Richard and Rhoda Goldman Distinguished Chair in the Biological Sciences & Professor of Genetics, Genomics and Development*Lab Homepage: http://mcb.berkeley.edu/labs/koshland/
**And Affiliate, Division of Cell and Developmental Biology
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My laboratory uses budding yeast to study fundamental processes in cell biology. Our approach has been to develop novel genetic reagents and cell biological methods to analyze these complex processes in vivo, coupled with the development and exploitation of in vitro assays to reveal underlying molecular mechanisms. Together these approaches have allowed us to make significant contributions to the following three areas of research.
Higher Order Chromosome Structure is important for the integrity, transmission and expression of chromosomes. The molecular bases for the formation, maintenance, and disassembly of higher order chromosome organization are major unsolved problems in cell biology.
The Maintenance of Genome Integrity (chromosome number and integrity) is critical to prevent cell inviability, inherited disorders, and disease. A major threat to genome integrity is broken DNA that can be misrepaired to cause gross chromosomal rearrangements (GCR) such as translocations, internal deletions or terminal truncations. While the cause of DSBs and their repair have been studied intensively, major new discoveries will be required to explain the massive rearrangement of chromosomes associated with cancer.
Stress Tolerance is fundamental to an organisms ability to survive internal and environmental perturbations. We study stress response through the lens of desiccation tolerance, a remarkable trait found in rare species in all kingdoms of life. Desiccation tolerance has significant biomedical potential and will likely provide novel insights into the role of different cell biological processes in water homeostasis. We are currently identifying additional extremophiles as novel systems to study stress biology
Higher order chromosome structure is important for transcription, chromosome segregation and DNA repair. Higher order chromosome structure is mediated by a conserved set of protein complexes called SMC for structural maintenance of chromosomes. These SMC complexes provide a powerful platform to understand both the biological function and molecular basis for different types of higher order chromosome structure. SMC complexes facilitate higher order organization of chromosomes by their ability to tether together two different regions of DNA, either within the same chromosome or between different chromosomes My laboratory has shown that different types of higher order chromosome organization are coordinated because the function of SMC complexes are highly interdependent. Different SMC complexes interact in at least three distinct ways to mediate proper chromosome morphogenesis in mitosis, meiosis and DNA repair. They regulate each other's assembly on chromosomes, regulate each other's disassembly from chromosomes and cooperate to build other chromosomal structures like synaptonemal complex. However, what is the molecular basis for the tethering activity of SMC complexes and how this activity is modulated by regulatory modifications of the complex or auxillary factors remain unanswered.
To address these two questions we have studied a prototypic SMC complex, cohesin. The tethering activity of cohesin is used for sister chromatid cohesion, chromosome condensation, DNA repair and regulation of gene expression, including studies implicating a potential role in stem cell gene expression. We have shown that cohesins bind chromatin and then become cohesive. We also have shown that this conversion to the cohesive state is regulated by complex post-translational modifications in response to cell cycle and DNA damage. Our understanding of cohesin regulation allows us to lock cohesin in either the non-cohesive or cohesive-competent state, providing critical new tools to facilitate powerful genetic suppressor studies, to assess specificity of in vitro activities as well as to generate sufficient quantities of active complex for in-depth biochemical and structural studies. Our current genetic, molecular, biochemical and imaging studies of cohesin and its regulation have revealed novel roles for cohesin ATPase function, cohesin acetylation and cohesin oligomerization that dramatically reshape current models for the molecular mechanism by which cohesin modulates chromosome structure. In collaboration with the Meyer lab, we are leveraging the genetic tools developed to study cohesin in budding yeast to interrogate in metazoans the roles of its tethering and oligomerization activities in sister chromatid cohesion and gene expression.
Dissecting the molecular basis for chromosome integrity is challenging because changes in chromosome integrity like GCRs (Gross Chromosomal Rearrangement) are usually rare and often either lethal or genetically silent.To identify novel processes that prevent GCR, we developed a high throughput assay to follow GCR using a yeast artificial chromosome (YAC). Our studies identified novel proteins required to promote chromosome integrity. As one example, we find that factors required for general mRNA metabolism play an active role in masking newly formed RNA molecules to prevent them from hybridizing back to DNA. When RNA-DNA hybrids do form, two evolutionarily conserved RNases H acts as a surveillance mechanism for their removal, thereby safeguarding the genome. We have shown that hybrids form in trans (that is RNA hybridizes to homologous DNA sequences distinct from their site of synthesis), catalyzed by the homologous DNA repair machinery. Fundamental questions remain unanswered including 1) where do hybrids form in the genome?; 2) why are there two RNAses H and what are their roles in hybrid removal; 3) what type of DNA damage is induced by hybrids, and 4) what are the repair mechanisms of hybrid induced damage? To address these questions, we have developed new genetic and molecular reagents in yeast including novel genome-wide methods to map the position of hybrids and the regions of DNA damage that are associated with a subset of hybrids. These tools have defined causal elements for hybrid formation, revealed distinct spacial functions of the RNAses H, and implicated hybrids not only in damage formation but also modulating DNA repair.
Stress Tolerance through the Lens of Desiccation Tolerance
Studies of biological extremes have transformed biology, for example, the study of telomeres in Tetrahymena, the giant axons of squids, or the identification thermo-resistant polymerases in thermophiles. With this precedent in mind, we study desiccation tolerance in yeast as a mechanism to provide novel insights into water homeostasis and stress biology. Two fundamental questions about desiccation tolerance remain unanswered. What is the stress(es) that kill desiccation sensitive cells and how do tolerant cells mitigate these stresses to survive. While the rare trait of desiccation has been studied for many years, almost all studies have succeeded in establishing only correlations (for example the presence of specific small molecules like special sugars or peptides) without any means of testing causality. Indeed, desiccation tolerance has been correlated with a number of stress response pathways including, heat shock, osmotic, DNA damage or high-salt. We have established budding yeast as a genetic model to study desiccation tolerance and demonstrated that the lethal stresses of desiccation are likely protein aggregation and membrane damage, and not salt, oxidation, DNA damage or osmotic stresses as previously proposed. Hugo Tapia has shown that trehalose, a small sugar, and HSP12, a small intrinsically disordered protein (IDP), are necessary and sufficient to promote desiccation tolerance yeast. These exciting new observations identify critical desiccation tolerant factors and connect them with the propagation of amyloids, associated with a number of human diseases. We are currently investigating the potential uses of these factors to promote drought tolerance in plants and to identify protein targets that are particularly prone to desiccation introduced aggregation. Intrinsically disordered proteins and domains represent a huge unexplored proportion of the proteome. The study of IDPs in stress tolerance provides a powerful tool to unlock the mysteries of their biological and molecular functions.
Çamdere, G.Ö., Carlborg, K.K., and Koshland, D. (2018). Intermediate step of cohesin’s ATPase cycle allows cohesin to entrap DNA. Proceedings of the National Academy of Sciences 4, 201807213.
Bloom, M. S., Koshland, D., & Guacci, V. (2018). Cohesin Function in Cohesion, Condensation, and DNA Repair Is Regulated by Wpl1p via a Common Mechanism in Saccharomyces cerevisiae. Genetics, 208(1), 111–124. http://doi.org/10.1534/genetics.117.300537.
Robison, B., Guacci, V., & Koshland, D. (2017). A role for the Smc3 hinge domain in the maintenance of sister chromatid cohesion. Molecular Biology of the Cell, mbc.E17–08–0511. http://doi.org/10.1091/mbc.E17-08-0511
Stigler, J., Çamdere, G.Ö., Koshland, D.E., and Greene, E.C. (2016). Single-Molecule Imaging Reveals a Collapsed Conformational State for DNA-Bound Cohesin. Cell Rep 15, 988–998.
Camdere, G., Guacci, V., Stricklin, J., and Koshland, D. (2015). The ATPases of cohesin interface with regulators to modulate cohesin-mediated DNA tethering. Elife 4, e11315.
Guacci, V., Stricklin, J., Bloom, M.S., Guō, X., Bhatter, M., and Koshland, D. (2015). A novel mechanism for the establishment of sister chromatid cohesion by the ECO1 acetyltransferase. Mol Biol Cell 26, 117–133.
Eng, T., Guacci, V., and Koshland, D. (2015). Interallelic complementation provides functional evidence for cohesin-cohesin interactions on DNA. Mol. Biol. Cell 26, 4224–4235.
Eng, T., Guacci, V., and Koshland, D. (2014). ROCC, a conserved region in Cohesin's Mcd1 Subunit, is essential for the proper regulation of the maintenance of cohesion and establishment of condensation. Mol Biol Cell 25, 2351–2364.
Costantino, L., and Koshland, D. (2018). Genome-wide Map of R-Loop-Induced Damage Reveals How a Subset of R-Loops Contributes to Genomic Instability. Mol. Cell 71, 487–497.e3.
Amon, J.D., and Koshland, D. (2016). RNase H enables efficient repair of R-loop induced DNA damage. Elife 5, e20533.
Zimmer, A.D., and Koshland, D. (2016). Differential roles of the RNases H in preventing chromosome instability. Proc. Natl. Acad. Sci. U.S.a. 113, 12220–12225.
Wahba, L., Costantino, L., Tan, F.J., Zimmer, A., and Koshland, D. (2016). S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation. Genes Dev. 30, 1327–1338.
Costantino, L., and Koshland, D. (2015). The Yin and Yang of R-loop biology. Curr Opin Cell Biol 34, 39–45.
Wahba, L., Gore, S. K., & Koshland, D. (2013). The homologous recombination machinery modulates the formation of RNA-DNA hybrids and associated chromosome instability. eLife, 2(0), e00505–e00505. doi:10.7554/eLife.00505.027
Wahba, L., Amon, J.D., Koshland, D., and Vuica-Ross, M. (2011). RNase H and Multiple RNA Biogenesis Factors Cooperate to Prevent RNA:DNA Hybrids from Generating Genome Instability. Mol Cell 44, 978–988.
Kim, S.X., Camdere, G., Hu, X., Koshland, D., and Tapia, H. (2018). Synergy between the small intrinsically disordered protein Hsp12 and trehalose sustain viability after severe desiccation. Elife 7, 959.
Boothby, T. C., Tapia, H., Brozena, A. H., Piszkiewicz, S., Smith, A. E., Giovannini, I., et al. (2017). Tardigrades Use Intrinsically Disordered Proteins to Survive Desiccation. Molecular Cell, 65(6), 975–984.e5. http://doi.org/10.1016/j.molcel.2017.02.018
Tapia, H., Young, L., Fox, D., Bertozzi, C.R., and Koshland, D. (2015). Increasing intracellular trehalose is sufficient to confer desiccation tolerance to Saccharomyces cerevisiae. Proc Natl Acad Sci USA 112, 6122–6127.
Tapia, H., and Koshland, D.E. (2014). Trehalose is a versatile and long-lived chaperone for desiccation tolerance. Curr Biol 24, 2758–2766.
Welch, A. Z., Gibney, P. A., Botstein, D., & Koshland, D. E. (2013). TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae. Molecular biology of the cell, 24(2), 115–128. doi:10.1091/mbc.E12-07-0524
Calahan, D., Dunham, M., Desevo, C., and Koshland, D.E. (2011). Genetic Analysis of Desiccation Tolerance in Sachharomyces cerevisiae. Genetics 189, 507–519.
Photo Credit: Mark Hanson of Mark Joseph Studios
Last Updated 2019-03-08