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James M. Berger
James M. Berger
Biophysics and Biophysical Chemistry
725 N. Wolfe Street
Baltimore MD 21205
Structural and molecular mechanisms of nucleic-acid machines and assemblies; control of DNA replication and chromosome superstructure
Research Interests: My laboratory's research is focused on understanding how multi-subunit assemblies use ATP for overcoming topological challenges within the chromosome and controlling the flow of genetic information. We are particularly interested in developing mechanistic models that explain how macromolecular machines transduce chemical energy into force and motion, and in determining how cells exploit these complexes and their activities for regulating the initiation of DNA replication, chromosome superstructure, and other essential nucleic acid transactions. Our principal approaches rely on a variety of structural, biochemical, and biophysical methods to define the architecture, function, evolution, and regulation of biological complexes. We also have extensive interests in mechanistic enzymology and the study of small-molecule inhibitors of therapeutic potential, the development of chemical approaches to trapping weak protein/protein and protein/nucleic acid interactions, and in using microfluidics for biochemical investigations of protein dynamics and structure.
Ongoing project areas:
Replication initiation and replisome assembly. The initiation of DNA replication relies on a large and multi-faceted complement of proteins that coordinately recognize origin sequences, unwind the origin DNA, and assemble the replisome. Initially, phylogenetic analyses suggested that replication factors fell into two general classes, bacterial and eukaryl/archaeal; however, structural and biochemical data have since indicated that nearly all initiation proteins share certain 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 biochemically and structurally dissecting the reaction cycles of these initiation proteins, both individually and complexed with various targets, to better understand their molecular and cellular function.
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, helicase/translocases, and chromosome-condensation assemblies to modulate and reorganize DNA or RNA superstructure. Many of these proteins utilize ATP, but direct it toward different purposes, such as transporting one DNA duplex through a transient break in another, or moving along a DNA or RNA chain while concomitantly unwinding paired nucleic-acid strands. Despite such significant 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 a variety of DNA- and RNA-dependent motor proteins. Using structural and solution-based 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.
Bleichert F, Botchan MR, Berger JM. Mechanisms for initiating cellular DNA replication. Science. 2017 Feb 24;355(6327).
Thomsen ND, Lawson MR, Witkowsky LB, Qu S, Berger JM. Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor. Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):E7691-E7700.
Lawson MR, Dyer K, Berger JM. Ligand-induced and small-molecule control of substrate loading in a hexameric helicase. Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):13714-13719.
Hood IV, Berger JM. Viral hijacking of a replicative helicase loader and its implications for helicase loading control and phage replication. Elife. 2016 May 31;5.
Arias-Palomo E, Berger JM. An Atypical AAA+ ATPase Assembly Controls Efficient Transposition through DNA Remodeling and Transposase Recruitment. Cell. 2015 Aug 13;162(4):860-71.
Bleichert F, Botchan MR*, Berger JM* (*co-corresponding authors). “Crystal structure of the eukaryotic origin recognition complex.” Nature. 2015 519:321-6.
Costa A, Renault L, Swuec P, Petojevic T, Pesavento JJ, Ilves I, MacLellan-Gibson K, Fleck RA, Botchan MR*, Berger JM* (*co-corresponding authors). “DNA binding polarity, dimerization, and ATPase ring remodeling in the CMG helicase of the eukaryotic replisome.” Elife. 2014 3:e03273.
Vos SM, Lyubimov AY, Hershey DM, Schoeffler AJ, Sengupta S, Nagaraja V, Berger JM. “Direct control of type IIA topoisomerase activity by a chromosomally encoded regulatory protein.” Genes Dev. 2014 28(13):1485-97.
Arias-Palomo E, Puri N, O'Shea Murray VL, Yan Q, Berger JM. Physical Basis for the Loading of a Bacterial Replicative Helicase onto DNA. Mol Cell. 2019 Apr 4;74(1):173-184.
Lawson MR, Ma W, Bellecourt MJ, Artsimovitch I, Martin A, Landick R, Schulten K, Berger JM. Mechanism for the Regulated Control of Bacterial Transcription Termination by a Universal Adaptor Protein. Mol Cell. 2018.
Bleichert F, Leitner A, Aebersold R, Botchan MR*, Berger JM* (*co-corresponding authors). Conformational control and DNA-binding mechanism of the metazoan origin recognition complex. Proc Natl Acad Sci U S A. 2018;115(26):E5906-E5915.
Wendorff TJ and Berger JM. Topoisomerase VI senses and exploits both DNA crossings and bends to facilitate strand passage. Elife. 2018, Mar 29;7. PMCID: in progress