Contact Information:

Dept. of Microbiology and
Molecular Genetics

Division of Microbiology

NEPRC

Harvard Medical School

One Pine Hill Drive

Southborough, MA 01772

USA

phone: 508-624-8041

fax: 508-786-3317

welkin_johnson@hms.harvard.edu

Research Summary

The genomes of all metazoan species are riddled with the remnants of ancient retroviral epidemics in the form of integrated proviruses.  These DNA “fossils” are a testament to the great adaptability of the retroviridae and serve as proof that the lineages of all living species have been subject to retroviral onslaughts for tens of millions of years.  Although we are generally not aware of it, when we study infection and replication of retroviruses in cells we are studying relationships that have been fine-tuned by millions of years of co-evolution of retroviruses and their animal hosts.

In our laboratory we specifically want to understand how the primate lentiviruses, including HIV-1 and its cousins, the simian immunodeficiency viruses (SIV), accomplish the feat of continuous, long term replication in hosts that are, at least initially, fully competent to mount virus-specific immune responses.  Our focus at this time is on understanding the antibody-resistant phenotype displayed by primary isolates (viruses isolated directly from patients or animals with little or no adaptation to tissue culture), bringing to bear on the problem techniques of molecular and cellular biology, recombinant antibody technology, tissue culture, surface plasmon resonance (SPR) and phage-display.  The hope is to identify the adaptations that permit these viruses to replicate in spite of vigorous antiviral antibody responses, and to apply this knowledge to the rational design of vaccine immunogens or viral entry inhibitors.  

We are also interested in identifying and studying non-immunologic genes that influence inherent susceptibility to infection and cross-species transmission of retroviruses.  One recently discovered host factor that affects retroviral replication in cultured cells is the TRIM5α protein.  We have found that the TRIM5 locus of old world monkeys is highly polymorphic, suggesting that this locus is evolving under the influence of balancing selection (selection that maintains equilibrium between two or more functionally distinguishable alleles). In striking contrast, the human TRIM5 locus appears to be relatively monomorphic, a condition that may well have contributed to the extent and severity of the AIDS pandemic.  The classic examples of loci operating under balancing selection are genes of the major histocompatibility complex (MHC).  Highly polymorphic sites in MHC class I and class II proteins, for example, define individual binding pockets for key residues in the processed peptides that constitute CTL epitopes.  By analogy, we hypothesize that polymorphic sites in primate TRIM5α homologues represent residues that govern specificity for target structures on virions.  Thus, the use of comparative genomics and population genetics is helping us reconstruct the evolution of the TRIM5 locus while at the same time providing us with hypotheses and raw material for molecular dissection of TRIM5α function.  This approach, which combines molecular genetics, phylogenetics and molecular virology, will also serve as a template for future investigation of other loci that influence viral replication and disease progression. 

Selected Reading

Newman et al.2006. Balancing selection and the evolution of functional polymorphism in Old World monkey TRIM5alpha. Proceedings of the National Academy of Sciences 103(50) 19134-19139.  The paper describes our initial phylogenetic and functional analyses of polymorphic variants in old world monkey orthologues of the antiviral factor TRIM5alpha.

Johnson, W. E., Desrosiers, R. C. 2002. Viral persistance: HIV's strategies of immune system evasion. Annual Review of Medicine 53: 499-518.  This is an overview of immune evasion mechanisms used by the immunodeficiency viruses, with an emphasis on comparisons between HIV and SIV.

Johnson, W.E. and Coffin, J.M.1999. Constructing Primate Phylogenies from Endogenous Retrovirus Sequences. Proceedings of the National Academy of Sciences 96(18):10254-60.  This paper describes the novel properties of ancient retrovirus sequences, such as those found in the human genome, and how these are useful for reconstructing evolutionary history.

Yuste, E., Sanford, H.B., Carmody, J., Bixby, J., Little, S., Zwick, M., Greenough, T., Burton, D.R., Richman, D.D., Desrosiers, R.C., Johnson, W.E. 2005. Simian Immunodeficiency Virus Engrafted with HIV-1 Specific Epitopes: Replication, Neutralization, and Survey of HIV-1-Positive Plasma. Journal of Virology: In Press (March ’06).  A unique approach to understanding the neutralizing antibody response using SIV strains engrafted with HIV-1-specific epitope structures.