Bruce Bowerman - US grants

9317993 Dahlquist Partial funding of the hardware needed to perform pulsed field gradient experiments to enhance the use of nuclear magnetic resonance to study the solution properties of proteins and nucleic acids has been requested. The requested capability will greatly aid in 8 projects outlined in this proposal. These include investigations of the substrate binding site of galactose oxidase, the solution structure of the SYMBOL 101 \f "Symbol" subunit of the mitochondrial ATP synthase, the structure of an unusual DNA binding domain found in the project of the skn-1 gene of C. elegans, the structural basis of the interaction of two yeast transcription factors a1 and a2, the structural changes associated with mutations of the prosequence of the yeast carboxypeptidase and the folding pathway of the heterodimeric bacterial luciferase. s t g ? r StringFileInfo ^ 040904E4 ' CompanyName Microsoft Corporation : & FileDescription Windows Task Manager app9317993 Dahlquist Partial funding of the hardware needed to perform pulsed field gradient experiments to enhance the use of 4 5 K L o q $ $ $ D Y Y ? CG Times Symbol & Arial Tms Rmn Times New Roman Y 9 A A " h B e ~ < 1 Shauna Benson Deseree King, BIR

We use the nematode Caenorhabditis elegans as a model system for studying the molecular mechanisms by which developmental determinants specify the different fates of early embryonic cells (blastomeres). We have shown that the maternally expressed C. elegans gene skn-1 is required to specify the fate of a 4-cell stage blastomere called EMS. The ventrally-positioned EMS blastomere produces many different cell fates, contributing to both mesodermal and endodermal tissues. In skn-1 mutant embryos, EMS instead adopts a fate more like that of its sister blastomere in the 4-cell stage embryo. Genetic and molecular analyses suggest that skn-1 may encode an early embryonic determinant that acts by regulating the transcription of zygotic genes in descendants if EMS, and that other maternal genes restrict skn-1(+) activity to only the EMS blastomere. We propose experiments designed to address three fundamental issues concerning the regulation and function of skn1 as a developmental determinant in the early C. elegans embryo. (1) How is the expression of maternal skn-1 mRNA regulated such that high levels of Skn-1 protein accumulate only in a subset of early blastomeres? (2) What other maternally expressed genes are required for the EMS blastomere to produce its proper pattern of cell fates? (3) What zygotically expressed genes are targets of skn-1 transcriptional regulation in an EMS pathway of blastomere development? Our goal is to use skn-1 as an entry point for defining the steps in a genetic pathway that controls blastomere fate. We think this information will be interesting particularly in comparison to the much more detailed understanding we currently have of early embryogenesis in the fruit fly, Drosophila melanogaster. In Drosophila, the fate map of the embryo is largely determined during a time in which all embryonic nuclei share a common syncytial cytoplasm, before cell membranes partition the embryo into cellular compartments. In contrast, C. elegans embryos are completely cellularized during development. Studies of blastomere fate specification, in embryos that have their nuclei partitioned by cell membranes, will contribute to our general understanding of how different animal body plans develop and evolve.

We propose to use the powerful genetics and the impressive cytological properties of the early C. elegans embryo to investigate cytokinesis and its relationship to mitotic spindle orientation in a developing animal. The early C. elegans embryo offers two key advantages for these studies: (i) the ability to rapidly identify genes required for cytokinesis and for mitotic spindle orientation in early embryonic cells, and (ii) the ability to visualize with high resolution the subcellular localization of functionally important proteins in the large (approximately 22 x 55 micron) 1-cell stage zygote. We have three long term goals: (1) To use genetic and molecular methods to define cytokinesis as a series of discrete molecular interactions that execute cytokinesis in the early embryo. (2) To determine the mechanistic relationship between the termination of cytokinesis and the mechanisms that orient mitotic spindles during asymmetric divisions in early embryonic cells. (3) To identify motor proteins important for cytokinesis and the generation of asymmetric cell divisions. These studies will provide significant insight into the molecular basis for human pathologies: cytoskeleton/plasma membrane interactions have proven relevant to our understanding of cancer and of other significant diseases, including muscular dystrophy, deafness, and sterility. In preliminary studies, we have identified a gene called cyk-1 that is required for a late step in cytokinesis. This is the first gene identified in C. elegans that is specifically required for cytokinesis in the early embryo. Intriguingly, the CYK-1 protein localizes to the leading edge of the cleavage furrow late in cytokinesis, where we hypothesize it bridges the actin and tubulin cytoskeleton. While CYK-1 provides a starting point for identifying functionally protein/protein interactions that occur during cytokinesis, we first propose to identify as comprehensively as possible the genes required for cytokinesis and mitotic spindle orientation. To this end, we have begun a large-scale screen for temperature-sensitive, embryonic-lethal mutants, and we are using a functional genomics approach that involves the use of a recently discovered technology called RNA interference. We will molecularly clone genes that are most specifically required for cytokinesis and mitotic spindle orientation. By using genetic and molecular epistasis experiments, and by examining how the different proteins we identify interact, we will define the molecular interactions and pathways that control these fundamental cellular and developmental processes.

DESCRIPTION (provided by applicant): In our original application (funded from May 1, 1998-April 30, 2002), we proposed to identify genes required for early embryonic cell divisions in C. elegans, focusing on the isolation and investigation of conditional, embryonic-lethal mutants. In this funding period, we have identified 1600 conditional mutants, including several with defects in cytokineis that are the focus of this proposal. We have identified several intriguing classes of cytokinesis mutants, some required positively and others required for novel negative forms of regulation not previously documented. In our new Specific Aims, we propose to investigate the regulation and role of the Nedd8/Rub1p ubiquitin-like protein conjugation pathway, which negatively regulating cortical microfilament contractility outside the cleavage furrow during cytokinesis. We also propose to characterize the phenotypes of several new cytokinesis mutants we have identified, and to use positional cloning to determine the molecular identities of the mutated genes. These include one mutant with defects in furrow assembly and progression, one mutant with a late defect in cytokinesis, and two mutants with ectopic cleavage furrows either during or before mitosis. Finally, we propose to continue our screens for conditional, embryonic-lethal mutants with defects in cell division, and we also propose a novel screen that takes advantage of RNAi and our conditional mutants to identify more comprehensively genes that participate in cytokinesis and other processes. These genetic and molecular studies should provide new insight into the regulation and function of the microfilament and microtubule cytoskeleton, which mediate essential and conserved cellular processes, and are often associated with human disease.

DESCRIPTION (provided by applicant): In our first renewal application (funded from May 1,1998-April 30, 2002), we proposed to examine the role of Wnt signaling during endoderm induction in C. elegans. We have since shown that a conserved MAP Kinase module converges with Wnt signaling to polarize endoderm potential within a single embryonic cell called EMS. We also showed that Wnt signaling induces a rotation of the mitotic spindle in EMS, such that its posterior daughter inherits endoderm potential. Our findings provide important mechanistic insights about a key signal transduction pathway that is widely conserved, being involved in several important human cancers and in many different developmental processes. Four other cell divisions in the early embryo are intrinsically asymmetric. In each case, as in EMS, the mitotic spindle rotates to align with the axis of polarization. We have identified new mutants with mitotic spindle positioning defects in two intrinsically polarized embryonic cells called P0 and P1. We propose new specific aims that focus largely on intrinsic polarity in these two cells. We are investigating a gene we discovered called spn-4, which encodes a conserved RNA binding protein that acts downstream of the PAR polarity proteins to regulate mitotic spindle orientation and cell polarity in P1. We also proposed to study another mutant we recently identified, called spn-5, that exhibits P1 spindle orientation defects, and four new mutants (spn-6-9) with defects in P0 mitotic spindle positioning. Finally, we propose a novel and powerful screen to identify genes required for spindle orientation and asymmetric cell division. We are using RNA interference to identify loci throughout the genome that, when reduced in function, can enhance or suppress conditional mutants grown at just-viable or just-lethal temperatures. Our long-term goal is to attain a comprehensive view of the pathways that regulate cell polarity in the early C. elegans embryo.

[unreadable] DESCRIPTION (provided by applicant): The use of asymmetric cell division is central to generating cell type diversity during development. This process has been studied extensively using genetic and molecular approaches in both Caenorhabditis elegans and Drosophila melanogaster. However, both of these organisms are evolutionarily very high derived and may be relatively closely related. Thus it is difficult to define conserved core components of key regulatory pathways without comparison to a more distantly related and less derived experimental system For this purpose, we propose to initiate studies of a bilaterian organism more likely to resemble a primitive state, the annelid Platynereis dumerilii. This marine polychaete exhibits developmental features that link invertebrates and vertebrates, and provides impressive technical advantages. During early embryogenesis of Platynereis stereotypic asymmetric cell divisions generate distinct founder cell lineages, such as a mesodermal cell lineage called 4d. Thousands of synchronous embryonic stages can be easily obtained, the embryos are transparent and gene function can be reduced using RNA interference. To identify important regulators of early development, we propose to generate a P. dumerilii EST library and an in situ data base, and to examine gene requirements using both parental dsRNA interference and specific inhibitors of target genes. We also will employ microarray techniques to examine global changes in gene expression in mutant embryos. Our goals are to explore and exploit this new model system for studies of asymmetric cell division and nervous system development, and to use it as a comparative tool for defining the most highly conserved, functionally required core components of cellular machineries. Newly discovered and conserved loci will also be studied in C. elegans and Drosophila. [unreadable] [unreadable]

Project Summary The early C. elegans embryo provides a powerful model system for molecular genetic studies of cell division. During the current funding period, (i) we have obtained evidence that receptor-independent G[unreadable] proteins regulate non-muscle myosin II to influence positioning of the first mitotic spindle in one-cell zygotes. (ii) We have isolated a large collection of mutants with mitotic spindle defects led to our discovery that the spindle assembly checkpoint is active in early C. elegans embryos, and to our identification of several genes required for spindle assembly or function. (iii) We developed a powerful genome-wide RNA interference-based modifier screen that has identified conserved genes not previously known to influence mitotic spindle assembly and function. In addition, through our use of this modifier screen we have found that dynein light chains can negatively regulate dynein heavy chain function, which to our knowledge has not been documented previously. In this renewal, we propose (i) to further study a group of 21 specific suppressors of conditional dynein heavy chain mutants, and test our hypothesis that dynein light chains negatively regulate dynein function in early embryonic cells. We also will (ii) extend our use of novel particle tracking methods, and other approaches, to further test our hypothesis that a network of cortical and cytoplasmic actomyosin is regulated by G[unreadable] proteins and applies forces to astral microtubules that contribute to mitotic spindle positioning. In a final aim (iii), we will characterize and positionally clone the genes mutated in new conditional mutants we have identified in five different loci that are required for mitotic spindle assembly, positioning, or function. We also will pursue further analysis of several specific suppressors of two conditional mutants with defects in centrosome maturation, to extend our identification and analysis of conserved genes that influence mitotic spindle assembly and function. These studies of cell division and cytoskeletal function are relevant to several important human diseases. Advances in our understanding of these processes, and in the identification of conserved genes that influence them, may prove useful in developing therapeutic interventions for the treatment of human disease. Project Narrative The essential cell division processes we study, using the early Caenorhabditis elegans embryo as a model system, are highly conserved in all animals, including humans, and are relevant not only to cancer, but also to many other human illnesses, including neurodegenerative diseases. Chemotherapeutic agents such as taxol, which target the cell division machinery, can be useful for inhibiting cancer cell growth: a better understanding of the machinery, including further identification of the parts, will provide more candidate targets for therapeutic intervention. Lastly, our studies of the asymmetric cell divisions that characterize early embryogenesis in C. elegans also are relevant to our understanding of stem cell biology, and our ability to manipulate stem cell development for therapeutic applications.

DESCRIPTION (provided by applicant): Conditional (heat-sensitive) mutations remain the most valuable genetic tool available for the in vivo investigation of essential gene requirements, and C. elegans is unique as an animal model in which one can feasibly isolate large numbers of rare conditional mutations. This proposal seeks to expand our identification of conditional mutations in essential C. elegans genes by (i) exploring previously ignored mutant phenotypes, and (ii) developing next generation DNA sequencing-based approaches to greatly reduce the time and labor required to map and positionally clone mutant C. elegans loci isolated after chemical mutagenesis screens. Specific Aim 1 focuses on the identification of 2000 new temperature-sensitive, embryonic-lethal C. elegans mutants; the systematic classification of all mutants into several phenotypic categories; the distribution of multiple mutant classes to collaborators; and the isolation of a large collection of mutants with previously unexplored gonad morphogenesis-defective phenotypes. Specific Aim 2 focuses on developing an Illumina DNA sequencing-based genome-wide approach to Single Nucleotide Polymorphism (SNP) mapping called Restriction-site Associated DNA polymorphism (RAD) mapping. To our knowledge, we are the first laboratory to explore applying this recently developed technology to the mapping of mutant loci in C. elegans. It promises to provide a high throughput and cost-effective approach to the mapping and positional cloning of large numbers of mutant loci. Specific Aim 3 explores Illumina DNA sequencing-based whole genome sequencing to identify the mutational lesions responsible for conditional embryonic-lethality in the mutants isolated in Aim 1 and mapped to small intervals in Aim 2. Our ultimate goal is to greatly expand the use of chemical mutagenesis screens to identify conditional mutations in essential C. elegans genes. By developing high throughput approaches to the positional cloning of conditionally mutant loci, our proposed exploratory research will substantially impact research by laboratories throughout the world that use C. elegans as an animal model for investigating many different and fundamentally important biological processes. PUBLIC HEALTH RELEVANCE: The nematode Caenorhabditis elegans is unique as an animal model in which one can feasibly isolate large numbers of rare conditional mutations in essential genes. Conditional (heat-sensitive) mutations remain the most valuable genetic tool available for the investigation of essential gene requirements, which often have multiple essential requirements, in many cases even during a single cell division cycle. Moreover, essential C. elegans genes are with few exceptions widely conserved in other organisms including humans, and are in many cases of direct relevance to our understanding of and ability to detect and treat cancers and other important human diseases. By promoting the isolation of large collections of these valuable genetic tools for the study of conserved and essential genes, we will contribute substantially to our basic understanding of numerous fundamental biological processes under investigation in laboratories throughout the world. The investigation of biological processes in model organisms like C. elegans is of fundamental importance for understanding human disease mechanisms, and for identifying possible therapeutic targets and opportunities.

? DESCRIPTION (provided by applicant): We propose to combine powerful new technologies to investigate at a systems level an almost entirely neglected area of developmental biology research-late embryogenesis in the nematode Caenorhabditis elegans-and to greatly expand the availability of conditional mutations in essential genes for the investigation of biological processes in this model animal. We will use Illumina-based whole genome sequencing to rapidly identify the causal mutations in a collection of 250 temperature-sensitive, embryonic-lethal C. elegans mutants that progress normally through the early stages of embryogenesis but arrest late in embryogenesis. About 30 of these mutants arrest with severe defects in morphogenesis - the elongation of an oval mass of largely post-mitotic cells into a long thin worm. The remainder arrest later in development after extensive morphogenesis. While embryonic morphogenesis in C. elegans has been a subject of investigation for many years, our understanding of it remains incomplete. Our mutant collection promises important new insights into the genetic networks that regulate and mediate this complex process. In addition to identifying the causal genes, we will systematically identify the developmental defects in late embryos at cellular resolution, which has been almost entirely neglected due to technical difficulties. To characterize the developmental defects at high resolution in both classes of mutants, and assemble our data into a systems view of late embryogenesis, we will (i) apply recently developed automated embryonic cell lineage analysis as well as new methods for quantitative image analysis to identify abnormalities throughout embryogenesis, (ii) use CRISPR/Cas9 technology to generate transgenic strains bearing translational fusions of GFP to the genes we identify so as to determine when and where in embryogenesis they are expressed, and to guide our phenotype analysis, and (iii) assemble the phenotype and expression data into a multi-scale view of late embryonic development from genes to organismal morphology. We also will take advantage of the conditional mutations we have isolated to determine when in development the affected genes perform their essential embryonic functions, and to identify additional essential functions throughout the nematode life cycle. Genome-wide RNA interference screens have identified about 2500 essential genes in C. elegans, most of which are conserved in other animals. Temperature-sensitive mutations provide a uniquely powerful tool for investigating the requirements for essential genes, as many if not most of them have multiple functions throughout the life of the animal. Moreover, C. elegans is unique as an animal model in which one can feasibly isolate large numbers of relatively rare conditional mutations in essential genes, and yet conditional mutations have been identified in only about one hundred of the 2500 essential C. elegans genes. In addition to substantially advancing our understanding of morphogenesis and late embryogenesis, we also will greatly expand the availability of these powerful genetic tools to investigators throughout th world who use C. elegans as an animal model.

Project Summary Oocyte meiosis ends with two rounds of cell division that produce an egg with a haploid genome. While mitosis uses bipolar spindles that assemble using two centrosomes, oocytes assemble bipolar spindles in the absence of centrosomes. While the assembly and function of mitotic spindles have been studied extensively, acentrosomal oocyte spindle assembly remains poorly understood, and C. elegans provides an appealing model system for investigating the mechanisms that govern this process. Moreover, our understanding of oocyte spindle assembly remains incomplete in all widely used model systems, with live cell imaging only recently beginning to shed light on the dynamics of spindle assembly, and somewhat piecemeal genetic studies having provided a partial but incomplete catalogue of the important players. We propose a systematic and quantitative analysis of oocyte meiotic spindle assembly and spindle bipolarity, using a valuable collection of temperature-sensitive mutants we have isolated. We also will use RNA interference to identify the genes and pathways that operate during oocyte spindle assembly in C. elegans, along with live-cell fluorescent video-microscopy and genome editing to provide a more complete and mechanistic understanding of this fundamentally important process. In 2014, we published a manuscript describing our initial work on oocyte spindle pole assembly in Molecular Biology of the Cell, and in 2015 another manuscript in The Journal of Cell Biology and describing our evidence that the microtubule depolymerase KLP- 7/MCAK acts through kinetochores to promote the coalescence of oocyte spindle poles. These results, together with our identification of additional temperature-sensitive mutants with oocyte spindle defects and a thorough survey of the literature covering the most widely used model systems, provide the foundation for the specific aims we now propose to advance our understanding of acentrosomal oocyte meiotic spindle assembly. Even though mitotic spindles rely extensively on centrosomes to organize bipolar spindles, oocyte meiosis and somatic mitosis share the use of acentrosomal pathways for nucleating and organizing microtubules. Thus investigating oocyte spindle assembly will improve our understanding the abnormal mitotic proliferations that result in cancer. Moreover, human oocytes are remarkably prone to errors in spindle assembly and often produce aneuploid oocytes that upon fertilization develop abnormally. A better understanding of oocyte meiotic spindle assembly is therefore relevant to human fertility and development.

Project Summary Oocyte meiosis ends with two rounds of cell division that produce an egg with a haploid genome. While mitosis uses bipolar spindles that assemble using two centrosomes, oocytes assemble bipolar spindles in the absence of centrosomes. While the assembly and function of mitotic spindles have been studied extensively, acentrosomal oocyte spindle assembly remains poorly understood, and C. elegans provides an appealing model system for investigating the mechanisms that govern this process. Moreover, our understanding of oocyte spindle assembly remains incomplete in all widely used model systems, with live cell imaging only recently beginning to shed light on the dynamics of spindle assembly, and somewhat piecemeal genetic studies having provided a partial but incomplete catalogue of the important players. We propose a systematic and quantitative analysis of oocyte meiotic spindle assembly and spindle bipolarity, using a valuable collection of temperature-sensitive mutants we have isolated. We also will use RNA interference to identify the genes and pathways that operate during oocyte spindle assembly in C. elegans, along with live-cell fluorescent video-microscopy and genome editing to provide a more complete and mechanistic understanding of this fundamentally important process. In 2014, we published a manuscript describing our initial work on oocyte spindle pole assembly in Molecular Biology of the Cell, and in 2015 another manuscript in The Journal of Cell Biology and describing our evidence that the microtubule depolymerase KLP- 7/MCAK acts through kinetochores to promote the coalescence of oocyte spindle poles. These results, together with our identification of additional temperature-sensitive mutants with oocyte spindle defects and a thorough survey of the literature covering the most widely used model systems, provide the foundation for the specific aims we now propose to advance our understanding of acentrosomal oocyte meiotic spindle assembly. Even though mitotic spindles rely extensively on centrosomes to organize bipolar spindles, oocyte meiosis and somatic mitosis share the use of acentrosomal pathways for nucleating and organizing microtubules. Thus investigating oocyte spindle assembly will improve our understanding the abnormal mitotic proliferations that result in cancer. Moreover, human oocytes are remarkably prone to errors in spindle assembly and often produce aneuploid oocytes that upon fertilization develop abnormally. A better understanding of oocyte meiotic spindle assembly is therefore relevant to human fertility and development.

Project Summary For 25 years now, our laboratory has used live cell imaging with fluorescently marked proteins, and the forward genetics approach of isolating temperature-sensitive (TS) and embryonic-lethal C. elegans mutants, to investigate cytoskeletal function during embryonic cell divisions. More recently, we have (i) incorporated higher throughput positional cloning methods made possible by Illumina DNA sequencing technology to expand our effort to identify TS mutations in essential C. elegans genes as a community resource, and (ii) employed CRISPR/Cas9 genome editing technology to augment our genetics and live cell imaging approaches. Over the past five years, in addition to developing higher throughput positional cloning approaches, we have focused on two fundamentally important cell biological processes: (i) the orientation of cell division axes during development to establish multicellular architectures, and (ii) the mechanisms that nucleate and organize microtubules into a bipolar structure during oocyte meiotic spindle assembly, which occurs in the absence of the centrosomal microtubule organizing centers that mediate mitotic spindle assembly. Our research program over the next five years will focus on expanding our identification of TS mutations in essential C. elegans genes and making them generally available to the research community, extending our analysis of a previously unknown but widely conserved microtubule- independent and cortical actomyosin-dependent mechanism for orienting cell division axes during animal development, and improving our understanding of acentrosomal oocyte meiotic spindle assembly and function.

Project Summary/Abstract We request funds to purchase of a second CherryTemp device, produced by a company in France called Cherry Biotech, that provides precise temperature control of specimens mounted on slides during live cell imaging, and allows for very rapid changes in sample temperature (see Narrative for details). In the Specific Aims for our most recent renewal of R01GM049869, and in our research program outlined in R35GM131749, we proposed to use temperature-sensitive, embryonic-lethal (TS-EL) C. elegans mutants to investigate the genetic pathways that mediate the acentrosomal assembly of bipolar spindles during oocyte meiotic cell division, relying in large part on live-imaging of TS-EL mutants to define gene requirements. The temperature control provided by the CherryTemp device has greatly improve our ability to accurately and reproducibly assess gene requirements using our TS-EL mutants. Our Institute recently obtain funds from the Murdock Foundation to purchase a second Nikon spinning disk confocal microscope. This second CherryTemp device we now wish to purchase will come with components that allow it to be used on both our current Andor system and the new Nikon spinning disk confocal system. This new device will serve both as a backup for our current device when it breaks down (which it has at times, with one thermostat that is sensitive to wear and tear), and more importantly will allow my lab members to use both our Andor System and the new Nikon system simultaneously, with one lab member working on each scope, doubling our rate of data acquisition. Thus these devices not only will improve the rigor and reproducibility of our data, but also greatly accelerate our rate of data collection and how quickly we can achieve our research goals and initiate new projects.