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Urso SJ, Sathaseevan A, Brent Derry W, Lamitina T. Regulation of the hypertonic stress response by the 3' mRNA cleavage and polyadenylation complex. Genetics 2023; 224:iyad051. [PMID: 36972377 PMCID: PMC10490458 DOI: 10.1093/genetics/iyad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 03/29/2023] Open
Abstract
Maintenance of osmotic homeostasis is one of the most aggressively defended homeostatic set points in physiology. One major mechanism of osmotic homeostasis involves the upregulation of proteins that catalyze the accumulation of solutes called organic osmolytes. To better understand how osmolyte accumulation proteins are regulated, we conducted a forward genetic screen in Caenorhabditis elegans for mutants with no induction of osmolyte biosynthesis gene expression (Nio mutants). The nio-3 mutant encoded a missense mutation in cpf-2/CstF64, while the nio-7 mutant encoded a missense mutation in symk-1/Symplekin. Both cpf-2 and symk-1 are nuclear components of the highly conserved 3' mRNA cleavage and polyadenylation complex. cpf-2 and symk-1 block the hypertonic induction of gpdh-1 and other osmotically induced mRNAs, suggesting they act at the transcriptional level. We generated a functional auxin-inducible degron (AID) allele for symk-1 and found that acute, post-developmental degradation in the intestine and hypodermis was sufficient to cause the Nio phenotype. symk-1 and cpf-2 exhibit genetic interactions that strongly suggest they function through alterations in 3' mRNA cleavage and/or alternative polyadenylation. Consistent with this hypothesis, we find that inhibition of several other components of the mRNA cleavage complex also cause a Nio phenotype. cpf-2 and symk-1 specifically affect the osmotic stress response since heat shock-induced upregulation of a hsp-16.2::GFP reporter is normal in these mutants. Our data suggest a model in which alternative polyadenylation of 1 or more mRNAs is essential to regulate the hypertonic stress response.
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Affiliation(s)
- Sarel J Urso
- Graduate Program in Cell Biology and Molecular Physiology, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Anson Sathaseevan
- Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - W Brent Derry
- Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Todd Lamitina
- Graduate Program in Cell Biology and Molecular Physiology, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
- Division of Child Neurology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
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52
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Clancy JC, Vo AA, Myles KM, Levenson MT, Ragle JM, Ward JD. Experimental considerations for study of C. elegans lysosomal proteins. G3 (BETHESDA, MD.) 2023; 13:jkad032. [PMID: 36748711 PMCID: PMC10085801 DOI: 10.1093/g3journal/jkad032] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 06/20/2022] [Accepted: 01/27/2023] [Indexed: 02/08/2023]
Abstract
Lysosomes are an important organelle required for the degradation of a range of cellular components. Lysosome function is critical for development and homeostasis as dysfunction can lead to inherited genetic disorders, cancer, and neurodegenerative and metabolic diseases. The acidic and protease-rich environment of lysosomes poses experimental challenges. Many fluorescent proteins are quenched or degraded, while specific red fluorescent proteins can be cleaved from translational fusion partners and accumulate. While studying MLT-11, a Caenorhabditis elegans molting factor that localizes to lysosomes and the cuticle, we sought to optimize several experimental parameters. We found that, in contrast to mNeonGreen fusions, mScarlet fusions to MLT-11 missed cuticular and rectal epithelial localization. Rapid sample lysis and denaturation were critical for preventing MLT-11 fragmentation while preparing lysates for western blots. Using a model lysosomal substrate (NUC-1), we found that rigid polyproline linkers and truncated mCherry constructs do not prevent cleavage of mCherry from NUC-1. We provide evidence that extended localization in lysosomal environments prevents the detection of FLAG epitopes in western blots. Finally, we optimize an acid-tolerant green fluorescent protein (Gamillus) for use in C. elegans. These experiments provide important experimental considerations and new reagents for the study of C. elegans lysosomal proteins.
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Affiliation(s)
- John C Clancy
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - An A Vo
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Krista M Myles
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Max T Levenson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jordan D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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53
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Peterson ND, Tse SY, Huang QJ, Wani KA, Schiffer CA, Pukkila-Worley R. Non-canonical pattern recognition of a pathogen-derived metabolite by a nuclear hormone receptor identifies virulent bacteria in C. elegans. Immunity 2023; 56:768-782.e9. [PMID: 36804958 PMCID: PMC10101930 DOI: 10.1016/j.immuni.2023.01.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/27/2022] [Accepted: 01/25/2023] [Indexed: 02/19/2023]
Abstract
Distinguishing infectious pathogens from harmless microorganisms is essential for animal health. The mechanisms used to identify infectious microbes are not fully understood, particularly in metazoan hosts that eat bacteria as their food source. Here, we characterized a non-canonical pattern-recognition system in Caenorhabditis elegans (C. elegans) that assesses the relative threat of virulent Pseudomonas aeruginosa (P. aeruginosa) to activate innate immunity. We discovered that the innate immune response in C. elegans was triggered by phenazine-1-carboxamide (PCN), a toxic metabolite produced by pathogenic strains of P. aeruginosa. We identified the nuclear hormone receptor NHR-86/HNF4 as the PCN sensor in C. elegans and validated that PCN bound to the ligand-binding domain of NHR-86/HNF4. Activation of NHR-86/HNF4 by PCN directly engaged a transcriptional program in intestinal epithelial cells that protected against P. aeruginosa. Thus, a bacterial metabolite is a pattern of pathogenesis surveilled by nematodes to identify a pathogen in its bacterial diet.
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Affiliation(s)
- Nicholas D Peterson
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Samantha Y Tse
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Qiuyu Judy Huang
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Khursheed A Wani
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Read Pukkila-Worley
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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54
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Gibney TV, Favichia M, Latifi L, Medwig-Kinney TN, Matus DQ, McIntyre DC, Arrigo AB, Branham KR, Bubrig LT, Ghaddar A, Jiranek JA, Liu KE, Marcucci CG, Porter RJ, Pani AM. A simple method to dramatically increase C. elegans germline microinjection efficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533855. [PMID: 36993165 PMCID: PMC10055348 DOI: 10.1101/2023.03.23.533855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Genome manipulation methods in C. elegans require microinjecting DNA or ribonucleoprotein complexes into the microscopic core of the gonadal syncytium. These microinjections are technically demanding and represent a key bottleneck for all genome engineering and transgenic approaches in C. elegans . While there have been steady improvements in the ease and efficiency of genetic methods for C. elegans genome manipulation, there have not been comparable advances in the physical process of microinjection. Here, we report a simple and inexpensive method for handling worms using a paintbrush during the injection process that nearly tripled average microinjection rates compared to traditional worm handling methods. We found that the paintbrush increased injection throughput by substantially increasing both injection speeds and post-injection survival rates. In addition to dramatically and universally increasing injection efficiency for experienced personnel, the paintbrush method also significantly improved the abilities of novice investigators to perform key steps in the microinjection process. We expect that this method will benefit the C. elegans community by increasing the speed at which new strains can be generated and will also make microinjection-based approaches less challenging and more accessible to personnel and labs without extensive experience.
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Affiliation(s)
- Theresa V. Gibney
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Michelle Favichia
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Laila Latifi
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - David Q. Matus
- Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, NY, USA
- David Matus is a paid consultant of Arcadia Science
| | | | - Angelo B. Arrigo
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - Louis T. Bubrig
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Abbas Ghaddar
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - Kendra E. Liu
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA
| | - Charles G. Marcucci
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA
| | - Robert J. Porter
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Ariel M. Pani
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- Department of Cell Biology, University of Virginia, Charlottesville, VA, USA
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55
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Pu L, Zhao L, Lu Q, Chen C. Hypoxia induces food leaving in C. elegans. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000776. [PMID: 37033703 PMCID: PMC10077061 DOI: 10.17912/micropub.biology.000776] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/05/2023] [Accepted: 03/21/2023] [Indexed: 04/11/2023]
Abstract
Hypoxia alters eating behavior in different animals. In C. elegans , hypoxia induces a strong food leaving response. We found that this behavior was independent of the known O 2 response mechanisms including acute O 2 sensation and HIF-1 signaling of chronic hypoxia response. Mutating egl-3 and egl-21 , encoding the neuropeptide pro-protein convertase and carboxypeptidase, led to defects in hypoxia induced food leaving, suggesting that neuropeptidergic signaling was required for this response. However, we failed to identify any neuropeptide mutants that were severely defective in hypoxia induced food leaving, suggesting that multiple neuropeptides act redundantly to modulate this behavior.
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Affiliation(s)
- Longjun Pu
- Umeå Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Lina Zhao
- Umeå Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Qiongxuan Lu
- Umeå Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Changchun Chen
- Umeå Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
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56
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Kurashina M, Mizumoto K. Targeting endogenous proteins for spatial and temporal knockdown using auxin-inducible degron in Caenorhabditis elegans. STAR Protoc 2023; 4:102028. [PMID: 36640369 PMCID: PMC9860162 DOI: 10.1016/j.xpro.2022.102028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/21/2022] [Accepted: 12/27/2022] [Indexed: 01/15/2023] Open
Abstract
The auxin-inducible degron (AID) provides reversible, spatiotemporal control for the knockdown of target proteins. Here, we present a protocol for AID-mediated protein knockdown in Caenorhabditis elegans. We describe steps for generating the knock-in mutants using two CRISPR-Cas9 genome editing techniques and preparing the auxin-containing nematode growth media (NGM) plates. We also detail AID-mediated spatiotemporal protein knockdown. For complete details on the use and execution of this protocol, please refer to Kurashina et al. (2021).1.
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Affiliation(s)
- Mizuki Kurashina
- Department of Zoology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Graduate Program in Cell & Developmental Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; The Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Kota Mizumoto
- Department of Zoology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Graduate Program in Cell & Developmental Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; The Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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57
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Kim HM, Hong Y, Chen J. A Decade of CRISPR-Cas Gnome Editing in C. elegans. Int J Mol Sci 2022; 23:ijms232415863. [PMID: 36555505 PMCID: PMC9781986 DOI: 10.3390/ijms232415863] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
CRISPR-Cas allows us to introduce desired genome editing, including mutations, epitopes, and deletions, with unprecedented efficiency. The development of CRISPR-Cas has progressed to such an extent that it is now applicable in various fields, with the help of model organisms. C. elegans is one of the pioneering animals in which numerous CRISPR-Cas strategies have been rapidly established over the past decade. Ironically, the emergence of numerous methods makes the choice of the correct method difficult. Choosing an appropriate selection or screening approach is the first step in planning a genome modification. This report summarizes the key features and applications of CRISPR-Cas methods using C. elegans, illustrating key strategies. Our overview of significant advances in CRISPR-Cas will help readers understand the current advances in genome editing and navigate various methods of CRISPR-Cas genome editing.
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58
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Rochester JD, Min H, Gajjar GA, Sharp CS, Maki NJ, Rollins JA, Keiper BD, Graber JH, Updike DL. GLH-1/Vasa represses neuropeptide expression and drives spermiogenesis in the C. elegans germline. Dev Biol 2022; 492:200-211. [PMID: 36273621 PMCID: PMC9677334 DOI: 10.1016/j.ydbio.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/26/2022] [Accepted: 10/07/2022] [Indexed: 01/09/2023]
Abstract
Germ granules harbor processes that maintain germline integrity and germline stem cell capacity. Depleting core germ granule components in C. elegans leads to the reprogramming of germ cells, causing them to express markers of somatic differentiation in day-two adults. Somatic reprogramming is associated with complete sterility at this stage. The resulting germ cell atrophy and other pleiotropic defects complicate our understanding of the initiation of reprogramming and how processes within germ granules safeguard the totipotency and immortal potential of germline stem cells. To better understand the initial events of somatic reprogramming, we examined total mRNA (transcriptome) and polysome-associated mRNA (translatome) changes in a precision full-length deletion of glh-1, which encodes a homolog of the germline-specific Vasa/DDX4 DEAD-box RNA helicase. Fertile animals at a permissive temperature were analyzed as young adults, a stage that precedes by 24 h the previously determined onset of somatic reporter-gene expression in the germline. Two significant changes are observed at this early stage. First, the majority of neuropeptide-encoding transcripts increase in both the total and polysomal mRNA fractions, suggesting that GLH-1 or its effectors suppress this expression. Second, there is a significant decrease in Major Sperm Protein (MSP)-domain mRNAs when glh-1 is deleted. We find that the presence of GLH-1 helps repress spermatogenic expression during oogenesis, but boosts MSP expression to drive spermiogenesis and sperm motility. These insights define an early role for GLH-1 in repressing somatic reprogramming to maintain germline integrity.
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Affiliation(s)
- Jesse D Rochester
- Kathryn W. Davis Center for Regenerative Biology and Aging, The Mount Desert Island Biological Laboratory, Bar Harbor, ME, United States; Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, United States
| | - Hyemin Min
- Kathryn W. Davis Center for Regenerative Biology and Aging, The Mount Desert Island Biological Laboratory, Bar Harbor, ME, United States
| | - Gita A Gajjar
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC, United States
| | - Catherine S Sharp
- Kathryn W. Davis Center for Regenerative Biology and Aging, The Mount Desert Island Biological Laboratory, Bar Harbor, ME, United States
| | - Nathaniel J Maki
- Kathryn W. Davis Center for Regenerative Biology and Aging, The Mount Desert Island Biological Laboratory, Bar Harbor, ME, United States
| | - Jarod A Rollins
- Kathryn W. Davis Center for Regenerative Biology and Aging, The Mount Desert Island Biological Laboratory, Bar Harbor, ME, United States
| | - Brett D Keiper
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC, United States
| | - Joel H Graber
- Kathryn W. Davis Center for Regenerative Biology and Aging, The Mount Desert Island Biological Laboratory, Bar Harbor, ME, United States
| | - Dustin L Updike
- Kathryn W. Davis Center for Regenerative Biology and Aging, The Mount Desert Island Biological Laboratory, Bar Harbor, ME, United States.
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59
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Ragle JM, Morrison KN, Vo AA, Johnson ZE, Hernandez Lopez J, Rechtsteiner A, Shakes DC, Ward JD. NHR-23 and SPE-44 regulate distinct sets of genes during Caenorhabditis elegans spermatogenesis. G3 (BETHESDA, MD.) 2022; 12:6711396. [PMID: 36135804 PMCID: PMC9635660 DOI: 10.1093/g3journal/jkac256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/19/2022] [Indexed: 11/28/2022]
Abstract
Spermatogenesis is the process through which mature male gametes are formed and is necessary for the transmission of genetic information. While much work has established how sperm fate is promoted and maintained, less is known about how the sperm morphogenesis program is executed. We previously identified a novel role for the nuclear hormone receptor transcription factor, NHR-23, in promoting Caenorhabditis elegans spermatogenesis. The depletion of NHR-23 along with SPE-44, another transcription factor that promotes spermatogenesis, caused additive phenotypes. Through RNA-seq, we determined that NHR-23 and SPE-44 regulate distinct sets of genes. The depletion of both NHR-23 and SPE-44 produced yet another set of differentially regulated genes. NHR-23-regulated genes are enriched in phosphatases, consistent with the switch from genome quiescence to post-translational regulation in spermatids. In the parasitic nematode Ascaris suum, MFP1 and MFP2 control the polymerization of Major Sperm Protein, the molecule that drives sperm motility and serves as a signal to promote ovulation. NHR-23 and SPE-44 regulate several MFP2 paralogs, and NHR-23 depletion from the male germline caused defective localization of MSD/MFP1 and NSPH-2/MFP2. Although NHR-23 and SPE-44 do not transcriptionally regulate the casein kinase gene spe-6, a key regulator of sperm development, SPE-6 protein is lost following NHR-23+SPE-44 depletion. Together, these experiments provide the first mechanistic insight into how NHR-23 promotes spermatogenesis and an entry point to understanding the synthetic genetic interaction between nhr-23 and spe-44.
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Affiliation(s)
- James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
| | | | - An A Vo
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
| | - Zoe E Johnson
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
| | - Javier Hernandez Lopez
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
| | - Andreas Rechtsteiner
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
| | - Diane C Shakes
- Department of Biology, William & Mary, Williamsburg, VA 23185, USA
| | - Jordan D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
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60
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Broitman-Maduro G, Sun S, Kikuchi T, Maduro MF. The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network. Development 2022; 149:277064. [PMID: 36196618 PMCID: PMC9720673 DOI: 10.1242/dev.200984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022]
Abstract
ABSTRACT
Endoderm specification in Caenorhabditis elegans occurs through a network in which maternally provided SKN-1/Nrf, with additional input from POP-1/TCF, activates the GATA factor cascade MED-1,2→END-1,3→ELT-2,7. Orthologues of the MED, END and ELT-7 factors are found only among nematodes closely related to C. elegans, raising the question of how gut is specified in their absence in more distant species in the genus. We find that the C. angaria, C. portoensis and C. monodelphis orthologues of the GATA factor gene elt-3 are expressed in the early E lineage, just before their elt-2 orthologues. In C. angaria, Can-pop-1(RNAi), Can-elt-3(RNAi) and a Can-elt-3 null mutation result in a penetrant ‘gutless’ phenotype. Can-pop-1 is necessary for Can-elt-3 activation, showing that it acts upstream. Forced early E lineage expression of Can-elt-3 in C. elegans can direct the expression of a Can-elt-2 transgene and rescue an elt-7 end-1 end-3; elt-2 quadruple mutant strain to viability. Our results demonstrate an ancestral mechanism for gut specification and differentiation in Caenorhabditis involving a simpler POP-1→ELT-3→ELT-2 gene network.
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Affiliation(s)
- Gina Broitman-Maduro
- University of California 1 Department of Molecular, Cell and Systems Biology , , Riverside, CA 92521 , USA
| | - Simo Sun
- Faculty of Medicine, University of Miyazaki 2 Department of Infectious Diseases , , 5200 Kihara, Miyazaki 889-1692 , Japan
- Graduate School of Frontier Sciences, The University of Tokyo 3 Department of Integrated Biosciences , , Chiba 277-8562 , Japan
| | - Taisei Kikuchi
- Faculty of Medicine, University of Miyazaki 2 Department of Infectious Diseases , , 5200 Kihara, Miyazaki 889-1692 , Japan
- Graduate School of Frontier Sciences, The University of Tokyo 3 Department of Integrated Biosciences , , Chiba 277-8562 , Japan
| | - Morris F. Maduro
- University of California 1 Department of Molecular, Cell and Systems Biology , , Riverside, CA 92521 , USA
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61
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Beacham GM, Wei DT, Beyrent E, Zhang Y, Zheng J, Camacho MMK, Florens L, Hollopeter G. The Caenorhabditis elegans ASPP homolog APE-1 is a junctional protein phosphatase 1 modulator. Genetics 2022; 222:iyac102. [PMID: 35792852 PMCID: PMC9434228 DOI: 10.1093/genetics/iyac102] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/28/2022] [Indexed: 08/19/2023] Open
Abstract
How serine/threonine phosphatases are spatially and temporally tuned by regulatory subunits is a fundamental question in cell biology. Ankyrin repeat, SH3 domain, proline-rich-region-containing proteins are protein phosphatase 1 catalytic subunit binding partners associated with cardiocutaneous diseases. Ankyrin repeat, SH3 domain, proline-rich-region-containing proteins localize protein phosphatase 1 catalytic subunit to cell-cell junctions, but how ankyrin repeat, SH3 domain, proline-rich-region-containing proteins localize and whether they regulate protein phosphatase 1 catalytic subunit activity in vivo is unclear. Through a Caenorhabditis elegans genetic screen, we find that loss of the ankyrin repeat, SH3 domain, proline-rich-region-containing protein homolog, APE-1, suppresses a pathology called "jowls," providing us with an in vivo assay for APE-1 activity. Using immunoprecipitations and mass spectrometry, we find that APE-1 binds the protein phosphatase 1 catalytic subunit called GSP-2. Through structure-function analysis, we discover that APE-1's N-terminal half directs the APE-1-GSP-2 complex to intercellular junctions. Additionally, we isolated mutations in highly conserved residues of APE-1's ankyrin repeats that suppress jowls yet do not preclude GSP-2 binding, implying APE-1 does more than simply localize GSP-2. Indeed, in vivo reconstitution of APE-1 suggests the ankyrin repeats modulate phosphatase output, a function we find to be conserved among vertebrate homologs.
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Affiliation(s)
| | - Derek T Wei
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Erika Beyrent
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jian Zheng
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Mari M K Camacho
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Gunther Hollopeter
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
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62
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Fakieh R, Duong T, Wu Y, Rasmussen N, Reiner D. A simple strategy for addition of degron tags to endogenous genes harboring prior insertions of fluorescent protein. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000622. [PMID: 36035777 PMCID: PMC9412190 DOI: 10.17912/micropub.biology.000622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/04/2022] [Accepted: 08/06/2022] [Indexed: 11/13/2022]
Abstract
There exist insufficient validated "entry portal" sites in the C. elegans genome for CRISPR/Cas9-dependent insertion into endogenous genes to confer diverse spatiotemporal patterns and levels of expression on exogenous sequences. Consequently, we recognized the most common potential "entry portal" sequences: genes previously tagged with fluorescent proteins using CRISPR/Cas9. As proof of concept, we used existing mKate2-encoding sequences inserted in the 5' end of genes as an insertion point for the auxin inducible degron, AID*. This sequence permits reasonably efficient insertion that can be employed using a variety of approaches for different end goals. Our strategy is thus generalizable to many needs.
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Affiliation(s)
| | | | | | | | - David Reiner
- Texas A&M University
,
Correspondence to: David Reiner (
)
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63
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Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in C. elegans. J Biol Chem 2022; 298:102343. [PMID: 35933017 PMCID: PMC9437848 DOI: 10.1016/j.jbc.2022.102343] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022] Open
Abstract
Proximity-dependent protein labeling provides a powerful in vivo strategy to characterize the interactomes of specific proteins. We previously optimized a proximity labeling protocol for Caenorhabditis elegans using the highly active biotin ligase TurboID. A significant constraint on the sensitivity of TurboID is the presence of abundant endogenously biotinylated proteins that take up bandwidth in the mass spectrometer, notably carboxylases that use biotin as a cofactor. In C. elegans, these comprise POD-2/acetyl-CoA carboxylase alpha, PCCA-1/propionyl-CoA carboxylase alpha, PYC-1/pyruvate carboxylase, and MCCC-1/methylcrotonyl-CoA carboxylase alpha. Here, we developed ways to remove these carboxylases prior to streptavidin purification and mass spectrometry by engineering their corresponding genes to add a C-terminal His10 tag. This allows us to deplete them from C. elegans lysates using immobilized metal affinity chromatography. To demonstrate the method's efficacy, we use it to expand the interactome map of the presynaptic active zone protein ELKS-1. We identify many known active zone proteins, including UNC-10/RIM, SYD-2/liprin-alpha, SAD-1/BRSK1, CLA-1/CLArinet, C16E9.2/Sentryn, as well as previously uncharacterized potentially synaptic proteins such as the ortholog of human angiomotin, F59C12.3 and the uncharacterized protein R148.3. Our approach provides a quick and inexpensive solution to a common contaminant problem in biotin-dependent proximity labeling. The approach may be applicable to other model organisms and will enable deeper and more complete analysis of interactors for proteins of interest.
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64
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ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. PLoS Biol 2022; 20:e3001684. [PMID: 35727855 PMCID: PMC9249223 DOI: 10.1371/journal.pbio.3001684] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/01/2022] [Accepted: 05/20/2022] [Indexed: 12/02/2022] Open
Abstract
The ability to detect and respond to acute oxygen (O2) shortages is indispensable to aerobic life. The molecular mechanisms and circuits underlying this capacity are poorly understood. Here, we characterize the behavioral responses of feeding Caenorhabditis elegans to approximately 1% O2. Acute hypoxia triggers a bout of turning maneuvers followed by a persistent switch to rapid forward movement as animals seek to avoid and escape hypoxia. While the behavioral responses to 1% O2 closely resemble those evoked by 21% O2, they have distinct molecular and circuit underpinnings. Disrupting phosphodiesterases (PDEs), specific G proteins, or BBSome function inhibits escape from 1% O2 due to increased cGMP signaling. A primary source of cGMP is GCY-28, the ortholog of the atrial natriuretic peptide (ANP) receptor. cGMP activates the protein kinase G EGL-4 and enhances neuroendocrine secretion to inhibit acute responses to 1% O2. Triggering a rise in cGMP optogenetically in multiple neurons, including AIA interneurons, rapidly and reversibly inhibits escape from 1% O2. Ca2+ imaging reveals that a 7% to 1% O2 stimulus evokes a Ca2+ decrease in several neurons. Defects in mitochondrial complex I (MCI) and mitochondrial complex I (MCIII), which lead to persistently high reactive oxygen species (ROS), abrogate acute hypoxia responses. In particular, repressing the expression of isp-1, which encodes the iron sulfur protein of MCIII, inhibits escape from 1% O2 without affecting responses to 21% O2. Both genetic and pharmacological up-regulation of mitochondrial ROS increase cGMP levels, which contribute to the reduced hypoxia responses. Our results implicate ROS and precise regulation of intracellular cGMP in the modulation of acute responses to hypoxia by C. elegans. The ability to detect and respond to acute oxygen shortages is indispensable to aerobic life, but the molecular mechanisms underlying this capacity are poorly understood. This study reveals that high levels of cGMP and reactive oxygen species (ROS) prevent the nematode Caenorhabditis elegans from escaping hypoxia.
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65
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Volodina OV, Smirnikhina SA. The Choice of a Donor Molecule in Genome Editing Experiments in Animal Cells. Mol Biol 2022. [DOI: 10.1134/s002689332203013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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66
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Marnik EA, Almeida MV, Cipriani PG, Chung G, Caspani E, Karaulanov E, Gan HH, Zinno J, Isolehto IJ, Kielisch F, Butter F, Sharp CS, Flanagan RM, Bonnet FX, Piano F, Ketting RF, Gunsalus KC, Updike DL. The Caenorhabditis elegans TDRD5/7-like protein, LOTR-1, interacts with the helicase ZNFX-1 to balance epigenetic signals in the germline. PLoS Genet 2022; 18:e1010245. [PMID: 35657999 PMCID: PMC9200344 DOI: 10.1371/journal.pgen.1010245] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 06/15/2022] [Accepted: 05/09/2022] [Indexed: 11/24/2022] Open
Abstract
LOTUS and Tudor domain containing proteins have critical roles in the germline. Proteins that contain these domains, such as Tejas/Tapas in Drosophila, help localize the Vasa helicase to the germ granules and facilitate piRNA-mediated transposon silencing. The homologous proteins in mammals, TDRD5 and TDRD7, are required during spermiogenesis. Until now, proteins containing both LOTUS and Tudor domains in Caenorhabditis elegans have remained elusive. Here we describe LOTR-1 (D1081.7), which derives its name from its LOTUS and Tudor domains. Interestingly, LOTR-1 docks next to P granules to colocalize with the broadly conserved Z-granule helicase, ZNFX-1. The Tudor domain of LOTR-1 is required for its Z-granule retention. Like znfx-1 mutants, lotr-1 mutants lose small RNAs from the 3’ ends of WAGO and mutator targets, reminiscent of the loss of piRNAs from the 3’ ends of piRNA precursor transcripts in mouse Tdrd5 mutants. Our work shows that LOTR-1 acts with ZNFX-1 to bring small RNA amplifying mechanisms towards the 3’ ends of its RNA templates. Germ granules are protein and RNA complexes that are critical for maintaining an animal’s fertility. Central to the composition of germ granules are their small RNAs, which have the capacity to convey a memory of germline-licensed expression from one generation to the next. Here we describe and characterize a new germ-granule protein in C. elegans that we’ve named LOTR-1, after its LOTUS and Tudor domains. This combination of LOTUS and Tudor domains can be found in the mammalian proteins TDRD5 and TDRD7, which are required during spermatogenesis. During C. elegans embryogenesis, germ granules demix or partition into subgranules with refined functions. We show that LOTR-1 partitions with a specific class of subgranules called Z granules, interacting with a Z-granule helicase called ZNFX-1. Here, LOTR-1 functions with ZNFX-1 to position small RNA amplification from RNA templates, ensuring a memory of germline expression across generations. These findings may provide new insight into the function of TDRD5 and TDRD7 during human germline development.
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Affiliation(s)
- Elisabeth A. Marnik
- The MDI Biological Laboratory, Bar Harbor, Maine, United States of America
- Husson University, Bangor, Maine, United States of America
| | - Miguel V. Almeida
- Institute of Molecular Biology, Mainz, Germany
- International PhD Programme on Gene Regulation, Epigenetics & Genome Stability, Mainz, Germany
| | - P. Giselle Cipriani
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - George Chung
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
| | - Edoardo Caspani
- Institute of Molecular Biology, Mainz, Germany
- International PhD Programme on Gene Regulation, Epigenetics & Genome Stability, Mainz, Germany
| | | | - Hin Hark Gan
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
| | - John Zinno
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
| | - Ida J. Isolehto
- Institute of Molecular Biology, Mainz, Germany
- International PhD Programme on Gene Regulation, Epigenetics & Genome Stability, Mainz, Germany
| | | | - Falk Butter
- Institute of Molecular Biology, Mainz, Germany
| | - Catherine S. Sharp
- The MDI Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Roisin M. Flanagan
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
| | - Frederic X. Bonnet
- The MDI Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Fabio Piano
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - René F. Ketting
- Institute of Molecular Biology, Mainz, Germany
- * E-mail: (RFK); (KCG); (DLU)
| | - Kristin C. Gunsalus
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- * E-mail: (RFK); (KCG); (DLU)
| | - Dustin L. Updike
- The MDI Biological Laboratory, Bar Harbor, Maine, United States of America
- * E-mail: (RFK); (KCG); (DLU)
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67
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Vicencio J, Sánchez-Bolaños C, Moreno-Sánchez I, Brena D, Vejnar CE, Kukhtar D, Ruiz-López M, Cots-Ponjoan M, Rubio A, Melero NR, Crespo-Cuadrado J, Carolis C, Pérez-Pulido AJ, Giráldez AJ, Kleinstiver BP, Cerón J, Moreno-Mateos MA. Genome editing in animals with minimal PAM CRISPR-Cas9 enzymes. Nat Commun 2022; 13:2601. [PMID: 35552388 PMCID: PMC9098488 DOI: 10.1038/s41467-022-30228-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 04/22/2022] [Indexed: 01/21/2023] Open
Abstract
The requirement for Cas nucleases to recognize a specific PAM is a major restriction for genome editing. SpCas9 variants SpG and SpRY, recognizing NGN and NRN PAMs, respectively, have contributed to increase the number of editable genomic sites in cell cultures and plants. However, their use has not been demonstrated in animals. Here we study the nuclease activity of SpG and SpRY by targeting 40 sites in zebrafish and C. elegans. Delivered as mRNA-gRNA or ribonucleoprotein (RNP) complexes, SpG and SpRY were able to induce mutations in vivo, albeit at a lower rate than SpCas9 in equivalent formulations. This lower activity was overcome by optimizing mRNA-gRNA or RNP concentration, leading to mutagenesis at regions inaccessible to SpCas9. We also found that the CRISPRscan algorithm could help to predict SpG and SpRY targets with high activity in vivo. Finally, we applied SpG and SpRY to generate knock-ins by homology-directed repair. Altogether, our results expand the CRISPR-Cas targeting genomic landscape in animals.
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Affiliation(s)
- Jeremy Vicencio
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Carlos Sánchez-Bolaños
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Ismael Moreno-Sánchez
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - David Brena
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Dmytro Kukhtar
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Miguel Ruiz-López
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Mariona Cots-Ponjoan
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Alejandro Rubio
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Natalia Rodrigo Melero
- Biomolecular Screening and Protein Technologies Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | - Jesús Crespo-Cuadrado
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Carlo Carolis
- Biomolecular Screening and Protein Technologies Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | - Antonio J Pérez-Pulido
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Antonio J Giráldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, 06510, USA
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - Julián Cerón
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain.
| | - Miguel A Moreno-Mateos
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain.
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain.
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68
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Jin EJ, Jin Y. A mutation linked to degt-1(ok3307) in C. elegans strain VC2633 affects rpm-1. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000565. [PMID: 35622515 PMCID: PMC9073554 DOI: 10.17912/micropub.biology.000565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 12/01/2022]
Abstract
C. elegans
strain VC2633 is described to contain the
degt-1(ok3307)
mutation. Here, we report the identification of a loss of function mutation in
rpm-1
that is linked to
degt-1(ok3307)
in VC2633. In homozygous animals of
degt-1(ok3307)
derived from VC2633, we observed neuronal morphology defects that resemble
rpm-1
loss of function. Based on complementation test with
rpm-1
mutants, sanger sequencing of
rpm-1
locus and genome editing, we verified a single nucleotide change designated
rpm-1(ju1928)
in
degt-1(ok3307)
chromosome in VC2633 and derivatives. This mutation alters a conserved Glutamine at amino acid 3089 to Histidine in RPM-1. We generated a new strain of
degt-1(ok3307)
without
ju1928;
the updated genotype of VC2633 strain is
rpm-1(ju1928) degt-1(ok3307).
While currently there are no reported binding partners for the region of RPM-1 containing Glu3089, the neuronal defects associated with the mutant RPM-1 suggest that this region may play roles in regulating RPM-1 activity.
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Affiliation(s)
- Eugene Jennifer Jin
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, CA, USA
,
Correspondence to: Eugene Jennifer Jin (
)
| | - Yishi Jin
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, CA, USA
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69
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Identification and characterization of Crumbs polarity complex proteins in Caenorhabditis elegans. J Biol Chem 2022; 298:101786. [PMID: 35247383 PMCID: PMC9006659 DOI: 10.1016/j.jbc.2022.101786] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/12/2022] [Accepted: 02/16/2022] [Indexed: 11/23/2022] Open
Abstract
Crumbs proteins are evolutionarily conserved transmembrane proteins with essential roles in promoting the formation of the apical domain in epithelial cells. The short intracellular tail of Crumbs proteins are known to interact with several proteins, including the scaffolding protein PALS1 (protein associated with LIN7, Stardust in Drosophila). PALS1 in turn binds to a second scaffolding protein PATJ (PALS1-associated tight junction protein) to form the core Crumbs/PALS1/PATJ complex. While essential roles in epithelial organization have been shown for Crumbs proteins in Drosophila and mammalian systems, the three Caenorhabditis elegans crumbs genes are dispensable for epithelial polarization and development. Here, we investigated the presence and function of PALS1 and PATJ orthologs in C. elegans. We identified MAGU-2 as the C. elegans ortholog of PALS1 and show that MAGU-2 interacts with all three Crumbs proteins and localizes to the apical membrane domain of intestinal epithelial cells in a Crumbs-dependent fashion. Similar to crumbs mutants, magu-2 deletion showed no epithelial polarity defects. We also identified MPZ-1 as a candidate ortholog of PATJ based on the physical interaction with MAGU-2 and sequence similarity with PATJ proteins. However, MPZ-1 is not broadly expressed in epithelial tissues and, therefore, not likely a core component of the C. elegans Crumbs complex. Finally, we show overexpression of the Crumbs proteins EAT-20 or CRB-3 can lead to apical membrane expansion in the intestine. Our results shed light on the composition of the C. elegans Crumbs complex and indicate that the role of Crumbs proteins in promoting apical domain formation is conserved.
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70
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Snoozy J, Breen PC, Ruvkun G, Warnhoff K. moc-6/MOCS2A is necessary for molybdenum cofactor synthesis in C. elegans. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000531. [PMID: 35224462 PMCID: PMC8864482 DOI: 10.17912/micropub.biology.000531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 11/05/2022]
Abstract
Molybdenum cofactor (Moco) is an essential prosthetic group that mediates the activity of 4 animal oxidases and is required for viability. Humans with mutations in the genes encoding Moco-biosynthetic enzymes suffer from Moco deficiency, a neonatal lethal inborn error of metabolism. Caenorhabditis elegans has recently emerged as a useful and tractable genetic discovery engine for Moco biology. Here, we identify and characterize K10D2.7/moc-6, the C. elegans ortholog of human MOCS2A, a sulfur-carrier protein essential for Moco synthesis. Using CRISPR/Cas9 gene editing, we generate 3 null mutations in K10D2.7/moc-6 and with these alleles genetically demonstrate that K10D2.7/moc-6 is necessary for endogenous Moco synthesis in C. elegans.
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Affiliation(s)
- Jennifer Snoozy
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD 57104, USA
| | - Peter C Breen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kurt Warnhoff
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD 57104, USA,
Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105 USA,
Correspondence to: Kurt Warnhoff ()
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71
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Peterson ND, Icso JD, Salisbury JE, Rodríguez T, Thompson PR, Pukkila-Worley R. Pathogen infection and cholesterol deficiency activate the C. elegans p38 immune pathway through a TIR-1/SARM1 phase transition. eLife 2022; 11:e74206. [PMID: 35098926 PMCID: PMC8923663 DOI: 10.7554/elife.74206] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
Intracellular signaling regulators can be concentrated into membrane-free, higher ordered protein assemblies to initiate protective responses during stress - a process known as phase transition. Here, we show that a phase transition of the Caenorhabditis elegans Toll/interleukin-1 receptor domain protein (TIR-1), an NAD+ glycohydrolase homologous to mammalian sterile alpha and TIR motif-containing 1 (SARM1), underlies p38 PMK-1 immune pathway activation in C. elegans intestinal epithelial cells. Through visualization of fluorescently labeled TIR-1/SARM1 protein, we demonstrate that physiologic stresses, both pathogen and non-pathogen, induce multimerization of TIR-1/SARM1 into visible puncta within intestinal epithelial cells. In vitro enzyme kinetic analyses revealed that, like mammalian SARM1, the NAD+ glycohydrolase activity of C. elegans TIR-1 is dramatically potentiated by protein oligomerization and a phase transition. Accordingly, C. elegans with genetic mutations that specifically block either multimerization or the NAD+ glycohydrolase activity of TIR-1/SARM1 fail to induce p38 PMK phosphorylation, are unable to increase immune effector expression, and are dramatically susceptible to bacterial infection. Finally, we demonstrate that a loss-of-function mutation in nhr-8, which alters cholesterol metabolism and is used to study conditions of sterol deficiency, causes TIR-1/SARM1 to oligomerize into puncta in intestinal epithelial cells. Cholesterol scarcity increases p38 PMK-1 phosphorylation, primes immune effector induction in a manner that requires TIR-1/SARM1 oligomerization and its intrinsic NAD+ glycohydrolase activity, and reduces pathogen accumulation in the intestine during a subsequent infection. These data reveal a new adaptive response that allows a metazoan host to anticipate pathogen threats during cholesterol deprivation, a time of relative susceptibility to infection. Thus, a phase transition of TIR-1/SARM1 as a prerequisite for its NAD+ glycohydrolase activity is strongly conserved across millions of years of evolution and is essential for diverse physiological processes in multiple cell types.
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Affiliation(s)
- Nicholas D Peterson
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Janneke D Icso
- Program in Chemical Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - J Elizabeth Salisbury
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Tomás Rodríguez
- RNA Therapeutics Institute, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Paul R Thompson
- Program in Chemical Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Read Pukkila-Worley
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
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72
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Floxed exon (Flexon): A flexibly positioned stop cassette for recombinase-mediated conditional gene expression. Proc Natl Acad Sci U S A 2022; 119:2117451119. [PMID: 35027456 PMCID: PMC8784106 DOI: 10.1073/pnas.2117451119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2021] [Indexed: 12/15/2022] Open
Abstract
Tools that afford spatiotemporal control of gene expression are crucial for studying genes and processes in multicellular organisms. Stop cassettes consist of exogenous sequences that interrupt gene expression and flanking site-specific recombinase sites to allow for tissue-specific excision and restoration of function by expression of the cognate recombinase. We describe a stop cassette called a flexon, composed of an artificial exon flanked by artificial introns that can be flexibly positioned in a gene. We demonstrate its efficacy in Caenorhabditis elegans for lineage-specific control of gene expression and for tissue-specific RNA interference and discuss other potential uses. The Flexon approach should be feasible in any system amenable to site-specific recombination-based methods and applicable to diverse areas including development, neuroscience, and metabolism. Conditional gene expression is a powerful tool for genetic analysis of biological phenomena. In the widely used “lox-stop-lox” approach, insertion of a stop cassette consisting of a series of stop codons and polyadenylation signals flanked by lox sites into the 5′ untranslated region (UTR) of a gene prevents expression until the cassette is excised by tissue-specific expression of Cre recombinase. Although lox-stop-lox and similar approaches using other site-specific recombinases have been successfully used in many experimental systems, this design has certain limitations. Here, we describe the Floxed exon (Flexon) approach, which uses a stop cassette composed of an artificial exon flanked by artificial introns, designed to cause premature termination of translation and nonsense-mediated decay of the mRNA and allowing for flexible placement into a gene. We demonstrate its efficacy in Caenorhabditis elegans by showing that, when promoters that cause weak and/or transient cell-specific expression are used to drive Cre in combination with a gfp(flexon) transgene, strong and sustained expression of green fluorescent protein (GFP) is obtained in specific lineages. We also demonstrate its efficacy in an endogenous gene context: we inserted a flexon into the Argonaute gene rde-1 to abrogate RNA interference (RNAi), and restored RNAi tissue specifically by expression of Cre. Finally, we describe several potential additional applications of the Flexon approach, including more precise control of gene expression using intersectional methods, tissue-specific protein degradation, and generation of genetic mosaics. The Flexon approach should be feasible in any system where a site-specific recombination-based method may be applied.
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73
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Medley JC, Hebbar S, Sydzyik JT, Zinovyeva AY. Single nucleotide substitutions effectively block Cas9 and allow for scarless genome editing in Caenorhabditis elegans. Genetics 2022; 220:iyab199. [PMID: 34791245 PMCID: PMC8733430 DOI: 10.1093/genetics/iyab199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
In Caenorhabditis elegans, germline injection of Cas9 complexes is reliably used to achieve genome editing through homology-directed repair of Cas9-generated DNA breaks. To prevent Cas9 from targeting repaired DNA, additional blocking mutations are often incorporated into homologous repair templates. Cas9 can be blocked either by mutating the PAM sequence that is essential for Cas9 activity or by mutating the guide sequence that targets Cas9 to a specific genomic location. However, it is unclear how many nucleotides within the guide sequence should be mutated, since Cas9 can recognize "off-target" sequences that are imperfectly paired to its guide. In this study, we examined whether single-nucleotide substitutions within the guide sequence are sufficient to block Cas9 and allow for efficient genome editing. We show that a single mismatch within the guide sequence effectively blocks Cas9 and allows for recovery of edited animals. Surprisingly, we found that a low rate of edited animals can be recovered without introducing any blocking mutations, suggesting a temporal block to Cas9 activity in C. elegans. Furthermore, we show that the maternal genome of hermaphrodite animals is preferentially edited over the paternal genome. We demonstrate that maternally provided haplotypes can be selected using balancer chromosomes and propose a method of mutant isolation that greatly reduces screening efforts postinjection. Collectively, our findings expand the repertoire of genome editing strategies in C. elegans and demonstrate that extraneous blocking mutations are not required to recover edited animals when the desired mutation is located within the guide sequence.
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Affiliation(s)
- Jeffrey C Medley
- Division of Biology, Kansas State University, Manhattan, KS 66502, USA
| | - Shilpa Hebbar
- Division of Biology, Kansas State University, Manhattan, KS 66502, USA
| | - Joel T Sydzyik
- Division of Biology, Kansas State University, Manhattan, KS 66502, USA
| | - Anna Y Zinovyeva
- Division of Biology, Kansas State University, Manhattan, KS 66502, USA
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74
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Abstract
The clustered, regularly interspaced, short, palindromic repeat (CRISPR)-associated (CAS) nuclease Cas9 has been used in many organisms to generate specific mutations and transgene insertions. Here we describe our most up-to-date protocols using the S. pyogenes Cas9 in C. elegans that provides a convenient and effective approach for making heritable changes to the worm genome. We present several considerations when deciding which strategy best suits the needs of the experiment.
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Affiliation(s)
- Charlotte J Martin
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - John A Calarco
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
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75
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Ding C, Wu Y, Dabas H, Hammarlund M. Activation of the CaMKII-Sarm1-ASK1-p38 MAP kinase pathway protects against axon degeneration caused by loss of mitochondria. eLife 2022; 11:73557. [PMID: 35285800 PMCID: PMC8920508 DOI: 10.7554/elife.73557] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/25/2022] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial defects are tightly linked to axon degeneration, yet the underlying cellular mechanisms remain poorly understood. In Caenorhabditis elegans, PVQ axons that lack mitochondria degenerate spontaneously with age. Using an unbiased genetic screen, we found that cell-specific activation of CaMKII/UNC-43 suppresses axon degeneration due to loss of mitochondria. Unexpectedly, CaMKII/UNC-43 activates the conserved Sarm1/TIR-1-ASK1/NSY-1-p38 MAPK pathway and eventually the transcription factor CEBP-1 to protect against degeneration. In addition, we show that disrupting a trafficking complex composed of calsyntenin/CASY-1, Mint/LIN-10, and kinesin suppresses axon degeneration. Further analysis indicates that disruption of this trafficking complex activates the CaMKII-Sarm1-MAPK pathway through L-type voltage-gated calcium channels. Our findings identify CaMKII as a pivot point between mitochondrial defects and axon degeneration, describe how it is regulated, and uncover a surprising neuroprotective role for the Sarm1-p38 MAPK pathway in this context.
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Affiliation(s)
- Chen Ding
- Department of Neuroscience, Yale University School of MedicineNew HavenUnited States
| | - Youjun Wu
- Department of Genetics, Yale University School of MedicineNew HavenUnited States
| | - Hadas Dabas
- Department of Genetics, Yale University School of MedicineNew HavenUnited States
| | - Marc Hammarlund
- Department of Neuroscience, Yale University School of MedicineNew HavenUnited States,Department of Genetics, Yale University School of MedicineNew HavenUnited States
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76
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Stolpner N, Dickinson DJ. Single-Cell Single-Molecule Pull-Down (sc-SiMPull) for Detection of Protein Complexes from Embryonic Lysates. Methods Mol Biol 2022; 2438:59-81. [PMID: 35147935 PMCID: PMC8851684 DOI: 10.1007/978-1-0716-2035-9_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Mapping how proteins form complexes and change binding partners is central to understanding cell signaling. Bulk biochemistry can provide a summary of what complexes are present in a cell, but information about the diversity of individual protein complexes is lost. Here, we describe single-cell , single-molecule pull-down (sc-SiMPull), a TIRF microscopy-based coimmunoprecipitation method, to visualize thousands of individual proteins, their binding partners, and protein complex stoichiometry directly from single-cell lysate. By iterating sc-SiMPull over time, temporal dynamics of protein complexes in response to signaling can be constructed.
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Affiliation(s)
- Naomi Stolpner
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Daniel J Dickinson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
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77
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Hiraga H, Ishita Y, Chihara T, Okumura M. Efficient visual screening of CRISPR/Cas9 genome editing in the nematode Pristionchus pacificus. Dev Growth Differ 2021; 63:488-500. [PMID: 34813661 DOI: 10.1111/dgd.12761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/17/2021] [Accepted: 09/30/2021] [Indexed: 12/22/2022]
Abstract
CRISPR/Cas9 genome editing has been applied to a wide variety of organisms, including nematodes such as Caenorhabditis elegans and Pristionchus pacificus. In these nematodes, genome editing is achieved by microinjection of Cas9 protein and guide RNA into the hermaphrodite gonads. However, P. pacificus is less efficient in CRISPR/Cas9 genome editing and exogenous gene expression. Therefore, it takes considerable time and effort to screen for target mutants if there are no visual markers that indicate successful injection. To overcome this problem, co-injection markers (gRNA for Ppa-prl-1, which induces the roller phenotype, and Ppa-egl-20p::turboRFP, a plasmid expressing a fluorescent protein) have been developed in P. pacificus. By selecting worms with the roller phenotype or turboRFP expression, screening efficiency is substantially increased to obtain worms with desired mutations. Here, we describe a step-by-step protocol for the visual screening system for CRISPR/Cas9 genome editing in P. pacificus. We also describe technical tips for microinjection, which is difficult for beginners. This protocol will facilitate genome editing in P. pacificus and may be applied to other nematode species.
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Affiliation(s)
- Hirokuni Hiraga
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Yuuki Ishita
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takahiro Chihara
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan.,Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Misako Okumura
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan.,Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
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78
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DeMott E, Dickinson DJ, Doonan R. Highly improved cloning efficiency for plasmid-based CRISPR knock-in in C. elegans. MICROPUBLICATION BIOLOGY 2021; 2021:10.17912/micropub.biology.000499. [PMID: 34816097 PMCID: PMC8606032 DOI: 10.17912/micropub.biology.000499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 11/06/2022]
Abstract
Plasmid-based CRISPR knock-in is a streamlined, scalable, and versatile approach for generating fluorescent protein tags in C. elegans (Dickinson et al. 2015; Schwartz and Jorgensen 2016). However, compared to more recent protocols that utilize commercially available Cas9/RNP products and linear DNA repair templates (Dokshin et al. 2018; Ghanta and Mello 2020), the cloning required for plasmid-based protocols has been cited as a drawback of this knock-in approach. Using thorough quantitative assessment, we have found that cloning efficiency can reproducibly reach 90% for the plasmids of the self-excising cassette (SEC) selection method, essentially resolving cloning as a burden for plasmid-based CRISPR knock-in.
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Affiliation(s)
- Ella DeMott
- Glow Worms Stream, Freshman Research Initiative, Texas Institute for Discovery Education in Science, College of Natural Sciences, The University of Texas at Austin, Austin TX, USA
| | - Daniel J Dickinson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin TX, USA
| | - Ryan Doonan
- Glow Worms Stream, Freshman Research Initiative, Texas Institute for Discovery Education in Science, College of Natural Sciences, The University of Texas at Austin, Austin TX, USA,
Correspondence to: Ryan Doonan ()
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79
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Sarıkaya S, Dickinson DJ. Rapid extraction and kinetic analysis of protein complexes from single cells. Biophys J 2021; 120:5018-5031. [PMID: 34653388 PMCID: PMC8633716 DOI: 10.1016/j.bpj.2021.10.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/22/2021] [Accepted: 10/08/2021] [Indexed: 11/22/2022] Open
Abstract
Proteins contribute to cell biology by forming dynamic, regulated interactions, and measuring these interactions is a foundational approach in biochemistry. We present a rapid, quantitative in vivo assay for protein-protein interactions, based on optical cell lysis followed by time-resolved single-molecule analysis of protein complex binding to an antibody-coated substrate. We show that our approach has better reproducibility, higher dynamic range, and lower background than previous single-molecule pull-down assays. Furthermore, we demonstrate that by monitoring cellular protein complexes over time after cell lysis, we can measure the dissociation rate constant of a cellular protein complex, providing information about binding affinity and kinetics. Our dynamic single-cell, single-molecule pull-down method thus approaches the biochemical precision that is often sought from in vitro assays while being applicable to native protein complexes isolated from single cells in vivo.
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Affiliation(s)
- Sena Sarıkaya
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas
| | - Daniel J Dickinson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas.
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80
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Price IF, Hertz HL, Pastore B, Wagner J, Tang W. Proximity labeling identifies LOTUS domain proteins that promote the formation of perinuclear germ granules in C. elegans. eLife 2021; 10:e72276. [PMID: 34730513 PMCID: PMC8616582 DOI: 10.7554/elife.72276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 11/01/2021] [Indexed: 11/30/2022] Open
Abstract
The germ line produces gametes that transmit genetic and epigenetic information to the next generation. Maintenance of germ cells and development of gametes require germ granules-well-conserved membraneless and RNA-rich organelles. The composition of germ granules is elusive owing to their dynamic nature and their exclusive expression in the germ line. Using Caenorhabditis elegans germ granule, called P granule, as a model system, we employed a proximity-based labeling method in combination with mass spectrometry to comprehensively define its protein components. This set of experiments identified over 200 proteins, many of which contain intrinsically disordered regions (IDRs). An RNA interference-based screen identified factors that are essential for P granule assembly, notably EGGD-1 and EGGD-2, two putative LOTUS-domain proteins. Loss of eggd-1 and eggd-2 results in separation of P granules from the nuclear envelope, germline atrophy, and reduced fertility. We show that IDRs of EGGD-1 are required to anchor EGGD-1 to the nuclear periphery while its LOTUS domains are required to promote the perinuclear localization of P granules. Taken together, our work expands the repertoire of P granule constituents and provides new insights into the role of LOTUS-domain proteins in germ granule organization.
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Affiliation(s)
- Ian F Price
- Department of Biological Chemistry and PharmacologyColumbusUnited States
- Center for RNA BiologyColumbusUnited States
- Ohio State Biochemistry ProgramColumbusUnited States
| | - Hannah L Hertz
- Department of Biological Chemistry and PharmacologyColumbusUnited States
- Center for RNA BiologyColumbusUnited States
| | - Benjamin Pastore
- Department of Biological Chemistry and PharmacologyColumbusUnited States
- Center for RNA BiologyColumbusUnited States
- Ohio State Biochemistry ProgramColumbusUnited States
| | - Jillian Wagner
- Department of Biological Chemistry and PharmacologyColumbusUnited States
- Department of Molecular Genetics, Ohio State UniversityColumbusUnited States
| | - Wen Tang
- Department of Biological Chemistry and PharmacologyColumbusUnited States
- Center for RNA BiologyColumbusUnited States
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81
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Schwartz ML, Davis MW, Rich MS, Jorgensen EM. High-efficiency CRISPR gene editing in C. elegans using Cas9 integrated into the genome. PLoS Genet 2021; 17:e1009755. [PMID: 34748534 PMCID: PMC8601624 DOI: 10.1371/journal.pgen.1009755] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/18/2021] [Accepted: 10/16/2021] [Indexed: 11/24/2022] Open
Abstract
Gene editing in C. elegans using plasmid-based CRISPR reagents requires microinjection of many animals to produce a single edit. Germline silencing of plasmid-borne Cas9 is a major cause of inefficient editing. Here, we present a set of C. elegans strains that constitutively express Cas9 in the germline from an integrated transgene. These strains markedly improve the success rate for plasmid-based CRISPR edits. For simple, short homology arm GFP insertions, 50-100% of injected animals typically produce edited progeny, depending on the target locus. Template-guided editing from an extrachromosomal array is maintained over multiple generations. We have built strains with the Cas9 transgene on multiple chromosomes. Additionally, each Cas9 locus also contains a heatshock-driven Cre recombinase for selectable marker removal and a bright fluorescence marker for easy outcrossing. These integrated Cas9 strains greatly reduce the workload for producing individual genome edits.
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Affiliation(s)
- Matthew L. Schwartz
- Howard Hughes Medical Institute and School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - M. Wayne Davis
- Howard Hughes Medical Institute and School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Matthew S. Rich
- Howard Hughes Medical Institute and School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Erik M. Jorgensen
- Howard Hughes Medical Institute and School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
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82
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Riga A, Cravo J, Schmidt R, Pires HR, Castiglioni VG, van den Heuvel S, Boxem M. Caenorhabditis elegans LET-413 Scribble is essential in the epidermis for growth, viability, and directional outgrowth of epithelial seam cells. PLoS Genet 2021; 17:e1009856. [PMID: 34673778 PMCID: PMC8570498 DOI: 10.1371/journal.pgen.1009856] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 11/05/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022] Open
Abstract
The conserved adapter protein Scribble (Scrib) plays essential roles in a variety of cellular processes, including polarity establishment, proliferation, and directed cell migration. While the mechanisms through which Scrib promotes epithelial polarity are beginning to be unraveled, its roles in other cellular processes including cell migration remain enigmatic. In C. elegans, the Scrib ortholog LET-413 is essential for apical–basal polarization and junction formation in embryonic epithelia. However, whether LET-413 is required for postembryonic development or plays a role in migratory events is not known. Here, we use inducible protein degradation to investigate the functioning of LET-413 in larval epithelia. We find that LET-413 is essential in the epidermal epithelium for growth, viability, and junction maintenance. In addition, we identify a novel role for LET-413 in the polarized outgrowth of the epidermal seam cells. These stem cell-like epithelial cells extend anterior and posterior directed apical protrusions in each larval stage to reconnect to their neighbors. We show that the role of LET-413 in seam cell outgrowth is likely mediated largely by the junctional component DLG-1 discs large, which we demonstrate is also essential for directed outgrowth of the seam cells. Our data uncover multiple essential functions for LET-413 in larval development and show that the polarized outgrowth of the epithelial seam cells is controlled by LET-413 Scribble and DLG-1 Discs large. Most cells in multicellular organisms are organized along a directional axis of cell polarity. One protein that is important for this polarized organization is the conserved polarity regulator Scribble. This protein has several functions, including forming the basolateral domains of cells, promoting the formation of cell junctions, and promoting cell migration. How Scribble performs these functions is not fully understood. In this paper we study the role of Scribble during larval development of the small nematode Caenorhabditis elegans using an inducible protein degradation system. We show that Scribble, called LET-413 in C. elegans, is essential in the epidermal epithelium for animal development, as depletion of LET-413 in only this tissue blocks growth. We also demonstrate that LET-413 is required for the polarized outgrowth of an epithelial cell type called the seam cells, a process resembling cell migration. Finally, we show that one major function of LET-413 in seam cell outgrowth is the localization of the junctional component Discs large (DLG-1), which we demonstrate is also essential for this process. Our data thus uncover multiple essential functions for LET-413 in larval development and provide new insights into how the directional outgrowth of epithelial seam cells is controlled.
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Affiliation(s)
- Amalia Riga
- Division of Developmental Biology, Institute of Biodynamics and Biocomplexity, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Janine Cravo
- Division of Developmental Biology, Institute of Biodynamics and Biocomplexity, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Ruben Schmidt
- Division of Developmental Biology, Institute of Biodynamics and Biocomplexity, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Helena R. Pires
- Division of Developmental Biology, Institute of Biodynamics and Biocomplexity, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Victoria G. Castiglioni
- Division of Developmental Biology, Institute of Biodynamics and Biocomplexity, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Sander van den Heuvel
- Division of Developmental Biology, Institute of Biodynamics and Biocomplexity, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Mike Boxem
- Division of Developmental Biology, Institute of Biodynamics and Biocomplexity, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- * E-mail:
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83
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Ghanta KS, Chen Z, Mir A, Dokshin GA, Krishnamurthy PM, Yoon Y, Gallant J, Xu P, Zhang XO, Ozturk AR, Shin M, Idrizi F, Liu P, Gneid H, Edraki A, Lawson ND, Rivera-Pérez JA, Sontheimer EJ, Watts JK, Mello CC. 5'-Modifications improve potency and efficacy of DNA donors for precision genome editing. eLife 2021; 10:e72216. [PMID: 34665130 PMCID: PMC8568340 DOI: 10.7554/elife.72216] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/09/2021] [Indexed: 12/22/2022] Open
Abstract
Nuclease-directed genome editing is a powerful tool for investigating physiology and has great promise as a therapeutic approach to correct mutations that cause disease. In its most precise form, genome editing can use cellular homology-directed repair (HDR) pathways to insert information from an exogenously supplied DNA-repair template (donor) directly into a targeted genomic location. Unfortunately, particularly for long insertions, toxicity and delivery considerations associated with repair template DNA can limit HDR efficacy. Here, we explore chemical modifications to both double-stranded and single-stranded DNA-repair templates. We describe 5'-terminal modifications, including in its simplest form the incorporation of triethylene glycol (TEG) moieties, that consistently increase the frequency of precision editing in the germlines of three animal models (Caenorhabditis elegans, zebrafish, mice) and in cultured human cells.
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Affiliation(s)
- Krishna S Ghanta
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Zexiang Chen
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Aamir Mir
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Gregoriy A Dokshin
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | | | - Yeonsoo Yoon
- Department of Pediatrics, Division of Genes and Development, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Judith Gallant
- Department of Pediatrics, Division of Genes and Development, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Ping Xu
- Department of Pediatrics, Division of Genes and Development, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Xiao-Ou Zhang
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Ahmet Rasit Ozturk
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Masahiro Shin
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Feston Idrizi
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Hassan Gneid
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Alireza Edraki
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Nathan D Lawson
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical SchoolWorcesterUnited States
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical SchoolWorcesterUnited States
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Jaime A Rivera-Pérez
- Department of Pediatrics, Division of Genes and Development, University of Massachusetts Medical SchoolWorcesterUnited States
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical SchoolWorcesterUnited States
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical SchoolWorcesterUnited States
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Craig C Mello
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
- Howard Hughes Medical Institute, University of Massachusetts Medical SchoolWorcesterUnited States
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84
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The nuclear ubiquitin ligase adaptor SPOP is a conserved regulator of C9orf72 dipeptide toxicity. Proc Natl Acad Sci U S A 2021; 118:2104664118. [PMID: 34593637 DOI: 10.1073/pnas.2104664118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2021] [Indexed: 12/29/2022] Open
Abstract
A hexanucleotide repeat expansion in the C9orf72 gene is the most common cause of inherited amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Unconventional translation of the C9orf72 repeat produces dipeptide repeat proteins (DPRs). Previously, we showed that the DPRs PR50 and GR50 are highly toxic when expressed in Caenorhabditis elegans, and this toxicity depends on nuclear localization of the DPR. In an unbiased genome-wide RNA interference (RNAi) screen for suppressors of PR50 toxicity, we identified 12 genes that consistently suppressed either the developmental arrest and/or paralysis phenotype evoked by PR50 expression. All of these genes have vertebrate homologs, and 7 of 12 contain predicted nuclear localization signals. One of these genes was spop-1, the C. elegans homolog of SPOP, a nuclear localized E3 ubiquitin ligase adaptor only found in metazoans. SPOP is also required for GR50 toxicity and functions in a genetic pathway that includes cul-3, which is the canonical E3 ligase partner for SPOP Genetic or pharmacological inhibition of SPOP in mammalian primary spinal cord motor neurons suppressed DPR toxicity without affecting DPR expression levels. Finally, we find that knockdown of bromodomain proteins in both C. elegans and mammalian neurons, which are known SPOP ubiquitination targets, suppresses the protective effect of SPOP inhibition. Together, these data suggest a model in which SPOP promotes the DPR-dependent ubiquitination and degradation of BRD proteins. We speculate the pharmacological manipulation of this pathway, which is currently underway for multiple cancer subtypes, could also represent an entry point for therapeutic intervention to treat C9orf72 FTD/ALS.
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85
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Park S, Sohn J, Kwon S, Kim EJE, Jung Y, Park HEH, Kim SS, Lee SJV. Age-dependent upregulation of Y RNAs in Caenorhabditis elegans. MICROPUBLICATION BIOLOGY 2021; 2021. [PMID: 34604714 PMCID: PMC8477234 DOI: 10.17912/micropub.biology.000452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/02/2021] [Accepted: 09/02/2021] [Indexed: 11/10/2022]
Abstract
Y RNA is a conserved small non-coding RNA whose functions in aging remain unknown. Here, we sought to determine the role of C. elegans Y RNA homologs, CeY RNA (CeY) and stem-bulge RNAs (sbRNAs), in aging. We found that the levels of CeY and sbRNAs generally increased during aging. We showed that CeY was downregulated by oxidative and thermal stresses, whereas several sbRNAs were upregulated by oxidative stress. We did not observe lifespan phenotypes by mutations in CeY-coding yrn-1. Future research under various genetic and environmental conditions is required to further evaluate the role of Y RNA in C. elegans aging.
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Affiliation(s)
- Sangsoon Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Jooyeon Sohn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Sujeong Kwon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Eun Ji E Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Yoonji Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Hae-Eun H Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Sieun S Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Seung-Jae V Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
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86
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Makeyeva YV, Shirayama M, Mello CC. Cues from mRNA splicing prevent default Argonaute silencing in C. elegans. Dev Cell 2021; 56:2636-2648.e4. [PMID: 34547227 DOI: 10.1016/j.devcel.2021.08.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 06/28/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022]
Abstract
In animals, Argonaute small-RNA pathways scan germline transcripts to silence self-replicating genetic elements. However, little is known about how endogenous gene expression is recognized and licensed. Here, we show that the presence of introns and, by inference, the process of mRNA splicing prevents default Argonaute-mediated silencing in the C. elegans germline. The silencing of intronless genes is initiated independently of the piRNA pathway but nevertheless engages multiple components of the downstream amplification and maintenance mechanisms that mediate transgenerational silencing, including both nuclear and cytoplasmic members of the worm-specific Argonaute gene family (WAGOs). Small RNAs amplified from intronless mRNAs can trans-silence cognate intron-containing genes. Interestingly, a second, small RNA-independent cis-acting mode of silencing also acts on intronless mRNAs. Our findings suggest that cues put in place during mRNA splicing license germline gene expression and provide evidence for a splicing-dependent and dsRNA- and piRNA-independent mechanism that can program Argonaute silencing.
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Affiliation(s)
- Yekaterina V Makeyeva
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Masaki Shirayama
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, Worcester, MA 01605, USA
| | - Craig C Mello
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, Worcester, MA 01605, USA.
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87
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Huang G, de Jesus B, Koh A, Blanco S, Rettmann A, DeMott E, Sylvester M, Ren C, Meng C, Waterland S, Rhodes A, Alicea P, Flynn A, Dickinson DJ, Doonan R. Improved CRISPR/Cas9 knock-in efficiency via the self-excising cassette (SEC) selection method in C. elegans. MICROPUBLICATION BIOLOGY 2021; 2021. [PMID: 34549176 PMCID: PMC8449260 DOI: 10.17912/micropub.biology.000460] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 11/08/2022]
Abstract
Streamlined, selection-based CRISPR knock-in protocols for C. elegans were first introduced six years ago (Dickinson et al. 2015; Schwartz and Jorgensen 2016). Though these selection-based approaches are powerful, one drawback has been the requirement to inject large numbers of P0 worms (~30-60 per gene target). We have found that a combination of high-purity DNA and a lower concentration of Cas9/sgRNA plasmid dramatically improves efficiency, often resulting in multiple independent CRISPR knock-ins via as few as 10 injected worms, comparable to the efficiency of melted dsDNA templates and purified Cas9 protein (Dokshin et al. 2018; Ghanta and Mello 2020).
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Affiliation(s)
- George Huang
- Glow Worms Stream, Freshman Research Initiative, Texas Institute for Discovery Education in Science, College of Natural Sciences, The University of Texas at Austin, Austin TX, USA
| | - Bailey de Jesus
- Glow Worms Stream, Freshman Research Initiative, Texas Institute for Discovery Education in Science, College of Natural Sciences, The University of Texas at Austin, Austin TX, USA
| | - Alex Koh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin TX, USA
| | - Sara Blanco
- Glow Worms Stream, Freshman Research Initiative, Texas Institute for Discovery Education in Science, College of Natural Sciences, The University of Texas at Austin, Austin TX, USA
| | - Aubrie Rettmann
- Glow Worms Stream, Freshman Research Initiative, Texas Institute for Discovery Education in Science, College of Natural Sciences, The University of Texas at Austin, Austin TX, USA
| | - Ella DeMott
- Glow Worms Stream, Freshman Research Initiative, Texas Institute for Discovery Education in Science, College of Natural Sciences, The University of Texas at Austin, Austin TX, USA
| | - Melynda Sylvester
- Glow Worms Stream, Freshman Research Initiative, Texas Institute for Discovery Education in Science, College of Natural Sciences, The University of Texas at Austin, Austin TX, USA
| | - Cassie Ren
- Glow Worms Stream, Freshman Research Initiative, Texas Institute for Discovery Education in Science, College of Natural Sciences, The University of Texas at Austin, Austin TX, USA
| | - Carrie Meng
- Glow Worms Stream, Freshman Research Initiative, Texas Institute for Discovery Education in Science, College of Natural Sciences, The University of Texas at Austin, Austin TX, USA
| | - Skye Waterland
- Glow Worms Stream, Freshman Research Initiative, Texas Institute for Discovery Education in Science, College of Natural Sciences, The University of Texas at Austin, Austin TX, USA
| | - Anita Rhodes
- Glow Worms Stream, Freshman Research Initiative, Texas Institute for Discovery Education in Science, College of Natural Sciences, The University of Texas at Austin, Austin TX, USA
| | - Persephone Alicea
- Glow Worms Stream, Freshman Research Initiative, Texas Institute for Discovery Education in Science, College of Natural Sciences, The University of Texas at Austin, Austin TX, USA
| | - Abbey Flynn
- Glow Worms Stream, Freshman Research Initiative, Texas Institute for Discovery Education in Science, College of Natural Sciences, The University of Texas at Austin, Austin TX, USA
| | - Daniel J Dickinson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin TX, USA
| | - Ryan Doonan
- Glow Worms Stream, Freshman Research Initiative, Texas Institute for Discovery Education in Science, College of Natural Sciences, The University of Texas at Austin, Austin TX, USA.,Department of Molecular Biosciences, The University of Texas at Austin, Austin TX, USA
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88
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Abstract
In Caenorhabditis elegans, targeted genome editing techniques are now routinely used to generate germline edits. The remarkable ease of C. elegans germline editing is attributed to the syncytial nature of the pachytene ovary which is easily accessed by microinjection. This protocol describes the step-by-step details and troubleshooting tips for the entire CRISPR-Cas genome editing procedure, including gRNA design and microinjection of ribonucleoprotein complexes, followed by screening and genotyping in C. elegans, to help accessing this powerful genetic animal system. For complete details on the use and execution of this protocol, please refer to Ghanta and Mello (2020).
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Affiliation(s)
- Krishna S. Ghanta
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Takao Ishidate
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
- Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Craig C. Mello
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
- Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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89
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Medwig-Kinney TN, Palmisano NJ, Matus DQ. Deletion of a putative HDA-1 binding site in the hlh-2 promoter eliminates expression in C. elegans dorsal uterine cells. MICROPUBLICATION BIOLOGY 2021; 2021:10.17912/micropub.biology.000449. [PMID: 34514358 PMCID: PMC8414078 DOI: 10.17912/micropub.biology.000449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 01/04/2023]
Abstract
The helix-loop-helix transcription factor hlh-2 (E/Daughterless) has been shown to play an important role in regulating cell fate patterning, cell cycle, and basement membrane invasion in the context of the development of the C. elegans somatic gonad. Here, using CRISPR/Cas9 genome engineering, we generated a new hlh-2 allele (hlh-2(Δ-1303-702)) in the endogenous, GFP-tagged hlh-2 locus. This allele represents a deletion of a 601 bp region in the hlh-2 promoter that contains a putative binding site of the histone deacetylase hda-1 (HDAC) according to publicly available ChIP-sequencing data. Strikingly, we find that HLH-2 expression is virtually absent in the dorsal uterine cells of hlh-2(Δ-1303-702) animals compared to wild type controls. Levels of HLH-2 in the anchor cell and ventral uterine cells are only modestly reduced in the mutant; however, this does not seem to be functionally significant based on the lack of relevant phenotypes and expression levels of a downstream gene, NHR-67 (TLX/Tailless/NR2E1), in these cells. Taken together, these results support growing evidence that HDACs can potentially positively regulate transcription and provide a new reagent for studying hlh-2 regulation.
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Affiliation(s)
| | | | - David Q Matus
- Stony Brook University,
Correspondence to: David Q Matus ()
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90
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Pastore B, Hertz HL, Price IF, Tang W. pre-piRNA trimming and 2'-O-methylation protect piRNAs from 3' tailing and degradation in C. elegans. Cell Rep 2021; 36:109640. [PMID: 34469728 PMCID: PMC8459939 DOI: 10.1016/j.celrep.2021.109640] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/24/2021] [Accepted: 08/10/2021] [Indexed: 11/30/2022] Open
Abstract
The Piwi-interacting RNA (piRNA) pathway suppresses transposable elements and promotes fertility in diverse organisms. Maturation of piRNAs involves pre-piRNA trimming followed by 2'-O-methylation at their 3' termini. Here, we report that the 3' termini of Caenorhabditis elegans piRNAs are subject to nontemplated nucleotide addition, and piRNAs with 3' addition exhibit extensive base-pairing interaction with their target RNAs. Animals deficient for PARN-1 (pre-piRNA trimmer) and HENN-1 (2'-O-methyltransferase) accumulate piRNAs with 3' nontemplated nucleotides. In henn-1 mutants, piRNAs are shortened prior to 3' addition, whereas long isoforms of untrimmed piRNAs are preferentially modified in parn-1 mutant animals. Loss of either PARN-1 or HENN-1 results in modest reduction in steady-state levels of piRNAs. Deletion of both enzymes leads to depletion of piRNAs, desilenced piRNA targets, and impaired fecundity. Together, our findings suggest that pre-piRNA trimming and 2'-O-methylation act collaboratively to protect piRNAs from tailing and degradation.
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Affiliation(s)
- Benjamin Pastore
- Department of Biological Chemistry and Pharmacology, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, Columbus, OH 43210, USA
| | - Hannah L Hertz
- Department of Biological Chemistry and Pharmacology, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Ian F Price
- Department of Biological Chemistry and Pharmacology, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, Columbus, OH 43210, USA
| | - Wen Tang
- Department of Biological Chemistry and Pharmacology, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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91
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Mosquera JV, Bacher MC, Priess JR. Nuclear lipid droplets and nuclear damage in Caenorhabditis elegans. PLoS Genet 2021; 17:e1009602. [PMID: 34133414 PMCID: PMC8208577 DOI: 10.1371/journal.pgen.1009602] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/14/2021] [Indexed: 01/01/2023] Open
Abstract
Fat stored in the form of lipid droplets has long been considered a defining characteristic of cytoplasm. However, recent studies have shown that nuclear lipid droplets occur in multiple cells and tissues, including in human patients with fatty liver disease. The function(s) of stored fat in the nucleus has not been determined, and it is possible that nuclear fat is beneficial in some situations. Conversely, nuclear lipid droplets might instead be deleterious by disrupting nuclear organization or triggering aggregation of hydrophobic proteins. We show here that nuclear lipid droplets occur normally in C. elegans intestinal cells and germ cells, but appear to be associated with damage only in the intestine. Lipid droplets in intestinal nuclei can be associated with novel bundles of microfilaments (nuclear actin) and membrane tubules that might have roles in damage repair. To increase the normal, low frequency of nuclear lipid droplets in wild-type animals, we used a forward genetic screen to isolate mutants with abnormally large or abundant nuclear lipid droplets. Genetic analysis and cloning of three such mutants showed that the genes encode the lipid regulator SEIP-1/seipin, the inner nuclear membrane protein NEMP-1/Nemp1/TMEM194A, and a component of COPI vesicles called COPA-1/α-COP. We present several lines of evidence that the nuclear lipid droplet phenotype of copa-1 mutants results from a defect in retrieving mislocalized membrane proteins that normally reside in the endoplasmic reticulum. The seip-1 mutant causes most germ cells to have nuclear lipid droplets, the largest of which occupy more than a third of the nuclear volume. Nevertheless, the nuclear lipid droplets do not trigger apoptosis, and the germ cells differentiate into gametes that produce viable, healthy progeny. Thus, our results suggest that nuclear lipid droplets are detrimental to intestinal nuclei, but have no obvious deleterious effect on germ nuclei. Several human disorders such as obesity are associated with abnormal fat storage. Cells normally store fat in cytoplasmic organelles called lipid droplets. However, recent studies have shown that fat can also form inside of the cell nucleus, and the effects of nuclear fat are not known. Here we use the cell biology and genetics of the model organism C. elegans to study the causes and consequences of nuclear fat. We show that intestinal cells can contain nuclear fat, particularly during high-low-high changes in cytoplasmic fat that involve de novo fat synthesis. Nuclear fat is associated with multiple changes in intestinal nuclei that appear to represent damage and repair. Germ nuclei that normally differentiate into oocytes can also contain nuclear fat. In germ cells, however, even high levels of nuclear fat appear to cause little or no damage. Our results suggest that intestinal nuclei and germ cell nuclei might have different responses to nuclear fat in part because they differ in chromosomal organization at the nuclear envelope.
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Affiliation(s)
| | - Meghan C. Bacher
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - James R. Priess
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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92
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Amran A, Pigatto L, Pocock R, Gopal S. Functions of the extracellular matrix in development: Lessons from Caenorhabditis elegans. Cell Signal 2021; 84:110006. [PMID: 33857577 DOI: 10.1016/j.cellsig.2021.110006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/04/2021] [Accepted: 04/05/2021] [Indexed: 12/30/2022]
Abstract
Cell-extracellular matrix interactions are crucial for the development of an organism from the earliest stages of embryogenesis. The main constituents of the extracellular matrix are collagens, laminins, proteoglycans and glycosaminoglycans that form a network of interactions. The extracellular matrix and its associated molecules provide developmental cues and structural support from the outside of cells during development. The complex nature of the extracellular matrix and its ability for continuous remodeling poses challenges when investigating extracellular matrix-based signaling during development. One way to address these challenges is to employ invertebrate models such as Caenorhabditis elegans, which are easy to genetically manipulate and have an invariant developmental program. C. elegans also expresses fewer extracellular matrix protein isoforms and exhibits reduced redundancy compared to mammalian models, thus providing a simpler platform for exploring development. This review summarizes our current understanding of how the extracellular matrix controls the development of neurons, muscles and the germline in C. elegans.
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Affiliation(s)
- Aqilah Amran
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Lara Pigatto
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Roger Pocock
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Sandeep Gopal
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria 3800, Australia; Department of Experimental Medical Science, Lund University, Lund, Sweden.
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93
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Ashley GE, Duong T, Levenson MT, Martinez MAQ, Johnson LC, Hibshman JD, Saeger HN, Palmisano NJ, Doonan R, Martinez-Mendez R, Davidson BR, Zhang W, Ragle JM, Medwig-Kinney TN, Sirota SS, Goldstein B, Matus DQ, Dickinson DJ, Reiner DJ, Ward JD. An expanded auxin-inducible degron toolkit for Caenorhabditis elegans. Genetics 2021; 217:iyab006. [PMID: 33677541 PMCID: PMC8045686 DOI: 10.1093/genetics/iyab006] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/10/2021] [Indexed: 12/30/2022] Open
Abstract
The auxin-inducible degron (AID) system has emerged as a powerful tool to conditionally deplete proteins in a range of organisms and cell types. Here, we describe a toolkit to augment the use of the AID system in Caenorhabditis elegans. We have generated a set of single-copy, tissue-specific (germline, intestine, neuron, muscle, pharynx, hypodermis, seam cell, anchor cell) and pan-somatic TIR1-expressing strains carrying a co-expressed blue fluorescent reporter to enable use of both red and green channels in experiments. These transgenes are inserted into commonly used, well-characterized genetic loci. We confirmed that our TIR1-expressing strains produce the expected depletion phenotype for several nuclear and cytoplasmic AID-tagged endogenous substrates. We have also constructed a set of plasmids for constructing repair templates to generate fluorescent protein::AID fusions through CRISPR/Cas9-mediated genome editing. These plasmids are compatible with commonly used genome editing approaches in the C. elegans community (Gibson or SapTrap assembly of plasmid repair templates or PCR-derived linear repair templates). Together these reagents will complement existing TIR1 strains and facilitate rapid and high-throughput fluorescent protein::AID tagging of genes. This battery of new TIR1-expressing strains and modular, efficient cloning vectors serves as a platform for straightforward assembly of CRISPR/Cas9 repair templates for conditional protein depletion.
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Affiliation(s)
- Guinevere E Ashley
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tam Duong
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M Health Science Center, Texas A&M University, Houston, TX 77030, USA
| | - Max T Levenson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Michael A Q Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Londen C Johnson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jonathan D Hibshman
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hannah N Saeger
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nicholas J Palmisano
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ryan Doonan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Raquel Martinez-Mendez
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brittany R Davidson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Taylor N Medwig-Kinney
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Sydney S Sirota
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Bob Goldstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Daniel J Dickinson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - David J Reiner
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M Health Science Center, Texas A&M University, Houston, TX 77030, USA
| | - Jordan D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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94
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Spichal M, Heestand B, Billmyre KK, Frenk S, Mello CC, Ahmed S. Germ granule dysfunction is a hallmark and mirror of Piwi mutant sterility. Nat Commun 2021; 12:1420. [PMID: 33658512 PMCID: PMC7930041 DOI: 10.1038/s41467-021-21635-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/29/2021] [Indexed: 01/31/2023] Open
Abstract
In several species, Piwi/piRNA genome silencing defects cause immediate sterility that correlates with transposon expression and transposon-induced genomic instability. In C. elegans, mutations in the Piwi-related gene (prg-1) and other piRNA deficient mutants cause a transgenerational decline in fertility over a period of several generations. Here we show that the sterility of late generation piRNA mutants correlates poorly with increases in DNA damage signaling. Instead, sterile individuals consistently exhibit altered perinuclear germ granules. We show that disruption of germ granules does not activate transposon expression but induces multiple phenotypes found in sterile prg-1 pathway mutants. Furthermore, loss of the germ granule component pgl-1 enhances prg-1 mutant infertility. Environmental restoration of germ granule function for sterile pgl-1 mutants restores their fertility. We propose that Piwi mutant sterility is a reproductive arrest phenotype that is characterized by perturbed germ granule structure and is phenocopied by germ granule dysfunction, independent of genomic instability.
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Affiliation(s)
- Maya Spichal
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Biology, University of North Carolina, Chapel Hill, NC USA ,grid.168645.80000 0001 0742 0364RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA USA
| | - Bree Heestand
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Biology, University of North Carolina, Chapel Hill, NC USA
| | - Katherine Kretovich Billmyre
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Biology, University of North Carolina, Chapel Hill, NC USA ,grid.250820.d0000 0000 9420 1591Present Address: Stowers Institute for Medical Research, Kansas City, MO USA
| | - Stephen Frenk
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Biology, University of North Carolina, Chapel Hill, NC USA ,Present Address: Achilles Therapeutics Limited, London, UK
| | - Craig C. Mello
- grid.168645.80000 0001 0742 0364RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA USA ,grid.413575.10000 0001 2167 1581Howard Hughes Medical Institute, Worcester, MA USA
| | - Shawn Ahmed
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Biology, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC USA
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95
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Urso SJ, Lamitina T. The C. elegans Hypertonic Stress Response: Big Insights from Shrinking Worms. Cell Physiol Biochem 2021; 55:89-105. [PMID: 33626269 DOI: 10.33594/000000332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 12/23/2022] Open
Abstract
Cell volume is one of the most aggressively defended physiological set points in biology. Changes in intracellular ion and water concentrations, which are induced by changes in metabolism or environmental exposures, disrupt protein folding, enzymatic activity, and macromolecular assemblies. To counter these challenges, cells and organisms have evolved multifaceted, evolutionarily conserved molecular mechanisms to restore cell volume and repair stress induced damage. However, many unanswered questions remain regarding the nature of cell volume 'sensing' as well as the molecular signaling pathways involved in activating physiological response mechanisms. Unbiased genetic screening in the model organism C. elegans is providing new and unexpected insights into these questions, particularly questions relating to the hypertonic stress response (HTSR) pathway. One surprising characteristic of the HTSR pathway in C. elegans is that it is under strong negative regulation by proteins involved in protein homeostasis and the extracellular matrix (ECM). The role of the ECM in particular highlights the importance of studying the HTSR in the context of a live organism where native ECM-tissue associations are preserved. A second novel and recently discovered characteristic is that the HTSR is regulated at the post-transcriptional level. The goal of this review is to describe these discoveries, to provide context for their implications, and to raise outstanding questions to guide future research.
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Affiliation(s)
- Sarel J Urso
- University of Pittsburgh, Graduate Program in Cell Biology and Physiology, Pittsburgh, PA, USA.,University of Pittsburgh, Departments of Pediatrics and Cell Biology, Pittsburgh, PA, USA
| | - Todd Lamitina
- University of Pittsburgh, Graduate Program in Cell Biology and Physiology, Pittsburgh, PA, USA, .,University of Pittsburgh, Departments of Pediatrics and Cell Biology, Pittsburgh, PA, USA
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Duan Y, Choi S, Nelson C, Ambros V. Engineering essential genes with a "jump board" strategy using CRISPR/Cas9. MICROPUBLICATION BIOLOGY 2020; 2020:10.17912/micropub.biology.000315. [PMID: 33274316 PMCID: PMC7704125 DOI: 10.17912/micropub.biology.000315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ye Duan
- University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sungwook Choi
- University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Charles Nelson
- University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Victor Ambros
- University of Massachusetts Medical School, Worcester, MA 01605, USA,
Correspondence to: Victor Ambros ()
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