1
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Kong S, Zhu M, Scarpin MR, Pan D, Jia L, Martinez RE, Alamos S, Vadde BVL, Garcia HG, Qian SB, Brunkard JO, Roeder AHK. DRMY1 promotes robust morphogenesis by sustaining the translation of cytokinin signaling inhibitor proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.07.536060. [PMID: 37066395 PMCID: PMC10104159 DOI: 10.1101/2023.04.07.536060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Robustness is the invariant development of phenotype despite environmental changes and genetic perturbations. In the Arabidopsis flower bud, four sepals robustly initiate and grow to constant size to enclose and protect the inner floral organs. We previously characterized the mutant development related myb-like1 ( drmy1 ), where 3-5 sepals initiate variably and grow to different sizes, compromising their protective function. The molecular mechanism underlying this loss of robustness was unclear. Here, we show that drmy1 has reduced TARGET OF RAPAMYCIN (TOR) activity, ribosomal content, and translation. Translation reduction decreases the protein level of ARABIDOPSIS RESPONSE REGULATOR7 (ARR7) and ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 (AHP6), two cytokinin signaling inhibitors that are normally rapidly produced before sepal initiation. The resultant upregulation of cytokinin signaling disrupts robust auxin patterning and sepal initiation. Our work shows that the homeostasis of translation, a ubiquitous cellular process, is crucial for the robust spatiotemporal patterning of organogenesis.
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2
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Godthi A, Min S, Das S, Cruz-Corchado J, Deonarine A, Misel-Wuchter K, Issuree PD, Prahlad V. Neuronal IL-17 controls Caenorhabditis elegans developmental diapause through CEP-1/p53. Proc Natl Acad Sci U S A 2024; 121:e2315248121. [PMID: 38483995 PMCID: PMC10963014 DOI: 10.1073/pnas.2315248121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/06/2024] [Indexed: 03/19/2024] Open
Abstract
During metazoan development, how cell division and metabolic programs are coordinated with nutrient availability remains unclear. Here, we show that nutrient availability signaled by the neuronal cytokine, ILC-17.1, switches Caenorhabditis elegans development between reproductive growth and dormancy by controlling the activity of the tumor suppressor p53 ortholog, CEP-1. Specifically, upon food availability, ILC-17.1 signaling by amphid neurons promotes glucose utilization and suppresses CEP-1/p53 to allow growth. In the absence of ILC-17.1, CEP-1/p53 is activated, up-regulates cell-cycle inhibitors, decreases phosphofructokinase and cytochrome C expression, and causes larvae to arrest as stress-resistant, quiescent dauers. We propose a model whereby ILC-17.1 signaling links nutrient availability and energy metabolism to cell cycle progression through CEP-1/p53. These studies describe ancestral functions of IL-17 s and the p53 family of proteins and are relevant to our understanding of neuroimmune mechanisms in cancer. They also reveal a DNA damage-independent function of CEP-1/p53 in invertebrate development and support the existence of a previously undescribed C. elegans dauer pathway.
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Affiliation(s)
- Abhishiktha Godthi
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY14263
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
| | - Sehee Min
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY14263
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
| | - Srijit Das
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
| | - Johnny Cruz-Corchado
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY14263
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
| | - Andrew Deonarine
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
| | - Kara Misel-Wuchter
- Department of Internal Medicine, The University of Iowa, Iowa City, IA52242
| | - Priya D. Issuree
- Department of Internal Medicine, The University of Iowa, Iowa City, IA52242
| | - Veena Prahlad
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY14263
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
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3
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Morton EA, Hall AN, Cuperus JT, Queitsch C. Substantial rDNA copy number reductions alter timing of development and produce variable tissue-specific phenotypes in C. elegans. Genetics 2023; 224:iyad039. [PMID: 36919976 PMCID: PMC10474940 DOI: 10.1093/genetics/iyad039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
The genes that encode ribosomal RNAs are present in several hundred copies in most eukaryotes. These vast arrays of repetitive ribosomal DNA (rDNA) have been implicated not just in ribosome biogenesis, but also aging, cancer, genome stability, and global gene expression. rDNA copy number is highly variable among and within species; this variability is thought to associate with traits relevant to human health and disease. Here we investigate the phenotypic consequences of multicellular life at the lower bounds of rDNA copy number. We use the model Caenorhabditis elegans, which has previously been found to complete embryogenesis using only maternally provided ribosomes. We find that individuals with rDNA copy number reduced to ∼5% of wild type are capable of further development with variable penetrance. Such individuals are sterile and exhibit severe morphological defects, particularly in post-embryonically dividing tissues such as germline and vulva. Developmental completion and fertility are supported by an rDNA copy number ∼10% of wild type, with substantially delayed development. Worms with rDNA copy number reduced to ∼33% of wild type display a subtle developmental timing defect that was absent in worms with higher copy numbers. Our results support the hypothesis that rDNA requirements vary across tissues and indicate that the minimum rDNA copy number for fertile adulthood is substantially less than the lowest naturally observed total copy number. The phenotype of individuals with severely reduced rDNA copy number is highly variable in penetrance and presentation, highlighting the need for continued investigation into the biological consequences of rDNA copy number variation.
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Affiliation(s)
| | - Ashley N Hall
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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4
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Huang G, Ma Y, Xie D, Zhao C, Zhu L, Xie G, Wu P, Wang W, Zhao Z, Cai Z. Evaluation of nanoplastics toxicity in the soil nematode Caenorhabditis elegans by iTRAQ-based quantitative proteomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 862:160646. [PMID: 36493839 DOI: 10.1016/j.scitotenv.2022.160646] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Plastic pollution is recognized as a major threat to ecosystems in the 21st century. Large plastic objects undergo biotic and abiotic degradation to generate micro- and nano-sized plastic pieces. Despite tremendous efforts to evaluate the adverse effects of microplastics, a comprehensive understanding of the toxicity of nanoplastics remains elusive, especially at the protein level. To this end, we used isobaric-tag-for-relative-and-absolute-quantitation-based quantitative proteomics to investigate the proteome dynamics of the soil nematode Caenorhabditis elegans in response to exposure to 100 nm polystyrene nanoplastics (PS-NPs). After 48 h of exposure to 0.1, 1, or 10 mg/L PS-NPs, 136 out of 1684 proteins were differentially expressed and 108 of these proteins were upregulated. These proteins were related to ribosome biogenesis, translation, proteolysis, kinases, protein processing in the endoplasmic reticulum, and energy metabolism. Remarkably, changes in proteome dynamics in response to exposure to PS-NPs were consistent with the phenotypic defects of C. elegans. Collectively, our findings demonstrate that disruption of proteome homeostasis is a biological consequence of PS-NPs accumulation in C. elegans, which provides insights into the molecular mechanisms underlying the toxicology of nanoplastics.
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Affiliation(s)
- Gefei Huang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 999077, Hong Kong
| | - Yiming Ma
- Department of Biology, Hong Kong Baptist University, 999077, Hong Kong
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, 999077, Hong Kong
| | - Cunmin Zhao
- Department of Biology, Hong Kong Baptist University, 999077, Hong Kong
| | - Lin Zhu
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 999077, Hong Kong
| | - Guangshan Xie
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 999077, Hong Kong
| | - Pengfei Wu
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 999077, Hong Kong
| | - Wei Wang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 999077, Hong Kong
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, 999077, Hong Kong
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 999077, Hong Kong.
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5
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Breznak SM, Kotb NM, Rangan P. Dynamic regulation of ribosome levels and translation during development. Semin Cell Dev Biol 2023; 136:27-37. [PMID: 35725716 DOI: 10.1016/j.semcdb.2022.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/20/2022] [Accepted: 06/12/2022] [Indexed: 01/11/2023]
Abstract
The ability of ribosomes to translate mRNAs into proteins is the basis of all life. While ribosomes are essential for cell viability, reduction in levels of ribosomes can affect cell fate and developmental transitions in a tissue specific manner and can cause a plethora of related diseases called ribosomopathies. How dysregulated ribosomes homeostasis influences cell fate and developmental transitions is not fully understood. Model systems such as Drosophila and C. elegans oogenesis have been used to address these questions since defects in conserved steps in ribosome biogenesis result in stem cell differentiation and developmental defects. In this review, we first explore how ribosome levels affect stem cell differentiation. Second, we describe how ribosomal modifications and incorporation of ribosomal protein paralogs contribute to development. Third, we summarize how cells with perturbed ribosome biogenesis are sensed and eliminated during organismal growth.
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Affiliation(s)
- Shane M Breznak
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, 12222, USA
| | - Noor M Kotb
- Department of Biomedical Sciences, The School of Public Health, University at Albany SUNY, 11 Albany, NY 12222, USA
| | - Prashanth Rangan
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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6
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Wahba L, Hansen L, Fire AZ. An essential role for the piRNA pathway in regulating the ribosomal RNA pool in C. elegans. Dev Cell 2021; 56:2295-2312.e6. [PMID: 34388368 PMCID: PMC8387450 DOI: 10.1016/j.devcel.2021.07.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/11/2021] [Accepted: 07/15/2021] [Indexed: 01/08/2023]
Abstract
Piwi-interacting RNAs (piRNAs) are RNA effectors with key roles in maintaining genome integrity and promoting fertility in metazoans. In Caenorhabditis elegans loss of piRNAs leads to a transgenerational sterility phenotype. The plethora of piRNAs and their ability to silence transcripts with imperfect complementarity have raised several (non-exclusive) models for the underlying drivers of sterility. Here, we report the extranuclear and transferable nature of the sterility driver, its suppression via mutations disrupting the endogenous RNAi and poly-uridylation machinery, and copy-number amplification at the ribosomal DNA locus. In piRNA-deficient animals, several small interfering RNA (siRNA) populations become increasingly overabundant in the generations preceding loss of germline function, including ribosomal siRNAs (risiRNAs). A concomitant increase in uridylated sense rRNA fragments suggests that poly-uridylation may potentiate RNAi-mediated gene silencing of rRNAs. We conclude that loss of the piRNA machinery allows for unchecked amplification of siRNA populations, originating from abundant highly structured RNAs, to deleterious levels.
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Affiliation(s)
- Lamia Wahba
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Loren Hansen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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7
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Liao S, Chen X, Xu T, Jin Q, Xu Z, Xu D, Zhou X, Zhu C, Guang S, Feng X. Antisense ribosomal siRNAs inhibit RNA polymerase I-directed transcription in C. elegans. Nucleic Acids Res 2021; 49:9194-9210. [PMID: 34365510 PMCID: PMC8450093 DOI: 10.1093/nar/gkab662] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/13/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Eukaryotic cells express a wide variety of endogenous small regulatory RNAs that function in the nucleus. We previously found that erroneous rRNAs induce the generation of antisense ribosomal siRNAs (risiRNAs) which silence the expression of rRNAs via the nuclear RNAi defective (Nrde) pathway. To further understand the biological roles and mechanisms of this class of small regulatory RNAs, we conducted forward genetic screening to identify factors involved in risiRNA generation in Caenorhabditis elegans. We found that risiRNAs accumulated in the RNA exosome mutants. risiRNAs directed the association of NRDE proteins with pre-rRNAs and the silencing of pre-rRNAs. In the presence of risiRNAs, NRDE-2 accumulated in the nucleolus and colocalized with RNA polymerase I. risiRNAs inhibited the transcription elongation of RNA polymerase I by decreasing RNAP I occupancy downstream of the RNAi-targeted site. Meanwhile, exosomes mislocalized from the nucleolus to nucleoplasm in suppressor of siRNA (susi) mutants, in which erroneous rRNAs accumulated. These results established a novel model of rRNA surveillance by combining ribonuclease-mediated RNA degradation with small RNA-directed nucleolar RNAi system.
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Affiliation(s)
- Shimiao Liao
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Xiangyang Chen
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Ting Xu
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Qile Jin
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Zongxiu Xu
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Demin Xu
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Xufei Zhou
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Chengming Zhu
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Shouhong Guang
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Hefei, Anhui 230027, P.R. China
| | - Xuezhu Feng
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
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8
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von Diezmann L, Rog O. Single-Molecule Tracking of Chromatin-Associated Proteins in the C. elegans Gonad. J Phys Chem B 2021; 125:6162-6170. [PMID: 34097417 DOI: 10.1021/acs.jpcb.1c03040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biomolecules are distributed within cells by molecular-scale diffusion and binding events that are invisible in standard fluorescence microscopy. These molecular search kinetics are key to understanding nuclear signaling and chromosome organization and can be directly observed by single-molecule tracking microscopy. Here, we report a method to track individual proteins within intact C. elegans gonads and apply it to study the molecular dynamics of the axis, a proteinaceous backbone that organizes meiotic chromosomes. Using either fluorescent proteins or enzymatically ligated dyes, we obtain multisecond trajectories with a localization precision of 15-25 nm in nuclei actively undergoing meiosis. Correlation with a reference channel allows for accurate measurement of protein dynamics, compensating for movements of the nuclei and chromosomes within the gonad. We find that axis proteins exhibit either static binding to chromatin or free diffusion in the nucleoplasm, and we separately quantify the motion parameters of these distinct populations. Freely diffusing axis proteins selectively explore chromatin-rich regions, suggesting they are circumventing the central phase-separated region of the nucleus. This work demonstrates that single-molecule microscopy can infer nanoscale-resolution dynamics within living tissue, expanding the possible applications of this approach.
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9
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Baral SS, Lieux ME, DiMario PJ. Nucleolar stress in Drosophila neuroblasts, a model for human ribosomopathies. Biol Open 2020; 9:bio046565. [PMID: 32184230 PMCID: PMC7197718 DOI: 10.1242/bio.046565] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 03/03/2020] [Indexed: 12/11/2022] Open
Abstract
Different stem cells or progenitor cells display variable threshold requirements for functional ribosomes. This is particularly true for several human ribosomopathies in which select embryonic neural crest cells or adult bone marrow stem cells, but not others, show lethality due to failures in ribosome biogenesis or function (now known as nucleolar stress). To determine if various Drosophila neuroblasts display differential sensitivities to nucleolar stress, we used CRISPR-Cas9 to disrupt the Nopp140 gene that encodes two splice variant ribosome biogenesis factors (RBFs). Disruption of Nopp140 induced nucleolar stress that arrested larvae in the second instar stage. While the majority of larval neuroblasts arrested development, the mushroom body (MB) neuroblasts continued to proliferate as shown by their maintenance of deadpan, a neuroblast-specific transcription factor, and by their continued EdU incorporation. MB neuroblasts in wild-type larvae appeared to contain more fibrillarin and Nopp140 in their nucleoli as compared to other neuroblasts, indicating that MB neuroblasts stockpile RBFs as they proliferate in late embryogenesis while other neuroblasts normally enter quiescence. A greater abundance of Nopp140 encoded by maternal transcripts in Nopp140-/- MB neuroblasts of 1----2-day-old larvae likely rendered these cells more resilient to nucleolar stress.
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Affiliation(s)
- Sonu Shrestha Baral
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Molly E Lieux
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Patrick J DiMario
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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10
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Chen PH, Chen YT, Chu TY, Ma TH, Wu MH, Lin HH, Chang YS, Tan BCM, Lo SJ. Nucleolar control by a non-apoptotic p53-caspases-deubiquitinylase axis promotes resistance to bacterial infection. FASEB J 2020; 34:1107-1121. [PMID: 31914708 DOI: 10.1096/fj.201901959r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/02/2019] [Accepted: 10/15/2019] [Indexed: 11/11/2022]
Abstract
The nucleolus is best known for its cellular role in regulating ribosome production and growth. More recently, an unanticipated role for the nucleolus in innate immunity has recently emerged whereby downregulation of fibrillarin and nucleolar contraction confers pathogen resistance across taxa. The mechanism of this downregulation, however, remains obscure. Here we report that rather than fibrillarin itself being the proximal factor in this pathway, the key player is a fibrillarin-stabilizing deubiquitinylase USP-33. This was discovered by a candidate-gene search of Caenorhabditis elegans in which CED-3 caspase was revealed to execute targeted cleavage of USP-33, thus destabilizing fibrillarin. We also showed that cep-1 and ced-3 mutant worms altered nucleolar size and decreased antimicrobial peptide gene, spp-1, expression rendering susceptibility to bacterial infection. These phenotypes were reversed by usp-33 knockdown, thus linking the CEP-1-CED-3-USP-33 pathway with nucleolar control and resistance to bacterial infection in worms. Parallel experiments with the human analogs of caspases and USP36 revealed similar roles in coordinating these two processes. In summary, our work outlined a conserved cascade that connects cell death signaling to nucleolar control and innate immune response.
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Affiliation(s)
- Po-Hsiang Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Tung Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tai-Ying Chu
- Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan
| | - Tian-Hsiang Ma
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Mei-Hsuan Wu
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hsi-Hsien Lin
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Sun Chang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Bertrand Chin-Ming Tan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Szecheng J Lo
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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11
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Trinh DA, Shirakawa R, Kimura T, Sakata N, Goto K, Horiuchi H. Inhibitor of Growth 4 (ING4) is a positive regulator of rRNA synthesis. Sci Rep 2019; 9:17235. [PMID: 31754246 PMCID: PMC6872537 DOI: 10.1038/s41598-019-53767-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 08/30/2019] [Indexed: 01/29/2023] Open
Abstract
Ribosome biogenesis is essential for maintaining basic cellular activities although its mechanism is not fully understood. Inhibitor of growth 4 (ING4) is a member of ING family while its cellular functions remain controversial. Here, we identified several nucleolar proteins as novel ING4 interacting proteins. ING4 localized in the nucleus with strong accumulation in the nucleolus through its plant homeodomain, which is known to interact with histone trimethylated H3K4, commonly present in the promoter of active genes. ING4 deficient cells exhibited slower proliferation and the alteration in nucleolar structure with reduced rRNA transcription, which was rescued by exogenous expression of GFP-ING4 to the similar levels of wild type cells. In the ING4 deficient cells, histone H3K9 acetylation and the key rRNA transcription factor UBF at the promoter of rDNA were reduced, both of which were also recovered by exogenous GFP-ING4 expression. Thus, ING4 could positively regulate rRNA transcription through modulation of histone modifications at the rDNA promoter.
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Affiliation(s)
- Duc-Anh Trinh
- Department of Oral Cancer Therapeutics, Graduate School of Dentistry, Tohoku University, Sendai, Japan.,Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Ryutaro Shirakawa
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Tomohiro Kimura
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Research Center for Molecular Genetics, Institute for Promotion of Medical Science Research, Yamagata University Faculty of Medicine, Yamagata, Yamagata, Japan
| | - Natsumi Sakata
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Kota Goto
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Hisanori Horiuchi
- Department of Oral Cancer Therapeutics, Graduate School of Dentistry, Tohoku University, Sendai, Japan. .,Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.
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12
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The Nopp140 gene in Drosophila melanogaster displays length polymorphisms in its large repetitive second exon. Mol Genet Genomics 2019; 294:1073-1083. [PMID: 31006039 DOI: 10.1007/s00438-019-01568-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 04/10/2019] [Indexed: 12/21/2022]
Abstract
Nopp140, often called the nucleolar and Cajal body phosphoprotein (NOLC1), is an evolutionarily conserved chaperone for the transcription and processing of rRNA during ribosome subunit assembly. Metazoan Nopp140 contains an amino terminal LisH dimerization domain and a highly conserved carboxyl domain. A large central domain consists of alternating basic and acidic motifs of low sequence complexity. Orthologous versions of Nopp140 contain variable numbers of repeating basic-acidic units. While vertebrate Nopp140 genes use multiple exons to encode the central domain, the Nopp140 gene in Drosophila uses exclusively exon 2 to encode the central domain. Here, we define three overlapping repeat sequence patterns (P, P', and P″) within the central domain of D. melanogaster Nopp140. These repeat patterns are poorly conserved in other Drosophila species. We also describe a length polymorphism in exon 2 that pertains specifically to the P' pattern in D. melanogaster. The pattern displays either two or three 96 base pair repeats, respectively, referred to as Nopp140-Short and Nopp140-Long. Fly lines homozygous for one or the other allele, or heterozygous for both alleles, show no discernible phenotypes. PCR characterization of the long and short alleles shows a poorly defined, artifactual bias toward amplifying the long allele over the short allele. The significance of this polymorphism will be in discerning the largely unknown properties of Nopp140's large central domain in rDNA transcription and ribosome biogenesis.
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West SM, Mecenas D, Gutwein M, Aristizábal-Corrales D, Piano F, Gunsalus KC. Developmental dynamics of gene expression and alternative polyadenylation in the Caenorhabditis elegans germline. Genome Biol 2018; 19:8. [PMID: 29368663 PMCID: PMC5784609 DOI: 10.1186/s13059-017-1369-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 12/03/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The 3' untranslated regions (UTRs) of mRNAs play a major role in post-transcriptional regulation of gene expression. Selection of transcript cleavage and polyadenylation sites is a dynamic process that produces multiple transcript isoforms for the same gene within and across different cell types. Using LITE-Seq, a new quantitative method to capture transcript 3' ends expressed in vivo, we have characterized sex- and cell type-specific transcriptome-wide changes in gene expression and 3'UTR diversity in Caenorhabditis elegans germline cells undergoing proliferation and differentiation. RESULTS We show that nearly half of germline transcripts are alternatively polyadenylated, that differential regulation of endogenous 3'UTR variants is common, and that alternative isoforms direct distinct spatiotemporal protein expression patterns in vivo. Dynamic expression profiling also reveals temporal regulation of X-linked gene expression, selective stabilization of transcripts, and strong evidence for a novel developmental program that promotes nucleolar dissolution in oocytes. We show that the RNA-binding protein NCL-1/Brat is a posttranscriptional regulator of numerous ribosome-related transcripts that acts through specific U-rich binding motifs to down-regulate mRNAs encoding ribosomal protein subunits, rRNA processing factors, and tRNA synthetases. CONCLUSIONS These results highlight the pervasive nature and functional potential of patterned gene and isoform expression during early animal development.
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Affiliation(s)
- Sean M West
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - Desirea Mecenas
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - Michelle Gutwein
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - David Aristizábal-Corrales
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - Fabio Piano
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA.
- Center for Genomics & Systems Biology, NYU Abu Dhabi, P.O. Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates.
| | - Kristin C Gunsalus
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA.
- Center for Genomics & Systems Biology, NYU Abu Dhabi, P.O. Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates.
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Ma TH, Lee LW, Lee CC, Yi YH, Chan SP, Tan BCM, Lo SJ. Genetic control of nucleolar size: An evolutionary perspective. Nucleus 2016; 7:112-20. [PMID: 27003693 DOI: 10.1080/19491034.2016.1166322] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Exploiting a C. elegans mutant (ncl-1) exhibiting nucleolar abnormalities, we recently identified the let-7/ncl-1/fib-1 genetic cascade underlying proper rRNA abundance and nucleolar size. These 3 factors, let-7 (a miRNA), NCL-1 (a member of the TRIM-NHL family), and fibrillarin (a nucleolar methyltransferase), are evolutionarily conserved across metazoans. In this article, we provide several lines of bioinformatic evidence showing that human and Drosophila homologues of C. elegans NCL-1, TRIM-71 and Brat, respectively, likely act as translational suppressors of fibrillarin. Moreover, since their 3'-UTRs contain putative target sites, they may also be under the control of the let-7 miRNA. We hypothesize that let-7, TRIM and fibrillarin contribute activities in concert, and constitute a conserved network controlling nucleolar size in eukaryotes. We provide an in-depth literature review of various molecular pathways, including the let-7/ncl-1/fib-1 genetic cascade, implicated in the regulation of nucleolar size.
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Affiliation(s)
- Tian-Hsiang Ma
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,b Graduate Institute of Biomedical Sciences , College of Medicine , Chang Gung University , TaoYuan , Taiwan
| | - Li-Wei Lee
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,c Molecular Medicine Research Center , College of Medicine , Chang Gung University , TaoYuan , Taiwan
| | - Chi-Chang Lee
- d Institute of Chemistry , Academia Sinica , Taipei , Taiwan
| | - Yung-Hsiang Yi
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,c Molecular Medicine Research Center , College of Medicine , Chang Gung University , TaoYuan , Taiwan
| | - Shih-Peng Chan
- e Graduate Institute of Microbiology , College of Medicine , National Taiwan University , Taipei , Taiwan
| | - Bertrand Chin-Ming Tan
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,b Graduate Institute of Biomedical Sciences , College of Medicine , Chang Gung University , TaoYuan , Taiwan.,c Molecular Medicine Research Center , College of Medicine , Chang Gung University , TaoYuan , Taiwan
| | - Szecheng J Lo
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,b Graduate Institute of Biomedical Sciences , College of Medicine , Chang Gung University , TaoYuan , Taiwan.,c Molecular Medicine Research Center , College of Medicine , Chang Gung University , TaoYuan , Taiwan
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Abstract
Caenorhabditis elegans is a well-established model organism which allows, among others, to investigate the link between nucleolar structure/function on the one hand and cell fate choices and cellular differentiation on the other. In addition, C. elegans can be used to study the role of the nucleolus in processes that can be difficult to faithfully reproduce in vitro, such as gametogenesis, disease development, and aging. Here I present two complementary techniques, immunofluorescent staining and DNA fluorescence in situ hybridization, that have been adapted to label nucleolar components at various stages of the life cycle of the worm.
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Affiliation(s)
- Christian Lanctôt
- Institute of Cellular Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Albertov 4, 128 00, Prague, Czech Republic.
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16
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Abstract
A veritable explosion of primary research papers within the past 10 years focuses on nucleolar and ribosomal stress, and for good reason: with ribosome biosynthesis consuming ~80% of a cell’s energy, nearly all metabolic and signaling pathways lead ultimately to or from the nucleolus. We begin by describing p53 activation upon nucleolar stress resulting in cell cycle arrest or apoptosis. The significance of this mechanism cannot be understated, as oncologists are now inducing nucleolar stress strategically in cancer cells as a potential anti-cancer therapy. We also summarize the human ribosomopathies, syndromes in which ribosome biogenesis or function are impaired leading to birth defects or bone narrow failures; the perplexing problem in the ribosomopathies is why only certain cells are affected despite the fact that the causative mutation is systemic. We then describe p53-independent nucleolar stress, first in yeast which lacks p53, and then in other model metazoans that lack MDM2, the critical E3 ubiquitin ligase that normally inactivates p53. Do these presumably ancient p53-independent nucleolar stress pathways remain latent in human cells? If they still exist, can we use them to target >50% of known human cancers that lack functional p53?
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Affiliation(s)
- Allison James
- a Department of Biological Sciences; Louisiana State University; Baton Rouge, LA USA
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Loss of DNase II function in the gonad is associated with a higher expression of antimicrobial genes in Caenorhabditis elegans. Biochem J 2015; 470:145-54. [PMID: 26251453 DOI: 10.1042/bj20150563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/30/2015] [Indexed: 11/17/2022]
Abstract
Three waves of apoptosis shape the development of Caenorhabditis elegans. Although the exact roles of the three DNase II genes (nuc-1, crn-6 and crn-7), which are known to mediate degradation of apoptotic DNA, in the embryonic and larval phases of apoptosis have been characterized, the DNase II acting in the third wave of germ cell apoptosis remains undetermined. In the present study, we performed in vitro and in vivo assays on various mutant nematodes to demonstrate that NUC-1 and CRN-7, but not CRN-6, function in germ cell apoptosis. In addition, in situ DNA-break detection and anti-phosphorylated ERK (extracellular-signal-regulated kinase) staining illustrated the sequential and spatially regulated actions of NUC-1 and CRN-7, at the pachytene zone of the gonad and at the loop respectively. In line with the notion that UV-induced DNA fragment accumulation in the gonad activates innate immunity responses, we also found that loss of NUC-1 and CRN-7 lead to up-regulation of antimicrobial genes (abf-2, spp-1, nlp-29, cnc-2, and lys-7). Our observations suggest that an incomplete digestion of DNA fragments resulting from the absence of NUC-1 or CRN-7 in the gonad could induce the ERK signalling, consequently activating antimicrobial gene expression. Taken together, the results of the present study demonstrate for the first time that nuc-1 and crn-7 play a role in degrading apoptotic DNA in distinct sites of the gonad, and act as negative regulators of innate immunity in C. elegans.
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Zhu L, Brangwynne CP. Nuclear bodies: the emerging biophysics of nucleoplasmic phases. Curr Opin Cell Biol 2015; 34:23-30. [PMID: 25942753 DOI: 10.1016/j.ceb.2015.04.003] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/16/2015] [Accepted: 04/14/2015] [Indexed: 01/02/2023]
Abstract
The cell nucleus contains a large number of membrane-less bodies that play important roles in the spatiotemporal regulation of gene expression. Recent work suggests that low complexity/disordered protein motifs and repetitive binding domains drive assembly of droplets of nuclear RNA/protein by promoting nucleoplasmic phase separation. Nucleation and maturation of these structures is regulated by, and may in turn affect, factors including post-translational modifications, protein concentration, transcriptional activity, and chromatin state. Here we present a concise review of these exciting recent advances, and discuss current and future challenges in understanding the assembly, regulation, and function of nuclear RNA/protein bodies.
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Affiliation(s)
- Lian Zhu
- Princeton University, Department of Chemical and Biological Engineering, Princeton, NJ 08544, USA
| | - Clifford P Brangwynne
- Princeton University, Department of Chemical and Biological Engineering, Princeton, NJ 08544, USA.
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