Research Program

• Blood Cell Development and Function

Slide 1
The single cell reproductive cycle of the alpharetrovirus, ALV. The virus life cycle is 46 divided into an early phase that includes steps from virus infection to establishment of the provirus, and a late phase that includes expression of the provirus and formation of progeny virions. Adapted from: Principles of Virology, 4rd edition Vol. I. 2015. S.J Flint, V.R Racaniello, G.F. Rall. and A.M. Skalka. ASM Press Washington DC, Vol. I Appendix, Figure 30.

Slide 2
Steps in the synthesis of retroviral DNA and its integration into host DNA. The viral RNA genome (green line) is reverse transcribed in the cytoplasm of the cell within a subviral nucleoprotein structure (called the reverse transcription complex) to form a duplex DNA containing long terminal repeats (LTRs) of sequences unique to the 5 (U5) and 3 (U3) ends of the viral RNA. The organization of the genes common to all retroviruses ( gag, pro, pol, and env) is colinear with the RNA genome. Imperfect inverted repeats at the LTR duplex termini are recognized and nicked by cognate integrase (IN) proteins, following a conserved CA dinucleotide at each 3 end ( purple arrowheads in inset), producing recessed 3-OH ends. This first reaction catalyzed by IN is called processing and takes place within a nucleoprotein assembly called a preintegration complex. A tetramer of IN bound to the processed viral DNA (vDNA) ends enters the nucleus, where a joining reaction catalyzed by IN connects the 3-OH ends of the vDNA to staggered phosphates at a target site in the host DNA. The length of the stagger (4–6 bp) is characteristic of the viral IN protein. The conserved CA dinucleotide and steps catalyzed by IN are highlighted in purple. Removal of the noncomplementary 5 nucleotides of vDNA and repair of the gaps in host DNA by host enzymes generate a covalently integrated provirus, shorter by 2 bp on either end and flanked by duplications of the target site (red arrows). From: MD Andrake and AM Skalka, Retroviral Integrase: Then and Now. Ann. Rev. Virol. Vol.2. 2015.

Slide 3
Domain organization of integrase (IN) proteins from different retroviruses. (a) Maps for the organization of IN proteins from the alpharetrovirus avian sarcoma/leukosis virus (ASLV), the gammaretrovirus murine leukemia virus (MLV), the lentivirus human immunodeficiency virus type 1 (HIV-1), and the spumavirus prototype foamy virus (PFV). Amino acid numbers delineate the start and end of each domain: the N-terminal extension domain (NED; purple); the N-terminal domain (NTD; red ), including the HHCC motif; the catalytic core domain (CCD; blue), including the D,D(35)E motif; and the C-terminal domain (CTD; green). The lengths of linkers that connect the domains are indicated below the lines between domains. Domains for which there is no experimentally determined structure from crystallography are in muted colors. (b) Domain models from crystal structures of the HIV-1 NTD (PDB 1K6Y), CCD (PDB 1BIU), and CTD (PDB 1EX4). The Zn2+ ion in the NTD is shown as an aqua sphere; one of the two Mg2+ ions bound in the active site of the CCD is shown as a green sphere. The conserved Glu residue of the D,D(35)E motif is presumed to chelate the second metal ion together with the first conserved Asp residue.
From: MD Andrake and AM Skalka, Retroviral Integrase: Then and Now. Ann. Rev. Virol. Vol.2. 2015.

Slide 4
Models for architectures of full-length human immunodeficiency virus type 1 (HIV-1) apo-integrase (IN) protein in solution. (a) Structures for HIV-1 IN protein in the absence of DNA substrates were derived by HADDOCK data-driven modeling of the HIV-1 IN monomer, dimer, and tetramer in solution, based on small-angle X-ray scattering and protein cross-linking data. Catalytic core domains (CCDs) are rendered in muted surface representation to emphasize their locations in the structures. It is not yet known which of these forms is competent for the viral DNA binding that leads to assembly of an HIV-1 intasome.
(b) An HIV-1 intasome model (90) with DNA shown in yellow ladder representation. Structures, colored as in Figure 3, are in a ribbon rendering and were generated using Chimera software. From: MD Andrake and AM Skalka, Retroviral Integrase: Then and Now. Ann. Rev. Virol. Vol.2. 2015.

Slide 5
Model for the roles of the human Daxx protein in the initiation and maintenance of epigenetic silencing. Daxx acts as a scaffolding protein to recruit DNA methyltransferases (DNMTs) and histone deacetylases (HDACs) to avian sarcoma virus (ASV) DNA via binding to integrase (IN). Bottom- Post-integration repressive marks are depicted as circles. The mechanism by which Daxx is positions on viral DNA to during silencing maintenance is unknow, as indicated by the question mark. Black rectangles = long terminal repeats (LTRs) in retroviral DNA. See: Shalginskikh N. et al. Retroviral DNA methylation ond epigeneic repression are mediated by the antiviral host protein Daxx. J. Virol. 87:2137.2013.

Skalka lab staff, 2015: George Merkel, Kate Buettner, Maria Shubina, Valentina Medvedeva, Richard Katz, Alison Beister, Adam Maynard, Jason Wasserman, Mark Andrake
Marie Estes

Educational Background

• Postdoctoral Fellow, Genetics, Carnegie Insitution, Cold Spring Harbor, NY
• PhD, Candidate, Microbiology, Yale University, New Haven CT, 1959-60
• PhD, Microbiology, New York University Medical School, New York, NY
• BA, Biology, Adelphi University, Garden City, NY, 1959

Memberships

• Editorial Board, Journal of Virology, 1974 - 1985
• NIH Working Group on Safer Hosts and Vectors, (for Recombinant DNA Research), Recombinant DNA Advisory Committee   1976 - 1980
• Editor, Gene, 1976 - 1997
• Member, Memorial Sloan-Kettering Cancer Center,  Standing Committee on Recombinant DNA Research, 1977 - 1979
• NIH Study Section, Experimental Virology, 1977 - 1981
• IUPHAR (International Union of Pharmacology), Representative to the International Congress of Scientific Union's Committee on Genetic Experimentation (COGENE), 1977 - 1985
• Member, American Cancer Society Advisory Committee  on Microbiology and Virology, 1982 - 1985
• Editorial Board, Journal of Molecular and Cellular Biology, 1983 - 1987
• Commissioner, New Jersey State Commission on Cancer Research, (Governor's Appointment), 1983 - date
• Editor, BioEssay, 1984 - 1989
• Editor, Journal of Virology, 1985 – 1989
• Outstanding Woman Scientist Award,  American Association of Women in Science, 1985
• Member, Board of Scientific Counselors for National Institute of Diabetes, Digestive and Kidney Diseases, 1989 - 1993
• Member, General Motors Cancer Research Foundation Awards Assembly, 1989 - 1993
• Chairperson, 1991 Sloan Prize Selection Committee, 1990
• National Cancer Institute, Outstanding Investigator Grant, 1990-1997
• Recipient, Bristol-Myers Squibb Special Unrestricted Grant, Research in Infectious Diseases, 1992-1997
• Member, External Advisory Board, NCI-designated Comprehensive Cancer Center, Albert Einstein College of Medicine, NY, 1992 - 1995
• Member, Selection Committee for Bristol-Myers Squibb Award, Outstanding Achievement in Infectious Diseases, 1992 - 1997
• Chair, Scientific Advisory Board, NCI designated Cancer Center, McArdle Laboratory for Cancer Research, Madison, WI, 1992 - 1999
• Editorial Board, Cancer Research, 1993 – 2005
• Elected, American Academy of Arts and Sciences, 1994
• Chair, Microbiological and Immunological Special Emphasis Panel, Experimental Virology Study Section, 1994 - 1995
• Member, NCI Board of Scientific Counselors, Division of Cancer Treatment, 1994 - 1995
• Editorial Board, Journal of Biological Chemistry, 1994 - 2006
• Member, Selection Committee, Chiron Corporation Biotechnology Research Award, 1995 - 1998
• Member, Scientific Advisory Board, Case Western Reserve University, Center for AIDS Research, 1995 – 2000
• Elected, American Association for the Advancement of Science, 1996
• Member, Naval Research Advisory Committee, 1996 - 2000
• Chairperson, Selection Committee for Bristol-Myers Squibb Award, Outstanding Achievement in Infectious Diseases, 1997 - 1998
• Member, NCI Board of Scientific Counselors for Basic Science, 1997 – 2001
• Elected, American Academy of Microbiology – Board of Governors, 1998
• Elected Fellow, New York Academy of Sciences, 2000
• Vice Chair, New Jersey State Commission on Cancer Research, 2000 - 2005
• Member, United States Department of Defense Science Board, 2000 - 2011
• Member, Scientific Advisory Board, Onconova Therapeutics, Inc, 2001 – date
• Governor Appointed Chair, New Jersey Commission on Cancer Research, 2005 - 2014
• Member, AIDS Molecular and Cellular Biology Study Section (AMCB), 2006 - 2010
• Member, John Scott Award Advisory Committee, 2008 - date
• Outstanding Women of Science Award, N.J. Assoc. Biomedical Research, 2008
• American Cancer Society Scientific Research Award, PA Div, 2008
• Visiting Member, Institute for Advanced Study, Princeton, NJ, 2009 - date
• Co-Organizer, Centennial Retrovirus Meeting. Prague Czech Republic, 2010
• Elected Member, AAAS Nominating Committee, Biological Sciences, 2011 - 2014
• P50 Center Grant Study Section, Washington, DC, 2012
• Elected Member, Committee on Elections to the American Academy of Microbiology, 2012 - 2016

Honors & Awards

• Distinguished Research Award, Center for Retroviral Research, Ohio State University, 2013

Research Program

• Blood Cell Development and Function

Research Interests

Lab Overview

Selected Publications

Additional Publications

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