it does not appear to be due to deamination of their genomes. 

APOBEC3A:  a potent inhibitor of retrotransposons and parvovirus.  The roles of the various APOBEC3 family members are not yet known but an attractive hypothesis is that they act against different viruses.  In support of this possibility, we have studied APOBEC3A.  APOBEC3A has no activity against HIV-1 or SIV, but is a potent inhibitor of retrotransposons.  Retrotransposons are a class of endogenous genetic elements that are present in thousands of copies in mammalian genomes.  They resemble retroviruses in genome structure and some have the ability to transpose, or jump in the genome, an event that occasionally cause diseases such as muscular dystrophy or hemophilia. APOBEC3A also inhibits adeno-associated virus, a small DNA virus that replicates in the nucleus through a single strand DNA intermediate.  APOBEC3 proteins are active against single-stranded DNA and APOBEC3A localizes to the nucleus, allowing it to be in the vicinity of reverse transcribing retroelements and replicating parvovirus.  APOBEC3A is strongly induced by type-1 interferon, further supporting its role as an antiviral protein.  We have produced pure, catalytically active recombinant APOBEC3A in milligram quantities and found that the enzyme acts nonprocessively and strongly binds to single-stranded DNA.  We are interested to understand how this works in vitro and in vivo.

II. SAMHD1:  a host restriction factor that starves the virus of deoxynucleotides.   HIV-2 and SIV encode the accessory protein viral protein X (Vpx).  Vpx is unusual among the lentivirus nonstructural proteins in that it is present in the virus particles.  Its packaging during virus assembly is the result of a short amino acid motif in Gag, the major structural protein of the virus.  The role of Vpx is to degrade SAMHD1, an antiviral host protein that blocks the infection of myeloid cells (macrophages and dendritic cells).  Its mechanism is quite interesting. It is a phosphohydrolase that dephosphorylates the deoxynucleotide triphosphates (dNTP) of the cell.  Because the virus uses the cell’s dNTPs to synthesize its DNA through the process of reverse transcription, in a cell that has active SAMHD1, the virus genome is not generated and infection is blocked.  When HIV-2 or SIV infects such a cell, the Vpx in the virion is released and targets SAMHD1 for degradation, thereby relieving the block to infection.  In activated T cells, SAMHD1 does not reduce the size of the dNTP pool and does not block infection.  However, in resting cells, SAMHD1 is active.  As a result, the cell cannot be infected.  To induce the degradation of SAMHD1, Vpx associates with an E3 ubiquitin ligase.  These multi-subunit complexes are molecular machines that target specific host proteins for degradation.  We’re trying to understand how Vpx targets SAMHD1 for degradation and to understand how SAMHD1 activity is regulated in the cell so that it does not deplete the dNTPs of dividing cells.  HIV-1 doesn’t have a Vpx, and we’re working on understanding how the virus manages to replicate in vivo without it.  As a tool in these studies, we have generated a modified HIV-1 that packages Vpx. 

III.  Vpr: searching for a function.  HIV-1 encodes another accessory protein, viral protein R (Vpr), the function of which is poorly understood.  When expressed in a cell, Vpr arrests the cell cycle in the G2 phase.  However, that is most likely not the biologically relevant role for Vpr.  We hypothesize that like Vpx, it counteracts a host restriction factor.  Vpr is conserved in HIV-1 isolates but is not required for the virus to replicate on cultured cells.  Its importance for virus replication and disease pathogenesis in vivo has been demonstrated in the rhesus macaque model.  Vpr associates with the same E3 ubiquitin ligase as Vpx and is packaged into virions as is Vpx.  This would suggest that it, like Vpx, counteracts a host restriction by inducing the degradation of an antiviral host protein.  Understanding this mechanism may uncover yet another target for antiretroviral drug development.  We are trying to identify the protein using various genomic and proteomic approaches.

IV.  The development of Vpx-containing dendritic cell vaccines.  Lentiviral vectors have been used in human gene therapy trials as a means to stably express biologically active proteins long-term in human cells in vivo.  Until recently, it was not possible to use lentiviral vectors to express proteins in dendritic cells because the vectors were blocked by SAMHD1.  To overcome this limitation, we transferred the Vpx packaging motif into HIV-1 Gag, allowing us to generate lentivirus vectors that contain packaged Vpx.  We are developing these vectors as “DC vaccines”.  The vectors express an antigenic peptide from a viral pathogen and CD40L, the ligand for CD40 on dendritic cells that promotes antigen presentation by dendritic cells and induces them to secrete cytokines that activate T cells.  We are developing these vectors for use as therapeutic vaccine vectors for cancer and for HIV-1 infection.

Dr. Landau’s review of recent findings regarding DNA sensing of HIV infection in dendritic cells was published in DNA and Cell Biology and an image from the review produced by Nicolin Bloch, a graduate student in the lab, made the cover of the May issue.  Sensing of HIV by cytosolic signaling molecules such as cGAS is currently a topic that is both exciting and controversial.  The review provides insight into this important research area in AIDS research. 

PUBLICATIONS

The cargo-binding domain of transportin 3 is required for lentivirus nuclear import.
Logue E, Taylor K, Goff P, Landau NR.
J Virol. 2011 Dec;85(24):12950-61. Epub 2011 Oct 5.

Human immunodeficiency virus type 1 modified to package Simian immunodeficiency virus Vpx efficiently infects macrophages and dendritic cells.
Sunseri N, O’Brien M, Bhardwaj N, Landau NR. J Virol. 2011.
PMID: 21507971

Evidence for an activation domain at the amino terminus of simian immunodeficiency virus Vpx.
Gramberg T, Sunseri N, Landau NR. J Virol. 2010.
PMID: 19923175

Restriction of HIV-1 by APOBEC3G is cytidine deaminase-dependent.
Browne EP, Allers C, Landau NR. Virology. 2009.
PMID: 19304304

HIV-1 Vpr function is mediated by interaction with the damage-specific DNA-binding protein DDB1.
Schröfelbauer B, Senger T, Manning G, Landau NR.
Proc. Natl. Acad. Sci. USA. 2007.
PMID: 17360488

Analysis of Vif-induced APOBEC3G degradation using an alpha-complementation assay.
Fang L, Landau NR.
Virology. 2007.
PMID: 17049578

Reversed functional organization of mouse and human APOBEC3G cytidine deaminase domains.
Hakata Y, Landau NR.
J Biol. Chem. 2006.
PMID: 17020885

Mutational alteration of human immunodeficiency virus type 1 Vif allows for functional interaction with nonhuman primate APOBEC3G.
Schröfelbauer B, Senger T, Manning G, Landau NR.
J Virol. 2006.
PMID: 16731937

Human immunodeficiency virus type 1 Vpr induces the degradation of the UNG and SMUG uracil-DNA glycosylases.
Schröfelbauer B, Yu Q, Zeitlin SG, Landau NR.
J Virol. 2005.
PMID: 16103149

Complementary function of the two catalytic domains of APOBEC3G.
Navarro F, Bollman B, Chen H, König R, Yu Q, Chiles K, Landau NR.
Virology. 2005.
PMID: 15721369

APOBEC3B and APOBEC3C are potent inhibitors of simian immunodeficiency virus replication.
Yu Q, Chen D, König R, Mariani R, Unutmaz D, Landau NR.
J Biol. Chem. 2004.
PMID: 15466872

Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome.
Yu Q, König R, Pillai S, Chiles K, Kearney M, Palmer S, Richman D, Coffin JM, Landau NR.
Nat. Struct. Mol. Biol. 2004.
PMID: 15098018

Species-specific exclusion of APOBEC3G from HIV-1 virions by Vif.
Mariani R, Chen D, Schröfelbauer B, Navarro F, König R, Bollman B, Münk C, Nymark-McMahon H, Landau NR.
Cell. 2003.
PMID: 12859895

The role of a mutant CCR5 allele in HIV-1 transmission and disease progression.
Huang Y, Paxton WA, Wolinsky SM, Neumann AU, Zhang L, He T, Kang S, Ceradini D, Jin Z, Tazdanbakhsh K, Kunstman K, Erickson D, Dragon E, Landau NR, Phair J, Ho DD, Koup RA.
Nat. Med. 1996.
PMID: 8898752

Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection.
Liu R, Paxton WA, Choe S, Ceradini D, Martin SR, Horuk R, MacDonald ME, Stuhlmann H, Koup RA, Landau NR.
Cell. 1996.
PMID: 8756719

Identification of a major co-receptor for primary isolates of HIV-1.
Deng H, Liu R, Ellmeier W, Choe S, Unutmaz D, Burkhart M, Di Marzio P, Marmon S, Sutton RE, Hill CM, Davis CB, Peiper SC, Schall TJ, Littman DR, Landau NR.
Nature. 1996.

Lab Members

Nicolin Bloch, Graduate Student
Henning Hofmann, Postdoctoral Fellow
Tom Norton, MD Fellow
Stephanie Fung, Research Assistant
Megan Schultz, Research Assistant
Paula Jauregui, Postdoctoral Fellow
Ruonan Zhang, Postdoctoral Fellow

Past Lab Members

Eric Logue
Carolina Allers
Brooke Bollman
Ed Browne
Hui Chen
Erica Dhuey
Lei Fang
Peter Goff
Thomas Gramberg
Yoshi Hakata
Cecile Herate
Anne Holland
Renate König
Roberto Mariani
Carsten Münk
Francisco Navarro
Bärbel Schröfelbauer
Tilo Senger
Nicole Sunseri
Kayleigh Taylor
Qin Yu

Job Opportunities/Positions Available

Postdoctoral Scientist
Individuals holding a Ph.D. with experience in protein chemistry, molecular biology, immunology or cell biology are welcome to apply at any time.  
 
Research Assistant
Recent college graduates with a strong background in molecular and cell biology and previous laboratory experience should submit a cover letter, resume and three references.



Related Links: Joan and Joel Smilow Research Center