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Kociemba J, Jørgensen ACS, Tadić N, Harris A, Sideri T, Chan WY, Ibrahim F, Ünal E, Skehel M, Shahrezaei V, Argüello-Miranda O, van Werven FJ. Multi-signal regulation of the GSK-3β homolog Rim11 controls meiosis entry in budding yeast. EMBO J 2024; 43:3256-3286. [PMID: 38886580 PMCID: PMC11294583 DOI: 10.1038/s44318-024-00149-7] [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: 09/28/2023] [Revised: 04/22/2024] [Accepted: 05/27/2024] [Indexed: 06/20/2024] Open
Abstract
Starvation in diploid budding yeast cells triggers a cell-fate program culminating in meiosis and spore formation. Transcriptional activation of early meiotic genes (EMGs) hinges on the master regulator Ime1, its DNA-binding partner Ume6, and GSK-3β kinase Rim11. Phosphorylation of Ume6 by Rim11 is required for EMG activation. We report here that Rim11 functions as the central signal integrator for controlling Ume6 phosphorylation and EMG transcription. In nutrient-rich conditions, PKA suppresses Rim11 levels, while TORC1 retains Rim11 in the cytoplasm. Inhibition of PKA and TORC1 induces Rim11 expression and nuclear localization. Remarkably, nuclear Rim11 is required, but not sufficient, for Rim11-dependent Ume6 phosphorylation. In addition, Ime1 is an anchor protein enabling Ume6 phosphorylation by Rim11. Subsequently, Ume6-Ime1 coactivator complexes form and induce EMG transcription. Our results demonstrate how various signaling inputs (PKA/TORC1/Ime1) converge through Rim11 to regulate EMG expression and meiosis initiation. We posit that the signaling-regulatory network elucidated here generates robustness in cell-fate control.
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Affiliation(s)
- Johanna Kociemba
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Andreas Christ Sølvsten Jørgensen
- Department of Mathematics, Imperial College London, London, SW7 2BX, UK
- I-X Centre for AI In Science, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
| | - Nika Tadić
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695-7612, USA
| | - Anthony Harris
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Theodora Sideri
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Wei Yee Chan
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Fairouz Ibrahim
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Mark Skehel
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Vahid Shahrezaei
- Department of Mathematics, Imperial College London, London, SW7 2BX, UK.
| | - Orlando Argüello-Miranda
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695-7612, USA.
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Pfaltzgraff NG, Liu B, de Rooij DG, Page DC, Mikedis MM. Destabilization of mRNAs enhances competence to initiate meiosis in mouse spermatogenic cells. Development 2024; 151:dev202740. [PMID: 38884383 PMCID: PMC11273298 DOI: 10.1242/dev.202740] [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: 01/29/2024] [Accepted: 06/07/2024] [Indexed: 06/18/2024]
Abstract
The specialized cell cycle of meiosis transforms diploid germ cells into haploid gametes. In mammals, diploid spermatogenic cells acquire the competence to initiate meiosis in response to retinoic acid. Previous mouse studies revealed that MEIOC interacts with RNA-binding proteins YTHDC2 and RBM46 to repress mitotic genes and to promote robust meiotic gene expression in spermatogenic cells that have initiated meiosis. Here, we have used the enhanced resolution of scRNA-seq and bulk RNA-seq of developmentally synchronized spermatogenesis to define how MEIOC molecularly supports early meiosis in spermatogenic cells. We demonstrate that MEIOC mediates transcriptomic changes before meiotic initiation, earlier than previously appreciated. MEIOC, acting with YTHDC2 and RBM46, destabilizes its mRNA targets, including the transcriptional repressors E2f6 and Mga, in mitotic spermatogonia. MEIOC thereby derepresses E2F6- and MGA-repressed genes, including Meiosin and other meiosis-associated genes. This confers on spermatogenic cells the molecular competence to, in response to retinoic acid, fully activate the transcriptional regulator STRA8-MEIOSIN, which is required for the meiotic G1/S phase transition and for meiotic gene expression. We conclude that, in mice, mRNA decay mediated by MEIOC-YTHDC2-RBM46 enhances the competence of spermatogenic cells to initiate meiosis.
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Affiliation(s)
- Natalie G. Pfaltzgraff
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Bingrun Liu
- Whitehead Institute, Cambridge, MA 02142, USA
| | | | - David C. Page
- Whitehead Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maria M. Mikedis
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Whitehead Institute, Cambridge, MA 02142, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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3
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Pfaltzgraff NG, Liu B, de Rooij DG, Page DC, Mikedis MM. Destabilization of mRNAs enhances competence to initiate meiosis in mouse spermatogenic cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.20.557439. [PMID: 37781613 PMCID: PMC10541148 DOI: 10.1101/2023.09.20.557439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The specialized cell cycle of meiosis transforms diploid germ cells into haploid gametes. In mammals, diploid spermatogenic cells acquire the competence to initiate meiosis in response to retinoic acid. Previous mouse studies revealed that MEIOC interacts with RNA-binding proteins YTHDC2 and RBM46 to repress mitotic genes and promote robust meiotic gene expression in spermatogenic cells that have initiated meiosis. Here, we used the enhanced resolution of scRNA-seq, and bulk RNA-seq of developmentally synchronized spermatogenesis, to define how MEIOC molecularly supports early meiosis in spermatogenic cells. We demonstrate that MEIOC mediates transcriptomic changes before meiotic initiation, earlier than previously appreciated. MEIOC, acting with YTHDC2 and RBM46, destabilizes its mRNA targets, including transcriptional repressors E2f6 and Mga , in mitotic spermatogonia. MEIOC thereby derepresses E2F6- and MGA-repressed genes, including Meiosin and other meiosis-associated genes. This confers on spermatogenic cells the molecular competence to, in response to retinoic acid, fully activate transcriptional regulator STRA8-MEIOSIN, required for the meiotic G1/S phase transition and meiotic gene expression. We conclude that in mice, mRNA decay mediated by MEIOC-YTHDC2-RBM46 enhances the competence of spermatogenic cells to initiate meiosis. SUMMARY STATEMENT RNA-binding complex MEIOC-YTHDC2-RBM46 destabilizes its mRNA targets, including transcriptional repressors. This activity facilitates the retinoic acid-dependent activation of Meiosin gene expression and transition into meiosis.
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Ramakanth S, Kennedy T, Yalcinkaya B, Neupane S, Tadic N, Buchler NE, Argüello-Miranda O. Deep learning-driven imaging of cell division and cell growth across an entire eukaryotic life cycle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591211. [PMID: 38712227 PMCID: PMC11071524 DOI: 10.1101/2024.04.25.591211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The life cycle of biomedical and agriculturally relevant eukaryotic microorganisms involves complex transitions between proliferative and non-proliferative states such as dormancy, mating, meiosis, and cell division. New drugs, pesticides, and vaccines can be created by targeting specific life cycle stages of parasites and pathogens. However, defining the structure of a microbial life cycle often relies on partial observations that are theoretically assembled in an ideal life cycle path. To create a more quantitative approach to studying complete eukaryotic life cycles, we generated a deep learning-driven imaging framework to track microorganisms across sexually reproducing generations. Our approach combines microfluidic culturing, life cycle stage-specific segmentation of microscopy images using convolutional neural networks, and a novel cell tracking algorithm, FIEST, based on enhancing the overlap of single cell masks in consecutive images through deep learning video frame interpolation. As proof of principle, we used this approach to quantitatively image and compare cell growth and cell cycle regulation across the sexual life cycle of Saccharomyces cerevisiae . We developed a fluorescent reporter system based on a fluorescently labeled Whi5 protein, the yeast analog of mammalian Rb, and a new High-Cdk1 activity sensor, LiCHI, designed to report during DNA replication, mitosis, meiotic homologous recombination, meiosis I, and meiosis II. We found that cell growth preceded the exit from non-proliferative states such as mitotic G1, pre-meiotic G1, and the G0 spore state during germination. A decrease in the total cell concentration of Whi5 characterized the exit from non-proliferative states, which is consistent with a Whi5 dilution model. The nuclear accumulation of Whi5 was developmentally regulated, being at its highest during meiotic exit and spore formation. The temporal coordination of cell division and growth was not significantly different across three sexually reproducing generations. Our framework could be used to quantitatively characterize other single-cell eukaryotic life cycles that remain incompletely described. An off-the-shelf user interface Yeastvision provides free access to our image processing and single-cell tracking algorithms.
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Higdon AL, Won NH, Brar GA. Truncated protein isoforms generate diversity of protein localization and function in yeast. Cell Syst 2024; 15:388-408.e4. [PMID: 38636458 PMCID: PMC11075746 DOI: 10.1016/j.cels.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/21/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
Genome-wide measurement of ribosome occupancy on mRNAs has enabled empirical identification of translated regions, but high-confidence detection of coding regions that overlap annotated coding regions has remained challenging. Here, we report a sensitive and robust algorithm that revealed the translation of 388 N-terminally truncated proteins in budding yeast-more than 30-fold more than previously known. We extensively experimentally validated them and defined two classes. The first class lacks large portions of the annotated protein and tends to be produced from a truncated transcript. We show that two such cases, Yap5truncation and Pus1truncation, have condition-specific regulation and distinct functions from their respective annotated isoforms. The second class of truncated protein isoforms lacks only a small region of the annotated protein and is less likely to be produced from an alternative transcript isoform. Many display different subcellular localizations than their annotated counterpart, representing a common strategy for dual localization of otherwise functionally identical proteins. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Andrea L Higdon
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nathan H Won
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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Su AJ, Yendluri SC, Ünal E. Control of meiotic entry by dual inhibition of a key mitotic transcription factor. eLife 2024; 12:RP90425. [PMID: 38411169 PMCID: PMC10939502 DOI: 10.7554/elife.90425] [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] [Indexed: 02/28/2024] Open
Abstract
The mitosis to meiosis transition requires dynamic changes in gene expression, but whether and how the mitotic transcriptional machinery is regulated during this transition is unknown. In budding yeast, SBF and MBF transcription factors initiate the mitotic gene expression program. Here, we report two mechanisms that work together to restrict SBF activity during meiotic entry: repression of the SBF-specific Swi4 subunit through LUTI-based regulation and inhibition of SBF by Whi5, a functional homolog of the Rb tumor suppressor. We find that untimely SBF activation causes downregulation of early meiotic genes and delays meiotic entry. These defects are largely driven by the SBF-target G1 cyclins, which block the interaction between the central meiotic regulator Ime1 and its cofactor Ume6. Our study provides insight into the role of SWI4LUTI in establishing the meiotic transcriptional program and demonstrates how the LUTI-based regulation is integrated into a larger regulatory network to ensure timely SBF activity.
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Affiliation(s)
- Amanda J Su
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Siri C Yendluri
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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Su AJ, Yendluri SC, Ünal E. Control of meiotic entry by dual inhibition of a key mitotic transcription factor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533246. [PMID: 36993411 PMCID: PMC10055192 DOI: 10.1101/2023.03.17.533246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The mitosis to meiosis transition requires dynamic changes in gene expression, but whether and how the mitotic transcriptional machinery is regulated during this transition is unknown. In budding yeast, SBF and MBF transcription factors initiate the mitotic gene expression program. Here, we report two mechanisms that work together to restrict SBF activity during meiotic entry: repression of the SBF-specific Swi4 subunit through LUTI-based regulation and inhibition of SBF by Whi5, a homolog of the Rb tumor suppressor. We find that untimely SBF activation causes downregulation of early meiotic genes and delays meiotic entry. These defects are largely driven by the SBF-target G1 cyclins, which block the interaction between the central meiotic regulator Ime1 and its cofactor Ume6. Our study provides insight into the role of SWI4LUTI in establishing the meiotic transcriptional program and demonstrates how the LUTI-based regulation is integrated into a larger regulatory network to ensure timely SBF activity.
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Gaspary A, Laureau R, Dyatel A, Dursuk G, Simon Y, Berchowitz LE. Rie1 and Sgn1 form an RNA-binding complex that enforces the meiotic entry cell fate decision. J Cell Biol 2023; 222:e202302074. [PMID: 37638885 PMCID: PMC10460998 DOI: 10.1083/jcb.202302074] [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: 02/17/2023] [Revised: 06/28/2023] [Accepted: 08/08/2023] [Indexed: 08/29/2023] Open
Abstract
Budding yeast cells have the capacity to adopt few but distinct physiological states depending on environmental conditions. Vegetative cells proliferate rapidly by budding while spores can survive prolonged periods of nutrient deprivation and/or desiccation. Whether or not a yeast cell will enter meiosis and sporulate represents a critical decision that could be lethal if made in error. Most cell fate decisions, including those of yeast, are understood as being triggered by the activation of master transcription factors. However, mechanisms that enforce cell fates posttranscriptionally have been more difficult to attain. Here, we perform a forward genetic screen to determine RNA-binding proteins that affect meiotic entry at the posttranscriptional level. Our screen revealed several candidates with meiotic entry phenotypes, the most significant being RIE1, which encodes an RRM-containing protein. We demonstrate that Rie1 binds RNA, is associated with the translational machinery, and acts posttranscriptionally to enhance protein levels of the master transcription factor Ime1 in sporulation conditions. We also identified a physical binding partner of Rie1, Sgn1, which is another RRM-containing protein that plays a role in timely Ime1 expression. We demonstrate that these proteins act independently of cell size regulation pathways to promote meiotic entry. We propose a model explaining how constitutively expressed RNA-binding proteins, such as Rie1 and Sgn1, can act in cell fate decisions both as switch-like enforcers and as repressors of spurious cell fate activation.
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Affiliation(s)
- Alec Gaspary
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Raphaelle Laureau
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Annie Dyatel
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Gizem Dursuk
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Yael Simon
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Luke E. Berchowitz
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer’s and the Aging Brain, New York, NY, USA
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Foltman M, Sanchez-Diaz A. TOR Complex 1: Orchestrating Nutrient Signaling and Cell Cycle Progression. Int J Mol Sci 2023; 24:15745. [PMID: 37958727 PMCID: PMC10647266 DOI: 10.3390/ijms242115745] [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] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
The highly conserved TOR signaling pathway is crucial for coordinating cellular growth with the cell cycle machinery in eukaryotes. One of the two TOR complexes in budding yeast, TORC1, integrates environmental cues and promotes cell growth. While cells grow, they need to copy their chromosomes, segregate them in mitosis, divide all their components during cytokinesis, and finally physically separate mother and daughter cells to start a new cell cycle apart from each other. To maintain cell size homeostasis and chromosome stability, it is crucial that mechanisms that control growth are connected and coordinated with the cell cycle. Successive periods of high and low TORC1 activity would participate in the adequate cell cycle progression. Here, we review the known molecular mechanisms through which TORC1 regulates the cell cycle in the budding yeast Saccharomyces cerevisiae that have been extensively used as a model organism to understand the role of its mammalian ortholog, mTORC1.
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Affiliation(s)
- Magdalena Foltman
- Mechanisms and Regulation of Cell Division Research Unit, Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, 39011 Santander, Spain
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain
| | - Alberto Sanchez-Diaz
- Mechanisms and Regulation of Cell Division Research Unit, Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, 39011 Santander, Spain
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain
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10
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Harris A, Ünal E. The transcriptional regulator Ume6 is a major driver of early gene expression during gametogenesis. Genetics 2023; 225:iyad123. [PMID: 37431893 PMCID: PMC10550318 DOI: 10.1093/genetics/iyad123] [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: 04/07/2023] [Revised: 06/07/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
The process of gametogenesis is orchestrated by a dynamic gene expression program, where a vital subset constitutes the early meiotic genes. In budding yeast, the transcription factor Ume6 represses early meiotic gene expression during mitotic growth. However, during the transition from mitotic to meiotic cell fate, early meiotic genes are activated in response to the transcriptional regulator Ime1 through its interaction with Ume6. While it is known that binding of Ime1 to Ume6 promotes early meiotic gene expression, the mechanism of early meiotic gene activation remains elusive. Two competing models have been proposed whereby Ime1 either forms an activator complex with Ume6 or promotes Ume6 degradation. Here, we resolve this controversy. First, we identify the set of genes that are directly regulated by Ume6, including UME6 itself. While Ume6 protein levels increase in response to Ime1, Ume6 degradation occurs much later in meiosis. Importantly, we found that depletion of Ume6 shortly before meiotic entry is detrimental to early meiotic gene activation and gamete formation, whereas tethering of Ume6 to a heterologous activation domain is sufficient to trigger early meiotic gene expression and produce viable gametes in the absence of Ime1. We conclude that Ime1 and Ume6 form an activator complex. While Ume6 is indispensable for early meiotic gene expression, Ime1 primarily serves as a transactivator for Ume6.
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Affiliation(s)
- Anthony Harris
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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11
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Park ZM, Sporer AJ, Kraft K, Lum KK, Blackman E, Belnap E, Yellman CM, Rose MD. Kar4, the yeast homolog of METTL14, is required for mRNA m6A methylation and meiosis. PLoS Genet 2023; 19:e1010896. [PMID: 37603553 PMCID: PMC10470960 DOI: 10.1371/journal.pgen.1010896] [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: 02/08/2023] [Revised: 08/31/2023] [Accepted: 08/03/2023] [Indexed: 08/23/2023] Open
Abstract
KAR4, the yeast homolog of the mammalian mRNA N6A-methyltransferase complex component METTL14, is required for two disparate developmental programs in Saccharomyces cerevisiae: mating and meiosis. To understand KAR4's role in yeast mating and meiosis, we used a genetic screen to isolate 25 function-specific mutant alleles, which map to non-overlapping surfaces on a predicted structure of the Kar4 protein (Kar4p). Most of the mating-specific alleles (Mat-) abolish Kar4p's interaction with the transcription factor Ste12p, indicating that Kar4p's mating function is through Ste12p. In yeast, the mRNA methyltransferase complex was previously defined as comprising Ime4p (Kar4p's paralog and the homolog of mammalian METTL3), Mum2p (homolog of mammalian WTAP), and Slz1p (MIS), but not Kar4p. During meiosis, Kar4p interacts with Ime4p, Mum2p, and Slz1p. Moreover, cells lacking Kar4p have highly reduced levels of mRNA methylation during meiosis indicating that Kar4p is a key member of the methyltransferase complex, as it is in humans. Analysis of kar4Δ/Δ and 7 meiosis-specific alleles (Mei-) revealed that Kar4p is required early in meiosis, before initiation of S-phase and meiotic recombination. High copy expression of the meiotic transcriptional activator IME1 rescued the defect of these Mei- alleles. Surprisingly, Kar4p was also found to be required at a second step for the completion of meiosis and sporulation. Over-expression of IME1 in kar4Δ/Δ permits pre-meiotic S-phase, but most cells remained arrested with a monopolar spindle. Analysis of the function-specific mutants revealed that roughly half became blocked after premeiotic DNA synthesis and did not sporulate (Spo-). Loss of Kar4p's Spo function was suppressed by overexpression of RIM4, a meiotic translational regulator. Overexpression of IME1 and RIM4 together allowed sporulation of kar4Δ/Δ cells. Taken together, these data suggest that Kar4p regulates meiosis at multiple steps, presumably reflecting requirements for methylation in different stages of meiotic gene expression.
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Affiliation(s)
- Zachory M. Park
- Department of Biology, Georgetown University, Washington DC, United States of America
| | - Abigail J. Sporer
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Katherine Kraft
- Department of Biology, Georgetown University, Washington DC, United States of America
| | - Krystal K. Lum
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Edith Blackman
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Ethan Belnap
- Department of Biology, Georgetown University, Washington DC, United States of America
| | | | - Mark D. Rose
- Department of Biology, Georgetown University, Washington DC, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
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12
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Park ZM, Remillard M, Belnap E, Rose MD. Kar4 is required for the normal pattern of meiotic gene expression. PLoS Genet 2023; 19:e1010898. [PMID: 37639444 PMCID: PMC10491391 DOI: 10.1371/journal.pgen.1010898] [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: 02/08/2023] [Revised: 09/08/2023] [Accepted: 08/03/2023] [Indexed: 08/31/2023] Open
Abstract
Kar4p, the yeast homolog of the mammalian methyltransferase subunit METTL14, is required for efficient mRNA m6A methylation, which regulates meiotic entry. Kar4p is also required for a second seemingly non-catalytic function during meiosis. Overexpression of the early meiotic transcription factor, IME1, can bypass the requirement for Kar4p in meiotic entry but the additional overexpression of the translational regulator, RIM4, is required to permit sporulation in kar4Δ/Δ. Using microarray analysis and RNA sequencing, we sought to determine the impact of removing Kar4p and consequently mRNA methylation on the early meiotic transcriptome in a strain background (S288c) that is sensitive to the loss of early meiotic regulators. We found that kar4Δ/Δ mutants have a largely wild type transcriptional profile with the exception of two groups of genes that show delayed and reduced expression: (1) a set of Ime1p-dependent early genes as well as IME1, and (2) a set of late genes dependent on the mid-meiotic transcription factor, Ndt80p. The early gene expression defect is likely the result of the loss of mRNA methylation and is rescued by overexpressing IME1, but the late defect is only suppressed by overexpression of both IME1 and RIM4. The requirement for RIM4 led us to predict that the non-catalytic function of Kar4p, like methyltransferase complex orthologs in other systems, may function at the level of translation. Mass spectrometry analysis identified several genes involved in meiotic recombination with strongly reduced protein levels, but with little to no reduction in transcript levels in kar4Δ/Δ after IME1 overexpression. The low levels of these proteins were rescued by overexpression of RIM4 and IME1, but not by the overexpression of IME1 alone. These data expand our understanding of the role of Kar4p in regulating meiosis and provide key insights into a potential mechanism of Kar4p's later meiotic function that is independent of mRNA methylation.
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Affiliation(s)
- Zachory M. Park
- Department of Biology, Georgetown University, Washington DC, United States of America
| | - Matthew Remillard
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Ethan Belnap
- Department of Biology, Georgetown University, Washington DC, United States of America
| | - Mark D. Rose
- Department of Biology, Georgetown University, Washington DC, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
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13
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Zhang X, Liu Y, Sosa F, Gunewardena S, Crawford PA, Zielen AC, Orwig KE, Wang N. Transcriptional metabolic reprogramming implements meiotic fate decision in mouse testicular germ cells. Cell Rep 2023; 42:112749. [PMID: 37405912 PMCID: PMC10529640 DOI: 10.1016/j.celrep.2023.112749] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 05/24/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
Nutrient starvation drives yeast meiosis, whereas retinoic acid (RA) is required for mammalian meiosis through its germline target Stra8. Here, by using single-cell transcriptomic analysis of wild-type and Stra8-deficient juvenile mouse germ cells, our data show that the expression of nutrient transporter genes, including Slc7a5, Slc38a2, and Slc2a1, is downregulated in germ cells during meiotic initiation, and this process requires Stra8, which binds to these genes and induces their H3K27 deacetylation. Consequently, Stra8-deficient germ cells sustain glutamine and glucose uptake in response to RA and exhibit hyperactive mTORC1/protein kinase A (PKA) activities. Importantly, expression of Slc38a2, a glutamine importer, is negatively correlated with meiotic genes in the GTEx dataset, and Slc38a2 knockdown downregulates mTORC1/PKA activities and induces meiotic gene expression. Thus, our study indicates that RA via Stra8, a chordate morphogen pathway, induces meiosis partially by generating a conserved nutrient restriction signal in mammalian germ cells by downregulating their nutrient transporter expression.
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Affiliation(s)
- Xiaoyu Zhang
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA; Center for Reproductive Sciences, Institute for Reproductive and Developmental Sciences (IRDS), University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Yan Liu
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA; Center for Reproductive Sciences, Institute for Reproductive and Developmental Sciences (IRDS), University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Froylan Sosa
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA; Center for Reproductive Sciences, Institute for Reproductive and Developmental Sciences (IRDS), University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Sumedha Gunewardena
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Peter A Crawford
- Department of Medicine, Division of Molecular Medicine, University of Minnesota, Minneapolis, MN 55455, USA; Department of Molecular Biology, Biochemistry, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Amanda C Zielen
- Department of Obstetrics, Gynecology and Reproductive Sciences and Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Kyle E Orwig
- Department of Obstetrics, Gynecology and Reproductive Sciences and Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Ning Wang
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA; Center for Reproductive Sciences, Institute for Reproductive and Developmental Sciences (IRDS), University of Kansas Medical Center, Kansas City, KS 66160, USA.
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14
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Higdon AL, Won NH, Brar GA. Truncated protein isoforms generate diversity of protein localization and function in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548938. [PMID: 37503254 PMCID: PMC10369987 DOI: 10.1101/2023.07.13.548938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Genome-wide measurements of ribosome occupancy on mRNA transcripts have enabled global empirical identification of translated regions. These approaches have revealed an unexpected diversity of protein products, but high-confidence identification of new coding regions that entirely overlap annotated coding regions - including those that encode truncated protein isoforms - has remained challenging. Here, we develop a sensitive and robust algorithm focused on identifying N-terminally truncated proteins genome-wide, identifying 388 truncated protein isoforms, a more than 30-fold increase in the number known in budding yeast. We perform extensive experimental validation of these truncated proteins and define two general classes. The first set lack large portions of the annotated protein sequence and tend to be produced from a truncated transcript. We show two such cases, Yap5 truncation and Pus1 truncation , to have condition-specific regulation and functions that appear distinct from their respective annotated isoforms. The second set of N-terminally truncated proteins lack only a small region of the annotated protein and are less likely to be regulated by an alternative transcript isoform. Many localize to different subcellular compartments than their annotated counterpart, representing a common strategy for achieving dual localization of otherwise functionally identical proteins.
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15
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Park ZM, Sporer A, Kraft K, Lum K, Blackman E, Belnap E, Yellman C, Rose MD. Kar4, the Yeast Homolog of METTL14, is Required for mRNA m 6 A Methylation and Meiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.29.526094. [PMID: 36747717 PMCID: PMC9900893 DOI: 10.1101/2023.01.29.526094] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
KAR4 , the yeast homolog of the mammalian mRNA N 6 A-methyltransferase complex component METTL14 , is required for two disparate developmental programs in Saccharomyces cerevisiae : mating and meiosis. To understand KAR4 's role in yeast mating and meiosis, we used a genetic screen to isolate 25 function-specific mutant alleles, which map to non-overlapping surfaces on a predicted structure of the Kar4 protein (Kar4p). Most of the mating-specific alleles (Mat - ) abolish Kar4p's interaction with the transcription factor Ste12p, indicating that Kar4p's mating function is through Ste12p. In yeast, the mRNA methyltransferase complex was previously defined as comprising Ime4p (Kar4p's paralog and the homolog of mammalian METTL3), Mum2p (homolog of mammalian WTAP), and Slz1p (MIS), but not Kar4p. During meiosis, Kar4p interacts with Ime4p, Mum2p, and Slz1p. Moreover, cells lacking Kar4p have highly reduced levels of mRNA methylation during meiosis indicating that Kar4p is a key member of the methyltransferase complex, as it is in humans. Analysis of kar4 Δ/Δ and 7 meiosis-specific alleles (Mei - ) revealed that Kar4p is required early in meiosis, before initiation of S-phase and meiotic recombination. High copy expression of the meiotic transcriptional activator IME1 rescued the defect of these Mei- alleles. Surprisingly, Kar4p was also found to be required at a second step for the completion of meiosis and sporulation. Over-expression of IME1 in kar4 Δ/Δ permits pre-meiotic S-phase, but most cells remained arrested with a monopolar spindle. Analysis of the function-specific mutants revealed that roughly half became blocked after premeiotic DNA synthesis and did not sporulate (Spo - ). Loss of Kar4p's Spo function was suppressed by overexpression of RIM4 , a meiotic translational regulator. Overexpression of IME1 and RIM4 together allowed sporulation of kar4 Δ/Δ cells. Taken together, these data suggest that Kar4p regulates meiosis at multiple steps, presumably reflecting requirements for methylation in different stages of meiotic gene expression. Author Summary In yeast, KAR4 is required for mating and meiosis. A genetic screen for function-specific mutations identified 25 alleles that map to different surfaces on a predicted structure of the Kar4 protein (Kar4p). The mating-specific alleles interfere with Kar4p's ability to interact with the transcription factor Ste12p, its known partner in mating. The meiosis-specific alleles revealed an independent function: Kar4p is required for entry into meiosis and initiation of S-phase. During meiosis, Kar4p interacts with all components of the mRNA methyltransferase complex and kar4 Δ/Δ mutants have greatly reduced levels of mRNA methylation. Thus, Kar4p is a member of the yeast methyltransferase complex. Overexpression of the meiotic transcriptional activator IME1 rescued the meiotic entry defect but did not lead to sporulation, implying that Kar4p has more than one meiotic function. Suppression by Ime1p overexpression led to arrest after premeiotic DNA synthesis, but before sporulation. Loss of Kar4's sporulation function can be suppressed by overexpression of a translation regulator, Rim4p. Overexpression of both IME1 and RIM4 allowed sporulation in kar4 Δ/Δ cells.
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Affiliation(s)
- Zachory M. Park
- Department of Biology, Georgetown University, Washington DC, 20057, USA
| | - Abigail Sporer
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Katherine Kraft
- Department of Biology, Georgetown University, Washington DC, 20057, USA
| | - Krystal Lum
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Edith Blackman
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Ethan Belnap
- Department of Biology, Georgetown University, Washington DC, 20057, USA
| | | | - Mark D. Rose
- Department of Biology, Georgetown University, Washington DC, 20057, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
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16
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Park ZM, Remillard M, Rose MD. Kar4 is Required for the Normal Pattern of Meiotic Gene Expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.29.526097. [PMID: 36747654 PMCID: PMC9900936 DOI: 10.1101/2023.01.29.526097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Kar4p, the yeast homolog of the mammalian methyltransferase subunit METTL14, is required for the initiation of meiosis and has at least two distinct functions in regulating the meiotic program. Cells lacking Kar4p can be driven to sporulate by co-overexpressing the master meiotic transcription factor, IME1 , and the translational regulator, RIM4 , suggesting that Kar4p functions at both the transcriptional and translational level to regulate meiosis. Using microarray analysis and RNA sequencing, we found that kar4 Δ/Δ mutants have a largely wild type transcriptional profile with the exception of two groups of genes that show delayed and reduced expression: (1) a set of Ime1p-dependent early genes as well as IME1 , and (2) a set of late genes dependent on the mid-meiotic transcription factor, Ndt80p. The early gene expression defect is rescued by overexpressing IME1 , but the late defect is only suppressed by overexpression of both IME1 and RIM4 . Mass spectrometry analysis identified several genes involved in meiotic recombination with strongly reduced protein levels, but with little to no reduction in transcript levels in kar4 Δ/Δ after IME1 overexpression. The low levels of these proteins were rescued by overexpression of RIM4 and IME1 , but not by the overexpression of IME1 alone. These data expand our understanding of the role of Kar4p in regulating meiosis and provide key insights into a potential mechanism of Kar4p's later meiotic function that is independent of mRNA methylation. Author Summary Kar4p is required at two stages during meiosis. Cells lacking Kar4p have a severe loss of mRNA methylation and arrest early in the meiotic program, failing to undergo either pre-meiotic DNA synthesis or meiotic recombination. The early block is rescued by overexpression of the meiotic transcription factor, IME1 . The kar4 Δ/Δ cells show delayed and reduced expression of a set of Ime1p-dependent genes expressed early in meiosis as well as a set of later genes that are largely Ndt80p-dependent. Overexpression of IME1 rescues the expression defect of these early genes and expedites the meiotic program in the wild type S288C strain background. However, IME1 overexpression is not sufficient to facilitate sporulation in kar4 Δ/Δ. Completion of meiosis and sporulation requires the additional overexpression of a translational regulator, RIM4 . Analysis of kar4 Δ/Δ's proteome during meiosis with IME1 overexpression revealed that proteins important for meiotic recombination have reduced levels that cannot be explained by equivalent reductions in transcript abundance. IME1 overexpression by itself rescues the defect associated with a catalytic mutant of Ime4p, implying that the early defect reflects mRNA methylation. The residual defects in protein levels likely reflect the loss of a non-catalytic function of Kar4p, and the methylation complex, which requires overexpression of RIM4 to suppress.
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Affiliation(s)
- Zachory M. Park
- Department of Biology, Georgetown University, Washington DC, 20057, USA
| | - Matthew Remillard
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Mark D. Rose
- Department of Biology, Georgetown University, Washington DC, 20057, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
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17
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Varier RA, Sideri T, Capitanchik C, Manova Z, Calvani E, Rossi A, Edupuganti RR, Ensinck I, Chan VWC, Patel H, Kirkpatrick J, Faull P, Snijders AP, Vermeulen M, Ralser M, Ule J, Luscombe NM, van Werven FJ. N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast. eLife 2022; 11:e84034. [PMID: 36422864 PMCID: PMC9731578 DOI: 10.7554/elife.84034] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/13/2022] [Indexed: 11/25/2022] Open
Abstract
N6- methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here, we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3'end of meiotic mRNAs in both an m6A-dependent and independent manner. Within cells, Pho92 transitions from the nucleus to the cytoplasm, and associates with translating ribosomes. In the nucleus Pho92 associates with target loci through its interaction with transcriptional elongator Paf1C. Functionally, we show that Pho92 promotes and links protein synthesis to mRNA decay. As such, the Pho92-mediated m6A-mRNA decay is contingent on active translation and the CCR4-NOT complex. We propose that the m6A reader Pho92 is loaded co-transcriptionally to facilitate protein synthesis and subsequent decay of m6A modified transcripts, and thereby promotes meiosis.
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Affiliation(s)
| | | | | | | | | | - Alice Rossi
- The Francis Crick InstituteLondonUnited Kingdom
| | - Raghu R Edupuganti
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University NijmegenNijmegenNetherlands
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Biomedical Research BuildingMiamiUnited States
| | | | | | | | | | - Peter Faull
- The Francis Crick InstituteLondonUnited Kingdom
- Biological Mass Spectrometry Facility, The University of Texas at AustinAustinUnited States
| | | | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University NijmegenNijmegenNetherlands
| | - Markus Ralser
- The Francis Crick InstituteLondonUnited Kingdom
- Department of Biochemistry, Charité Universitätsmedizin BerlinBerlinGermany
| | - Jernej Ule
- The Francis Crick InstituteLondonUnited Kingdom
- Dementia Research Institute, King's College LondonLondonUnited Kingdom
| | - Nicholas M Luscombe
- The Francis Crick InstituteLondonUnited Kingdom
- Department of Genetics, Evolution and Environment, UCL Genetics InstituteLondonUnited Kingdom
- Okinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
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18
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Palozzi JM, Jeedigunta SP, Minenkova AV, Monteiro VL, Thompson ZS, Lieber T, Hurd TR. Mitochondrial DNA quality control in the female germline requires a unique programmed mitophagy. Cell Metab 2022; 34:1809-1823.e6. [PMID: 36323236 DOI: 10.1016/j.cmet.2022.10.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/22/2022] [Accepted: 10/06/2022] [Indexed: 11/07/2022]
Abstract
Mitochondria have their own DNA (mtDNA), which is susceptible to the accumulation of disease-causing mutations. To prevent deleterious mutations from being inherited, the female germline has evolved a conserved quality control mechanism that remains poorly understood. Here, through a large-scale screen, we uncover a unique programmed germline mitophagy (PGM) that is essential for mtDNA quality control. We find that PGM is developmentally triggered as germ cells enter meiosis by inhibition of the target of rapamycin complex 1 (TORC1). We identify a role for the RNA-binding protein Ataxin-2 (Atx2) in coordinating the timing of PGM with meiosis. We show that PGM requires the mitophagy receptor BNIP3, mitochondrial fission and translation factors, and members of the Atg1 complex, but not the mitophagy factors PINK1 and Parkin. Additionally, we report several factors that are critical for germline mtDNA quality control and show that pharmacological manipulation of one of these factors promotes mtDNA quality control.
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Affiliation(s)
- Jonathan M Palozzi
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Swathi P Jeedigunta
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Anastasia V Minenkova
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Vernon L Monteiro
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Zoe S Thompson
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Toby Lieber
- HHMI and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Thomas R Hurd
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
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19
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Cairo G, MacKenzie A, Tsuchiya D, Lacefield S. Use of Time-Lapse Microscopy and Stage-Specific Nuclear Depletion of Proteins to Study Meiosis in S. Cerevisiae. J Vis Exp 2022:10.3791/64580. [PMID: 36314815 PMCID: PMC10114469 DOI: 10.3791/64580] [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: 11/13/2022] Open
Abstract
Time-lapse fluorescence microscopy has revolutionized the understanding of meiotic cell-cycle events by providing temporal and spatial data that is often not seen by imaging fixed cells. Budding yeast has proved to be an important model organism to study meiotic chromosome segregation because many meiotic genes are highly conserved. Time-lapse microscopy of meiosis in budding yeast allows the monitoring of different meiotic mutants to show how the mutation disrupts meiotic processes. However, many proteins function at multiple points in meiosis. The use of loss-of-function or meiotic null mutants can therefore disrupt an early process, blocking or disturbing the later process and making it difficult to determine the phenotypes associated with each individual role. To circumvent this challenge, this protocol describes how the proteins can be conditionally depleted from the nucleus at specific stages of meiosis while monitoring meiotic events using time-lapse microscopy. Specifically, this protocol describes how the cells are synchronized in prophase I, how the anchor away technique is used to deplete proteins from the nucleus at specific meiotic stages, and how time-lapse imaging is used to monitor meiotic chromosome segregation. As an example of the usefulness of the technique, the kinetochore protein Ctf19 was depleted from the nucleus at different time points during meiosis, and the number of chromatin masses was analyzed at the end of meiosis II. Overall, this protocol can be adapted to deplete different nuclear proteins from the nucleus while monitoring the meiotic divisions.
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Affiliation(s)
| | | | - Dai Tsuchiya
- Department of Biology, Indiana University; Stowers Institute for Biomedical Research
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20
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Scutenaire J, Plassard D, Matelot M, Villa T, Zumsteg J, Libri D, Séraphin B. The S. cerevisiae m6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts. Nucleic Acids Res 2022; 51:517-535. [PMID: 35934316 PMCID: PMC9881176 DOI: 10.1093/nar/gkac640] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/05/2022] [Accepted: 07/20/2022] [Indexed: 02/06/2023] Open
Abstract
N6-Methyladenosine (m6A), one of the most abundant internal modification of eukaryotic mRNAs, participates in the post-transcriptional control of gene expression through recruitment of specific m6A readers. In Saccharomyces cerevisiae, the m6A methyltransferase Ime4 is expressed only during meiosis and its deletion impairs this process. To elucidate how m6A control gene expression, we investigated the function of the budding yeast m6A reader Pho92. We show that Pho92 is an early meiotic factor that promotes timely meiotic progression. High-throughput RNA sequencing and mapping of Pho92-binding sites following UV-crosslinking reveal that Pho92 is recruited to specific mRNAs in an m6A-dependent manner during the meiotic prophase, preceding their down-regulation. Strikingly, point mutations altering m6A sites in mRNAs targeted by Pho92 are sufficient to delay their down-regulation and, in one case, to slow down meiotic progression. Altogether, our results indicate that Pho92 facilitate the meiotic progression by accelerating the down-regulation of timely-regulated mRNAs during meiotic recombination.
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Affiliation(s)
- Jérémy Scutenaire
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France,Centre National de Recherche Scientifique (CNRS) UMR 7104, 67400 Illkirch, France,Institut National de Santé et de Recherche Médicale (INSERM) U1258, 67400 Illkirch, France,Université de Strasbourg, 67400 Illkirch, France
| | - Damien Plassard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France,Centre National de Recherche Scientifique (CNRS) UMR 7104, 67400 Illkirch, France,Institut National de Santé et de Recherche Médicale (INSERM) U1258, 67400 Illkirch, France,Université de Strasbourg, 67400 Illkirch, France
| | - Mélody Matelot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France,Centre National de Recherche Scientifique (CNRS) UMR 7104, 67400 Illkirch, France,Institut National de Santé et de Recherche Médicale (INSERM) U1258, 67400 Illkirch, France,Université de Strasbourg, 67400 Illkirch, France
| | - Tommaso Villa
- Université de Paris Cité, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Julie Zumsteg
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Domenico Libri
- Université de Paris Cité, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Bertrand Séraphin
- To whom correspondence should be addressed. Tel: +33 3 88 65 33 36; Fax: +33 3 88 65 32 01;
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21
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Zhang J, Tian M, Chen K, Yan G, Xiong J, Miao W. Zfp1, a Cys2His2 zinc finger protein is required for meiosis initiation in Tetrahymena thermophila. Cell Cycle 2022; 21:1422-1433. [PMID: 35293272 PMCID: PMC9345619 DOI: 10.1080/15384101.2022.2053449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Meiosis is an important and highly conserved process that occurs during eukaryotic sexual reproduction. Diverse mechanisms are responsible for meiosis initiation among eukaryotes, and transcription factors have been established to have an important role in many species. However, the specific function of transcription factors in initiating meiosis in ciliates is unknown. Here we show that a putative Cys2His2 zinc finger-containing transcription factor encoded by the ZFP1 gene is specifically expressed during sexual reproduction in Tetrahymena thermophila. Meiosis is not initiated in the cells lacking ZFP1. Transcriptome sequencing analyses reveal that Zfp1 is required for the expression of many meiosis-specific genes. Our results indicate that Zfp1 could be a transcriptional activator required for meiosis initiation in T. thermophila.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Miao Tian
- Department of Chromosome Biology and Max F. Perutz Laboratories, Center for Molecular Biology, University of Vienna, Vienna, Austria
| | - Kai Chen
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Guanxiong Yan
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, Shanghai, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China.,State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China.,CAS Center for Excellence in Animal Evolution and Genetics, Kunming, Yunnan, China
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22
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Abstract
Meiosis is critical for germ cell development in multicellular organisms. Initiation of meiosis coincides with pre-meiotic S phase, which is followed by meiotic prophase, a prolonged G2 phase that ensures numerous meiosis-specific chromosome events. Meiotic prophase is accompanied by robust alterations of gene expression. In mouse germ cells, MEIOSIN and STRA8 direct cell cycle switch from mitosis to meiosis. MEIOSIN and STRA8 coordinate meiotic initiation with cell cycle, by activating the meiotic genes to have meiotic prophase program installed at S phase. This review mainly focuses on the mechanism of meiotic initiation in mouse germ cells from the viewpoint of the transcription of meiotic genes. Furthermore, signaling pathways that regulate meiotic initiation will be discussed in the context of germ cell development, pointing out the sexual differences in the mode of meiotic initiation.
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Affiliation(s)
- Kei-Ichiro Ishiguro
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan.
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23
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Hernández-Sánchez F, Peraza-Reyes L. Spatiotemporal Dynamic Regulation of Organelles During Meiotic Development, Insights From Fungi. Front Cell Dev Biol 2022; 10:886710. [PMID: 35547805 PMCID: PMC9081346 DOI: 10.3389/fcell.2022.886710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/08/2022] [Indexed: 12/02/2022] Open
Abstract
Eukaryotic cell development involves precise regulation of organelle activity and dynamics, which adapt the cell architecture and metabolism to the changing developmental requirements. Research in various fungal model organisms has disclosed that meiotic development involves precise spatiotemporal regulation of the formation and dynamics of distinct intracellular membrane compartments, including peroxisomes, mitochondria and distinct domains of the endoplasmic reticulum, comprising its peripheral domains and the nuclear envelope. This developmental regulation implicates changes in the constitution and dynamics of these organelles, which modulate their structure, abundance and distribution. Furthermore, selective degradation systems allow timely organelle removal at defined meiotic stages, and regulated interactions between membrane compartments support meiotic-regulated organelle dynamics. This dynamic organelle remodeling is implicated in conducting organelle segregation during meiotic differentiation, and defines quality control regulatory systems safeguarding the inheritance of functional membrane compartments, promoting meiotic cell rejuvenation. Moreover, organelle remodeling is important for proper activity of the cytoskeletal system conducting meiotic nucleus segregation, as well as for meiotic differentiation. The orchestrated regulation of organelle dynamics has a determinant contribution in the formation of the renewed genetically-diverse offspring of meiosis.
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24
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Gavade JN, Puccia CM, Herod SG, Trinidad JC, Berchowitz LE, Lacefield S. Identification of 14-3-3 proteins, Polo kinase, and RNA-binding protein Pes4 as key regulators of meiotic commitment in budding yeast. Curr Biol 2022; 32:1534-1547.e9. [PMID: 35240051 PMCID: PMC9007917 DOI: 10.1016/j.cub.2022.02.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/04/2022] [Accepted: 02/04/2022] [Indexed: 01/25/2023]
Abstract
The initiation of the cell division process of meiosis requires exogenous signals that activate internal gene regulatory networks. Meiotic commitment ensures the irreversible continuation of meiosis, even upon withdrawal of the meiosis-inducing signals. A loss of meiotic commitment can cause highly abnormal polyploid cells and can ultimately lead to germ cell tumors. Despite the importance of meiotic commitment, only a few genes involved in commitment are known. In this study, we have discovered six new regulators of meiotic commitment in budding yeast: the Bcy1 protein involved in nutrient sensing, the meiosis-specific kinase Ime2, Polo kinase Cdc5, RNA-binding protein Pes4, and the 14-3-3 proteins Bmh1 and Bmh2. Decreased levels of these proteins cause a failure to establish or maintain meiotic commitment. Importantly, we found that Bmh1 and Bmh2 are involved in multiple processes throughout meiosis and in meiotic commitment. First, cells depleted of both Bmh1 and Bmh2 trigger the pachytene checkpoint, likely due to a role in DNA double-strand break repair. Second, Bmh1 interacts directly with the middle meiosis transcription factor Ndt80, and both Bmh1 and Bmh2 maintain Ndt80 levels. Third, Bmh1 and Bmh2 bind to Cdc5 and enhance its kinase activity. Finally, Bmh1 binds to Pes4, which regulates the timing of the translation of several mRNAs in meiosis II and is required to maintain meiotic commitment. Our results demonstrate that meiotic commitment is actively maintained throughout meiosis, with the 14-3-3 proteins and Polo kinase serving as key regulators of this developmental program.
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Affiliation(s)
| | - Chris M Puccia
- Indiana University, Department of Biology, Bloomington, IN, USA
| | - S Grace Herod
- Columbia University Irving Medical Center, Department of Genetics and Development, Hammer Health Sciences Center, New York, NY, USA
| | | | - Luke E Berchowitz
- Columbia University Irving Medical Center, Department of Genetics and Development, Hammer Health Sciences Center, New York, NY, USA
| | - Soni Lacefield
- Indiana University, Department of Biology, Bloomington, IN, USA.
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25
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Piccirillo S, Morgan AP, Leon AY, Smith AL, Honigberg SM. Investigating cell autonomy in microorganisms. Curr Genet 2022; 68:305-318. [PMID: 35119506 PMCID: PMC9101301 DOI: 10.1007/s00294-022-01231-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/04/2022] [Accepted: 01/18/2022] [Indexed: 11/28/2022]
Abstract
Cell-cell signaling in microorganisms is still poorly characterized. In this Methods paper, we describe a genetic procedure for detecting cell-nonautonomous genetic effects, and in particular cell-cell signaling, termed the chimeric colony assay (CCA). The CCA measures the effect of a gene on a biological response in a neighboring cell. This assay can measure cell autonomy for range of biological activities including transcript or protein accumulation, subcellular localization, and cell differentiation. To date, the CCA has been used exclusively to investigate colony patterning in the budding yeast Saccharomyces cerevisiae. To demonstrate the wider potential of the assay, we applied this assay to two other systems: the effect of Grr1 on glucose repression of GAL1 transcription in yeast and the effect of rpsL on stop-codon translational readthrough in Escherichia coli. We also describe variations of the standard CCA that address specific aspects of cell-cell signaling, and we delineate essential controls for this assay. Finally, we discuss complementary approaches to the CCA. Taken together, this Methods paper demonstrates how genetic assays can reveal and explore the roles of cell-cell signaling in microbial processes.
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Affiliation(s)
- Sarah Piccirillo
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| | - Andrew P. Morgan
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| | - Andy Y. Leon
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| | - Annika L. Smith
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| | - Saul M. Honigberg
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
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26
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Feng W, Argüello-Miranda O, Qian S, Wang F. Cdc14 spatiotemporally dephosphorylates Atg13 to activate autophagy during meiotic divisions. J Cell Biol 2022; 221:213046. [PMID: 35238874 PMCID: PMC8919667 DOI: 10.1083/jcb.202107151] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/07/2022] [Accepted: 02/03/2022] [Indexed: 02/07/2023] Open
Abstract
Autophagy is a conserved eukaryotic lysosomal degradation pathway that responds to environmental and cellular cues. Autophagy is essential for the meiotic exit and sporulation in budding yeast, but the underlying molecular mechanisms remain unknown. Here, we show that autophagy is maintained during meiosis and stimulated in anaphase I and II. Cells with higher levels of autophagy complete meiosis faster, and genetically enhanced autophagy increases meiotic kinetics and sporulation efficiency. Strikingly, our data reveal that the conserved phosphatase Cdc14 regulates meiosis-specific autophagy. Cdc14 is activated in anaphase I and II, accompanying its subcellular relocation from the nucleolus to the cytoplasm, where it dephosphorylates Atg13 to stimulate Atg1 kinase activity and thus autophagy. Together, our findings reveal a meiosis-tailored mechanism that spatiotemporally controls meiotic autophagy activity to ensure meiosis progression, exit, and sporulation.
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Affiliation(s)
- Wenzhi Feng
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | | | - Suhong Qian
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Fei Wang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX,Correspondence to Fei Wang:
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27
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Liu X, Wang H, Liu B, Qi Z, Li J, Xu B, Liu W, Xu Z, Deng Y. The Latest Research Progress of m 6A Modification and Its Writers, Erasers, Readers in Infertility: A Review. Front Cell Dev Biol 2021; 9:681238. [PMID: 34568313 PMCID: PMC8461070 DOI: 10.3389/fcell.2021.681238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/06/2021] [Indexed: 01/22/2023] Open
Abstract
Eukaryotic messenger mRNAs contain many RNA methyl chemical modifications, in which N6-methyladenosine (m6A) plays a very important role. The modification process of RNA methylation is a dynamic reversible regulatory process that is mainly catalyzed by "Writer" m6A methyltransferase, removed by "Eraser" m6A demethylase, and recognized by the m6A binding protein, thereby, linking m6A modification with other mRNA pathways. At various stages of the life cycle, m6A modification plays an extremely important role in regulating mRNA splicing, processing, translation, as well as degradation, and is associated with gametogenesis and fertility for both sexes. Normal gametogenesis is a basic guarantee of fertility. Infertility leads to trauma, affects harmony in the family and seriously affects the quality of life. We review the roles and mechanisms of RNA m6A methylation modification in infertility and provide a potential target for infertility treatment, which can be used for drug development.
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Affiliation(s)
- Xuda Liu
- Department of Public Health, China Medical University, Shenyang, China
| | - Haiying Wang
- Department of Public Health, China Medical University, Shenyang, China
| | - Bingchen Liu
- Department of Public Health, China Medical University, Shenyang, China
| | - Zhipeng Qi
- Department of Public Health, China Medical University, Shenyang, China
| | - Jiashuo Li
- Department of Public Health, China Medical University, Shenyang, China
| | - Bin Xu
- Department of Public Health, China Medical University, Shenyang, China
| | - Wei Liu
- Department of Public Health, China Medical University, Shenyang, China
| | - Zhaofa Xu
- Department of Public Health, China Medical University, Shenyang, China
| | - Yu Deng
- Department of Public Health, China Medical University, Shenyang, China
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28
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Shi J, Ma Y, Hua H, Liu Y, Li W, Yu H, Liu C. Dynamic Histone H3 Modifications Regulate Meiosis Initiation via Respiration. Front Cell Dev Biol 2021; 9:646214. [PMID: 33869198 PMCID: PMC8047140 DOI: 10.3389/fcell.2021.646214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/08/2021] [Indexed: 01/02/2023] Open
Abstract
Meiosis is essential for genetic stability and diversity during sexual reproduction in most eukaryotes. Chromatin structure and gene expression are drastically changed during meiosis, and various histone modifications have been reported to participate in this unique process. However, the dynamic of histone modifications during meiosis is still not well investigated. Here, by using multiple reaction monitoring (MRM) based LC-MS/MS, we detected dynamic changes of histone H3 lysine post-translational modifications (PTMs). We firstly quantified the precise percentage of H3 modifications on different lysine sites during mouse and yeast meiosis, and found H3 acetylation and methylation were dramatically changed. To further study the potential functions of H3 acetylation and methylation in meiosis, we performed histone H3 lysine mutant screening in yeast, and found that yeast strains lacking H3K18 acetylation (H3K18ac) failed to initiate meiosis due to insufficient IME1 expression. Further studies showed that the absence of H3K18ac impaired respiration, leading to the reduction of Rim101p, which further upregulated a negative regulator of IME1 transcription, Smp1p. Together, our studies reveal a novel meiosis initiation pathway mediated by histone H3 modifications.
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Affiliation(s)
- Jian Shi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, College of Life Sciences, University of Chinese Academy of Sciences, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, China
| | - Yanjie Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, College of Life Sciences, University of Chinese Academy of Sciences, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, China
| | - Hui Hua
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Yujiao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, College of Life Sciences, University of Chinese Academy of Sciences, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, College of Life Sciences, University of Chinese Academy of Sciences, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, China
| | - Hongxiu Yu
- Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, College of Life Sciences, University of Chinese Academy of Sciences, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, China
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29
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Chen J, Ünal E. Meiotic regulation of the Ndc80 complex composition and function. Curr Genet 2021; 67:511-518. [PMID: 33745061 PMCID: PMC8254699 DOI: 10.1007/s00294-021-01174-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 11/30/2022]
Abstract
This review describes the current models for how the subunit abundance of the Ndc80 complex, a key kinetochore component, is regulated in budding yeast and metazoan meiosis. The past decades of kinetochore research have established the Ndc80 complex to be a key microtubule interactor and a central hub for regulating chromosome segregation. Recent studies further demonstrate that Ndc80 is the limiting kinetochore subunit that dictates the timing of kinetochore activation in budding yeast meiosis. Here, we discuss the molecular circuits that regulate Ndc80 protein synthesis and degradation in budding yeast meiosis and compare the findings with those from metazoans. We envision the regulatory principles discovered in budding yeast to be conserved in metazoans, thereby providing guidance into future investigations on kinetochore regulation in human health and disease.
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Affiliation(s)
- Jingxun Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
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30
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Moretto F, Wood NE, Chia M, Li C, Luscombe NM, van Werven FJ. Transcription levels of a noncoding RNA orchestrate opposing regulatory and cell fate outcomes in yeast. Cell Rep 2021; 34:108643. [PMID: 33472063 PMCID: PMC7816125 DOI: 10.1016/j.celrep.2020.108643] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/28/2020] [Accepted: 12/22/2020] [Indexed: 12/21/2022] Open
Abstract
Transcription through noncoding regions of the genome is pervasive. How these transcription events regulate gene expression remains poorly understood. Here, we report that, in S. cerevisiae, the levels of transcription through a noncoding region, IRT2, located upstream in the promoter of the inducer of meiosis, IME1, regulate opposing chromatin and transcription states. At low levels, the act of IRT2 transcription promotes histone exchange, delivering acetylated histone H3 lysine 56 to chromatin locally. The subsequent open chromatin state directs transcription factor recruitment and induces downstream transcription to repress the IME1 promoter and meiotic entry. Conversely, increasing transcription turns IRT2 into a repressor by promoting transcription-coupled chromatin assembly. The two opposing functions of IRT2 transcription shape a regulatory circuit, which ensures a robust cell-type-specific control of IME1 expression and yeast meiosis. Our data illustrate how intergenic transcription levels are key to controlling local chromatin state, gene expression, and cell fate outcomes.
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Affiliation(s)
- Fabien Moretto
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Crete 70013, Greece
| | - N Ezgi Wood
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Minghao Chia
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore
| | - Cai Li
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Nicholas M Luscombe
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan; UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Folkert J van Werven
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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31
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Chia M, Li C, Marques S, Pelechano V, Luscombe NM, van Werven FJ. High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts. Genome Biol 2021; 22:34. [PMID: 33446241 PMCID: PMC7807719 DOI: 10.1186/s13059-020-02245-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The start and end sites of messenger RNAs (TSSs and TESs) are highly regulated, often in a cell-type-specific manner. Yet the contribution of transcript diversity in regulating gene expression remains largely elusive. We perform an integrative analysis of multiple highly synchronized cell-fate transitions and quantitative genomic techniques in Saccharomyces cerevisiae to identify regulatory functions associated with transcribing alternative isoforms. RESULTS Cell-fate transitions feature widespread elevated expression of alternative TSS and, to a lesser degree, TES usage. These dynamically regulated alternative TSSs are located mostly upstream of canonical TSSs, but also within gene bodies possibly encoding for protein isoforms. Increased upstream alternative TSS usage is linked to various effects on canonical TSS levels, which range from co-activation to repression. We identified two key features linked to these outcomes: an interplay between alternative and canonical promoter strengths, and distance between alternative and canonical TSSs. These two regulatory properties give a plausible explanation of how locally transcribed alternative TSSs control gene transcription. Additionally, we find that specific chromatin modifiers Set2, Set3, and FACT play an important role in mediating gene repression via alternative TSSs, further supporting that the act of upstream transcription drives the local changes in gene transcription. CONCLUSIONS The integrative analysis of multiple cell-fate transitions suggests the presence of a regulatory control system of alternative TSSs that is important for dynamic tuning of gene expression. Our work provides a framework for understanding how TSS heterogeneity governs eukaryotic gene expression, particularly during cell-fate changes.
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Affiliation(s)
- Minghao Chia
- The Francis Crick Institute, London, UK
- Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672, Singapore
| | - Cai Li
- The Francis Crick Institute, London, UK
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sueli Marques
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Vicente Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Nicholas M Luscombe
- The Francis Crick Institute, London, UK
- Okinawa Institute of Science & Technology Graduate University, Okinawa, 904-0495, Japan
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
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32
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Higdon AL, Brar GA. Rules are made to be broken: a "simple" model organism reveals the complexity of gene regulation. Curr Genet 2020; 67:49-56. [PMID: 33130938 DOI: 10.1007/s00294-020-01121-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 11/27/2022]
Abstract
Global methods for assaying translation have greatly improved our understanding of the protein-coding capacity of the genome. In particular, it is now possible to perform genome-wide and condition-specific identification of translation initiation sites through modified ribosome profiling methods that selectively capture initiating ribosomes. Here we discuss our recent study applying such an approach to meiotic and mitotic timepoints in the simple eukaryote, budding yeast, as an example of the surprising diversity of protein products-many of which are non-canonical-that can be revealed by such methods. We also highlight several key challenges in studying non-canonical protein isoforms that have precluded their prior systematic discovery. A growing body of work supports expanded use of empirical protein-coding region identification, which can help relieve some of the limitations and biases inherent to traditional genome annotation approaches. Our study also argues for the adoption of less static views of gene identity and a broader framework for considering the translational capacity of the genome.
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Affiliation(s)
- Andrea L Higdon
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
- Center for Computational Biology, University of California, Berkeley, CA, 94720, USA
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
- Center for Computational Biology, University of California, Berkeley, CA, 94720, USA.
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33
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Modeling the Control of Meiotic Cell Divisions: Entry, Progression, and Exit. Biophys J 2020; 119:1015-1024. [PMID: 32783879 DOI: 10.1016/j.bpj.2020.07.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 12/20/2022] Open
Abstract
Upon nitrogen starvation, Schizosaccharomyces pombe exit the mitotic cell cycle and become irreversibly committed to the completion of meiosis program. Meiotic cell divisions are coordinated with sporulation events to produce haploid spores. In the last few decades, experiments on fission yeast have revealed different molecular players involved in two meiotic cell divisions, meiosis I (MI) and meiosis II (MII). How the MI entry, MI-to-MII transition, and MII exit occur because of the dynamics of the regulatory network is not well understood. In this work, we developed a comprehensive mathematical model of the network that describes the temporal dynamics of meiotic progression. The model accounts for the phenotypes of several experimental data (single and multiple mutations). We demonstrate the control strategy involving multiple feedback loops to yield two successive division cycles. The differential regulation of anaphase-promoting complex/cyclosome (APC/C) coactivators and its inhibitors is crucial for the dynamics of both MI-to-MII transition and MII exit. This model generates mechanistic insights that help in further experiments and modeling.
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34
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CDK Regulation of Meiosis: Lessons from S. cerevisiae and S. pombe. Genes (Basel) 2020; 11:genes11070723. [PMID: 32610611 PMCID: PMC7397238 DOI: 10.3390/genes11070723] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 12/13/2022] Open
Abstract
Meiotic progression requires precise orchestration, such that one round of DNA replication is followed by two meiotic divisions. The order and timing of meiotic events is controlled through the modulation of the phosphorylation state of proteins. Key components of this phospho-regulatory system include cyclin-dependent kinase (CDK) and its cyclin regulatory subunits. Over the past two decades, studies in budding and fission yeast have greatly informed our understanding of the role of CDK in meiotic regulation. In this review, we provide an overview of how CDK controls meiotic events in both budding and fission yeast. We discuss mechanisms of CDK regulation through post-translational modifications and changes in the levels of cyclins. Finally, we highlight the similarities and differences in CDK regulation between the two yeast species. Since CDK and many meiotic regulators are highly conserved, the findings in budding and fission yeasts have revealed conserved mechanisms of meiotic regulation among eukaryotes.
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35
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Tam J, van Werven FJ. Regulated repression governs the cell fate promoter controlling yeast meiosis. Nat Commun 2020; 11:2271. [PMID: 32385261 PMCID: PMC7210989 DOI: 10.1038/s41467-020-16107-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 04/14/2020] [Indexed: 12/11/2022] Open
Abstract
Intrinsic signals and external cues from the environment drive cell fate decisions. In budding yeast, the decision to enter meiosis is controlled by nutrient and mating-type signals that regulate expression of the master transcription factor for meiotic entry, IME1. How nutrient signals control IME1 expression remains poorly understood. Here, we show that IME1 transcription is regulated by multiple sequence-specific transcription factors (TFs) that mediate association of Tup1-Cyc8 co-repressor to its promoter. We find that at least eight TFs bind the IME1 promoter when nutrients are ample. Remarkably, association of these TFs is highly regulated by different nutrient cues. Mutant cells lacking three TFs (Sok2/Phd1/Yap6) displayed reduced Tup1-Cyc8 association, increased IME1 expression, and earlier onset of meiosis. Our data demonstrate that the promoter of a master regulator is primed for rapid activation while repression by multiple TFs mediating Tup1-Cyc8 recruitment dictates the fate decision to enter meiosis.
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Affiliation(s)
- Janis Tam
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Folkert J van Werven
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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36
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MEIOSIN Directs the Switch from Mitosis to Meiosis in Mammalian Germ Cells. Dev Cell 2020; 52:429-445.e10. [DOI: 10.1016/j.devcel.2020.01.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/10/2019] [Accepted: 01/09/2020] [Indexed: 01/12/2023]
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37
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Wei Y, Bettedi L, Ting CY, Kim K, Zhang Y, Cai J, Lilly MA. The GATOR complex regulates an essential response to meiotic double-stranded breaks in Drosophila. eLife 2019; 8:e42149. [PMID: 31650955 PMCID: PMC6834368 DOI: 10.7554/elife.42149] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/13/2019] [Indexed: 01/18/2023] Open
Abstract
The TORC1 regulator GATOR1/SEACIT controls meiotic entry and early meiotic events in yeast. However, how metabolic pathways influence meiotic progression in metazoans remains poorly understood. Here we examine the role of the TORC1 regulators GATOR1 and GATOR2 in the response to meiotic double-stranded breaks (DSB) during Drosophila oogenesis. We find that in mutants of the GATOR2 component mio, meiotic DSBs trigger the constitutive downregulation of TORC1 activity and a permanent arrest in oocyte growth. Conversely, in GATOR1 mutants, high TORC1 activity results in the delayed repair of meiotic DSBs and the hyperactivation of p53. Unexpectedly, we found that GATOR1 inhibits retrotransposon expression in the presence of meiotic DSBs in a pathway that functions in parallel to p53. Thus, our studies have revealed a link between oocyte metabolism, the repair of meiotic DSBs and retrotransposon expression.
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Affiliation(s)
- Youheng Wei
- Cell Biology and Neurobiology BranchNational Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouChina
| | - Lucia Bettedi
- Cell Biology and Neurobiology BranchNational Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Chun-Yuan Ting
- Cell Biology and Neurobiology BranchNational Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Kuikwon Kim
- Cell Biology and Neurobiology BranchNational Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Yingbiao Zhang
- Cell Biology and Neurobiology BranchNational Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Jiadong Cai
- College of Bioscience and BiotechnologyYangzhou UniversityYangzhouChina
| | - Mary A Lilly
- Cell Biology and Neurobiology BranchNational Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
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38
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Pearson GA, Martins N, Madeira P, Serrão EA, Bartsch I. Sex-dependent and -independent transcriptional changes during haploid phase gametogenesis in the sugar kelp Saccharina latissima. PLoS One 2019; 14:e0219723. [PMID: 31513596 PMCID: PMC6742357 DOI: 10.1371/journal.pone.0219723] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/27/2019] [Indexed: 11/26/2022] Open
Abstract
In haplodiplontic lineages, sexual reproduction occurs in haploid parents without meiosis. Although widespread in multicellular lineages such as brown algae (Phaeophyceae), haplodiplontic gametogenesis has been little studied at the molecular level. We addressed this by generating an annotated reference transcriptome for the gametophytic phase of the sugar kelp, Saccharina latissima. Transcriptional profiles of microscopic male and female gametophytes were analysed at four time points during the transition from vegetative growth to gametogenesis. Gametogenic signals resulting from a switch in culture irradiance from red to white light activated a core set of genes in a sex-independent manner, involving rapid activation of ribosome biogenesis, transcription and translation related pathways, with several acting at the post-transcriptional or post-translational level. Additional genes regulating nutrient acquisition and key carbohydrate-energy pathways were also identified. Candidate sex-biased genes under gametogenic conditions had potentially key roles in controlling female- and male-specific gametogenesis. Among these were several sex-biased or -specific E3 ubiquitin-protein ligases that may have important regulatory roles. Females specifically expressed several genes that coordinate gene expression and/or protein degradation, and the synthesis of inositol-containing compounds. Other female-biased genes supported parallels with oogenesis in divergent multicellular lineages, in particular reactive oxygen signalling via an NADPH-oxidase. Males specifically expressed the hypothesised brown algal sex-determining factor. Male-biased expression mainly involved upregulation of genes that control mitotic cell proliferation and spermatogenesis in other systems, as well as multiple flagella-related genes. Our data and results enhance genome-level understanding of gametogenesis in this ecologically and economically important multicellular lineage.
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Affiliation(s)
- Gareth A. Pearson
- Centre for Marine Sciences (CCMAR)-CIMAR, University of Algarve, Portugal
| | - Neusa Martins
- Centre for Marine Sciences (CCMAR)-CIMAR, University of Algarve, Portugal
| | - Pedro Madeira
- Centre for Marine Sciences (CCMAR)-CIMAR, University of Algarve, Portugal
| | - Ester A. Serrão
- Centre for Marine Sciences (CCMAR)-CIMAR, University of Algarve, Portugal
| | - Inka Bartsch
- Alfred-Wegener-Institute, Helmholtz Center for Polar and Marine Research, Am Handelshafen, Germany
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39
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Kojima ML, de Rooij DG, Page DC. Amplification of a broad transcriptional program by a common factor triggers the meiotic cell cycle in mice. eLife 2019; 8:43738. [PMID: 30810530 PMCID: PMC6392498 DOI: 10.7554/elife.43738] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 02/10/2019] [Indexed: 12/22/2022] Open
Abstract
The germ line provides the cellular link between generations of multicellular organisms, its cells entering the meiotic cell cycle only once each generation. However, the mechanisms governing this initiation of meiosis remain poorly understood. Here, we examined cells undergoing meiotic initiation in mice, and we found that initiation involves the dramatic upregulation of a transcriptional network of thousands of genes whose expression is not limited to meiosis. This broad gene expression program is directly upregulated by STRA8, encoded by a germ cell-specific gene required for meiotic initiation. STRA8 binds its own promoter and those of thousands of other genes, including meiotic prophase genes, factors mediating DNA replication and the G1-S cell-cycle transition, and genes that promote the lengthy prophase unique to meiosis I. We conclude that, in mice, the robust amplification of this extraordinarily broad transcription program by a common factor triggers initiation of meiosis.
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Affiliation(s)
- Mina L Kojima
- Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | | | - David C Page
- Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, United States
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40
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Sawyer EM, Joshi PR, Jorgensen V, Yunus J, Berchowitz LE, Ünal E. Developmental regulation of an organelle tether coordinates mitochondrial remodeling in meiosis. J Cell Biol 2018; 218:559-579. [PMID: 30538140 PMCID: PMC6363441 DOI: 10.1083/jcb.201807097] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/26/2018] [Accepted: 11/21/2018] [Indexed: 12/25/2022] Open
Abstract
Cellular differentiation involves remodeling cellular architecture to transform one cell type to another. By investigating mitochondrial dynamics during meiotic differentiation in budding yeast, we sought to understand how organelle morphogenesis is developmentally controlled in a system where regulators of differentiation and organelle architecture are known, but the interface between them remains unexplored. We analyzed the regulation of mitochondrial detachment from the cell cortex, a known meiotic alteration to mitochondrial morphology. We found that mitochondrial detachment is enabled by the programmed destruction of the mitochondria-endoplasmic reticulum-cortex anchor (MECA), an organelle tether that bridges mitochondria and the plasma membrane. MECA regulation is governed by a meiotic transcription factor, Ndt80, which promotes the activation of a conserved kinase, Ime2. We further present evidence for Ime2-dependent phosphorylation and degradation of MECA in a temporally controlled manner. Our study defines a key mechanism that coordinates mitochondrial morphogenesis with the landmark events of meiosis and demonstrates that cells can developmentally regulate tethering to induce organelle remodeling.
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Affiliation(s)
- Eric M Sawyer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Pallavi R Joshi
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Victoria Jorgensen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Julius Yunus
- Department of Genetics and Development, Columbia University Medical Center, New York, NY
| | - Luke E Berchowitz
- Department of Genetics and Development, Columbia University Medical Center, New York, NY
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
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41
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Liu L, He GJ, Chen L, Zheng J, Chen Y, Shen L, Tian X, Li E, Yang E, Liao G, Wang L. Genetic basis for coordination of meiosis and sexual structure maturation in Cryptococcus neoformans. eLife 2018; 7:38683. [PMID: 30281018 PMCID: PMC6235564 DOI: 10.7554/elife.38683] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 10/02/2018] [Indexed: 12/19/2022] Open
Abstract
In the human fungal pathogen Cryptococcus neoformans, sex can benefit its pathogenicity through production of meiospores, which are believed to offer both physical and meiosis-created lineage advantages for its infections. Cryptococcus sporulation occurs following two parallel events, meiosis and differentiation of the basidium, the characteristic sexual structure of the basidiomycetes. However, the circuit integrating these events to ensure subsequent sporulation is unclear. Here, we show the spatiotemporal coordination of meiosis and basidial maturation by visualizing event-specific molecules in developing basidia defined by a quantitative approach. Monitoring of gene induction timing together with genetic analysis reveals co-regulation of the coordinated events by a shared regulatory program. Two RRM family regulators, Csa1 and Csa2, are crucial components that bridge meiosis and basidial maturation, further determining sporulation. We propose that the regulatory coordination of meiosis and basidial development serves as a determinant underlying the production of infectious meiospores in C. neoformans.
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Affiliation(s)
- Linxia Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guang-Jun He
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lei Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jiao Zheng
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Yingying Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lan Shen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiuyun Tian
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Erwei Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ence Yang
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Guojian Liao
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Linqi Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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42
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Romer KA, de Rooij DG, Kojima ML, Page DC. Isolating mitotic and meiotic germ cells from male mice by developmental synchronization, staging, and sorting. Dev Biol 2018; 443:19-34. [PMID: 30149006 DOI: 10.1016/j.ydbio.2018.08.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 08/23/2018] [Accepted: 08/23/2018] [Indexed: 01/06/2023]
Abstract
Isolating discrete populations of germ cells from the mouse testis is challenging, because the adult testis contains germ cells at every step of spermatogenesis, in addition to somatic cells. We present a novel method for isolating precise, high-purity populations of male germ cells. We first synchronize germ cell development in vivo by manipulating retinoic acid metabolism, and perform histological staging to verify synchronization. We use fluorescence-activated cell sorting to separate the synchronized differentiating germ cells from contaminating somatic cells and undifferentiated spermatogonia. We achieve ~90% purity at each step of development from undifferentiated spermatogonia through late meiotic prophase. Utilizing this "3 S" method (synchronize, stage, and sort), we can separate germ cell types that were previously challenging or impossible to distinguish, with sufficient yield for epigenetic and biochemical studies. 3 S expands the toolkit of germ cell sorting methods, and should facilitate detailed characterization of molecular and biochemical changes that occur during the mitotic and meiotic phases of spermatogenesis.
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Affiliation(s)
- Katherine A Romer
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dirk G de Rooij
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA
| | - Mina L Kojima
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David C Page
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA.
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43
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Filarsky M, Fraschka SA, Niederwieser I, Brancucci NMB, Carrington E, Carrió E, Moes S, Jenoe P, Bártfai R, Voss TS. GDV1 induces sexual commitment of malaria parasites by antagonizing HP1-dependent gene silencing. Science 2018; 359:1259-1263. [PMID: 29590075 DOI: 10.1126/science.aan6042] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 01/17/2018] [Indexed: 11/02/2022]
Abstract
Malaria is caused by Plasmodium parasites that proliferate in the bloodstream. During each replication cycle, some parasites differentiate into gametocytes, the only forms able to infect the mosquito vector and transmit malaria. Sexual commitment is triggered by activation of AP2-G, the master transcriptional regulator of gametocytogenesis. Heterochromatin protein 1 (HP1)-dependent silencing of ap2-g prevents sexual conversion in proliferating parasites. In this study, we identified Plasmodium falciparum gametocyte development 1 (GDV1) as an upstream activator of sexual commitment. We found that GDV1 targeted heterochromatin and triggered HP1 eviction, thus derepressing ap2-g Expression of GDV1 was responsive to environmental triggers of sexual conversion and controlled via a gdv1 antisense RNA. Hence, GDV1 appears to act as an effector protein that induces sexual differentiation by antagonizing HP1-dependent gene silencing.
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Affiliation(s)
- Michael Filarsky
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland.,University of Basel, 4003 Basel, Switzerland
| | - Sabine A Fraschka
- Department of Molecular Biology, Radboud University, 6525 GA Nijmegen, Netherlands
| | - Igor Niederwieser
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland.,University of Basel, 4003 Basel, Switzerland
| | - Nicolas M B Brancucci
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland.,University of Basel, 4003 Basel, Switzerland
| | - Eilidh Carrington
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland.,University of Basel, 4003 Basel, Switzerland
| | - Elvira Carrió
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland.,University of Basel, 4003 Basel, Switzerland
| | - Suzette Moes
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Paul Jenoe
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Richárd Bártfai
- Department of Molecular Biology, Radboud University, 6525 GA Nijmegen, Netherlands
| | - Till S Voss
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland. .,University of Basel, 4003 Basel, Switzerland
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44
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Moretto F, Wood NE, Kelly G, Doncic A, van Werven FJ. A regulatory circuit of two lncRNAs and a master regulator directs cell fate in yeast. Nat Commun 2018; 9:780. [PMID: 29472539 PMCID: PMC5823921 DOI: 10.1038/s41467-018-03213-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/24/2018] [Indexed: 12/27/2022] Open
Abstract
Transcription of long noncoding RNAs (lncRNAs) regulates local gene expression in eukaryotes. Many examples of how a single lncRNA controls the expression of an adjacent or nearby protein-coding gene have been described. Here we examine the regulation of a locus consisting of two contiguous lncRNAs and the master regulator for entry into yeast meiosis, IME1. We find that the cluster of two lncRNAs together with several transcription factors form a regulatory circuit by which IME1 controls its own promoter and thereby promotes its own expression. Inhibition or stimulation of this unusual feedback circuit affects timing and rate of IME1 accumulation, and hence the ability for cells to enter meiosis. Our data demonstrate that orchestrated transcription through two contiguous lncRNAs promotes local gene expression and determines a critical cell fate decision.
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Affiliation(s)
- Fabien Moretto
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - N Ezgi Wood
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Gavin Kelly
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Andreas Doncic
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX, 75390, USA
- Green Center for Systems Biology, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA
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45
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A Role for the Respiratory Chain in Regulating Meiosis Initiation in Saccharomyces cerevisiae. Genetics 2018; 208:1181-1194. [PMID: 29301906 DOI: 10.1534/genetics.118.300689] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 12/29/2017] [Indexed: 01/01/2023] Open
Abstract
Meiosis is a specific type of cell division that is essential for sexual reproduction in most eukaryotes. Mitochondria are crucial cellular organelles that play important roles in reproduction, though the detailed mechanism by which the mitochondrial respiratory chain functions during meiosis remains elusive. Here, we show that components of the respiratory chain (Complexes I-V) play essential roles in meiosis initiation during the sporulation of budding yeast, Saccharomyces cerevisiae Any functional defects in the Complex I component Ndi1p resulted in the abolishment of sporulation. Further studies revealed that respiratory deficiency resulted in the failure of premeiotic DNA replication due to insufficient IME1 expression. In addition, respiration promoted the expression of RIM101, whose product inhibits Smp1p, a negative transcriptional regulator of IME1, to promote meiosis initiation. In summary, our studies unveiled the close relationship between mitochondria and sporulation, and uncover a novel meiosis initiation pathway that is regulated by the respiratory chain.
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46
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Navarro FJ, Chakravarty P, Nurse P. Phosphorylation of the RNA-binding protein Zfs1 modulates sexual differentiation in fission yeast. J Cell Sci 2017; 130:4144-4154. [PMID: 29084823 PMCID: PMC5769579 DOI: 10.1242/jcs.208066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/24/2017] [Indexed: 12/21/2022] Open
Abstract
Sexual differentiation in the fission yeast Schizosaccharomyces pombe promotes cell cycle arrest and extensive changes in gene expression, resulting in cell-to-cell fusion, the exchange of hereditary material and specialized cell division. These events are detrimental to the cell if they are triggered in inappropriate conditions, and therefore the decision to differentiate must be precisely controlled. Here, we investigated the role of the RNA-binding protein Zfs1 in this process by identifying its targets and characterizing novel post-translational regulatory mechanisms. We found that Zfs1 negatively regulates the G1 cyclin Puc1, and deregulated Puc1 levels inhibit differentiation in the zfs1Δ mutant. We also found that Zfs1 undergoes phosphorylation, which is stimulated upon nitrogen depletion or inhibition of the TOR pathway. Phosphorylation of Zfs1 modulates accumulation of Puc1 and plays an important role in the response of the cell to sexual differentiation signals. We propose that Zfs1 functions as an integrator of nutrient information to modulate sexual differentiation, contributing to the establishment of the differentiation-activating threshold.
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Affiliation(s)
| | - Probir Chakravarty
- Bioinformatics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Paul Nurse
- Cell Cycle Laboratory, The Francis Crick Institute, London NW1 1AT, UK
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47
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One-two punch mechanism of gene repression: a fresh perspective on gene regulation. Curr Genet 2017; 64:581-588. [PMID: 29218463 PMCID: PMC5948300 DOI: 10.1007/s00294-017-0793-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 11/30/2017] [Accepted: 12/02/2017] [Indexed: 02/04/2023]
Abstract
Cellular differentiation depends on temporally controlled waves of gene activation and inactivation that ultimately transform one cell type into another. It is well established that transcription factor cascades coordinate the timely activation of gene expression clusters during development. In comparison, much less is understood about how gene repression events are coordinated with the transcription factor-driven waves of gene activation and how this repression is achieved at a mechanistic level. Using budding yeast as a model, we recently discovered a new gene regulatory event, whereby a central meiotic transcription factor induces the expression of an mRNA isoform to repress gene expression through an integrated transcriptional and translational mechanism. This new model could explain how gene activation and inactivation waves can be temporally coordinated. In this review, we discuss our findings and their potential implications.
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48
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Jakobsson E, Argüello-Miranda O, Chiu SW, Fazal Z, Kruczek J, Nunez-Corrales S, Pandit S, Pritchet L. Towards a Unified Understanding of Lithium Action in Basic Biology and its Significance for Applied Biology. J Membr Biol 2017; 250:587-604. [PMID: 29127487 PMCID: PMC5696506 DOI: 10.1007/s00232-017-9998-2] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 10/21/2017] [Indexed: 01/14/2023]
Abstract
Lithium has literally been everywhere forever, since it is one of the three elements created in the Big Bang. Lithium concentration in rocks, soil, and fresh water is highly variable from place to place, and has varied widely in specific regions over evolutionary and geologic time. The biological effects of lithium are many and varied. Based on experiments in which animals are deprived of lithium, lithium is an essential nutrient. At the other extreme, at lithium ingestion sufficient to raise blood concentration significantly over 1 mM/, lithium is acutely toxic. There is no consensus regarding optimum levels of lithium intake for populations or individuals-with the single exception that lithium is a generally accepted first-line therapy for bipolar disorder, and specific dosage guidelines for sufferers of that condition are generally agreed on. Epidemiological evidence correlating various markers of social dysfunction and disease vs. lithium level in drinking water suggest benefits of moderately elevated lithium compared to average levels of lithium intake. In contrast to other biologically significant ions, lithium is unusual in not having its concentration in fluids of multicellular animals closely regulated. For hydrogen ions, sodium ions, potassium ions, calcium ions, chloride ions, and magnesium ions, blood and extracellular fluid concentrations are closely and necessarily regulated by systems of highly selective channels, and primary and secondary active transporters. Lithium, while having strong biological activity, is tolerated over body fluid concentrations ranging over many orders of magnitude. The lack of biological regulation of lithium appears due to lack of lithium-specific binding sites and selectivity filters. Rather lithium exerts its myriad physiological and biochemical effects by competing for macromolecular sites that are relatively specific for other cations, most especially for sodium and magnesium. This review will consider what is known about the nature of this competition and suggest using and extending this knowledge towards the goal of a unified understanding of lithium in biology and the application of that understanding in medicine and nutrition.
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Affiliation(s)
- Eric Jakobsson
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | | | - See-Wing Chiu
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zeeshan Fazal
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - James Kruczek
- Department of Physics, University of South Florida, Tampa, FL, USA
| | - Santiago Nunez-Corrales
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sagar Pandit
- Department of Physics, University of South Florida, Tampa, FL, USA
| | - Laura Pritchet
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Psychological and Brain Sciences, University of California at Santa Barbara, Santa Barbara, CA, USA
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49
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Zhou S, Sternglanz R, Neiman AM. Developmentally regulated internal transcription initiation during meiosis in budding yeast. PLoS One 2017; 12:e0188001. [PMID: 29136644 PMCID: PMC5685637 DOI: 10.1371/journal.pone.0188001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/30/2017] [Indexed: 02/07/2023] Open
Abstract
Sporulation of budding yeast is a developmental process in which cells undergo meiosis to generate stress-resistant progeny. The dynamic nature of the budding yeast meiotic transcriptome has been well established by a number of genome-wide studies. Here we develop an analysis pipeline to systematically identify novel transcription start sites that reside internal to a gene. Application of this pipeline to data from a synchronized meiotic time course reveals over 40 genes that display specific internal initiations in mid-sporulation. Consistent with the time of induction, motif analysis on upstream sequences of these internal transcription start sites reveals a significant enrichment for the binding site of Ndt80, the transcriptional activator of middle sporulation genes. Further examination of one gene, MRK1, demonstrates the Ndt80 binding site is necessary for internal initiation and results in the expression of an N-terminally truncated protein isoform. When the MRK1 paralog RIM11 is downregulated, the MRK1 internal transcript promotes efficient sporulation, indicating functional significance of the internal initiation. Our findings suggest internal transcriptional initiation to be a dynamic, regulated process with potential functional impacts on development.
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Affiliation(s)
- Sai Zhou
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, United States of America
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, United States of America
| | - Rolf Sternglanz
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, United States of America
| | - Aaron M. Neiman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, United States of America
- * E-mail:
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50
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Parasex Generates Phenotypic Diversity de Novo and Impacts Drug Resistance and Virulence in Candida albicans. Genetics 2017; 207:1195-1211. [PMID: 28912344 DOI: 10.1534/genetics.117.300295] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 09/05/2017] [Indexed: 01/06/2023] Open
Abstract
Candida albicans is a diploid fungus that is a frequent cause of mucosal and systemic infections in humans. This species exhibits an unusual parasexual cycle in which mating produces tetraploid cells that undergo a nonmeiotic program of concerted chromosome loss to return to a diploid or aneuploid state. In this work, we used a multipronged approach to examine the capacity of parasex to generate diversity in C. albicans First, we compared the phenotypic properties of 32 genotyped progeny and observed wide-ranging differences in fitness, filamentation, biofilm formation, and virulence. Strikingly, one parasexual isolate displayed increased virulence relative to parental strains using a Galleria mellonella model of infection, establishing that parasex has the potential to enhance pathogenic traits. Next, we examined parasexual progeny derived from homothallic, same-sex mating events, and reveal that parasex can generate diversity de novo from identical parental strains. Finally, we generated pools of parasexual progeny and examined resistance of these pools to environmental stresses. Parasexual progeny were generally less fit than control strains across most test conditions, but showed an increased ability to grow in the presence of the antifungal drug fluconazole (FL). FL-resistant progeny were aneuploid isolates, often being diploid strains trisomic for both Chr3 and Chr6. Passaging of these aneuploid strains frequently led to loss of the supernumerary chromosomes and a concomitant decrease in drug resistance. These experiments establish that parasex generates extensive phenotypic diversity de novo, and that this process has important consequences for both virulence and drug resistance in C. albicans populations.
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