1
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Elaswad MT, Gao M, Tice VE, Bright CG, Thomas GM, Munderloh C, Trombley NJ, Haddad CN, Johnson UG, Cichon AN, Schisa JA. The CCT chaperonin and actin modulate the ER and RNA-binding protein condensation during oogenesis and maintain translational repression of maternal mRNA and oocyte quality. Mol Biol Cell 2024; 35:ar131. [PMID: 39167497 DOI: 10.1091/mbc.e24-05-0216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024] Open
Abstract
The regulation of maternal mRNAs is essential for proper oogenesis, the production of viable gametes, and to avoid birth defects and infertility. Many oogenic RNA-binding proteins have been identified with roles in mRNA metabolism, some of which localize to dynamic ribonucleoprotein granules and others that appear dispersed. Here, we use a combination of in vitro condensation assays and the in vivo Caenorhabditis elegans oogenesis model to characterize the properties of the conserved KH-domain MEX-3 protein and to identify novel regulators of MEX-3 and three other translational regulators. We demonstrate that MEX-3 undergoes phase separation and appears to have intrinsic gel-like properties in vitro. We also identify novel roles for the chaperonin-containing tailless complex polypeptide 1 (CCT) chaperonin and actin in preventing ectopic RNA-binding protein condensates in maturing oocytes that appear to be independent of MEX-3 folding. The CCT chaperonin and actin also oppose the expansion of endoplasmic reticulum sheets that may promote ectopic condensation of RNA-binding proteins. These novel regulators of condensation are also required for the translational repression of maternal mRNA which is essential for oocyte quality and fertility. The identification of this regulatory network may also have implications for understanding the role of hMex3 phase transitions in cancer.
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Affiliation(s)
- Mohamed T Elaswad
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859
- Biochemistry Cell and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI 48859
| | - Mingze Gao
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859
- Biochemistry Cell and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI 48859
| | - Victoria E Tice
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859
- Biochemistry Cell and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI 48859
| | - Cora G Bright
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859
| | - Grace M Thomas
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859
| | - Chloe Munderloh
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859
| | - Nicholas J Trombley
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859
| | - Christya N Haddad
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859
| | - Ulysses G Johnson
- Biochemistry Cell and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI 48859
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI 48859
| | - Ashley N Cichon
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859
| | - Jennifer A Schisa
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859
- Biochemistry Cell and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI 48859
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2
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Vidya E, Jami-Alahmadi Y, Mayank AK, Rizwan J, Xu JMS, Cheng T, Leventis R, Sonenberg N, Wohlschlegel JA, Vera M, Duchaine TF. EDC-3 and EDC-4 regulate embryonic mRNA clearance and biomolecular condensate specialization. Cell Rep 2024; 43:114781. [PMID: 39331503 DOI: 10.1016/j.celrep.2024.114781] [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: 03/20/2024] [Revised: 08/09/2024] [Accepted: 09/05/2024] [Indexed: 09/29/2024] Open
Abstract
Animal development is dictated by the selective and timely decay of mRNAs in developmental transitions, but the impact of mRNA decapping scaffold proteins in development is unclear. This study unveils the roles and interactions of the DCAP-2 decapping scaffolds EDC-3 and EDC-4 in the embryonic development of C. elegans. EDC-3 facilitates the timely removal of specific embryonic mRNAs, including cgh-1, car-1, and ifet-1 by reducing their expression and preventing excessive accumulation of DCAP-2 condensates in somatic cells. We further uncover a role for EDC-3 in defining the boundaries between P bodies, germ granules, and stress granules. Finally, we show that EDC-4 counteracts EDC-3 and engenders the assembly of DCAP-2 with the GID (CTLH) complex, a ubiquitin ligase involved in maternal-to-zygotic transition (MZT). Our findings support a model where multiple RNA decay mechanisms temporally clear maternal and zygotic mRNAs throughout embryonic development.
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Affiliation(s)
- Elva Vidya
- Department of Biochemistry, McGill University, Montréal QC H3G 1Y6, Canada; Rosalind and Morris Goodman Cancer Institute, Montréal QC H3G 1Y6, Canada
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Adarsh K Mayank
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Javeria Rizwan
- Department of Biochemistry, McGill University, Montréal QC H3G 1Y6, Canada
| | - Jia Ming Stella Xu
- Department of Biochemistry, McGill University, Montréal QC H3G 1Y6, Canada
| | - Tianhao Cheng
- Department of Biochemistry, McGill University, Montréal QC H3G 1Y6, Canada; Rosalind and Morris Goodman Cancer Institute, Montréal QC H3G 1Y6, Canada
| | - Rania Leventis
- Department of Biochemistry, McGill University, Montréal QC H3G 1Y6, Canada; Rosalind and Morris Goodman Cancer Institute, Montréal QC H3G 1Y6, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montréal QC H3G 1Y6, Canada; Rosalind and Morris Goodman Cancer Institute, Montréal QC H3G 1Y6, Canada
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Maria Vera
- Department of Biochemistry, McGill University, Montréal QC H3G 1Y6, Canada
| | - Thomas F Duchaine
- Department of Biochemistry, McGill University, Montréal QC H3G 1Y6, Canada; Rosalind and Morris Goodman Cancer Institute, Montréal QC H3G 1Y6, Canada.
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3
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Tatnell HR, Novakovic S, Boag PR, Davis GM. EYA-1 is required for genomic integrity independent of H2AX signalling in Caenorhabditis elegans. Mol Biol Rep 2024; 51:1009. [PMID: 39316168 PMCID: PMC11422256 DOI: 10.1007/s11033-024-09933-4] [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: 05/02/2024] [Accepted: 09/10/2024] [Indexed: 09/25/2024]
Abstract
BACKGROUND Resolving genomic insults is essential for the survival of any species. In the case of eukaryotes, several pathways comprise the DNA damage repair network, and many components have high evolutionary conservation. These pathways ensure that DNA damage is resolved which prevents disease associated mutations from occurring in a de novo manner. In this study, we investigated the role of the Eyes Absent (EYA) homologue in Caenorhabditis elegans and its role in DNA damage repair. Current understanding of mammalian EYA1 suggests that EYA1 is recruited in response to H2AX signalling to dsDNA breaks. C. elegans do not possess a H2AX homologue, although they do possess homologues of the core DNA damage repair proteins. Due to this, we aimed to determine if eya-1 contributes to DNA damage repair independent of H2AX. METHODS AND RESULTS We used a putative null mutant for eya-1 in C. elegans and observed that absence of eya-1 results in abnormal chromosome morphology in anaphase embryos, including chromosomal bridges, missegregated chromosomes, and embryos with abnormal nuclei. Additionally, inducing different types of genomic insults, we show that eya-1 mutants are highly sensitive to induction of DNA damage, yet show little change to induced DNA replication stress and display a mortal germline resulting in sterility over successive generations. CONCLUSIONS Collectively, this study suggests that the EYA family of proteins may have a greater involvement in maintaining genomic integrity than previously thought and unveils novel roles of EYA associated DNA damage repair.
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Affiliation(s)
- Hannah R Tatnell
- Institute of Innovation, Science and Sustainability, Federation University, Churchill, VIC, Australia
| | - Stevan Novakovic
- 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
| | - Gregory M Davis
- Institute of Innovation, Science and Sustainability, Federation University, Churchill, VIC, Australia.
- Department of Health Sciences and Biostatistics, Swinburne University of Technology, Hawthorn, Australia.
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4
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Su Y, Shea J, Destephanis D, Su Z. Transcriptomic analysis of the spatiotemporal axis of oogenesis and fertilization in C. elegans. Front Cell Dev Biol 2024; 12:1436975. [PMID: 39224437 PMCID: PMC11366716 DOI: 10.3389/fcell.2024.1436975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Caenorhabditis elegans hermaphrodite presents a unique model to study the formation of oocytes. However, the size of the model animal and difficulties in retrieval of specific stages of the germline have obviated closer systematic studies of this process throughout the years. Here, we present a transcriptomic level analysis into the oogenesis of C. elegans hermaphrodites. We dissected a hermaphrodite gonad into seven sections corresponding to the mitotic distal region, the pachytene region, the diplotene region, the early diakinesis region and the 3 most proximal oocytes, and deeply sequenced the transcriptome of each of them along with that of the fertilized egg using a single-cell RNA-seq (scRNA-seq) protocol. We identified specific gene expression events as well as gene splicing events in finer detail along the gonad and provided novel insights into underlying mechanisms of the oogenesis process. Furthermore, through careful review of relevant research literature coupled with patterns observed in our analysis, we delineate transcripts that may serve functions in the interactions between the germline and cells of the somatic gonad. These results expand our knowledge of the transcriptomic space of the C. elegans germline and lay a foundation on which future studies of the germline can be based upon.
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Affiliation(s)
| | | | | | - Zhengchang Su
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, United States
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5
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Elaswad MT, Gao M, Tice VE, Bright CG, Thomas GM, Munderloh C, Trombley NJ, Haddad CN, Johnson UG, Cichon AN, Schisa JA. The CCT chaperonin and actin modulate the ER and RNA-binding protein condensation during oogenesis to maintain translational repression of maternal mRNA and oocyte quality. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601596. [PMID: 39005301 PMCID: PMC11244991 DOI: 10.1101/2024.07.01.601596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The regulation of maternal mRNAs is essential for proper oogenesis, the production of viable gametes, and to avoid birth defects and infertility. Many oogenic RNA-binding proteins have been identified with roles in mRNA metabolism, some of which localize to dynamic ribonucleoprotein granules and others that appear dispersed. Here, we use a combination of in vitro condensation assays and the in vivo C. elegans oogenesis model to determine the intrinsic properties of the conserved KH-domain MEX-3 protein and to identify novel regulators of MEX-3 and the Lsm protein, CAR-1. We demonstrate that MEX-3 undergoes liquid-liquid phase separation and appears to have intrinsic gel-like properties in vitro . We also identify novel roles for the CCT chaperonin and actin in preventing ectopic RNA-binding protein condensates in maturing oocytes that appear to be independent of MEX-3 folding. CCT and actin also oppose the expansion of ER sheets that may promote ectopic condensation of RNA-binding proteins that are associated with de-repression of maternal mRNA. This regulatory network is essential to preserve oocyte quality, prevent infertility, and may have implications for understanding the role of hMex3 phase transitions in cancer. Significance statement The molecular mechanisms that regulate phase transitions of oogenic RNA-binding proteins are critical to elucidate but are not fully understood.We identify novel regulators of RNA-binding protein phase transitions in maturing oocytes that are required to maintain translational repression of maternal mRNAs and oocyte quality.This study is the first to elucidate a regulatory network involving the CCT chaperonin, actin, and the ER for phase transitions of RNA-binding proteins during oogenesis. Our findings for the conserved MEX-3 protein may also be applicable to better understanding the role of hMex3 phase transitions in cancer.
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6
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Yin F, Zhou Y, Xie D, Liang Y, Luo X. Evaluating the adverse effects and mechanisms of nanomaterial exposure on longevity of C. elegans: A literature meta-analysis and bioinformatics analysis of multi-transcriptome data. ENVIRONMENTAL RESEARCH 2024; 247:118106. [PMID: 38224941 DOI: 10.1016/j.envres.2024.118106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024]
Abstract
Exposure to large-size particulate air pollution (PM2.5 or PM10) has been reported to increase risks of aging-related diseases and human death, indicating the potential pro-aging effects of airborne nanomaterials with ultra-fine particle size (which have been widely applied in various fields). However, this hypothesis remains inconclusive. Here, a meta-analysis of 99 published literatures collected from electronic databases (PubMed, EMBASE and Cochrane Library; from inception to June 2023) was performed to confirm the effects of nanomaterial exposure on aging-related indicators and molecular mechanisms in model animal C. elegans. The pooled analysis by Stata software showed that compared with the control, nanomaterial exposure significantly shortened the mean lifespan [standardized mean difference (SMD) = -2.30], reduced the survival rate (SMD = -4.57) and increased the death risk (hazard ratio = 1.36) accompanied by upregulation of ced-3, ced-4 and cep-1, while downregulation of ctl-2, ape-1, aak-2 and pmk-1. Furthermore, multi-transcriptome data associated with nanomaterial exposure were retrieved from Gene Expression Omnibus (GSE32521, GSE41486, GSE24847, GSE59470, GSE70509, GSE14932, GSE93187, GSE114881, and GSE122728) and bioinformatics analyses showed that pseudogene prg-2, mRNAs of abu, car-1, gipc-1, gsp-3, kat-1, pod-2, acdh-8, hsp-60 and egrh-2 were downregulated, while R04A9.7 was upregulated after exposure to at least two types of nanomaterials. Resveratrol (abu, hsp-60, pod-2, egrh-2, acdh-8, gsp-3, car-1, kat-1, gipc-1), naringenin (kat-1, egrh-2), coumestrol (egrh-2) or swainsonine/niacin/ferulic acid (R04A9.7) exerted therapeutic effects by reversing the expression levels of target genes. In conclusion, our study demonstrates the necessity to use phytomedicines that target hub genes to delay aging for populations with nanomaterial exposure.
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Affiliation(s)
- Fei Yin
- College of Textile and Clothing Engineering, Soochow University, 199 Ren-Ai Road, Suzhou, 215123, China
| | - Yang Zhou
- School of Textile Science and Engineering/National Engineering Laboratory for Advanced Yarn and Clean Production, Wuhan Textile University, Wuhan, 430200, China.
| | - Dongli Xie
- College of Textile and Clothing Engineering, Soochow University, 199 Ren-Ai Road, Suzhou, 215123, China
| | - Yunxia Liang
- College of Textile and Clothing Engineering, Soochow University, 199 Ren-Ai Road, Suzhou, 215123, China.
| | - Xiaogang Luo
- College of Textile and Clothing Engineering, Soochow University, 199 Ren-Ai Road, Suzhou, 215123, China.
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7
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Cassani M, Seydoux G. P-body-like condensates in the germline. Semin Cell Dev Biol 2024; 157:24-32. [PMID: 37407370 PMCID: PMC10761593 DOI: 10.1016/j.semcdb.2023.06.010] [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: 05/08/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023]
Abstract
P-bodies are cytoplasmic condensates that accumulate low-translation mRNAs for temporary storage before translation or degradation. P-bodies have been best characterized in yeast and mammalian tissue culture cells. We describe here related condensates in the germline of animal models. Germline P-bodies have been reported at all stages of germline development from primordial germ cells to gametes. The activity of the universal germ cell fate regulator, Nanos, is linked to the mRNA decay function of P-bodies, and spatially-regulated condensation of P-body like condensates in embryos is required to localize mRNA regulators to primordial germ cells. In most cases, however, it is not known whether P-bodies represent functional compartments or non-functional condensation by-products that arise when ribonucleoprotein complexes saturate the cytoplasm. We speculate that the ubiquity of P-body-like condensates in germ cells reflects the strong reliance of the germline on cytoplasmic, rather than nuclear, mechanisms of gene regulation.
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Affiliation(s)
- Madeline Cassani
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Geraldine Seydoux
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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8
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Zhang H, Zhang T, Wan X, Chen C, Wang S, Qin D, Li L, Yu L, Wu X. LSM14B coordinates protein component expression in the P-body and controls oocyte maturation. J Genet Genomics 2024; 51:48-60. [PMID: 37481122 DOI: 10.1016/j.jgg.2023.07.006] [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: 03/23/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/24/2023]
Abstract
The generation of mature and healthy oocytes is the most critical event in the entire female reproductive process, and the mechanisms regulating this process remain to be studied. Here, we demonstrate that Smith-like (LSM) family member 14B (LSM14B) regulates oocyte maturation, and the loss of LSM14B in mouse ovaries leads to abnormal oocyte MII arrest and female infertility. Next, we find the aberrant transcriptional activation, indicated by abnormal non-surrounded nucleolus and surrounded nucleolus oocyte proportions, and abnormal chromosome assembly and segregation in Lsm14b-deficient mouse oocytes. The global transcriptome analysis suggests that many transcripts involved in cytoplasmic processing body (P-body) function are altered in Lsm14b-deficient mouse oocytes. Deletion of Lsm14b results in the expression and/or localization changes of P-body components (such as LSM14A, DCP1A, and 4E-T). Notably, DDX6, a key component of the P-body, is downregulated and accumulates in the nuclei in Lsm14b-deficient mouse oocytes. Taken together, our data suggest that LSM14B links mouse oocyte maturation to female fertility through the regulation of the P-body.
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Affiliation(s)
- Huiru Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Tao Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Xiang Wan
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Chang Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Shu Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Dongdong Qin
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Lufan Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Luping Yu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu 210029, China.
| | - Xin Wu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China.
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9
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Fuentes-Jiménez DA, Salinas LS, Morales-Oliva E, Ramírez-Ramírez VA, Arciniega M, Navarro RE. Two predicted α-helices within the prion-like domain of TIAR-1 play a crucial role in its association with stress granules in Caenorhabditis elegans. Front Cell Dev Biol 2023; 11:1265104. [PMID: 38161334 PMCID: PMC10757852 DOI: 10.3389/fcell.2023.1265104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/14/2023] [Indexed: 01/03/2024] Open
Abstract
Stress granules (SGs) are sites for mRNA storage, protection, and translation repression. TIA1 and TIAR1 are two RNA-binding proteins that are key players in SGs formation in mammals. TIA1/TIAR have a prion-like domain (PrD) in their C-terminal that promotes liquid-phase separation. Lack of any TIA1/TIAR has severe consequences in mice. However, it is not clear whether the failure to form proper SGs is the cause of any of these problems. We disrupted two predicted α-helices within the prion-like domain of the Caenohabditis elegans TIA1/TIAR homolog, TIAR-1, to test whether its association with SGs is important for the nematode. We found that tiar-1 PrD mutant animals continued to form TIAR-1 condensates under stress in the C. elegans gonad. Nonetheless, TIAR-1 condensates appeared fragile and disassembled quickly after stress. Apparently, the SGs continued to associate regularly as observed with CGH-1, an SG marker. Like tiar-1-knockout nematodes, tiar-1 PrD mutant animals exhibited fertility problems and a shorter lifespan. Notwithstanding this, tiar-1 PrD mutant nematodes were no sensitive to stress. Our data demonstrate that the predicted prion-like domain of TIAR-1 is important for its association with stress granules. Moreover, this domain may also play a significant role in various TIAR-1 functions unrelated to stress, such as fertility, embryogenesis and lifespan.
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Affiliation(s)
- D. A. Fuentes-Jiménez
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - L. S. Salinas
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - E. Morales-Oliva
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - V. A. Ramírez-Ramírez
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - M. Arciniega
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - R. E. Navarro
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
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10
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He F, Jacobson A. Eukaryotic mRNA decapping factors: molecular mechanisms and activity. FEBS J 2023; 290:5057-5085. [PMID: 36098474 PMCID: PMC10008757 DOI: 10.1111/febs.16626] [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: 06/30/2022] [Revised: 08/11/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022]
Abstract
Decapping is the enzymatic removal of 5' cap structures from mRNAs in eukaryotic cells. Cap structures normally enhance mRNA translation and stability, and their excision commits an mRNA to complete 5'-3' exoribonucleolytic digestion and generally ends the physical and functional cellular presence of the mRNA. Decapping plays a pivotal role in eukaryotic cytoplasmic mRNA turnover and is a critical and highly regulated event in multiple 5'-3' mRNA decay pathways, including general 5'-3' decay, nonsense-mediated mRNA decay (NMD), AU-rich element-mediated mRNA decay, microRNA-mediated gene silencing, and targeted transcript-specific mRNA decay. In the yeast Saccharomyces cerevisiae, mRNA decapping is carried out by a single Dcp1-Dcp2 decapping enzyme in concert with the accessory activities of specific regulators commonly known as decapping activators or enhancers. These regulatory proteins include the general decapping activators Edc1, 2, and 3, Dhh1, Scd6, Pat1, and the Lsm1-7 complex, as well as the NMD-specific factors, Upf1, 2, and 3. Here, we focus on in vivo mRNA decapping regulation in yeast. We summarize recently uncovered molecular mechanisms that control selective targeting of the yeast decapping enzyme and discuss new roles for specific decapping activators in controlling decapping enzyme targeting, assembly of target-specific decapping complexes, and the monitoring of mRNA translation. Further, we discuss the kinetic contribution of mRNA decapping for overall decay of different substrate mRNAs and highlight experimental evidence pointing to the functional coordination and physical coupling between events in mRNA deadenylation, decapping, and 5'-3' exoribonucleolytic decay.
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Affiliation(s)
- Feng He
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
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11
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Shao Y, Wang Y, Hua X, Li Y, Wang D. Polylactic acid microparticles in the range of μg/L reduce reproductive capacity by affecting the gonad development and the germline apoptosis in Caenorhabditis elegans. CHEMOSPHERE 2023; 336:139193. [PMID: 37315859 DOI: 10.1016/j.chemosphere.2023.139193] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 06/16/2023]
Abstract
Polylactic acid (PLA) accounts for approximately 45% of the global market of biodegradable plastics. Using Caenorhabditis elegans as an animal model, we examined the effect of long-term exposure to PLA microplastic (MP) on reproductive capacity and the underlying mechanism. Brood size, number of fertilized eggs in uterus, and number of hatched eggs were significantly reduced by exposure to 10 and 100 μg/L PLA MP. Number of mitotic cells per gonad, area of gonad arm, and length of gonad arm were further significantly decreased by exposure to 10 and 100 μg/L PLA MP. In addition, exposure to 10 and 100 μg/L PLA MP enhanced germline apoptosis in the gonad. Accompanied with the enhancement in germline apoptosis, exposure to 10 and 100 μg/L PLA MP decreased expression of ced-9 and increased expressions of ced-3, ced-4, and egl-1. Moreover, the induction of germline apoptosis in PLA MP exposed nematodes was suppressed by RNAi of ced-3, ced-4, and egl-1, and strengthened by RNAi of ced-9. Meanwhile, we did not detect the obvious effect of leachate of 10 and 100 μg/L PLA MPs on reproductive capacity, gonad development, germline apoptosis, and expression of apoptosis related genes. Therefore, exposure to 10 and 100 μg/L PLA MPs potentially reduces the reproductive capacity by influencing the gonad development and enhancing the germline apoptosis in nematodes.
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Affiliation(s)
- Yuting Shao
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Yuxing Wang
- Medical School, Southeast University, Nanjing, China
| | - Xin Hua
- Medical School, Southeast University, Nanjing, China
| | - Yunhui Li
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, China.
| | - Dayong Wang
- Medical School, Southeast University, Nanjing, China; Shenzhen Ruipuxun Academy for Stem Cell & Regenerative Medicine, Shenzhen, China.
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12
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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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13
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Cassani M, Seydoux G. Specialized germline P-bodies are required to specify germ cell fate in Caenorhabditis elegans embryos. Development 2022; 149:dev200920. [PMID: 36196602 PMCID: PMC9686995 DOI: 10.1242/dev.200920] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/06/2022] [Indexed: 07/30/2023]
Abstract
In animals with germ plasm, specification of the germline involves 'germ granules', cytoplasmic condensates that enrich maternal transcripts in the germline founder cells. In Caenorhabditis elegans embryos, P granules enrich maternal transcripts, but surprisingly P granules are not essential for germ cell fate specification. Here, we describe a second condensate in the C. elegans germ plasm. Like canonical P-bodies found in somatic cells, 'germline P-bodies' contain regulators of mRNA decapping and deadenylation and, in addition, the intrinsically-disordered proteins MEG-1 and MEG-2 and the TIS11-family RNA-binding protein POS-1. Embryos lacking meg-1 and meg-2 do not stabilize P-body components, misregulate POS-1 targets, mis-specify the germline founder cell and do not develop a germline. Our findings suggest that specification of the germ line involves at least two distinct condensates that independently enrich and regulate maternal mRNAs in the germline founder cells. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Madeline Cassani
- Howard Hughes Medical Institute and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Geraldine Seydoux
- Howard Hughes Medical Institute and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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14
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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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15
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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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16
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Grzejda D, Mach J, Schweizer JA, Hummel B, Rezansoff AM, Eggenhofer F, Panhale A, Lalioti ME, Cabezas Wallscheid N, Backofen R, Felsenberg J, Hilgers V. The long noncoding RNA mimi scaffolds neuronal granules to maintain nervous system maturity. SCIENCE ADVANCES 2022; 8:eabo5578. [PMID: 36170367 PMCID: PMC9519039 DOI: 10.1126/sciadv.abo5578] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/15/2022] [Indexed: 05/29/2023]
Abstract
RNA binding proteins and messenger RNAs (mRNAs) assemble into ribonucleoprotein granules that regulate mRNA trafficking, local translation, and turnover. The dysregulation of RNA-protein condensation disturbs synaptic plasticity and neuron survival and has been widely associated with human neurological disease. Neuronal granules are thought to condense around particular proteins that dictate the identity and composition of each granule type. Here, we show in Drosophila that a previously uncharacterized long noncoding RNA, mimi, is required to scaffold large neuronal granules in the adult nervous system. Neuronal ELAV-like proteins directly bind mimi and mediate granule assembly, while Staufen maintains condensate integrity. mimi granules contain mRNAs and proteins involved in synaptic processes; granule loss in mimi mutant flies impairs nervous system maturity and neuropeptide-mediated signaling and causes phenotypes of neurodegeneration. Our work reports an architectural RNA for a neuronal granule and provides a handle to interrogate functions of a condensate independently of those of its constituent proteins.
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Affiliation(s)
- Dominika Grzejda
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
- Faculty of Biology, Albert Ludwig University of Freiburg, Freiburg 79104, Germany
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS- MCB), Freiburg 79108, Germany
| | - Jana Mach
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Johanna Aurelia Schweizer
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel 4058, Switzerland
- University of Basel, Basel 4001, Switzerland
| | - Barbara Hummel
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | | | - Florian Eggenhofer
- Department of Computer Science, Albert Ludwig University of Freiburg, Freiburg 79110, Germany
| | - Amol Panhale
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Maria-Eleni Lalioti
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | | | - Rolf Backofen
- Department of Computer Science, Albert Ludwig University of Freiburg, Freiburg 79110, Germany
- BIOSS and CIBSS Centres for Biological Signalling Studies, University of Freiburg, Freiburg 79104, Germany
| | - Johannes Felsenberg
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel 4058, Switzerland
| | - Valérie Hilgers
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg 79104, Germany
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17
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Elaswad MT, Munderloh C, Watkins BM, Sharp KG, Breton E, Schisa JA. Imaging-associated stress causes divergent phase transitions of RNA-binding proteins in the Caenorhabditis elegans germ line. G3 GENES|GENOMES|GENETICS 2022; 12:6633935. [PMID: 35801939 PMCID: PMC9434235 DOI: 10.1093/g3journal/jkac172] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/29/2022] [Indexed: 11/25/2022]
Abstract
One emerging paradigm of cellular organization of RNA and RNA-binding proteins is the formation of membraneless organelles. Examples of membraneless organelles include several types of ribonucleoprotein granules that form via phase separation. A variety of intracellular pH changes and posttranslational modifications, as well as extracellular stresses, can stimulate the condensation of proteins into granules. For example, the assembly of stress granules induced by oxidative stress, osmotic stress, and heat stress has been well characterized in a variety of somatic cell types. In the germ line, similar stress-induced condensation of proteins occurs; however, less is known about the role of phase separation during gamete production. Researchers who study phase transitions often make use of fluorescent reporters to study the dynamics of RNA-binding proteins during live cell imaging. In this report, we demonstrate that common conditions of live-imaging Caenorhabditis elegans can cause an inadvertent stress and trigger phase transitions of RNA-binding proteins. We show that this imaging-associated stress stimulates decondensation of multiple germ granule proteins and condensation of several P-body proteins. Proteins within larger ribonucleoprotein granules in meiotically arrested oocytes do not appear to be as sensitive to the stress as proteins in diakinesis oocytes of young hermaphrodites, with the exception of the germ granule protein PGL-1. Our results have important methodological implications for all researchers using live-cell imaging techniques. The data also suggest that the RNA-binding proteins within large ribonucleoprotein granules of arrested oocytes may have distinct phases, which we characterize in our companion article.
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Affiliation(s)
- Mohamed T Elaswad
- Biochemistry, Cell and Molecular Biology Program, Central Michigan University , Mt. Pleasant, MI 48859, USA
- Department of Biology, Central Michigan University , Mt. Pleasant, MI 48859, USA
| | - Chloe Munderloh
- Department of Biology, Central Michigan University , Mt. Pleasant, MI 48859, USA
- Present address Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brooklynne M Watkins
- Biochemistry, Cell and Molecular Biology Program, Central Michigan University , Mt. Pleasant, MI 48859, USA
- Department of Biology, Central Michigan University , Mt. Pleasant, MI 48859, USA
| | - Katherine G Sharp
- Department of Biology, Central Michigan University , Mt. Pleasant, MI 48859, USA
- Present address Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Elizabeth Breton
- Department of Biology, Central Michigan University , Mt. Pleasant, MI 48859, USA
- Present address Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Jennifer A Schisa
- Biochemistry, Cell and Molecular Biology Program, Central Michigan University , Mt. Pleasant, MI 48859, USA
- Department of Biology, Central Michigan University , Mt. Pleasant, MI 48859, USA
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18
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Phillips CM, Updike DL. Germ granules and gene regulation in the Caenorhabditis elegans germline. Genetics 2022; 220:6541922. [PMID: 35239965 PMCID: PMC8893257 DOI: 10.1093/genetics/iyab195] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 10/10/2021] [Indexed: 01/27/2023] Open
Abstract
The transparency of Caenorhabditis elegans provides a unique window to observe and study the function of germ granules. Germ granules are specialized ribonucleoprotein (RNP) assemblies specific to the germline cytoplasm, and they are largely conserved across Metazoa. Within the germline cytoplasm, they are positioned to regulate mRNA abundance, translation, small RNA production, and cytoplasmic inheritance to help specify and maintain germline identity across generations. Here we provide an overview of germ granules and focus on the significance of more recent observations that describe how they further demix into sub-granules, each with unique compositions and functions.
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Affiliation(s)
- Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA,Corresponding author: (C.M.P.); (D.L.U.)
| | - Dustin L Updike
- The Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA,Corresponding author: (C.M.P.); (D.L.U.)
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19
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Zhang Y, Wang K, Yang K, Shi Y, Hong J. Insight into the interaction between the RNA helicase CGH-1 and EDC-3 and its implications. Sci Rep 2021; 11:20359. [PMID: 34645931 PMCID: PMC8514580 DOI: 10.1038/s41598-021-99919-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 09/30/2021] [Indexed: 12/03/2022] Open
Abstract
Previous studies indicated that the P-body components, CGH-1 and EDC-3 may play a crucial role in the regulation of lifespan in Caenorhabditis elegans. Homo sapiens DDX6 or Saccharomyces cerevisiae Dhh1p (CGH-1 in C. elegans) could form complexes with EDC3 (Edc3p in yeast), respectively, which is significant for translation inhibition and mRNA decay. However, it is currently unclear how CGH-1 can be recognized by EDC-3 in C. elegans. Here, we provided structural and biochemical insights into the interaction between CGH-1 and EDC-3. Combined with homology modeling, mutation, and ITC assays, we uncovered an interface between CGH-1 RecA2 domain and EDC-3 FDF-FEK. Additionally, GST-pulldown and co-localization experiments confirmed the interaction between CGH-1 and EDC-3 in vitro and in vivo. We also analyzed PATR-1-binding interface on CGH-1 RecA2 by ITC assays. Moreover, we unveiled the similarity and differences of the binding mode between EDC-3 and CAR-1 or PATR-1. Taken together, these findings provide insights into the recognition of DEAD-box protein CGH-1 by EDC-3 FDF-FEK motif, suggesting important functional implications.
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Affiliation(s)
- Yong Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, People's Republic of China
| | - Ke Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, People's Republic of China
| | - Kanglong Yang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, People's Republic of China
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, People's Republic of China
| | - Jingjun Hong
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, People's Republic of China.
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20
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Sundby AE, Molnar RI, Claycomb JM. Connecting the Dots: Linking Caenorhabditis elegans Small RNA Pathways and Germ Granules. Trends Cell Biol 2021; 31:387-401. [PMID: 33526340 DOI: 10.1016/j.tcb.2020.12.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 12/15/2022]
Abstract
Germ granules are non-membrane bound, phase-separated organelles, composed of RNAs and proteins. Germ granules are present only within the germ cells of animals, including model systems such as Caenorhabditis elegans, Drosophila, mice, and zebrafish, where they play critical roles in specifying the germ lineage, the inheritance of epigenetic information, and post-transcriptional gene regulation. Across species, conserved germ granule proteins reflect these essential functions. A significant proportion of proteins that localize to germ granules are components of RNA metabolism and small RNA (sRNA) gene regulatory pathways. Here we synthesize our current knowledge of the roles that germ granules and their components play in sRNA pathway functions, transgenerational inheritance, and fertility in the C. elegans germline.
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Affiliation(s)
- Adam E Sundby
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ruxandra I Molnar
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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21
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Wang J, Li T, Deng S, Ma E, Zhang J, Xing S. DDX6 Is Essential for Oocyte Development and Maturation in Locusta migratoria. INSECTS 2021; 12:70. [PMID: 33466820 PMCID: PMC7830464 DOI: 10.3390/insects12010070] [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] [Received: 12/13/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 11/16/2022]
Abstract
DEAD-box protein 6 (DDX6) is a member of the DDX RNA helicase family that exists in all eukaryotes. It has been extensively studied in yeast and mammals and has been shown to be involved in messenger ribonucleoprotein assembly, mRNA storage, and decay, as well as in miRNA-mediated gene silencing. DDX6 participates in many developmental processes but the biological function of DDX6 in insects has not yet been adequately addressed. Herein, we characterized the LmDDX6 gene that encodes the LmDDX6 protein in Locusta migratoria, a global, destructive pest. LmDDX6 possesses five motifs unique to the DDX6 subfamily. In the phylogenetic tree, LmDDX6 was closely related to its orthologs in Apis dorsata and Zootermopsis nevadensis. RT-qPCR data revealed high expression of LmDDX6 in the ovary, muscle, and fat body, with a declining trend in the ovary after adult ecdysis. LmDDX6 knockdown downregulated the expression levels of the juvenile hormone receptor Met, and genes encoding Met downstream targeted Grp78-1 and Grp78-2, reduced LmVg expression, and impaired ovary development and oocyte maturation. These results demonstrate that LmDDX6 plays an essential role in locust female reproduction and, thus, could be a novel target for locust biological control.
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Affiliation(s)
- Junxiu Wang
- Research Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China; (J.W.); (T.L.); (S.D.); (E.M.); (J.Z.)
- College of Life Science, Shanxi University, Taiyuan 030006, Shanxi, China
| | - Tingting Li
- Research Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China; (J.W.); (T.L.); (S.D.); (E.M.); (J.Z.)
- College of Life Science, Shanxi University, Taiyuan 030006, Shanxi, China
| | - Sufang Deng
- Research Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China; (J.W.); (T.L.); (S.D.); (E.M.); (J.Z.)
- College of Life Science, Shanxi University, Taiyuan 030006, Shanxi, China
- College of Biological Sciences and Technology, Jinzhong University, Jinzhong 030600, Shanxi, China
| | - Enbo Ma
- Research Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China; (J.W.); (T.L.); (S.D.); (E.M.); (J.Z.)
- Shanxi Provincial Key Laboratory of Agricultural Integrated Pest Management, Taiyuan 030006, Shanxi, China
| | - Jianzhen Zhang
- Research Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China; (J.W.); (T.L.); (S.D.); (E.M.); (J.Z.)
- Shanxi Provincial Key Laboratory of Agricultural Integrated Pest Management, Taiyuan 030006, Shanxi, China
| | - Shuping Xing
- Research Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China; (J.W.); (T.L.); (S.D.); (E.M.); (J.Z.)
- Shanxi Provincial Key Laboratory of Agricultural Integrated Pest Management, Taiyuan 030006, Shanxi, China
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22
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Nocua PA, Requena JM, Puerta CJ. Identification of the interactomes associated with SCD6 and RBP42 proteins in Leishmania braziliensis. J Proteomics 2020; 233:104066. [PMID: 33296709 DOI: 10.1016/j.jprot.2020.104066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/16/2020] [Accepted: 11/29/2020] [Indexed: 02/04/2023]
Abstract
Leishmania are protozoan parasites responsible for leishmaniasis. These parasites present a precise gene regulation that allows them to survive different environmental conditions during their digenetic life cycle. This adaptation depends on the regulation of the expression of a wide variety of genes, which occurs, mainly at the post-transcriptional level. This differential gene expression is achieved by mechanisms based mainly in RNA binding proteins that regulate the translation and/or stability of mRNA targets by interaction with cis elements principally located in the untranslated regions (UTR). In recent studies, our group identified and characterized two proteins, SCD6 and RBP42, as RNA binding proteins in Leishmania braziliensis. To find clues about the cellular processes in which these proteins are involved, this work was aimed to determine the SCD6- and RBP42-interacting proteins (interactome) in L. braziliensis promastigotes. For this purpose, after an in vivo UV cross-linking, cellular extracts were used to immunoprecipitated, by specific antibodies, protein complexes in which SCD6 or RBP42 were present. Protein mass spectrometry analysis of the immunoprecipitated proteins identified 96 proteins presumably associated with SCD6 and 173 proteins associated with RBP42. Notably, a significant proportion of the identified proteins were shared in both interactomes, indicating a possible functional relationship between SCD6 and RBP42. Remarkably, many of the proteins identified in the SCD6 and RBP42 interactomes are related to RNA metabolism and translation processes, and many of them have been described as components of ribonucleoprotein (RNP) granules in Leishmania and related trypanosomatids. Thus, these results support a role of SCD6 and RBP42 in the assembly and/or function of mRNA-protein complexes, participating in the fate (decay/accumulation/translation) of L. braziliensis transcripts. SIGNIFICANCE: Parasites of the Leishmania genus present a particular regulation of gene expression, operating mainly at the post-transcriptional level, surely aimed to modulate quickly both mRNA and protein levels to survive the sudden environmental changes that occur during a parasite's life cycle as it moves from one host to another. This regulation of gene expression processes would be governed by the interaction of mRNA with RNA binding proteins. Nevertheless, the entirety of protein networks involved in these regulatory processes is far from being understood. In this regard, our work is contributing to stablish protein networks in which the L. braziliensis SCD6 and RBP42 proteins are involved; these proteins, in previous works, have been described as RNA binding proteins and found to participate in gene regulation in different cells and organisms. Additionally, our data point out a possible functional relationship between SCD6 and RBP42 proteins as constituents of mRNA granules, like processing bodies or stress granules, which are essential structures in the regulation of gene expression. This knowledge could provide a new approach for the development of therapeutic targets to control Leishmania infections.
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Affiliation(s)
- Paola A Nocua
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia; Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
| | - José M Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
| | - Concepción J Puerta
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.
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23
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Dodson AE, Kennedy S. Phase Separation in Germ Cells and Development. Dev Cell 2020; 55:4-17. [PMID: 33007213 DOI: 10.1016/j.devcel.2020.09.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/28/2020] [Accepted: 09/05/2020] [Indexed: 12/20/2022]
Abstract
The animal germline is an immortal cell lineage that gives rise to eggs and/or sperm each generation. Fusion of an egg and sperm, or fertilization, sets off a cascade of developmental events capable of producing an array of different cell types and body plans. How germ cells develop, function, and eventually give rise to entirely new organisms is an important question in biology. A growing body of evidence suggests that phase separation events likely play a significant and multifaceted role in germ cells and development. Here, we discuss the organization, dynamics, and potential functions of phase-separated compartments in germ cells and examine the various ways in which phase separation might contribute to the development of multicellular organisms.
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Affiliation(s)
- Anne E Dodson
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA.
| | - Scott Kennedy
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
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24
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Nguyen LTS, Robinson DN. The Unusual Suspects in Cytokinesis: Fitting the Pieces Together. Front Cell Dev Biol 2020; 8:441. [PMID: 32626704 PMCID: PMC7314909 DOI: 10.3389/fcell.2020.00441] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/11/2020] [Indexed: 01/24/2023] Open
Abstract
Cytokinesis is the step of the cell cycle in which the cell must faithfully separate the chromosomes and cytoplasm, yielding two daughter cells. The assembly and contraction of the contractile network is spatially and temporally coupled with the formation of the mitotic spindle to ensure the successful completion of cytokinesis. While decades of studies have elucidated the components of this machinery, the so-called usual suspects, and their functions, many lines of evidence are pointing to other unexpected proteins and sub-cellular systems as also being involved in cytokinesis. These we term the unusual suspects. In this review, we introduce recent discoveries on some of these new unusual suspects and begin to consider how these subcellular systems snap together to help complete the puzzle of cytokinesis.
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Affiliation(s)
- Ly T. S. Nguyen
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Douglas N. Robinson
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD, United States
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, United States
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, United States
- Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD, United States
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25
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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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26
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Tang NH, Kim KW, Xu S, Blazie SM, Yee BA, Yeo GW, Jin Y, Chisholm AD. The mRNA Decay Factor CAR-1/LSM14 Regulates Axon Regeneration via Mitochondrial Calcium Dynamics. Curr Biol 2020; 30:865-876.e7. [PMID: 31983639 DOI: 10.1016/j.cub.2019.12.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/26/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022]
Abstract
mRNA decay factors regulate mRNA turnover by recruiting non-translating mRNAs and targeting them for translational repression and mRNA degradation. How mRNA decay pathways regulate cellular function in vivo with specificity is poorly understood. Here, we show that C. elegans mRNA decay factors, including the translational repressors CAR-1/LSM14 and CGH-1/DDX6, and the decapping enzymes DCAP-1/DCP1, function in neurons to differentially regulate axon development, maintenance, and regrowth following injury. In neuronal cell bodies, CAR-1 fully colocalizes with CGH-1 and partially colocalizes with DCAP-1, suggesting that mRNA decay components form at least two types of cytoplasmic granules. Following axon injury in adult neurons, loss of CAR-1 or CGH-1 results in increased axon regrowth and growth cone formation, whereas loss of DCAP-1 or DCAP-2 results in reduced regrowth. To determine how CAR-1 inhibits regrowth, we analyzed mRNAs bound to pan-neuronally expressed GFP::CAR-1 using a crosslinking and immunoprecipitation-based approach. Among the putative mRNA targets of CAR-1, we characterized the roles of micu-1, a regulator of the mitochondrial calcium uniporter MCU-1, in axon injury. We show that loss of car-1 results increased MICU-1 protein levels, and that enhanced axon regrowth in car-1 mutants is dependent on micu-1 and mcu-1. Moreover, axon injury induces transient calcium influx into axonal mitochondria, dependent on MCU-1. In car-1 loss-of-function mutants and in micu-1 overexpressing animals, the axonal mitochondrial calcium influx is more sustained, which likely underlies enhanced axon regrowth. Our data uncover a novel pathway that controls axon regrowth through axonal mitochondrial calcium uptake.
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Affiliation(s)
- Ngang Heok Tang
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kyung Won Kim
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Suhong Xu
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephen M Blazie
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yishi Jin
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Andrew D Chisholm
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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27
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Dokshin GA, Davis GM, Sawle AD, Eldridge MD, Nicholls PK, Gourley TE, Romer KA, Molesworth LW, Tatnell HR, Ozturk AR, de Rooij DG, Hannon GJ, Page DC, Mello CC, Carmell MA. GCNA Interacts with Spartan and Topoisomerase II to Regulate Genome Stability. Dev Cell 2020; 52:53-68.e6. [PMID: 31839538 PMCID: PMC7227305 DOI: 10.1016/j.devcel.2019.11.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 08/14/2019] [Accepted: 11/13/2019] [Indexed: 12/22/2022]
Abstract
GCNA proteins are expressed across eukarya in pluripotent cells and have conserved functions in fertility. GCNA homologs Spartan (DVC-1) and Wss1 resolve DNA-protein crosslinks (DPCs), including Topoisomerase-DNA adducts, during DNA replication. Here, we show that GCNA mutants in mouse and C. elegans display defects in genome maintenance including DNA damage, aberrant chromosome condensation, and crossover defects in mouse spermatocytes and spontaneous genomic rearrangements in C. elegans. We show that GCNA and topoisomerase II (TOP2) physically interact in both mice and worms and colocalize on condensed chromosomes during mitosis in C. elegans embryos. Moreover, C. elegans gcna-1 mutants are hypersensitive to TOP2 poison. Together, our findings support a model in which GCNA provides genome maintenance functions in the germline and may do so, in part, by promoting the resolution of TOP2 DPCs.
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Affiliation(s)
- Gregoriy A Dokshin
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Gregory M Davis
- School of Health and Life Sciences, Federation University, VIC 3841, Australia
| | - Ashley D Sawle
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Matthew D Eldridge
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Taylin E Gourley
- School of Health and Life Sciences, Federation University, VIC 3841, Australia
| | - Katherine A Romer
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Luke W Molesworth
- School of Health and Life Sciences, Federation University, VIC 3841, Australia
| | - Hannah R Tatnell
- School of Health and Life Sciences, Federation University, VIC 3841, Australia
| | - Ahmet R Ozturk
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Dirk G de Rooij
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Reproductive Biology Group, Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584, the Netherlands; Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam 1105, the Netherlands
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David C Page
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Craig C Mello
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Michelle A Carmell
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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28
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Zheleva A, Gómez-Orte E, Sáenz-Narciso B, Ezcurra B, Kassahun H, de Toro M, Miranda-Vizuete A, Schnabel R, Nilsen H, Cabello J. Reduction of mRNA export unmasks different tissue sensitivities to low mRNA levels during Caenorhabditis elegans development. PLoS Genet 2019; 15:e1008338. [PMID: 31525188 PMCID: PMC6762213 DOI: 10.1371/journal.pgen.1008338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 09/26/2019] [Accepted: 07/31/2019] [Indexed: 12/25/2022] Open
Abstract
Animal development requires the execution of specific transcriptional programs in different sets of cells to build tissues and functional organs. Transcripts are exported from the nucleus to the cytoplasm where they are translated into proteins that, ultimately, carry out the cellular functions. Here we show that in Caenorhabditis elegans, reduction of mRNA export strongly affects epithelial morphogenesis and germline proliferation while other tissues remain relatively unaffected. Epithelialization and gamete formation demand a large number of transcripts in the cytoplasm for the duration of these processes. In addition, our findings highlight the existence of a regulatory feedback mechanism that activates gene expression in response to low levels of cytoplasmic mRNA. We expand the genetic characterization of nuclear export factor NXF-1 to other members of the mRNA export pathway to model mRNA export and recycling of NXF-1 back to the nucleus. Our model explains how mutations in genes involved in general processes, such as mRNA export, may result in tissue-specific developmental phenotypes.
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Affiliation(s)
- Angelina Zheleva
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Eva Gómez-Orte
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | | | - Begoña Ezcurra
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Henok Kassahun
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - María de Toro
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Antonio Miranda-Vizuete
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Ralf Schnabel
- Institute of Genetics, Technische Universität Braunschweig, Germany
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Juan Cabello
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
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29
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Vastenhouw NL, Cao WX, Lipshitz HD. The maternal-to-zygotic transition revisited. Development 2019; 146:146/11/dev161471. [PMID: 31189646 DOI: 10.1242/dev.161471] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The development of animal embryos is initially directed by maternal gene products. Then, during the maternal-to-zygotic transition (MZT), developmental control is handed to the zygotic genome. Extensive research in both vertebrate and invertebrate model organisms has revealed that the MZT can be subdivided into two phases, during which very different modes of gene regulation are implemented: initially, regulation is exclusively post-transcriptional and post-translational, following which gradual activation of the zygotic genome leads to predominance of transcriptional regulation. These changes in the gene expression program of embryos are precisely controlled and highly interconnected. Here, we review current understanding of the mechanisms that underlie handover of developmental control during the MZT.
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Affiliation(s)
- Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Wen Xi Cao
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
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30
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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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31
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Wei S, Chen H, Dzakah EE, Yu B, Wang X, Fu T, Li J, Liu L, Fang S, Liu W, Shan G. Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants. Genome Biol 2019; 20:7. [PMID: 30621757 PMCID: PMC6325887 DOI: 10.1186/s13059-018-1619-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 12/27/2018] [Indexed: 12/04/2022] Open
Abstract
Background Long intergenic RNAs (lincRNAs) play critical roles in eukaryotic cells, but systematic analyses of the lincRNAs of an animal for phenotypes are lacking. We generate CRISPR knockout strains for Caenorhabditis elegans lincRNAs and evaluate their phenotypes. Results C. elegans lincRNAs demonstrate global features such as shorter length and fewer exons than mRNAs. For the systematic evaluation of C. elegans lincRNAs, we produce CRISPR knockout strains for 155 of the total 170 C. elegans lincRNAs. Mutants of 23 lincRNAs show phenotypes in 6 analyzed traits. We investigate these lincRNAs by phenotype for their gene expression patterns and potential functional mechanisms. Some C. elegans lincRNAs play cis roles to modulate the expression of their neighboring genes, and several lincRNAs play trans roles as ceRNAs against microRNAs. We also examine the regulation of lincRNA expression by transcription factors, and we dissect the pathway by which two transcription factors, UNC-30 and UNC-55, together control the expression of linc-73. Furthermore, linc-73 possesses a cis function to modulate the expression of its neighboring kinesin gene unc-104 and thus plays roles in C. elegans locomotion. Conclusions By using CRISPR/cas9 technology, we generate knockout strains of 155 C. elegans lincRNAs as valuable resources for studies in noncoding RNAs, and we provide biological insights for 23 lincRNAs with the phenotypes identified in this study. Electronic supplementary material The online version of this article (10.1186/s13059-018-1619-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuai Wei
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - He Chen
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Emmanuel Enoch Dzakah
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.,Department of Molecular Biology and Biotechnology, School of Biological Sciences, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Bin Yu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.,Present address: Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Xiaolin Wang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Tao Fu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Jingxin Li
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Lei Liu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Shucheng Fang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Weihong Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Present address: Hanwang Technology Co., Ltd., Haidian District, Beijing, 100193, China
| | - Ge Shan
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China. .,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, CAS, Shanghai, 200031, China.
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32
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Keiper BD. Cap-Independent mRNA Translation in Germ Cells. Int J Mol Sci 2019; 20:ijms20010173. [PMID: 30621249 PMCID: PMC6337596 DOI: 10.3390/ijms20010173] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 02/07/2023] Open
Abstract
Cellular mRNAs in plants and animals have a 5'-cap structure that is accepted as the recognition point to initiate translation by ribosomes. Consequently, it was long assumed that the translation initiation apparatus was built solely for a cap-dependent (CD) mechanism. Exceptions that emerged invoke structural damage (proteolytic cleavage) to eukaryotic initiation factor 4 (eIF4) factors that disable cap recognition. The residual eIF4 complex is thought to be crippled, but capable of cap-independent (CI) translation to recruit viral or death-associated mRNAs begrudgingly when cells are in great distress. However, situations where CI translation coexists with CD translation are now known. In such cases, CI translation is still a minor mechanism in the major background of CD synthesis. In this review, I propose that germ cells do not fit this mold. Using observations from various animal models of oogenesis and spermatogenesis, I suggest that CI translation is a robust partner to CD translation to carry out the translational control that is so prevalent in germ cell development. Evidence suggests that CI translation provides surveillance of germ cell homeostasis, while CD translation governs the regulated protein synthesis that ushers these meiotic cells through the remarkable steps in sperm/oocyte differentiation.
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Affiliation(s)
- Brett D Keiper
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA.
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33
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3′-UTRs and the Control of Protein Expression in Space and Time. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:133-148. [DOI: 10.1007/978-3-030-31434-7_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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34
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Davis GM, Tu S, Anderson JW, Colson RN, Gunzburg MJ, Francisco MA, Ray D, Shrubsole SP, Sobotka JA, Seroussi U, Lao RX, Maity T, Wu MZ, McJunkin K, Morris QD, Hughes TR, Wilce JA, Claycomb JM, Weng Z, Boag PR. The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. e legans. eLife 2018; 7:35478. [PMID: 30575518 PMCID: PMC6351104 DOI: 10.7554/elife.35478] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 12/20/2018] [Indexed: 12/26/2022] Open
Abstract
Proper regulation of germline gene expression is essential for fertility and maintaining species integrity. In the C. elegans germline, a diverse repertoire of regulatory pathways promote the expression of endogenous germline genes and limit the expression of deleterious transcripts to maintain genome homeostasis. Here we show that the conserved TRIM-NHL protein, NHL-2, plays an essential role in the C. elegans germline, modulating germline chromatin and meiotic chromosome organization. We uncover a role for NHL-2 as a co-factor in both positively (CSR-1) and negatively (HRDE-1) acting germline 22G-small RNA pathways and the somatic nuclear RNAi pathway. Furthermore, we demonstrate that NHL-2 is a bona fide RNA binding protein and, along with RNA-seq data point to a small RNA independent role for NHL-2 in regulating transcripts at the level of RNA stability. Collectively, our data implicate NHL-2 as an essential hub of gene regulatory activity in both the germline and soma.
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Affiliation(s)
- Gregory M Davis
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.,School of Health and Life Sciences, Federation University, Victoria, Australia
| | - Shikui Tu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
| | - Joshua Wt Anderson
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Rhys N Colson
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Menachem J Gunzburg
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | | | - Debashish Ray
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Sean P Shrubsole
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Julia A Sobotka
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Uri Seroussi
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Robert X Lao
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Tuhin Maity
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Monica Z Wu
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Katherine McJunkin
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Quaid D Morris
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Jacqueline A Wilce
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
| | - Peter R Boag
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
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Langerak S, Trombley A, Patterson JR, Leroux D, Couch A, Wood MP, Schisa JA. Remodeling of the endoplasmic reticulum in Caenorhabditis elegans oocytes is regulated by CGH-1. Genesis 2018; 57:e23267. [PMID: 30489010 DOI: 10.1002/dvg.23267] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 11/12/2022]
Abstract
A key aspect of development in all metazoans is remodeling at the cellular level. During the development of gametes, remodeling occurs throughout the germ line. When Caenorhabditis elegans hermaphrodites become depleted of sperm after 4 days of adulthood, significant cellular remodeling occurs within the meiotically-arrested oocytes, including the formation of ribonucleoprotein granules. Since major remodeling of the endoplasmic reticulum (ER) occurs in early embryos, we investigated the extent of ER remodeling in meiotically-arrested oocytes. We found, using a combination of fluorescence reporters and transmission electron microscopy, that the ER in arrested oocytes accumulates in patches and sheets that are enriched at the cortex. Our findings suggest this remodeling is not due to simple displacement by large amounts of yolk that accumulate in arrested oocytes, and instead may be genetically regulated. We further identified the Ddx6 RNA helicase, CGH-1, as a key regulator of ER in the germ line. In cgh-1(tn691) oocytes, we detected cortical ER patches as well as aberrant granules of the RNA-binding proteins, PAB-1, MEX-3, and CGH-1. Taken together, our results suggest the possibility that the spatial organization of RNA binding proteins may regulate the translation of mRNAs associated with the ER that in turn, controls the organization of the ER in the adult germ line.
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Affiliation(s)
- Shaughna Langerak
- Department of Biology, Central Michigan University, Mount Pleasant, Michigan
| | - Alicia Trombley
- Department of Biology, Central Michigan University, Mount Pleasant, Michigan
| | - Joseph R Patterson
- Department of Biology, Central Michigan University, Mount Pleasant, Michigan
| | - Devon Leroux
- Department of Biology, Central Michigan University, Mount Pleasant, Michigan
| | - Alexandra Couch
- Department of Biology, Central Michigan University, Mount Pleasant, Michigan
| | - Megan P Wood
- Department of Biology, Central Michigan University, Mount Pleasant, Michigan
| | - Jennifer A Schisa
- Department of Biology, Central Michigan University, Mount Pleasant, Michigan
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Yin J, Liu R, Jian Z, Yang D, Pu Y, Yin L, Wang D. Di (2-ethylhexyl) phthalate-induced reproductive toxicity involved in dna damage-dependent oocyte apoptosis and oxidative stress in Caenorhabditis elegans. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 163:298-306. [PMID: 30056344 DOI: 10.1016/j.ecoenv.2018.07.066] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 07/15/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
Di-(2-ethylhexyl) phthalate (DEHP) is a widely used plasticizer with a high environmental exposure level. As a persistent organic pollutant, DEHP causes reproductive and developmental toxicity in mammals. In this paper, the reproductive toxicity of DEHP was discussed using the model organism Caenorhabditis elegans to determine the sensitivity indices for evaluating the ecotoxicological effects of DEHP. L4 C. elegans larvae to evaluate the LC50 of DEHP and the changes in brood size and generation time, we found that the LC50 of DEHP to C. elegans exceeded 100 mg/L. And 10 mg/L DEHP exposure significantly reduced the brood sizes but not the generation time. Results of oocyte and distal-tip cell (DTC) counting suggested that the number of oocytes were decreased and apoptotic cells that from the unilateral gonad arm were increased in the 1 mg/L and 10 mg/L DEHP exposed groups. In contrast, there was no significant difference in the fluorescence intensity of DTC. Fluorescence analysis of HUS-1 showed that HUS-1 protein was overexpressed after DEHP exposure. The H2O2 level and DNA damage were measured by Bradford protein assay and AP staining respectively. The results showed that there was no significant difference in H2O2 level after DEHP exposure, in contrast, DNA damage was increased significantly. Moreover, 10 mg/L concentration DEHP exposure significantly increased the expression levels of apoptosis-related genes cep-1, egl-1, ced-4, and ced-3 and decreased the expression levels of ced-9. It suggested that cep-1, egl-1, ced-4, and ced-3 genes promote apoptosis and the ced-9 gene inhibits apoptosis. Meanwhile, 10 mg/L concentration DEHP exposure decreased the expression of oxidative stress-related genes mev-1 and gas-1. The mev-1 and gas-1 are mainly involved in the inhibition of oxidative stress in nematodes. In short, the decreased oocyte numbers and increased apoptosis oocyte numbers in C. elegans when exposed to DEHP, which may involve in the DNA damage induced by oxidative stress.
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Affiliation(s)
- Jiechen Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Zihai Jian
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Dong Yang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Dayong Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
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Moll L, Roitenberg N, Bejerano-Sagie M, Boocholez H, Carvalhal Marques F, Volovik Y, Elami T, Siddiqui AA, Grushko D, Biram A, Lampert B, Achache H, Ravid T, Tzur YB, Cohen E. The insulin/IGF signaling cascade modulates SUMOylation to regulate aging and proteostasis in Caenorhabditis elegans. eLife 2018; 7:38635. [PMID: 30403374 PMCID: PMC6277199 DOI: 10.7554/elife.38635] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 11/06/2018] [Indexed: 12/02/2022] Open
Abstract
Although aging-regulating pathways were discovered a few decades ago, it is not entirely clear how their activities are orchestrated, to govern lifespan and proteostasis at the organismal level. Here, we utilized the nematode Caenorhabditis elegans to examine whether the alteration of aging, by reducing the activity of the Insulin/IGF signaling (IIS) cascade, affects protein SUMOylation. We found that IIS activity promotes the SUMOylation of the germline protein, CAR-1, thereby shortening lifespan and impairing proteostasis. In contrast, the expression of mutated CAR-1, that cannot be SUMOylated at residue 185, extends lifespan and enhances proteostasis. A mechanistic analysis indicated that CAR-1 mediates its aging-altering functions, at least partially, through the notch-like receptor glp-1. Our findings unveil a novel regulatory axis in which SUMOylation is utilized to integrate the aging-controlling functions of the IIS and of the germline and provide new insights into the roles of SUMOylation in the regulation of organismal aging. Aging may seem inescapable, but there are many factors, from diet to genetic mutations, that can affect this process. In fact, scientists have started to uncover the mechanisms that control and influence this slow decline. For example, in the small worm Caenorhabditis elegans, removing the germs cells – which give rise to eggs – extends the lifespan. Similarly, interfering with the activity of the Insulin/IGF-1 signaling (IIS) pathway leads to a longer life for the animals. However, it is unclear whether these two mechanisms work together, or if they operate in parallel. To explore this, Moll, Roitenberg et al. first looked at how the IIS pathway regulates a type of protein modification known as SUMOylation in C. elegans. Reducing the activity of the IIS pathway slowed down aging in the worms. It also decreased the levels of SUMOylation of certain proteins, including CAR-1, which is found in the structures that produce germ cells. Further experiments showed that stopping the SUMOylation of CAR-1 extended the lifespan of the animals. In fact, replacing the protein with a mutated version of CAR-1 that cannot accept the SUMO element makes the worms live longer and resist a toxic protein that causes Alzheimer’s disease in humans. These results therefore show that, in C. elegans, the IIS pathway and a mechanism that involves CAR-1 in germ cells work together to determine the pace of aging. Further studies are now needed to dissect how the IIS pathway influences SUMOylation, and whether the findings hold true in mammals.
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Affiliation(s)
- Lorna Moll
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Noa Roitenberg
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Michal Bejerano-Sagie
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Hana Boocholez
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Filipa Carvalhal Marques
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Yuli Volovik
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Tayir Elami
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Atif Ahmed Siddiqui
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Danielle Grushko
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Adi Biram
- Departments of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Bar Lampert
- Departments of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hana Achache
- Departments of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tommer Ravid
- Departments of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yonatan B Tzur
- Departments of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ehud Cohen
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
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Spike CA, Huelgas-Morales G, Tsukamoto T, Greenstein D. Multiple Mechanisms Inactivate the LIN-41 RNA-Binding Protein To Ensure a Robust Oocyte-to-Embryo Transition in Caenorhabditis elegans. Genetics 2018; 210:1011-1037. [PMID: 30206186 PMCID: PMC6218228 DOI: 10.1534/genetics.118.301421] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/10/2018] [Indexed: 12/23/2022] Open
Abstract
In the nematode Caenorhabditis elegans, the conserved LIN-41 RNA-binding protein is a translational repressor that coordinately controls oocyte growth and meiotic maturation. LIN-41 exerts these effects, at least in part, by preventing the premature activation of the cyclin-dependent kinase CDK-1 Here we investigate the mechanism by which LIN-41 is rapidly eliminated upon the onset of meiotic maturation. Elimination of LIN-41 requires the activities of CDK-1 and multiple SCF (Skp1, Cul1, and F-box protein)-type E3 ubiquitin ligase subunits, including the conserved substrate adaptor protein SEL-10/Fbw7/Cdc4, suggesting that LIN-41 is a target of ubiquitin-mediated protein degradation. Within the LIN-41 protein, two nonoverlapping regions, Deg-A and Deg-B, are individually necessary for LIN-41 degradation; both contain several potential phosphodegron sequences, and at least one of these sequences is required for LIN-41 degradation. Finally, Deg-A and Deg-B are sufficient, in combination, to mediate SEL-10-dependent degradation when transplanted into a different oocyte protein. Although LIN-41 is a potent inhibitor of protein translation and M phase entry, the failure to eliminate LIN-41 from early embryos does not result in the continued translational repression of LIN-41 oocyte messenger RNA targets. Based on these observations, we propose a model for the elimination of LIN-41 by the SEL-10 E3 ubiquitin ligase and suggest that LIN-41 is inactivated before it is degraded. Furthermore, we provide evidence that another RNA-binding protein, the GLD-1 tumor suppressor, is regulated similarly. Redundant mechanisms to extinguish translational repression by RNA-binding proteins may both control and provide robustness to irreversible developmental transitions, including meiotic maturation and the oocyte-to-embryo transition.
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Affiliation(s)
- Caroline A Spike
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - Gabriela Huelgas-Morales
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - Tatsuya Tsukamoto
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - David Greenstein
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455
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Somatic and Germline MicroRNAs Form Distinct Silencing Complexes to Regulate Their Target mRNAs Differently. Dev Cell 2018; 47:239-247.e4. [PMID: 30245155 DOI: 10.1016/j.devcel.2018.08.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/31/2018] [Accepted: 08/23/2018] [Indexed: 11/23/2022]
Abstract
Animal germ cells possess a specific post-transcriptional regulatory context allowing the storage of maternal transcripts in the oocyte until their translation at a specific point in early development. As key regulators of gene expression, miRNAs repress translation mainly through mRNA destabilization. Thus, germline miRNAs likely use distinct ways to regulate their targets. Here, we use C. elegans to compare miRNA function within germline and somatic tissues. We show that the same miRNA displays tissue-specific gene regulatory mechanisms. While translational repression occurs in both tissues, targeted mRNAs are instead stabilized in the germline. Comparative analyses of miRNA silencing complexes (miRISC) demonstrate that their composition differs from germline to soma. We show that germline miRNA targets preferentially localize to perinuclear regions adjacent to P granules, and their repression is dependent on the core P granule component GLH-1. Together, our findings reveal the existence of different miRISC in animals that affect targeted mRNAs distinctively.
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40
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Wu E, Vashisht AA, Chapat C, Flamand MN, Cohen E, Sarov M, Tabach Y, Sonenberg N, Wohlschlegel J, Duchaine TF. A continuum of mRNP complexes in embryonic microRNA-mediated silencing. Nucleic Acids Res 2018; 45:2081-2098. [PMID: 28204614 PMCID: PMC5389717 DOI: 10.1093/nar/gkw872] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 09/21/2016] [Accepted: 09/28/2016] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) impinge on the translation and stability of their target mRNAs, and play key roles in development, homeostasis and disease. The gene regulation mechanisms they instigate are largely mediated through the CCR4–NOT deadenylase complex, but the molecular events that occur on target mRNAs are poorly resolved. We observed a broad convergence of interactions of germ granule and P body mRNP components on AIN-1/GW182 and NTL-1/CNOT1 in Caenorhabditis elegans embryos. We show that the miRISC progressively matures on the target mRNA from a scanning form into an effector mRNP particle by sequentially recruiting the CCR4–NOT complex, decapping and decay, or germ granule proteins. Finally, we implicate intrinsically disordered proteins, key components in mRNP architectures, in the embryonic function of lsy-6 miRNA. Our findings define dynamic steps of effector mRNP assembly in miRNA-mediated silencing, and identify a functional continuum between germ granules and P bodies in the C. elegans embryo.
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Affiliation(s)
| | - Ajay A Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Clément Chapat
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3G 1Y6 Canada
| | - Mathieu N Flamand
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3G 1Y6 Canada
| | - Emiliano Cohen
- Department of Developmental Biology and Cancer Research, The Institute For Medical Research-Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, The Institute For Medical Research-Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3G 1Y6 Canada
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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Raiders SA, Eastwood MD, Bacher M, Priess JR. Binucleate germ cells in Caenorhabditis elegans are removed by physiological apoptosis. PLoS Genet 2018; 14:e1007417. [PMID: 30024879 PMCID: PMC6053125 DOI: 10.1371/journal.pgen.1007417] [Citation(s) in RCA: 32] [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: 03/13/2018] [Accepted: 05/15/2018] [Indexed: 12/27/2022] Open
Abstract
Cell death plays a major role during C. elegans oogenesis, where over half of the oogenic germ cells die in a process termed physiological apoptosis. How germ cells are selected for physiological apoptosis, or instead become oocytes, is not understood. Most oocytes produce viable embryos when apoptosis is blocked, suggesting that physiological apoptosis does not function to cull defective germ cells. Instead, cells targeted for apoptosis may function as nurse cells; the germline is syncytial, and all germ cells appear to contribute cytoplasm to developing oocytes. C. elegans has been a leading model for the genetics and molecular biology of apoptosis and phagocytosis, but comparatively few studies have examined the cell biology of apoptotic cells. We used live imaging to identify and examine pre-apoptotic germ cells in the adult gonad. After initiating apoptosis, germ cells selectively export their mitochondria into the shared pool of syncytial cytoplasm; this transport appears to use the microtubule motor kinesin. The apoptotic cells then shrink as they expel most of their remaining cytoplasm, and close off from the syncytium. Shortly thereafter the apoptotic cells restructure their microtubule and actin cytoskeletons, possibly to maintain cell integrity; the microtubules form a novel, cortical array of stabilized microtubules, and actin and cofilin organize into giant cofilin-actin rods. We discovered that some apoptotic germ cells are binucleate; the binucleate germ cells can develop into binucleate oocytes in apoptosis-defective strains, and appear capable of producing triploid offspring. Our results suggest that the nuclear layer of the germline syncytium becomes folded during mitosis and growth, and that binucleate cells arise as the layer unfolds or everts; all of the binucleate cells are subsequently removed by apoptosis. These results show that physiological apoptosis targets at least two distinct populations of germ cells, and that the apoptosis machinery efficiently recognizes cells with two nuclei. Many germ cells die by apoptosis during the development of animal oocytes, including more than half of all germ cells in the model system C. elegans. How individual germ cells are selected for apoptosis, or survival, is not known. Here we study the cell biology of apoptosis. The C. elegans gonad is a syncytium, with nearly 1000 germ “cells” connected to a shared, core cytoplasm. Once apoptosis is initiated, germ cells selectively transport their mitochondria into the gonad core, apparently using the microtubule motor protein kinesin. The apoptotic cells next constrict, expelling most of their remaining cytoplasm into the core, and close off from the gonad core. The microtubule and actin cytoskeletons are remodeled and stabilized, presumably to maintain the integrity of the dying cell. The apoptotic cells form giant cofilin-actin rods, similar to rods described in stressed cultured cells and in human myopathies and neuropathies such as Alzheimer’s and Huntington’s disease. We show that some germ cells are binucleate; these cells appear to form during germline morphogenesis, and are removed by apoptosis. These results demonstrate heterogeneity between oogenic germ cells, and show that the apoptosis machinery efficiently recognizes and removes cells with two nuclei.
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Affiliation(s)
- Stephan A. Raiders
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michael D. Eastwood
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Meghan Bacher
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - James R. Priess
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Roy D, Rajyaguru PI. Suppressor of clathrin deficiency (Scd6)-An emerging RGG-motif translation repressor. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1479. [DOI: 10.1002/wrna.1479] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/07/2018] [Accepted: 03/07/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Debadrita Roy
- Department of Biochemistry; Indian Institute of Science; Bangalore India
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43
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Zhang S, Fan Z, Qiao P, Zhao Y, Wang Y, Jiang D, Wang X, Zhu X, Zhang Y, Huang B, Lu J, Li X. miR-51 regulates GABAergic synapses by targeting Rab GEF GLO-4 and lysosomal trafficking-related GLO/AP-3 pathway in Caenorhabditis elegans. Dev Biol 2018; 436:66-74. [DOI: 10.1016/j.ydbio.2018.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 01/30/2018] [Accepted: 02/17/2018] [Indexed: 01/22/2023]
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Nocua PA, Ramirez CA, Requena JM, Puerta CJ. Leishmania braziliensis SCD6 and RBP42 proteins, two factors with RNA binding capacity. Parasit Vectors 2017; 10:610. [PMID: 29258569 PMCID: PMC5735676 DOI: 10.1186/s13071-017-2557-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/26/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The study of RNA binding proteins (RBPs) is of great relevance for understanding processes like post-transcriptional control of gene expression. The post-transcriptional mechanisms are particularly important in Leishmania parasites and related trypanosomatids since transcriptional regulation is almost absent in them. Thus, RBPs should be essential during the development of these parasites and for survival strategies against the adverse conditions that they face during their life-cycle. This work was aimed to do a structural and biochemical characterization of two Leishmania braziliensis proteins, which were previously found in pull-down assays using an HSP70 RNA as bait. At that time, these proteins were annotated as hypothetical proteins (LbrM.25.2210 and LbrM.30.3080) in the GeneDB database. RESULTS Structural analysis indicated that these two proteins belong to evolutionarily conserved families; thus, they have been renamed accordingly as LbSCD6 (LbrM.25.2210) and LbRBP42 (LbrM.30.3080). We have demonstrated experimentally that these proteins are RBPs, in agreement with their structural features. Both proteins were able to bind to the complete 3' UTR-II region of HSP70-type II mRNA, and to an A + U rich element (ARE) present in that UTR. Cellular localization assays suggested that both proteins are mainly distributed in the cytoplasm of promastigotes growing at 26 °C, but they accumulate in foci around the nucleus when the parasites are under heat-shock conditions. Also, our study showed that steady-state levels of LbSCD6 and LbRBP42 transcripts decreased significantly during incubation of L. braziliensis promastigotes at heat-shock temperatures. However, in these conditions, the cellular content of both proteins remained unaltered. CONCLUSIONS Our data suggest that LbSCD6 and LbRBP42, as occurs for their orthologues in other organisms, are involved in mRNA regulation, and probably they have a relevant role facing the stress conditions that L. braziliensis encounters during insect-to-mammalian transmission.
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Affiliation(s)
- Paola A Nocua
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.,Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Cesar A Ramirez
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - José M Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
| | - Concepción J Puerta
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.
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45
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Automated three-dimensional reconstruction of the Caenorhabditis elegans germline. Dev Biol 2017; 432:222-228. [DOI: 10.1016/j.ydbio.2017.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/09/2017] [Accepted: 10/09/2017] [Indexed: 11/24/2022]
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46
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Dawson JA, Methven-Kelley C, Davis GM. atz-1 Influences meiosis to maintain germline chromosomal stability in Caenorhabditis elegans. Cell Biol Int 2017; 41:1160-1168. [PMID: 28696027 DOI: 10.1002/cbin.10821] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/07/2017] [Indexed: 11/07/2022]
Abstract
Exchange of genetic information during meiosis occurs in all sexually reproducing species to produce haploid gametes from diploid cells. This process involves tight coordination of a meiotic specific cohesin complex, the synaptonemal complex, and DNA damage repair mechanisms. In this study, we describe a putative myosin heavy chain protein orthologous to human myosin 1, F28D1.2, which we named Abnormal Transition Zone (atz-1). Deletion of atz-1 results in embryonic lethality and a depleted transition zone, accompanied by reduced expression of the meiotic cohesin protein, REC-8. atz-1 mutants display disorganized and aggregated chromosomal bodies in diakinetic oocytes. In addition to this, atz-1 mutants are hypersensitive to mild inhibition of DNA damage repair, suggesting that DNA replication in atz-1 mutants is impaired. Moreover, the atz-1 mutant phenotype is germline specific and resupplying somatically expressed atz-1 does not rescue the reproductive defects associated with atz-1 mutants. Overall, our data suggest that atz-1 contributes to meiosis and maintains germline chromosomal stability.
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Affiliation(s)
- Joseph A Dawson
- School of Applied and Biomedical Sciences, Federation University, Churchill, Australia
| | | | - Gregory M Davis
- School of Applied and Biomedical Sciences, Federation University, Churchill, Australia
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47
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Götze M, Dufourt J, Ihling C, Rammelt C, Pierson S, Sambrani N, Temme C, Sinz A, Simonelig M, Wahle E. Translational repression of the Drosophila nanos mRNA involves the RNA helicase Belle and RNA coating by Me31B and Trailer hitch. RNA (NEW YORK, N.Y.) 2017; 23:1552-1568. [PMID: 28701521 PMCID: PMC5602113 DOI: 10.1261/rna.062208.117] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/10/2017] [Indexed: 05/10/2023]
Abstract
Translational repression of maternal mRNAs is an essential regulatory mechanism during early embryonic development. Repression of the Drosophila nanos mRNA, required for the formation of the anterior-posterior body axis, depends on the protein Smaug binding to two Smaug recognition elements (SREs) in the nanos 3' UTR. In a comprehensive mass spectrometric analysis of the SRE-dependent repressor complex, we identified Smaug, Cup, Me31B, Trailer hitch, eIF4E, and PABPC, in agreement with earlier data. As a novel component, the RNA-dependent ATPase Belle (DDX3) was found, and its involvement in deadenylation and repression of nanos was confirmed in vivo. Smaug, Cup, and Belle bound stoichiometrically to the SREs, independently of RNA length. Binding of Me31B and Tral was also SRE-dependent, but their amounts were proportional to the length of the RNA and equimolar to each other. We suggest that "coating" of the RNA by a Me31B•Tral complex may be at the core of repression.
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Affiliation(s)
- Michael Götze
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Jérémy Dufourt
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34396 Montpellier Cedex 5, France
| | - Christian Ihling
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Christiane Rammelt
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Stephanie Pierson
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34396 Montpellier Cedex 5, France
| | - Nagraj Sambrani
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34396 Montpellier Cedex 5, France
| | - Claudia Temme
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Martine Simonelig
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34396 Montpellier Cedex 5, France
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
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48
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Wang M, Ly M, Lugowski A, Laver JD, Lipshitz HD, Smibert CA, Rissland OS. ME31B globally represses maternal mRNAs by two distinct mechanisms during the Drosophila maternal-to-zygotic transition. eLife 2017; 6:27891. [PMID: 28875934 PMCID: PMC5779226 DOI: 10.7554/elife.27891] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 09/04/2017] [Indexed: 12/27/2022] Open
Abstract
In animal embryos, control of development is passed from exclusively maternal gene products to those encoded by the embryonic genome in a process referred to as the maternal-to-zygotic transition (MZT). We show that the RNA-binding protein, ME31B, binds to and represses the expression of thousands of maternal mRNAs during the Drosophila MZT. However, ME31B carries out repression in different ways during different phases of the MZT. Early, it represses translation while, later, its binding leads to mRNA destruction, most likely as a consequence of translational repression in the context of robust mRNA decay. In a process dependent on the PNG kinase, levels of ME31B and its partners, Cup and Trailer Hitch (TRAL), decrease by over 10-fold during the MZT, leading to a change in the composition of mRNA-protein complexes. We propose that ME31B is a global repressor whose regulatory impact changes based on its biological context.
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Affiliation(s)
- Miranda Wang
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Michael Ly
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Andrew Lugowski
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - John D Laver
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Olivia S Rissland
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, United States.,RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, United States
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49
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Boateng R, Nguyen KCQ, Hall DH, Golden A, Allen AK. Novel functions for the RNA-binding protein ETR-1 in Caenorhabditis elegans reproduction and engulfment of germline apoptotic cell corpses. Dev Biol 2017; 429:306-320. [PMID: 28648844 PMCID: PMC5603194 DOI: 10.1016/j.ydbio.2017.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 06/01/2017] [Accepted: 06/08/2017] [Indexed: 01/31/2023]
Abstract
RNA-binding proteins (RBPs) are essential regulators of gene expression that act through a variety of mechanisms to ensure the proper post-transcriptional regulation of their target RNAs. RBPs in multiple species have been identified as playing crucial roles during development and as having important functions in various adult organ systems, including the heart, nervous, muscle, and reproductive systems. ETR-1, a highly conserved ELAV-Type RNA-binding protein belonging to the CELF/Bruno protein family, has been previously reported to be involved in C. elegans muscle development. Animals depleted of ETR-1 have been previously characterized as arresting at the two-fold stage of embryogenesis. In this study, we show that ETR-1 is expressed in the hermaphrodite somatic gonad and germ line, and that reduction of ETR-1 via RNA interference (RNAi) results in reduced hermaphrodite fecundity. Detailed characterization of this fertility defect indicates that ETR-1 is required in both the somatic tissue and the germ line to ensure wild-type reproductive levels. Additionally, the ability of ETR-1 depletion to suppress the published WEE-1.3-depletion infertility phenotype is dependent on ETR-1 being reduced in the soma. Within the germline of etr-1(RNAi) hermaphrodite animals, we observe a decrease in average oocyte size and an increase in the number of germline apoptotic cell corpses as evident by an increased number of CED-1::GFP and acridine orange positive apoptotic germ cells. Transmission Electron Microscopy (TEM) studies confirm the significant increase in apoptotic cells in ETR-1-depleted animals, and reveal a failure of the somatic gonadal sheath cells to properly engulf dying germ cells in etr-1(RNAi) animals. Through investigation of an established engulfment pathway in C. elegans, we demonstrate that co-depletion of CED-1 and ETR-1 suppresses both the reduced fecundity and the increase in the number of apoptotic cell corpses observed in etr-1(RNAi) animals. Combined, this data identifies a novel role for ETR-1 in hermaphrodite gametogenesis and in the process of engulfment of germline apoptotic cell corpses.
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Affiliation(s)
- Ruby Boateng
- Department of Biology, Howard University, Washington, DC 20059, USA
| | - Ken C Q Nguyen
- Center for C. elegans Anatomy, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - David H Hall
- Center for C. elegans Anatomy, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Andy Golden
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna K Allen
- Department of Biology, Howard University, Washington, DC 20059, USA
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50
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Singh KD, Zheng X, Milstein S, Keller M, Roschitzki B, Grossmann J, Hengartner MO. Differential regulation of germ line apoptosis and germ cell differentiation by CPEB family members in C. elegans. PLoS One 2017; 12:e0182270. [PMID: 28759574 PMCID: PMC5536308 DOI: 10.1371/journal.pone.0182270] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 07/14/2017] [Indexed: 11/21/2022] Open
Abstract
Cytoplasmic polyadenylation element binding (CPEB) proteins are evolutionary conserved RNA-binding proteins that control mRNA polyadenylation and translation. Orthologs in humans and other vertebrates are mainly involved in oogenesis. This is also the case for the C. elegans CPEB family member CPB-3, whereas two further CPEB proteins (CPB-1 and FOG-1) are involved in spermatogenesis. Here we describe the characterisation of a new missense allele of cpb-3 and show that loss of cpb-3 function leads to an increase in physiological germ cell death. To better understand the interaction and effect of C. elegans CPEB proteins on processes such as physiological apoptosis, germ cell differentiation, and regulation of gene expression, we characterised changes in the transcriptome and proteome of C. elegans CPEB mutants. Our results show that, despite their sequence similarities CPEB family members tend to have distinct overall effects on gene expression (both at the transcript and protein levels). This observation is consistent with the distinct phenotypes observed in the various CPEB family mutants.
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Affiliation(s)
- Kapil Dev Singh
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- PhD Program in Molecular Life Science, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Xue Zheng
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- PhD Program in Molecular Life Science, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Stuart Milstein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Martin Keller
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- PhD Program in Molecular Life Science, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Bernd Roschitzki
- Functional Genomics Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Jonas Grossmann
- Functional Genomics Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Michael O. Hengartner
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- * E-mail:
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