1
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Riggs CL, Kedersha N, Amarsanaa M, Zubair SN, Ivanov P, Anderson P. UBAP2L contributes to formation of P-bodies and modulates their association with stress granules. J Cell Biol 2024; 223:e202307146. [PMID: 39007803 PMCID: PMC11248227 DOI: 10.1083/jcb.202307146] [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: 07/28/2023] [Revised: 03/06/2024] [Accepted: 06/10/2024] [Indexed: 07/16/2024] Open
Abstract
Stress triggers the formation of two distinct cytoplasmic biomolecular condensates: stress granules (SGs) and processing bodies (PBs), both of which may contribute to stress-responsive translation regulation. Though PBs can be present constitutively, stress can increase their number and size and lead to their interaction with stress-induced SGs. The mechanism of such interaction, however, is largely unknown. Formation of canonical SGs requires the RNA binding protein Ubiquitin-Associated Protein 2-Like (UBAP2L), which is a central SG node protein in the RNA-protein interaction network of SGs and PBs. UBAP2L binds to the essential SG and PB proteins G3BP and DDX6, respectively. Research on UBAP2L has mostly focused on its role in SGs, but not its connection to PBs. We find that UBAP2L is not solely an SG protein but also localizes to PBs in certain conditions, contributes to PB biogenesis and SG-PB interactions, and can nucleate hybrid granules containing SG and PB components in cells. These findings inform a new model for SG and PB formation in the context of UBAP2L's role.
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Affiliation(s)
- Claire L Riggs
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nancy Kedersha
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Misheel Amarsanaa
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Biological Sciences, Wellesley College, Wellesley, MA, USA
| | - Safiyah Noor Zubair
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Paul Anderson
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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2
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Xie Y, Shu T, Liu T, Spindler MC, Mahamid J, Hocky GM, Gresham D, Holt LJ. Polysome collapse and RNA condensation fluidize the cytoplasm. Mol Cell 2024; 84:2698-2716.e9. [PMID: 39059370 DOI: 10.1016/j.molcel.2024.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 03/25/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024]
Abstract
The cell interior is packed with macromolecules of mesoscale size, and this crowded milieu significantly influences cellular physiology. Cellular stress responses almost universally lead to inhibition of translation, resulting in polysome collapse and release of mRNA. The released mRNA molecules condense with RNA-binding proteins to form ribonucleoprotein (RNP) condensates known as processing bodies and stress granules. Here, we show that polysome collapse and condensation of RNA transiently fluidize the cytoplasm, and coarse-grained molecular dynamic simulations support this as a minimal mechanism for the observed biophysical changes. Increased mesoscale diffusivity correlates with the efficient formation of quality control bodies (Q-bodies), membraneless organelles that compartmentalize misfolded peptides during stress. Synthetic, light-induced RNA condensation also fluidizes the cytoplasm. Together, our study reveals a functional role for stress-induced translation inhibition and formation of RNP condensates in modulating the physical properties of the cytoplasm to enable efficient response of cells to stress conditions.
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Affiliation(s)
- Ying Xie
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Tong Shu
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA
| | - Tiewei Liu
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Marie-Christin Spindler
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany; Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
| | - Glen M Hocky
- Department of Chemistry and Simons Center for Computational Physical Chemistry, New York University, New York, NY, USA
| | - David Gresham
- Department of Biology, New York University, New York, NY, USA.
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA.
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3
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Shen X, Peng X, Guo Y, Dai Z, Cui L, Yu W, Liu Y, Liu CY. YAP/TAZ enhances P-body formation to promote tumorigenesis. eLife 2024; 12:RP88573. [PMID: 39046443 PMCID: PMC11268890 DOI: 10.7554/elife.88573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024] Open
Abstract
The role of processing bodies (P-bodies) in tumorigenesis and tumor progression is not well understood. Here, we showed that the oncogenes YAP/TAZ promote P-body formation in a series of cancer cell lines. Mechanistically, both transcriptional activation of the P-body-related genes SAMD4A, AJUBA, and WTIP and transcriptional suppression of the tumor suppressor gene PNRC1 are involved in enhancing the effects of YAP/TAZ on P-body formation in colorectal cancer (CRC) cells. By reexpression of PNRC1 or knockdown of P-body core genes (DDX6, DCP1A, and LSM14A), we determined that disruption of P-bodies attenuates cell proliferation, cell migration, and tumor growth induced by overexpression of YAP5SA in CRC. Analysis of a pancancer CRISPR screen database (DepMap) revealed co-dependencies between YAP/TEAD and the P-body core genes and correlations between the mRNA levels of SAMD4A, AJUBA, WTIP, PNRC1, and YAP target genes. Our study suggests that the P-body is a new downstream effector of YAP/TAZ, which implies that reexpression of PNRC1 or disruption of P-bodies is a potential therapeutic strategy for tumors with active YAP.
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Affiliation(s)
- Xia Shen
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Colorectal Cancer Research CenterShanghaiChina
| | - Xiang Peng
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Colorectal Cancer Research CenterShanghaiChina
| | - YueGui Guo
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Colorectal Cancer Research CenterShanghaiChina
| | - Zhujiang Dai
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Colorectal Cancer Research CenterShanghaiChina
| | - Long Cui
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Colorectal Cancer Research CenterShanghaiChina
| | - Wei Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan UniversityShanghaiChina
| | - Yun Liu
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Colorectal Cancer Research CenterShanghaiChina
| | - Chen-Ying Liu
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Colorectal Cancer Research CenterShanghaiChina
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4
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Rajan AAN, Hutchins EJ. Post-transcriptional regulation as a conserved driver of neural crest and cancer-cell migration. Curr Opin Cell Biol 2024; 89:102400. [PMID: 39032482 DOI: 10.1016/j.ceb.2024.102400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/26/2024] [Accepted: 06/26/2024] [Indexed: 07/23/2024]
Abstract
Cells have evolved mechanisms to migrate for diverse biological functions. A process frequently deployed during metazoan cell migration is the epithelial-mesenchymal transition (EMT). During EMT, adherent epithelial cells undergo coordinated cellular transitions to mesenchymalize and reduce their intercellular attachments. This is achieved via tightly regulated changes in gene expression, which modulates cell-cell and cell-matrix adhesion to allow movement. The acquisition of motility and invasive properties following EMT allows some mesenchymal cells to migrate through complex environments to form tissues during embryogenesis; however, these processes may also be leveraged by cancer cells, which often co-opt these endogenous programs to metastasize. Post-transcriptional regulation is now emerging as a major conserved mechanism by which cells modulate EMT and migration, which we discuss here in the context of vertebrate development and cancer.
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Affiliation(s)
- Arvind Arul Nambi Rajan
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Erica J Hutchins
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
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5
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Huang Y, Xia P. Biomolecular condensates in plant cells: mediating and integrating environmental signals and development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 347:112178. [PMID: 38971467 DOI: 10.1016/j.plantsci.2024.112178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/23/2024] [Accepted: 06/30/2024] [Indexed: 07/08/2024]
Abstract
In response to the spatiotemporal coordination of various biochemical reactions and membrane-encapsulated organelles, plants appear to provide another effective mechanism for cellular organization by phase separation that allows the internal compartmentalization of cells to form a variety of membrane-less organelles. Most of the research on phase separation has centralized in various non-plant systems, such as yeast and animal systems. Recent studies have shown a remarkable correlation between the formation of condensates in plant systems and the formation of condensates in these systems. Moreover, the last decade has made new advances in phase separation research in the context of plant biology. Here, we provide an overview of the physicochemical forces and molecular factors that drive liquid-liquid phase separation in plant cells and the biochemical characterization of condensates. We then explore new developments in phase separation research specific to plants, discussing examples of condensates found in green plants and detailing their role in plant growth and development. We propose that phase separation may be a conserved organizational mechanism in plant evolution to help plants respond rapidly and effectively to various environmental stresses as sessile organisms.
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Affiliation(s)
- Yang Huang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Pengguo Xia
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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6
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Taeb S, Rostamzadeh D, Amini SM, Rahmati M, Eftekhari M, Safari A, Najafi M. MicroRNAs targeted mTOR as therapeutic agents to improve radiotherapy outcome. Cancer Cell Int 2024; 24:233. [PMID: 38965615 PMCID: PMC11229485 DOI: 10.1186/s12935-024-03420-3] [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: 11/03/2023] [Accepted: 06/22/2024] [Indexed: 07/06/2024] Open
Abstract
MicroRNAs (miRNAs) are small RNA molecules that regulate genes and are involved in various biological processes, including cancer development. Researchers have been exploring the potential of miRNAs as therapeutic agents in cancer treatment. Specifically, targeting the mammalian target of the rapamycin (mTOR) pathway with miRNAs has shown promise in improving the effectiveness of radiotherapy (RT), a common cancer treatment. This review provides an overview of the current understanding of miRNAs targeting mTOR as therapeutic agents to enhance RT outcomes in cancer patients. It emphasizes the importance of understanding the specific miRNAs that target mTOR and their impact on radiosensitivity for personalized cancer treatment approaches. The review also discusses the role of mTOR in cell homeostasis, cell proliferation, and immune response, as well as its association with oncogenesis. It highlights the different ways in which miRNAs can potentially affect the mTOR pathway and their implications in immune-related diseases. Preclinical findings suggest that combining mTOR modulators with RT can inhibit tumor growth through anti-angiogenic and anti-vascular effects, but further research and clinical trials are needed to validate the efficacy and safety of using miRNAs targeting mTOR as therapeutic agents in combination with RT. Overall, this review provides a comprehensive understanding of the potential of miRNAs targeting mTOR to enhance RT efficacy in cancer treatment and emphasizes the need for further research to translate these findings into improved clinical outcomes.
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Affiliation(s)
- Shahram Taeb
- Department of Radiology, School of Paramedical Sciences, Guilan University of Medical Sciences, Rasht, Iran
| | - Davoud Rostamzadeh
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Seyed Mohammad Amini
- Radiation Biology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Rahmati
- Department of Medical Biotechnology, Faculty of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Mohammad Eftekhari
- Department of Medical Biotechnology, Faculty of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Arash Safari
- Department of Radiology, Ionizing and Non-Ionizing Radiation Protection Research Center (INIRPRC), School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, 71439-14693, Iran
| | - Masoud Najafi
- Radiology and Nuclear Medicine Department, School of Paramedical Sciences, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Medical Biology Research Center, Institute of Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Medical Technology Research Center, Institute of Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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7
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Wang JY, Liu YJ, Zhang XL, Liu YH, Jiang LL, Hu HY. PolyQ-expanded ataxin-2 aggregation impairs cellular processing-body homeostasis via sequestering the RNA helicase DDX6. J Biol Chem 2024; 300:107413. [PMID: 38810698 PMCID: PMC11254730 DOI: 10.1016/j.jbc.2024.107413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/02/2024] [Accepted: 04/10/2024] [Indexed: 05/31/2024] Open
Abstract
Ataxin-2 (Atx2) is a polyglutamine (polyQ) tract-containing RNA-binding protein, while its polyQ expansion may cause protein aggregation that is implicated in the pathogenesis of neurodegenerative diseases such as spinocerebellar ataxia type 2 (SCA2). However, the molecular mechanism underlying how Atx2 aggregation contributes to the proteinopathies remains elusive. Here, we investigated the influence of Atx2 aggregation on the assembly and functionality of cellular processing bodies (P-bodies) by using biochemical and fluorescence imaging approaches. We have revealed that polyQ-expanded (PQE) Atx2 sequesters the DEAD-box RNA helicase (DDX6), an essential component of P-bodies, into aggregates or puncta via some RNA sequences. The N-terminal like-Sm (LSm) domain of Atx2 (residues 82-184) and the C-terminal helicase domain of DDX6 are responsible for the interaction and specific sequestration. Moreover, sequestration of DDX6 may aggravate pre-mRNA mis-splicing, and interfere with the assembly of cellular P-bodies, releasing the endoribonuclease MARF1 that promotes mRNA decay and translational repression. Rescuing the DDX6 protein level can recover the assembly and functionality of P-bodies, preventing targeted mRNA from degradation. This study provides a line of evidence for sequestration of the P-body components and impairment of the P-body homeostasis in dysregulating RNA metabolism, which is implicated in the disease pathologies and a potential therapeutic target.
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Affiliation(s)
- Jian-Yang Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Ya-Jun Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Xiang-Le Zhang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Yin-Hu Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Lei-Lei Jiang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, PR China
| | - Hong-Yu Hu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, PR China.
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8
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Rathnayaka-Mudiyanselage IW, Nandana V, Schrader JM. Proteomic composition of eukaryotic and bacterial RNA decay condensates suggests convergent evolution. Curr Opin Microbiol 2024; 79:102467. [PMID: 38569418 PMCID: PMC11162941 DOI: 10.1016/j.mib.2024.102467] [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: 12/19/2023] [Revised: 02/21/2024] [Accepted: 03/12/2024] [Indexed: 04/05/2024]
Abstract
Bacterial cells have a unique challenge to organize their cytoplasm without the use of membrane-bound organelles. Biomolecular condensates (henceforth BMCs) are a class of nonmembrane-bound organelles, which, through the physical process of phase separation, can form liquid-like droplets with proteins/nucleic acids. BMCs have been broadly characterized in eukaryotic cells, and BMCs have been recently identified in bacteria, with the first and best studied example being bacterial ribonucleoprotein bodies (BR-bodies). BR-bodies contain the RNA decay machinery and show functional parallels to eukaryotic P-bodies (PBs) and stress granules (SGs). Due to the finding that mRNA decay machinery is compartmentalized in BR-bodies and in eukaryotic PBs/SGs, we will explore the functional similarities in the proteins, which are known to enrich in these structures based on recent proteomic studies. Interestingly, despite the use of different mRNA decay and post-transcriptional regulatory machinery, this analysis has revealed evolutionary convergence in the classes of enriched enzymes in these structures.
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Affiliation(s)
- I W Rathnayaka-Mudiyanselage
- Wayne State University, Department of Biological Sciences, Detroit, MI, USA; Wayne State University, Department of Chemistry, Detroit, MI, USA
| | - V Nandana
- Wayne State University, Department of Biological Sciences, Detroit, MI, USA
| | - J M Schrader
- Wayne State University, Department of Biological Sciences, Detroit, MI, USA.
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9
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Murai T. Transmembrane signaling through single-spanning receptors modulated by phase separation at the cell surface. Eur J Cell Biol 2024; 103:151413. [PMID: 38631097 DOI: 10.1016/j.ejcb.2024.151413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024] Open
Abstract
A wide variety of transmembrane signals are transduced by cell-surface receptors that activate intracellular signaling molecules. In particular, receptor clustering in the plasma membrane plays a critical role in these processes. Single-spanning or single-pass transmembrane proteins are among the most significant types of membrane receptors, which include adhesion receptors, such as integrins, CD44, cadherins, and receptor tyrosine kinases. Elucidating the molecular mechanisms underlying the regulation of the activity of these receptors is of great significance. Liquid-liquid phase separation (LLPS) is a recently emerging paradigm in cellular physiology for the ubiquitous regulation of the spatiotemporal dynamics of various signaling pathways. This study describes the emerging features of transmembrane signaling through single-spanning receptors from the perspective of phase separation. Possible physicochemical modulations of LLPS-based transmembrane signaling are also discussed.
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Affiliation(s)
- Toshiyuki Murai
- Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan.
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10
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Bonsor M, Ammar O, Schnoegl S, Wanker EE, Silva Ramos E. Polyglutamine disease proteins: Commonalities and differences in interaction profiles and pathological effects. Proteomics 2024; 24:e2300114. [PMID: 38615323 DOI: 10.1002/pmic.202300114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/16/2024]
Abstract
Currently, nine polyglutamine (polyQ) expansion diseases are known. They include spinocerebellar ataxias (SCA1, 2, 3, 6, 7, 17), spinal and bulbar muscular atrophy (SBMA), dentatorubral-pallidoluysian atrophy (DRPLA), and Huntington's disease (HD). At the root of these neurodegenerative diseases are trinucleotide repeat mutations in coding regions of different genes, which lead to the production of proteins with elongated polyQ tracts. While the causative proteins differ in structure and molecular mass, the expanded polyQ domains drive pathogenesis in all these diseases. PolyQ tracts mediate the association of proteins leading to the formation of protein complexes involved in gene expression regulation, RNA processing, membrane trafficking, and signal transduction. In this review, we discuss commonalities and differences among the nine polyQ proteins focusing on their structure and function as well as the pathological features of the respective diseases. We present insights from AlphaFold-predicted structural models and discuss the biological roles of polyQ-containing proteins. Lastly, we explore reported protein-protein interaction networks to highlight shared protein interactions and their potential relevance in disease development.
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Affiliation(s)
- Megan Bonsor
- Department of Neuroproteomics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Orchid Ammar
- Department of Neuroproteomics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Sigrid Schnoegl
- Department of Neuroproteomics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Erich E Wanker
- Department of Neuroproteomics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Eduardo Silva Ramos
- Department of Neuroproteomics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
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11
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Firdous Z, Kalra S, Chattopadhyay R, Bari VK. Current insight into the role of mRNA decay pathways in fungal pathogenesis. Microbiol Res 2024; 283:127671. [PMID: 38479232 DOI: 10.1016/j.micres.2024.127671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 04/17/2024]
Abstract
Pathogenic fungal species can cause superficial and mucosal infections, to potentially fatal systemic or invasive infections in humans. These infections are more common in immunocompromised or critically ill patients and have a significant morbidity and fatality rate. Fungal pathogens utilize several strategies to adapt the host environment resulting in efficient and comprehensive alterations in their cellular metabolism. Fungal virulence is regulated by several factors and post-transcriptional regulation mechanisms involving mRNA molecules are one of them. Post-transcriptional controls have emerged as critical regulatory mechanisms involved in the pathogenesis of fungal species. The untranslated upstream and downstream regions of the mRNA, as well as RNA-binding proteins, regulate morphogenesis and virulence by controlling mRNA degradation and stability. The limited number of available therapeutic drugs, the emergence of multidrug resistance, and high death rates associated with systemic fungal illnesses pose a serious risk to human health. Therefore, new antifungal treatments that specifically target mRNA pathway components can decrease fungal pathogenicity and when combined increase the effectiveness of currently available antifungal drugs. This review summarizes the mRNA degradation pathways and their role in fungal pathogenesis.
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Affiliation(s)
- Zulikha Firdous
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Sapna Kalra
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Rituja Chattopadhyay
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Vinay Kumar Bari
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India.
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12
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Paul S, Arias MA, Wen L, Liao SE, Zhang J, Wang X, Regev O, Fei J. RNA molecules display distinctive organization at nuclear speckles. iScience 2024; 27:109603. [PMID: 38638569 PMCID: PMC11024929 DOI: 10.1016/j.isci.2024.109603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/05/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024] Open
Abstract
RNA molecules often play critical roles in assisting the formation of membraneless organelles in eukaryotic cells. Yet, little is known about the organization of RNAs within membraneless organelles. Here, using super-resolution imaging and nuclear speckles as a model system, we demonstrate that different sequence domains of RNA transcripts exhibit differential spatial distributions within speckles. Specifically, we image transcripts containing a region enriched in binding motifs of serine/arginine-rich (SR) proteins and another region enriched in binding motifs of heterogeneous nuclear ribonucleoproteins (hnRNPs). We show that these transcripts localize to the outer shell of speckles, with the SR motif-rich region localizing closer to the speckle center relative to the hnRNP motif-rich region. Further, we identify that this intra-speckle RNA organization is driven by the strength of RNA-protein interactions inside and outside speckles. Our results hint at novel functional roles of nuclear speckles and likely other membraneless organelles in organizing RNA substrates for biochemical reactions.
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Affiliation(s)
- Sneha Paul
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Mauricio A. Arias
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
- Institute for System Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Li Wen
- Department of Physics, The University of Chicago, Chicago, IL 60637, USA
| | - Susan E. Liao
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | - Jiacheng Zhang
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Xiaoshu Wang
- The College, The University of Chicago, Chicago, IL 60637, USA
| | - Oded Regev
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
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13
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Li J, Zhang Y, Gu J, Zhou Y, Liu J, Cui H, Zhao T, Jin Z. Stress Granule Core Protein-Derived Peptides Inhibit Assembly of Stress Granules and Improve Sorafenib Sensitivity in Cancer Cells. Molecules 2024; 29:2134. [PMID: 38731625 PMCID: PMC11085366 DOI: 10.3390/molecules29092134] [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: 03/14/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024] Open
Abstract
Upon a variety of environmental stresses, eukaryotic cells usually recruit translational stalled mRNAs and RNA-binding proteins to form cytoplasmic condensates known as stress granules (SGs), which minimize stress-induced damage and promote stress adaptation and cell survival. SGs are hijacked by cancer cells to promote cell survival and are consequently involved in the development of anticancer drug resistance. However, the design and application of chemical compounds targeting SGs to improve anticancer drug efficacy have rarely been studied. Here, we developed two types of SG inhibitory peptides (SIPs) derived from SG core proteins Caprin1 and USP10 and fused with cell-penetrating peptides to generate TAT-SIP-C1/2 and SIP-U1-Antp, respectively. We obtained 11 SG-inducing anticancer compounds from cell-based screens and explored the potential application of SIPs in overcoming resistance to the SG-inducing anticancer drug sorafenib. We found that SIPs increased the sensitivity of HeLa cells to sorafenib via the disruption of SGs. Therefore, anticancer drugs which are competent to induce SGs could be combined with SIPs to sensitize cancer cells, which might provide a novel therapeutic strategy to alleviate anticancer drug resistance.
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Affiliation(s)
- Juan Li
- College of Life Sciences, Office of Student Entrepreneurship, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
| | - Yaobin Zhang
- College of Life Sciences, Office of Student Entrepreneurship, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
| | - Jinxuan Gu
- College of Life Sciences, Office of Student Entrepreneurship, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
| | - Yulin Zhou
- College of Life Sciences, Office of Student Entrepreneurship, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
| | - Jie Liu
- College of Life Sciences, Office of Student Entrepreneurship, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
| | - Haiyan Cui
- College of Life Sciences, Office of Student Entrepreneurship, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
| | - Tiejun Zhao
- College of Life Sciences, Office of Student Entrepreneurship, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou 310015, China
| | - Zhigang Jin
- College of Life Sciences, Office of Student Entrepreneurship, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
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14
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Min H, Liang X, Wang C, Qin J, Boonhok R, Muneer A, Brashear AM, Li X, Minns AM, Adapa SR, Jiang RHY, Ning G, Cao Y, Lindner SE, Miao J, Cui L. The DEAD-box RNA helicase PfDOZI imposes opposing actions on RNA metabolism in Plasmodium falciparum. Nat Commun 2024; 15:3747. [PMID: 38702310 PMCID: PMC11068891 DOI: 10.1038/s41467-024-48140-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/19/2024] [Indexed: 05/06/2024] Open
Abstract
In malaria parasites, the regulation of mRNA translation, storage and degradation during development and life-stage transitions remains largely unknown. Here, we functionally characterized the DEAD-box RNA helicase PfDOZI in P. falciparum. Disruption of pfdozi enhanced asexual proliferation but reduced sexual commitment and impaired gametocyte development. By quantitative transcriptomics, we show that PfDOZI is involved in the regulation of invasion-related genes and sexual stage-specific genes during different developmental stages. PfDOZI predominantly participates in processing body-like mRNPs in schizonts but germ cell granule-like mRNPs in gametocytes to impose opposing actions of degradation and protection on different mRNA targets. We further show the formation of stress granule-like mRNPs during nutritional deprivation, highlighting an essential role of PfDOZI-associated mRNPs in stress response. We demonstrate that PfDOZI participates in distinct mRNPs to maintain mRNA homeostasis in response to life-stage transition and environmental changes by differentially executing post-transcriptional regulation on the target mRNAs.
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Affiliation(s)
- Hui Min
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Xiaoying Liang
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases, Department of Global Health, College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Junling Qin
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
| | - Rachasak Boonhok
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
- Department of Medical Technology, School of Allied Health Sciences, and Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat, 80160, Thailand
| | - Azhar Muneer
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
| | - Awtum M Brashear
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
| | - Xiaolian Li
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
| | - Allen M Minns
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Swamy Rakesh Adapa
- Center for Global Health and Infectious Diseases, Department of Global Health, College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases, Department of Global Health, College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Gang Ning
- Electron Microscopy Facility, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Scott E Lindner
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Jun Miao
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA.
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA.
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15
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Mir DA, Ma Z, Horrocks J, Rogers AN. Stress-induced Eukaryotic Translational Regulatory Mechanisms. ARXIV 2024:arXiv:2405.01664v1. [PMID: 38745702 PMCID: PMC11092689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The eukaryotic protein synthesis process entails intricate stages governed by diverse mechanisms to tightly regulate translation. Translational regulation during stress is pivotal for maintaining cellular homeostasis, ensuring the accurate expression of essential proteins crucial for survival. This selective translational control mechanism is integral to cellular adaptation and resilience under adverse conditions. This review manuscript explores various mechanisms involved in selective translational regulation, focusing on mRNA-specific and global regulatory processes. Key aspects of translational control include translation initiation, which is often a rate-limiting step, and involves the formation of the eIF4F complex and recruitment of mRNA to ribosomes. Regulation of translation initiation factors, such as eIF4E, eIF4E2, and eIF2, through phosphorylation and interactions with binding proteins, modulates translation efficiency under stress conditions. This review also highlights the control of translation initiation through factors like the eIF4F complex and the ternary complex and also underscores the importance of eIF2α phosphorylation in stress granule formation and cellular stress responses. Additionally, the impact of amino acid deprivation, mTOR signaling, and ribosome biogenesis on translation regulation and cellular adaptation to stress is also discussed. Understanding the intricate mechanisms of translational regulation during stress provides insights into cellular adaptation mechanisms and potential therapeutic targets for various diseases, offering valuable avenues for addressing conditions associated with dysregulated protein synthesis.
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Affiliation(s)
- Dilawar Ahmad Mir
- Kathryn W. Davis Center for Regenerative Biology and Aging, Mount Desert Island Biological Laboratory, Bar Harbor, ME
| | - Zhengxin Ma
- Kathryn W. Davis Center for Regenerative Biology and Aging, Mount Desert Island Biological Laboratory, Bar Harbor, ME
| | - Jordan Horrocks
- Kathryn W. Davis Center for Regenerative Biology and Aging, Mount Desert Island Biological Laboratory, Bar Harbor, ME
| | - Aric N Rogers
- Kathryn W. Davis Center for Regenerative Biology and Aging, Mount Desert Island Biological Laboratory, Bar Harbor, ME
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16
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Liu W, Deng J, Song S, Sethi S, Walther A. A facile DNA coacervate platform for engineering wetting, engulfment, fusion and transient behavior. Commun Chem 2024; 7:100. [PMID: 38693272 PMCID: PMC11063173 DOI: 10.1038/s42004-024-01185-4] [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: 11/02/2023] [Accepted: 04/19/2024] [Indexed: 05/03/2024] Open
Abstract
Biomolecular coacervates are emerging models to understand biological systems and important building blocks for designer applications. DNA can be used to build up programmable coacervates, but often the processes and building blocks to make those are only available to specialists. Here, we report a simple approach for the formation of dynamic, multivalency-driven coacervates using long single-stranded DNA homopolymer in combination with a series of palindromic binders to serve as a synthetic coacervate droplet. We reveal details on how the length and sequence of the multivalent binders influence coacervate formation, how to introduce switching and autonomous behavior in reaction circuits, as well as how to engineer wetting, engulfment and fusion in multi-coacervate system. Our simple-to-use model DNA coacervates enhance the understanding of coacervate dynamics, fusion, phase transition mechanisms, and wetting behavior between coacervates, forming a solid foundation for the development of innovative synthetic and programmable coacervates for fundamental studies and applications.
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Affiliation(s)
- Wei Liu
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Jie Deng
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Luoyu Road 1037, 430074, Wuhan, China
| | - Siyu Song
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Soumya Sethi
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Andreas Walther
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128, Mainz, Germany.
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17
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Ibrahim KA, Naidu AS, Miljkovic H, Radenovic A, Yang W. Label-Free Techniques for Probing Biomolecular Condensates. ACS NANO 2024; 18:10738-10757. [PMID: 38609349 DOI: 10.1021/acsnano.4c01534] [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: 04/14/2024]
Abstract
Biomolecular condensates play important roles in a wide array of fundamental biological processes, such as cellular compartmentalization, cellular regulation, and other biochemical reactions. Since their discovery and first observations, an extensive and expansive library of tools has been developed to investigate various aspects and properties, encompassing structural and compositional information, material properties, and their evolution throughout the life cycle from formation to eventual dissolution. This Review presents an overview of the expanded set of tools and methods that researchers use to probe the properties of biomolecular condensates across diverse scales of length, concentration, stiffness, and time. In particular, we review recent years' exciting development of label-free techniques and methodologies. We broadly organize the set of tools into 3 categories: (1) imaging-based techniques, such as transmitted-light microscopy (TLM) and Brillouin microscopy (BM), (2) force spectroscopy techniques, such as atomic force microscopy (AFM) and the optical tweezer (OT), and (3) microfluidic platforms and emerging technologies. We point out the tools' key opportunities, challenges, and future perspectives and analyze their correlative potential as well as compatibility with other techniques. Additionally, we review emerging techniques, namely, differential dynamic microscopy (DDM) and interferometric scattering microscopy (iSCAT), that have huge potential for future applications in studying biomolecular condensates. Finally, we highlight how some of these techniques can be translated for diagnostics and therapy purposes. We hope this Review serves as a useful guide for new researchers in this field and aids in advancing the development of new biophysical tools to study biomolecular condensates.
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18
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Yuan S, Zhou G, Xu G. Translation machinery: the basis of translational control. J Genet Genomics 2024; 51:367-378. [PMID: 37536497 DOI: 10.1016/j.jgg.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/23/2023] [Accepted: 07/23/2023] [Indexed: 08/05/2023]
Abstract
Messenger RNA (mRNA) translation consists of initiation, elongation, termination, and ribosome recycling, carried out by the translation machinery, primarily including tRNAs, ribosomes, and translation factors (TrFs). Translational regulators transduce signals of growth and development, as well as biotic and abiotic stresses, to the translation machinery, where global or selective translational control occurs to modulate mRNA translation efficiency (TrE). As the basis of translational control, the translation machinery directly determines the quality and quantity of newly synthesized peptides and, ultimately, the cellular adaption. Thus, regulating the availability of diverse machinery components is reviewed as the central strategy of translational control. We provide classical signaling pathways (e.g., integrated stress responses) and cellular behaviors (e.g., liquid-liquid phase separation) to exemplify this strategy within different physiological contexts, particularly during host-microbe interactions. With new technologies developed, further understanding this strategy will speed up translational medicine and translational agriculture.
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Affiliation(s)
- Shu Yuan
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guilong Zhou
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guoyong Xu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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19
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Cassani M, Seydoux G. P-body-like condensates in the germline. Semin Cell Dev Biol 2024; 157:24-32. [PMID: 37407370 PMCID: PMC10761593 DOI: 10.1016/j.semcdb.2023.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023]
Abstract
P-bodies are cytoplasmic condensates that accumulate low-translation mRNAs for temporary storage before translation or degradation. P-bodies have been best characterized in yeast and mammalian tissue culture cells. We describe here related condensates in the germline of animal models. Germline P-bodies have been reported at all stages of germline development from primordial germ cells to gametes. The activity of the universal germ cell fate regulator, Nanos, is linked to the mRNA decay function of P-bodies, and spatially-regulated condensation of P-body like condensates in embryos is required to localize mRNA regulators to primordial germ cells. In most cases, however, it is not known whether P-bodies represent functional compartments or non-functional condensation by-products that arise when ribonucleoprotein complexes saturate the cytoplasm. We speculate that the ubiquity of P-body-like condensates in germ cells reflects the strong reliance of the germline on cytoplasmic, rather than nuclear, mechanisms of gene regulation.
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Affiliation(s)
- Madeline Cassani
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Geraldine Seydoux
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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20
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Guo D, Xiong Y, Fu B, Sha Z, Li B, Wu H. Liquid-Liquid phase separation in bacteria. Microbiol Res 2024; 281:127627. [PMID: 38262205 DOI: 10.1016/j.micres.2024.127627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/16/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
Cells are the essential building blocks of living organisms, responsible for carrying out various biochemical reactions and performing specific functions. In eukaryotic cells, numerous membrane organelles have evolved to facilitate these processes by providing specific spatial locations. In recent years, it has also been discovered that membraneless organelles play a crucial role in the subcellular organization of bacteria, which are single-celled prokaryotic microorganisms characterized by their simple structure and small size. These membraneless organelles in bacteria have been found to undergo Liquid-Liquid phase separation (LLPS), a molecular mechanism that allows for their assembly. Through extensive research, the occurrence of LLPS and its role in the spatial organization of bacteria have been better understood. Various biomacromolecules have been identified to exhibit LLPS properties in different bacterial species. LLPS which is introduced into synthetic biology applies to bacteria has important implications, and three recent research reports have shed light on its potential applications in this field. Overall, this review investigates the molecular mechanisms of LLPS occurrence and its significance in bacteria while also considering the future prospects of implementing LLPS in synthetic biology.
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Affiliation(s)
- Dong Guo
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yan Xiong
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Beibei Fu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Zhou Sha
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Bohao Li
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Chongqing 401331, China.
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21
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Blake LA, Watkins L, Liu Y, Inoue T, Wu B. A rapid inducible RNA decay system reveals fast mRNA decay in P-bodies. Nat Commun 2024; 15:2720. [PMID: 38548718 PMCID: PMC10979015 DOI: 10.1038/s41467-024-46943-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 03/14/2024] [Indexed: 04/01/2024] Open
Abstract
RNA decay is vital for regulating mRNA abundance and gene expression. Existing technologies lack the spatiotemporal precision or transcript specificity to capture the stochastic and transient decay process. We devise a general strategy to inducibly recruit protein factors to modulate target RNA metabolism. Specifically, we introduce a Rapid Inducible Decay of RNA (RIDR) technology to degrade target mRNAs within minutes. The fast and synchronous induction enables direct visualization of mRNA decay dynamics in cells. Applying RIDR to endogenous ACTB mRNA reveals rapid formation and dissolution of RNA granules in pre-existing P-bodies. Time-resolved RNA distribution measurements demonstrate rapid RNA decay inside P-bodies, which is further supported by knocking down P-body constituent proteins. Light and oxidative stress modulate P-body behavior, potentially reconciling the contradictory literature about P-body function. This study reveals compartmentalized RNA decay kinetics, establishing RIDR as a pivotal tool for exploring the spatiotemporal RNA metabolism in cells.
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Affiliation(s)
- Lauren A Blake
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Leslie Watkins
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yang Liu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biochemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Takanari Inoue
- The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- The Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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Lu Q, Xi P, Xu S, Zhang Z, Gong B, Liu J, Zhu Q, Sun T, Zhu S, Chen R. A novel risk signature based on liquid-liquid phase separation-related genes reveals prognostic and tumour microenvironmental features in clear cell renal cell carcinoma. Aging (Albany NY) 2024; 16:6118-6134. [PMID: 38546385 PMCID: PMC11042959 DOI: 10.18632/aging.205691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/07/2024] [Indexed: 04/23/2024]
Abstract
BACKGROUND Clear cell renal cell carcinoma(ccRCC) is one of the most common malignancies. However, there are still many barriers to its underlying causes, early diagnostic techniques and therapeutic approaches. MATERIALS AND METHODS The Cancer Genome Atlas (TCGA)- Kidney renal clear cell (KIRC) cohort differentially analysed liquid-liquid phase separation (LLPS)-related genes from the DrLLPS website. Univariate and multivariate Cox regression analyses and LASSO regression analyses were used to construct prognostic models. The E-MTAB-1980 cohort was used for external validation. Then, potential functions, immune infiltration analysis, and mutational landscapes were analysed for the high-risk and low-risk groups. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) experiments as well as single-cell analyses validated the genes key to the model. RESULTS We screened 174 LLPS-related genes in ccRCC and constructed a risk signature consisting of five genes (CLIC5, MXD3, NUF2, PABPC1L, PLK1). The high-risk group was found to be associated with worse prognosis in different subgroups. A nomogram constructed by combining age and tumour stage had a strong predictive power for the prognosis of ccRCC patients. In addition, there were differences in pathway enrichment, immune cell infiltration, and mutational landscapes between the two groups. The results of qRT-PCR in renal cancer cell lines and renal cancer tissues were consistent with the biosignature prediction. Three single-cell data of GSE159115, GSE139555, and GSE121636 were analysed for differences in the presence of these five genes in different cells. CONCLUSIONS We developed a risk signature constructed based on the five LLPS-related genes and can have a high ability to predict the prognosis of ccRCC patients, further providing a strong support for clinical decision-making.
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Affiliation(s)
- Qing Lu
- Department of Urology, Fujian Medical University Union Hospital, Fuzhou 350001, Fujian, P.R. China
| | - Ping Xi
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Suling Xu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Zhicheng Zhang
- Department of Surgery, Fuzhou First People’s Hospital, Fuzhou 344000, Jiangxi, China
| | - Binbin Gong
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Ji Liu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Qiqi Zhu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Ting Sun
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Shaoxing Zhu
- Department of Urology, Fujian Medical University Union Hospital, Fuzhou 350001, Fujian, P.R. China
| | - Ru Chen
- Department of Urology, Fujian Medical University Union Hospital, Fuzhou 350001, Fujian, P.R. China
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23
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Romagnoli BAA, Lucena ACR, Freire ER, Munhoz da Rocha IF, Alves LR, Goldenberg S. TcZC3HTTP, a regulatory element that contributes to Trypanosoma cruzi cell proliferation. Microbiol Spectr 2024; 12:e0288023. [PMID: 38270449 PMCID: PMC10913370 DOI: 10.1128/spectrum.02880-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024] Open
Abstract
Post-transcriptional regulation of gene expression is a critical process for adapting to and surviving Trypanosoma cruzi, a parasite with a complex life cycle. RNA-binding proteins (RBPs) are key players in this regulation, forming ribonucleoprotein complexes (messenger ribonucleoproteins) and RNA granules that control transcript stability, localization, degradation, and translation modulation. Understanding the specific roles of individual RBPs is crucial for unraveling the details of this regulatory network. In this study, we generated null mutants of the TcZC3HTTP gene, a specific RBP in the Trypanosoma family characterized by a C3H zinc finger and a DNAJ domain associated with RNA and protein binding, respectively. Through cell growth assays, we demonstrated that the absence of TcZC3HTTP or the expression of an additional tagged version impacted epimastigote growth, indicating its contribution to cell proliferation. TcZC3HTTP was found to associate with mRNAs involved in cell cycle and division in epimastigotes, while in nutritionally stressed parasites it exhibited associations with mRNAs coding for other RBPs and rRNA. Furthermore, our analysis identified that TcZC3HTTP protein partners were different during normal growth conditions compared to starvation conditions, with the latter showing enrichment of ribosomal proteins and other RBPs. Therefore, this study provides insights into TcZC3HTTP's role in the post-transcriptional regulation of gene expression during normal growth and nutritional stress in T. cruzi, uncovering its versatile functions in different cellular contexts.IMPORTANCEUnderstanding how Trypanosoma cruzi, the causative agent of Chagas disease, regulates gene expression is crucial for developing targeted interventions. In this study, we investigated the role of TcZC3HTTP, an RNA-binding protein, in post-transcriptional regulation. Our findings demonstrate that TcZC3HTTP is relevant for the growth and proliferation of epimastigotes, a stage of the parasite's life cycle. We identified its associations with specific mRNAs involved in cell cycle and division and its interactions with enzymes and other RNA-binding proteins (RBPs) under normal and starvation conditions. These insights shed light on the regulatory network underlying gene expression in T. cruzi and reveal the multifaceted functions of RBPs in this parasite. Such knowledge enhances our understanding of the parasite's biology and opens avenues for developing novel therapeutic strategies targeting post-transcriptional gene regulation in T. cruzi.
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Affiliation(s)
| | - Aline Castro Rodrigues Lucena
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Fiocruz PR, Curitiba, Paraná, Brazil
| | - Eden Ribeiro Freire
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz PR, Curitiba, Paraná, Brazil
| | | | - Lysangela Ronalte. Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz PR, Curitiba, Paraná, Brazil
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity, CHU de Quebec Research Center, University Laval, Quebec, Canada
| | - Samuel Goldenberg
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz PR, Curitiba, Paraná, Brazil
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24
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Huai Y, Wang X, Mao W, Wang X, Zhao Y, Chu X, Huang Q, Ru K, Zhang L, Li Y, Chen Z, Qian A. HuR-positive stress granules: Potential targets for age-related osteoporosis. Aging Cell 2024; 23:e14053. [PMID: 38375951 PMCID: PMC10928564 DOI: 10.1111/acel.14053] [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: 07/17/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 02/21/2024] Open
Abstract
Aging impairs osteoblast function and bone turnover, resulting in age-related bone degeneration. Stress granules (SGs) are membrane-less organelles that assemble in response to stress via the recruitment of RNA-binding proteins (RBPs), and have emerged as a novel mechanism in age-related diseases. Here, we identified HuR as a bone-related RBP that aggregated into SGs and facilitated osteogenesis during aging. HuR-positive SG formation increased during osteoblast differentiation, and HuR overexpression mitigated the reduction in SG formation observed in senescent osteoblasts. Moreover, HuR positively regulated the mRNA stability and expression of its target β-catenin by binding and recruiting β-catenin into SGs. As a potential therapeutic target, HuR activator apigenin (API) enhanced its expression and thus aided osteoblasts differentiation. API treatment increased HuR nuclear export, enhanced the recruitment of β-catenin into HuR-positive SGs, facilitated β-catenin nuclear translocation, and contributed osteogenesis. Our findings highlight the roles of HuR and its SGs in promoting osteogenesis during skeletal aging and lay the groundwork for novel therapeutic strategies against age-related skeletal disorders.
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Affiliation(s)
- Ying Huai
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
- Department of OrthopedicsTangdu Hospital, Air Force Military Medical UniversityXi'anChina
| | - Xue Wang
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Wenjing Mao
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Xuehao Wang
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Yipu Zhao
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Xiaohua Chu
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Qian Huang
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Kang Ru
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Ling Zhang
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Yu Li
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Zhihao Chen
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
| | - Airong Qian
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health EngineeringNorthwestern Polytechnical UniversityXi'anChina
- Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems EngineeringNorthwestern Polytechnical UniversityXi'anChina
- NPU‐UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'anChina
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25
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Doan VS, Alshareedah I, Singh A, Banerjee PR, Shin S. Diffusiophoresis promotes phase separation and transport of biomolecular condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.03.547532. [PMID: 37461689 PMCID: PMC10350024 DOI: 10.1101/2023.07.03.547532] [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: 07/25/2023]
Abstract
The internal microenvironment of a living cell is heterogeneous and comprises a multitude of organelles with distinct biochemistry. Amongst them are biomolecular condensates, which are membrane-less, phase-separated compartments enriched in system-specific proteins and nucleic acids. The heterogeneity of the cell engenders the presence of multiple spatiotemporal gradients in chemistry, charge, concentration, temperature, and pressure. Such thermodynamic gradients can lead to non-equilibrium driving forces for the formation and transport of biomolecular condensates. Here, we report how ion gradients impact the transport processes of biomolecular condensates on the mesoscale and biomolecules on the microscale. Utilizing a microfluidic platform, we demonstrate that the presence of ion concentration gradients can accelerate the transport of biomolecules, including nucleic acids and proteins, via diffusiophoresis. This hydrodynamic transport process allows localized enrichment of biomolecules, thereby promoting the location-specific formation of biomolecular condensates via phase separation. The ion gradients further impart active motility of condensates, allowing them to exhibit enhanced diffusion along the gradient. Coupled with a reentrant phase behavior, the gradient-induced active motility leads to a dynamical redistribution of condensates that ultimately extends their lifetime. Together, our results demonstrate diffusiophoresis as a non-equilibrium thermodynamic force that governs the formation and transport of biomolecular condensates.
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Affiliation(s)
- Viet Sang Doan
- Department of Mechanical and Aerospace Engineering, University at Buffalo, The State University of New York, Buffalo, NY 14260
| | - Ibraheem Alshareedah
- Department of Physics, University at Buffalo, The State University of New York, Buffalo, NY 14260
| | - Anurag Singh
- Department of Physics, University at Buffalo, The State University of New York, Buffalo, NY 14260
| | - Priya R Banerjee
- Department of Physics, University at Buffalo, The State University of New York, Buffalo, NY 14260
| | - Sangwoo Shin
- Department of Mechanical and Aerospace Engineering, University at Buffalo, The State University of New York, Buffalo, NY 14260
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26
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Blake LA, De La Cruz A, Wu B. Imaging spatiotemporal translation regulation in vivo. Semin Cell Dev Biol 2024; 154:155-164. [PMID: 36963991 PMCID: PMC10514244 DOI: 10.1016/j.semcdb.2023.03.006] [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: 03/23/2022] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/26/2023]
Abstract
Translation is regulated spatiotemporally to direct protein synthesis when and where it is needed. RNA localization and local translation have been observed in various subcellular compartments, allowing cells to rapidly and finely adjust their proteome post-transcriptionally. Local translation on membrane-bound organelles is important to efficiently synthesize proteins targeted to the organelles. Protein-RNA phase condensates restrict RNA spatially in membraneless organelles and play essential roles in translation regulation and RNA metabolism. In addition, the temporal translation kinetics not only determine the amount of protein produced, but also serve as an important checkpoint for the quality of ribosomes, mRNAs, and nascent proteins. Translation imaging provides a unique capability to study these fundamental processes in the native environment. Recent breakthroughs in imaging enabled real-time visualization of translation of single mRNAs, making it possible to determine the spatial distribution and key biochemical parameters of in vivo translation dynamics. Here we reviewed the recent advances in translation imaging methods and their applications to study spatiotemporal translation regulation in vivo.
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Affiliation(s)
- Lauren A Blake
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ana De La Cruz
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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27
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Zhang X, Li Y, Cao Y, Wu Y, Cheng G. The Role of Noncoding RNA in the Transmission and Pathogenicity of Flaviviruses. Viruses 2024; 16:242. [PMID: 38400018 PMCID: PMC10892091 DOI: 10.3390/v16020242] [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: 12/11/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
Noncoding RNAs (ncRNAs) constitute a class of RNA molecules that lack protein-coding capacity. ncRNAs frequently modulate gene expression through specific interactions with target proteins or messenger RNAs, thereby playing integral roles in a wide array of cellular processes. The Flavivirus genus comprises several significant members, such as dengue virus (DENV), Zika virus (ZIKV), and yellow fever virus (YFV), which have caused global outbreaks, resulting in high morbidity and mortality in human populations. The life cycle of arthropod-borne flaviviruses encompasses their transmission between hematophagous insect vectors and mammalian hosts. During this process, a complex three-way interplay occurs among the pathogen, vector, and host, with ncRNAs exerting a critical regulatory influence. ncRNAs not only constitute a crucial regulatory mechanism that has emerged from the coevolution of viruses and their hosts but also hold potential as antiviral targets for controlling flavivirus epidemics. This review introduces the biogenesis of flavivirus-derived ncRNAs and summarizes the regulatory roles of ncRNAs in viral replication, vector-mediated viral transmission, antiviral innate immunity, and viral pathogenicity. A profound comprehension of the interplay between ncRNAs and flaviviruses will help formulate efficacious prophylactic and therapeutic strategies against flavivirus-related diseases.
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Affiliation(s)
- Xianwen Zhang
- Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen 518000, China
| | - Yuhan Li
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
| | - Yingyi Cao
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
| | - Ying Wu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School, Wuhan University, Wuhan 430072, China;
| | - Gong Cheng
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
- Southwest United Graduate School, Kunming 650092, China
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28
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Kannaiah S, Goldberger O, Alam N, Barnabas G, Pozniak Y, Nussbaum-Shochat A, Schueler-Furman O, Geiger T, Amster-Choder O. MinD-RNase E interplay controls localization of polar mRNAs in E. coli. EMBO J 2024; 43:637-662. [PMID: 38243117 PMCID: PMC10897333 DOI: 10.1038/s44318-023-00026-9] [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: 02/03/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024] Open
Abstract
The E. coli transcriptome at the cell's poles (polar transcriptome) is unique compared to the membrane and cytosol. Several factors have been suggested to mediate mRNA localization to the membrane, but the mechanism underlying polar localization of mRNAs remains unknown. Here, we combined a candidate system approach with proteomics to identify factors that mediate mRNAs localization to the cell poles. We identified the pole-to-pole oscillating protein MinD as an essential factor regulating polar mRNA localization, although it is not able to bind RNA directly. We demonstrate that RNase E, previously shown to interact with MinD, is required for proper localization of polar mRNAs. Using in silico modeling followed by experimental validation, the membrane-binding site in RNase E was found to mediate binding to MinD. Intriguingly, not only does MinD affect RNase E interaction with the membrane, but it also affects its mode of action and dynamics. Polar accumulation of RNase E in ΔminCDE cells resulted in destabilization and depletion of mRNAs from poles. Finally, we show that mislocalization of polar mRNAs may prevent polar localization of their protein products. Taken together, our findings show that the interplay between MinD and RNase E determines the composition of the polar transcriptome, thus assigning previously unknown roles for both proteins.
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Affiliation(s)
- Shanmugapriya Kannaiah
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63110, USA.
| | - Omer Goldberger
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
| | - Nawsad Alam
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Georgina Barnabas
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 6997801, Tel-Aviv, Israel
- Department of Pathology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Yair Pozniak
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 6997801, Tel-Aviv, Israel
| | - Anat Nussbaum-Shochat
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 6997801, Tel-Aviv, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, 76100001, Rehovot, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel.
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29
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Perez RC, Yang X, Familari M, Martinez G, Lovicu FJ, Hime GR, de Iongh RU. TOB1 and TOB2 mark distinct RNA processing granules in differentiating lens fiber cells. J Mol Histol 2024; 55:121-138. [PMID: 38165569 DOI: 10.1007/s10735-023-10177-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/12/2023] [Indexed: 01/04/2024]
Abstract
Differentiation of lens fiber cells involves a complex interplay of signals from growth factors together with tightly regulated gene expression via transcriptional and post-transcriptional regulators. Various studies have demonstrated that RNA-binding proteins, functioning in ribonucleoprotein granules, have important roles in regulating post-transcriptional expression during lens development. In this study, we examined the expression and localization of two members of the BTG/TOB family of RNA-binding proteins, TOB1 and TOB2, in the developing lens and examined the phenotype of mice that lack Tob1. By RT-PCR, both Tob1 and Tob2 mRNA were detected in epithelial and fiber cells of embryonic and postnatal murine lenses. In situ hybridization showed Tob1 and Tob2 mRNA were most intensely expressed in the early differentiating fibers, with weaker expression in anterior epithelial cells, and both appeared to be downregulated in the germinative zone of E15.5 lenses. TOB1 protein was detected from E11.5 to E16.5 and was predominantly detected in large cytoplasmic puncta in early differentiating fiber cells, often co-localizing with the P-body marker, DCP2. Occasional nuclear puncta were also observed. By contrast, TOB2 was detected in a series of interconnected peri-nuclear granules, in later differentiating fiber cells of the inner cortex. TOB2 did not appear to co-localize with DCP2 but did partially co-localize with an early stress granule marker (EIF3B). These data suggest that TOB1 and TOB2 are involved with different aspects of the mRNA processing cycle in lens fiber cells. In vitro experiments using rat lens epithelial explants treated with or without a fiber differentiating dose of FGF2 showed that both TOB1 and TOB2 were up-regulated during FGF-induced differentiation. In differentiating explants, TOB1 also co-localized with DCP2 in large cytoplasmic granules. Analyses of Tob1-/- mice revealed relatively normal lens morphology but a subtle defect in cell cycle arrest of some cells at the equator and in the lens fiber mass of E13.5 embryos. Overall, these findings suggest that TOB proteins play distinct regulatory roles in RNA processing during lens fiber differentiation.
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Affiliation(s)
- Rafaela C Perez
- Ocular Development Laboratory, Anatomy & Physiology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Xenia Yang
- Ocular Development Laboratory, Anatomy & Physiology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mary Familari
- School of Biosciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Gemma Martinez
- Ocular Development Laboratory, Anatomy & Physiology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Frank J Lovicu
- Molecular and Cellular Biomedicine, School of Medical Sciences and Save Sight Institute, University of Sydney, Sydney, NSW, 2006, Australia
| | - Gary R Hime
- Stem Cell Genetics Laboratory, Anatomy & Physiology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Robb U de Iongh
- Ocular Development Laboratory, Anatomy & Physiology, University of Melbourne, Parkville, VIC, 3010, Australia.
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30
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Turan G, Olgun ÇE, Ayten H, Toker P, Ashyralyyev A, Savaş B, Karaca E, Muyan M. Dynamic proximity interaction profiling suggests that YPEL2 is involved in cellular stress surveillance. Protein Sci 2024; 33:e4859. [PMID: 38145972 PMCID: PMC10804680 DOI: 10.1002/pro.4859] [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: 08/17/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 12/27/2023]
Abstract
YPEL2 is a member of the evolutionarily conserved YPEL family involved in cellular proliferation, mobility, differentiation, senescence, and death. However, the mechanism by which YPEL2, or YPEL proteins, mediates its effects is largely unknown. Proteins perform their functions in a network of proteins whose identities, amounts, and compositions change spatiotemporally in a lineage-specific manner in response to internal and external stimuli. Here, we explored interaction partners of YPEL2 by using dynamic TurboID-coupled mass spectrometry analyses to infer a function for the protein. Our results using inducible transgene expressions in COS7 cells indicate that proximity interaction partners of YPEL2 are mainly involved in RNA and mRNA metabolic processes, ribonucleoprotein complex biogenesis, regulation of gene silencing by miRNA, and cellular responses to stress. We showed that YPEL2 interacts with the RNA-binding protein ELAVL1 and the selective autophagy receptor SQSTM1. We also found that YPEL2 localizes stress granules in response to sodium arsenite, an oxidative stress inducer, which suggests that YPEL2 participates in stress granule-related processes. Establishing a point of departure in the delineation of structural/functional features of YPEL2, our results suggest that YPEL2 may be involved in stress surveillance mechanisms.
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Affiliation(s)
- Gizem Turan
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTürkiye
| | - Çağla Ece Olgun
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTürkiye
| | - Hazal Ayten
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTürkiye
| | - Pelin Toker
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTürkiye
| | | | - Büşra Savaş
- İzmir Biomedicine and Genome CenterİzmirTürkiye
- Izmir International Biomedicine and Genome InstituteDokuz Eylül UniversityIzmirTürkiye
| | - Ezgi Karaca
- İzmir Biomedicine and Genome CenterİzmirTürkiye
- Izmir International Biomedicine and Genome InstituteDokuz Eylül UniversityIzmirTürkiye
| | - Mesut Muyan
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTürkiye
- CanSyl LaboratoriesMiddle East Technical UniversityAnkaraTürkiye
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31
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Fu Q, Zhang B, Chen X, Chu L. Liquid-liquid phase separation in Alzheimer's disease. J Mol Med (Berl) 2024; 102:167-181. [PMID: 38167731 DOI: 10.1007/s00109-023-02407-3] [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: 04/17/2023] [Revised: 11/26/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
The pathological aggregation and misfolding of tau and amyloid-β play a key role in Alzheimer's disease (AD). However, the underlying pathological mechanisms remain unclear. Emerging evidences indicate that liquid-liquid phase separation (LLPS) has great impacts on regulating human health and diseases, especially neurodegenerative diseases. A series of studies have revealed the significance of LLPS in AD. In this review, we summarize the latest progress of LLPS in AD, focusing on the impact of metal ions, small-molecule inhibitors, and proteinaceous partners on tau LLPS and aggregation, as well as toxic oligomerization, the role of LLPS on amyloid-β (Aβ) aggregation, and the cross-interactions between amyloidogenic proteins in AD. Eventually, the fundamental methods and techniques used in LLPS study are introduced. We expect to present readers a deeper understanding of the relationship between LLPS and AD.
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Affiliation(s)
- Qinggang Fu
- Hepatic Surgery Center and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Bixiang Zhang
- Hepatic Surgery Center and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Xiaoping Chen
- Hepatic Surgery Center and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Liang Chu
- Hepatic Surgery Center and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
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32
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Liu Q, Liu W, Niu Y, Wang T, Dong J. Liquid-liquid phase separation in plants: Advances and perspectives from model species to crops. PLANT COMMUNICATIONS 2024; 5:100663. [PMID: 37496271 PMCID: PMC10811348 DOI: 10.1016/j.xplc.2023.100663] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/23/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023]
Abstract
Membraneless biomolecular condensates play important roles in both normal biological activities and responses to environmental stimuli in living organisms. Liquid‒liquid phase separation (LLPS) is an organizational mechanism that has emerged in recent years to explain the formation of biomolecular condensates. In the past decade, advances in LLPS research have contributed to breakthroughs in disease fields. By contrast, although LLPS research in plants has progressed over the past 5 years, it has been concentrated on the model plant Arabidopsis, which has limited relevance to agricultural production. In this review, we provide an overview of recently reported advances in LLPS in plants, with a particular focus on photomorphogenesis, flowering, and abiotic and biotic stress responses. We propose that many potential LLPS proteins also exist in crops and may affect crop growth, development, and stress resistance. This possibility presents a great challenge as well as an opportunity for rigorous scientific research on the biological functions and applications of LLPS in crops.
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Affiliation(s)
- Qianwen Liu
- College of Biological Sciences, China Agricultural University, Beijing 100193, China; College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Wenxuan Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Yiding Niu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Tao Wang
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jiangli Dong
- College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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33
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Cheung SWM, Yiu JHC, Chin KTC, Cai J, Xu A, Wong CM, Woo CW. Content of stress granules reveals a sex difference at the early phase of cold exposure in mice. Am J Physiol Endocrinol Metab 2024; 326:E29-E37. [PMID: 37991452 PMCID: PMC11193528 DOI: 10.1152/ajpendo.00317.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023]
Abstract
Adaptive thermogenesis is a vital physiological process for small endotherms. Female animals usually are more sensitive to cold temperature due to anatomical differences. Whether there is a sex difference at a molecular level is unclear. Stress granules (SGs) are dynamic organelles in which untranslated mRNAs reside during cellular stress. We hypothesize that the prompt response of SGs to cold stress can reveal the molecular difference between sexes. By analyzing the content in SGs of brown adipose tissue (BAT) at the early phase of cold stress for both sexes, we found more diverse mRNAs docked in the SGs in male mice and these mRNAs representing an extensive cellular reprogramming including apoptosis process and cold-induced thermogenesis. In female mice, the mRNAs in SGs dominantly were comprised of genes regulating ribonucleoprotein complex biogenesis. Conversely, the proteome in SGs was commonly characterized as structure molecules and RNA processing for both sexes. A spectrum of eukaryotic initiation factors (eIFs) was detected in the SGs of both female and male BAT, while those remained unchanged upon cold stress in male mice, various eIF3 and eIF4G isoforms were found reduced in female mice. Taken together, the unique features in SGs of male BAT reflected a prompt uncoupling protein-1 (UCP1) induction which was absent in female, and female, by contrast, were prepared for long-term transcriptional and translational adaptations.NEW & NOTEWORTHY The proteome analysis reveals that stress granules are the predominant form of cytosolic messenger ribonucleoproteins of brown adipose tissue (BAT) at the early phase of cold exposure in mice for both sexes. The transcriptome of stress granules of BAT unveils a sex difference of molecular response in early phase of cold exposure in mice, and such difference prepares for a prompt response to cold stress in male mice while for long-term adaptation in female mice.
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Affiliation(s)
- Samson W M Cheung
- State Key Laboratory of Pharmaceutical Biotechnology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Jensen H C Yiu
- State Key Laboratory of Pharmaceutical Biotechnology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Karie T C Chin
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Jieling Cai
- State Key Laboratory of Pharmaceutical Biotechnology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Aimin Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Chi Ming Wong
- State Key Laboratory of Pharmaceutical Biotechnology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, People's Republic of China
| | - Connie W Woo
- State Key Laboratory of Pharmaceutical Biotechnology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Micon Analytics, Toronto, Ontario, Canada
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Gorsheneva NA, Sopova JV, Azarov VV, Grizel AV, Rubel AA. Biomolecular Condensates: Structure, Functions, Methods of Research. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S205-S223. [PMID: 38621751 DOI: 10.1134/s0006297924140116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 04/17/2024]
Abstract
The term "biomolecular condensates" is used to describe membraneless compartments in eukaryotic cells, accumulating proteins and nucleic acids. Biomolecular condensates are formed as a result of liquid-liquid phase separation (LLPS). Often, they demonstrate properties of liquid-like droplets or gel-like aggregates; however, some of them may appear to have a more complex structure and high-order organization. Membraneless microcompartments are involved in diverse processes both in cytoplasm and in nucleus, among them ribosome biogenesis, regulation of gene expression, cell signaling, and stress response. Condensates properties and structure could be highly dynamic and are affected by various internal and external factors, e.g., concentration and interactions of components, solution temperature, pH, osmolarity, etc. In this review, we discuss variety of biomolecular condensates and their functions in live cells, describe their structure variants, highlight domain and primary sequence organization of the constituent proteins and nucleic acids. Finally, we describe current advances in methods that characterize structure, properties, morphology, and dynamics of biomolecular condensates in vitro and in vivo.
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Affiliation(s)
| | - Julia V Sopova
- St. Petersburg State University, St. Petersburg, 199034, Russia.
| | | | - Anastasia V Grizel
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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35
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Shan T, Liu F, Wen M, Chen Z, Li S, Wang Y, Cheng H, Zhou Y. m 6A modification negatively regulates translation by switching mRNA from polysome to P-body via IGF2BP3. Mol Cell 2023; 83:4494-4508.e6. [PMID: 38016476 DOI: 10.1016/j.molcel.2023.10.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 07/10/2023] [Accepted: 10/26/2023] [Indexed: 11/30/2023]
Abstract
In the cytoplasm, mRNAs are dynamically partitioned into translating and non-translating pools, but the mechanism for this regulation has largely remained elusive. Here, we report that m6A regulates mRNA partitioning between polysome and P-body where a pool of non-translating mRNAs resides. By quantifying the m6A level of polysomal and cytoplasmic mRNAs with m6A-LAIC-seq and m6A-LC-MS/MS in HeLa cells, we observed that polysome-associated mRNAs are hypo-m6A-methylated, whereas those enriched in P-body are hyper-m6A-methylated. Downregulation of the m6A writer METTL14 enhances translation by switching originally hyper-m6A-modified mRNAs from P-body to polysome. Conversely, by proteomic analysis, we identify a specific m6A reader IGF2BP3 enriched in P-body, and via knockdown and molecular tethering assays, we demonstrate that IGF2BP3 is both necessary and sufficient to switch target mRNAs from polysome to P-body. These findings suggest a model for the dynamic regulation of mRNA partitioning between the translating and non-translating pools in an m6A-dependent manner.
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Affiliation(s)
- Ting Shan
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, State Key Laboratory of Virology, Wuhan University, Wuhan, China
| | - Feiyan Liu
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, State Key Laboratory of Virology, Wuhan University, Wuhan, China
| | - Miaomiao Wen
- Institute of Advanced Studies, Wuhan University, Wuhan, China
| | - Zonggui Chen
- Institute of Advanced Studies, Wuhan University, Wuhan, China
| | - Shaopeng Li
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, State Key Laboratory of Virology, Wuhan University, Wuhan, China
| | - Yafen Wang
- School of Public Health, Wuhan University, Wuhan, China
| | - Hong Cheng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yu Zhou
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China; Institute of Advanced Studies, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, State Key Laboratory of Virology, Wuhan University, Wuhan, China.
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36
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Romero-Romero ML, Garcia-Seisdedos H. Agglomeration: when folded proteins clump together. Biophys Rev 2023; 15:1987-2003. [PMID: 38192350 PMCID: PMC10771401 DOI: 10.1007/s12551-023-01172-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/25/2023] [Indexed: 01/10/2024] Open
Abstract
Protein self-association is a widespread phenomenon that results in the formation of multimeric protein structures with critical roles in cellular processes. Protein self-association can lead to finite protein complexes or open-ended, and potentially, infinite structures. This review explores the concept of protein agglomeration, a process that results from the infinite self-assembly of folded proteins. We highlight its differences from other better-described processes with similar macroscopic features, such as aggregation and liquid-liquid phase separation. We review the sequence, structural, and biophysical factors influencing protein agglomeration. Lastly, we briefly discuss the implications of agglomeration in evolution, disease, and aging. Overall, this review highlights the need to study protein agglomeration for a better understanding of cellular processes.
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Affiliation(s)
- M. L. Romero-Romero
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
| | - H. Garcia-Seisdedos
- Department of Structural and Molecular Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
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37
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Ocharán-Mercado A, Loaeza-Loaeza J, Castro-Coronel Y, Acosta-Saavedra LC, Hernández-Kelly LC, Hernández-Sotelo D, Ortega A. RNA-Binding Proteins: A Role in Neurotoxicity? Neurotox Res 2023; 41:681-697. [PMID: 37776476 PMCID: PMC10682104 DOI: 10.1007/s12640-023-00669-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 03/15/2023] [Accepted: 09/19/2023] [Indexed: 10/02/2023]
Abstract
Despite sustained efforts to treat neurodegenerative diseases, little is known at the molecular level to understand and generate novel therapeutic approaches for these malignancies. Therefore, it is not surprising that neurogenerative diseases are among the leading causes of death in the aged population. Neurons require sophisticated cellular mechanisms to maintain proper protein homeostasis. These cells are generally sensitive to loss of gene expression control at the post-transcriptional level. Post-translational control responds to signals that can arise from intracellular processes or environmental factors that can be regulated through RNA-binding proteins. These proteins recognize RNA through one or more RNA-binding domains and form ribonucleoproteins that are critically involved in the regulation of post-transcriptional processes from splicing to the regulation of association of the translation machinery allowing a relatively rapid and precise modulation of the transcriptome. Neurotoxicity is the result of the biological, chemical, or physical interaction of agents with an adverse effect on the structure and function of the central nervous system. The disruption of the proper levels or function of RBPs in neurons and glial cells triggers neurotoxic events that are linked to neurodegenerative diseases such as spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS), fragile X syndrome (FXS), and frontotemporal dementia (FTD) among many others. The connection between RBPs and neurodegenerative diseases opens a new landscape for potentially novel therapeutic targets for the intervention of these neurodegenerative pathologies. In this contribution, a summary of the recent findings of the molecular mechanisms involved in the plausible role of RBPs in RNA processing in neurodegenerative disease is discussed.
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Affiliation(s)
- Andrea Ocharán-Mercado
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México
| | - Jaqueline Loaeza-Loaeza
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México
| | - Yaneth Castro-Coronel
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas 88, Chilpancingo, Guerrero, 39086, México
| | - Leonor C Acosta-Saavedra
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México
| | - Luisa C Hernández-Kelly
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México
| | - Daniel Hernández-Sotelo
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas 88, Chilpancingo, Guerrero, 39086, México
| | - Arturo Ortega
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México.
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38
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Dong H, Zhang H, Jalin J, He Z, Wang R, Huang L, Liu Z, Zhang S, Dai B, Li D. Nucleocapsid proteins from human coronaviruses possess phase separation capabilities and promote FUS pathological aggregation. Protein Sci 2023; 32:e4826. [PMID: 37906538 PMCID: PMC10659942 DOI: 10.1002/pro.4826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/16/2023] [Accepted: 10/27/2023] [Indexed: 11/02/2023]
Abstract
The nucleocapsid (N) protein is an essential structural component necessary for genomic packaging and replication in various human coronaviruses (HCoVs), such as SARS-CoV-2 and MERS-CoV. Recent studies have revealed that the SARS-CoV-2 N protein exhibits a high capacity for liquid-liquid phase separation (LLPS), which plays multiple roles in viral infection and replication. In this study, we systematically investigate the LLPS capabilities of seven homologous N proteins from different HCoVs using a high-throughput protein phase separation assay. We found that LLPS is a shared intrinsic property among these N proteins. However, the phase separation profiles of the various N protein homologs differ, and they undergo phase separation under distinct in vitro conditions. Moreover, we demonstrate that N protein homologs can co-phase separate with FUS, a SG-containing protein, and accelerate its liquid-to-solid phase transition and amyloid aggregation, which is closely related to amyotrophic lateral sclerosis. Further study shows that N protein homologs can directly bind to the low complexity domain of FUS. Together, our work demonstrates that N proteins of different HCoVs possess phase separation capabilities, which may contribute to promoting pathological aggregation of host proteins and disrupting SG homeostasis during the infection and replication of various HCoVs.
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Affiliation(s)
- Hui Dong
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- Present address:
Interdisciplinary Research Center on Biology and ChemistryShanghai Institute of Organic Chemistry, Chinese Academy of SciencesShanghaiChina
| | - Hong Zhang
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Julie Jalin
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ziqi He
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
| | - Runhan Wang
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Leqi Huang
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zibo Liu
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Shenqing Zhang
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
- Zhangjiang Institute for Advanced StudyShanghai Jiao Tong UniversityShanghaiChina
| | - Bin Dai
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Dan Li
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
- Zhangjiang Institute for Advanced StudyShanghai Jiao Tong UniversityShanghaiChina
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39
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Hu S, Zhang Y, Yi Q, Yang C, Liu Y, Bai Y. Time-resolved proteomic profiling reveals compositional and functional transitions across the stress granule life cycle. Nat Commun 2023; 14:7782. [PMID: 38012130 PMCID: PMC10682001 DOI: 10.1038/s41467-023-43470-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
Stress granules (SGs) are dynamic, membrane-less organelles. With their formation and disassembly processes characterized, it remains elusive how compositional transitions are coordinated during prolonged stress to meet changing functional needs. Here, using time-resolved proteomic profiling of the acute to prolonged heat-shock SG life cycle, we identify dynamic SG proteins, further segregated into early and late proteins. Comparison of different groups of SG proteins suggests that their biochemical properties help coordinate SG compositional and functional transitions. In particular, early proteins, with high phase-separation-propensity, drive the rapid formation of the initial SG platform, while late proteins are subsequently recruited as discrete modules to further functionalize SGs. This model, supported by immunoblotting and immunofluorescence imaging, provides a conceptual framework for the compositional transitions throughout the acute to prolonged SG life cycle. Additionally, an early SG constituent, non-muscle myosin II, is shown to promote SG formation by increasing SG fusion, underscoring the strength of this dataset in revealing the complexity of SG regulation.
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Affiliation(s)
- Shuyao Hu
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
| | - Yufeng Zhang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Qianqian Yi
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Cuiwei Yang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Yanfen Liu
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
| | - Yun Bai
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
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40
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Hatfield D, Rodriguez W, Mehrmann T, Muller M. The antiviral protein Shiftless blocks p-body formation during KSHV infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567185. [PMID: 38014318 PMCID: PMC10680731 DOI: 10.1101/2023.11.16.567185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
P-bodies (PB) are non-membranous foci involved in determining mRNA fate by affecting translation and mRNA decay. In this study, we identify the anti-viral factor SHFL as a potent disassembly factor of PB. We show that PBs remain sparse in the presence of SHFL even in the context of oxidative stress, a major trigger for PB induction. Mutational approaches revealed that SHFL RNA binding activity is not required for its PB disassembly function. However, we have identified a new region of SHFL which bridges two distant domains as responsible for PB disassembly. Furthermore, we show that SHFL ability to disrupt PB formation is directly linked to its anti-viral activity during KSHV infection. While WT SHFL efficiently restricts KSHV lytic cycle, PB disruption defective mutants no longer lead to reactivation defects. SHFL-mediated PB disassembly also leads to increased expression of key anti-viral cytokines, further expanding SHFL dependent anti-viral state. Taken together, our observations suggest a role of SHFL in PB disassembly, which could have important anti-viral consequences during infection.
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41
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Poruthoor AJ, Sharma A, Grossfield A. Understanding the free-energy landscape of phase separation in lipid bilayers using molecular dynamics. Biophys J 2023; 122:4144-4159. [PMID: 37742069 PMCID: PMC10645549 DOI: 10.1016/j.bpj.2023.09.012] [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: 03/06/2023] [Revised: 08/28/2023] [Accepted: 09/19/2023] [Indexed: 09/25/2023] Open
Abstract
Liquid-liquid phase separation inside the cell often results in biological condensates that can critically affect cell homeostasis. Such phase separation events occur in multiple parts of cells, including the cell membranes, where the "lipid raft" hypothesis posits the formation of ordered domains floating in a sea of disordered lipids. The resulting lipid domains often have functional roles. However, the thermodynamics of lipid phase separation and their resulting mechanistic effects on cell function and dysfunction are poorly understood. Understanding such complex phenomena in cell membranes, with their diverse lipid compositions, is exceptionally difficult. For these reasons, simple model systems that can recapitulate similar behavior are widely used to study this phenomenon. Despite these simplifications, the timescale and length scales of domain formation pose a challenge for molecular dynamics (MD) simulations. Thus, most MD studies focus on spontaneous lipid phase separation-essentially measuring the sign (but not the amplitude) of the free-energy change upon separation-rather than directly interrogating the thermodynamics. Here, we propose a proof-of-concept pipeline that can directly measure this free energy by combining coarse-grained MD with enhanced sampling protocols using a novel collective variable. This approach will be a useful tool to help connect the thermodynamics of phase separation with the mechanistic insights already available from MD simulations.
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Affiliation(s)
- Ashlin J Poruthoor
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Akshara Sharma
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Alan Grossfield
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
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42
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He F, Jacobson A. Eukaryotic mRNA decapping factors: molecular mechanisms and activity. FEBS J 2023; 290:5057-5085. [PMID: 36098474 PMCID: PMC10008757 DOI: 10.1111/febs.16626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/11/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022]
Abstract
Decapping is the enzymatic removal of 5' cap structures from mRNAs in eukaryotic cells. Cap structures normally enhance mRNA translation and stability, and their excision commits an mRNA to complete 5'-3' exoribonucleolytic digestion and generally ends the physical and functional cellular presence of the mRNA. Decapping plays a pivotal role in eukaryotic cytoplasmic mRNA turnover and is a critical and highly regulated event in multiple 5'-3' mRNA decay pathways, including general 5'-3' decay, nonsense-mediated mRNA decay (NMD), AU-rich element-mediated mRNA decay, microRNA-mediated gene silencing, and targeted transcript-specific mRNA decay. In the yeast Saccharomyces cerevisiae, mRNA decapping is carried out by a single Dcp1-Dcp2 decapping enzyme in concert with the accessory activities of specific regulators commonly known as decapping activators or enhancers. These regulatory proteins include the general decapping activators Edc1, 2, and 3, Dhh1, Scd6, Pat1, and the Lsm1-7 complex, as well as the NMD-specific factors, Upf1, 2, and 3. Here, we focus on in vivo mRNA decapping regulation in yeast. We summarize recently uncovered molecular mechanisms that control selective targeting of the yeast decapping enzyme and discuss new roles for specific decapping activators in controlling decapping enzyme targeting, assembly of target-specific decapping complexes, and the monitoring of mRNA translation. Further, we discuss the kinetic contribution of mRNA decapping for overall decay of different substrate mRNAs and highlight experimental evidence pointing to the functional coordination and physical coupling between events in mRNA deadenylation, decapping, and 5'-3' exoribonucleolytic decay.
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Affiliation(s)
- Feng He
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
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43
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Kumari P, Sarovar Bhavesh N. Birth and death view of DNA, RNA, and proteins. Gene 2023; 883:147672. [PMID: 37506987 DOI: 10.1016/j.gene.2023.147672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/26/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
The potential of cells to guide their genome and configure genes to express at a given time and in response to specific stimuli is pivotal to regulate cellular processes such as tissue differentiation, organogenesis, organismal development, homeostasis, and disease. In this review, we focus on the diverse mechanisms involved in DNA replication and its degradation, mRNA synthesis, and associated regulation such as RNA capping, splicing, tailing, and export. mRNA turnover including Decapping, deadenylation, RNA interference, and Nonsense mediated mRNA decay followed by protein translation, post-translational modification, and protein turnover. We highlight recent advances in understanding the complex series of molecular mechanisms responsible for the remarkable cellular regulatory mechanisms.
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Affiliation(s)
- Pooja Kumari
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, Jharkhand 834001, India.
| | - Neel Sarovar Bhavesh
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India.
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44
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Arora S, Roy DS, Maiti S, Ainavarapu SRK. Phase Separation and Aggregation of a Globular Folded Protein Small Ubiquitin-like Modifier 1 (SUMO1). J Phys Chem Lett 2023; 14:9060-9068. [PMID: 37782899 DOI: 10.1021/acs.jpclett.3c02092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Liquid-liquid phase separation (LLPS) plays a crucial role in cellular organization, primarily driven by intrinsically disordered proteins (IDPs) leading to the formation of biomolecular condensates. A folded protein SUMO that post-translationally modifies cellular proteins has recently emerged as a regulator of LLPS. Given its compact structure and limited flexibility, the precise role of SUMO in condensate formation remains to be investigated. Here, we show the rapid phase separation of SUMO1 into micrometer-sized liquid-like condensates in inert crowders under physiological conditions. Subsequent time-dependent conformational changes and aggregation are probed by label-free methods (tryptophan fluorescence and Raman spectroscopy). Remarkably, experiments on a SUMO1 variant lacking the N-terminal disordered region further corroborate the role of its structured part in phase transitions. Our findings highlight the potential of folded proteins to engage in LLPS and emphasize further investigation into the influence of the SUMO tag on IDPs associated with membrane-less assemblies in cells.
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Affiliation(s)
- Simran Arora
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Debsankar Saha Roy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
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45
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Gallo R, Rai AK, McIntyre ABR, Meyer K, Pelkmans L. DYRK3 enables secretory trafficking by maintaining the liquid-like state of ER exit sites. Dev Cell 2023; 58:1880-1897.e11. [PMID: 37643612 DOI: 10.1016/j.devcel.2023.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/16/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023]
Abstract
The dual-specificity kinase DYRK3 controls the formation and dissolution of multiple biomolecular condensates, regulating processes including stress recovery and mitotic progression. Here, we report that DYRK3 functionally interacts with proteins associated with endoplasmic reticulum (ER) exit sites (ERESs) and that inhibition of DYRK3 perturbs the organization of the ERES-Golgi interface and secretory trafficking. DYRK3-mediated regulation of ERES depends on the N-terminal intrinsically disordered region (IDR) of the peripheral membrane protein SEC16A, which co-phase separates with ERES components to form liquid-like condensates on the surface of the ER. By modulating the liquid-like properties of ERES, we show that their physical state is essential for functional cargo trafficking through the early secretory pathway. Our findings support a mechanism whereby phosphorylation by DYRK3 and its reversal by serine-threonine phosphatases regulate the material properties of ERES to create a favorable physicochemical environment for directional membrane traffic in eukaryotic cells.
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Affiliation(s)
- Raffaella Gallo
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Arpan Kumar Rai
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland.
| | - Alexa B R McIntyre
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Katrina Meyer
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland.
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46
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Zhu WS, Wheeler BD, Ansel KM. RNA circuits and RNA-binding proteins in T cells. Trends Immunol 2023; 44:792-806. [PMID: 37599172 PMCID: PMC10890840 DOI: 10.1016/j.it.2023.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023]
Abstract
RNA is integral to the regulatory circuits that control cell identity and behavior. Cis-regulatory elements in mRNAs interact with RNA-binding proteins (RBPs) that can alter RNA sequence, stability, and translation into protein. Similarly, long noncoding RNAs (lncRNAs) scaffold ribonucleoprotein complexes that mediate transcriptional and post-transcriptional regulation of gene expression. Indeed, cell programming is fundamental to multicellular life and, in this era of cellular therapies, it is of particular interest in T cells. Here, we review key concepts and recent advances in our understanding of the RNA circuits and RBPs that govern mammalian T cell differentiation and immune function.
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Affiliation(s)
- Wandi S Zhu
- Department of Microbiology & Immunology, Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Benjamin D Wheeler
- Department of Microbiology & Immunology, Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - K Mark Ansel
- Department of Microbiology & Immunology, Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA 94143, USA.
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47
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Németh-Szatmári O, Nagy-Mikó B, Györkei Á, Varga D, Kovács BBH, Igaz N, Bognár B, Rázga Z, Nagy G, Zsindely N, Bodai L, Papp B, Erdélyi M, Kiricsi M, Blastyák A, Collart MA, Boros IM, Villányi Z. Phase-separated ribosome-nascent chain complexes in genotoxic stress response. RNA (NEW YORK, N.Y.) 2023; 29:1557-1574. [PMID: 37460154 PMCID: PMC10578487 DOI: 10.1261/rna.079755.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 09/20/2023]
Abstract
Assemblysomes are EDTA- and RNase-resistant ribonucleoprotein (RNP) complexes of paused ribosomes with protruding nascent polypeptide chains. They have been described in yeast and human cells for the proteasome subunit Rpt1, and the disordered amino-terminal part of the nascent chain was found to be indispensable for the accumulation of the Rpt1-RNP into assemblysomes. Motivated by this, to find other assemblysome-associated RNPs we used bioinformatics to rank subunits of Saccharomyces cerevisiae protein complexes according to their amino-terminal disorder propensity. The results revealed that gene products involved in DNA repair are enriched among the top candidates. The Sgs1 DNA helicase was chosen for experimental validation. We found that indeed nascent chains of Sgs1 form EDTA-resistant RNP condensates, assemblysomes by definition. Moreover, upon exposure to UV, SGS1 mRNA shifted from assemblysomes to polysomes, suggesting that external stimuli are regulators of assemblysome dynamics. We extended our studies to human cell lines. The BLM helicase, ortholog of yeast Sgs1, was identified upon sequencing assemblysome-associated RNAs from the MCF7 human breast cancer cell line, and mRNAs encoding DNA repair proteins were overall enriched. Using the radiation-resistant A549 cell line, we observed by transmission electron microscopy that 1,6-hexanediol, an agent known to disrupt phase-separated condensates, depletes ring ribosome structures compatible with assemblysomes from the cytoplasm of cells and makes the cells more sensitive to X-ray treatment. Taken together, these findings suggest that assemblysomes may be a component of the DNA damage response from yeast to human.
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Affiliation(s)
- Orsolya Németh-Szatmári
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Bence Nagy-Mikó
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Ádám Györkei
- Institute of Biochemistry, Biological Research Centre, 6726 Szeged, Hungary
- Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Dániel Varga
- Department of Optics and Quantum Electronics, University of Szeged, 6720 Szeged, Hungary
| | - Bálint Barna H Kovács
- Department of Optics and Quantum Electronics, University of Szeged, 6720 Szeged, Hungary
| | - Nóra Igaz
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Bence Bognár
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Zsolt Rázga
- Department of Pathology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary
| | - Gábor Nagy
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Nóra Zsindely
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - László Bodai
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Balázs Papp
- Institute of Biochemistry, Biological Research Centre, 6726 Szeged, Hungary
| | - Miklós Erdélyi
- Department of Optics and Quantum Electronics, University of Szeged, 6720 Szeged, Hungary
| | - Mónika Kiricsi
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - András Blastyák
- Institute of Genetics, Biological Research Centre, 6726 Szeged, Hungary
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland
| | - Imre M Boros
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Zoltán Villányi
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
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48
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Dallastella M, de Oliveira WK, Rodrigues ML, Goldenberg S, Alves LR. The characterization of RNA-binding proteins and RNA metabolism-related proteins in fungal extracellular vesicles. Front Cell Infect Microbiol 2023; 13:1247329. [PMID: 37780856 PMCID: PMC10539620 DOI: 10.3389/fcimb.2023.1247329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 08/23/2023] [Indexed: 10/03/2023] Open
Abstract
RNA-binding proteins (RBPs) are essential for regulating RNA metabolism, stability, and translation within cells. Recent studies have shown that RBPs are not restricted to intracellular functions and can be found in extracellular vesicles (EVs) in different mammalian cells. EVs released by fungi contain a variety of proteins involved in RNA metabolism. These include RNA helicases, which play essential roles in RNA synthesis, folding, and degradation. Aminoacyl-tRNA synthetases, responsible for acetylating tRNA molecules, are also enriched in EVs, suggesting a possible link between these enzymes and tRNA fragments detected in EVs. Proteins with canonical RNA-binding domains interact with proteins and RNA, such as the RNA Recognition Motif (RRM), Zinc finger, and hnRNP K-homology (KH) domains. Polyadenylate-binding protein (PABP) plays a critical role in the regulation of gene expression by binding the poly(A) tail of messenger RNA (mRNA) and facilitating its translation, stability, and localization, making it a key factor in post-transcriptional control of gene expression. The presence of proteins related to the RNA life cycle in EVs from different fungal species suggests a conserved mechanism of EV cargo packing. Various models have been proposed for selecting RNA molecules for release into EVs. Still, the actual loading processes are unknown, and further molecular characterization of these proteins may provide insight into the mechanism of RNA sorting into EVs. This work reviews the current knowledge of RBPs and proteins related to RNA metabolism in EVs derived from distinct fungi species, and presents an analysis of proteomic datasets through GO term and orthology analysis, Our investigation identified orthologous proteins in fungal EVs on different fungal species.
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Affiliation(s)
- Marianna Dallastella
- Gene Expression Regulation Laboratory, Carlos Chagas Institute (ICC), Oswaldo Cruz Foundation, FIOCRUZ, Curitiba, Brazil
| | - Willian Klassen de Oliveira
- Laboratory for Applied Sciences and Technology in Health, Carlos Chagas Institute, FIOCRUZ PR, Curitiba, Brazil
| | - Marcio L. Rodrigues
- Gene Expression Regulation Laboratory, Carlos Chagas Institute (ICC), Oswaldo Cruz Foundation, FIOCRUZ, Curitiba, Brazil
- Microbiology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Samuel Goldenberg
- Gene Expression Regulation Laboratory, Carlos Chagas Institute (ICC), Oswaldo Cruz Foundation, FIOCRUZ, Curitiba, Brazil
| | - Lysangela R. Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute (ICC), Oswaldo Cruz Foundation, FIOCRUZ, Curitiba, Brazil
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center, University Laval, Quebec, QC, Canada
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49
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Hoffmann G, López-González S, Mahboubi A, Hanson J, Hafrén A. Cauliflower mosaic virus protein P6 is a multivalent node for RNA granule proteins and interferes with stress granule responses during plant infection. THE PLANT CELL 2023; 35:3363-3382. [PMID: 37040611 PMCID: PMC10473198 DOI: 10.1093/plcell/koad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/06/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Biomolecular condensation is a multipurpose cellular process that viruses use ubiquitously during their multiplication. Cauliflower mosaic virus replication complexes are condensates that differ from those of most viruses, as they are nonmembranous assemblies that consist of RNA and protein, mainly the viral protein P6. Although these viral factories (VFs) were described half a century ago, with many observations that followed since, functional details of the condensation process and the properties and relevance of VFs have remained enigmatic. Here, we studied these issues in Arabidopsis thaliana and Nicotiana benthamiana. We observed a large dynamic mobility range of host proteins within VFs, while the viral matrix protein P6 is immobile, as it represents the central node of these condensates. We identified the stress granule (SG) nucleating factors G3BP7 and UBP1 family members as components of VFs. Similarly, as SG components localize to VFs during infection, ectopic P6 localizes to SGs and reduces their assembly after stress. Intriguingly, it appears that soluble rather than condensed P6 suppresses SG formation and mediates other essential P6 functions, suggesting that the increased condensation over the infection time-course may accompany a progressive shift in selected P6 functions. Together, this study highlights VFs as dynamic condensates and P6 as a complex modulator of SG responses.
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Affiliation(s)
- Gesa Hoffmann
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
- Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Silvia López-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
- Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Amir Mahboubi
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90736 Umeå, Sweden
| | - Johannes Hanson
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90736 Umeå, Sweden
| | - Anders Hafrén
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
- Linnean Center for Plant Biology, 75007 Uppsala, Sweden
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50
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Wen J, Qin Z, Sun L, Zhang Y, Wang D, Peng H, Yao Y, Hu Z, Ni Z, Sun Q, Xin M. Alternative splicing of TaHSFA6e modulates heat shock protein-mediated translational regulation in response to heat stress in wheat. THE NEW PHYTOLOGIST 2023; 239:2235-2247. [PMID: 37403528 DOI: 10.1111/nph.19100] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/30/2023] [Indexed: 07/06/2023]
Abstract
Heat stress greatly threatens crop production. Plants have evolved multiple adaptive mechanisms, including alternative splicing, that allow them to withstand this stress. However, how alternative splicing contributes to heat stress responses in wheat (Triticum aestivum) is unclear. We reveal that the heat shock transcription factor gene TaHSFA6e is alternatively spliced in response to heat stress. TaHSFA6e generates two major functional transcripts: TaHSFA6e-II and TaHSFA6e-III. TaHSFA6e-III enhances the transcriptional activity of three downstream heat shock protein 70 (TaHSP70) genes to a greater extent than does TaHSFA6e-II. Further investigation reveals that the enhanced transcriptional activity of TaHSFA6e-III is due to a 14-amino acid peptide at its C-terminus, which arises from alternative splicing and is predicted to form an amphipathic helix. Results show that knockout of TaHSFA6e or TaHSP70s increases heat sensitivity in wheat. Moreover, TaHSP70s are localized in stress granule following exposure to heat stress and are involved in regulating stress granule disassembly and translation re-initiation upon stress relief. Polysome profiling analysis confirms that the translational efficiency of stress granule stored mRNAs is lower at the recovery stage in Tahsp70s mutants than in the wild types. Our finding provides insight into the molecular mechanisms by which alternative splicing improves the thermotolerance in wheat.
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Affiliation(s)
- Jingjing Wen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhen Qin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Lv Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yumei Zhang
- Qingdao Agricultural University, Qingdao, 266109, China
| | - Dongli Wang
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
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