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Khorsand FR, Aziziyan F, Khajeh K. Factors influencing amyloid fibril formation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:55-83. [PMID: 38811089 DOI: 10.1016/bs.pmbts.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Protein aggregation is a complex process with several stages that lead to the formation of complex structures and shapes with a broad variability in stability and toxicity. The aggregation process is affected by various factors and environmental conditions that disrupt the protein's original state, including internal factors like mutations, expression levels, and polypeptide chain truncation, as well as external factors, such as dense molecular surroundings, post-translation modifications, and interactions with other proteins, nucleic acids, small molecules, metal ions, chaperones, and lipid membranes. During the aggregation process, the biological activity of an aggregating protein may be reduced or eliminated, whereas the resulting aggregates may have the potential to be immunogenic, or they may have other undesirable properties. Finding the cause(s) of protein aggregation and controlling it to an acceptable level is among the most crucial topics of research in academia and biopharmaceutical companies. This chapter aims to review intrinsic pathways of protein aggregation and potential extrinsic variables that influence this process.
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Affiliation(s)
| | - Fatemeh Aziziyan
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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2
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Mirza Agha M, Tavili E, Dabirmanesh B. Functional amyloids. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:389-434. [PMID: 38811086 DOI: 10.1016/bs.pmbts.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
While amyloid has traditionally been viewed as a harmful formation, emerging evidence suggests that amyloids may also play a functional role in cell biology, contributing to normal physiological processes that have been conserved throughout evolution. Functional amyloids have been discovered in several creatures, spanning from bacteria to mammals. These amyloids serve a multitude of purposes, including but not limited to, forming biofilms, melanin synthesis, storage, information transfer, and memory. The functional role of amyloids has been consistently validated by the discovery of more functional amyloids, indicating a conceptual convergence. The biology of amyloids is well-represented by non-pathogenic amyloids, given the numerous ones already identified and the ongoing rate of new discoveries. In this chapter, functional amyloids in microorganisms, animals, and plants are described.
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Affiliation(s)
- Mansoureh Mirza Agha
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Elaheh Tavili
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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3
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Zheng H, Zhang H. More than a bystander: RNAs specify multifaceted behaviors of liquid-liquid phase-separated biomolecular condensates. Bioessays 2024; 46:e2300203. [PMID: 38175843 DOI: 10.1002/bies.202300203] [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: 10/24/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024]
Abstract
Cells contain a myriad of membraneless ribonucleoprotein (RNP) condensates with distinct compositions of proteins and RNAs. RNP condensates participate in different cellular activities, including RNA storage, mRNA translation or decay, stress response, etc. RNP condensates are assembled via liquid-liquid phase separation (LLPS) driven by multivalent interactions. Transition of RNP condensates into bodies with abnormal material properties, such as solid-like amyloid structures, is associated with the pathogenesis of various diseases. In this review, we focus on how RNAs regulate multiple aspects of RNP condensates, such as dynamic assembly and/or disassembly and biophysical properties. RNA properties - including concentration, sequence, length and structure - also determine the phase behaviors of RNP condensates. RNA is also involved in specifying autophagic degradation of RNP condensates. Unraveling the role of RNA in RNPs provides novel insights into pathological accumulation of RNPs in various diseases. This new understanding can potentially be harnessed to develop therapeutic strategies.
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Affiliation(s)
- Hui Zheng
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, P.R. China
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4
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Durant M, Mucelli X, Huang LS. Meiotic Cytokinesis in Saccharomyces cerevisiae: Spores That Just Need Closure. J Fungi (Basel) 2024; 10:132. [PMID: 38392804 PMCID: PMC10890087 DOI: 10.3390/jof10020132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/24/2024] Open
Abstract
In the budding yeast Saccharomyces cerevisiae, sporulation occurs during starvation of a diploid cell and results in the formation of four haploid spores forming within the mother cell ascus. Meiosis divides the genetic material that is encapsulated by the prospore membrane that grows to surround the haploid nuclei; this membrane will eventually become the plasma membrane of the haploid spore. Cellularization of the spores occurs when the prospore membrane closes to capture the haploid nucleus along with some cytoplasmic material from the mother cell, and thus, closure of the prospore membrane is the meiotic cytokinetic event. This cytokinetic event involves the removal of the leading-edge protein complex, a complex of proteins that localizes to the leading edge of the growing prospore membrane. The development and closure of the prospore membrane must be coordinated with other meiotic exit events such as spindle disassembly. Timing of the closure of the prospore membrane depends on the meiotic exit pathway, which utilizes Cdc15, a Hippo-like kinase, and Sps1, an STE20 family GCKIII kinase, acting in parallel to the E3 ligase Ama1-APC/C. This review describes the sporulation process and focuses on the development of the prospore membrane and the regulation of prospore membrane closure.
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Affiliation(s)
- Matthew Durant
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Xheni Mucelli
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Linda S Huang
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
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5
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Obsilova V, Obsil T. The yeast 14-3-3 proteins Bmh1 and Bmh2 regulate key signaling pathways. Front Mol Biosci 2024; 11:1327014. [PMID: 38328397 PMCID: PMC10847541 DOI: 10.3389/fmolb.2024.1327014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
Cell signaling regulates several physiological processes by receiving, processing, and transmitting signals between the extracellular and intracellular environments. In signal transduction, phosphorylation is a crucial effector as the most common posttranslational modification. Selectively recognizing specific phosphorylated motifs of target proteins and modulating their functions through binding interactions, the yeast 14-3-3 proteins Bmh1 and Bmh2 are involved in catabolite repression, carbon metabolism, endocytosis, and mitochondrial retrograde signaling, among other key cellular processes. These conserved scaffolding molecules also mediate crosstalk between ubiquitination and phosphorylation, the spatiotemporal control of meiosis, and the activity of ion transporters Trk1 and Nha1. In humans, deregulation of analogous processes triggers the development of serious diseases, such as diabetes, cancer, viral infections, microbial conditions and neuronal and age-related diseases. Accordingly, the aim of this review article is to provide a brief overview of the latest findings on the functions of yeast 14-3-3 proteins, focusing on their role in modulating the aforementioned processes.
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Affiliation(s)
- Veronika Obsilova
- Institute of Physiology of the Czech Academy of Sciences, Laboratory of Structural Biology of Signaling Proteins, Division, BIOCEV, Vestec, Czechia
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czechia
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6
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Zhang R, Li S, Feng W, Qian S, Chellappa AJ, Wang F. Rim4 is a Thermal Sensor and Driver of Meiosis-specific Stress Granules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574866. [PMID: 38260504 PMCID: PMC10802437 DOI: 10.1101/2024.01.09.574866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Rim4 is a meiosis-specific RNA-binding protein (RBP) that sequesters mRNAs to suppress their translation. Previous work has defined the Rim4 C-terminal low-complexity domain (LCD) as sequences that form self-propagating amyloid-like aggregates. Here, we uncovered a dynamic and reversible form of Rim4 self-assembly primarily triggered by heat during meiosis, proportionally from 30°C to 42°C. The formed thermal Rim4 condensates in cell promptly stimulates stress granule (SG) assembly, recruiting SG-resident proteins, such as Pab1 and Pbp1, and strikingly, decreases the required temperature for meiotic SG formation (∼33°C) by ∼9°C as compared to mitosis (∼42°C). This sensitization of meiotic SG formation to heat effectively prevents meiosis progression and sporulation under harmful thermal turbulence. Meanwhile, the Rim4-positive meiotic SGs protect Rim4 and Rim4-sequestered mRNAs from autophagy to allow a rapid recovery from stalled meiosis upon the stress relief. Mechanistically, we found that the yeast 14-3-3 proteins (Bmh1 and Bmh2) and nucleic acids brake initiation of heat-induced Rim4 self-assembly, and Hsp104 facilitates the restoration of intracellular Rim4 distribution during the recovery.
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7
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Ottoz DSM, Tang LC, Dyatel AE, Jovanovic M, Berchowitz LE. Assembly and function of the amyloid-like translational repressor Rim4 is coupled with nutrient conditions. EMBO J 2023; 42:e113332. [PMID: 37921330 PMCID: PMC10690475 DOI: 10.15252/embj.2022113332] [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: 12/19/2022] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 11/04/2023] Open
Abstract
Amyloid-like protein assemblies have been associated with toxic phenotypes because of their repetitive and stable structure. However, evidence that cells exploit these structures to control function and activity of some proteins in response to stimuli has questioned this paradigm. How amyloid-like assembly can confer emergent functions and how cells couple assembly with environmental conditions remains unclear. Here, we study Rim4, an RNA-binding protein that forms translation-repressing assemblies during yeast meiosis. We demonstrate that in its assembled and repressive state, Rim4 binds RNA more efficiently than in its monomeric and idle state, revealing a causal connection between assembly and function. The Rim4-binding site location within the transcript dictates whether the assemblies can repress translation, underscoring the importance of the architecture of this RNA-protein structure for function. Rim4 assembly depends exclusively on its intrinsically disordered region and is prevented by the Ras/protein kinase A signaling pathway, which promotes growth and suppresses meiotic entry in yeast. Our results suggest a mechanism whereby cells couple a functional protein assembly with a stimulus to enforce a cell fate decision.
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Affiliation(s)
- Diana SM Ottoz
- Department of Genetics and Development, Hammer Health Sciences CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Lauren C Tang
- Department of Biological SciencesColumbia UniversityNew YorkNYUSA
| | - Annie E Dyatel
- Department of Genetics and Development, Hammer Health Sciences CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Marko Jovanovic
- Department of Biological SciencesColumbia UniversityNew YorkNYUSA
| | - Luke E Berchowitz
- Department of Genetics and Development, Hammer Health Sciences CenterColumbia University Irving Medical CenterNew YorkNYUSA
- Taub Institute for Research on Alzheimer's and the Aging BrainNew YorkNYUSA
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8
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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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9
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Rojas J, Oz T, Jonak K, Lyzak O, Massaad V, Biriuk O, Zachariae W. Spo13/MEIKIN ensures a Two-Division meiosis by preventing the activation of APC/C Ama1 at meiosis I. EMBO J 2023; 42:e114288. [PMID: 37728253 PMCID: PMC10577557 DOI: 10.15252/embj.2023114288] [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: 04/14/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/21/2023] Open
Abstract
Genome haploidization at meiosis depends on two consecutive nuclear divisions, which are controlled by an oscillatory system consisting of Cdk1-cyclin B and the APC/C bound to the Cdc20 activator. How the oscillator generates exactly two divisions has been unclear. We have studied this question in yeast where exit from meiosis involves accumulation of the APC/C activator Ama1 at meiosis II. We show that inactivation of the meiosis I-specific protein Spo13/MEIKIN results in a single-division meiosis due to premature activation of APC/CAma1 . In the wild type, Spo13 bound to the polo-like kinase Cdc5 prevents Ama1 synthesis at meiosis I by stabilizing the translational repressor Rim4. In addition, Cdc5-Spo13 inhibits the activity of Ama1 by converting the B-type cyclin Clb1 from a substrate to an inhibitor of Ama1. Cdc20-dependent degradation of Spo13 at anaphase I unleashes a feedback loop that increases Ama1's synthesis and activity, leading to irreversible exit from meiosis at the second division. Thus, by repressing the exit machinery at meiosis I, Cdc5-Spo13 ensures that cells undergo two divisions to produce haploid gametes.
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Affiliation(s)
- Julie Rojas
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
- Present address:
Laboratory of GeneticsUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Tugce Oz
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
| | - Katarzyna Jonak
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
- Present address:
Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Oleksii Lyzak
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
| | - Vinal Massaad
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
| | - Olha Biriuk
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
| | - Wolfgang Zachariae
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
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10
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Zhang R, Feng W, Qian S, Li S, Wang F. Regulation of Rim4 distribution, function, and stability during meiosis by PKA, Cdc14, and 14-3-3 proteins. Cell Rep 2023; 42:113052. [PMID: 37659077 PMCID: PMC10591911 DOI: 10.1016/j.celrep.2023.113052] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 07/13/2023] [Accepted: 08/15/2023] [Indexed: 09/04/2023] Open
Abstract
Meiotic gene expression in budding yeast is tightly controlled by RNA-binding proteins (RBPs), with the meiosis-specific RBP Rim4 playing a key role in sequestering mid-late meiotic transcripts to prevent premature translation. However, the mechanisms governing assembly and disassembly of the Rim4-mRNA complex, critical for Rim4's function and stability, remain poorly understood. In this study, we unveil regulation of the Rim4 ribonucleoprotein (RNP) complex by the yeast 14-3-3 proteins Bmh1 and Bmh2. These proteins form a Rim4-Bmh1-Bmh2 heterotrimeric complex that expels mRNAs from Rim4 binding. We identify four Bmh1/2 binding sites (BBSs) on Rim4, with two residing within the RNA recognition motifs (RRMs). Phosphorylation and dephosphorylation of serine/threonine (S/T) residues at these BBSs by PKA kinase and Cdc14 phosphatase activities primarily control formation of Rim4-Bmh1/2, regulating Rim4's subcellular distribution, function, and stability. These findings shed light on the intricate post-transcriptional regulatory mechanisms governing meiotic gene expression.
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Affiliation(s)
- Rudian Zhang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenzhi Feng
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Suhong Qian
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shunjin Li
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Fei Wang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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11
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Zhang R, Feng W, Qian S, Wang F. Autophagy-mediated surveillance of Rim4-mRNA interaction safeguards programmed meiotic translation. Cell Rep 2023; 42:113051. [PMID: 37659076 PMCID: PMC10591816 DOI: 10.1016/j.celrep.2023.113051] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 07/13/2023] [Accepted: 08/15/2023] [Indexed: 09/04/2023] Open
Abstract
In yeast meiosis, autophagy is active and essential. Here, we investigate the fate of Rim4, a meiosis-specific RNA-binding protein (RBP), and its associated transcripts during meiotic autophagy. We demonstrate that Rim4 employs a nuclear localization signal (NLS) to enter the nucleus, where it loads its mRNA substrates before nuclear export. Upon reaching the cytoplasm, active autophagy selectively spares the Rim4-mRNA complex. During meiotic divisions, autophagy preferentially degrades Rim4 in an Atg11-dependent manner, coinciding with the release of Rim4-bound mRNAs for translation. Intriguingly, these released mRNAs also become vulnerable to autophagy. In vitro, purified Rim4 and its RRM-motif-containing variants activate Atg1 kinase in meiotic cell lysates and in immunoprecipitated (IP) Atg1 complexes. This suggests that the conserved RNA recognition motifs (RRMs) of Rim4 are involved in stimulating Atg1 and thereby facilitating selective autophagy. Taken together, our findings indicate that autophagy surveils Rim4-mRNA interaction to ensure stage-specific translation during meiosis.
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Affiliation(s)
- Rudian Zhang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenzhi Feng
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Suhong Qian
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Fei Wang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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12
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Seitz BC, Mucelli X, Majano M, Wallis Z, Dodge AC, Carmona C, Durant M, Maynard S, Huang LS. Meiosis II spindle disassembly requires two distinct pathways. Mol Biol Cell 2023; 34:ar98. [PMID: 37436806 PMCID: PMC10551701 DOI: 10.1091/mbc.e23-03-0096] [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: 03/15/2023] [Revised: 06/26/2023] [Accepted: 07/03/2023] [Indexed: 07/13/2023] Open
Abstract
During exit from meiosis II, cells undergo several structural rearrangements, including disassembly of the meiosis II spindles and cytokinesis. Each of these changes is regulated to ensure that they occur at the proper time. Previous studies have demonstrated that both SPS1, which encodes a STE20-family GCKIII kinase, and AMA1, which encodes a meiosis-specific activator of the Anaphase Promoting Complex, are required for both meiosis II spindle disassembly and cytokinesis in the budding yeast Saccharomyces cerevisiae. We examine the relationship between meiosis II spindle disassembly and cytokinesis and find that the meiosis II spindle disassembly failure in sps1Δ and ama1∆ cells is not the cause of the cytokinesis defect. We also see that the spindle disassembly defects in sps1Δ and ama1∆ cells are phenotypically distinct. We examined known microtubule-associated proteins Ase1, Cin8, and Bim1, and found that AMA1 is required for the proper loss of Ase1 and Cin8 on meiosis II spindles while SPS1 is required for Bim1 loss in meiosis II. Taken together, these data indicate that SPS1 and AMA1 promote distinct aspects of meiosis II spindle disassembly, and that both pathways are required for the successful completion of meiosis.
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Affiliation(s)
- Brian C. Seitz
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
| | - Xheni Mucelli
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
| | - Maira Majano
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
| | - Zoey Wallis
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
| | - Ashley C. Dodge
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
| | - Catherine Carmona
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
| | - Matthew Durant
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
| | - Sharra Maynard
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
| | - Linda S. Huang
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125
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13
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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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14
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Park ZM, Belnap E, Remillard M, Rose MD. Vir1p, the Yeast Homolog of Virilizer, is Required for mRNA m 6 A Methylation and Meiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527493. [PMID: 36798303 PMCID: PMC9934557 DOI: 10.1101/2023.02.07.527493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
N 6 -Methyladenosine (m 6 A) is one of the most abundant modifications found on eukaryotic mRNAs. mRNA methylation regulates a host of biological processes including meiosis, a specialized diploid cell division program that results in the formation of haploid cells (gametes). During budding yeast meiosis, m 6 A levels peak early, before the initiation of the meiotic divisions. High-throughput studies and work from our lab showed that Ygl036wp, a previously uncharacterized protein interacts with Kar4p, a meiotic protein required for mRNA m 6 A-methylation. Ygl036wp has no discernable domains except for several intrinsically disordered regions. However, protein folding prediction tools showed that Ygl036wp folds like VIRMA/Virilizer/VIR, which is involved in mRNA m 6 A-methylation in higher eukaryotes. In addition, Ygl036wp has several conserved motifs shared with VIRMA/Virilizer/VIR proteins. Accordingly, we propose to call the gene VIR1 for budding yeast ortholog of VIR MA/Virilizer/VIR 1 . In support, Vir1p interacts with all other members of the yeast methyltransferase complex and is required for mRNA m 6 A methylation and meiosis. Vir1p is required for the stability of proteins comprising the methyltransferase complex, suggesting that Vir1p acts as a scaffold to stabilize the complex. The vir1 Δ/Δ mutant is defective for premeiotic S-phase, which is suppressed by overexpression of the early meiotic transcription factor IME1; additional overexpression of the translational regulator RIM4 is required for sporulation. Consistent with IME1 suppression, vir1 Δ/Δ exhibits a defect in the abundance of IME1 mRNA, as well as transcripts within Ime1p's regulon. Suppression by IME1 revealed a defect in the expression of the middle meiotic transcription factor, Ndt80p (and genes in its regulon), which is rescued by additional overexpression of RIM4 . Together, these data suggest that Vir1p is required for cells to initiate the meiotic program and for progression through the meiotic divisions and spore formation. Author Summary Ygl036wp is a previously uncharacterized protein that we propose to name Vir1p (budding yeast ortholog of VIR MA/Virilizer/VIR 1 ). Work from our lab and others initially found an interaction between Vir1p and members of the yeast mRNA methyltransferase complex (Kar4p and Mum2p). We found that Vir1p interacts with all known members of the methyltransferase complex and is required for mRNA methylation. Vir1p is required early in meiosis; vir1 Δ/Δ mutants arrest due to the reduced expression of Ime1p. Lower levels of Ime1p cause severe disruption to the meiotic transcriptome in vir1 Δ/Δ. The vir1 Δ/Δ meiotic defect can be partially suppressed by the overexpression of IME1 ; full suppression requires overexpression of both IME1 and RIM4 . Using recent advances in protein folding predictions, we found that Vir1p is a remote homolog of VIRMA/Virilizer/VIR and shares conserved motifs with the protein from other organisms. Vir1p, like VIRMA/Virilizer/VIR, stabilizes the methyltransferase complex.
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Affiliation(s)
- Zachory M. Park
- Department of Biology, Georgetown University, Washington DC, 20057, USA
| | - Ethan Belnap
- 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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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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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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Sing TL, Brar GA, Ünal E. Gametogenesis: Exploring an Endogenous Rejuvenation Program to Understand Cellular Aging and Quality Control. Annu Rev Genet 2022; 56:89-112. [PMID: 35878627 PMCID: PMC9712276 DOI: 10.1146/annurev-genet-080320-025104] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Gametogenesis is a conserved developmental program whereby a diploid progenitor cell differentiates into haploid gametes, the precursors for sexually reproducing organisms. In addition to ploidy reduction and extensive organelle remodeling, gametogenesis naturally rejuvenates the ensuing gametes, leading to resetting of life span. Excitingly, ectopic expression of the gametogenesis-specific transcription factor Ndt80 is sufficient to extend life span in mitotically dividing budding yeast, suggesting that meiotic rejuvenation pathways can be repurposed outside of their natural context. In this review, we highlight recent studies of gametogenesis that provide emerging insight into natural quality control, organelle remodeling, and rejuvenation strategies that exist within a cell. These include selective inheritance, programmed degradation, and de novo synthesis, all of which are governed by the meiotic gene expression program entailing many forms of noncanonical gene regulation. Finally, we highlight critical questions that remain in the field and provide perspective on the implications of gametogenesis research on human health span.
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Affiliation(s)
- Tina L Sing
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
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18
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Herod SG, Dyatel A, Hodapp S, Jovanovic M, Berchowitz LE. Clearance of an amyloid-like translational repressor is governed by 14-3-3 proteins. Cell Rep 2022; 39:110753. [PMID: 35508136 PMCID: PMC9156962 DOI: 10.1016/j.celrep.2022.110753] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/24/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Amyloids are fibrous protein aggregates associated with age-related diseases. While these aggregates are typically described as irreversible and pathogenic, some cells use reversible amyloid-like structures that serve important functions. The RNA-binding protein Rim4 forms amyloid-like assemblies that are essential for translational control during Saccharomyces cerevisiae meiosis. Rim4 amyloid-like assemblies are disassembled in a phosphorylation-dependent manner at meiosis II onset. By investigating Rim4 clearance, we elucidate co-factors that mediate clearance of amyloid-like assemblies in a physiological setting. We demonstrate that yeast 14-3-3 proteins bind to Rim4 assemblies and facilitate their subsequent phosphorylation and timely clearance. Furthermore, distinct 14-3-3 proteins play non-redundant roles in facilitating phosphorylation and clearance of amyloid-like Rim4. Additionally, we find that 14-3-3 proteins contribute to global protein aggregate homeostasis. Based on the role of 14-3-3 proteins in aggregate homeostasis and their interactions with disease-associated assemblies, we propose that these proteins may protect against pathological protein aggregates.
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Affiliation(s)
- S Grace Herod
- 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
| | - Annie Dyatel
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Stefanie Hodapp
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, 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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19
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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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20
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Su Y, Guo X, Zang M, Xie Z, Zhao T, Xu EY. RNA binding protein BOULE forms aggregates in mammalian testis. J Biomed Res 2022; 36:255-268. [PMID: 35965435 PMCID: PMC9376728 DOI: 10.7555/jbr.36.20220072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Yujuan Su
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xinghui Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Min Zang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Zhengyao Xie
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Tingting Zhao
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Eugene Yujun Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Neurology, and Center for Reproductive Sciences, Northwestern University, Chicago, IL 60611, USA
- Eugene Yujun Xu, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Avenue, Nanjing, Jiangsu 211166, China. Tel: +86-25-86869505, E-mail:
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21
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Fassler JS, Skuodas S, Weeks DL, Phillips BT. Protein Aggregation and Disaggregation in Cells and Development. J Mol Biol 2021; 433:167215. [PMID: 34450138 PMCID: PMC8530975 DOI: 10.1016/j.jmb.2021.167215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/01/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022]
Abstract
Protein aggregation is a feature of numerous neurodegenerative diseases. However, regulated, often reversible, formation of protein aggregates, also known as condensates, helps control a wide range of cellular activities including stress response, gene expression, memory, cell development and differentiation. This review presents examples of aggregates found in biological systems, how they are used, and cellular strategies that control aggregation and disaggregation. We include features of the aggregating proteins themselves, environmental factors, co-aggregates, post-translational modifications and well-known aggregation-directed activities that influence their formation, material state, stability and dissolution. We highlight the emerging roles of biomolecular condensates in early animal development, and disaggregation processing proteins that have recently been shown to play key roles in gametogenesis and embryogenesis.
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Affiliation(s)
- Jan S Fassler
- Department of Biology, University of Iowa, Iowa City, IA 52242, United States.
| | - Sydney Skuodas
- Department of Biology, University of Iowa, Iowa City, IA 52242, United States. https://twitter.com/@sskuodas
| | - Daniel L Weeks
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Bryan T Phillips
- Department of Biology, University of Iowa, Iowa City, IA 52242, United States. https://twitter.com/@bt4phillips
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22
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Sternburg EL, Gruijs da Silva LA, Dormann D. Post-translational modifications on RNA-binding proteins: accelerators, brakes, or passengers in neurodegeneration? Trends Biochem Sci 2021; 47:6-22. [PMID: 34366183 DOI: 10.1016/j.tibs.2021.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 02/07/2023]
Abstract
RNA-binding proteins (RBPs) are critical players in RNA expression and metabolism, thus, the proper regulation of this class of proteins is critical for cellular health. Regulation of RBPs often occurs through post-translational modifications (PTMs), which allow the cell to quickly and efficiently respond to cellular and environmental stimuli. PTMs have recently emerged as important regulators of RBPs implicated in neurodegenerative disorders, in particular amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here, we summarize how disease-associated PTMs influence the biophysical properties, molecular interactions, subcellular localization, and function of ALS/FTD-linked RBPs, such as FUS and TDP-43. We will discuss how PTMs are believed to play pathological, protective, or ambiguous roles in these neurodegenerative disorders.
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Affiliation(s)
- Erin L Sternburg
- Johannes Gutenberg-Universität (JGU) Mainz, Faculty of Biology, Mainz, Germany
| | - Lara A Gruijs da Silva
- Johannes Gutenberg-Universität (JGU) Mainz, Faculty of Biology, Mainz, Germany; Graduate School of Systemic Neurosciences (GSN), Munich, Germany
| | - Dorothee Dormann
- Johannes Gutenberg-Universität (JGU) Mainz, Faculty of Biology, Mainz, Germany; Institute of Molecular Biology (IMB), Mainz, Germany.
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23
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Ismail H, Liu X, Yang F, Li J, Zahid A, Dou Z, Liu X, Yao X. Mechanisms and regulation underlying membraneless organelle plasticity control. J Mol Cell Biol 2021; 13:239-258. [PMID: 33914074 PMCID: PMC8339361 DOI: 10.1093/jmcb/mjab028] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Evolution has enabled living cells to adopt their structural and functional complexity by organizing intricate cellular compartments, such as membrane-bound and membraneless organelles (MLOs), for spatiotemporal catalysis of physiochemical reactions essential for cell plasticity control. Emerging evidence and view support the notion that MLOs are built by multivalent interactions of biomolecules via phase separation and transition mechanisms. In healthy cells, dynamic chemical modifications regulate MLO plasticity, and reversible phase separation is essential for cell homeostasis. Emerging evidence revealed that aberrant phase separation results in numerous neurodegenerative disorders, cancer, and other diseases. In this review, we provide molecular underpinnings on (i) mechanistic understanding of phase separation, (ii) unifying structural and mechanistic principles that underlie this phenomenon, (iii) various mechanisms that are used by cells for the regulation of phase separation, and (iv) emerging therapeutic and other applications.
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Affiliation(s)
- Hazrat Ismail
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
| | - Xu Liu
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity Control, Atlanta, GA 30310, USA
| | - Fengrui Yang
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity Control, Atlanta, GA 30310, USA
| | - Junying Li
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei 230027, China
| | - Ayesha Zahid
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
| | - Zhen Dou
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
| | - Xing Liu
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei 230027, China
| | - Xuebiao Yao
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei 230027, China
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24
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Lu J, Qian J, Xu Z, Yin S, Zhou L, Zheng S, Zhang W. Emerging Roles of Liquid-Liquid Phase Separation in Cancer: From Protein Aggregation to Immune-Associated Signaling. Front Cell Dev Biol 2021; 9:631486. [PMID: 34235141 PMCID: PMC8255971 DOI: 10.3389/fcell.2021.631486] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/14/2021] [Indexed: 12/12/2022] Open
Abstract
Liquid-liquid Phase Separation (LLPS) of proteins and nucleic acids has emerged as a new paradigm in the study of cellular activities. It drives the formation of liquid-like condensates containing biomolecules in the absence of membrane structures in living cells. In addition, typical membrane-less condensates such as nuclear speckles, stress granules and cell signaling clusters play important roles in various cellular activities, including regulation of transcription, cellular stress response and signal transduction. Previous studies highlighted the biophysical and biochemical principles underlying the formation of these liquid condensates. The studies also showed how these principles determine the molecular properties, LLPS behavior, and composition of liquid condensates. While the basic rules driving LLPS are continuously being uncovered, their function in cellular activities is still unclear, especially within a pathological context. Therefore, the present review summarizes the recent progress made on the existing roles of LLPS in cancer, including cancer-related signaling pathways, transcription regulation and maintenance of genome stability. Additionally, the review briefly introduces the basic rules of LLPS, and cellular signaling that potentially plays a role in cancer, including pathways relevant to immune responses and autophagy.
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Affiliation(s)
- Jiahua Lu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences, Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China
| | - Junjie Qian
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences, Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China.,Organ Transplantation Institute, Zhejiang University, Hangzhou, China
| | - Zhentian Xu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences, Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China
| | - Shengyong Yin
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences, Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China.,Organ Transplantation Institute, Zhejiang University, Hangzhou, China
| | - Lin Zhou
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences, Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China.,Organ Transplantation Institute, Zhejiang University, Hangzhou, China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences, Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China.,Organ Transplantation Institute, Zhejiang University, Hangzhou, China.,Shulan (Hangzhou) Hospital Affiliated to Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Wu Zhang
- Organ Transplantation Institute, Zhejiang University, Hangzhou, China.,Shulan (Hangzhou) Hospital Affiliated to Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
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25
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Kar FM, Hochwagen A. Phospho-Regulation of Meiotic Prophase. Front Cell Dev Biol 2021; 9:667073. [PMID: 33928091 PMCID: PMC8076904 DOI: 10.3389/fcell.2021.667073] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
Germ cells undergoing meiosis rely on an intricate network of surveillance mechanisms that govern the production of euploid gametes for successful sexual reproduction. These surveillance mechanisms are particularly crucial during meiotic prophase, when cells execute a highly orchestrated program of chromosome morphogenesis and recombination, which must be integrated with the meiotic cell division machinery to ensure the safe execution of meiosis. Dynamic protein phosphorylation, controlled by kinases and phosphatases, has emerged as one of the main signaling routes for providing readout and regulation of chromosomal and cellular behavior throughout meiotic prophase. In this review, we discuss common principles and provide detailed examples of how these phosphorylation events are employed to ensure faithful passage of chromosomes from one generation to the next.
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Affiliation(s)
- Funda M Kar
- Department of Biology, New York University, New York, NY, United States
| | - Andreas Hochwagen
- Department of Biology, New York University, New York, NY, United States
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26
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Abstract
Retrotransposons provide both threats and evolutionary opportunities for their hosts. In this issue of Developmental Cell, Laureau et al. describe a fascinating host-retrotransposon relationship that may lead to retrotransposon domestication: Ty3/Gypsy exploit meiosis networks to sustain their transcription, while the host deploys RNA-binding proteins to prevent their translation.
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27
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Noda NN, Wang Z, Zhang H. Liquid-liquid phase separation in autophagy. J Cell Biol 2021; 219:151909. [PMID: 32603410 PMCID: PMC7401820 DOI: 10.1083/jcb.202004062] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 01/05/2023] Open
Abstract
Liquid–liquid phase separation (LLPS) compartmentalizes and concentrates biomacromolecules into distinct condensates. Liquid-like condensates can transition into gel and solid states, which are essential for fulfilling their different functions. LLPS plays important roles in multiple steps of autophagy, mediating the assembly of autophagosome formation sites, acting as an unconventional modulator of TORC1-mediated autophagy regulation, and triaging protein cargos for degradation. Gel-like, but not solid, protein condensates can trigger formation of surrounding autophagosomal membranes. Stress and pathological conditions cause aberrant phase separation and transition of condensates, which can evade surveillance by the autophagy machinery. Understanding the mechanisms underlying phase separation and transition will provide potential therapeutic targets for protein aggregation diseases.
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Affiliation(s)
- Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
| | - Zheng Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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28
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Matiiv AB, Trubitsina NP, Matveenko AG, Barbitoff YA, Zhouravleva GA, Bondarev SA. Amyloid and Amyloid-Like Aggregates: Diversity and the Term Crisis. BIOCHEMISTRY (MOSCOW) 2021; 85:1011-1034. [PMID: 33050849 DOI: 10.1134/s0006297920090035] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Active accumulation of the data on new amyloids continuing nowadays dissolves boundaries of the term "amyloid". Currently, it is most often used to designate aggregates with cross-β structure. At the same time, amyloids also exhibit a number of other unusual properties, such as: detergent and protease resistance, interaction with specific dyes, and ability to induce transition of some proteins from a soluble form to an aggregated one. The same features have been also demonstrated for the aggregates lacking cross-β structure, which are commonly called "amyloid-like" and combined into one group, although they are very diverse. We have collected and systematized information on the properties of more than two hundred known amyloids and amyloid-like proteins with emphasis on conflicting examples. In particular, a number of proteins in membraneless organelles form aggregates with cross-β structure that are morphologically indistinguishable from the other amyloids, but they can be dissolved in the presence of detergents, which is not typical for amyloids. Such paradoxes signify the need to clarify the existing definition of the term amyloid. On the other hand, the demonstrated structural diversity of the amyloid-like aggregates shows the necessity of their classification.
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Affiliation(s)
- A B Matiiv
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - N P Trubitsina
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - A G Matveenko
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Y A Barbitoff
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia.,Bioinformatics Institute, St. Petersburg, 197342, Russia
| | - G A Zhouravleva
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - S A Bondarev
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia. .,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
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29
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Zhou X, Li W, Liu Y, Amon A. Cross-compartment signal propagation in the mitotic exit network. eLife 2021; 10:e63645. [PMID: 33481703 PMCID: PMC7822594 DOI: 10.7554/elife.63645] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/06/2021] [Indexed: 12/26/2022] Open
Abstract
In budding yeast, the mitotic exit network (MEN), a GTPase signaling cascade, integrates spatial and temporal cues to promote exit from mitosis. This signal integration requires transmission of a signal generated on the cytoplasmic face of spindle pole bodies (SPBs; yeast equivalent of centrosomes) to the nucleolus, where the MEN effector protein Cdc14 resides. Here, we show that the MEN activating signal at SPBs is relayed to Cdc14 in the nucleolus through the dynamic localization of its terminal kinase complex Dbf2-Mob1. Cdc15, the protein kinase that activates Dbf2-Mob1 at SPBs, also regulates its nuclear access. Once in the nucleus, priming phosphorylation of Cfi1/Net1, the nucleolar anchor of Cdc14, by the Polo-like kinase Cdc5 targets Dbf2-Mob1 to the nucleolus. Nucleolar Dbf2-Mob1 then phosphorylates Cfi1/Net1 and Cdc14, activating Cdc14. The kinase-primed transmission of the MEN signal from the cytoplasm to the nucleolus exemplifies how signaling cascades can bridge distant inputs and responses.
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Affiliation(s)
- Xiaoxue Zhou
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Wenxue Li
- Yale Cancer Biology Institute, Department of Pharmacology, Yale UniversityWest HavenUnited States
| | - Yansheng Liu
- Yale Cancer Biology Institute, Department of Pharmacology, Yale UniversityWest HavenUnited States
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States
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30
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Durant M, Roesner JM, Mucelli X, Slubowski CJ, Klee E, Seitz BC, Wallis Z, Huang LS. The Smk1 MAPK and Its Activator, Ssp2, Are Required for Late Prospore Membrane Development in Sporulating Saccharomyces cerevisiae. J Fungi (Basel) 2021; 7:jof7010053. [PMID: 33466572 PMCID: PMC7828665 DOI: 10.3390/jof7010053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/29/2020] [Accepted: 01/09/2021] [Indexed: 11/16/2022] Open
Abstract
During sporulation in the budding yeast Saccharomyces cerevisiae, proper development of the prospore membrane is necessary for the formation of viable spores. The prospore membrane will eventually become the plasma membrane of the newly formed haploid spore and also serves as the template for the deposition of the spore wall. The prospore membrane is generated de novo during meiosis II and the growing edge of the prospore membrane is associated with the Leading Edge Protein (LEP) complex. We find that the Smk1 MAP kinase, along with its activator Ssp2, transiently localizes with the LEP during late meiosis II. SSP2 is required for the leading edge localization of Smk1; this localization is independent of the activation state of Smk1. Like other LEP components, the localization of Smk1 at the leading edge also depends on Ady3. Although prospore membrane development begins normally in smk1 and ssp2 mutants, late prospore membrane formation is disrupted, with the formation of ectopic membrane compartments. Thus, MAP kinase signaling plays an important role in the formation of the prospore membrane.
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31
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Abstract
Most RNA-binding modules are small and bind few nucleotides. RNA-binding proteins typically attain the physiological specificity and affinity for their RNA targets by combining several RNA-binding modules. Here, we review how disordered linkers connecting RNA-binding modules govern the specificity and affinity of RNA-protein interactions by regulating the effective concentration of these modules and their relative orientation. RNA-binding proteins also often contain extended intrinsically disordered regions that mediate protein-protein and RNA-protein interactions with multiple partners. We discuss how these regions can connect proteins and RNA resulting in heterogeneous higher-order assemblies such as membrane-less compartments and amyloid-like structures that have the characteristics of multi-modular entities. The assembled state generates additional RNA-binding specificity and affinity properties that contribute to further the function of RNA-binding proteins within the cellular environment.
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Affiliation(s)
- Diana S M Ottoz
- Department of Genetics and Development, Columbia University Irving Medical Center New York, NY 10032, USA
| | - Luke E Berchowitz
- Department of Genetics and Development, Columbia University Irving Medical Center New York, NY 10032, USA.,Taub Institute for Research on Alzheimer's and the Aging Brain, Columbia University Irving Medical Center New York, NY 10032, USA
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32
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Laureau R, Dyatel A, Dursuk G, Brown S, Adeoye H, Yue JX, De Chiara M, Harris A, Ünal E, Liti G, Adams IR, Berchowitz LE. Meiotic Cells Counteract Programmed Retrotransposon Activation via RNA-Binding Translational Repressor Assemblies. Dev Cell 2020; 56:22-35.e7. [PMID: 33278343 DOI: 10.1016/j.devcel.2020.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/25/2020] [Accepted: 11/06/2020] [Indexed: 12/14/2022]
Abstract
Retrotransposon proliferation poses a threat to germline integrity. While retrotransposons must be activated in developing germ cells in order to survive and propagate, how they are selectively activated in the context of meiosis is unclear. We demonstrate that the transcriptional activation of Ty3/Gypsy retrotransposons and host defense are controlled by master meiotic regulators. We show that budding yeast Ty3/Gypsy co-opts binding sites of the essential meiotic transcription factor Ndt80 upstream of the integration site, thereby tightly linking its transcriptional activation to meiotic progression. We also elucidate how yeast cells thwart Ty3/Gypsy proliferation by blocking translation of the retrotransposon mRNA using amyloid-like assemblies of the RNA-binding protein Rim4. In mammals, several inactive Ty3/Gypsy elements are undergoing domestication. We show that mammals utilize equivalent master meiotic regulators (Stra8, Mybl1, Dazl) to regulate Ty3/Gypsy-derived genes in developing gametes. Our findings inform how genes that are evolving from retrotransposons can build upon existing regulatory networks during domestication.
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Affiliation(s)
- Raphaelle Laureau
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Annie Dyatel
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Gizem Dursuk
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Samantha Brown
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hannah Adeoye
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jia-Xing Yue
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice 06107, France
| | | | - Anthony Harris
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice 06107, France
| | - Ian R Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Luke E Berchowitz
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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33
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Gnügge R, Symington LS. Efficient DNA double-strand break formation at single or multiple defined sites in the Saccharomyces cerevisiae genome. Nucleic Acids Res 2020; 48:e115. [PMID: 33053188 PMCID: PMC7672422 DOI: 10.1093/nar/gkaa833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 08/18/2020] [Accepted: 09/28/2020] [Indexed: 01/08/2023] Open
Abstract
DNA double-strand breaks (DSBs) are common genome lesions that threaten genome stability and cell survival. Cells use sophisticated repair machineries to detect and heal DSBs. To study DSB repair pathways and associated factors, inducible site-specific endonucleases have proven to be fundamental tools. In Saccharomyces cerevisiae, galactose-inducible rare-cutting endonucleases are commonly used to create a single DSB at a unique cleavage site. Galactose induction requires cell cultivation in suboptimal growth media, which is tedious especially when working with slow growing DSB repair mutants. Moreover, endonucleases that simultaneously create DSBs in multiple defined and unique loci of the yeast genome are not available, hindering studies of DSB repair in different genomic regions and chromatin contexts. Here, we present new tools to overcome these limitations. We employ a heterologous media-independent induction system to express the yeast HO endonuclease or bacterial restriction enzymes for single or multiple DSB formation, respectively. The systems facilitate tightly controlled and efficient DSB formation at defined genomic sites and will be valuable tools to study DSB repair at a local and genome-wide scale.
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Affiliation(s)
- Robert Gnügge
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.,Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
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34
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Rekstina VV, Sabirzyanova TA, Sabirzyanov FA, Adzhubei AA, Tkachev YV, Kudryashova IB, Snalina NE, Bykova AA, Alessenko AV, Ziganshin RH, Kuznetsov SA, Kalebina TS. The Post-Translational Modifications, Localization, and Mode of Attachment of Non-Covalently Bound Glucanosyltransglycosylases of Yeast Cell Wall as a Key to Understanding their Functioning. Int J Mol Sci 2020; 21:ijms21218304. [PMID: 33167499 PMCID: PMC7663962 DOI: 10.3390/ijms21218304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 01/27/2023] Open
Abstract
Glucan linked to proteins is a natural mega-glycoconjugate (mGC) playing the central role as a structural component of a yeast cell wall (CW). Regulation of functioning of non-covalently bound glucanosyltransglycosylases (ncGTGs) that have to remodel mGC to provide CW extension is poorly understood. We demonstrate that the main ncGTGs Bgl2 and Scw4 have phosphorylated and glutathionylated residues and are represented in CW as different pools of molecules having various firmness of attachment. Identified pools contain Bgl2 molecules with unmodified peptides, but differ from each other in the presence and combination of modified ones, as well as in the presence or absence of other CW proteins. Correlation of Bgl2 distribution among pools and its N-glycosylation was not found. Glutathione affects Bgl2 conformation, probably resulting in the mode of its attachment and enzymatic activity. Bgl2 from the pool of unmodified and monophosphorylated molecules demonstrates the ability to fibrillate after isolation from CW. Revealing of Bgl2 microcompartments and their mosaic arrangement summarized with the results obtained give the evidence that the functioning of ncGTGs in CW can be controlled by reversible post-translational modifications and facilitated due to their compact localization. The hypothetical scheme of distribution of Bgl2 inside CW is represented.
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Affiliation(s)
- Valentina V. Rekstina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Tatyana A. Sabirzyanova
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Fanis A. Sabirzyanov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Alexei A. Adzhubei
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (A.A.A.); (Y.V.T.)
| | - Yaroslav V. Tkachev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (A.A.A.); (Y.V.T.)
| | - Irina B. Kudryashova
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Natalia E. Snalina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia; (N.E.S.); (A.V.A.)
| | - Anastasia A. Bykova
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Alice V. Alessenko
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia; (N.E.S.); (A.V.A.)
| | - Rustam H. Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia;
| | - Sergei A. Kuznetsov
- Institute of Biological Sciences, University of Rostock, 18059 Rostock, Germany;
| | - Tatyana S. Kalebina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
- Correspondence: ; Tel.: +7-(495)-939-50-75
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35
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Levkovich SA, Gazit E, Laor Bar-Yosef D. Two Decades of Studying Functional Amyloids in Microorganisms. Trends Microbiol 2020; 29:251-265. [PMID: 33041179 DOI: 10.1016/j.tim.2020.09.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/19/2020] [Accepted: 09/07/2020] [Indexed: 12/22/2022]
Abstract
In the past two decades, amyloids, typically associated with human diseases, have been described to play various functional roles in nearly all life forms. The structural and functional diversity of microbial 'functional amyloids' has dramatically increased in recent years, expanding the canonical definition of these assembled molecules. Here, we provide a broad review of the current understanding of microbial functional amyloids and their diverse roles, putting the spotlight on recent discoveries in the field. We discuss their functions as structural scaffolds, surface-tension modulators, adhesion molecules, cell-cycle and gametogenesis regulators, toxins, and mediators of host-pathogen interactions. We outline how noncanonical amyloid morphologies and sophisticated regulatory mechanisms underlie their functional diversity and emphasize their therapeutic and biotechnological implications and applications.
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Affiliation(s)
- Shon A Levkovich
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ehud Gazit
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; BLAVATNIK CENTER for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel; Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel; Sagol Interdisciplinary School of Neurosciences, Tel Aviv University, Tel Aviv, Israel.
| | - Dana Laor Bar-Yosef
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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36
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Yamamoto S, Kitagawa D. Emerging insights into symmetry breaking in centriole duplication: updated view on centriole duplication theory. Curr Opin Struct Biol 2020; 66:8-14. [PMID: 32956908 DOI: 10.1016/j.sbi.2020.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 11/15/2022]
Abstract
Centriole duplication occurs once per cell cycle. Since only a single daughter centriole is assembled adjacent to each mother centriole, symmetry around the mother centriole must be broken in the process of centriole duplication. Recent studies have established that Plk4, a master kinase for centriole duplication, can self-assemble into condensates, and have suggested that this Plk4 self-assembly is the key to symmetry breaking. Here, we present the current hypotheses for how Plk4 could break symmetry around the mother centriole via autonomous regulation. After this initial symmetry-breaking process, the ring-to-dot conversion of Plk4 around the mother centriole completes the selection of the site for procentriole formation. We also discuss how this dynamic transition contributes to the strict regulation of centriole duplication.
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Affiliation(s)
- Shohei Yamamoto
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Daiju Kitagawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo 113-0033, Japan.
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37
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Yu C, Shen B, You K, Huang Q, Shi M, Wu C, Chen Y, Zhang C, Li T. Proteome-scale analysis of phase-separated proteins in immunofluorescence images. Brief Bioinform 2020; 22:5900570. [PMID: 34020549 DOI: 10.1093/bib/bbaa187] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 12/25/2022] Open
Abstract
Phase separation is an important mechanism that mediates the spatial distribution of proteins in different cellular compartments. While phase-separated proteins share certain sequence characteristics, including intrinsically disordered regions (IDRs) and prion-like domains, such characteristics are insufficient for making accurate predictions; thus, a proteome-wide understanding of phase separation is currently lacking. Here, we define phase-separated proteomes based on the systematic analysis of immunofluorescence images of 12 073 proteins in the Human Protein Atlas. The analysis of these proteins reveals that phase-separated candidate proteins exhibit higher IDR contents, higher mean net charge and lower hydropathy and prefer to bind to RNA. Kinases and transcription factors are also enriched among these candidate proteins. Strikingly, both phase-separated kinases and phase-separated transcription factors display significantly reduced substrate specificity. Our work provides the first global view of the phase-separated proteome and suggests that the spatial proximity resulting from phase separation reduces the requirement for motif specificity and expands the repertoire of substrates. The source code and data are available at https://github.com/cheneyyu/deepphase.
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Affiliation(s)
- Chunyu Yu
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Boyan Shen
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Kaiqiang You
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Qi Huang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Minglei Shi
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; School of Medicine, Tsinghua University, Beijing, China
| | - Congying Wu
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yang Chen
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; School of Medicine, Tsinghua University, Beijing, China
| | - Chaolin Zhang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, USA
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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38
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Tsvetkov P, Eisen TJ, Heinrich SU, Brune Z, Hallacli E, Newby GA, Kayatekin C, Pincus D, Lindquist S. Persistent Activation of mRNA Translation by Transient Hsp90 Inhibition. Cell Rep 2020; 32:108001. [PMID: 32783929 PMCID: PMC10088179 DOI: 10.1016/j.celrep.2020.108001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022] Open
Abstract
The heat shock protein 90 (Hsp90) chaperone functions as a protein-folding buffer and plays a role promoting the evolution of new heritable traits. To better understand how Hsp90 can affect mRNA translation, we screen more than 1,600 factors involved in mRNA regulation for physical interactions with Hsp90 in human cells. The mRNA binding protein CPEB2 strongly binds Hsp90 via its prion domain. In a yeast model, transient inhibition of Hsp90 results in persistent activation of a CPEB translation reporter even in the absence of exogenous CPEB that persists for 30 generations after the inhibitor is removed. Ribosomal profiling reveals that some endogenous yeast mRNAs, including HAC1, show a persistent change in translation efficiency following transient Hsp90 inhibition. Thus, transient loss of Hsp90 function can promote a nongenetic inheritance of a translational state affecting specific mRNAs, introducing a mechanism by which Hsp90 can promote phenotypic variation.
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Affiliation(s)
- Peter Tsvetkov
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Timothy J Eisen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Sven U Heinrich
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Zarina Brune
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Erinc Hallacli
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Greg A Newby
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Can Kayatekin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - David Pincus
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
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39
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Releasing the Lockdown: An Emerging Role for the Ubiquitin-Proteasome System in the Breakdown of Transient Protein Inclusions. Biomolecules 2020; 10:biom10081168. [PMID: 32784966 PMCID: PMC7463783 DOI: 10.3390/biom10081168] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/06/2020] [Accepted: 08/08/2020] [Indexed: 12/20/2022] Open
Abstract
Intracellular protein inclusions are diverse cellular entities with distinct biological properties. They vary in their protein content, sequestration sites, physiological function, conditions for their generation, and turnover rates. Major distinctions have been recognized between stationary amyloids and dynamic, misfolded protein deposits. The former being a dead end for irreversibly misfolded proteins, hence, cleared predominantly by autophagy, while the latter consists of a protein-quality control mechanism, important for cell endurance, where proteins are sequestered during proteotoxic stress and resolved upon its relief. Accordingly, the disaggregation of transient inclusions is a regulated process consisting of protein solubilization, followed by a triage step to either refolding or to ubiquitin-mediated degradation. Recent studies have demonstrated an indispensable role in disaggregation for components of the chaperone and the ubiquitin-proteasome systems. These include heat-shock chaperones of the 40/70/100 kDa families, the proteasome, proteasome substrate shuttling factors, and deubiquitylating enzymes. Thus, a functional link has been established between the chaperone machinery that extracts proteins from transient deposits and 26S proteasome-dependent disaggregation, indicative of a coordinated process. In this review, we discuss data emanating from these important studies and subsequently consolidate the information in the form of a working model for the disaggregation mechanism.
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40
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Isc10, an Inhibitor That Links the Anaphase-Promoting Complex to a Meiosis-Specific Mitogen-Activated Protein Kinase. Mol Cell Biol 2020; 40:MCB.00097-20. [PMID: 32423992 DOI: 10.1128/mcb.00097-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/13/2020] [Indexed: 11/20/2022] Open
Abstract
Smk1 is a meiosis-specific mitogen-activated protein kinase (MAPK) in yeast that controls spore differentiation. It is activated by a MAPK binding protein, Ssp2, upon completion of the meiotic divisions. The activation of Smk1 by Ssp2 is positively regulated by a meiosis-specific coactivator of the anaphase promoting complex (APC/C) E3 ubiquitin ligase, Ama1. Here, we identify Isc10 as an inhibitor that links APC/CAma1 to Smk1 activation. Isc10 and Smk1 form an inhibited complex during meiosis I (MI). Ssp2 is produced later in the program, and it forms a ternary complex with Isc10 and Smk1 during MII that is poised for activation. Upon completion of MII, Isc10 is ubiquitylated and degraded in an AMA1-dependent manner, thereby triggering the activation of Smk1 by Ssp2. Mutations that caused Ssp2 to be produced before MII, or isc10Δ mutations, modestly reduced the efficiency of spore differentiation whereas spores were nearly absent in the double mutant. These findings define a pathway that couples spore differentiation to the G0-like phase of the cell cycle.
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41
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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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42
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Nil Z, Hervás R, Gerbich T, Leal P, Yu Z, Saraf A, Sardiu M, Lange JJ, Yi K, Unruh J, Slaughter B, Si K. Amyloid-like Assembly Activates a Phosphatase in the Developing Drosophila Embryo. Cell 2020; 178:1403-1420.e21. [PMID: 31491385 DOI: 10.1016/j.cell.2019.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/07/2019] [Accepted: 08/08/2019] [Indexed: 12/30/2022]
Abstract
Prion-like proteins can assume distinct conformational and physical states in the same cell. Sequence analysis suggests that prion-like proteins are prevalent in various species; however, it remains unclear what functional space they occupy in multicellular organisms. Here, we report the identification of a prion-like protein, Herzog (CG5830), through a multimodal screen in Drosophila melanogaster. Herzog functions as a membrane-associated phosphatase and controls embryonic patterning, likely being involved in TGF-β/BMP and FGF/EGF signaling pathways. Remarkably, monomeric Herzog is enzymatically inactive and becomes active upon amyloid-like assembly. The prion-like domain of Herzog is necessary for both its assembly and membrane targeting. Removal of the prion-like domain impairs activity, while restoring assembly on the membrane using a heterologous prion-like domain and membrane-targeting motif can restore phosphatase activity. This study provides an example of a prion-like domain that allows an enzyme to gain essential functionality via amyloid-like assembly to control animal development.
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Affiliation(s)
- Zelha Nil
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Rubén Hervás
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Therese Gerbich
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Paulo Leal
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Zulin Yu
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Mihaela Sardiu
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Jeffrey J Lange
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Kexi Yi
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Brian Slaughter
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Kausik Si
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA.
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43
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Functional amyloids of eukaryotes: criteria, classification, and biological significance. Curr Genet 2020; 66:849-866. [DOI: 10.1007/s00294-020-01079-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 11/26/2022]
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44
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Abstract
The traditional view of protein aggregation as being strictly disease-related has been challenged by many examples of cellular aggregates that regulate beneficial biological functions. When coupled with the emerging view that many regulatory proteins undergo phase separation to form dynamic cellular compartments, it has become clear that supramolecular assembly plays wide-ranging and critical roles in cellular regulation. This presents opportunities to develop new tools to probe and illuminate this biology, and to harness the unique properties of these self-assembling systems for synthetic biology for the purposeful manipulation of biological function.
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Affiliation(s)
- Giulio Chiesa
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Szilvia Kiriakov
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA, 02215, USA. .,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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45
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Wang F, Zhang R, Feng W, Tsuchiya D, Ballew O, Li J, Denic V, Lacefield S. Autophagy of an Amyloid-like Translational Repressor Regulates Meiotic Exit. Dev Cell 2020; 52:141-151.e5. [PMID: 31991104 DOI: 10.1016/j.devcel.2019.12.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 09/26/2019] [Accepted: 12/26/2019] [Indexed: 12/30/2022]
Abstract
We explored the potential for autophagy to regulate budding yeast meiosis. Following pre-meiotic DNA replication, we blocked autophagy by chemical inhibition of Atg1 kinase or engineered degradation of Atg14 and observed homologous chromosome segregation followed by sister chromatid separation; cells then underwent additional rounds of spindle formation and disassembly without DNA re-replication, leading to aberrant chromosome segregation. Analysis of cell-cycle regulators revealed that autophagy inhibition prevents meiosis II-specific expression of Clb3 and leads to the aberrant persistence of Clb1 and Cdc5, two substrates of a meiotic ubiquitin ligase activated by Ama1. Lastly, we found that during meiosis II, autophagy degrades Rim4, an amyloid-like translational repressor whose timed clearance regulates protein production from its mRNA targets, which include CLB3 and AMA1. Strikingly, engineered Clb3 or Ama1 production restored meiotic termination in the absence of autophagy. Thus, autophagy destroys a master regulator of meiotic gene expression to enable irreversible meiotic exit.
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Affiliation(s)
- Fei Wang
- Department of Internal Medicine, Center for Autophagy Research, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Rudian Zhang
- Department of Internal Medicine, Center for Autophagy Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Wenzhi Feng
- Department of Internal Medicine, Center for Autophagy Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Dai Tsuchiya
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Olivia Ballew
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Jiajia Li
- Department of Internal Medicine, Center for Autophagy Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Vladimir Denic
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
| | - Soni Lacefield
- Department of Biology, Indiana University, Bloomington, IN, USA.
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46
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Ou J, Rosa S, Berchowitz LE, Li W. Induced pluripotent stem cells as a tool for comparative physiology: lessons from the thirteen-lined ground squirrel. J Exp Biol 2019; 222:jeb196493. [PMID: 31585999 PMCID: PMC6806009 DOI: 10.1242/jeb.196493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Comparative physiologists are often interested in adaptive physiological phenomena found in unconventional model organisms; however, research on these species is frequently constrained by the limited availability of investigative tools. Here, we propose that induced pluripotent stem cells (iPSCs) from unconventional model organisms may retain certain species-specific features that can consequently be investigated in depth in vitro; we use hibernating mammals as an example. Many species (including ground squirrels, bats and bears) can enter a prolonged state of physiological dormancy known as hibernation to survive unfavorable seasonal conditions. Our understanding of the mechanisms underpinning the rapid transition and adaptation to a hypothermic, metabolically suppressed winter torpor state remains limited partially because of the lack of an easily accessible model. To address the fascinating unanswered questions underlying hibernation biology, we have developed a powerful model system: iPSCs from a hibernating species, the thirteen-lined ground squirrel (Ictidomys tridecemlineatus). These stem cells can potentially be differentiated into any cell type, and can be used for the analysis of cell-autonomous mechanisms that facilitate adaptation to hibernation and for comparisons with non-hibernators. Furthermore, we can manipulate candidate molecular and cellular pathways underlying relevant physiological phenomena by pharmacological or RNAi-based methods, and CRISPR/Cas9 gene editing. Moreover, iPSC strategies can be applied to other species (e.g. seals, naked mole rats, humming birds) for in vitro studies on adaptation to extreme physiological conditions. In this Commentary, we discuss factors to consider when attempting to generate iPSCs from unconventional model organisms, based on our experience with the thirteen-lined ground squirrel.
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Affiliation(s)
- Jingxing Ou
- Retinal Neurophysiology Section, National Eye Institute, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah Rosa
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
- Taub Institute for Research on Alzheimer's and the Aging Brain, New York, NY 10032, USA
| | - Luke E Berchowitz
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
- Taub Institute for Research on Alzheimer's and the Aging Brain, New York, NY 10032, USA
| | - Wei Li
- Retinal Neurophysiology Section, National Eye Institute, US National Institutes of Health, Bethesda, MD 20892, USA
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47
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Cable J, Brangwynne C, Seydoux G, Cowburn D, Pappu RV, Castañeda CA, Berchowitz LE, Chen Z, Jonikas M, Dernburg A, Mittag T, Fawzi NL. Phase separation in biology and disease-a symposium report. Ann N Y Acad Sci 2019; 1452:3-11. [PMID: 31199001 DOI: 10.1111/nyas.14126] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 01/28/2023]
Abstract
Phase separation of multivalent protein and RNA molecules enables cells the formation of reversible nonstoichiometric, membraneless assemblies. These assemblies, referred to as biomolecular condensates, help with the spatial organization and compartmentalization of cellular matter. Each biomolecular condensate is defined by a distinct macromolecular composition. Distinct condensates have distinct preferential locations within cells, and they are associated with distinct biological functions, including DNA replication, RNA metabolism, signal transduction, synaptic transmission, and stress response. Several proteins found in biomolecular condensates have also been implicated in disease, including Huntington's disease, amyotrophic lateral sclerosis, and several types of cancer. Disease-associated mutations in these proteins have been found to affect the material properties of condensates as well as the driving forces for phase separation. Understanding the intrinsic and extrinsic forces driving the formation and dissolution of biomolecular condensates via spontaneous and driven phase separation is an important step in understanding the processes associated with biological regulation in health and disease.
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Affiliation(s)
| | - Clifford Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - Geraldine Seydoux
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - David Cowburn
- Departments of Biochemistry and Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York
| | - Rohit V Pappu
- Department of Biomedical Engineering, Center for Science and Engineering of Living Systems, McKelvey School of Engineering, St. Louis, Missouri
| | - Carlos A Castañeda
- Departments of Biology and Chemistry, Program in Neuroscience, Syracuse University, Syracuse, New York
| | - Luke E Berchowitz
- Departments of Genetics and Development, Columbia University, New York, New York
| | - Zhijuan Chen
- University of Texas Southwestern Medical Center, Dallas, Texas
| | - Martin Jonikas
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | - Abby Dernburg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island
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48
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Kleino A, Silverman N. Regulation of the Drosophila Imd pathway by signaling amyloids. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 108:16-23. [PMID: 30857831 PMCID: PMC6474834 DOI: 10.1016/j.ibmb.2019.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/19/2019] [Accepted: 03/05/2019] [Indexed: 05/09/2023]
Abstract
Fruit flies elicit effective defense responses against numerous microbes. The responses against Gram-negative bacteria are mediated by the Imd pathway, an evolutionarily conserved NF-κB pathway recognizing meso-diaminopimelic acid (DAP)-type peptidoglycan from bacterial cell walls. Several reviews already provide a detailed view of ligand recognition and signal transduction during Imd signaling, but the formation and regulation of the signaling complex immediately downstream of the peptidoglycan-sensing receptors is still elusive. In this review, we focus on the formation of the Imd amyloidal signaling center and post-translational modifications in the assembly and disassembly of the Imd signaling complex.
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Affiliation(s)
- Anni Kleino
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, 8000, Aarhus C, Denmark
| | - Neal Silverman
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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49
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Yamamoto S, Kitagawa D. Self-organization of Plk4 regulates symmetry breaking in centriole duplication. Nat Commun 2019; 10:1810. [PMID: 31000710 PMCID: PMC6472344 DOI: 10.1038/s41467-019-09847-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 04/01/2019] [Indexed: 01/01/2023] Open
Abstract
During centriole duplication, a single daughter centriole is formed next to the mother centriole. The molecular mechanism that determines a single duplication site remains a long-standing question. Here, we show that intrinsic self-organization of Plk4 is implicated in symmetry breaking in the process of centriole duplication. We demonstrate that Plk4 has an ability to phase-separate into condensates via an intrinsically disordered linker and that the condensation properties of Plk4 are regulated by autophosphorylation. Consistently, the dissociation dynamics of centriolar Plk4 are controlled by autophosphorylation. We further found that autophosphorylated Plk4 is already distributed as a single focus around the mother centriole before the initiation of procentriole formation, and is subsequently targeted for STIL-HsSAS6 loading. Perturbation of Plk4 self-organization affects the asymmetry of centriolar Plk4 distribution and proper centriole duplication. Overall, we propose that the spatial pattern formation of Plk4 is a determinant of a single duplication site per mother centriole.
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Affiliation(s)
- Shohei Yamamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo, 113-0033, Japan
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Hongo, Tokyo, 113-0033, Japan
| | - Daiju Kitagawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo, 113-0033, Japan.
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50
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Rencus-Lazar S, DeRowe Y, Adsi H, Gazit E, Laor D. Yeast Models for the Study of Amyloid-Associated Disorders and Development of Future Therapy. Front Mol Biosci 2019; 6:15. [PMID: 30968029 PMCID: PMC6439353 DOI: 10.3389/fmolb.2019.00015] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/01/2019] [Indexed: 12/28/2022] Open
Abstract
First described almost two decades ago, the pioneering yeast models of neurodegenerative disorders, including Alzheimer's, Parkinson's, and Huntington's diseases, have become well-established research tools, providing both basic mechanistic insights as well as a platform for the development of therapeutic agents. These maladies are associated with the formation of aggregative amyloid protein structures showing common characteristics, such as the assembly of soluble oligomeric species, binding of indicative dyes, and apoptotic cytotoxicity. The canonical yeast models have recently been expanded by the establishment of a model for type II diabetes, a non-neurological amyloid-associated disease. While these model systems require the exogenous expression of mammalian proteins in yeast, an additional amyloid-associated disease model, comprising solely mutations of endogenous yeast genes, has been recently described. Mutated in the adenine salvage pathway, this yeast model exhibits adenine accumulation, thereby recapitulating adenine inborn error of metabolism disorders. Moreover, in line with the recent extension of the amyloid hypothesis to include metabolite amyloids, in addition to protein-associated ones, the intracellular assembly of adenine amyloid-like structures has been demonstrated using this yeast model. In this review, we describe currently available yeast models of diverse amyloid-associated disorders, as well as their impact on our understanding of disease mechanisms and contribution to future potential drug development.
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Affiliation(s)
- Sigal Rencus-Lazar
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yasmin DeRowe
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hanaa Adsi
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,BLAVATNIK CENTER for Drug Discovery, Tel Aviv University, Tel Aviv, Israel.,Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Dana Laor
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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