1
|
Benchorin G, Cho RJ, Li MJ, Molotkova N, Kohwi M. Dan forms condensates in neuroblasts and regulates nuclear architecture and progenitor competence in vivo. Nat Commun 2024; 15:5097. [PMID: 38877037 PMCID: PMC11178893 DOI: 10.1038/s41467-024-49326-6] [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] [Received: 01/22/2024] [Accepted: 05/30/2024] [Indexed: 06/16/2024] Open
Abstract
Genome organization is thought to underlie cell type specific gene expression, yet how it is regulated in progenitors to produce cellular diversity is unknown. In Drosophila, a developmentally-timed genome reorganization in neural progenitors terminates competence to produce early-born neurons. These events require downregulation of Distal antenna (Dan), part of the conserved pipsqueak DNA-binding superfamily. Here we find that Dan forms liquid-like condensates with high protein mobility, and whose size and subnuclear distribution are balanced with its DNA-binding. Further, we identify a LARKS domain, a structural motif associated with condensate-forming proteins. Deleting just 13 amino acids from LARKS abrogates Dan's ability to retain the early-born neural fate gene, hunchback, in the neuroblast nuclear interior and maintain competence in vivo. Conversely, domain-swapping with LARKS from known phase-separating proteins rescues Dan's effects on competence. Together, we provide in vivo evidence for condensate formation and the regulation of progenitor nuclear architecture underlying neuronal diversification.
Collapse
Affiliation(s)
- Gillie Benchorin
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Richard Jangwon Cho
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Neuroscience, Columbia University, New York, NY, USA
| | - Maggie Jiaqi Li
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Neuroscience, Columbia University, New York, NY, USA
| | - Natalia Molotkova
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Neuroscience, Columbia University, New York, NY, USA
| | - Minoree Kohwi
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
- Department of Neuroscience, Columbia University, New York, NY, USA.
- Kavli Institute for Brain Science, Columbia University, New York, NY, USA.
| |
Collapse
|
2
|
He Z, Fang Y, Zhang F, Liu Y, Cheng X, Wang J, Li D, Chen D, Wu F. Adenine nucleotide translocase 2 (Ant2) is required for individualization of spermatogenesis of Drosophila melanogaster. INSECT SCIENCE 2023. [PMID: 38112480 DOI: 10.1111/1744-7917.13309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/12/2023] [Accepted: 11/16/2023] [Indexed: 12/21/2023]
Abstract
Successful completion of spermatogenesis is crucial for the perpetuation of the species. In Drosophila, spermatid individualization, a process involving changes in mitochondrial structure and function is critical to produce functional mature sperm. Ant2, encoding a mitochondrial adenine nucleotide translocase, is highly expressed in male testes and plays a role in energy metabolism in the mitochondria. However, its molecular function remains unclear. Here, we identified an important role of Ant2 in spermatid individualization. In Ant2 knockdown testes, spermatid individualization complexes composed of F-actin cones exhibited a diffuse distribution, and mature sperms were absent in the seminal vesicle, thus leading to male sterility. The most striking effects in Ant2-knockdown spermatids were decrease in tubulin polyglycylation and disruption of proper mitochondria derivatives function. Excessive apoptotic cells were also observed in Ant2-knockdown testes. To further investigate the phenotype of Ant2 knockdown in testes at the molecular level, complementary transcriptome and proteome analyses were performed. At the mRNA level, 868 differentially expressed genes were identified, of which 229 genes were upregulated and 639 were downregulated induced via Ant2 knockdown. iTRAQ-labeling proteome analysis revealed 350 differentially expressed proteins, of which 117 proteins were upregulated and 233 were downregulated. The expression of glutathione transferase (GstD5, GstE5, GstE8, and GstD3), proteins involved in reproduction were significantly regulated at both the mRNA and protein levels. These results indicate that Ant2 is crucial for spermatid maturation by affecting mitochondrial morphogenesis.
Collapse
Affiliation(s)
- Zhen He
- Industrial Crops Institute, Hubei Academy of Agriculture Sciences, Wuhan, China
| | - Yang Fang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Fengchao Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Yang Liu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Xinkai Cheng
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Jiajia Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Dechen Li
- Industrial Crops Institute, Hubei Academy of Agriculture Sciences, Wuhan, China
| | - Dengsong Chen
- Industrial Crops Institute, Hubei Academy of Agriculture Sciences, Wuhan, China
| | - Fan Wu
- Industrial Crops Institute, Hubei Academy of Agriculture Sciences, Wuhan, China
| |
Collapse
|
3
|
Myles KM, Vo AA, Ragle JM, Ward JD. A spontaneous TIR1 loss-of-function allele in C. elegans. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000994. [PMID: 37908494 PMCID: PMC10613879 DOI: 10.17912/micropub.biology.000994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/12/2023] [Accepted: 10/11/2023] [Indexed: 11/02/2023]
Abstract
The auxin-inducible degron (AID) system is a widely-used system for conditional protein depletion. During the course of an experiment, we depleted the nuclear hormone receptor transcription factor NHR-23 to study molting, and we recovered a spontaneous suppressor allele that bypassed the L1 larval arrest caused by NHR-23 depletion. These mutants also failed to deplete a BFP::AID reporter in the strain background, suggesting a broader defect in the AID system. These animals carried an in-frame 18 base pair insertion that produced a 6 amino acid repeat in TIR1. The larval arrest in these animals could be restored by expressing a wild-type TIR1 transgene from an extrachromosomal array. Sister siblings that lost this array developed normally on auxin. Together, these experiments indicate that the TIR1 mutation was causing the loss of developmental arrest in the nhr-23::AID strain. This result highlights the importance of setting up a robust secondary screen to detect such mutants if performing forward genetic screens in conjunction with the AID system.
Collapse
Affiliation(s)
- Krista M. Myles
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States
| | - An A. Vo
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States
| | - Jordan D. Ward
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States
| |
Collapse
|
4
|
Vo AA, Levenson MT, Ragle JM, Ward JD. Efficient generation of a single-copy eft-3p::TIR1::F2A:: BFP::AID*::NLS allele in the C. elegans ttTi5605 insertion site through recombination-mediated cassette exchange. MICROPUBLICATION BIOLOGY 2021; 2021. [PMID: 34355140 PMCID: PMC8335552 DOI: 10.17912/micropub.biology.000425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/17/2022]
Abstract
The auxin-inducible degron (AID) system is a widely used system to conditionally deplete proteins. Using CRISPR/Cas9-based genome editing in C. elegans, we recently generated a set of single-copy, tissue-specific and pan-somatic TIR1-expressing strains carrying a BFP reporter inserted in single-copy into two commonly used, well-characterized genetic loci. However, we were unable to obtain a strain carrying a pan-somatic eft-3p::TIR1::F2A::BFP::AID*::NLS transgene inserted into the chromosome II ttTi5605 insertion site. Using recombination-mediated cassette exchange (RMCE) we were able to efficiently obtain this knock-in. The resulting strain displayed equivalent depletion of an AID*::GFP reporter compared to our previously generated eft-3p::TIR1::F2A::BFP::AID*::NLS transgene knocked into the chromosome I ttTi4348 insertion site. This work highlights the power of RMCE for generating new reagents for the AID system and provides an eft-3p::TIR1::F2A::BFP::AID*::NLS allele on chromosome II which will simplify genetic crossing schemes when using the AID system.
Collapse
Affiliation(s)
- An A Vo
- Department of Molecular, Cell, and Developmental Biology, University of California - Santa Cruz, Santa Cruz, CA, USA
| | - Max T Levenson
- Department of Molecular, Cell, and Developmental Biology, University of California - Santa Cruz, Santa Cruz, CA, USA
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California - Santa Cruz, Santa Cruz, CA, USA
| | - Jordan D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California - Santa Cruz, Santa Cruz, CA, USA
| |
Collapse
|
5
|
Ashley GE, Duong T, Levenson MT, Martinez MAQ, Johnson LC, Hibshman JD, Saeger HN, Palmisano NJ, Doonan R, Martinez-Mendez R, Davidson BR, Zhang W, Ragle JM, Medwig-Kinney TN, Sirota SS, Goldstein B, Matus DQ, Dickinson DJ, Reiner DJ, Ward JD. An expanded auxin-inducible degron toolkit for Caenorhabditis elegans. Genetics 2021; 217:iyab006. [PMID: 33677541 PMCID: PMC8045686 DOI: 10.1093/genetics/iyab006] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/10/2021] [Indexed: 12/30/2022] Open
Abstract
The auxin-inducible degron (AID) system has emerged as a powerful tool to conditionally deplete proteins in a range of organisms and cell types. Here, we describe a toolkit to augment the use of the AID system in Caenorhabditis elegans. We have generated a set of single-copy, tissue-specific (germline, intestine, neuron, muscle, pharynx, hypodermis, seam cell, anchor cell) and pan-somatic TIR1-expressing strains carrying a co-expressed blue fluorescent reporter to enable use of both red and green channels in experiments. These transgenes are inserted into commonly used, well-characterized genetic loci. We confirmed that our TIR1-expressing strains produce the expected depletion phenotype for several nuclear and cytoplasmic AID-tagged endogenous substrates. We have also constructed a set of plasmids for constructing repair templates to generate fluorescent protein::AID fusions through CRISPR/Cas9-mediated genome editing. These plasmids are compatible with commonly used genome editing approaches in the C. elegans community (Gibson or SapTrap assembly of plasmid repair templates or PCR-derived linear repair templates). Together these reagents will complement existing TIR1 strains and facilitate rapid and high-throughput fluorescent protein::AID tagging of genes. This battery of new TIR1-expressing strains and modular, efficient cloning vectors serves as a platform for straightforward assembly of CRISPR/Cas9 repair templates for conditional protein depletion.
Collapse
Affiliation(s)
- Guinevere E Ashley
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tam Duong
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M Health Science Center, Texas A&M University, Houston, TX 77030, USA
| | - Max T Levenson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Michael A Q Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Londen C Johnson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jonathan D Hibshman
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hannah N Saeger
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nicholas J Palmisano
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ryan Doonan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Raquel Martinez-Mendez
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brittany R Davidson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Taylor N Medwig-Kinney
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Sydney S Sirota
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Bob Goldstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Daniel J Dickinson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - David J Reiner
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M Health Science Center, Texas A&M University, Houston, TX 77030, USA
| | - Jordan D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| |
Collapse
|
6
|
Raich N, Mahmoudi S, Emre D, Karess RE. Mad1 influences interphase nucleoplasm organization and chromatin regulation in Drosophila. Open Biol 2018; 8:rsob.180166. [PMID: 30333236 PMCID: PMC6223205 DOI: 10.1098/rsob.180166] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 09/21/2018] [Indexed: 12/15/2022] Open
Abstract
The Drosophila Mad1 spindle checkpoint protein helps organize several nucleoplasmic components, and flies lacking Mad1 present changes in gene expression reflecting altered chromatin conformation. In interphase, checkpoint protein Mad1 is usually described as localizing to the inner nuclear envelope by binding the nucleoporin Tpr, an interaction believed to contribute to proper mitotic regulation. Whether Mad1 has other nuclear interphase functions is unknown. We found in Drosophila that Mad1 is present in nuclei of both mitotic and postmitotic tissues. Three proteins implicated in various aspects of chromatin organization co-immunoprecipitated with Mad1 from fly embryos: Mtor/Tpr, the SUMO peptidase Ulp1 and Raf2, a subunit of a Polycomb-like complex. In primary spermatocytes, all four proteins colocalized in a previously undescribed chromatin-associated structure called here a MINT (Mad1-containing IntraNuclear Territory). MINT integrity required all four proteins. In mad1 mutant spermatocytes, the other proteins were no longer confined to chromatin domains but instead dispersed throughout the nucleoplasm. mad1 flies also presented phenotypes indicative of excessive chromatin of heterochromatic character during development of somatic tissues. Together these results suggest that Drosophila Mad1, by helping organize its interphase protein partners in the nucleoplasm, contributes to proper chromatin regulation.
Collapse
Affiliation(s)
- Natacha Raich
- CNRS, Institut Jacques Monod, UMR7592, Université Paris Diderot, Sorbonne Paris Cité, Paris Cedex 13 75205, France
| | - Souhir Mahmoudi
- CNRS, Institut Jacques Monod, UMR7592, Université Paris Diderot, Sorbonne Paris Cité, Paris Cedex 13 75205, France
| | - Doruk Emre
- CNRS, Institut Jacques Monod, UMR7592, Université Paris Diderot, Sorbonne Paris Cité, Paris Cedex 13 75205, France
| | - Roger E Karess
- CNRS, Institut Jacques Monod, UMR7592, Université Paris Diderot, Sorbonne Paris Cité, Paris Cedex 13 75205, France
| |
Collapse
|