1
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Cao W, Fan Q, Amparado G, Begic D, Godini R, Gopal S, Pocock R. A nucleic acid binding protein map of germline regulation in Caenorhabditis elegans. Nat Commun 2024; 15:6884. [PMID: 39128930 PMCID: PMC11317507 DOI: 10.1038/s41467-024-51212-0] [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: 05/31/2024] [Accepted: 08/01/2024] [Indexed: 08/13/2024] Open
Abstract
Fertility requires the faithful proliferation of germ cells and their differentiation into gametes. Controlling these cellular states demands precise timing and expression of gene networks. Nucleic acid binding proteins (NBPs) play critical roles in gene expression networks that influence germ cell development. There has, however, been no functional analysis of the entire NBP repertoire in controlling in vivo germ cell development. Here, we analyzed germ cell states and germline architecture to systematically investigate the function of 364 germline-expressed NBPs in the Caenorhabditis elegans germ line. Using germline-specific knockdown, automated germ cell counting, and high-content analysis of germ cell nuclei and plasma membrane organization, we identify 156 NBPs with discrete autonomous germline functions. By identifying NBPs that control the germ cell cycle, proliferation, differentiation, germline structure and fertility, we have created an atlas for mechanistic dissection of germ cell behavior and gamete production.
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Affiliation(s)
- Wei Cao
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia.
| | - Qi Fan
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Gemmarie Amparado
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Dean Begic
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Rasoul Godini
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Sandeep Gopal
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia.
- Lund Stem Cell Center, Department of Experimental Medical Science, Lund University, Lund, Sweden.
| | - Roger Pocock
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia.
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2
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Brinkley DM, Smith KC, Fink EC, Kwen W, Yoo NH, West Z, Sullivan NL, Farthing AS, Hale VA, Goutte C. Notch signaling without the APH-2/nicastrin subunit of gamma secretase in Caenorhabditis elegans germline stem cells. Genetics 2024; 227:iyae076. [PMID: 38717968 DOI: 10.1093/genetics/iyae076] [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: 03/22/2024] [Accepted: 05/01/2024] [Indexed: 07/09/2024] Open
Abstract
The final step in Notch signaling activation is the transmembrane cleavage of Notch receptor by γ secretase. Thus far, genetic and biochemical evidence indicates that four subunits are essential for γ secretase activity in vivo: presenilin (the catalytic core), APH-1, PEN-2, and APH-2/nicastrin. Although some γ secretase activity has been detected in APH-2/nicastrin-deficient mammalian cell lines, the lack of biological relevance for this activity has left the quaternary γ secretase model unchallenged. Here, we provide the first example of in vivo Notch signal transduction without APH-2/nicastrin. The surprising dispensability of APH-2/nicastrin is observed in Caenorhabditis elegans germline stem cells (GSCs) and contrasts with its essential role in previously described C. elegans Notch signaling events. Depletion of GLP-1/Notch, presenilin, APH-1, or PEN-2 causes a striking loss of GSCs. In contrast, aph-2/nicastrin mutants maintain GSCs and exhibit robust and localized expression of the downstream Notch target sygl-1. Interestingly, APH-2/nicastrin is normally expressed in GSCs and becomes essential under conditions of compromised Notch function. Further insight is provided by reconstituting the C. elegans γ secretase complex in yeast, where we find that APH-2/nicastrin increases but is not essential for γ secretase activity. Together, our results are most consistent with a revised model of γ secretase in which the APH-2/nicastrin subunit has a modulatory, rather than obligatory role. We propose that a trimeric presenilin-APH-1-PEN-2 γ secretase complex can provide a low level of γ secretase activity, and that cellular context determines whether or not APH-2/nicastrin is essential for effective Notch signal transduction.
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Affiliation(s)
- David M Brinkley
- Program in Biochemistry and Biophysics, Amherst College, Amherst, MA 01002, USA
| | - Karen C Smith
- Department of Biology, Amherst College, Amherst, MA 01002, USA
| | - Emma C Fink
- Department of Biology, Amherst College, Amherst, MA 01002, USA
| | - Woohyun Kwen
- Department of Biology, Amherst College, Amherst, MA 01002, USA
| | - Nina H Yoo
- Department of Biology, Amherst College, Amherst, MA 01002, USA
| | - Zachary West
- Department of Biology, Amherst College, Amherst, MA 01002, USA
| | - Nora L Sullivan
- Department of Biology, Amherst College, Amherst, MA 01002, USA
| | - Alex S Farthing
- Program in Biochemistry and Biophysics, Amherst College, Amherst, MA 01002, USA
| | - Valerie A Hale
- Department of Biology, Amherst College, Amherst, MA 01002, USA
| | - Caroline Goutte
- Program in Biochemistry and Biophysics, Amherst College, Amherst, MA 01002, USA
- Department of Biology, Amherst College, Amherst, MA 01002, USA
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3
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Qiu C, Crittenden SL, Carrick BH, Dillard LB, Costa Dos Santos SJ, Dandey VP, Dutcher RC, Viverette EG, Wine RN, Woodworth J, Campbell ZT, Wickens M, Borgnia MJ, Kimble J, Tanaka Hall TM. A higher order PUF complex is central to regulation of C. elegans germline stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599074. [PMID: 38915480 PMCID: PMC11195197 DOI: 10.1101/2024.06.14.599074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
PUF RNA-binding proteins are broadly conserved stem cell regulators. Nematode PUF proteins maintain germline stem cells (GSCs) and, with key partner proteins, repress differentiation mRNAs, including gld-1. Here we report that PUF protein FBF-2 and its partner LST-1 form a ternary complex that represses gld-1 via a pair of adjacent FBF-2 binding elements (FBEs) in its 3ÚTR. One LST-1 molecule links two FBF-2 molecules via motifs in the LST-1 intrinsically-disordered region; the gld-1 FBE pair includes a well-established 'canonical' FBE and a newly-identified noncanonical FBE. Remarkably, this FBE pair drives both full RNA repression in GSCs and full RNA activation upon differentiation. Discovery of the LST-1-FBF-2 ternary complex, the gld-1 adjacent FBEs, and their in vivo significance predicts an expanded regulatory repertoire of different assemblies of PUF-partner complexes in nematode germline stem cells. It also suggests analogous PUF controls may await discovery in other biological contexts and organisms.
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Affiliation(s)
- Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | | | - Brian H. Carrick
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Current address: MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Lucas B. Dillard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- Current address: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stephany J. Costa Dos Santos
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- These authors contributed equally to the manuscript and are listed in alphabetical order
| | - Venkata P. Dandey
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- These authors contributed equally to the manuscript and are listed in alphabetical order
| | - Robert C. Dutcher
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- These authors contributed equally to the manuscript and are listed in alphabetical order
| | - Elizabeth G. Viverette
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- These authors contributed equally to the manuscript and are listed in alphabetical order
- Current address: Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert N. Wine
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- These authors contributed equally to the manuscript and are listed in alphabetical order
| | - Jennifer Woodworth
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- These authors contributed equally to the manuscript and are listed in alphabetical order
| | - Zachary T. Campbell
- Department of Anesthesiology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Mario J. Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Traci M. Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- Lead contact
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4
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Jones M, Norman M, Tiet AM, Lee J, Lee MH. C. elegans Germline as Three Distinct Tumor Models. BIOLOGY 2024; 13:425. [PMID: 38927305 PMCID: PMC11200432 DOI: 10.3390/biology13060425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Tumor cells display abnormal growth and division, avoiding the natural process of cell death. These cells can be benign (non-cancerous growth) or malignant (cancerous growth). Over the past few decades, numerous in vitro or in vivo tumor models have been employed to understand the molecular mechanisms associated with tumorigenesis in diverse regards. However, our comprehension of how non-tumor cells transform into tumor cells at molecular and cellular levels remains incomplete. The nematode C. elegans has emerged as an excellent model organism for exploring various phenomena, including tumorigenesis. Although C. elegans does not naturally develop cancer, it serves as a valuable platform for identifying oncogenes and the underlying mechanisms within a live organism. In this review, we describe three distinct germline tumor models in C. elegans, highlighting their associated mechanisms and related regulators: (1) ectopic proliferation due to aberrant activation of GLP-1/Notch signaling, (2) meiotic entry failure resulting from the loss of GLD-1/STAR RNA-binding protein, (3) spermatogenic dedifferentiation caused by the loss of PUF-8/PUF RNA-binding protein. Each model requires the mutations of specific genes (glp-1, gld-1, and puf-8) and operates through distinct molecular mechanisms. Despite these differences in the origins of tumorigenesis, the internal regulatory networks within each tumor model display shared features. Given the conservation of many of the regulators implicated in C. elegans tumorigenesis, it is proposed that these unique models hold significant potential for enhancing our comprehension of the broader control mechanisms governing tumorigenesis.
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Affiliation(s)
- Mariah Jones
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA; (M.J.); (M.N.)
| | - Mina Norman
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA; (M.J.); (M.N.)
| | - Alex Minh Tiet
- Neuroscience Program, East Carolina University, Greenville, NC 27858, USA;
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Jiwoo Lee
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Myon Hee Lee
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA; (M.J.); (M.N.)
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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5
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Zhang Z, Yang H, Fang L, Zhao G, Xiang J, Zheng JC, Qin Z. DOS-3 mediates cell-non-autonomous DAF-16/FOXO activity in antagonizing age-related loss of C. elegans germline stem/progenitor cells. Nat Commun 2024; 15:4904. [PMID: 38851828 PMCID: PMC11162419 DOI: 10.1038/s41467-024-49318-6] [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: 09/09/2023] [Accepted: 05/29/2024] [Indexed: 06/10/2024] Open
Abstract
Age-related depletion of stem cells causes tissue degeneration and failure to tissue regeneration, driving aging at the organismal level. Previously we reported a cell-non-autonomous DAF-16/FOXO activity in antagonizing the age-related loss of germline stem/progenitor cells (GSPCs) in C. elegans, indicating that regulation of stem cell aging occurs at the organ system level. Here we discover the molecular effector that links the cell-non-autonomous DAF-16/FOXO activity to GSPC maintenance over time by performing a tissue-specific DAF-16/FOXO transcriptome analysis. Our data show that dos-3, which encodes a non-canonical Notch ligand, is a direct transcriptional target of DAF-16/FOXO and mediates the effect of the cell-non-autonomous DAF-16/FOXO activity on GSPC maintenance through activating Notch signaling in the germ line. Importantly, expression of a human homologous protein can functionally substitute for DOS-3 in this scenario. As Notch signaling controls the specification of many tissue stem cells, similar mechanisms may exist in other aging stem cell systems.
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Affiliation(s)
- Zhifei Zhang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
| | - Haiyan Yang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
| | - Lei Fang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
| | - Guangrong Zhao
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
| | - Jun Xiang
- Department of Urology, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China.
| | - Jialin C Zheng
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital Affiliated to Tongji University, Shanghai, 200065, China.
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China.
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200080, China.
- Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital affiliated to Tongji University School of Medicine, Shanghai, 200080, China.
- Innovation Center of Medical Basic Research for Brain Aging and Associated Diseases, Ministry of Education, Tongji University, Shanghai, 200331, China.
- Collaborative Innovation Center for Brain Science, Tongji University, Shanghai, 200331, China.
- Shanghai Frontiers Science Center of Nanocatalytic Medicine, Tongji University School of Medicine, Shanghai, 200331, China.
| | - Zhao Qin
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China.
- Innovation Center of Medical Basic Research for Brain Aging and Associated Diseases, Ministry of Education, Tongji University, Shanghai, 200331, China.
- Collaborative Innovation Center for Brain Science, Tongji University, Shanghai, 200331, China.
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6
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Agarwal P, Berger S, Shemesh T, Zaidel-Bar R. Active nuclear positioning and actomyosin contractility maintain leader cell integrity during gonadogenesis. Curr Biol 2024; 34:2373-2386.e5. [PMID: 38776903 DOI: 10.1016/j.cub.2024.03.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 02/01/2024] [Accepted: 03/25/2024] [Indexed: 05/25/2024]
Abstract
Proper distribution of organelles can play an important role in a moving cell's performance. During C. elegans gonad morphogenesis, the nucleus of the leading distal tip cell (DTC) is always found at the front, yet the significance of this localization is unknown. Here, we identified the molecular mechanism that keeps the nucleus at the front, despite a frictional force that pushes it backward. The Klarsicht/ANC-1/Syne homology (KASH) domain protein UNC-83 links the nucleus to the motor protein kinesin-1 that moves along a polarized acentrosomal microtubule network. Interestingly, disrupting nuclear positioning on its own did not affect gonad morphogenesis. However, reducing actomyosin contractility on top of nuclear mispositioning led to a dramatic phenotype: DTC splitting and gonad bifurcation. Long-term live imaging of the double knockdown revealed that, while the gonad attempted to perform a planned U-turn, the DTC was stretched due to the lagging nucleus until it fragmented into a nucleated cell and an enucleated cytoplast, each leading an independent gonadal arm. Remarkably, the enucleated cytoplast had polarity and invaded, but it could only temporarily support germ cell proliferation. Based on a qualitative biophysical model, we conclude that the leader cell employs two complementary mechanical approaches to preserve its integrity and ensure proper organ morphogenesis while navigating through a complex 3D environment: active nuclear positioning by microtubule motors and actomyosin-driven cortical contractility.
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Affiliation(s)
- Priti Agarwal
- Department of Cell and Developmental Biology, Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Simon Berger
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Tom Shemesh
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Ronen Zaidel-Bar
- Department of Cell and Developmental Biology, Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.
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7
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Aprison EZ, Dzitoyeva S, Ruvinsky I. The roles of TGFβ and serotonin signaling in regulating proliferation of oocyte precursors and germline aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593208. [PMID: 38766220 PMCID: PMC11100717 DOI: 10.1101/2024.05.08.593208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The decline of oocyte quality in aging but otherwise relatively healthy individuals compels a search for underlying mechanisms. Building upon a finding that exposure to male pheromone ascr#10 improves oocyte quality in C. elegans, we uncovered a regulatory cascade that promotes proliferation of oocyte precursors in adults and regulates oocyte quality. We found that the male pheromone promotes proliferation of oocyte precursors by upregulating LAG-2, a ligand of the Notch-like pathway in the germline stem cell niche. LAG-2 is upregulated by a TGFβ-like ligand DAF-7 revealing similarity of regulatory mechanisms that promote germline proliferation in adults and larvae. A serotonin circuit that also regulates food search and consumption upregulates DAF-7 specifically in adults. The serotonin/DAF-7 signaling promotes germline expansion to compensate for oocyte expenditure which is increased by the male pheromone. Finally, we show that the earliest events in reproductive aging may be due to declining expression of LAG-2 and DAF-7. Our findings highlight neuronal signals that promote germline proliferation in response to the environment and argue that deteriorating oocyte quality may be due to reduced neuronal expression of key germline regulators.
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Affiliation(s)
- Erin Z. Aprison
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Svetlana Dzitoyeva
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Ilya Ruvinsky
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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8
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Osterli E, Ellenbecker M, Wang X, Terzo M, Jacobson K, Cuello D, Voronina E. COP9 signalosome component CSN-5 stabilizes PUF proteins FBF-1 and FBF-2 in Caenorhabditis elegans germline stem and progenitor cells. Genetics 2024; 227:iyae033. [PMID: 38427913 PMCID: PMC11075551 DOI: 10.1093/genetics/iyae033] [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: 01/02/2024] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 03/03/2024] Open
Abstract
RNA-binding proteins FBF-1 and FBF-2 (FBFs) are required for germline stem cell maintenance and the sperm/oocyte switch in Caenorhabditis elegans, although the mechanisms controlling FBF protein levels remain unknown. We identified an interaction between both FBFs and CSN-5), a component of the constitutive photomorphogenesis 9 (COP9) signalosome best known for its role in regulating protein degradation. Here, we find that the Mpr1/Pad1 N-terminal metalloprotease domain of CSN-5 interacts with the Pumilio and FBF RNA-binding domain of FBFs and the interaction is conserved for human homologs CSN5 and PUM1. The interaction between FBF-2 and CSN-5 can be detected in vivo by proximity ligation. csn-5 mutation results in the destabilization of FBF proteins, which may explain previously observed decrease in the numbers of germline stem and progenitor cells, and disruption of oogenesis. The loss of csn-5 does not decrease the levels of a related PUF protein PUF-3, and csn-5(lf) phenotype is not enhanced by fbf-1/2 knockdown, suggesting that the effect is specific to FBFs. The effect of csn-5 on oogenesis is largely independent of the COP9 signalosome and is cell autonomous. Surprisingly, the regulation of FBF protein levels involves a combination of COP9-dependent and COP9-independent mechanisms differentially affecting FBF-1 and FBF-2. This work supports a previously unappreciated role for CSN-5 in the stabilization of germline stem cell regulatory proteins FBF-1 and FBF-2.
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Affiliation(s)
- Emily Osterli
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Mary Ellenbecker
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Xiaobo Wang
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Mikaya Terzo
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Ketch Jacobson
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - DeAnna Cuello
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
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9
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Carrick BH, Crittenden SL, Chen F, Linsley M, Woodworth J, Kroll-Conner P, Ferdous AS, Keleş S, Wickens M, Kimble J. PUF partner interactions at a conserved interface shape the RNA-binding landscape and cell fate in Caenorhabditis elegans. Dev Cell 2024; 59:661-675.e7. [PMID: 38290520 PMCID: PMC11253550 DOI: 10.1016/j.devcel.2024.01.005] [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: 07/31/2023] [Revised: 11/10/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Protein-RNA regulatory networks underpin much of biology. C. elegans FBF-2, a PUF-RNA-binding protein, binds over 1,000 RNAs to govern stem cells and differentiation. FBF-2 interacts with multiple protein partners via a key tyrosine, Y479. Here, we investigate the in vivo significance of partnerships using a Y479A mutant. Occupancy of the Y479A mutant protein increases or decreases at specific sites across the transcriptome, varying with RNAs. Germline development also changes in a specific fashion: Y479A abolishes one FBF-2 function-the sperm-to-oocyte cell fate switch. Y479A's effects on the regulation of one mRNA, gld-1, are critical to this fate change, though other network changes are also important. FBF-2 switches from repression to activation of gld-1 RNA, likely by distinct FBF-2 partnerships. The role of RNA-binding protein partnerships in governing RNA regulatory networks will likely extend broadly, as such partnerships pervade RNA controls in virtually all metazoan tissues and species.
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Affiliation(s)
- Brian H Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fan Chen
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - MaryGrace Linsley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jennifer Woodworth
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peggy Kroll-Conner
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ahlan S Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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10
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Urman MA, John NS, Jung T, Lee C. Aging disrupts spatiotemporal regulation of germline stem cells and niche integrity. Biol Open 2024; 13:bio060261. [PMID: 38156664 PMCID: PMC10810562 DOI: 10.1242/bio.060261] [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: 11/30/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024] Open
Abstract
A major factor driving stem cell decline is stem cell niche aging, but its molecular mechanism remains elusive. We use the Caenorhabditis elegans distal tip cell (DTC), the mesenchymal niche that employs Notch signaling to regulate germline stem cells (GSCs), as an in vivo niche aging model and delineate the molecular details of the DTC/niche aging process. Here, we demonstrate that a drastic decrease in C. elegans germline fecundity, which begins even in early adulthood, is mainly due to an age-induced disruption in spatial regulation of Notch-dependent transcription in the germline combined with a moderate reduction in Notch transcription at both tissue and cellular levels. Consequently, the Notch-responsive GSC pool shifts from the distal end of the gonad to a more proximal region, disrupting the distal-to-proximal germline polarity. We find that this GSC pool shift is due to a dislocation of the DTC/niche nucleus, which is associated with age-induced changes in the structure and morphology of the DTC/niche. Our findings reveal a critical link between physiological changes in the aging niche, their consequences in stem cell regulation, and germline tissue functions.
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Affiliation(s)
- Michelle A. Urman
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Nimmy S. John
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Tyler Jung
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - ChangHwan Lee
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
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11
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Qiu C, Zhang Z, Wine RN, Campbell ZT, Zhang J, Hall TMT. Intra- and inter-molecular regulation by intrinsically-disordered regions governs PUF protein RNA binding. Nat Commun 2023; 14:7323. [PMID: 37953271 PMCID: PMC10641069 DOI: 10.1038/s41467-023-43098-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023] Open
Abstract
PUF proteins are characterized by globular RNA-binding domains. They also interact with partner proteins that modulate their RNA-binding activities. Caenorhabditis elegans PUF protein fem-3 binding factor-2 (FBF-2) partners with intrinsically disordered Lateral Signaling Target-1 (LST-1) to regulate target mRNAs in germline stem cells. Here, we report that an intrinsically disordered region (IDR) at the C-terminus of FBF-2 autoinhibits its RNA-binding affinity by increasing the off rate for RNA binding. Moreover, the FBF-2 C-terminal region interacts with its globular RNA-binding domain at the same site where LST-1 binds. This intramolecular interaction restrains an electronegative cluster of amino acid residues near the 5' end of the bound RNA to inhibit RNA binding. LST-1 binding in place of the FBF-2 C-terminus therefore releases autoinhibition and increases RNA-binding affinity. This regulatory mechanism, driven by IDRs, provides a biochemical and biophysical explanation for the interdependence of FBF-2 and LST-1 in germline stem cell self-renewal.
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Affiliation(s)
- Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Zihan Zhang
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert N Wine
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Zachary T Campbell
- Department of Anesthesiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Jun Zhang
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
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12
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Xu J, Jiang Y, Sherrard R, Ikegami K, Conradt B. PUF-8, a C. elegans ortholog of the RNA-binding proteins PUM1 and PUM2, is required for robustness of the cell death fate. Development 2023; 150:dev201167. [PMID: 37747106 PMCID: PMC10565243 DOI: 10.1242/dev.201167] [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: 07/29/2022] [Accepted: 09/11/2023] [Indexed: 09/26/2023]
Abstract
During C. elegans development, 1090 somatic cells are generated, of which 959 survive and 131 die, many through apoptosis. We present evidence that PUF-8, a C. elegans ortholog of the mammalian RNA-binding proteins PUM1 and PUM2, is required for the robustness of this 'survival and death' pattern. We found that PUF-8 prevents the inappropriate death of cells that normally survive, and we present evidence that this anti-apoptotic activity of PUF-8 is dependent on the ability of PUF-8 to interact with ced-3 (a C. elegans ortholog of caspase) mRNA, thereby repressing the activity of the pro-apoptotic ced-3 gene. PUF-8 also promotes the death of cells that are programmed to die, and we propose that this pro-apoptotic activity of PUF-8 may depend on the ability of PUF-8 to repress the expression of the anti-apoptotic ced-9 gene (a C. elegans ortholog of Bcl2). Our results suggest that stochastic differences in the expression of genes within the apoptosis pathway can disrupt the highly reproducible and robust survival and death pattern during C. elegans development, and that PUF-8 acts at the post-transcriptional level to level out these differences, thereby ensuring proper cell number homeostasis.
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Affiliation(s)
- Jimei Xu
- Faculty of Biology, Center for Integrative Protein Sciences Munich (CIPSM), Ludwig-Maximilians-University, Munich, 82152 Planegg-Martinsried, Germany
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Yanwen Jiang
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Ryan Sherrard
- Faculty of Biology, Center for Integrative Protein Sciences Munich (CIPSM), Ludwig-Maximilians-University, Munich, 82152 Planegg-Martinsried, Germany
| | - Kyoko Ikegami
- Faculty of Biology, Center for Integrative Protein Sciences Munich (CIPSM), Ludwig-Maximilians-University, Munich, 82152 Planegg-Martinsried, Germany
| | - Barbara Conradt
- Faculty of Biology, Center for Integrative Protein Sciences Munich (CIPSM), Ludwig-Maximilians-University, Munich, 82152 Planegg-Martinsried, Germany
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
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13
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Ferdous AS, Lynch TR, Costa Dos Santos SJ, Kapadia DH, Crittenden SL, Kimble J. LST-1 is a bifunctional regulator that feeds back on Notch-dependent transcription to regulate C. elegans germline stem cells. Proc Natl Acad Sci U S A 2023; 120:e2309964120. [PMID: 37729202 PMCID: PMC10523584 DOI: 10.1073/pnas.2309964120] [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: 06/13/2023] [Accepted: 08/15/2023] [Indexed: 09/22/2023] Open
Abstract
Notch signaling regulates stem cells across animal phylogeny. C. elegans Notch signaling activates transcription of two genes, lst-1 and sygl-1, that encode potent regulators of germline stem cells. The LST-1 protein regulates stem cells in two distinct ways: It promotes self-renewal posttranscriptionally and also restricts self-renewal by a poorly understood mechanism. Its self-renewal promoting activity resides in its N-terminal region, while its self-renewal restricting activity resides in its C-terminal region and requires the Zn finger. Here, we report that LST-1 limits self-renewal by down-regulating Notch-dependent transcription. We detect LST-1 in the nucleus, in addition to its previously known cytoplasmic localization. LST-1 lowers nascent transcript levels at both lst-1 and sygl-1 loci but not at let-858, a Notch-independent locus. LST-1 also lowers levels of two key components of the Notch activation complex, the LAG-1 DNA binding protein and Notch intracellular domain (NICD). Genetically, an LST-1 Zn finger mutant increases Notch signaling strength in both gain- and loss-of-function GLP-1/Notch receptor mutants. Biochemically, LST-1 co-immunoprecipitates with LAG-1 from nematode extracts, suggesting a direct effect. LST-1 is thus a bifunctional regulator that coordinates posttranscriptional and transcriptional mechanisms in a single protein. This LST-1 bifunctionality relies on its bipartite protein architecture and is bolstered by generation of two LST-1 isoforms, one specialized for Notch downregulation. A conserved theme from worms to human is the coupling of PUF-mediated RNA repression together with Notch feedback in the same protein.
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Affiliation(s)
- Ahlan S. Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
- Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Tina R. Lynch
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
- Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | | | - Deep H. Kapadia
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Sarah L. Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
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14
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Truong L, Chen YW, Barrere-Cain R, Levenson MT, Shuck K, Xiao W, da Veiga Beltrame E, Panter B, Reich E, Sternberg PW, Yang X, Allard P. Single-nucleus resolution mapping of the adult C. elegans and its application to elucidate inter- and trans-generational response to alcohol. Cell Rep 2023; 42:112535. [PMID: 37227821 PMCID: PMC10592506 DOI: 10.1016/j.celrep.2023.112535] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 03/16/2023] [Accepted: 05/03/2023] [Indexed: 05/27/2023] Open
Abstract
Single-cell transcriptomic platforms provide an opportunity to map an organism's response to environmental cues with high resolution. Here, we applied single-nucleus RNA sequencing (snRNA-seq) to establish the tissue and cell type-resolved transcriptome of the adult C. elegans and characterize the inter- and trans-generational transcriptional impact of ethanol. We profiled the transcriptome of 41,749 nuclei resolving into 31 clusters, representing a diverse array of adult cell types including syncytial tissues. Following exposure to human-relevant doses of alcohol, several germline, striated muscle, and neuronal clusters were identified as being the most transcriptionally impacted at the F1 and F3 generations. The effect on germline clusters was confirmed by phenotypic enrichment analysis as well as by functional validation, which revealed a remarkable inter- and trans-generational increase in germline apoptosis, aneuploidy, and embryonic lethality. Together, snRNA-seq represents a valuable approach for the detailed examination of an adult organism's response to environmental exposures.
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Affiliation(s)
- Lisa Truong
- Human Genetics Graduate Program, UCLA, Los Angeles, CA 90095, USA
| | - Yen-Wei Chen
- Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA
| | - Rio Barrere-Cain
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Max T Levenson
- Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA
| | - Karissa Shuck
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Wen Xiao
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | | | - Blake Panter
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Ella Reich
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Paul W Sternberg
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Xia Yang
- Integrative Biology and Physiology Department, UCLA, Los Angeles, CA 90095, USA
| | - Patrick Allard
- Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA; Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.
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15
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Davis GM, Hipwell H, Boag PR. Oogenesis in Caenorhabditis elegans. Sex Dev 2023; 17:73-83. [PMID: 37232019 PMCID: PMC10659005 DOI: 10.1159/000531019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND The nematode, Caenorhabditis elegans has proven itself as a valuable model for investigating metazoan biology. C. elegans have a transparent body, an invariant cell lineage, and a high level of genetic conservation which makes it a desirable model organism. Although used to elucidate many aspects of somatic biology, a distinct advantage of C. elegans is its well annotated germline which allows all aspects of oogenesis to be observed in real time within a single animal. C. elegans hermaphrodites have two U-shaped gonad arms which produce their own sperm that is later stored to fertilise their own oocytes. These two germlines take up much of the internal space of each animal and germ cells are therefore the most abundant cell present within each animal. This feature and the genetic phenotypes observed for mutant worm gonads have allowed many novel findings that established our early understanding of germ cell dynamics. The mutant phenotypes also allowed key features of meiosis and germ cell maturation to be unveiled. SUMMARY This review will focus on the key aspects that make C. elegans an outstanding model for exploring each feature of oogenesis. This will include the fundamental steps associated with germline function and germ cell maturation and will be of use for those interested in exploring reproductive metazoan biology. KEY MESSAGES Since germ cell biology is highly conserved in animals, much can be gained from study of a simple metazoan like C. elegans. Past findings have enhanced understanding on topics that would be more laborious or challenging in more complex animal models.
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Affiliation(s)
- Gregory M. Davis
- Institute of Innovation, Science and Sustainability, Federation University, Churchill, VIC, Australia
| | - Hayleigh Hipwell
- Department of Biochemistry and Molecular Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
| | - Peter R. Boag
- Department of Biochemistry and Molecular Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
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16
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Ferdous AS, Costa Dos Santos SJ, Kanzler CR, Shin H, Carrick BH, Crittenden SL, Wickens M, Kimble J. The in vivo functional significance of PUF hub partnerships in C. elegans germline stem cells. Development 2023; 150:dev201705. [PMID: 37070766 PMCID: PMC10259659 DOI: 10.1242/dev.201705] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/29/2023] [Indexed: 04/19/2023]
Abstract
PUF RNA-binding proteins are conserved stem cell regulators. Four PUF proteins govern self-renewal of Caenorhabditis elegans germline stem cells together with two intrinsically disordered proteins, LST-1 and SYGL-1. Based on yeast two-hybrid results, we previously proposed a composite self-renewal hub in the stem cell regulatory network, with eight PUF partnerships and extensive redundancy. Here, we investigate LST-1-PUF and SYGL-1-PUF partnerships and their molecular activities in their natural context - nematode stem cells. We confirm LST-1-PUF partnerships and their specificity to self-renewal PUFs by co-immunoprecipitation and show that an LST-1(AmBm) mutant defective for PUF-interacting motifs does not complex with PUFs in nematodes. LST-1(AmBm) is used to explore the in vivo functional significance of the LST-1-PUF partnership. Tethered LST-1 requires this partnership to repress expression of a reporter RNA, and LST-1 requires the partnership to co-immunoprecipitate with NTL-1/Not1 of the CCR4-NOT complex. We suggest that the partnership provides multiple molecular interactions that work together to form an effector complex on PUF target RNAs in vivo. Comparison of LST-1-PUF and Nanos-Pumilio reveals fundamental molecular differences, making LST-1-PUF a distinct paradigm for PUF partnerships.
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Affiliation(s)
- Ahlan S. Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Charlotte R. Kanzler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Heaji Shin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian H. Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sarah L. Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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17
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Ferdous AS, Costa Dos Santos SJ, Kanzler CR, Shin H, Carrick BH, Crittenden SL, Wickens M, Kimble J. Functional significance of PUF partnerships in C. elegans germline stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528708. [PMID: 36824876 PMCID: PMC9949348 DOI: 10.1101/2023.02.15.528708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
PUF RNA-binding proteins are conserved stem cell regulators. Four PUF proteins govern self-renewal of C. elegans germline stem cells together with two intrinsically disordered proteins, LST-1 and SYGL-1. Based on yeast two-hybrid results, we proposed a composite self-renewal hub in the stem cell regulatory network, with eight PUF partnerships and extensive redundancy. Here, we investigate LST-1-PUF and SYGL-1-PUF partnerships and their molecular activities in their natural context - nematode stem cells. We confirm LST-1-PUF partnerships and their specificity to self-renewal PUFs by co-immunoprecipitation and show that an LST-1(A m B m ) mutant defective for PUF-interacting motifs does not complex with PUFs in nematodes. LST-1(A m B m ) is used to explore the functional significance of the LST-1-PUF partnership. Tethered LST-1 requires the partnership to repress expression of a reporter RNA, and LST-1 requires the partnership to co-immunoprecipitate with NTL-1/Not1 of the CCR4-NOT complex. We suggest that the partnership provides multiple molecular interactions that work together to form an effector complex on PUF target RNAs. Comparison of PUF-LST-1 and Pumilio-Nanos reveals fundamental molecular differences, making PUF-LST-1 a distinct paradigm for PUF partnerships. Summary statement Partnerships between PUF RNA-binding proteins and intrinsically disordered proteins are essential for stem cell maintenance and RNA repression.
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Affiliation(s)
- Ahlan S Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Charlotte R Kanzler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Heaji Shin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian H Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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18
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Park Y, Gaddy M, Hyun M, Jones ME, Aslam HM, Lee MH. Genetic and Chemical Controls of Sperm Fate and Spermatocyte Dedifferentiation via PUF-8 and MPK-1 in Caenorhabditis elegans. Cells 2023; 12:cells12030434. [PMID: 36766775 PMCID: PMC9913519 DOI: 10.3390/cells12030434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/21/2023] [Accepted: 01/24/2023] [Indexed: 02/03/2023] Open
Abstract
Using the nematode C. elegans germline as a model system, we previously reported that PUF-8 (a PUF RNA-binding protein) and LIP-1 (a dual-specificity phosphatase) repress sperm fate at 20 °C and the dedifferentiation of spermatocytes into mitotic cells (termed "spermatocyte dedifferentiation") at 25 °C. Thus, double mutants lacking both PUF-8 and LIP-1 produce excess sperm at 20 °C, and their spermatocytes return to mitotically dividing cells via dedifferentiation at 25 °C, resulting in germline tumors. To gain insight into the molecular competence for spermatocyte dedifferentiation, we compared the germline phenotypes of three mutant strains that produce excess sperm-fem-3(q20gf), puf-8(q725); fem-3(q20gf), and puf-8(q725); lip-1(zh15). Spermatocyte dedifferentiation was not observed in fem-3(q20gf) mutants, but it was more severe in puf-8(q725); lip-1(zh15) than in puf-8(q725); fem-3(q20gf) mutants. These results suggest that MPK-1 (the C. elegans ERK1/2 MAPK ortholog) activation in the absence of PUF-8 is required to promote spermatocyte dedifferentiation. This idea was confirmed using Resveratrol (RSV), a potential activator of MPK-1 and ERK1/2 in C. elegans and human cells, respectively. Notably, spermatocyte dedifferentiation was significantly enhanced by RSV treatment in the absence of PUF-8, and its effect was blocked by mpk-1 RNAi. We, therefore, conclude that PUF-8 and MPK-1 are essential regulators for spermatocyte dedifferentiation and tumorigenesis. Since these regulators are broadly conserved, we suggest that similar regulatory circuitry may control cellular dedifferentiation and tumorigenesis in other organisms, including humans.
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Affiliation(s)
- Youngyong Park
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - Matthew Gaddy
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - Moonjung Hyun
- Biological Resources Research Group, Bioenvironmental Science & Toxicology Division, Korea Institute of Toxicology, Jinju 52834, Gyeongsangnam-do, Republic of Korea
| | - Mariah E. Jones
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - Hafiz M. Aslam
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - Myon Hee Lee
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
- Correspondence:
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19
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Crittenden SL, Seidel HS, Kimble J. Analysis of the C. elegans Germline Stem Cell Pool. Methods Mol Biol 2023; 2677:1-36. [PMID: 37464233 DOI: 10.1007/978-1-0716-3259-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The Caenorhabditis elegans germline is an excellent model for studying the genetic and molecular regulation of stem cell self-renewal and progression of cells from a stem cell state to a differentiated state. The germline tissue is organized in an assembly line with the germline stem cell (GSC) pool at one end and differentiated gametes at the other. A simple mesenchymal niche caps the GSC pool and maintains GSCs in an undifferentiated state by signaling through the conserved Notch pathway. Notch signaling activates transcription of the key GSC regulators lst-1 and sygl-1 proteins in a gradient through the GSC pool. LST-1 and SYGL-1 proteins work with PUF RNA regulators in a self-renewal hub to maintain the GSC pool. In this chapter, we present methods for characterizing the C. elegans GSC pool and early stages of germ cell differentiation. The methods include examination of germlines in living and fixed worms, cell cycle analysis, and analysis of markers. We also discuss assays to separate mutant phenotypes that affect the stem cell vs. differentiation decision from those that affect germ cell processes more generally.
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Affiliation(s)
- Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Hannah S Seidel
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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20
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Brenner JL, Jyo EM, Mohammad A, Fox P, Jones V, Mardis E, Schedl T, Maine EM. TRIM-NHL protein, NHL-2, modulates cell fate choices in the C. elegans germ line. Dev Biol 2022; 491:43-55. [PMID: 36063869 PMCID: PMC9922029 DOI: 10.1016/j.ydbio.2022.08.010] [Citation(s) in RCA: 2] [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: 04/05/2022] [Revised: 07/19/2022] [Accepted: 08/27/2022] [Indexed: 12/01/2022]
Abstract
Many tissues contain multipotent stem cells that are critical for maintaining tissue function. In Caenorhabditis elegans, germline stem cells allow gamete production to continue in adulthood. In the gonad, GLP-1/Notch signaling from the distal tip cell niche to neighboring germ cells activates a complex regulatory network to maintain a stem cell population. GLP-1/Notch signaling positively regulates production of LST-1 and SYGL-1 proteins that, in turn, interact with a set of PUF/FBF proteins to positively regulate the stem cell fate. We previously described sog (suppressor of glp-1 loss of function) and teg (tumorous enhancer of glp-1 gain of function) genes that limit the stem cell fate and/or promote the meiotic fate. Here, we show that sog-10 is allelic to nhl-2. NHL-2 is a member of the conserved TRIM-NHL protein family whose members can bind RNA and ubiquitinate protein substrates. We show that NHL-2 acts, at least in part, by inhibiting the expression of PUF-3 and PUF-11 translational repressor proteins that promote the stem cell fate. Two other negative regulators of stem cell fate, CGH-1 (conserved germline helicase) and ALG-5 (Argonaute protein), may work with NHL-2 to modulate the stem cell population. In addition, NHL-2 activity promotes the male germ cell fate in XX animals.
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Affiliation(s)
- John L Brenner
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Erin M Jyo
- Department of Biology, Syracuse University, Syracuse, NY, 13210, USA
| | - Ariz Mohammad
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Paul Fox
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Vovanti Jones
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Elaine Mardis
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tim Schedl
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Eleanor M Maine
- Department of Biology, Syracuse University, Syracuse, NY, 13210, USA.
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21
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Valet M, Narbonne P. Formation of benign tumors by stem cell deregulation. PLoS Genet 2022; 18:e1010434. [PMID: 36301803 PMCID: PMC9612571 DOI: 10.1371/journal.pgen.1010434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Within living organisms, stem cells respond to various cues, including to niche signals and growth factors. Niche signals originate from the stem cell's microenvironment and promote the undifferentiated state by preventing differentiation, allowing for stem cell self-renewal. On the other hand, growth factors promote stem cell growth and proliferation, while their sources comprise of a systemic input reflecting the animal's nutritional and metabolic status, and a localized, homeostatic feedback signal from the tissue that the stem cells serve. That homeostatic signal prevents unnecessary stem cell proliferation when the corresponding differentiated tissues already have optimal cell contents. Here, we recapitulate progresses made in our understanding of in vivo stem cell regulation, largely using simple models, and draw the conclusion that 2 types of stem cell deregulations can provoke the formation of benign tumors. Namely, constitutive niche signaling promotes the formation of undifferentiated "stem cell" tumors, while defective homeostatic signaling leads to the formation of differentiated tumors. Finally, we provide evidence that these general principles may be conserved in mammals and as such, may underlie benign tumor formation in humans, while benign tumors can evolve into cancer.
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Affiliation(s)
- Matthieu Valet
- Département de biologie médicale, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Patrick Narbonne
- Département de biologie médicale, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
- * E-mail:
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22
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Mechanisms of germ cell survival and plasticity in Caenorhabditis elegans. Biochem Soc Trans 2022; 50:1517-1526. [PMID: 36196981 PMCID: PMC9704514 DOI: 10.1042/bst20220878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022]
Abstract
Animals constantly encounter environmental and physiological stressors that threaten survival and fertility. Somatic stress responses and germ cell arrest/repair mechanisms are employed to withstand such challenges. The Caenorhabditis elegans germline combats stress by initiating mitotic germ cell quiescence to preserve genome integrity, and by removing meiotic germ cells to prevent inheritance of damaged DNA or to tolerate lack of germline nutrient supply. Here, we review examples of germline recovery from distinct stressors - acute starvation and defective splicing - where quiescent mitotic germ cells resume proliferation to repopulate a germ line following apoptotic removal of meiotic germ cells. These protective mechanisms reveal the plastic nature of germline stem cells.
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23
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Tolkin T, Mohammad A, Starich TA, Nguyen KCQ, Hall DH, Schedl T, Hubbard EJA, Greenstein D. Innexin function dictates the spatial relationship between distal somatic cells in the Caenorhabditis elegans gonad without impacting the germline stem cell pool. eLife 2022; 11:e74955. [PMID: 36098634 PMCID: PMC9473689 DOI: 10.7554/elife.74955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 08/08/2022] [Indexed: 12/01/2022] Open
Abstract
Gap-junctional signaling mediates myriad cellular interactions in metazoans. Yet, how gap junctions control the positioning of cells in organs is not well understood. Innexins compose gap junctions in invertebrates and affect organ architecture. Here, we investigate the roles of gap-junctions in controlling distal somatic gonad architecture and its relationship to underlying germline stem cells in Caenorhabditis elegans. We show that a reduction of soma-germline gap-junctional activity causes displacement of distal sheath cells (Sh1) towards the distal end of the gonad. We confirm, by live imaging, transmission electron microscopy, and antibody staining, that bare regions-lacking somatic gonadal cell coverage of germ cells-are present between the distal tip cell (DTC) and Sh1, and we show that an innexin fusion protein used in a prior study encodes an antimorphic gap junction subunit that mispositions Sh1. We determine that, contrary to the model put forth in the prior study based on this fusion protein, Sh1 mispositioning does not markedly alter the position of the borders of the stem cell pool nor of the progenitor cell pool. Together, these results demonstrate that gap junctions can control the position of Sh1, but that Sh1 position is neither relevant for GLP-1/Notch signaling nor for the exit of germ cells from the stem cell pool.
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Affiliation(s)
- Theadora Tolkin
- Kimmel Center for Biology and Medicine at the Skirball Institute, NYU Grossman School of MedicineNew YorkUnited States
- Department of Cell Biology, NYU Grossman School of MedicineNew YorkUnited States
| | - Ariz Mohammad
- Department of Genetics, Washington University School of MedicineSt. LouisUnited States
| | - Todd A Starich
- Department of Genetics, Cell Biology and Development, University of MinnesotaMinneapolisUnited States
| | - Ken CQ Nguyen
- Department of Neuroscience, Albert Einstein College of MedicineThe BronxUnited States
| | - David H Hall
- Department of Neuroscience, Albert Einstein College of MedicineThe BronxUnited States
| | - Tim Schedl
- Department of Genetics, Washington University School of MedicineSt. LouisUnited States
| | - E Jane Albert Hubbard
- Kimmel Center for Biology and Medicine at the Skirball Institute, NYU Grossman School of MedicineNew YorkUnited States
- Department of Cell Biology, NYU Grossman School of MedicineNew YorkUnited States
- Department of Pathology, NYU Grossman School of MedicineNew YorkUnited States
| | - David Greenstein
- Department of Genetics, Cell Biology and Development, University of MinnesotaMinneapolisUnited States
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24
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Li X, Singh N, Miller C, Washington I, Sosseh B, Gordon KL. The C. elegans gonadal sheath Sh1 cells extend asymmetrically over a differentiating germ cell population in the proliferative zone. eLife 2022; 11:75497. [PMID: 36094368 PMCID: PMC9467509 DOI: 10.7554/elife.75497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 08/08/2022] [Indexed: 12/04/2022] Open
Abstract
The Caenorhabditis elegans adult hermaphrodite germline is surrounded by a thin tube formed by somatic sheath cells that support germ cells as they mature from the stem-like mitotic state through meiosis, gametogenesis, and ovulation. Recently, we discovered that the distal Sh1 sheath cells associate with mitotic germ cells as they exit the niche Gordon et al., 2020. Here, we report that these sheath-associated germ cells differentiate first in animals with temperature-sensitive mutations affecting germ cell state, and stem-like germ cells are maintained distal to the Sh1 boundary. We analyze several markers of the distal sheath, which is best visualized with endogenously tagged membrane proteins, as overexpressed fluorescent proteins fail to localize to distal membrane processes and can cause gonad morphology defects. However, such reagents with highly variable expression can be used to determine the relative positions of the two Sh1 cells, one of which often extends further distal than the other.
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Affiliation(s)
- Xin Li
- Department of Biology, The University of North Carolina at Chapel Hill
| | - Noor Singh
- Department of Biology, The University of North Carolina at Chapel Hill
| | - Camille Miller
- Department of Biology, The University of North Carolina at Chapel Hill
| | - India Washington
- Department of Biology, The University of North Carolina at Chapel Hill
| | - Bintou Sosseh
- Department of Biology, The University of North Carolina at Chapel Hill
| | - Kacy Lynn Gordon
- Department of Biology, The University of North Carolina at Chapel Hill
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25
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Vanden Broek K, Han X, Hansen D. Redundant mechanisms regulating the proliferation vs. differentiation balance in the C. elegans germline. Front Cell Dev Biol 2022; 10:960999. [PMID: 36120589 PMCID: PMC9479330 DOI: 10.3389/fcell.2022.960999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/15/2022] [Indexed: 11/21/2022] Open
Abstract
The proper production of gametes over an extended portion of the life of an organism is essential for a high level of fitness. The balance between germline stem cell (GSC) proliferation (self-renewal) and differentiation (production of gametes) must be tightly regulated to ensure proper gamete production and overall fitness. Therefore, organisms have evolved robust regulatory systems to control this balance. Here we discuss the redundancy in the regulatory system that controls the proliferation vs. differentiation balance in the C. elegans hermaphrodite germline, and how this redundancy may contribute to robustness. We focus on the various types of redundancy utilized to regulate this balance, as well as the approaches that have enabled these redundant mechanisms to be uncovered.
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26
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Lynch TR, Xue M, Czerniak CW, Lee C, Kimble J. Notch-dependent DNA cis-regulatory elements and their dose-dependent control of C. elegans stem cell self-renewal. Development 2022; 149:274985. [PMID: 35394007 PMCID: PMC9058496 DOI: 10.1242/dev.200332] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/16/2022] [Indexed: 11/20/2022]
Abstract
A long-standing biological question is how DNA cis-regulatory elements shape transcriptional patterns during metazoan development. Reporter constructs, cell culture assays and computational modeling have made major contributions to answering this question, but analysis of elements in their natural context is an important complement. Here, we mutate Notch-dependent LAG-1 binding sites (LBSs) in the endogenous Caenorhabditis elegans sygl-1 gene, which encodes a key stem cell regulator, and analyze the consequences on sygl-1 expression (nascent transcripts, mRNA, protein) and stem cell maintenance. Mutation of one LBS in a three-element cluster approximately halved both expression and stem cell pool size, whereas mutation of two LBSs essentially abolished them. Heterozygous LBS mutant clusters provided intermediate values. Our results lead to two major conclusions. First, both LBS number and configuration impact cluster activity: LBSs act additively in trans and synergistically in cis. Second, the SYGL-1 gradient promotes self-renewal above its functional threshold and triggers differentiation below the threshold. Our approach of coupling CRISPR/Cas9 LBS mutations with effects on both molecular and biological readouts establishes a powerful model for in vivo analyses of DNA cis-regulatory elements. Summary: Notch-dependent DNA cis-regulatory elements work together in their developmental context in C. elegans to shape a transcriptional gradient, control stem cell pool size, and govern differentiation onset.
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Affiliation(s)
- Tina R. Lynch
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Integrated Program in Biochemistry, Madison, WI 53706, USA
| | - Mingyu Xue
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Cazza W. Czerniak
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Joint Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - ChangHwan Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Integrated Program in Biochemistry, Madison, WI 53706, USA
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27
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Amar A, Hubbard EJA, Kugler H. Modeling the C. elegans germline stem cell genetic network using automated reasoning. Biosystems 2022; 217:104672. [PMID: 35469833 PMCID: PMC9142837 DOI: 10.1016/j.biosystems.2022.104672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 11/18/2022]
Abstract
Computational methods and tools are a powerful complementary approach to experimental work for studying regulatory interactions in living cells and systems. We demonstrate the use of formal reasoning methods as applied to the Caenorhabditis elegans germ line, which is an accessible system for stem cell research. The dynamics of the underlying genetic networks and their potential regulatory interactions are key for understanding mechanisms that control cellular decision-making between stem cells and differentiation. We model the “stem cell fate” versus entry into the “meiotic development” pathway decision circuit in the young adult germ line based on an extensive study of published experimental data and known/hypothesized genetic interactions. We apply a formal reasoning framework to derive predictive networks for control of differentiation. Using this approach we simultaneously specify many possible scenarios and experiments together with potential genetic interactions, and synthesize genetic networks consistent with all encoded experimental observations. In silico analysis of knock-down and overexpression experiments within our model recapitulate published phenotypes of mutant animals and can be applied to make predictions on cellular decision-making. A methodological contribution of this work is demonstrating how to effectively model within a formal reasoning framework a complex genetic network with a wealth of known experimental data and constraints. We provide a summary of the steps we have found useful for the development and analysis of this model and can potentially be applicable to other genetic networks. This work also lays a foundation for developing realistic whole tissue models of the C. elegans germ line where each cell in the model will execute a synthesized genetic network.
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Affiliation(s)
- Ani Amar
- The Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel.
| | - E Jane Albert Hubbard
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Department of Pathology, NYU Grossman School of Medicine, 540 First Avenue, New York, NY 10016, United States of America.
| | - Hillel Kugler
- The Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel.
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28
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Robinson-Thiewes S, Kershner AM, Shin H, Haupt KA, Kroll-Connor P, Kimble J. A sensitized genetic screen to identify regulators of Caenorhabditis elegans germline stem cells. G3 (BETHESDA, MD.) 2022; 12:jkab439. [PMID: 35100350 PMCID: PMC9210287 DOI: 10.1093/g3journal/jkab439] [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] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022]
Abstract
GLP-1/Notch signaling and a downstream RNA regulatory network maintain germline stem cells in Caenorhabditis elegans. In mutants lacking the GLP-1 receptor, all germline stem cells enter the meiotic cell cycle precociously and differentiate into sperm. This dramatic germline stem cell defect is called the "Glp" phenotype. The lst-1 and sygl-1 genes are direct targets of Notch transcriptional activation and functionally redundant. Whereas single lst-1 and sygl-1 mutants are fertile, lst-1 sygl-1 double mutants are sterile with a Glp phenotype. We set out to identify genes that function redundantly with either lst-1 or sygl-1 to maintain germline stem cells. To this end, we conducted forward genetic screens for mutants with a Glp phenotype in genetic backgrounds lacking functional copies of either lst-1 or sygl-1. The screens generated 9 glp-1 alleles, 2 lst-1 alleles, and 1 allele of pole-1, which encodes the catalytic subunit of DNA polymerase ε. Three glp-1 alleles reside in Ankyrin repeats not previously mutated. pole-1 single mutants have a low penetrance Glp phenotype that is enhanced by loss of sygl-1. Thus, the screen uncovered 1 locus that interacts genetically with sygl-1 and generated useful mutations for further studies of germline stem cell regulation.
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Affiliation(s)
| | | | - Heaji Shin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kimberly A Haupt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peggy Kroll-Connor
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith Kimble
- Department of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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29
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Qiu C, Wine RN, Campbell ZT, Hall T. Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal. Nucleic Acids Res 2022; 50:536-548. [PMID: 34908132 PMCID: PMC8754657 DOI: 10.1093/nar/gkab1220] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/23/2021] [Accepted: 12/08/2021] [Indexed: 01/09/2023] Open
Abstract
In C. elegans, PUF proteins promote germline stem cell self-renewal. Their functions hinge on partnerships with two proteins that are redundantly required for stem cell maintenance. Here we focus on understanding how the essential partner protein, LST-1, modulates mRNA regulation by the PUF protein, FBF-2. LST-1 contains two nonidentical sites of interaction with FBF-2, LST-1 A and B. Our crystal structures of complexes of FBF-2, LST-1 A, and RNA visualize how FBF-2 associates with LST-1 A versus LST-1 B. One commonality is that FBF-2 contacts the conserved lysine and leucine side chains in the KxxL motifs in LST-1 A and B. A key difference is that FBF-2 forms unique contacts with regions N- and C-terminal to the KxxL motif. Consequently, LST-1 A does not modulate the RNA-binding affinity of FBF-2, whereas LST-1 B decreases RNA-binding affinity of FBF-2. The N-terminal region of LST-1 B, which binds near the 5' end of RNA elements, is essential to modulate FBF-2 RNA-binding affinity, while the C-terminal residues of LST-1 B contribute strong binding affinity to FBF-2. We conclude that LST-1 has the potential to impact which mRNAs are regulated depending on the precise nature of engagement through its functionally distinct FBF binding sites.
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Affiliation(s)
- Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Robert N Wine
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Zachary T Campbell
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75025, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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30
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Mercer M, Jang S, Ni C, Buszczak M. The Dynamic Regulation of mRNA Translation and Ribosome Biogenesis During Germ Cell Development and Reproductive Aging. Front Cell Dev Biol 2021; 9:710186. [PMID: 34805139 PMCID: PMC8595405 DOI: 10.3389/fcell.2021.710186] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/07/2021] [Indexed: 01/21/2023] Open
Abstract
The regulation of mRNA translation, both globally and at the level of individual transcripts, plays a central role in the development and function of germ cells across species. Genetic studies using flies, worms, zebrafish and mice have highlighted the importance of specific RNA binding proteins in driving various aspects of germ cell formation and function. Many of these mRNA binding proteins, including Pumilio, Nanos, Vasa and Dazl have been conserved through evolution, specifically mark germ cells, and carry out similar functions across species. These proteins typically influence mRNA translation by binding to specific elements within the 3′ untranslated region (UTR) of target messages. Emerging evidence indicates that the global regulation of mRNA translation also plays an important role in germ cell development. For example, ribosome biogenesis is often regulated in a stage specific manner during gametogenesis. Moreover, oocytes need to produce and store a sufficient number of ribosomes to support the development of the early embryo until the initiation of zygotic transcription. Accumulating evidence indicates that disruption of mRNA translation regulatory mechanisms likely contributes to infertility and reproductive aging in humans. These findings highlight the importance of gaining further insights into the mechanisms that control mRNA translation within germ cells. Future work in this area will likely have important impacts beyond germ cell biology.
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Affiliation(s)
- Marianne Mercer
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Seoyeon Jang
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Chunyang Ni
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Michael Buszczak
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
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31
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Scharf A, Pohl F, Egan BM, Kocsisova Z, Kornfeld K. Reproductive Aging in Caenorhabditis elegans: From Molecules to Ecology. Front Cell Dev Biol 2021; 9:718522. [PMID: 34604218 PMCID: PMC8481778 DOI: 10.3389/fcell.2021.718522] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/04/2021] [Indexed: 11/13/2022] Open
Abstract
Aging animals display a broad range of progressive degenerative changes, and one of the most fascinating is the decline of female reproductive function. In the model organism Caenorhabditis elegans, hermaphrodites reach a peak of progeny production on day 2 of adulthood and then display a rapid decline; progeny production typically ends by day 8 of adulthood. Since animals typically survive until day 15 of adulthood, there is a substantial post reproductive lifespan. Here we review the molecular and cellular changes that occur during reproductive aging, including reductions in stem cell number and activity, slowing meiotic progression, diminished Notch signaling, and deterioration of germ line and oocyte morphology. Several interventions have been identified that delay reproductive aging, including mutations, drugs and environmental factors such as temperature. The detailed description of reproductive aging coupled with interventions that delay this process have made C. elegans a leading model system to understand the mechanisms that drive reproductive aging. While reproductive aging has dramatic consequences for individual fertility, it also has consequences for the ecology of the population. Population dynamics are driven by birth and death, and reproductive aging is one important factor that influences birth rate. A variety of theories have been advanced to explain why reproductive aging occurs and how it has been sculpted during evolution. Here we summarize these theories and discuss the utility of C. elegans for testing mechanistic and evolutionary models of reproductive aging.
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Affiliation(s)
- Andrea Scharf
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
| | - Franziska Pohl
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States.,Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Brian M Egan
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
| | - Zuzana Kocsisova
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
| | - Kerry Kornfeld
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
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32
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Singh R, Smit RB, Wang X, Wang C, Racher H, Hansen D. Reduction of Derlin activity suppresses Notch-dependent tumours in the C. elegans germ line. PLoS Genet 2021; 17:e1009687. [PMID: 34555015 PMCID: PMC8491880 DOI: 10.1371/journal.pgen.1009687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 10/05/2021] [Accepted: 09/08/2021] [Indexed: 11/19/2022] Open
Abstract
Regulating the balance between self-renewal (proliferation) and differentiation is key to the long-term functioning of all stem cell pools. In the Caenorhabditis elegans germline, the primary signal controlling this balance is the conserved Notch signaling pathway. Gain-of-function mutations in the GLP-1/Notch receptor cause increased stem cell self-renewal, resulting in a tumour of proliferating germline stem cells. Notch gain-of-function mutations activate the receptor, even in the presence of little or no ligand, and have been associated with many human diseases, including cancers. We demonstrate that reduction in CUP-2 and DER-2 function, which are Derlin family proteins that function in endoplasmic reticulum-associated degradation (ERAD), suppresses the C. elegans germline over-proliferation phenotype associated with glp-1(gain-of-function) mutations. We further demonstrate that their reduction does not suppress other mutations that cause over-proliferation, suggesting that over-proliferation suppression due to loss of Derlin activity is specific to glp-1/Notch (gain-of-function) mutations. Reduction of CUP-2 Derlin activity reduces the expression of a read-out of GLP-1/Notch signaling, suggesting that the suppression of over-proliferation in Derlin loss-of-function mutants is due to a reduction in the activity of the mutated GLP-1/Notch(GF) receptor. Over-proliferation suppression in cup-2 mutants is only seen when the Unfolded Protein Response (UPR) is functioning properly, suggesting that the suppression, and reduction in GLP-1/Notch signaling levels, observed in Derlin mutants may be the result of activation of the UPR. Chemically inducing ER stress also suppress glp-1(gf) over-proliferation but not other mutations that cause over-proliferation. Therefore, ER stress and activation of the UPR may help correct for increased GLP-1/Notch signaling levels, and associated over-proliferation, in the C. elegans germline. Notch signaling is a highly conserved signaling pathway that is utilized in many cell fate decisions in many organisms. In the C. elegans germline, Notch signaling is the primary signal that regulates the balance between stem cell proliferation and differentiation. Notch gain-of-function mutations cause the receptor to be active, even when a signal that is normally needed to activate the receptor is absent. In the germline of C. elegans, gain-of-function mutations in GLP-1, a Notch receptor, results in over-proliferation of the stem cells and tumour formation. Here we demonstrate that a reduction or loss of Derlin activity, which is a conserved family of proteins involved in endoplasmic reticulum-associated degradation (ERAD), suppresses over-proliferation due to GLP-1/Notch gain-of-function mutations. Furthermore, we demonstrate that a surveillance mechanism utilized in cells to monitor and react to proteins that are not folded properly (Unfolded Protein Response-UPR) must be functioning well in order for the loss of Derlin activity to supress over-proliferation caused by glp-1/Notch gain-of-function mutations. This suggests that activation of the UPR may be the mechanism at work for suppressing this type of over-proliferation, when Derlin activity is reduced. Therefore, decreasing Derlin activity may be a means of reducing the impact of phenotypes and diseases due to certain Notch gain-of-function mutations.
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Affiliation(s)
- Ramya Singh
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Ryan B. Smit
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Xin Wang
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Chris Wang
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Hilary Racher
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Dave Hansen
- Department of Biological Sciences, University of Calgary, Calgary, Canada
- * E-mail:
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33
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Pushpa K, Dagar S, Kumar H, Pathak D, Mylavarapu SVS. The exocyst complex regulates C. elegans germline stem cell proliferation by controlling membrane Notch levels. Development 2021; 148:271155. [PMID: 34338279 DOI: 10.1242/dev.196345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 06/30/2021] [Indexed: 11/20/2022]
Abstract
The conserved exocyst complex regulates plasma membrane-directed vesicle fusion in eukaryotes. However, its role in stem cell proliferation has not been reported. Germline stem cell (GSC) proliferation in the nematode Caenorhabditis elegans is regulated by conserved Notch signaling. Here, we reveal that the exocyst complex regulates C. elegans GSC proliferation by modulating Notch signaling cell autonomously. Notch membrane density is asymmetrically maintained on GSCs. Knockdown of exocyst complex subunits or of the exocyst-interacting GTPases Rab5 and Rab11 leads to Notch redistribution from the GSC-niche interface to the cytoplasm, suggesting defects in plasma membrane Notch deposition. The anterior polarity (aPar) protein Par6 is required for GSC proliferation, and for maintaining niche-facing membrane levels of Notch and the exocyst complex. The exocyst complex biochemically interacts with the aPar regulator Par5 (14-3-3ζ) and Notch in C. elegans and human cells. Exocyst components are required for Notch plasma membrane localization and signaling in mammalian cells. Our study uncovers a possibly conserved requirement of the exocyst complex in regulating GSC proliferation and in maintaining optimal membrane Notch levels.
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Affiliation(s)
- Kumari Pushpa
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India
| | - Sunayana Dagar
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India.,Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha 751024, India
| | - Harsh Kumar
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India.,Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Diksha Pathak
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India
| | - Sivaram V S Mylavarapu
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India.,Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha 751024, India.,Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
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34
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Tolkin T, Hubbard EJA. Germline Stem and Progenitor Cell Aging in C. elegans. Front Cell Dev Biol 2021; 9:699671. [PMID: 34307379 PMCID: PMC8297657 DOI: 10.3389/fcell.2021.699671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
Like many animals and humans, reproduction in the nematode C. elegans declines with age. This decline is the cumulative result of age-related changes in several steps of germline function, many of which are highly accessible for experimental investigation in this short-lived model organism. Here we review recent work showing that a very early and major contributing step to reproductive decline is the depletion of the germline stem and progenitor cell pool. Since many cellular and molecular aspects of stem cell biology and aging are conserved across animals, understanding mechanisms of age-related decline of germline stem and progenitor cells in C. elegans has broad implications for aging stem cells, germline stem cells, and reproductive aging.
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Affiliation(s)
- Theadora Tolkin
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, NYU Grossman School of Medicine, New York, NY, United States
| | - E Jane Albert Hubbard
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, NYU Grossman School of Medicine, New York, NY, United States
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Robinson-Thiewes S, Dufour B, Martel PO, Lechasseur X, Brou AAD, Roy V, Chen Y, Kimble J, Narbonne P. Non-autonomous regulation of germline stem cell proliferation by somatic MPK-1/MAPK activity in C. elegans. Cell Rep 2021; 35:109162. [PMID: 34038716 PMCID: PMC8182673 DOI: 10.1016/j.celrep.2021.109162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 02/17/2021] [Accepted: 04/30/2021] [Indexed: 11/03/2022] Open
Abstract
Extracellular-signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) is a major positive regulator of cell proliferation, which is often upregulated in cancer. However, few studies have addressed ERK/MAPK regulation of proliferation within a complete organism. The Caenorhabditis elegans ERK/MAPK ortholog MPK-1 is best known for its control of somatic organogenesis and germline differentiation, but it also stimulates germline stem cell proliferation. Here, we show that the germline-specific MPK-1B isoform promotes germline differentiation but has no apparent role in germline stem cell proliferation. By contrast, the soma-specific MPK-1A isoform promotes germline stem cell proliferation non-autonomously. Indeed, MPK-1A functions in the intestine or somatic gonad to promote germline proliferation independent of its other known roles. We propose that a non-autonomous role of ERK/MAPK in stem cell proliferation may be conserved across species and various tissue types, with major clinical implications for cancer and other diseases. The prevailing paradigm is that ERK/MAPK functions autonomously to promote cell proliferation upon mitogen stimulation. Robinson-Thiewes et al. now demonstrate that C. elegans ERK/MAPK acts within somatic tissues to non-autonomously promote the proliferation of germline stem cells. Germline ERK/MAPK is thus dispensable for germline stem cell proliferation.
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Affiliation(s)
| | - Benjamin Dufour
- Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada
| | - Pier-Olivier Martel
- Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada
| | - Xavier Lechasseur
- Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada
| | - Amani Ange Danielle Brou
- Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada
| | - Vincent Roy
- Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada; Département de Biologie Moléculaire, de Biochimie Médicale et de pathologie, Faculté de Médecine, Université Laval, QC G1R 3S3, Canada
| | - Yunqing Chen
- Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada
| | - Judith Kimble
- Department of Genetics, University of Wisconsin-Madison, Madison, WI 53706-1580, USA
| | - Patrick Narbonne
- Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada; Département de Biologie Moléculaire, de Biochimie Médicale et de pathologie, Faculté de Médecine, Université Laval, QC G1R 3S3, Canada.
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Fraga de Andrade I, Mehta C, Bresnick EH. Post-transcriptional control of cellular differentiation by the RNA exosome complex. Nucleic Acids Res 2020; 48:11913-11928. [PMID: 33119769 PMCID: PMC7708067 DOI: 10.1093/nar/gkaa883] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/21/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Given the complexity of intracellular RNA ensembles and vast phenotypic remodeling intrinsic to cellular differentiation, it is instructive to consider the role of RNA regulatory machinery in controlling differentiation. Dynamic post-transcriptional regulation of protein-coding and non-coding transcripts is vital for establishing and maintaining proteomes that enable or oppose differentiation. By contrast to extensively studied transcriptional mechanisms governing differentiation, many questions remain unanswered regarding the involvement of post-transcriptional mechanisms. Through its catalytic activity to selectively process or degrade RNAs, the RNA exosome complex dictates the levels of RNAs comprising multiple RNA classes, thereby regulating chromatin structure, gene expression and differentiation. Although the RNA exosome would be expected to control diverse biological processes, studies to elucidate its biological functions and how it integrates into, or functions in parallel with, cell type-specific transcriptional mechanisms are in their infancy. Mechanistic analyses have demonstrated that the RNA exosome confers expression of a differentiation regulatory receptor tyrosine kinase, downregulates the telomerase RNA component TERC, confers genomic stability and promotes DNA repair, which have considerable physiological and pathological implications. In this review, we address how a broadly operational RNA regulatory complex interfaces with cell type-specific machinery to control cellular differentiation.
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Affiliation(s)
- Isabela Fraga de Andrade
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
| | - Charu Mehta
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
| | - Emery H Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
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Wang X, Ellenbecker M, Hickey B, Day NJ, Osterli E, Terzo M, Voronina E. Antagonistic control of Caenorhabditis elegans germline stem cell proliferation and differentiation by PUF proteins FBF-1 and FBF-2. eLife 2020; 9:52788. [PMID: 32804074 PMCID: PMC7467723 DOI: 10.7554/elife.52788] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 08/14/2020] [Indexed: 02/07/2023] Open
Abstract
Stem cells support tissue maintenance, but the mechanisms that coordinate the rate of stem cell self-renewal with differentiation at a population level remain uncharacterized. We find that two PUF family RNA-binding proteins FBF-1 and FBF-2 have opposite effects on Caenorhabditis elegans germline stem cell dynamics: FBF-1 restricts the rate of meiotic entry, while FBF-2 promotes both cell division and meiotic entry rates. Antagonistic effects of FBFs are mediated by their distinct activities toward the shared set of target mRNAs, where FBF-1-mediated post-transcriptional control requires the activity of CCR4-NOT deadenylase, while FBF-2 is deadenylase-independent and might protect the targets from deadenylation. These regulatory differences depend on protein sequences outside of the conserved PUF family RNA-binding domain. We propose that the opposing FBF-1 and FBF-2 activities serve to modulate stem cell division rate simultaneously with the rate of meiotic entry.
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Affiliation(s)
- Xiaobo Wang
- Division of Biological Sciences, University of Montana, Missoula, United States
| | - Mary Ellenbecker
- Division of Biological Sciences, University of Montana, Missoula, United States
| | - Benjamin Hickey
- Division of Biological Sciences, University of Montana, Missoula, United States
| | - Nicholas J Day
- Division of Biological Sciences, University of Montana, Missoula, United States
| | - Emily Osterli
- Division of Biological Sciences, University of Montana, Missoula, United States
| | - Mikaya Terzo
- Division of Biological Sciences, University of Montana, Missoula, United States
| | - Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, United States
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Gordon K. Recent Advances in the Genetic, Anatomical, and Environmental Regulation of the C. elegans Germ Line Progenitor Zone. J Dev Biol 2020; 8:E14. [PMID: 32707774 PMCID: PMC7559772 DOI: 10.3390/jdb8030014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 12/16/2022] Open
Abstract
The C. elegans germ line and its gonadal support cells are well studied from a developmental genetics standpoint and have revealed many foundational principles of stem cell niche biology. Among these are the observations that a niche-like cell supports a self-renewing stem cell population with multipotential, differentiating daughter cells. While genetic features that distinguish stem-like cells from their differentiating progeny have been defined, the mechanisms that structure these populations in the germ line have yet to be explained. The spatial restriction of Notch activation has emerged as an important genetic principle acting in the distal germ line. Synthesizing recent findings, I present a model in which the germ stem cell population of the C. elegans adult hermaphrodite can be recognized as two distinct anatomical and genetic populations. This review describes the recent progress that has been made in characterizing the undifferentiated germ cells and gonad anatomy, and presents open questions in the field and new directions for research to pursue.
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Affiliation(s)
- Kacy Gordon
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Gordon KL, Zussman JW, Li X, Miller C, Sherwood DR. Stem cell niche exit in C. elegans via orientation and segregation of daughter cells by a cryptic cell outside the niche. eLife 2020; 9:e56383. [PMID: 32692313 PMCID: PMC7467730 DOI: 10.7554/elife.56383] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/17/2020] [Indexed: 12/17/2022] Open
Abstract
Stem cells reside in and rely upon their niche to maintain stemness but must balance self-renewal with the production of daughters that leave the niche to differentiate. We discovered a mechanism of stem cell niche exit in the canonical C. elegans distal tip cell (DTC) germ stem cell niche mediated by previously unobserved, thin, membranous protrusions of the adjacent somatic gonad cell pair (Sh1). A disproportionate number of germ cell divisions were observed at the DTC-Sh1 interface. Stem-like and differentiating cell fates segregated across this boundary. Spindles polarized, pairs of daughter cells oriented between the DTC and Sh1, and Sh1 grew over the Sh1-facing daughter. Impeding Sh1 growth by RNAi to cofilin and Arp2/3 perturbed the DTC-Sh1 interface, reduced germ cell proliferation, and shifted a differentiation marker. Because Sh1 membrane protrusions eluded detection for decades, it is possible that similar structures actively regulate niche exit in other systems.
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Affiliation(s)
- Kacy L Gordon
- Department of Biology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Jay W Zussman
- Department of Biology, Duke UniversityDurhamUnited States
| | - Xin Li
- Department of Biology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Camille Miller
- Department of Biology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - David R Sherwood
- Department of Biology, Duke UniversityDurhamUnited States
- Regeneration Next, Duke UniversityDurhamUnited States
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Chen J, Mohammad A, Pazdernik N, Huang H, Bowman B, Tycksen E, Schedl T. GLP-1 Notch-LAG-1 CSL control of the germline stem cell fate is mediated by transcriptional targets lst-1 and sygl-1. PLoS Genet 2020; 16:e1008650. [PMID: 32196486 PMCID: PMC7153901 DOI: 10.1371/journal.pgen.1008650] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/13/2020] [Accepted: 02/04/2020] [Indexed: 12/16/2022] Open
Abstract
Stem cell systems are essential for the development and maintenance of polarized tissues. Intercellular signaling pathways control stem cell systems, where niche cells signal stem cells to maintain the stem cell fate/self-renewal and inhibit differentiation. In the C. elegans germline, GLP-1 Notch signaling specifies the stem cell fate, employing the sequence-specific DNA binding protein LAG-1 to implement the transcriptional response. We undertook a comprehensive genome-wide approach to identify transcriptional targets of GLP-1 signaling. We expected primary response target genes to be evident at the intersection of genes identified as directly bound by LAG-1, from ChIP-seq experiments, with genes identified as requiring GLP-1 signaling for RNA accumulation, from RNA-seq analysis. Furthermore, we performed a time-course transcriptomics analysis following auxin inducible degradation of LAG-1 to distinguish between genes whose RNA level was a primary or secondary response of GLP-1 signaling. Surprisingly, only lst-1 and sygl-1, the two known target genes of GLP-1 in the germline, fulfilled these criteria, indicating that these two genes are the primary response targets of GLP-1 Notch and may be the sole germline GLP-1 signaling protein-coding transcriptional targets for mediating the stem cell fate. In addition, three secondary response genes were identified based on their timing following loss of LAG-1, their lack of a LAG-1 ChIP-seq peak and that their glp-1 dependent mRNA accumulation could be explained by a requirement for lst-1 and sygl-1 activity. Moreover, our analysis also suggests that the function of the primary response genes lst-1 and sygl-1 can account for the glp-1 dependent peak protein accumulation of FBF-2, which promotes the stem cell fate and, in part, for the spatial restriction of elevated LAG-1 accumulation to the stem cell region. Stem cell systems are central to tissue development, homeostasis and regeneration, where niche to stem cell signaling pathways promote the stem cell fate/self-renewal and inhibit differentiation. The evolutionarily conserved GLP-1 Notch signaling pathway in the C. elegans germline is an experimentally tractable system, allowing dissection of control of the stem cell fate and inhibition of meiotic development. However, as in many systems, the primary molecular targets of the signaling pathway in stem cells is incompletely known, as are secondary molecular targets, and this knowledge is essential for a deep understanding of stem cell systems. Here we focus on the identification of the primary transcriptional targets of the GLP-1 signaling pathway that promotes the stem cell fate, employing unbiased multilevel genomic approaches. We identify only lst-1 and sygl-1, two of a number of previously reported targets, as likely the sole primary mRNA transcriptional targets of GLP-1 signaling that promote the germline stem cell fate. We also identify secondary GLP-1 signaling RNA and protein targets, whose expression shows dependence on lst-1 and sygl-1, where the protein targets reinforce the importance of posttranscriptional regulation in control of the stem cell fate.
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Affiliation(s)
- Jian Chen
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Ariz Mohammad
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Nanette Pazdernik
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, United States of America
- Current address, Integrated DNA Technologies, Coralville, Iowa, United States of America
| | - Huiyan Huang
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Beth Bowman
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- Current address, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Eric Tycksen
- Genome Technology Access Center, McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Tim Schedl
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, United States of America
- * E-mail:
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Wang X, Voronina E. Diverse Roles of PUF Proteins in Germline Stem and Progenitor Cell Development in C. elegans. Front Cell Dev Biol 2020; 8:29. [PMID: 32117964 PMCID: PMC7015873 DOI: 10.3389/fcell.2020.00029] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/14/2020] [Indexed: 01/05/2023] Open
Abstract
Stem cell development depends on post-transcriptional regulation mediated by RNA-binding proteins (RBPs) (Zhang et al., 1997; Forbes and Lehmann, 1998; Okano et al., 2005; Ratti et al., 2006; Kwon et al., 2013). Pumilio and FBF (PUF) family RBPs are highly conserved post-transcriptional regulators that are critical for stem cell maintenance (Wickens et al., 2002; Quenault et al., 2011). The RNA-binding domains of PUF proteins recognize a family of related sequence motifs in the target mRNAs, yet individual PUF proteins have clearly distinct biological functions (Lu et al., 2009; Wang et al., 2018). The C. elegans germline is a simple and powerful model system for analyzing regulation of stem cell development. Studies in C. elegans uncovered specific physiological roles for PUFs expressed in the germline stem cells ranging from control of proliferation and differentiation to regulation of the sperm/oocyte decision. Importantly, recent studies started to illuminate the mechanisms behind PUF functional divergence. This review summarizes the many roles of PUF-8, FBF-1, and FBF-2 in germline stem and progenitor cells (SPCs) and discusses the factors accounting for their distinct biological functions. PUF proteins are conserved in evolution, and insights into PUF-mediated regulation provided by the C. elegans model system are likely relevant for other organisms.
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Affiliation(s)
- Xiaobo Wang
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
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Haupt KA, Law KT, Enright AL, Kanzler CR, Shin H, Wickens M, Kimble J. A PUF Hub Drives Self-Renewal in Caenorhabditis elegans Germline Stem Cells. Genetics 2020; 214:147-161. [PMID: 31740451 PMCID: PMC6944405 DOI: 10.1534/genetics.119.302772] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/05/2019] [Indexed: 01/12/2023] Open
Abstract
Stem cell regulation relies on extrinsic signaling from a niche plus intrinsic factors that respond and drive self-renewal within stem cells. A priori, loss of niche signaling and loss of the intrinsic self-renewal factors might be expected to have equivalent stem cell defects. Yet this simple prediction has not been borne out for most stem cells, including Caenorhabditis elegans germline stem cells (GSCs). The central regulators of C. elegans GSCs include extrinsically acting GLP-1/Notch signaling from the niche; intrinsically acting RNA-binding proteins in the PUF family, termed FBF-1 and FBF-2 (collectively FBF); and intrinsically acting PUF partner proteins that are direct Notch targets. Abrogation of either GLP-1/Notch signaling or its targets yields an earlier and more severe GSC defect than loss of FBF-1 and FBF-2, suggesting that additional intrinsic regulators must exist. Here, we report that those missing regulators are two additional PUF proteins, PUF-3 and PUF-11 Remarkably, an fbf-1fbf-2 ; puf-3puf-11 quadruple null mutant has a GSC defect virtually identical to that of a glp-1/Notch null mutant. PUF-3 and PUF-11 both affect GSC maintenance, both are expressed in GSCs, and epistasis experiments place them at the same position as FBF within the network. Therefore, action of PUF-3 and PUF-11 explains the milder GSC defect in fbf-1fbf-2 mutants. We conclude that a "PUF hub," comprising four PUF proteins and two PUF partners, constitutes the intrinsic self-renewal node of the C. elegans GSC RNA regulatory network. Discovery of this hub underscores the significance of PUF RNA-binding proteins as key regulators of stem cell maintenance.
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Affiliation(s)
- Kimberly A Haupt
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Kimberley T Law
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Amy L Enright
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Charlotte R Kanzler
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Heaji Shin
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
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Hubbard EJA, Schedl T. Biology of the Caenorhabditis elegans Germline Stem Cell System. Genetics 2019; 213:1145-1188. [PMID: 31796552 PMCID: PMC6893382 DOI: 10.1534/genetics.119.300238] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 09/09/2019] [Indexed: 12/14/2022] Open
Abstract
Stem cell systems regulate tissue development and maintenance. The germline stem cell system is essential for animal reproduction, controlling both the timing and number of progeny through its influence on gamete production. In this review, we first draw general comparisons to stem cell systems in other organisms, and then present our current understanding of the germline stem cell system in Caenorhabditis elegans In contrast to stereotypic somatic development and cell number stasis of adult somatic cells in C. elegans, the germline stem cell system has a variable division pattern, and the system differs between larval development, early adult peak reproduction and age-related decline. We discuss the cell and developmental biology of the stem cell system and the Notch regulated genetic network that controls the key decision between the stem cell fate and meiotic development, as it occurs under optimal laboratory conditions in adult and larval stages. We then discuss alterations of the stem cell system in response to environmental perturbations and aging. A recurring distinction is between processes that control stem cell fate and those that control cell cycle regulation. C. elegans is a powerful model for understanding germline stem cells and stem cell biology.
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Affiliation(s)
- E Jane Albert Hubbard
- Skirball Institute of Biomolecular Medicine, Departments of Cell Biology and Pathology, New York University School of Medicine, New York 10016
| | - Tim Schedl
- and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
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Haupt KA, Enright AL, Ferdous AS, Kershner AM, Shin H, Wickens M, Kimble J. The molecular basis of LST-1 self-renewal activity and its control of stem cell pool size. Development 2019; 146:dev.181644. [PMID: 31515205 DOI: 10.1242/dev.181644] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/05/2019] [Indexed: 01/01/2023]
Abstract
PUF RNA-binding proteins have diverse roles in animal development, with a broadly conserved role in stem cells. Two paradigmatic PUF proteins, FBF-1 and FBF-2, promote both self-renewal and differentiation in the C. elegans germline. The LST-1 protein is a pivotal regulator of self-renewal and is oncogenic when mis-expressed. Here, we demonstrate that LST-1 self-renewal activity resides within a predicted disordered region that harbors two KXXL motifs. We find that the KXXL motifs mediate the binding of LST-1 to FBF, and that point mutations of these motifs abrogate LST-1 self-renewal activity. The LST-1-FBF partnership is therefore crucial to stem cell maintenance and is a key element in the FBF regulatory network. A distinct region within LST-1 determines its spatial expression and size of the GSC pool. Most importantly, the molecular understanding of how an IDR-rich protein works in an essential partnership with a conserved stem cell regulator and RNA-binding protein suggests broad new avenues for combinatorial control.
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Affiliation(s)
- Kimberly A Haupt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amy L Enright
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ahlan S Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aaron M Kershner
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Heaji Shin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA .,Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
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Lee C, Shin H, Kimble J. Dynamics of Notch-Dependent Transcriptional Bursting in Its Native Context. Dev Cell 2019; 50:426-435.e4. [PMID: 31378588 PMCID: PMC6724715 DOI: 10.1016/j.devcel.2019.07.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 05/23/2019] [Accepted: 07/01/2019] [Indexed: 12/16/2022]
Abstract
Transcription is well known to be inherently stochastic and episodic, but the regulation of transcriptional dynamics is not well understood. Here, we analyze how Notch signaling modulates transcriptional bursting during animal development. Our focus is Notch regulation of transcription in germline stem cells of the nematode C. elegans. Using the MS2 system to visualize nascent transcripts and live imaging to record dynamics, we analyze bursting as a function of position within the intact animal. We find that Notch-dependent transcriptional activation is indeed "bursty"; that wild-type Notch modulates burst duration (ON-time) rather than duration of pauses between bursts (OFF-time) or mean burst intensity; and that a mutant Notch receptor, which is compromised for assembly into the Notch transcription factor complex, primarily modifies burst size (duration × intensity). These analyses thus visualize the effect of a canonical signaling pathway on metazoan transcriptional bursting in its native context.
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Affiliation(s)
- ChangHwan Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Heaji Shin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Crittenden SL, Lee C, Mohanty I, Battula S, Knobel K, Kimble J. Sexual dimorphism of niche architecture and regulation of the Caenorhabditis elegans germline stem cell pool. Mol Biol Cell 2019; 30:1757-1769. [PMID: 31067147 PMCID: PMC6727753 DOI: 10.1091/mbc.e19-03-0164] [Citation(s) in RCA: 15] [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: 03/19/2019] [Revised: 04/24/2019] [Accepted: 05/02/2019] [Indexed: 01/08/2023] Open
Abstract
Stem cell maintenance by niche signaling is a common theme across phylogeny. In the Caenorhabditis elegans gonad, the broad outlines of germline stem cell (GSC) regulation are the same for both sexes: GLP-1/Notch signaling from the mesenchymal distal tip cell niche maintains GSCs in the distal gonad of both sexes and does so via two key stem cell regulators, SYGL-1 and LST-1. Yet most recent analyses of niche signaling and GSC regulation have focused on XX hermaphrodites, an essentially female sex making sperm in larvae and oocytes in adults. Here we focus on GSC regulation in XO males. Sexual dimorphism of niche architecture, reported previously, suggested that the molecular responses to niche signaling or numbers of GSCs might also be sexually distinct. Remarkably, this is not the case. This work extends our understanding of the sexually dimorphic niche architecture, but also demonstrates that the dimorphic niches drive a similar molecular response and maintain a similar number of GSCs in their stem cell pools.
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Affiliation(s)
- Sarah L. Crittenden
- Howard Hughes Medical Institute, University of Wisconsin–Madison, Madison, WI 53706
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706
| | - ChangHwan Lee
- Howard Hughes Medical Institute, University of Wisconsin–Madison, Madison, WI 53706
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706
| | - Ipsita Mohanty
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706
| | - Sindhu Battula
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706
| | - Karla Knobel
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706
| | - Judith Kimble
- Howard Hughes Medical Institute, University of Wisconsin–Madison, Madison, WI 53706
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706
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Kocsisova Z, Kornfeld K, Schedl T. Rapid population-wide declines in stem cell number and activity during reproductive aging in C. elegans. Development 2019; 146:dev173195. [PMID: 30936182 PMCID: PMC6503983 DOI: 10.1242/dev.173195] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/13/2019] [Indexed: 01/03/2023]
Abstract
C. elegans hermaphrodites display dramatic age-related decline of reproduction early in life, while somatic functions are still robust. To understand reproductive aging, we analyzed the assembly line of oocyte production that generates fertilized eggs. Aging germlines displayed both sporadic and population-wide changes. A small fraction of aging animals displayed endomitotic oocytes in the germline and other defects. By contrast, all animals displayed age-related decreases in germline size and function. As early as day 3 of adulthood, animals displayed fewer stem cells and a slower cell cycle, which combine to substantially decrease progenitor zone output. The C. elegans germline is the only adult tissue that contains stem cells, allowing the analysis of stem cells in aging. To investigate the mechanism of the decrease in stem cell number, we analyzed the Notch signaling pathway. The Notch effectors LST-1 and SYGL-1 displayed age-related decreases in expression domains, suggesting a role for Notch signaling in germline aging. The results indicate that although sporadic defects account for the sterility of some animals, population-wide changes account for the overall pattern of reproductive aging.
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Affiliation(s)
- Zuzana Kocsisova
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Kerry Kornfeld
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Tim Schedl
- Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
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Porter DF, Prasad A, Carrick BH, Kroll-Connor P, Wickens M, Kimble J. Toward Identifying Subnetworks from FBF Binding Landscapes in Caenorhabditis Spermatogenic or Oogenic Germlines. G3 (BETHESDA, MD.) 2019; 9:153-165. [PMID: 30459181 PMCID: PMC6325917 DOI: 10.1534/g3.118.200300] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 11/09/2018] [Indexed: 12/31/2022]
Abstract
Metazoan PUF (Pumilio and FBF) RNA-binding proteins regulate various biological processes, but a common theme across phylogeny is stem cell regulation. In Caenorhabditis elegans, FBF (fem-3 Binding Factor) maintains germline stem cells regardless of which gamete is made, but FBF also functions in the process of spermatogenesis. We have begun to "disentangle" these biological roles by asking which FBF targets are gamete-independent, as expected for stem cells, and which are gamete-specific. Specifically, we compared FBF iCLIP binding profiles in adults making sperm to those making oocytes. Normally, XX adults make oocytes. To generate XX adults making sperm, we used a fem-3(gf) mutant requiring growth at 25°; for comparison, wild-type oogenic hermaphrodites were also raised at 25°. Our FBF iCLIP data revealed FBF binding sites in 1522 RNAs from oogenic adults and 1704 RNAs from spermatogenic adults. More than half of these FBF targets were independent of germline gender. We next clustered RNAs by FBF-RNA complex frequencies and found four distinct blocks. Block I RNAs were enriched in spermatogenic germlines, and included validated target fog-3, while Block II and III RNAs were common to both genders, and Block IV RNAs were enriched in oogenic germlines. Block II (510 RNAs) included almost all validated FBF targets and was enriched for cell cycle regulators. Block III (21 RNAs) was enriched for RNA-binding proteins, including previously validated FBF targets gld-1 and htp-1 We suggest that Block I RNAs belong to the FBF network for spermatogenesis, and that Blocks II and III are associated with stem cell functions.
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Affiliation(s)
- Douglas F Porter
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Aman Prasad
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Brian H Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Peggy Kroll-Connor
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Wisconsin 53706
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Wisconsin 53706
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Qiu C, Bhat VD, Rajeev S, Zhang C, Lasley AE, Wine RN, Campbell ZT, Hall TMT. A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity. eLife 2019; 8:48968. [PMID: 31397673 PMCID: PMC6697444 DOI: 10.7554/elife.48968] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/09/2019] [Indexed: 01/09/2023] Open
Abstract
In the Caenorhabditis elegans germline, fem-3 Binding Factor (FBF) partners with LST-1 to maintain stem cells. A crystal structure of an FBF-2/LST-1/RNA complex revealed that FBF-2 recognizes a short RNA motif different from the characteristic 9-nt FBF binding element, and compact motif recognition coincided with curvature changes in the FBF-2 scaffold. Previously, we engineered FBF-2 to favor recognition of shorter RNA motifs without curvature change (Bhat et al., 2019). In vitro selection of RNAs bound by FBF-2 suggested sequence specificity in the central region of the compact element. This bias, reflected in the crystal structure, was validated in RNA-binding assays. FBF-2 has the intrinsic ability to bind to this shorter motif. LST-1 weakens FBF-2 binding affinity for short and long motifs, which may increase target selectivity. Our findings highlight the role of FBF scaffold flexibility in RNA recognition and suggest a new mechanism by which protein partners refine target site selection.
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Affiliation(s)
- Chen Qiu
- Epigenetics and Stem Cell Biology LaboratoryNational Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle ParkUnited States
| | - Vandita D Bhat
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Sanjana Rajeev
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Chi Zhang
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Alexa E Lasley
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Robert N Wine
- Epigenetics and Stem Cell Biology LaboratoryNational Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle ParkUnited States
| | - Zachary T Campbell
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology LaboratoryNational Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle ParkUnited States
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