1
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Li Y, Feng Y, Geng S, Xu F, Guo H. The role of liquid-liquid phase separation in defining cancer EMT. Life Sci 2024; 353:122931. [PMID: 39038510 DOI: 10.1016/j.lfs.2024.122931] [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: 04/28/2024] [Revised: 07/08/2024] [Accepted: 07/19/2024] [Indexed: 07/24/2024]
Abstract
Cancer EMT is a pivotal process that drives carcinogenesis, metastasis, and cancer recurrence, with its initiation and regulation intricately governed by biochemical pathways in a precise spatiotemporal manner. Recently, the membrane-less biomolecular condensates formed via liquid-liquid phase separation (LLPS) have emerged as a universal mechanism underlying the spatiotemporal collaboration of biological activities in cancer EMT. In this review, we first elucidate the current understanding of LLPS formation and its cellular functions, followed by an overview of valuable tools for investigating LLPS. Secondly, we examine in detail the LLPS-mediated biological processes crucial for the initiation and regulation of cancer EMT. Lastly, we address current challenges in advancing LLPS research and explore the potential modulation of LLPS using therapeutic agents.
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Affiliation(s)
- Yuan Li
- MOE Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Yuqing Feng
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China; Department of Dermatology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, PR China
| | - Songmei Geng
- Department of Dermatology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, PR China
| | - Feng Xu
- MOE Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China.
| | - Hui Guo
- Department of Medical Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, PR China.
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2
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Wang H, Vant JW, Zhang A, Sanchez RG, Wu Y, Micou ML, Luczak V, Whiddon Z, Carlson NM, Yu SB, Jabbo M, Yoon S, Abushawish AA, Ghassemian M, Masubuchi T, Gan Q, Watanabe S, Griffis ER, Hammarlund M, Singharoy A, Pekkurnaz G. Organization of a functional glycolytic metabolon on mitochondria for metabolic efficiency. Nat Metab 2024:10.1038/s42255-024-01121-9. [PMID: 39261628 DOI: 10.1038/s42255-024-01121-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 08/02/2024] [Indexed: 09/13/2024]
Abstract
Glucose, the primary cellular energy source, is metabolized through glycolysis initiated by the rate-limiting enzyme hexokinase (HK). In energy-demanding tissues like the brain, HK1 is the dominant isoform, primarily localized on mitochondria, and is crucial for efficient glycolysis-oxidative phosphorylation coupling and optimal energy generation. This study unveils a unique mechanism regulating HK1 activity, glycolysis and the dynamics of mitochondrial coupling, mediated by the metabolic sensor enzyme O-GlcNAc transferase (OGT). OGT catalyses reversible O-GlcNAcylation, a post-translational modification influenced by glucose flux. Elevated OGT activity induces dynamic O-GlcNAcylation of the regulatory domain of HK1, subsequently promoting the assembly of the glycolytic metabolon on the outer mitochondrial membrane. This modification enhances the mitochondrial association with HK1, orchestrating glycolytic and mitochondrial ATP production. Mutation in HK1's O-GlcNAcylation site reduces ATP generation in multiple cell types, specifically affecting metabolic efficiency in neurons. This study reveals a previously unappreciated pathway that links neuronal metabolism and mitochondrial function through OGT and the formation of the glycolytic metabolon, providing potential strategies for tackling metabolic and neurological disorders.
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Affiliation(s)
- Haoming Wang
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - John W Vant
- Biodesign Institute, The School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Andrew Zhang
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Richard G Sanchez
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Youjun Wu
- Department of Genetics and Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Mary L Micou
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Thomas Jefferson University, Philadelphia, PA, USA
| | - Vincent Luczak
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Neurocrine Biosciences, San Diego, CA, USA
| | - Zachary Whiddon
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Natasha M Carlson
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Seungyoon B Yu
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | - Mirna Jabbo
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Seokjun Yoon
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- University of Southern California, Los Angeles, CA, USA
| | - Ahmed A Abushawish
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, University of California San Diego, La Jolla, CA, USA
| | - Takeya Masubuchi
- Cell and Developmental Biology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Quan Gan
- Department of Cell Biology, Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA
| | - Shigeki Watanabe
- Department of Cell Biology, Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA
| | - Eric R Griffis
- Nikon Imaging Center, University of California San Diego, La Jolla, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Marc Hammarlund
- Department of Genetics and Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Abhishek Singharoy
- Biodesign Institute, The School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Gulcin Pekkurnaz
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
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3
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Lin W, Nagy PD. Co-opted cytosolic proteins form condensate substructures within membranous replication organelles of a positive-strand RNA virus. THE NEW PHYTOLOGIST 2024; 243:1917-1935. [PMID: 38515267 DOI: 10.1111/nph.19691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024]
Abstract
Positive-strand RNA viruses co-opt organellar membranes for biogenesis of viral replication organelles (VROs). Tombusviruses also co-opt pro-viral cytosolic proteins to VROs. It is currently not known what type of molecular organization keeps co-opted proteins sequestered within membranous VROs. In this study, we employed tomato bushy stunt virus (TBSV) and carnation Italian ringspot virus (CIRV) - Nicotiana benthamiana pathosystems to identify biomolecular condensate formation in VROs. We show that TBSV p33 and the CIRV p36 replication proteins sequester glycolytic and fermentation enzymes in unique condensate substructures associated with membranous VROs. We find that p33 and p36 form droplets in vitro driven by intrinsically disordered region. The replication protein organizes partitioning of co-opted host proteins into droplets. VRO-associated condensates are critical for local adenosine triphosphate production to support energy for virus replication. We find that co-opted endoplasmic reticulum membranes and actin filaments form meshworks within and around VRO condensates, contributing to unique composition and structure. We propose that p33/p36 organize liquid-liquid phase separation of co-opted concentrated host proteins in condensate substructures within membranous VROs. Overall, we demonstrate that subverted membranes and condensate substructures co-exist and are critical for VRO functions. The replication proteins induce and connect the two substructures within VROs.
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Affiliation(s)
- Wenwu Lin
- Department of Plant Pathology, University of Kentucky, Lexington, KY, 40543, USA
| | - Peter D Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, KY, 40543, USA
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4
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DeMichele E, Buret AG, Taylor CT. Hypoxia-inducible factor-driven glycolytic adaptations in host-microbe interactions. Pflugers Arch 2024; 476:1353-1368. [PMID: 38570355 PMCID: PMC11310250 DOI: 10.1007/s00424-024-02953-w] [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: 02/06/2024] [Revised: 02/07/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Mammalian cells utilize glucose as a primary carbon source to produce energy for most cellular functions. However, the bioenergetic homeostasis of cells can be perturbed by environmental alterations, such as changes in oxygen levels which can be associated with bacterial infection. Reduction in oxygen availability leads to a state of hypoxia, inducing numerous cellular responses that aim to combat this stress. Importantly, hypoxia strongly augments cellular glycolysis in most cell types to compensate for the loss of aerobic respiration. Understanding how this host cell metabolic adaptation to hypoxia impacts the course of bacterial infection will identify new anti-microbial targets. This review will highlight developments in our understanding of glycolytic substrate channeling and spatiotemporal enzymatic organization in response to hypoxia, shedding light on the integral role of the hypoxia-inducible factor (HIF) during host-pathogen interactions. Furthermore, the ability of intracellular and extracellular bacteria (pathogens and commensals alike) to modulate host cellular glucose metabolism will be discussed.
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Affiliation(s)
- Emily DeMichele
- School of Medicine and Systems Biology Ireland, The Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Andre G Buret
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Cormac T Taylor
- School of Medicine and Systems Biology Ireland, The Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
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5
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Lynch EM, Hansen H, Salay L, Cooper M, Timr S, Kollman JM, Webb BA. Structural basis for allosteric regulation of human phosphofructokinase-1. Nat Commun 2024; 15:7323. [PMID: 39183237 PMCID: PMC11345425 DOI: 10.1038/s41467-024-51808-6] [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: 03/28/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024] Open
Abstract
Phosphofructokinase-1 (PFK1) catalyzes the rate-limiting step of glycolysis, committing glucose to conversion into cellular energy. PFK1 is highly regulated to respond to the changing energy needs of the cell. In bacteria, the structural basis of PFK1 regulation is a textbook example of allostery; molecular signals of low and high cellular energy promote transition between an active R-state and inactive T-state conformation, respectively. Little is known, however, about the structural basis for regulation of eukaryotic PFK1. Here, we determine structures of the human liver isoform of PFK1 (PFKL) in the R- and T-state by cryoEM, providing insight into eukaryotic PFK1 allosteric regulatory mechanisms. The T-state structure reveals conformational differences between the bacterial and eukaryotic enzyme, the mechanisms of allosteric inhibition by ATP binding at multiple sites, and an autoinhibitory role of the C-terminus in stabilizing the T-state. We also determine structures of PFKL filaments that define the mechanism of higher-order assembly and demonstrate that these structures are necessary for higher-order assembly of PFKL in cells.
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Affiliation(s)
- Eric M Lynch
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Heather Hansen
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV, USA
| | - Lauren Salay
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Madison Cooper
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV, USA
| | - Stepan Timr
- Department of Computational Chemistry, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - Bradley A Webb
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV, USA.
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6
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Glorieux C, Liu S, Trachootham D, Huang P. Targeting ROS in cancer: rationale and strategies. Nat Rev Drug Discov 2024; 23:583-606. [PMID: 38982305 DOI: 10.1038/s41573-024-00979-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2024] [Indexed: 07/11/2024]
Abstract
Reactive oxygen species (ROS) in biological systems are transient but essential molecules that are generated and eliminated by a complex set of delicately balanced molecular machineries. Disruption of redox homeostasis has been associated with various human diseases, especially cancer, in which increased ROS levels are thought to have a major role in tumour development and progression. As such, modulation of cellular redox status by targeting ROS and their regulatory machineries is considered a promising therapeutic strategy for cancer treatment. Recently, there has been major progress in this field, including the discovery of novel redox signalling pathways that affect the metabolism of tumour cells as well as immune cells in the tumour microenvironment, and the intriguing ROS regulation of biomolecular phase separation. Progress has also been made in exploring redox regulation in cancer stem cells, the role of ROS in determining cell fate and new anticancer agents that target ROS. This Review discusses these research developments and their implications for cancer therapy and drug discovery, as well as emerging concepts, paradoxes and future perspectives.
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Affiliation(s)
- Christophe Glorieux
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Shihua Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | | | - Peng Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.
- Metabolic Innovation Center, Sun Yat-Sen University, Guangzhou, China.
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7
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Zhang D, Wickramasinghe SR, Zydney AL, Smelko JP, Loman A, Wheeler A, Qian X. Proteomic analysis of host cell protein fouling during bioreactor harvesting. Biotechnol Prog 2024; 40:e3453. [PMID: 38477450 DOI: 10.1002/btpr.3453] [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: 07/25/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024]
Abstract
Chinese hamster ovary (CHO) cells are among the most common cell lines used for therapeutic protein production. Membrane fouling during bioreactor harvesting is a major limitation for the downstream purification of therapeutic proteins. Host cell proteins (HCP) are the most challenging impurities during downstream purification processes. The present work focuses on identification of HCP foulants during CHO bioreactor harvesting using reverse asymmetrical commercial membrane BioOptimal™ MF-SL. In order to investigate foulants and fouling behavior during cell clarification, for the first time a novel backwash process was developed to effectively elute almost all the HCP and DNA from the fouled membrane filter. The isoelectric points (pIs) and molecular weights (MWs) of major HCP in the bioreactor harvest and fouled on the membrane were successfully characterized using two-dimensional gel electrophoresis (2D SDS-PAGE). In addition, a total of 8 HCP were identified using matrix-assisted laser desorption/ionization-mass spectroscopy (MALDI-MS). The majority of these HCP are enzymes or associated with exosomes, both of which can form submicron-sized particles which could lead to the plugging of the filters.
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Affiliation(s)
- Da Zhang
- Ralph E. Martin Department of Chemical Engineering, University of Arkansas, Fayetteville, Arkansas, USA
| | - S Ranil Wickramasinghe
- Ralph E. Martin Department of Chemical Engineering, University of Arkansas, Fayetteville, Arkansas, USA
| | - Andrew L Zydney
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - John P Smelko
- Biogen, Research Triangle Park, Durham, North Carolina, USA
| | - Abdullah Loman
- Biogen, Research Triangle Park, Durham, North Carolina, USA
| | - April Wheeler
- Asahi Kasei Bioprocess American, Glenview, Illinois, USA
| | - Xianghong Qian
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, Arkansas, USA
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8
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Crawford RA, Eastham M, Pool MR, Ashe MP. Orchestrated centers for the production of proteins or "translation factories". WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1867. [PMID: 39048533 DOI: 10.1002/wrna.1867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/20/2024] [Accepted: 06/07/2024] [Indexed: 07/27/2024]
Abstract
The mechanics of how proteins are generated from mRNA is increasingly well understood. However, much less is known about how protein production is coordinated and orchestrated within the crowded intracellular environment, especially in eukaryotic cells. Recent studies suggest that localized sites exist for the coordinated production of specific proteins. These sites have been termed "translation factories" and roles in protein complex formation, protein localization, inheritance, and translation regulation have been postulated. In this article, we review the evidence supporting the translation of mRNA at these sites, the details of their mechanism of formation, and their likely functional significance. Finally, we consider the key uncertainties regarding these elusive structures in cells. This article is categorized under: Translation Translation > Mechanisms RNA Export and Localization > RNA Localization Translation > Regulation.
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Affiliation(s)
- Robert A Crawford
- Division of Molecular and Cellular Function, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Matthew Eastham
- Division of Molecular and Cellular Function, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Martin R Pool
- Division of Molecular and Cellular Function, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Mark P Ashe
- Division of Molecular and Cellular Function, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
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9
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Creamer DR, Beynon RJ, Hubbard SJ, Ashe MP, Grant CM. Isoform-specific sequestration of protein kinase A fine-tunes intracellular signaling during heat stress. Cell Rep 2024; 43:114360. [PMID: 38865242 DOI: 10.1016/j.celrep.2024.114360] [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: 12/22/2023] [Revised: 04/24/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
Protein kinase A (PKA) is a conserved kinase crucial for fundamental biological processes linked to growth, development, and metabolism. The PKA catalytic subunit is expressed as multiple isoforms in diverse eukaryotes; however, their contribution to ensuring signaling specificity in response to environmental cues remains poorly defined. Catalytic subunit activity is classically moderated via interaction with an inhibitory regulatory subunit. Here, a quantitative mass spectrometry approach is used to examine heat-stress-induced changes in the binding of yeast Tpk1-3 catalytic subunits to the Bcy1 regulatory subunit. We show that Tpk3 is not regulated by Bcy1 binding but, instead, is deactivated upon heat stress via reversible sequestration into cytoplasmic granules. These "Tpk3 granules" are enriched for multiple PKA substrates involved in various metabolic processes, with the Hsp42 sequestrase required for their formation. Hence, regulated sequestration of Tpk3 provides a mechanism to control isoform-specific kinase signaling activity during stress conditions.
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Affiliation(s)
- Declan R Creamer
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Simon J Hubbard
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Mark P Ashe
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Chris M Grant
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.
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10
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Nesterov SV, Ilyinsky NS, Plokhikh KS, Manuylov VD, Chesnokov YM, Vasilov RG, Kuznetsova IM, Turoverov KK, Gordeliy VI, Fonin AV, Uversky VN. Order wrapped in chaos: On the roles of intrinsically disordered proteins and RNAs in the arrangement of the mitochondrial enzymatic machines. Int J Biol Macromol 2024; 267:131455. [PMID: 38588835 DOI: 10.1016/j.ijbiomac.2024.131455] [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: 11/11/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
The analysis of cryo-electron tomography images of human and rat mitochondria revealed that the mitochondrial matrix is at least as crowded as the cytosol. To mitigate the crowding effects, metabolite transport in the mitochondria primarily occurs through the intermembrane space, which is significantly less crowded. The scientific literature largely ignores how enzyme systems and metabolite transport are organized in the crowded environment of the mitochondrial matrix. Under crowded conditions, multivalent interactions carried out by disordered protein regions (IDRs), may become extremely important. We analyzed the human mitochondrial proteome to determine the presence and physiological significance of IDRs. Despite mitochondrial proteins being generally more ordered than cytosolic or overall proteome proteins, disordered regions plays a significant role in certain mitochondrial compartments and processes. Even in highly ordered enzyme systems, there are proteins with long IDRs. Some IDRs act as binding elements between highly ordered subunits, while the roles of others are not yet established. Mitochondrial systems, like their bacterial ancestors, rely less on IDRs and more on RNA for LLPS compartmentalization. More evolutionarily advanced subsystems that enable mitochondria-cell interactions contain more IDRs. The study highlights the crucial and often overlooked role played by IDRs and non-coding RNAs in mitochondrial organization.
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Affiliation(s)
- Semen V Nesterov
- National Research Center "Kurchatov Institute", Moscow 123182, Russia; Moscow Institute of Physics and Techonology, Dolgoprudny, Moscow Region 141701, Russia; Institute of Cytology, Russian Academy of Sciences, Saint Petersburg 194064, Russia.
| | - Nikolay S Ilyinsky
- Moscow Institute of Physics and Techonology, Dolgoprudny, Moscow Region 141701, Russia.
| | | | - Vladimir D Manuylov
- Moscow Institute of Physics and Techonology, Dolgoprudny, Moscow Region 141701, Russia
| | - Yuriy M Chesnokov
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - Raif G Vasilov
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - Irina M Kuznetsova
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg 194064, Russia
| | | | - Valentin I Gordeliy
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, 38027 Grenoble, France
| | - Alexander V Fonin
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg 194064, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA.
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11
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Li C, Hao B, Yang H, Wang K, Fan L, Xiao W. Protein aggregation and biomolecular condensation in hypoxic environments (Review). Int J Mol Med 2024; 53:33. [PMID: 38362920 PMCID: PMC10903932 DOI: 10.3892/ijmm.2024.5357] [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: 11/08/2023] [Accepted: 01/15/2024] [Indexed: 02/17/2024] Open
Abstract
Due to molecular forces, biomacromolecules assemble into liquid condensates or solid aggregates, and their corresponding formation and dissolution processes are controlled. Protein homeostasis is disrupted by increasing age or environmental stress, leading to irreversible protein aggregation. Hypoxic pressure is an important factor in this process, and uncontrolled protein aggregation has been widely observed in hypoxia‑related conditions such as neurodegenerative disease, cardiovascular disease, hypoxic brain injury and cancer. Biomolecular condensates are also high‑order complexes assembled from macromolecules. Although they exist in different phase from protein aggregates, they are in dynamic balance under certain conditions, and their activation or assembly are considered as important regulatory processes in cell survival with hypoxic pressure. Therefore, a better understanding of the relationship between hypoxic stress, protein aggregation and biomolecular condensation will bring marked benefits in the clinical treatment of various diseases. The aim of the present review was to summarize the underlying mechanisms of aggregate assembly and dissolution induced by hypoxic conditions, and address recent breakthroughs in understanding the role of aggregates in hypoxic‑related diseases, given the hypotheses that hypoxia induces macromolecular assemblage changes from a liquid to a solid phase, and that adenosine triphosphate depletion and ATP‑driven inactivation of multiple protein chaperones play important roles among the process. Moreover, it is anticipated that an improved understanding of the adaptation in hypoxic environments could extend the overall survival of patients and provide new strategies for hypoxic‑related diseases.
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Affiliation(s)
- Chaoqun Li
- School of Exercise and Health, Shanghai University of Sport, Shanghai 200438, P.R. China
- Institute of Energy Metabolism and Health, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Bingjie Hao
- Institute of Energy Metabolism and Health, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Haiguang Yang
- Institute of Energy Metabolism and Health, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Kai Wang
- Institute of Energy Metabolism and Health, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Lihong Fan
- School of Exercise and Health, Shanghai University of Sport, Shanghai 200438, P.R. China
- Institute of Energy Metabolism and Health, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Weihua Xiao
- School of Exercise and Health, Shanghai University of Sport, Shanghai 200438, P.R. China
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12
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Lynch EM, Hansen H, Salay L, Cooper M, Timr S, Kollman JM, Webb BA. Structural basis for allosteric regulation of human phosphofructokinase-1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585110. [PMID: 38559074 PMCID: PMC10980016 DOI: 10.1101/2024.03.15.585110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Phosphofructokinase-1 (PFK1) catalyzes the rate-limiting step of glycolysis, committing glucose to conversion into cellular energy. PFK1 is highly regulated to respond to the changing energy needs of the cell. In bacteria, the structural basis of PFK1 regulation is a textbook example of allostery; molecular signals of low and high cellular energy promote transition between an active R-state and inactive T-state conformation, respectively Little is known, however, about the structural basis for regulation of eukaryotic PFK1. Here, we determine structures of the human liver isoform of PFK1 (PFKL) in the R- and T-state by cryoEM, providing insight into eukaryotic PFK1 allosteric regulatory mechanisms. The T-state structure reveals conformational differences between the bacterial and eukaryotic enzyme, the mechanisms of allosteric inhibition by ATP binding at multiple sites, and an autoinhibitory role of the C-terminus in stabilizing the T-state. We also determine structures of PFKL filaments that define the mechanism of higher-order assembly and demonstrate that these structures are necessary for higher-order assembly of PFKL in cells.
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Affiliation(s)
- Eric M Lynch
- Department of Biochemistry, University of Washington
| | - Heather Hansen
- Department of Biochemistry and Molecular Medicine, West Virginia University
| | - Lauren Salay
- Department of Biochemistry, University of Washington
| | - Madison Cooper
- Department of Biochemistry and Molecular Medicine, West Virginia University
| | - Stepan Timr
- Department of Computational Chemistry, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences
| | | | - Bradley A Webb
- Department of Biochemistry and Molecular Medicine, West Virginia University
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13
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Ikari N, Honjo K, Sagami Y, Nakamura Y, Arakawa H. Mieap forms membrane-less organelles involved in cardiolipin metabolism. iScience 2024; 27:108916. [PMID: 38322995 PMCID: PMC10845071 DOI: 10.1016/j.isci.2024.108916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 11/16/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024] Open
Abstract
Biomolecular condensates (BCs) are formed by proteins with intrinsically disordered regions (IDRs) via liquid-liquid phase separation. Mieap/Spata18, a p53-inducible protein, participates in suppression of colorectal tumors by promoting mitochondrial quality control. However, the regulatory mechanism involved remains unclear. Here, we report that Mieap is an IDR-containing protein that drives formation of BCs involved in cardiolipin metabolism. Mieap BCs specifically phase separate the mitochondrial phospholipid, cardiolipin. Mieap directly binds to cardiolipin in vitro. Lipidomic analysis of cardiolipin suggests that Mieap promotes enzymatic reactions in cardiolipin biosynthesis and remodeling. Accordingly, four cardiolipin biosynthetic enzymes, TAMM41, PGS1, PTPMT1, and CRLS1 and two remodeling enzymes, PLA2G6 and TAZ, are phase-separated by Mieap BCs. Mieap-deficient cells exhibit altered crista structure, leading to decreased respiration activity and ATP production in mitochondria. These results suggest that Mieap may form membrane-less organelles to compartmentalize and facilitate cardiolipin metabolism, thus potentially contributing to mitochondrial quality control.
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Affiliation(s)
- Naoki Ikari
- Division of Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Katsuko Honjo
- Division of Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Yoko Sagami
- Division of Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Yasuyuki Nakamura
- Division of Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Hirofumi Arakawa
- Division of Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
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14
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He Z, Li S, Zhao F, Sun H, Hu J, Wang J, Liu X, Li M, Zhao Z, Luo Y. LncRNA and Protein Expression Profiles Reveal Heart Adaptation to High-Altitude Hypoxia in Tibetan Sheep. Int J Mol Sci 2023; 25:385. [PMID: 38203557 PMCID: PMC10779337 DOI: 10.3390/ijms25010385] [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: 11/28/2023] [Revised: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
The Tibetan sheep has an intricate mechanism of adaptation to low oxygen levels, which is influenced by both genetic and environmental factors. The heart plays a crucial role in the adaptation of Tibetan sheep to hypoxia. In the present study, we utilized transcriptomic and proteomic technologies to comprehensively analyze and identify the long non-coding RNAs (lncRNAs), genes, proteins, pathways, and gene ontology (GO) terms associated with hypoxic adaptation in Tibetan sheep at three different altitudes (2500 m, 3500 m, and 4500 m). By integrating the differentially expressed (DE) lncRNA target genes, differentially expressed proteins (DEPs), and differentially expressed genes (DEGs), we were able to identify and characterize the mechanisms underlying hypoxic adaptation in Tibetan sheep. Through this integration, we identified 41 shared genes/proteins, and functional enrichment analyses revealed their close association with lipid metabolism, glycolysis/gluconeogenesis, and angiogenesis. Additionally, significant enrichment was observed in important pathways such as the PPAR signaling pathway, glycolysis/gluconeogenesis, the oxoacid metabolic process, and angiogenesis. Furthermore, the co-expression network of lncRNAs and mRNAs demonstrated that lncRNAs (MSTRG.4748.1, ENSOART00020025894, and ENSOART00020036371) may play a pivotal role in the adaptation of Tibetan sheep to the hypoxic conditions of the plateau. In conclusion, this study expands the existing database of lncRNAs and proteins in Tibetan sheep, and these findings may serve as a reference for the prevention of altitude sickness in humans.
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Affiliation(s)
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.H.); (F.Z.); (H.S.); (J.H.); (J.W.); (X.L.); (M.L.); (Z.Z.)
| | | | | | | | | | | | | | | | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.H.); (F.Z.); (H.S.); (J.H.); (J.W.); (X.L.); (M.L.); (Z.Z.)
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15
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Jeon M, Schmitt DL, Kyoung M, An S. Size-Specific Modulation of a Multienzyme Glucosome Assembly during the Cell Cycle. ACS BIO & MED CHEM AU 2023; 3:461-470. [PMID: 37876499 PMCID: PMC10591302 DOI: 10.1021/acsbiomedchemau.3c00037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 10/26/2023]
Abstract
Enzymes in glucose metabolism have been subjected to numerous studies, revealing the importance of their biological roles during the cell cycle. However, due to the lack of viable experimental strategies for measuring enzymatic activities particularly in living human cells, it has been challenging to address whether their enzymatic activities and thus anticipated glucose flux are directly associated with cell cycle progression. It has remained largely elusive how human cells regulate glucose metabolism at a subcellular level to meet the metabolic demands during the cell cycle. Meanwhile, we have characterized that rate-determining enzymes in glucose metabolism are spatially organized into three different sizes of multienzyme metabolic assemblies, termed glucosomes, to regulate the glucose flux between energy metabolism and building block biosynthesis. In this work, we first determined using cell synchronization and flow cytometric techniques that enhanced green fluorescent protein-tagged phosphofructokinase is adequate as an intracellular biomarker to evaluate the state of glucose metabolism during the cell cycle. We then applied fluorescence single-cell imaging strategies and discovered that the percentage of Hs578T cells showing small-sized glucosomes is drastically changed during the cell cycle, whereas the percentage of cells with medium-sized glucosomes is significantly elevated only in the G1 phase, but the percentage of cells showing large-sized glucosomes is barely or minimally altered along the cell cycle. Should we consider our previous localization-function studies that showed assembly size-dependent metabolic roles of glucosomes, this work strongly suggests that glucosome sizes are modulated during the cell cycle to regulate glucose flux between glycolysis and building block biosynthesis. Therefore, we propose the size-specific modulation of glucosomes as a behind-the-scenes mechanism that may explain functional association of glucose metabolism with the cell cycle and, thereby, their metabolic significance in human cell biology.
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Affiliation(s)
- Miji Jeon
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County (UMBC); 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
| | - Danielle L. Schmitt
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County (UMBC); 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
| | - Minjoung Kyoung
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County (UMBC); 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
- Program
in Oncology, Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, Maryland 21201, United States
| | - Songon An
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County (UMBC); 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
- Program
in Oncology, Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, Maryland 21201, United States
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16
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Wang T, Li X, Liu N, Yang Y, Gong Q. TurboID-based proximity labelling reveals a connection between VPS34 and cellular homeostasis. JOURNAL OF PLANT PHYSIOLOGY 2023; 289:154100. [PMID: 37748420 DOI: 10.1016/j.jplph.2023.154100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 09/27/2023]
Abstract
Unlike animals, plants and yeasts only have a class III phosphatidylinositol 3-kinase (PI3KC3). Its lipid product, phosphatidylinositol 3-phosphate (PtdIns-3-P, PI3P), organizes intracellular trafficking routes such as autophagosome formation, multivesicular body (MVB) formation, retro-transport from trans-Golgi network (TGN) to late Golgi, and the fusion events between autophagosomes and MVBs and the vacuole. The catalytic subunit of plant PI3KC3 is encoded by the essential gene Vacuolar Protein Sorting 34 (VPS34). Despite the importance of VPS34 in cellular homeostasis and plant development, a VPS34 interactome is lacking. Here we employed TurboID, an enzyme-catalyzed proximity labelling (PL) method, to describe a proximal interactome of Arabidopsis VPS34. TurboID catalyzed spatially restricted biotinylation and enabled VPS34-specific enrichment of 273 proteins from affinity purification coupled with mass spectrometry. The interactome confirmed known functions of VPS34 in endo-lysosomal trafficking. Intriguingly, carbohydrate metabolism was the most enriched Gene Ontology (GO) term, including glycolytic enzymes in the triose portion and enzymes functioning in chloroplast triose export and sucrose biosynthesis. The interaction between VPS34 and the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH, GAPC1/2) was validated in planta. Also verified was the interaction between VPS34 and the plasma membrane H+-ATPase AHA2, a primary determinant of membrane potential. Our study links PI3KC3 to carbohydrate metabolism and membrane potential, two key processes that maintain cellular homeostasis.
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Affiliation(s)
- Taotao Wang
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Xinjing Li
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Ningjing Liu
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Yi Yang
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Qingqiu Gong
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
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17
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Wang H, Vant J, Wu Y, Sanchez R, Micou ML, Zhang A, Luczak V, Yu SB, Jabbo M, Yoon S, Abushawish AA, Ghassemian M, Griffis E, Hammarlund M, Singharoy A, Pekkurnaz G. Functional Organization of Glycolytic Metabolon on Mitochondria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.26.554955. [PMID: 37662343 PMCID: PMC10473731 DOI: 10.1101/2023.08.26.554955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Glucose, the primary cellular energy source, is metabolized through glycolysis initiated by the rate-limiting enzyme Hexokinase (HK). In energy-demanding tissues like the brain, HK1 is the dominant isoform, primarily localized on mitochondria, crucial for efficient glycolysis-oxidative phosphorylation coupling and optimal energy generation. This study unveils a unique mechanism regulating HK1 activity, glycolysis, and the dynamics of mitochondrial coupling, mediated by the metabolic sensor enzyme O-GlcNAc transferase (OGT). OGT catalyzes reversible O-GlcNAcylation, a post-translational modification, influenced by glucose flux. Elevated OGT activity induces dynamic O-GlcNAcylation of HK1's regulatory domain, subsequently promoting the assembly of the glycolytic metabolon on the outer mitochondrial membrane. This modification enhances HK1's mitochondrial association, orchestrating glycolytic and mitochondrial ATP production. Mutations in HK1's O-GlcNAcylation site reduce ATP generation, affecting synaptic functions in neurons. The study uncovers a novel pathway that bridges neuronal metabolism and mitochondrial function via OGT and the formation of the glycolytic metabolon, offering new prospects for tackling metabolic and neurological disorders.
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18
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Flood D, Lee ES, Taylor CT. Intracellular energy production and distribution in hypoxia. J Biol Chem 2023; 299:105103. [PMID: 37507013 PMCID: PMC10480318 DOI: 10.1016/j.jbc.2023.105103] [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: 04/04/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
The hydrolysis of ATP is the primary source of metabolic energy for eukaryotic cells. Under physiological conditions, cells generally produce more than sufficient levels of ATP to fuel the active biological processes necessary to maintain homeostasis. However, mechanisms underpinning the distribution of ATP to subcellular microenvironments with high local demand remain poorly understood. Intracellular distribution of ATP in normal physiological conditions has been proposed to rely on passive diffusion across concentration gradients generated by ATP producing systems such as the mitochondria and the glycolytic pathway. However, subcellular microenvironments can develop with ATP deficiency due to increases in local ATP consumption. Alternatively, ATP production can be reduced during bioenergetic stress during hypoxia. Mammalian cells therefore need to have the capacity to alter their metabolism and energy distribution strategies to compensate for local ATP deficits while also controlling ATP production. It is highly likely that satisfying the bioenergetic requirements of the cell involves the regulated distribution of ATP producing systems to areas of high ATP demand within the cell. Recently, the distribution (both spatially and temporally) of ATP-producing systems has become an area of intense investigation. Here, we review what is known (and unknown) about intracellular energy production and distribution and explore potential mechanisms through which this targeted distribution can be altered in hypoxia, with the aim of stimulating investigation in this important, yet poorly understood field of research.
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Affiliation(s)
- Darragh Flood
- Conway Institute of Biomolecular and Biomedical Research and School of Medicine, University College Dublin, Dublin, Ireland
| | - Eun Sang Lee
- Conway Institute of Biomolecular and Biomedical Research and School of Medicine, University College Dublin, Dublin, Ireland
| | - Cormac T Taylor
- Conway Institute of Biomolecular and Biomedical Research and School of Medicine, University College Dublin, Dublin, Ireland.
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19
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Solis-Miranda J, Chodasiewicz M, Skirycz A, Fernie AR, Moschou PN, Bozhkov PV, Gutierrez-Beltran E. Stress-related biomolecular condensates in plants. THE PLANT CELL 2023; 35:3187-3204. [PMID: 37162152 PMCID: PMC10473214 DOI: 10.1093/plcell/koad127] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/07/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023]
Abstract
Biomolecular condensates are membraneless organelle-like structures that can concentrate molecules and often form through liquid-liquid phase separation. Biomolecular condensate assembly is tightly regulated by developmental and environmental cues. Although research on biomolecular condensates has intensified in the past 10 years, our current understanding of the molecular mechanisms and components underlying their formation remains in its infancy, especially in plants. However, recent studies have shown that the formation of biomolecular condensates may be central to plant acclimation to stress conditions. Here, we describe the mechanism, regulation, and properties of stress-related condensates in plants, focusing on stress granules and processing bodies, 2 of the most well-characterized biomolecular condensates. In this regard, we showcase the proteomes of stress granules and processing bodies in an attempt to suggest methods for elucidating the composition and function of biomolecular condensates. Finally, we discuss how biomolecular condensates modulate stress responses and how they might be used as targets for biotechnological efforts to improve stress tolerance.
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Affiliation(s)
- Jorge Solis-Miranda
- Institutode Bioquimica Vegetal y Fotosintesis, Consejo Superior de Investigaciones Cientificas (CSIC)-Universidad de Sevilla, 41092 Sevilla, Spain
| | - Monika Chodasiewicz
- Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | | | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
- Department of Biology, University of Crete, Heraklion 71409, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Emilio Gutierrez-Beltran
- Institutode Bioquimica Vegetal y Fotosintesis, Consejo Superior de Investigaciones Cientificas (CSIC)-Universidad de Sevilla, 41092 Sevilla, Spain
- Departamento de Bioquimica Vegetal y Biologia Molecular, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain
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20
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Tang HS, Gates CR, Schultz MC. Biochemical evidence that the whole compartment activity behavior of GAPDH differs between the cytoplasm and nucleus. PLoS One 2023; 18:e0290892. [PMID: 37651389 PMCID: PMC10470895 DOI: 10.1371/journal.pone.0290892] [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: 06/23/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023] Open
Abstract
Some metabolic enzymes normally occur in the nucleus and cytoplasm. These compartments differ in molecular composition. Since post-translational modification and interaction with allosteric effectors can tune enzyme activity, it follows that the behavior of an enzyme as a catalyst may differ between the cytoplasm and nucleus. We explored this possibility for the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Homogenates of pristine nuclei and cytoplasms isolated from Xenopus laevis oocytes were used for whole compartment activity profiling in a near-physiological buffer. Titrations of NAD+ revealed similar whole compartment activity profiles for GAPDH in nuclear and cytoplasmic homogenates. Surprisingly however GAPDH in these compartments did not have the same behavior in assays of the dependence of initial velocity (v0) on G3P concentration. First, the peak v0 for nuclear GAPDH was up to 2.5-fold higher than the peak for cytoplasmic GAPDH. Second, while Michaelis Menten-like behavior was observed in all assays of cytoplasm, the v0 versus [G3P] plots for nuclear GAPDH typically exhibited a non-Michaelis Menten (sigmoidal) profile. Apparent Km and Vmax (G3P) values for nuclear GAPDH activity were highly variable, even between replicates of the same sample. Possible sources of this variability include in vitro processing of a metabolite that allosterically regulates GAPDH, turnover of a post-translational modification of the enzyme, and fluctuation of the state of interaction of GAPDH with other proteins. Collectively these findings are consistent with the hypothesis that the environment of the nucleus is distinct from the environment of the cytoplasm with regard to GAPDH activity and its modulation. This finding warrants further comparison of the regulation of nuclear and cytoplasmic GAPDH, as well as whole compartment activity profiling of other enzymes of metabolism with cytosolic and nuclear pools.
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Affiliation(s)
- Helen S. Tang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Chelsea R. Gates
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Michael C. Schultz
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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21
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Kierans SJ, Fagundes RR, Malkov MI, Sparkes R, Dillon ET, Smolenski A, Faber KN, Taylor CT. Hypoxia induces a glycolytic complex in intestinal epithelial cells independent of HIF-1-driven glycolytic gene expression. Proc Natl Acad Sci U S A 2023; 120:e2208117120. [PMID: 37603756 PMCID: PMC10469334 DOI: 10.1073/pnas.2208117120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/11/2023] [Indexed: 08/23/2023] Open
Abstract
The metabolic adaptation of eukaryotic cells to hypoxia involves increasing dependence upon glycolytic adenosine triphosphate (ATP) production, an event with consequences for cellular bioenergetics and cell fate. This response is regulated at the transcriptional level by the hypoxia-inducible factor-1(HIF-1)-dependent transcriptional upregulation of glycolytic enzymes (GEs) and glucose transporters. However, this transcriptional upregulation alone is unlikely to account fully for the levels of glycolytic ATP produced during hypoxia. Here, we investigated additional mechanisms regulating glycolysis in hypoxia. We observed that intestinal epithelial cells treated with inhibitors of transcription or translation and human platelets (which lack nuclei and the capacity for canonical transcriptional activity) maintained the capacity for hypoxia-induced glycolysis, a finding which suggests the involvement of a nontranscriptional component to the hypoxia-induced metabolic switch to a highly glycolytic phenotype. In our investigations into potential nontranscriptional mechanisms for glycolytic induction, we identified a hypoxia-sensitive formation of complexes comprising GEs and glucose transporters in intestinal epithelial cells. Surprisingly, the formation of such glycolytic complexes occurs independent of HIF-1-driven transcription. Finally, we provide evidence for the presence of HIF-1α in cytosolic fractions of hypoxic cells which physically interacts with the glucose transporter GLUT1 and the GEs in a hypoxia-sensitive manner. In conclusion, we provide insights into the nontranscriptional regulation of hypoxia-induced glycolysis in intestinal epithelial cells.
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Affiliation(s)
- Sarah J. Kierans
- University College Dublin School of Medicine, University College Dublin, DublinD4, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, DublinD4, Ireland
| | - Raphael R. Fagundes
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, GroningenD4, The Netherlands
| | - Mykyta I. Malkov
- University College Dublin School of Medicine, University College Dublin, DublinD4, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, DublinD4, Ireland
| | - Ríona Sparkes
- University College Dublin School of Medicine, University College Dublin, DublinD4, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, DublinD4, Ireland
| | - Eugène T. Dillon
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, DublinD4, Ireland
| | - Albert Smolenski
- University College Dublin School of Medicine, University College Dublin, DublinD4, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, DublinD4, Ireland
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, GroningenD4, The Netherlands
| | - Cormac T. Taylor
- University College Dublin School of Medicine, University College Dublin, DublinD4, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, DublinD4, Ireland
- Systems Biology Ireland, University College Dublin, DublinD4, Ireland
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22
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Murata Y, Hirayama R, Miura N, Kataoka M. Large-scale preparation of yeast strains expressing condensates derived from a glycolytic enzyme via controlled dissolved oxygen levels under hypoxia. Lett Appl Microbiol 2023; 76:ovad095. [PMID: 37587018 DOI: 10.1093/lambio/ovad095] [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: 05/16/2023] [Revised: 08/01/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
Under hypoxia, Saccharomyces cerevisiae forms cytoplasmic condensates composed of proteins, including glycolytic enzymes, that are thought to regulate cellular metabolism. However, the hypoxic conditions required for condensate formation remain unclear. In this study, we developed a 300-mL-scale culture method to produce condensate-forming cells by precisely controlling the dissolved oxygen (DO) level in the media. Using enolase as a model, a foci formation rate of more than 50% was achieved at ∼0.1% DO, and the results showed that the DO level affected the foci formation rate. The foci formation rates of the previously reported foci-deficient strains and strains with single amino acid substitutions in the endogenous enolase were examined, and the effect of these amino acid substitutions on glucose consumption and ethanol and glycerol production under hypoxia was evaluated. The results of this study contribute to the investigation of the mechanisms that regulate biomacromolecular condensates under hypoxia.
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Affiliation(s)
- Yuki Murata
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Japan
| | - Reina Hirayama
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Japan
| | - Natsuko Miura
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Japan
- Department of Applied Biological Chemistry, Graduate School of Agriculture, Osaka Metropolitan University, Sakai 599-8531, Japan
| | - Michihiko Kataoka
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Japan
- Department of Applied Biological Chemistry, Graduate School of Agriculture, Osaka Metropolitan University, Sakai 599-8531, Japan
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23
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Zhang L, Liu Z, Lu Y, Nie J, Chen Y. Phase Separation in Kidney Diseases: Autosomal Dominant Polycystic Kidney Disease and Beyond. KIDNEY DISEASES (BASEL, SWITZERLAND) 2023; 9:229-238. [PMID: 37899998 PMCID: PMC10601909 DOI: 10.1159/000530250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/15/2023] [Indexed: 10/31/2023]
Abstract
Background The formation of biomolecular condensates via phase separation has emerged as a fundamental principle underlying the spatiotemporal coordination of biological activities in cells. Aberrant biomolecular condensates often directly regulate key cellular process involved in the pathogenesis of human diseases, including kidney diseases. Summary In this review, we summarize the physiological roles of phase separation and methodologies for phase separation studies. Taking autosomal dominant polycystic kidney disease as an example, we discuss recent advances toward elucidating the multiple mechanisms involved in kidney pathology arising from aberrant phase separation. We suggest that dysregulation of phase separation contributes to the pathogenesis of other important kidney diseases, including kidney injury and fibrosis. Key Messages Phase separation provides a useful new concept to understand the mechanisms underlying kidney disease development. Targeting aberrant phase-separated condensates offers new therapeutic avenues for combating kidney diseases.
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Affiliation(s)
- Lirong Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
| | - Zhiheng Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
| | - Yumei Lu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
| | - Jing Nie
- Division of Nephrology, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Guangdong Provincial Institute of Nephrology, Guangdong Provincial Key Laboratory of Renal Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yupeng Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
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24
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Abstract
Biomolecular condensates are reversible compartments that form through a process called phase separation. Post-translational modifications like ADP-ribosylation can nucleate the formation of these condensates by accelerating the self-association of proteins. Poly(ADP-ribose) (PAR) chains are remarkably transient modifications with turnover rates on the order of minutes, yet they can be required for the formation of granules in response to oxidative stress, DNA damage, and other stimuli. Moreover, accumulation of PAR is linked with adverse phase transitions in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. In this review, we provide a primer on how PAR is synthesized and regulated, the diverse structures and chemistries of ADP-ribosylation modifications, and protein-PAR interactions. We review substantial progress in recent efforts to determine the molecular mechanism of PAR-mediated phase separation, and we further delineate how inhibitors of PAR polymerases may be effective treatments for neurodegenerative pathologies. Finally, we highlight the need for rigorous biochemical interrogation of ADP-ribosylation in vivo and in vitro to clarify the exact pathway from PARylation to condensate formation.
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Affiliation(s)
- Kevin Rhine
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Hana M Odeh
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - James Shorter
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Sua Myong
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Physics Frontier Center (Center for the Physics of Living Cells), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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25
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Silva JL, Foguel D, Ferreira VF, Vieira TCRG, Marques MA, Ferretti GDS, Outeiro TF, Cordeiro Y, de Oliveira GAP. Targeting Biomolecular Condensation and Protein Aggregation against Cancer. Chem Rev 2023. [PMID: 37379327 DOI: 10.1021/acs.chemrev.3c00131] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Biomolecular condensates, membrane-less entities arising from liquid-liquid phase separation, hold dichotomous roles in health and disease. Alongside their physiological functions, these condensates can transition to a solid phase, producing amyloid-like structures implicated in degenerative diseases and cancer. This review thoroughly examines the dual nature of biomolecular condensates, spotlighting their role in cancer, particularly concerning the p53 tumor suppressor. Given that over half of the malignant tumors possess mutations in the TP53 gene, this topic carries profound implications for future cancer treatment strategies. Notably, p53 not only misfolds but also forms biomolecular condensates and aggregates analogous to other protein-based amyloids, thus significantly influencing cancer progression through loss-of-function, negative dominance, and gain-of-function pathways. The exact molecular mechanisms underpinning the gain-of-function in mutant p53 remain elusive. However, cofactors like nucleic acids and glycosaminoglycans are known to be critical players in this intersection between diseases. Importantly, we reveal that molecules capable of inhibiting mutant p53 aggregation can curtail tumor proliferation and migration. Hence, targeting phase transitions to solid-like amorphous and amyloid-like states of mutant p53 offers a promising direction for innovative cancer diagnostics and therapeutics.
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Affiliation(s)
- Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Debora Foguel
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Vitor F Ferreira
- Faculty of Pharmacy, Fluminense Federal University (UFF), Rio de Janeiro, RJ 21941-902, Brazil
| | - Tuane C R G Vieira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Mayra A Marques
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Giulia D S Ferretti
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center, 37075 Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne NE2 4HH, U.K
- Scientific employee with an honorary contract at Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 37075 Göttingen, Germany
| | - Yraima Cordeiro
- Faculty of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
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26
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Dahmani I, Qin K, Zhang Y, Fernie AR. The formation and function of plant metabolons. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1080-1092. [PMID: 36906885 DOI: 10.1111/tpj.16179] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/26/2023] [Accepted: 03/06/2023] [Indexed: 05/31/2023]
Abstract
Metabolons are temporary structural-functional complexes of sequential enzymes of a metabolic pathway that are distinct from stable multi-enzyme complexes. Here we provide a brief history of the study of enzyme-enzyme assemblies with a particular focus on those that mediate substrate channeling in plants. Large numbers of protein complexes have been proposed for both primary and secondary metabolic pathways in plants. However, to date only four substrate channels have been demonstrated. We provide an overview of current knowledge concerning these four metabolons and explain the methodologies that are currently being applied to unravel their functions. Although the assembly of metabolons has been documented to arise through diverse mechanisms, the physical interaction within the characterized plant metabolons all appear to be driven by interaction with structural elements of the cell. We therefore pose the question as to what methodologies could be brought to bear to enhance our knowledge of plant metabolons that assemble via different mechanisms? In addressing this question, we review recent findings in non-plant systems concerning liquid droplet phase separation and enzyme chemotaxis and propose strategies via which such metabolons could be identified in plants. We additionally discuss the possibilities that could be opened up by novel approaches based on: (i) subcellular-level mass spectral imaging, (ii) proteomics, and (iii) emergent methods in structural and computational biology.
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Affiliation(s)
- Ismail Dahmani
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Kezhen Qin
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
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27
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Vendruscolo M, Fuxreiter M. Towards sequence-based principles for protein phase separation predictions. Curr Opin Chem Biol 2023; 75:102317. [PMID: 37207400 DOI: 10.1016/j.cbpa.2023.102317] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/21/2023]
Abstract
The phenomenon of protein phase separation, which underlies the formation of biomolecular condensates, has been associated with numerous cellular functions. Recent studies indicate that the amino acid sequences of most proteins may harbour not only the code for folding into the native state but also for condensing into the liquid-like droplet state and the solid-like amyloid state. Here we review the current understanding of the principles for sequence-based methods for predicting the propensity of proteins for phase separation. A guiding concept is that entropic contributions are generally more important to stabilise the droplet state than they are for the native and amyloid states. Although estimating these entropic contributions has proven difficult, we describe some progress that has been recently made in this direction. To conclude, we discuss the challenges ahead to extend sequence-based prediction methods of protein phase separation to include quantitative in vivo characterisations of this process.
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Affiliation(s)
- Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
| | - Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, PD 35131, Italy; Department of Physics and Astronomy, University of Padova, PD 35131, Italy.
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28
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Ho T, Potapenko E, Davis DB, Merrins MJ. A plasma membrane-associated glycolytic metabolon is functionally coupled to K ATP channels in pancreatic α and β cells from humans and mice. Cell Rep 2023; 42:112394. [PMID: 37058408 PMCID: PMC10513404 DOI: 10.1016/j.celrep.2023.112394] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/25/2023] [Accepted: 03/30/2023] [Indexed: 04/15/2023] Open
Abstract
The ATP-sensitive K+ (KATP) channel is a key regulator of hormone secretion from pancreatic islet endocrine cells. Using direct measurements of KATP channel activity in pancreatic β cells and the lesser-studied α cells, from both humans and mice, we provide evidence that a glycolytic metabolon locally controls KATP channels on the plasma membrane. The two ATP-consuming enzymes of upper glycolysis, glucokinase and phosphofructokinase, generate ADP that activates KATP. Substrate channeling of fructose 1,6-bisphosphate through the enzymes of lower glycolysis fuels pyruvate kinase, which directly consumes the ADP made by phosphofructokinase to raise ATP/ADP and close the channel. We further show the presence of a plasma membrane-associated NAD+/NADH cycle whereby lactate dehydrogenase is functionally coupled to glyceraldehyde-3-phosphate dehydrogenase. These studies provide direct electrophysiological evidence of a KATP-controlling glycolytic signaling complex and demonstrate its relevance to islet glucose sensing and excitability.
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Affiliation(s)
- Thuong Ho
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Evgeniy Potapenko
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Dawn B Davis
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Wisconsin-Madison, Madison, WI 53705, USA; William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
| | - Matthew J Merrins
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Wisconsin-Madison, Madison, WI 53705, USA; William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA.
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29
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Shil S, Tsuruta M, Kawauchi K, Miyoshi D. Biomolecular Liquid-Liquid Phase Separation for Biotechnology. BIOTECH 2023; 12:26. [PMID: 37092470 PMCID: PMC10123627 DOI: 10.3390/biotech12020026] [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: 03/09/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
The liquid-liquid phase separation (LLPS) of biomolecules induces condensed assemblies called liquid droplets or membrane-less organelles. In contrast to organelles with lipid membrane barriers, the liquid droplets induced by LLPS do not have distinct barriers (lipid bilayer). Biomolecular LLPS in cells has attracted considerable attention in broad research fields from cellular biology to soft matter physics. The physical and chemical properties of LLPS exert a variety of functions in living cells: activating and deactivating biomolecules involving enzymes; controlling the localization, condensation, and concentration of biomolecules; the filtration and purification of biomolecules; and sensing environmental factors for fast, adaptive, and reversible responses. The versatility of LLPS plays an essential role in various biological processes, such as controlling the central dogma and the onset mechanism of pathological diseases. Moreover, biomolecular LLPS could be critical for developing new biotechnologies such as the condensation, purification, and activation of a series of biomolecules. In this review article, we introduce some fundamental aspects and recent progress of biomolecular LLPS in living cells and test tubes. Then, we discuss applications of biomolecular LLPS toward biotechnologies.
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Affiliation(s)
| | | | | | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Hyogo, Japan
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30
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Xie Q, Cheng J, Mei W, Yang D, Zhang P, Zeng C. Phase separation in cancer at a glance. J Transl Med 2023; 21:237. [PMID: 37005672 PMCID: PMC10067312 DOI: 10.1186/s12967-023-04082-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/25/2023] [Indexed: 04/04/2023] Open
Abstract
Eukaryotic cells are segmented into multiple compartments or organelles within the cell that regulate distinct chemical and biological processes. Membrane-less organelles are membrane-less microscopic cellular compartments that contain protein and RNA molecules that perform a wide range of functions. Liquid-liquid phase separation (LLPS) can reveal how membrane-less organelles develop via dynamic biomolecule assembly. LLPS either segregates undesirable molecules from cells or aggregates desired ones in cells. Aberrant LLPS results in the production of abnormal biomolecular condensates (BMCs), which can cause cancer. Here, we explore the intricate mechanisms behind the formation of BMCs and its biophysical properties. Additionally, we discuss recent discoveries related to biological LLPS in tumorigenesis, including aberrant signaling and transduction, stress granule formation, evading growth arrest, and genomic instability. We also discuss the therapeutic implications of LLPS in cancer. Understanding the concept and mechanism of LLPS and its role in tumorigenesis is crucial for antitumor therapeutic strategies.
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Affiliation(s)
- Qingqing Xie
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Guangdong Medical University, Shenzhen, 518110, China
| | - Jiejuan Cheng
- School of Pharmacy, Hubei University of Science and Technology, Xianning, 437100, Hubei, China
| | - Wuxuan Mei
- Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, Hubei, China
| | - Dexing Yang
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Guangdong Medical University, Shenzhen, 518110, China
| | - Pengfei Zhang
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Guangdong Medical University, Shenzhen, 518110, China
| | - Changchun Zeng
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Guangdong Medical University, Shenzhen, 518110, China.
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31
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Staples MI, Frazer C, Fawzi NL, Bennett RJ. Phase separation in fungi. Nat Microbiol 2023; 8:375-386. [PMID: 36782025 PMCID: PMC10081517 DOI: 10.1038/s41564-022-01314-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/16/2022] [Indexed: 02/15/2023]
Abstract
Phase separation, in which macromolecules partition into a concentrated phase that is immiscible with a dilute phase, is involved with fundamental cellular processes across the tree of life. We review the principles of phase separation and highlight how it impacts diverse processes in the fungal kingdom. These include the regulation of autophagy, cell signalling pathways, transcriptional circuits and the establishment of asymmetry in fungal cells. We describe examples of stable, phase-separated assemblies including membraneless organelles such as the nucleolus as well as transient condensates that also arise through phase separation and enable cells to rapidly and reversibly respond to important environmental cues. We showcase how research into phase separation in model yeasts, such as Saccharomyces cerevisiae and Schizosaccharomyces pombe, in conjunction with that in plant and human fungal pathogens, such as Ashbya gossypii and Candida albicans, is continuing to enrich our understanding of fundamental molecular processes.
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Affiliation(s)
- Mae I Staples
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Corey Frazer
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Nicolas L Fawzi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
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32
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Activation of L-lactate oxidase by the formation of enzyme assemblies through liquid-liquid phase separation. Sci Rep 2023; 13:1435. [PMID: 36697449 PMCID: PMC9877012 DOI: 10.1038/s41598-023-28040-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023] Open
Abstract
The assembly state of enzymes is gaining interest as a mechanism for regulating the function of enzymes in living cells. One of the current topics in enzymology is the relationship between enzyme activity and the assembly state due to liquid-liquid phase separation. In this study, we demonstrated enzyme activation via the formation of enzyme assemblies using L-lactate oxidase (LOX). LOX formed hundreds of nanometer-scale assemblies with poly-L-lysine (PLL). In the presence of ammonium sulfate, the LOX-PLL clusters formed micrometer-scale liquid droplets. The enzyme activities of LOX in clusters and droplets were one order of magnitude higher than those in the dispersed state, owing to a decrease in KM and an increase in kcat. Moreover, the clusters exhibited a higher activation effect than the droplets. In addition, the conformation of LOX changed in the clusters, resulting in increased enzyme activation. Understanding enzyme activation and assembly states provides important information regarding enzyme function in living cells, in addition to biotechnology applications.
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33
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Kim-Holzapfel DM, Dey R, Richardson BC, Arachchige D, Reddy K, De Vitto H, Bhandari J, French JB. Human uridine 5'-monophosphate synthase stores metabolic potential in inactive biomolecular condensates. J Biol Chem 2023; 299:102949. [PMID: 36708921 PMCID: PMC9978035 DOI: 10.1016/j.jbc.2023.102949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/02/2023] [Accepted: 01/06/2023] [Indexed: 01/27/2023] Open
Abstract
Human uridine 5'-monophosphate synthase (HsUMPS) is a bifunctional enzyme that catalyzes the final two steps in de novo pyrimidine biosynthesis. The individual orotate phosphoribosyl transferase and orotidine monophosphate domains have been well characterized, but little is known about the overall structure of the protein and how the organization of domains impacts function. Using a combination of chromatography, electron microscopy, and complementary biophysical methods, we report herein that HsUMPS can be observed in two structurally distinct states, an enzymatically active dimeric form and a nonactive multimeric form. These two states readily interconvert to reach an equilibrium that is sensitive to perturbations of the active site and the presence of substrate. We determined that the smaller molecular weight form of HsUMPS is an S-shaped dimer that can self-assemble into relatively well-ordered globular condensates. Our analysis suggests that the transition between dimer and multimer is driven primarily by oligomerization of the orotate phosphoribosyl transferase domain. While the cellular distribution of HsUMPS is unaffected, quantification by mass spectrometry revealed that de novo pyrimidine biosynthesis is dysregulated when this protein is unable to assemble into inactive condensates. Taken together, our data suggest that HsUMPS self-assembles into biomolecular condensates as a means to store metabolic potential for the regulation of metabolic rates.
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Affiliation(s)
- Deborah M Kim-Holzapfel
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA; Molecular and Cellular Biology PhD Program, Stony Brook University, Stony Brook, New York, USA
| | - Raja Dey
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | | | | | - Kanamata Reddy
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Humberto De Vitto
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Janarjan Bhandari
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Jarrod B French
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA.
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34
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Utsumi R, Murata Y, Ito-Harashima S, Akai M, Miura N, Kuroda K, Ueda M, Kataoka M. Foci-forming regions of pyruvate kinase and enolase at the molecular surface incorporate proteins into yeast cytoplasmic metabolic enzymes transiently assembling (META) bodies. PLoS One 2023; 18:e0283002. [PMID: 37053166 PMCID: PMC10101385 DOI: 10.1371/journal.pone.0283002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/28/2023] [Indexed: 04/14/2023] Open
Abstract
Spatial reorganization of metabolic enzymes to form the "metabolic enzymes transiently assembling (META) body" is increasingly recognized as a mechanism contributing to regulation of cellular metabolism in response to environmental changes. A number of META body-forming enzymes, including enolase (Eno2p) and phosphofructokinase, have been shown to contain condensate-forming regions. However, whether all META body-forming enzymes have condensate-forming regions or whether enzymes have multiple condensate-forming regions remains unknown. The condensate-forming regions of META body-forming enzymes have potential utility in the creation of artificial intracellular enzyme assemblies. In the present study, the whole sequence of yeast pyruvate kinase (Cdc19p) was searched for condensate-forming regions. Four peptide fragments comprising 27-42 amino acids were found to form condensates. Together with the fragment previously identified from Eno2p, these peptide regions were collectively termed "META body-forming sequences (METAfos)." METAfos-tagged yeast alcohol dehydrogenase (Adh1p) was found to co-localize with META bodies formed by endogenous Cdc19p under hypoxic conditions. The effect of Adh1p co-localization with META bodies on cell metabolism was further evaluated. Expression of Adh1p fused with a METAfos-tag increased production of ethanol compared to acetic acid, indicating that spatial reorganization of metabolic enzymes affects cell metabolism. These results contribute to understanding of the mechanisms and biological roles of META body formation.
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Affiliation(s)
- Ryotaro Utsumi
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | - Yuki Murata
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | - Sayoko Ito-Harashima
- Department of Applied Biological Chemistry, Graduate School of Agriculture, Osaka Metropolitan University, Sakai, Japan
| | - Misaki Akai
- School of Applied Life Sciences, College of Life, Environment, and Advanced Sciences, Osaka Prefecture University, Sakai, Japan
| | - Natsuko Miura
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
- Department of Applied Biological Chemistry, Graduate School of Agriculture, Osaka Metropolitan University, Sakai, Japan
- School of Applied Life Sciences, College of Life, Environment, and Advanced Sciences, Osaka Prefecture University, Sakai, Japan
- Research Institute for LAC-SYS (RILACS), Osaka Metropolitan University, Sakai, Japan
| | - Kouichi Kuroda
- Department of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Mitsuyoshi Ueda
- Department of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Michihiko Kataoka
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
- Department of Applied Biological Chemistry, Graduate School of Agriculture, Osaka Metropolitan University, Sakai, Japan
- School of Applied Life Sciences, College of Life, Environment, and Advanced Sciences, Osaka Prefecture University, Sakai, Japan
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35
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A brief guideline for studies of phase-separated biomolecular condensates. Nat Chem Biol 2022; 18:1307-1318. [DOI: 10.1038/s41589-022-01204-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/10/2022] [Indexed: 11/20/2022]
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36
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Wegener M, Dietz KJ. The mutual interaction of glycolytic enzymes and RNA in post-transcriptional regulation. RNA (NEW YORK, N.Y.) 2022; 28:1446-1468. [PMID: 35973722 PMCID: PMC9745834 DOI: 10.1261/rna.079210.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
About three decades ago, researchers suggested that metabolic enzymes participate in cellular processes that are unrelated to their catalytic activity, and the term "moonlighting functions" was proposed. Recently developed advanced technologies in the field of RNA interactome capture now unveil the unexpected RNA binding activity of many metabolic enzymes, as exemplified here for the enzymes of glycolysis. Although for most of these proteins a precise binding mechanism, binding conditions, and physiological relevance of the binding events still await in-depth clarification, several well explored examples demonstrate that metabolic enzymes hold crucial functions in post-transcriptional regulation of protein synthesis. This widely conserved RNA-binding function of glycolytic enzymes plays major roles in controlling cell activities. The best explored examples are glyceraldehyde 3-phosphate dehydrogenase, enolase, phosphoglycerate kinase, and pyruvate kinase. This review summarizes current knowledge about the RNA-binding activity of the ten core enzymes of glycolysis in plant, yeast, and animal cells, its regulation and physiological relevance. Apparently, a tight bidirectional regulation connects core metabolism and RNA biology, forcing us to rethink long established functional singularities.
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Affiliation(s)
- Melanie Wegener
- Biochemistry and Physiology of Plants, Bielefeld University, 33615 Bielefeld, Germany
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Bielefeld University, 33615 Bielefeld, Germany
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37
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Rhine K, Al-Azzam N, Yu T, Yeo GW. Aging RNA granule dynamics in neurodegeneration. Front Mol Biosci 2022; 9:991641. [PMID: 36188213 PMCID: PMC9523239 DOI: 10.3389/fmolb.2022.991641] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/22/2022] [Indexed: 12/30/2022] Open
Abstract
Disordered RNA-binding proteins and repetitive RNA sequences are the main genetic causes of several neurodegenerative diseases, including amyotrophic lateral sclerosis and Huntington's disease. Importantly, these components also seed the formation of cytoplasmic liquid-like granules, like stress granules and P bodies. Emerging evidence demonstrates that healthy granules formed via liquid-liquid phase separation can mature into solid- or gel-like inclusions that persist within the cell. These solidified inclusions are a precursor to the aggregates identified in patients, demonstrating that dysregulation of RNA granule biology is an important component of neurodegeneration. Here, we review recent literature highlighting how RNA molecules seed proteinaceous granules, the mechanisms of healthy turnover of RNA granules in cells, which biophysical properties underly a transition to solid- or gel-like material states, and why persistent granules disrupt the cellular homeostasis of neurons. We also identify various methods that will illuminate the contributions of disordered proteins and RNAs to neurodegeneration in ongoing research efforts.
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Affiliation(s)
- Kevin Rhine
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United States
- Stem Cell Program, University of California, San Diego, San Diego, CA, United States
- Institute for Genomic Medicine, University of California, San Diego, San Diego, CA, United States
| | - Norah Al-Azzam
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United States
- Stem Cell Program, University of California, San Diego, San Diego, CA, United States
- Institute for Genomic Medicine, University of California, San Diego, San Diego, CA, United States
- Neurosciences Graduate Program, University of California, San Diego, San Diego, CA, United States
| | - Tao Yu
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United States
- Stem Cell Program, University of California, San Diego, San Diego, CA, United States
- Institute for Genomic Medicine, University of California, San Diego, San Diego, CA, United States
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United States
- Stem Cell Program, University of California, San Diego, San Diego, CA, United States
- Institute for Genomic Medicine, University of California, San Diego, San Diego, CA, United States
- Neurosciences Graduate Program, University of California, San Diego, San Diego, CA, United States
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38
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Polo-Generelo S, Torres B, Guerrero-Martínez JA, Camafeita E, Vázquez J, Reyes JC, Pintor-Toro JA. TGF-β-Upregulated Lnc-Nr6a1 Acts as a Reservoir of miR-181 and Mediates Assembly of a Glycolytic Complex. Noncoding RNA 2022; 8:ncrna8050062. [PMID: 36136852 PMCID: PMC9498520 DOI: 10.3390/ncrna8050062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/06/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as key regulators in a wide range of biological processes. Here, we identified a mouse miRNA-host gene lncRNA (lnc-Nr6a1) upregulated early during epithelial-to-mesenchymal transition (EMT). We show that when lncRNA is processed, it gives rise to two abundant polyadenylated isoforms, lnc-Nr6a1-1 and lnc-Nr6a1-2, and a longer non-polyadenylated microprocessor-driven lnc-pri-miRNA containing clustered pre-miR-181a2 and pre-miR-181b2 hairpins. Ectopic expression of the lnc-Nr6a1-1 or lnc-Nr6a1-2 isoform enhanced cell migration and the invasive capacity of the cells, whereas the expression of the isoforms and miR-181a2 and miR-181b2 conferred anoikis resistance. Lnc-Nr6a1 gene deletion resulted in cells with lower adhesion capacity and reduced glycolytic metabolism, which are restored by lnc-Nr6a1-1 isoform expression. We performed identification of direct RNA interacting proteins (iDRIP) to identify proteins interacting directly with the lnc-Nr6a1-1 isoform. We defined a network of interacting proteins, including glycolytic enzymes, desmosome proteins and chaperone proteins; and we demonstrated that the lnc-Nr6a1-1 isoform directly binds and acts as a scaffold molecule for the assembly of ENO1, ALDOA, GAPDH, and PKM glycolytic enzymes, along with LDHA, supporting substrate channeling for efficient glycolysis. Our results unveil a role of Lnc-Nr6a1 as a multifunctional lncRNA acting as a backbone for multiprotein complex formation and primary microRNAs.
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Affiliation(s)
- Salvador Polo-Generelo
- Department of Cell Signalling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092 Sevilla, Spain
| | - Belén Torres
- Department of Cell Signalling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092 Sevilla, Spain
| | - José A. Guerrero-Martínez
- Department of Cell Signalling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092 Sevilla, Spain
| | - Emilio Camafeita
- Cardiovascular Proteomics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Jesús Vázquez
- Cardiovascular Proteomics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - José C. Reyes
- Department of Cell Signalling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092 Sevilla, Spain
| | - José A. Pintor-Toro
- Department of Cell Signalling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092 Sevilla, Spain
- Correspondence: ; Tel.: +34-954467995
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Chakravarty AK, McGrail DJ, Lozanoski TM, Dunn BS, Shih DJ, Cirillo KM, Cetinkaya SH, Zheng WJ, Mills GB, Yi SS, Jarosz DF, Sahni N. Biomolecular Condensation: A New Phase in Cancer Research. Cancer Discov 2022; 12:2031-2043. [PMID: 35852417 PMCID: PMC9437557 DOI: 10.1158/2159-8290.cd-21-1605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 01/09/2023]
Abstract
Multicellularity was a watershed development in evolution. However, it also meant that individual cells could escape regulatory mechanisms that restrict proliferation at a severe cost to the organism: cancer. From the standpoint of cellular organization, evolutionary complexity scales to organize different molecules within the intracellular milieu. The recent realization that many biomolecules can "phase-separate" into membraneless organelles, reorganizing cellular biochemistry in space and time, has led to an explosion of research activity in this area. In this review, we explore mechanistic connections between phase separation and cancer-associated processes and emerging examples of how these become deranged in malignancy. SIGNIFICANCE One of the fundamental functions of phase separation is to rapidly and dynamically respond to environmental perturbations. Importantly, these changes often lead to alterations in cancer-relevant pathways and processes. This review covers recent advances in the field, including emerging principles and mechanisms of phase separation in cancer.
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Affiliation(s)
- Anupam K. Chakravarty
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Daniel J. McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, Ohio
| | | | - Brandon S. Dunn
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David J.H. Shih
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas
| | - Kara M. Cirillo
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sueda H. Cetinkaya
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wenjin Jim Zheng
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas
| | - Gordon B. Mills
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health and Sciences University, Portland, Oregon
| | - S. Stephen Yi
- Department of Oncology, Livestrong Cancer Institutes, The University of Texas at Austin, Austin, Texas
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas
- Interdisciplinary Life Sciences Graduate Programs (ILSGP) and Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, Texas
| | - Daniel F. Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Program in Quantitative and Computational Biosciences (QCB), Baylor College of Medicine, Houston, Texas
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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40
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Peng Q, Tan S, Xia L, Wu N, Oyang L, Tang Y, Su M, Luo X, Wang Y, Sheng X, Zhou Y, Liao Q. Phase separation in Cancer: From the Impacts and Mechanisms to Treatment potentials. Int J Biol Sci 2022; 18:5103-5122. [PMID: 35982902 PMCID: PMC9379413 DOI: 10.7150/ijbs.75410] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/16/2022] [Indexed: 12/14/2022] Open
Abstract
Cancer is a public health problem of great concern, and it is also one of the main causes of death in the world. Cancer is a disease characterized by dysregulation of diverse cellular processes, including avoiding growth inhibitory factors, avoiding immune damage and promoting metastasis, etc. However, the precise mechanism of tumorigenesis and tumor progression still needs to be further elucidated. Formations of liquid-liquid phase separation (LLPS) condensates are a common strategy for cells to achieve diverse functions, such as chromatin organization, signal transduction, DNA repair and transcriptional regulation, etc. The biomolecular aggregates formed by LLPS are mainly driven by multivalent weak interactions mediated by intrinsic disordered regions (IDRs) in proteins. In recent years, aberrant phase separations and transition have been reported to be related to the process of various diseases, such as neurodegenerative diseases and cancer. Herein, we discussed recent findings that phase separation regulates tumor-related signaling pathways and thus contributes to tumor progression. We also reviewed some tumor virus-associated proteins to regulate the development of virus-associated tumors via phase separation. Finally, we discussed some possible strategies for treating tumors by targeting phase separation.
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Affiliation(s)
- Qiu Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Shiming Tan
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Longzheng Xia
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Nayiyuan Wu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Linda Oyang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Min Su
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Xia Luo
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Ying Wang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Xiaowu Sheng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.,Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.,Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China
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41
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Liu D, Wan Y, Qu N, Fu Q, Liang C, Zeng L, Yang Y. LncRNA-FAM66C Was Identified as a Key Regulator for Modulating Tumor Microenvironment and Hypoxia-Related Pathways in Glioblastoma. Front Public Health 2022; 10:898270. [PMID: 35874989 PMCID: PMC9299378 DOI: 10.3389/fpubh.2022.898270] [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: 03/17/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Although the role of hypoxia has been greatly explored and unveiled in glioblastoma (GBM), the mechanism of hypoxia-related long non-coding (lnc) RNAs has not been clearly understood. This study aims to reveal the crosstalk among hypoxia-related lncRNAs, tumor microenvironment (TME), and tumorigenesis for GBM. Gene expression profiles of GBM patients were used as a basis for identifying hypoxia-related lncRNAs. Unsupervised consensus clustering was conducted for classifying samples into different molecular subtypes. Gene set enrichment analysis (GSEA) was performed to analyze the enrichment of a series of genes or gene signatures. Three molecular subtypes were constructed based on eight identified hypoxia-related lncRNAs. Oncogenic pathways, such as epithelial mesenchymal transition (EMT), tumor necrosis factor-α (TNF-α) signaling, angiogenesis, hypoxia, P53 signaling, and glycolysis pathways, were significantly enriched in C1 subtype with poor overall survival. C1 subtype showed high immune infiltration and high expression of immune checkpoints. Furthermore, we identified 10 transcription factors (TFs) that were highly correlated with lncRNA-FAM66C. Three key lncRNAs (ADAMTS9-AS2, LINC00968, and LUCAT1) were screened as prognostic biomarkers for GBM. This study shed light on the important role of hypoxia-related lncRNAs for TME modulation and tumorigenesis in GBM. The eight identified hypoxia-related lncRNAs, especially FAM66C may serve as key regulators involving in hypoxia-related pathways.
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Affiliation(s)
- Dan Liu
- Oncology Department, Jinzhou Central Hospital, Jinzhou, China
| | - Yue Wan
- Oncology Department, Jinzhou Central Hospital, Jinzhou, China
| | - Ning Qu
- Department of Pediatrics, Jinzhou Central Hospital, Jinzhou, China
| | - Qiang Fu
- Department of Neurosurgery, Shengjing Hospital Affiliated to China Medical University, Shenyang, China
| | - Chao Liang
- Department of General Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Lingda Zeng
- Department of Otorhinolaryngology Surgery, Jinzhou Central Hospital, Jinzhou, China
| | - Yang Yang
- Department of Neurosurgery, Jinzhou Central Hospital, Jinzhou, China
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42
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Parker DM, Winkenbach LP, Osborne Nishimura E. It’s Just a Phase: Exploring the Relationship Between mRNA, Biomolecular Condensates, and Translational Control. Front Genet 2022; 13:931220. [PMID: 35832192 PMCID: PMC9271857 DOI: 10.3389/fgene.2022.931220] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Cells spatially organize their molecular components to carry out fundamental biological processes and guide proper development. The spatial organization of RNA within the cell can both promote and result from gene expression regulatory control. Recent studies have demonstrated diverse associations between RNA spatial patterning and translation regulatory control. One form of patterning, compartmentalization in biomolecular condensates, has been of particular interest. Generally, transcripts associated with cytoplasmic biomolecular condensates—such as germ granules, stress granules, and P-bodies—are linked with low translational status. However, recent studies have identified new biomolecular condensates with diverse roles associated with active translation. This review outlines RNA compartmentalization in various condensates that occur in association with repressed or active translational states, highlights recent findings in well-studied condensates, and explores novel condensate behaviors.
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Affiliation(s)
- Dylan M. Parker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
- Department of Biochemistry, University of Colorado, Boulder, CO, United States
| | - Lindsay P. Winkenbach
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Erin Osborne Nishimura
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
- *Correspondence: Erin Osborne Nishimura,
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43
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Hypoxia-driven metabolic heterogeneity and immune evasive behaviour of gastrointestinal cancers: Elements of a recipe for disaster. Cytokine 2022; 156:155917. [PMID: 35660715 DOI: 10.1016/j.cyto.2022.155917] [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: 02/01/2022] [Revised: 04/28/2022] [Accepted: 05/16/2022] [Indexed: 11/24/2022]
Abstract
Gastrointestinal (GI) cancers refer to a group of malignancies associated with the GI tract (GIT). Like other solid tumors, hypoxic regions consistently feature inside the GI tumor microenvironment (TME) and contribute towards metabolic reprogramming of tumor-resident cells by modulating hypoxia-induced factors. We highlight here how the metabolic crosstalk between cancer cells and immune cells generate immunosuppressive environment inside hypoxic tumors. Given the fluctuating nature of tumor hypoxia, the metabolic fluxes between immune cells and cancer cells change dynamically. These changes alter cellular phenotypes and functions, resulting in the acceleration of cancer progression. These evolved properties of hypoxic tumors make metabolism-targeting monotherapy approaches or immunotherapy-measures unsuccessful. The current review highlights the advantages of combined immunometabolic treatment strategies to target hypoxic GI cancers and also identifies research areas to develop better combinational therapeutics for future.
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44
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Petty HR. Enzyme Trafficking and Co-Clustering Precede and Accurately Predict Human Breast Cancer Recurrences: An Interdisciplinary Review. Am J Physiol Cell Physiol 2022; 322:C991-C1010. [PMID: 35385324 DOI: 10.1152/ajpcell.00042.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Although great effort has been expended to understand cancer's origins, less attention has been given to the primary cause of cancer deaths - cancer recurrences and their sequelae. This interdisciplinary review addresses mechanistic features of aggressive cancer by studying metabolic enzyme patterns within ductal carcinoma in situ (DCIS) of the breast lesions. DCIS lesions from patients who did or did not experience a breast cancer recurrence were compared. Several proteins, including phospho-Ser226-glucose transporter type 1, phosphofructokinase type L and phosphofructokinase/fructose 2,6-bisphosphatase type 4 are found in nucleoli of ductal epithelial cells in samples from patients who will not subsequently recur, but traffic to the cell periphery in samples from patients who will experience a cancer recurrence. Large co-clusters of enzymes near plasmalemmata will enhance product formation because enzyme concentrations in clusters are very high while solvent molecules and solutes diffuse through small channels. These structural changes will accelerate aerobic glycolysis. Agglomerations of pentose phosphate pathway and glutathione synthesis enzymes enhance GSH formation. As aggressive cancer lesions are incomplete at early stages, they may be unrecognizable. We have found that machine learning provides superior analyses of tissue images and may be used to identify biomarker patterns associated with recurrent and non-recurrent patients with high accuracy. This suggests a new prognostic test to predict DCIS patients who are likely to recur and those who are at low risk for recurrence. Mechanistic interpretations provide a deeper understanding of anti-cancer drug action and suggest that aggressive metastatic cancer cells are sensitive to reductive chemotherapy.
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Affiliation(s)
- Howard R Petty
- Dept. of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, MI, United States
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45
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Igelmann S, Lessard F, Ferbeyre G. Liquid-Liquid Phase Separation in Cancer Signaling, Metabolism and Anticancer Therapy. Cancers (Basel) 2022; 14:cancers14071830. [PMID: 35406602 PMCID: PMC8997759 DOI: 10.3390/cancers14071830] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 01/07/2023] Open
Abstract
The cancer state is thought to be maintained by genetic and epigenetic changes that drive a cancer-promoting gene expression program. However, recent results show that cellular states can be also stably maintained by the reorganization of cell structure leading to the formation of biological condensates via the process of liquid-liquid phase separation. Here, we review the data showing cancer-specific biological condensates initiated by mutant oncoproteins, RNA-binding proteins, or lincRNAs that regulate oncogenic gene expression programs and cancer metabolism. Effective anticancer drugs may specifically partition into oncogenic biological condensates (OBC).
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Affiliation(s)
- Sebastian Igelmann
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada;
- Montreal Cancer Institute, CR-CHUM, Université de Montréal, Montréal, QC H2X 0A9, Canada
| | - Frédéric Lessard
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, QC G1R 2J6, Canada;
| | - Gerardo Ferbeyre
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada;
- Montreal Cancer Institute, CR-CHUM, Université de Montréal, Montréal, QC H2X 0A9, Canada
- Correspondence: ; Tel.: +1-514-343-7571
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46
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Garde A, Kenny IW, Kelley LC, Chi Q, Mutlu AS, Wang MC, Sherwood DR. Localized glucose import, glycolytic processing, and mitochondria generate a focused ATP burst to power basement-membrane invasion. Dev Cell 2022; 57:732-749.e7. [PMID: 35316617 PMCID: PMC8969095 DOI: 10.1016/j.devcel.2022.02.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/18/2022] [Accepted: 02/18/2022] [Indexed: 11/27/2022]
Abstract
Invasive cells use transient, energy-consuming protrusions to breach basement membrane (BM) barriers. Using the ATP sensor PercevalHR during anchor cell (AC) invasion in Caenorhabditis elegans, we show that BM invasion is accompanied by an ATP burst from mitochondria at the invasive front. RNAi screening and visualization of a glucose biosensor identified two glucose transporters, FGT-1 and FGT-2, which bathe invasive front mitochondria with glucose and facilitate the ATP burst to form protrusions. FGT-1 localizes at high levels along the invasive membrane, while FGT-2 is adaptive, enriching most strongly during BM breaching and when FGT-1 is absent. Cytosolic glycolytic enzymes that process glucose for mitochondrial ATP production cluster with invasive front mitochondria and promote higher mitochondrial membrane potential and ATP levels. Finally, we show that UNC-6 (netrin), which polarizes invasive protrusions, also orients FGT-1. These studies reveal a robust and integrated energy acquisition, processing, and delivery network that powers BM breaching.
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Affiliation(s)
- Aastha Garde
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27708, USA
| | - Isabel W Kenny
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Laura C Kelley
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Qiuyi Chi
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Ayse Sena Mutlu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meng C Wang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - David R Sherwood
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA.
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Noda N, Jung Y, Ado G, Mizuhata Y, Higuchi M, Ogawa T, Ishidate F, Sato SI, Kurata H, Tokitoh N, Uesugi M. Glucose as a Protein-Condensing Cellular Solute. ACS Chem Biol 2022; 17:567-575. [PMID: 35188733 DOI: 10.1021/acschembio.1c00849] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The present study reports a surprising protein-condensing effect of glucose, prompted by our accidental observation during chemical library screening under a high-glucose condition. We noticed "glucosing-out" of certain compounds, in which physiological concentrations of glucose induced compound aggregation. Adapting the "glucosing-out" concept to proteins, our proteomic analysis identified three cellular proteins (calmodulin, rho guanine nucleotide exchange factor 40, and polyubiquitin-C) that displayed robust glucose-dependent precipitation. One of these proteins, calmodulin, formed glucose-dependent condensates that control cellular glycogenolysis in hepatic cells. Our findings suggest that glucose is a heretofore underappreciated driver of protein phase separation that may have profound effects on cellular homeostasis.
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Affiliation(s)
- Naotaka Noda
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yejin Jung
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Genyir Ado
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yoshiyuki Mizuhata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masakazu Higuchi
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tetsuya Ogawa
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Fumiyoshi Ishidate
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Shin-ichi Sato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hiroki Kurata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Norihiro Tokitoh
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Motonari Uesugi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Uji, Kyoto 611-0011, Japan
- School of Pharmacy, Fudan University, Shanghai 201203, China
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48
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Neurons undergo pathogenic metabolic reprogramming in models of familial ALS. Mol Metab 2022; 60:101468. [PMID: 35248787 PMCID: PMC8958550 DOI: 10.1016/j.molmet.2022.101468] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 11/21/2022] Open
Abstract
Objectives Methods Results Conclusions Our work is the first to perform a comprehensive and quantitative analysis of intermediary metabolism in neurons in the setting of fALS causing gene products. Because the cardinal feature of ALS is death of motor neurons, these new studies are directly relevant to the pathogenesis of ALS. Our functional interrogations begin to unpack how metabolic re-wiring is induced by fALS genes and it will be very interesting, in the future, to gain insight in amino acid fueling of the TCA cycle. We suspect pleiotropic effects of amino acid fueling, and this may lead to very targeted therapeutic interventions.
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49
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Miura N. Condensate Formation by Metabolic Enzymes in Saccharomyces cerevisiae. Microorganisms 2022; 10:232. [PMID: 35208686 PMCID: PMC8876316 DOI: 10.3390/microorganisms10020232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/31/2022] Open
Abstract
Condensate formation by a group of metabolic enzymes in the cell is an efficient way of regulating cell metabolism through the formation of "membrane-less organelles." Because of the use of green fluorescent protein (GFP) for investigating protein localization, various enzymes were found to form condensates or filaments in living Saccharomyces cerevisiae, mammalian cells, and in other organisms, thereby regulating cell metabolism in the certain status of the cells. Among different environmental stresses, hypoxia triggers the spatial reorganization of many proteins, including more than 20 metabolic enzymes, to form numerous condensates, including "Glycolytic body (G-body)" and "Purinosome." These individual condensates are collectively named "Metabolic Enzymes Transiently Assembling (META) body". This review overviews condensate or filament formation by metabolic enzymes in S. cerevisiae, focusing on the META body, and recent reports in elucidating regulatory machinery of META body formation.
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Affiliation(s)
- Natsuko Miura
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Japan
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Loh D, Reiter RJ. Melatonin: Regulation of Prion Protein Phase Separation in Cancer Multidrug Resistance. Molecules 2022; 27:705. [PMID: 35163973 PMCID: PMC8839844 DOI: 10.3390/molecules27030705] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 12/13/2022] Open
Abstract
The unique ability to adapt and thrive in inhospitable, stressful tumor microenvironments (TME) also renders cancer cells resistant to traditional chemotherapeutic treatments and/or novel pharmaceuticals. Cancer cells exhibit extensive metabolic alterations involving hypoxia, accelerated glycolysis, oxidative stress, and increased extracellular ATP that may activate ancient, conserved prion adaptive response strategies that exacerbate multidrug resistance (MDR) by exploiting cellular stress to increase cancer metastatic potential and stemness, balance proliferation and differentiation, and amplify resistance to apoptosis. The regulation of prions in MDR is further complicated by important, putative physiological functions of ligand-binding and signal transduction. Melatonin is capable of both enhancing physiological functions and inhibiting oncogenic properties of prion proteins. Through regulation of phase separation of the prion N-terminal domain which targets and interacts with lipid rafts, melatonin may prevent conformational changes that can result in aggregation and/or conversion to pathological, infectious isoforms. As a cancer therapy adjuvant, melatonin could modulate TME oxidative stress levels and hypoxia, reverse pH gradient changes, reduce lipid peroxidation, and protect lipid raft compositions to suppress prion-mediated, non-Mendelian, heritable, but often reversible epigenetic adaptations that facilitate cancer heterogeneity, stemness, metastasis, and drug resistance. This review examines some of the mechanisms that may balance physiological and pathological effects of prions and prion-like proteins achieved through the synergistic use of melatonin to ameliorate MDR, which remains a challenge in cancer treatment.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health San Antonio, San Antonio, TX 78229, USA
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