Defining gene function via the mass spectrometric analysis of multiprotein complexes

Abstract

The in vitro dissection of the life cycle of dendritic cells and of the dynamics of T cell activation has been instrumental to identify some of the critical steps that control the generation of effector and memory T cells. I will first discuss how recruitment of dendritic cells into inflamed tissues, their activation by pathogens and inflammatory cytokines and their migration to secondary lymphoid organs provide the optimal conditions for T cell priming and polarization.In particular I will show that different T cell responses (type 1, type 2 or unpolarized T cells) can be generated by modulating the state of activation of dendritic cells and the duration of the dendritic cell-T cell interaction. I will also discuss the differential roles played by 'central memory' and 'effector memory' T cells in secondary immune responses. References: Lanzavecchia, A., G. Iezzi, and A. Viola. 1999. From TCR engagement to T cell activation: a kinetic view of T cell behavior. Cell Lanzavecchia. 1999. Maturation, activation, and protection of dendritic cells induced by double-stranded RNA. J. Exp. Med. 189821-829. Sallusto, F., D. Lenig, R. Forster, M. Lipp, and A. Lanzavecchia. 1999. Two subsets of memory T lymphocytes with distinct homing potentials and effector functions. Nature 401:708-712. Sallusto, F., C.R. Mackay, and A. Lanzavecchia. 2000. The role of chemokine receptors in primary, effector and memory immune responses. Annu. Rev. Immunol. (2000) 18,593-620 287 From genome sequences to protein functions Box 951570, UCLA, Lor AEgefes CA 90095-1570 USANew computational methods have been developed for assigning protein functions and interactions to genome sequences. These methods make use of information from all fully sequenced genomes and are distinct from standard homology methods. They have been applied to assign functions for roughly half of the previously uncharacterized proteins of Saccharomyces cervisiae and Mycobacterium tuberculosis.The first method is called the phylogenetic profile method; it examines the correlated inheritance of proteins in different species. It is based on the assumption that proteins that evolve in a correlated fashion are likely to function together in a pathway or XNCturd complex. During evolution, such functionally linked proteins tend to be either all preserved or eliminated in a new species. This property of c o r r e k d evohnion is described by characterizing each protein by irr phylogenetic profile, a string that encodes the presence or absence of a protein in every fully squenced genome.Studies show that proteins having matching or similar phylogenetic profiles strongly tend to be functionally linked. Conversely, proteins having similar function tend to have similar phylogenetic profiles. This correlation permits us to assign functions to uncharacterized proteins that have phylogenetic profiles similar to proteins of known function.The second method examines correlated domains in proteins and its termed the Rosetta Stone method. It is based on the observation that some pairs of interac...