Program in Cellular Regulation and Metabolism
Alan G. Hinnebusch, PhD, Program Director
The Program in Cellular Regulation and Metabolism brings together two Laboratories whose investigators apply a combination of genetics, biochemistry, and structural biology to elucidate the molecular basis of processes that are fundamentally important in cell biology or animal development. Four of the eight groups in the Laboratory of Gene Regulation and Development (LGRD), which is headed by Alan Hinnebusch, study transcriptional and translational control of gene regulation, chromosome condensation and segregation, and the transposition of retroelements in budding or fission yeast. Two LGRD groups employ the fruit fly Drosophila to investigate molecular mechanisms in development, including the molecular basis of neuronal connection specificity in the visual system and of cell signaling by TGF-beta factors. The aneuran Xenopus laevis serves as a model system for the work of the other two groups, which focus on chromosome segregation and cell-cycle control and transcriptional programming of organ development during metamorphosis. The Laboratory of Genomic Integrity, headed by Roger Woodgate, studies translesion DNA replication.
Mary Dasso’s Section on Cell Cycle Regulation uses a variety of metazoan systems, including Xenopus laevis egg extracts, to study mitotic roles of the Ran GTPase, the nuclear pore complex (NPC), and the SUMO family of ubiquitin-like proteins. During the past year, analysis of the Ulp/SENP family of SUMO proteases demonstrated that these enzymes play essential roles at mitotic kinetochores as well as in the process of ribosome biogenesis. The Section also uncovered novel roles for NPC components in kinetochore function and spindle assembly.
The Section on Protein Biosynthesis, headed by Thomas Dever, is characterizing the structure and function of several translation initiation factors and the molecular principles of kinasesubstrate recognition by the stress-responsive eIF2a kinases. The Section recently characterized the dimerization-dependent activation of the dual kinase-endoribonuclease IRE1 that catalyzes the splicing of the mRNA encoding the transcription factor HAC1/Xbp1, a key modulator of ER stress and the unfolded protein response.
The Section on Nutrient Control of Gene Expression, headed by Alan Hinnebusch, studies the transcriptional and translational control of amino acid–biosynthetic genes. Recently, the Section identified specific residues of 18S rRNA in the P site of the small (40S) ribosomal subunit involved in recruiting initiator tRNA and AUG recognition, implicating a specific amino acid in the large (60S) subunit protein L33 in subunit joining and gene-specific translational repression of GCN4. The Section also demonstrated that the a/TIF32 subunit of initiation factor 3 (eIF3) interacts with sequences in GCN4 mRNA to stimulate re-initiation by post-termination 40S subunits. In addition, members of the Section provided evidence that SUS1, a subunit of transcriptional co-activator (SAGA) and nuclear export (TREX-2) complexes, plays a pivotal role in transcription elongation and mRNA export.
The Unit on Neuronal Connectivity, headed by Chi-Hon Lee, investigates the structure and development of color-vision circuitry in Drosophila. Recently, the Unit identified the neural substrate of spectral preference. The data indicate that Dm8, a specific amacrine neuron subtype, relays signals from several UV-sensing R7 photoreceptors to projection neurons, thus sacrificing spatial resolution for sensitivity. The Unit also investigated the roles of TGF-beta/Activin signaling in regulating synaptogenesis between R7 photoreceptors and their target neurons.
Henry Levin heads the Section on Eukaryotic Transposable Elements, which analyzes long term repeat retrotransposons and the integration of their cDNA into the chromosomes of host cells. Recently, the Section demonstrated that the preferential insertion of Tf1 into the 5′ regions of genes results from the recognition of sequences within the promoter. In the case of the fbp1 promoter, the Section found that integration occurred at the binding site for the transcription factor Atf1p and that the binding of Atf1p was required for integration. In addition, the Section’s recent study of Tf1 integrase revealed that the C-terminal chromodomain plays an important role in directing integration to pol II promoters.
The Unit on Cellular Communication, headed by Mihaela Serpe, uses the Drosophila system to investigate molecular mechanisms that regulate cellular signaling during development. The Unit focuses primarily on signaling by TGF-beta factors and on genes that modulate the function and distribution of the signaling ligands in time and space. The Unit’s studies have shown that secreted BMP-binding proteins such as Short gastrulation and Crossveinless-2 (Cv-2) have versatile effects on signaling and, depending on context, promote or inhibit signaling. Cv-2 binds to cell surfaces and forms a transient complex with BMP and the type I receptor. Through this complex, Cv-2 at moderate levels stimulates signaling by recruiting BMPs from the extracellular space onto receptors while Cv-2 at higher levels antagonizes signaling by sequestering BMPs.
The Section on Molecular Morphogenesis, headed by Yun-Bo Shi, studies the gene-regulatory mechanisms controlled by the thyroid hormone receptor (TR) that establish the developmental program of metamorphosis. The Section has demonstrated that TR is necessary and sufficient for metamorphosis; unliganded TR recruits co-repressors to control metamorphic timing, and liganded TR recruits co-activators for metamorphosis progression. The Section has also studied the roles of TR-regulated matrix metalloproteinases in extracellular matrix remodeling and cell-fate determination during metamorphosis.
Alexander Strunnikov’s Unit on Chromatin Structure and Function is studying SMC protein complexes, particularly the role of the condensin complex in mitotic chromosome condensation and segregation. Recently, the Unit characterized mitosis-specific sumoylation of condensin in yeast and demonstrated that it cooperates with sumoylated topoisomerases in rDNA and nucleolar chromatin. Using human cells, the Unit analyzed the structure of condensin-defective centromeres and kinetochores biochemically, genetically, and cytologically. The loss of condensin resulted in both depletion of CENP-A and a high incidence of merotelic attachments. The studies indicate that human condensins play a pivotal role in the proper spatial positioning of the kinetochore relative to the microtubule-regulating protein complexes in the inner centromere.
Scientists in the Laboratory of Genomic Integrity, headed by Roger Woodgate, are studying the mechanisms by which mutations are introduced into damaged DNA. Many of the proteins long implicated in the mutagenic process are now known to be low-fidelity DNA polymerases that can replicate past damaged DNA in a process termed translesion DNA synthesis (TLS). In the past year, experiments aimed at understanding TLS have spanned the evolutionary spectrum and include characterization of DNA polymerase switching in E. coli; interactions between archaeal Dpo4 and PCNA; and the in vivo and in vitro characterization of the eukaryotic TLS DNA polymerases eta, iota, and kappa.