CELL BIOLOGY AND METABOLISM PROGRAM
The Program in Cell Biology and Metabolism conducts studies in various areas of molecular cell biology, including mechanisms of intracellular protein trafficking and organelle biogenesis, adaptive responses to environmental stresses, regulation of the cell cycle during oogenesis, liver cell physiology, and biology of small non-coding RNAs and small proteins. A salient feature of the program is its outstanding capabilities in state-of-the-art fluorescence microscopy techniques, which include cell imaging in real time, photobleaching, fluorescence resonance energy transfer, and fluorescence correlation spectroscopy. We have greatly enhanced our imaging capabilities with the development of photoactivated localization microscopy (PALM). In addition, the program operates facilities that permit work with many model organisms, including bacteria, yeast, Drosophila, mice, and mammalian cells. The knowledge gained from the study of basic cellular processes elucidates the causes of human diseases, including disorders of protein trafficking and bile acid secretion, as well as neurodegeneration and viral pathogenesis.
The Unit on Cell Polarity, headed by Irwin Arias, studies the mechanisms responsible for selective trafficking of proteins to the apical domain of hepatocytes and other polarized cells. The unit’s main goals are to identify components and regulation of these processes, their role in creating and maintaining cellular polarity, and molecular defects responsible for heritable and acquired bile secretory failure (cholestasis). The unit has discovered the importance of rab11a and myosin Vb in canalicular formation and maintenance and of the myosin light chain for apical trafficking of ABC-type transporters. The unit also developed and characterized novel systems for long-term culture of hepatocytes and four-dimensional live-cell imaging of polarized epithelial cells.
The Section on Intracellular Protein Trafficking, led by Juan Bonifacino, has continued its work on the molecular machinery involved in protein sorting to endosomes and lysosomes. The section showed that two accessory proteins named p56 and GAK cooperate with clathrin adaptors in the sorting of mannose 6-phosphate receptors and their cargo lysosomal hydrolases from the Golgi complex to endosomes. In addition, the section defined the subunit composition, structure, and regulation of a protein complex named retromer, which is involved in the retrieval of unoccupied mannose 6-phosphate receptors from endosomes to the Golgi complex. Finally, the group contributed to the elucidation of the mechanism by which the Nef protein of HIV-1 downregulates the CD4 co-receptor.
The Unit on Protein Biogenesis, led by Ramanujan Hegde, has continued its investigations into the trafficking of newly synthesized secretory and membrane proteins. A notable advance this past year was the discovery of the first component (named TRC40) of a novel membrane protein insertion pathway for tail-anchored proteins. These proteins play critical roles in virtually all aspects of cell biology. Hence, the recently discovered novel protein-sorting pathway will likely be recognized for its fundamental importance in normal cellular function. The unit is now using TRC40 to identify additional components of the pathway. In parallel work, the unit identified a new protective pathway, termed pre-emptive quality control (pQC), that attenuates the adverse consequences of protein misfolding in the endoplasmic reticulum. The unit is now examining the importance of pQC in mouse models of neurodegeneration and is identifying the molecular basis of the pathway in vitro.
The Unit on Cell Cycle Regulation, headed by Mary Lilly, has continued to explore the developmental regulation of the cell cycle. The unit’s researchers have shown that the p27-like Cdk inhibitor (CKI) Dacapo promotes genomic integrity during pre-meiotic S phase by facilitating the licensing of DNA replication origins. The work demonstrated that CKIs commonly function during both mitosis and meiosis to promote genomic stability. In addition, the laboratory continued to study the pathways that coordinate meiotic progression with gamete differentiation during oogenesis. To this end, the unit initiated genetic screens to identify genes that regulate the highly conserved prophase I meiotic arrest. The unit also determined that the missing oocyte gene, which is required for the maintenance of the meiotic cycle, interacts both genetically and biochemically with components of the nuclear pore complex.
Jennifer Lippincott-Schwartz’s Section on Organelle Biology has continued to investigate new features of numerous cellular processes by using novel fluorescence imaging approaches combined with quantitative analysis and mathematical modeling. Among the areas of interest are (1) membrane partitioning and its role in protein sorting and transport in the Golgi apparatus; (2) biogenesis and turnover of peroxisomes; (3) mitochondrial morphology and its regulation of cell cycle progression; (4) control of primary cilia dynamics; (5) intercellular transfer between stem and niche cells; (6) origin of autophagosomes; (7) live cell photoactivation localization microscopy (PALM) for single-particle tracking; and (8) cytoskeletal and endomembrane crosstalk in three-dimensional polarized cells and developing Drosophila syncytial blastoderm embryos.
The Section on Environmental Gene Regulation, headed by Gisela Storz, has continued its studies of small, non-coding RNAs in E. coli. Many of these bacterial RNAs act analogously to eukaryotic miRNA and siRNAs to regulate mRNA stability and translation. Along with identifying additional noncoding RNAs and characterizing their functions, the section has helped develop general tools for the study of these regulators. The section also initiated a project to identify and characterize genes encoding small proteins (less than 50 amino acids)—a category of genes, along with regulatory RNAs, that has largely been overlooked.
