Profile of James M. Berger

Whether he is restoring his 1976 Triumph TR6 British roadster or analyzing proteins, James Berger is curious about how machines work and what fuels them. Berger, a professor in the Department of Biophysics and Biophysical Chemistry at Johns Hopkins University School of Medicine, primarily studies biological nanomachines, which are fueled by the cellular energy currency ATP and carry out coordinated mechanical tasks. For more than two decades, his work on molecular machines has shed light on DNA replication and chromosome topology at the atomic level.

Portrait of James Berger. Image courtesy of Keith Weller (Johns Hopkins Medicine, Baltimore).

Applying these endeavors to potential medical applications, Berger and his colleagues have described the function of enzymes underlying chemotherapy targets, research that could lead to more effective anticancer treatments. For example, Berger, a member of the National Academy of Sciences, has analyzed a class of antibiotics known as fluoroquinolones. His team has described the X-ray crystal structures of nine different fluoroquinolone–enzyme–DNA complexes for the Mycobacterium tuberculosis gyrase, a bacterial enzyme that relieves supercoiling in DNA. The findings help to explain the antibacterial resistance of the etiological agent for tuberculosis, a major public health threat. The findings also point to new approaches for overcoming the disease.

Growing Up in the “Cosmos” Era

As a child in Santa Fe, New Mexico, Berger enjoyed watching Carl Sagan’s televised science series “Cosmos,” admiring the host’s ability to explain complex matters using compelling lay language. Berger now uses a similar approach, complete with a toy box of colorful plastic models, when teaching his own students and the public about biophysics and biophysical chemistry. His mother and father were early role models as well. “My parents worked at Los Alamos National Laboratory, so science and appreciation for science was ever-present,” Berger says.

An advanced placement high school course in biology led to him spending a summer working in a research position at Los Alamos. He says, “The generosity and intellect of my host and mentor there, Paul Jackson [who is now at Livermore National Laboratory], cemented my desire to study biochemistry in college.” As an undergraduate in biochemistry at the University of Utah, Berger continued to work summers at the nuclear research facility. Jackson at the time was trying to understand how plants grow in contaminated soils. Biologist David Goldenberg also influenced Berger by fostering interest in proteins and biophysics. Goldenberg additionally allowed the undergraduate to work in his laboratory.

Graduate Work in Crystallography

After graduating summa cum laude from the University of Utah in biochemistry with minors in chemistry and mathematics, Berger went to Harvard University for his graduate studies. He first started his work in the laboratory of biochemist James Wang, who became his thesis advisor. Berger says, “Jim allowed me great freedom to choose my dissertation project [structure determination of a type II topoisomerase by X-ray crystallography] and was endlessly supportive even though a) the project was outside the normal wheelhouse of the lab, and b) it was not at all clear during my first three years in his lab whether I would ever succeed.”

Proteins are inherently fragile and flexible, Berger says, explaining a primary reason he struggled to produce the crystals necessary for the X-ray diffraction tool. His focus was yeast topoisomerase II, an enzyme that alters the supercoiled form of DNA. Stephen Harrison, director of Harvard’s laboratory of structural cell biology, became Berger’s coadvisor. Postdoctoral fellow Stephen Gamblin, now at the Francis Crick Institute, also took Berger under his wing to educate him on the finer details of X-ray crystallography. With their help, Berger eventually determined the structure of the primary DNA-cleaving region of yeast topoisomerase II, otherwise known as topo II (1).

DNA Replication Insights

Following Harrison’s kind urging and support, Berger become a fellow at the Whitehead Institute for Biomedical Research at the Massachusetts Institute of Technology from 1995 to 1998. Working frequently with Peter Kim, who provided invaluable advice on how to develop an independent research program, Berger continued to study the structure of topoisomerases (2) and molecular machinery affecting DNA. After his fellowship, Berger became an assistant professor and later professor of biochemistry and molecular biology at the University of California, Berkeley, where he stayed for 15 years. During his time at the university, he simultaneously worked as a staff research scientist at the Lawrence Berkeley National Laboratory (1999–2013) and served as director of University of California (UC) Berkeley’s Keck Macrolab (2006–2013).

In two articles concurrently published in the journal Nature Structural and Molecular Biology, Berger and colleagues showed that the core machinery for initiating DNA replication is the same for all three domains of life (3, 4). The researchers did so by identifying a helical substructure within a superfamily of proteins, called AAA+ ATPases, as the molecular initiator of DNA replication in the bacteria Escherichia coli, as well as in the eukaryote Drosophila melanogaster. For this and other achievements, Berger received the 2006 American Chemical Society Pfizer Award in Enzyme Chemistry and the 2006 American Society for Biochemistry and Molecular Biology Schering Plough Research Institute Scientific Achievement Award.

Images of Topo II, Bacterial Protein Motors

The following year, Berger and graduate student Ken Dong collected crystallographic data using the Advanced Light Source (ALS) at the Lawrence Berkeley National Laboratory to produce 3D structural images of a DNA-bound topo II that is responsible for untangling coiled strands of chromosomes during cell division. (5) “Topo II has been called nature’s magician because it literally can move one DNA segment through another,” Berger says. Because this enzyme is so critical to DNA transcription and replication, it has long been a prime target of antibacterial and anticancer drugs. The 3D images revealed how topo II binds and bends DNA duplexes.

In 2009, Berger and graduate student Nathan Thomsen again used the ALS to capture the atomic-level action of a type of ring-shaped hexameric motor protein known as the Rho transcription termination factor (6). The researchers determined that in bacteria, this protein motor binds to a specific region of mRNA and translocates along the chain to selectively terminate transcription at discrete points along the genome. Future research may focus on ways of stopping the motor from functioning, thereby hopefully preventing bacterial spread.

In two subsequent papers with other members of his team, Berger explored the function of two ATP-binding proteins, DnaA and DnaC, which help to initiate DNA replication in bacteria (7, 8). The first showed that DnaA melts replication origins by forming a filament that stretches DNA. In the second paper, Berger and colleagues showed that DnaC physically cracks open a ring-shaped, six-subunit helicase, DnaB (helicases are DNA-unwinding enzymes), to promote its loading onto DNA in support of bacterial replication. Following the research, Berger received the National Academy of Sciences Award in Molecular Biology. In 2012, he was elected to the American Academy of Arts and Sciences.

Move to Johns Hopkins

In 2013, Berger and his wife Marian Feldman, an art historian and Near Eastern studies scholar, left their positions at UC Berkeley and joined the faculty at Johns Hopkins University. The decision was not easy for them at first; both enjoyed and greatly valued their time at Berkeley. Feldman has family in Baltimore, however, and Berger appreciated the opportunity Johns Hopkins offered to pair his research with clinical and translational data for potential medical applications.

Such a collaborative effort occurred in 2015, when Berger and colleagues Franziska Bleichart and Michael Botchan studied the origin recognition complex (ORC), a protein complex that directs DNA replication (9). Using the Argonne National Laboratory’s powerful X-ray beam and gathering data from a beamline supported by the National Institute for General Medicine and the National Cancer Institute, the researchers obtained the first atomic-level insight into the ORC. Berger says, “We revealed the overall architecture of the molecular machinery responsible for loading helicases onto replication origins in eukaryotes such as humans, and uncovered new insights into how it accomplishes this task.” The work additionally helps to explain how ORC may be compromised in some individuals with Meier–Gorlin syndrome, a form of dwarfism in humans.

Berger’s Inaugural Article, published in early 2016, again paired clinical data with his ability to study biological nanomachines (10). Fluoroquinolone antibiotics often used to treat tuberculosis and other bacterial infections were the focus of the research. Berger says, “We established why different types of fluoroquinolones differ in the efficiency with which they poison their primary target, a type II topoisomerase known as gyrase. Our findings will hopefully help facilitate efforts aimed at making more specific and efficacious fluoroquinolone derivatives for treating bacterial infections.”

Broadening Scope

Berger and his team continue to examine how dynamic, multiprotein assemblies organize, express, and preserve genetic information in the cell. Their combined structure/function approach to this problem is to increasingly incorporate proteomic, chemical-biological, and biophysical methods to further broaden the scope of their efforts. “Our long-term goal is to try answer fundamental questions, such as how chemical energy is converted into force and motion, and to try to understand how these systems operate at a molecular level of detail, in real-time,” Berger says. “We also hope to begin to address how the formation, activity, and localization of protein/nucleic-acid complexes are regulated in the cell and how these systems can be targeted in some instances by small molecule agents of therapeutic potential.”