Faculty and Research
Faculty by Name
James Berger
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James Berger
Professor of Biochemistry and Molecular Biology*
*And Member, Physical Biosciences Division, Lawrence Berkeley National Laboratory; Member, Biophysics Graduate Program; Member, Chemistry and Biology Graduate Program.
Research Interests
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Our research interests lie in understanding the molecular basis of protein assembly and function. In particular, we aim to develop mechanistic models that explain how proteins physically exploit shape and chemistry to form large complexes and transduce energy into work. The primary focus of my group's investigations is on proteins that replicate, manipulate, and organize nucleic acids in the cell, and on metabolic enzymes required for maintaining nucleic acids in the pathogenic bacterium, M. tuberculosis. A combination of structural analyses, such as X-ray crystallography, small-angle X-ray scattering and EM, coupled with biphysical and biochemical experimentation, forms the core of our methodological approach.
Current Projects
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Replication initiation and replisome assembly. The initiation of DNA replication relies on a multifunctional complement of proteins that coordinately recognize origin sequences, unwind the origin DNA, and assemble the replisome. Initially, phylogenetic analyses suggested that replication factors fall into two general classes, bacterial and eukaryotic/archaeal; however, structural and biochemical data indicate that nearly all of these proteins share fundamental architectural and functional features. To better understand how cells regulate and initiate replication of their genomes, we are studying origin-binding proteins, helicases, primases, and accessory remodeling factors from a variety of organisms within the three cellular domains of life. Work from our group is revealing important information about the mechanisms of origin processing, primer synthesis, and macromolecular assembly that occur during replisome construction. We are now biochemically and structurally dissecting the reaction cycles of these initiation proteins, both individually and complexed with various targets, to better model their molecular activity.
Nucleic acid-dependent motors. The length and double-helical properties of DNA present the cell with topological and information processing challenges. For example, transcription and replication require melting of duplex DNA to read out the coded nucleotide sequence, while chromosomal tangles and knots can arise during replication, recombination, and DNA compaction. To resolve these problems, cells use a host of molecular motor proteins, including type II DNA topoisomerases, helicases, and chromosome-condensation assemblies to modulate and reorganize DNA or RNA superstructure. All of these motor proteins use ATP, but direct it toward different purposes, such as transporting one DNA duplex through a transient break in another, or translocating along a DNA or RNA chain while concomitantally unwinding paired nucleic acid strands. Despite general functional differences, each of these proteins nonetheless uses ATP binding and hydrolysis to trigger cascades of conformational changes that result in motion and force generation. We are currently studying DNA- and RNA-dependent motor proteins from bacterial, archaeal, and eukaryotic organisms. Using structural analyses of different conformational and substrate-bound states, combined with directed biochemical and enzymological studies, we are determining how such proteins interact with nucleic acids and partner proteins, and how they use ATP to drive the architectural changes required for catalysis and physical movement.
Nucleic acid metabolism in Mycobacterium tuberculosis. The bacterium M. tuberculosis is a widespread pathogen that is estimated to have infected nearly a third of the world population. We are working as part of an international consortium to determine the structures of essential proteins that regulate information flow in this organism. A major goal of this work is to produce structural data of essential M. tuberculosis proteins that may be used to speed vaccine and drug design to combat the spread of the pathogen. The efforts in my lab are focused in several areas including RNA metabolism, and DNA replication, segregation, and repair.
Selected Publications
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Skordalakes E., Berger J.M., “Structural Insights into RNA-Dependent Ring Closure and ATPase Activation by the Rho Termination Factor,” Cell, 127:553-64, 2006.
Erzberger J.P., Mott M.L., and Berger J.M., ”Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling,” Nat. Struct. Mol. Biol., 13:676-83, 2006.
Corn, J.E., Pease, P.J., Hura, G.L., and Berger, J.M., “Crosstalk between primase subunits can act to regulate primer synthesis in trans”, Mol. Cell, 20:391-401, 2005.
Fennell Fezzie, R., Gradia, S.D., Akey, D. and Berger, J.M., “The MukF subunit of E. coli condensin: architecture and functional relationship to kleisins,” EMBO J., 24:1924-1930, 2005
Corbett, K.D., Schoeffler, A.J., Thomsen, N.D. and Berger, J.M., “The structural basis for substrate specificity in DNA topoisomerase IV,” J. Mol. Biol., 351:545-561, 2005.
Corbett, K., Schultzaberger, R., and Berger, J.M., "The C-terminal domain of DNA Gyrase A adopts a DNA-bending 'β-pinwheel' fold," Proc. Nat. Acad. Sci. USA, 101:7293-7298, 2004.
Classen, D.S. and Berger, J.M., "Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic, ICRF-187," Proc. Nat. Acad. Sci. USA, 100:10629-10634, 2003.
Skordalakes, E. and Berger, J.M., "Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading," Cell, 114:135-146, 2003.
Last Updated 2006-12-15