Amy Lee Joins Biology Faculty

On August 1, Amy Lee joined the Biology department as an Assistant Professor. Previously, Amy was an American Cancer Society Postdoctoral Scholar in Jamie Cate’s lab at University of California, Berkeley. She received her Ph.D. in Virology from Harvard University in Sean Whelan’s lab and her Bachelors of Science in Biology from Massachusetts Institute of Technology.


eIF3d structure, see Figure 2 at

Amy’s research focuses on understanding how gene regulation shapes cell growth and differentiation, and how dysregulation leads to human diseases like carcinogenesis and neurodegeneration. She is interested in discovering new mechanisms of mRNA translation initiation and novel functions of RNA-binding proteins and eukaryotic translation factors. Her research combines genome-wide and computational approaches together with molecular genetics, cell biology, biochemistry, and structural biology techniques.

Amy recently published a paper in Nature together with the Jamie Cate, Jennifer Doudna, and Philip Kranzusch describing the discovery of a new translation pathway that controls the production of proteins critical to regulating the growth and proliferation of cells. Cancer is characterized by uncontrolled cell growth, which means the protein production machinery goes into overdrive to provide the building materials and control systems for new cells. Hence, biologists for decades have studied the proteins that control how genes are transcribed into mRNA and how the mRNA is read and translated into a functioning protein. One key insight more than 40 years ago was that a so-called initiation protein must bind to a chemical handle on the end of each mRNA to start it through the protein manufacturing plant, the ribosome. Until now, this initiation protein was thought to be eIF4E (eukaryotic initiation factor 4E) for all mRNAs.

Amy and her colleagues discovered that for a certain specialized subset of mRNAs – most of which have been linked somehow to cancer – initiation is triggered by a different protein, called eIF3d. The finding was a surprise because the protein is part of an assembly of 13 proteins called eIF3 -eukaryotic initiation factor 3 – that has been known and studied for nearly 50 years, and no one suspected its undercover role in the cell. This may be because eIF3’s ability to selectively control mRNA translation is turned on only when it binds to the set of specialized mRNAs. Binding between eIF3 and these mRNAs opens up a pocket in eIF3d that then latches onto the end-cap of mRNA to trigger the translation process. Subsequent X-ray crystallography of eIF3d revealed the structural rearrangements that must occur when eIF3 binds to the mRNA tag and which open up the cap-binding pocket. eIF3d thus presents a promising new drug target in cancer, as a drug blocking this binding protein could shut off translation of only the growth-promoting proteins and not other life-critical proteins inside the cell.

Lee AS, Kranzusch PJ, Doudna JA, Cate JH. eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation. Nature. 2016.


Deciding the fate of a stalled RNA polymerase

Ever wondered what happens when the transcription machinery runs into a DNA lesion or a protein roadblock? Alexandra M. Deaconescu, corresponding author and research associate in the Grigorieff laboratory together with HHMI Investigator and Biochemistry Professor Dr. Nikolaus Grigorieff and Dr. Irina Artsimovitch (Ohio State University) address this question in a new review “Interplay of DNA repair with transcription: from structures to mechanisms” featured in the latest issue of Trends in Biochemical Sciences. The review describes emerging mechanisms of transcription-coupled DNA repair with emphasis on the bacterial system.

Unraveling mutations in pediatric brain cancer

Medulloblastoma is the most common malignant brain tumor of childhood, with an overall mortality of 40 to 50 percent. Surviving children often have significant long-term cognitive and physical sequelae resulting from existing treatments. Therefore, identifying and understanding the genetic events that drive these tumors is critical for the development of more effective therapies.

In the 2 August issue of the journal Nature, Brandeis Biochemistry faculty member Daniel Pomeranz Krummel contributed his structural biological expertise in collaboration with colleagues at Children’s Hospital Boston, Dana-Farber Cancer Institute, Harvard University, the Broad Institute (MIT), Stanford and the Hospital for Sick Children in Toronto. The paper titled, “Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations,” unravels a landscape of mutations that are peculiar to medulloblastomas. This paper represents a landmark study of medulloblastomas. More specifically, Pomeranz Krummel’s collaborators noticed that a protein called DDX3X had numerous mutations in medulloblastoma. Pomeranz Krummel was able to create a structural model of DDX3X that provided insight into the functional significance of the critical mutations in children with medulloblastoma (below, image).

DDX3X is an ATP-dependent RNA helicase. RNA helicases are fascinating proteins that function to drive the restructuring of RNA and/or RNA-protein assemblies, and have proven to be of great importance in cancer biology and HIV research. Pomeranz Krummel’s long-standing interest is in RNA-protein interactions and application of methods to visualize the enzymes critical to processing of RNA in the human cell. Thus, thinking about the structure-function relationship of this RNA helicase DDX3X was a problem of much interest to Pomeranz Krummel. This collaboration involved forging links between basic and translational scientists, thus giving rise to promising new horizons of treatment options for children with medulloblastoma.



Children’s Leukemia Research Award to Fund Myosin Research

(from left to right) Director of Rosenstiel Center Jim Haber, Professor Carolyn Cohen, Dr. Jerry Brown, Anthony Pasqua, President of the Childrens Leukemia Research Association

On April 24, a Children’s Leukemia Research Association (CLRA) award was presented to Jerry Brown, a Senior Research Scientist who works with Carolyn Cohen at the Rosenstiel Basic Medical Sciences Research Center. The award will help fund research on structures of α-helical coiled-coils, in particular those from myosin implicated in certain leukemias. The α-helical coiled coil is a common dimerization motif in proteins and is implicated in many normal physiological as well as pathological processes. Many cases of acute myeloid leukemia involve the aberrant fusion of the transcription factor, CBFβ, to a long portion of the smooth muscle myosin rod, which is predicted from its amino acid sequence to form an α-helical coiled coil. A major aim of the proposed research is thus to crystallize and determine the atomic structures of the segment of the myosin rod nearest this fusion point, both in its normal unfused physiological state and when aberrantly fused to CBFβ. A related aim of the research is to understand how the conformations of α-helical coiled coils in general are affected by attached structures. Accomplishment of these aims may provide a structural basis for the rational design of drugs that can selectively disrupt the activity of the pathologically fused protein.

In addition to Dr. Brown and Professor Cohen, the award presentation was attended by their laboratory researchers Senthil Kumar, Ludmila Reshetnikova, and Elizabeth O’Neall-Hennessey, Rosenstiel Director James Haber, Brandeis Office of Research Administration Associate Director Patricia McDonough, Rosenstiel Department Operations Manager Anahid Keshgerian, CLRA President Anthony Pasqua, his daughter Susan (Pasqua) Bogue, a survivor of leukemia, and Nancy Golden and three of her children.   The award is named after another daughter of Nancy Golden, Amy Golden Uleis, who lost her battle with cancer at age 52 and was a graduate of Brandeis. The award presentation was accompanied by a photo-op and a small reception held at Rosenstiel.

Protein Flexing: A New Look at Transcription-Coupled DNA Repair

Alexandra M. Deaconescu, a research associate in the Rosenstiel Basic Medical Sciences Research Center and 2008-2010 Fellow of the Damon Runyon Cancer Research Foundation, together with Professor of Biochemistry and HHMI Investigator Nikolaus Grigorieff and collaborators in the Laboratory of Dr. Irina Artsimovitch at Ohio State University have just published a new study in PNAS, which delineates novel mechanistic details of transcription-coupled DNA repair.

In any cell, there is intense interplay between various DNA-based transactions, such as replication, transcription and DNA repair. More than twenty years ago, it was discovered that DNA lesions that cause stalling of RNA polymerase molecules elicit a form of preferential nucleotide excision repair (NER) that exists in both eubacteria and eukaryotes, and specifically targets the transcribed DNA strand. Termed transcription-coupled DNA repair (TCR), the process is found to be carried out in bacteria by an ATPase called Mfd or TRCF (see Figure, right). In TCR, TRCF performs two functions: 1) it recognizes a damage-stalled RNA polymerase (RNAP), then dissociates it off the DNA using energy derived from ATP hydrolysis and 2) it recruits DNA repair enzymes via binding to the UvrA subunit of the Uvr(A)BC NER machinery [1].   The Uvr(A)BC machinery is one of the main players in bacterial DNA repair, and distinguishes itself from other DNA repair proteins by its ability to repair a remarkably diverse repertoire of lesions by utilizing a “cut and patch” mechanism, whereby an oligonucleotide containing the damage is excised and the gap later filled.

The cellular role of TRCFs extends beyond TCR. Because of their ability to forward translocate and dissociate stalled RNAPs (or  “backtracked” RNAPs that have slid backwards on the template) [2], TRCFs are also involved in transcription elongation regulation [3, 4], resolution of head-on collisions of the transcription apparatus with the DNA replication machinery [5], and antibiotic resistance [6, 7]. In humans, the effects of impaired TCR are systemic and complex. Mutations in the transcription-repair coupling factor CSB lead to Cockayne Syndrome [8], a progeroid (accelerated-aging) disease characterized by severe developmental abnormalities and neurodegeneration, and whose etiology is currently poorly understood.

To elucidate the mechanism underpinning UvrA recruitment by TRCF, Deaconescu crystallized and solved the X-ray structure of a core UvrA-TRCF complex (Figure, left) demonstrating that UvrA binding involves unmasking of a conserved intramolecular surface within TRCF via a gating motion of the C-terminal domain (red in Figure above). Despite significant effort so far, Deaconescu is still trying to coax nucleotide-bound TRCF to form crystals suitable for X-ray diffraction. These would be highly informative because ATP is required for DNA binding, and its hydrolysis leads to TRCF translocation on dsDNA and ultimately release of RNAP off the damaged template.  Because diffracting crystals eluded her, and to further find out how ADP/ATP modulate the structure of TRCF, Deaconescu learned small-angle X-ray scattering techniques suitable for probing TRCF in solution in the absence and presence of nucleotides, thus circumventing the need for highly-ordered crystals. Then, the Brandeis team and their collaborators at Ohio State employed domain-locking disulfide engineering in conjunction with functional assays to gain a deeper understanding of what TRCF looks like during its catalytic cycle and upon binding to UvrA.  They find that the two main functions of TRCF (RNAP release and UvrA binding) can be uncoupled, suggesting that UvrA recruitment may only occur during/post RNAP release, and not upon RNAP binding as had been proposed earlier in the literature [9]. Furthermore, they show that the ternary elongation complex (consisting of RNAP, template and nascent RNA), but not naked DNA, significantly stimulates ATP hydrolysis by TRCF. Thus, bacterial TRCF operates in a manner reminiscent of that utilized by eukaryotic chromatin remodeling factors, and are preferentially stimulated by nucleosomes over naked DNA substrates.

Deaconescu previously “looked” at TCR using X-rays – as a graduate student she solved the first structure of an intact transcription-repair coupling factor from any organism using X-ray crystallography [10]. She now hopes to reconstitute the larger intermediates that form during TCR and bridge low- with high-resolution information using hybrid structural methods, particularly electron cryo-microscopy, and ultimately formulate a cogent model of how TRCFs operate in cells.

“Similar differences”: radial spokes are different from each other, but conserved across species

Eukaryotic cilia and flagella are highly conserved organelles present on the surfaces of many animal cells and protists. These organelles are important for cell motility and/or sensing of the environment. Virtually all motile cilia and flagella share the same microtubule-based core structure, the axoneme, composed of nine doublet microtubules (DMTs) surrounding a central pair of singlet microtubules known as the central pair complex (CPC) (Fig. 1). Structurally, each DMT is built from many copies of a 96 nm-long unit that repeats along the longitudinal DMT axis (Fig. 1A). The proper assembly and function of the components of these repeat units are necessary for the generation of the characteristic wave form of ciliary and flagellar movement. Mutations in these components have been linked to various human diseases termed ciliopathies.

”]Important components of the 96 nm repeat unit include the dyneins – molecular motors that convert chemical energy into motion – and complexes that regulate dynein activity, such as radial spokes (RSs) and the Nexin-Dynein Regulatory Complex (N-DRC). The dyneins are arranged in two rows: the inner-dynein arms (IDAs) and the outer-dynein arms (ODAs) (Fig. 1B). All dynein motors are permanently anchored on one DMT and generate force by walking along the neighboring DMT, causing both DMTs to slide against one another. Connections between neighboring DMTs, e.g.the nexin links, restrict this sliding motion between DMTs and transform it into the bending motion typical of cilia and flagella. Dynein motors can only move in one direction: towards the minus end of the DMT. Consequently, dyneins on one side of the axoneme cause the axoneme to bend in one direction, whereas dyneins on the opposite side of the axoneme cause it to bend in the opposite direction (Fig. 1B).

Figure 1 (right): A) Model of the 96nm axonemal repeat containing important regulatory structures. B) An overview of the axoneme in cross section. C and D) Axoneme bending in opposing directions is achieved by alternating activation of dynein motors between opposing DMT subsets. [Heuser et al., 2009]

To generate the characteristic flagellar beating patterns, only subsets of dyneins must be active at any given time. If the dyneins were all active at once, this would put the cilia and flagella in a rigor-like state, as opposite sides of the axoneme would be trying to bend in opposing directions. Precise regulation of  dyneins present on subsets of DMTs is thus required to achieve a normal beating pattern. The current model for how cilia and flagella achieve such regulation is that the dyneins receive chemical and mechanical cues from the CPC, through the RSs, to the IDAs or through the N-DRC and the I1-dynein complex to the ODAs. The RSs are key players in this signaling pathway that regulates motility. Previously, classical electron microscopy studies have described RSs as T-shaped structures that are present either as pairs (termed RS1 and RS2; e.g. in Chlamydomonas) or triplets (termed RS1, RS2, and RS3; e.g. in mammalian cilia, sea urchin flagella, and Tetrahymena).  It was thought that RSs within pairs or triplets were all structurally identical. Recently, however, the Nicastro group and collaborator Elizabeth Smith’s lab at Dartmouth University demonstrated that RS1 and RS2 (green and blue in Fig. 2 bottom) of the RS pair in Chlamydomonas exhibit heterogeneity, i.e. their docking to the DMT and the structure of their bases are different, suggesting different roles in motility regulation (Barber et al., 2012; Dymek et al. 2011).

The Nicastro lab at Brandeis University aims at understanding the structure and function of cilia and flagella. Using state-of-the-art structural methods, such as cryo-electron tomography and sub-tomogram averaging, the Nicastro lab is visualizing the axonemes of different model organisms such as protists (e.g. the bi-flagellated alga Chlamydomonas or the ciliate Tetrahymena with thousands of cilia) and metazoa (e.g. sea urchin sperm flagella) at unprecedented detail (Nicastro et al. 2006; Heuser et al. 2009).

In a new study, Dr. Jianfeng Lin (a post-doc in the Nicastro lab) and his colleagues from the Nicastro lab have revealed a remarkably distinct RS heterogeneity that is highly conserved across species (Fig. 2) (Lin et al., 2012). At a resolution of 3.6 nm, it became obvious that RS3 (orange in Fig. 2 top) is structurally unique; bearing no resemblance to RS1 and RS2 (green and blue in Fig. 2 top). In comparison to RS1 & 2, RS3 is larger in mass, and has a bulkier and irregular shape, including the RS head, which consists of two rotationally symmetric halves in RS1 & 2, but is asymmetric in RS3 (Fig. 2 top).

Figure 2 (left): Top) Isosurface renderings of RS1 (green), RS2 (blue) and RS3 (orange) in sea urchin sperm flagella. Center) Cross section model of a sea urchin sperm flagellum displaying doublet specific features of the RSs. Bottom) Isosurface renderings of RS1 (green), RS2 (blue) and RS3S (orange) in Chlamydomonas flagella.

Perhaps the most intriguing structural difference observed was that RS3 exhibits features which are specific to only some of the nine DMTs, so called doublet-specific features (Fig. 2 center). For example, a structure termed the Radial Spoke Joist (RSJ) is only present on DMTs 3, 4, and 7-9 (magenta in Fig. 2 center). These features seem to act as a triad that connects three major regularory complexes, RS2, RS3, and the N-DRC. The doublet-specific features observed on RS3 suggest that RS3 plays a unique and currently unknown role in generating typical cilia and flagella beating patterns in sea urchin flagella and Tetrahymena cilia.

Although the Chlamydomonas axoneme contains only RS pairs, it does possess a structure that occupies the same site in each axonemal repeat that a third RS would occupy in organisms with RS triplets (orange in Fig. 2 bottom). This structure was termed the RS3-stand in (RS3S) by Barber et al. (2012). A comparison of the Chlamydomonas RS3S to RS3 in RS triplets revealed that the basal region of RS3 and the entire RS3S are virtually identical in structure (Fig. 2), suggesting that the RS3S is a shorter homolog of RS3 (Lin et al., 2012).

Although past proteomic studies identified the protein composition of the Chlamydomonas RS pair, i.e. of RS1 & 2, the new data suggest that the proteome of RS3 has yet to be determined. RS3 may play a novel role in regulating ciliary and flagellar motility and determining its protein composition in future studies should provide valuable clues to its function.

Reference: Nicastro et al. (2006) Science 313: 944-8; Heuser et al. (2009) J Cell Biol 187: 921-33; Dymek et al. (2011) Mol Biol Cell 22: 2520-31; Barber et al. (2012) Mol Biol Cell 23: 111-20; Lin et al. (2012) Cytoskeleton [Epub ahead of print].

Quantitative Biology Bootcamp 2012

What do dinosaur DNA, calculating the global amount of carbon dioxide consumed in photosynthesis, and cooperation and cheating between yeast cells have in common?  They were all topics discussed at the sixth annual Quantitative Biology Bootcamp, held on the Brandeis campus January 12 and 13.

At the bootcamp, more than 40 Ph.D. students and faculty participated in lectures, discussions, and computational projects using both computers and pencil-on-paper approaches.  The Brandeis Quantitative Biology Program is a unique “add-on” graduate program open to students in all six of the natural sciences Ph.D. programs at Brandeis.  The main goal of the program is to train students to work effectively as a part of research teams that span the boundaries of traditional scientific disciplines.  To this end, Quantitative Biology students participate in both courses and out-of-classroom activities, like the Bootcamp, that highlight the diverse approaches to scientific problems taken by scientists from different disciplines.

A central feature of this year’s Bootcamp were the lectures and computer laboratory exercise presented by Jeffrey Boucher, a student in the Biochemistry Ph.D. program and the winner of Quantitative Biology Program’s 2012 HHMI Interfaces Scholar Award.  Boucher’s presentations described mathematical techniques and experimental methods that can be used to understand the processes of biological evolution by reconstructing genes and proteins present in the long-extinct progenitors of present animal, plant and microbial species. Prospective graduate students and others interested in learning more about Brandeis Quantitative Biology can consult the program’s web site at

Otten named Damon Runyon Fellow

Renee Otten, a postdoctoral fellow in the Kern lab at Brandeis, has been awarded a November 2011 Damon Runyon Fellowship to support his postdoctoral research. Otten received his Ph.D. in 2011 from the University of Groningen, working on applying NMR spectroscopic methods to studying the relationship between protein structure and dynamics. The fellowship will support his continued efforts to use NMR to study dynamics and enzyme catalysis in protein kinases.

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