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Glauninger H, Bard JAM, Wong Hickernell CJ, Airoldi EM, Li W, Singer RH, Paul S, Fei J, Sosnick TR, Wallace EWJ, Drummond DA. Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts. bioRxiv 2024:2024.04.15.589678. [PMID: 38659805 PMCID: PMC11042329 DOI: 10.1101/2024.04.15.589678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Stress-induced condensation of mRNA and proteins into stress granules is conserved across eukaryotes, yet the function, formation mechanisms, and relation to well-studied conserved transcriptional responses remain largely unresolved. Stress-induced exposure of ribosome-free mRNA following translational shutoff is thought to cause condensation by allowing new multivalent RNA-dependent interactions, with RNA length and associated interaction capacity driving increased condensation. Here we show that, in striking contrast, virtually all mRNA species condense in response to multiple unrelated stresses in budding yeast, length plays a minor role, and instead, stress-induced transcripts are preferentially excluded from condensates, enabling their selective translation. Using both endogenous genes and reporter constructs, we show that translation initiation blockade, rather than resulting ribosome-free RNA, causes condensation. These translation initiation-inhibited condensates (TIICs) are biochemically detectable even when stress granules, defined as microscopically visible foci, are absent or blocked. TIICs occur in unstressed yeast cells, and, during stress, grow before the appearance of visible stress granules. Stress-induced transcripts are excluded from TIICs primarily due to the timing of their expression, rather than their sequence features. Together, our results reveal a simple system by which cells redirect translational activity to newly synthesized transcripts during stress, with broad implications for cellular regulation in changing conditions.
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2
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Roscoe S, Guo Y, Vacratsis PO, Ananvoranich S. Proteomic profile of Toxoplasma gondii stress granules by high-resolution mass spectrometry. Can J Microbiol 2024; 70:32-39. [PMID: 37826860 DOI: 10.1139/cjm-2023-0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Ribonucleoprotein granules are bio-condensates that form a diverse group of dynamic membrane-less organelles implicated in several cellular functions, including stress response and cellular survival. In Toxoplasma gondii, a type of bio-condensates referred to as stress granules (SGs) are formed prior to the parasites' egress from the host cell and are implicated in the survival and invasion competency of extracellular tachyzoites. We used paraformaldehyde to fix and cross-link SG proteins to allow purification by centrifugation and analysis by mass spectrometry. We profiled protein components of SGs at 10 and 30 min post-egress when parasite's invasion ability is significantly diminished. Thirty-three proteins were identified from 10 min SGs, and additional 43 proteins were identified from 30 min SGs. Notably, common SG components such as proteins with intrinsically disordered domains were not identified. Gene ontology analysis of both 10 and 30 min SGs shows that overall molecular functions of SGs' proteins are ATP-binding, GTP-binding, and GTPase activity. Discernable differences between 10 and 30 min SGs are in the proportions of translation and microtubule-related proteins. Ten-minute SGs have a higher proportion of microtubule-related proteins and a lower proportion of ribosome-related proteins, while a reverse correlation was identified for those of 30 min. It remains to be investigated whether this reverse correlation contributes to the ability of extracellular tachyzoites to reinvade host cells.
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Affiliation(s)
- Scott Roscoe
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B3P4, Canada
| | - Yue Guo
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B3P4, Canada
| | - Panayiotis O Vacratsis
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B3P4, Canada
| | - Sirinart Ananvoranich
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B3P4, Canada
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3
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Jin Z, Ling C, Yim W, Chang YC, He T, Li K, Zhou J, Cheng Y, Li Y, Yeung J, Wang R, Fajtová P, Amer L, Mattoussi H, O'Donoghue AJ, Jokerst JV. Endoproteolysis of Oligopeptide-Based Coacervates for Enzymatic Modeling. ACS Nano 2023; 17:16980-16992. [PMID: 37579082 PMCID: PMC10614163 DOI: 10.1021/acsnano.3c04259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Better insights into the fate of membraneless organelles could strengthen the understanding of the transition from prebiotic components to multicellular organisms. Compartmentalized enzyme reactions in a synthetic coacervate have been investigated, yet there remains a gap in understanding the enzyme interactions with coacervate as a substrate hub. Here, we study how the molecularly crowded nature of the coacervate affects the interactions of the embedded substrate with a protease. We design oligopeptide-based coacervates that comprise an anionic Asp-peptide (D10) and a cationic Arg-peptide (R5R5) with a proteolytic cleavage site. The coacervates dissolve in the presence of the main protease (Mpro) implicated in the coronavirus lifecycle. We capitalize on the condensed structure, introduce a self-quenching mechanism, and model the enzyme kinetics by using Cy5.5-labeled peptides. The determined specificity constant (kcat/KM) is 5817 M-1 s-1 and is similar to that of the free substrate. We further show that the enzyme kinetics depend on the type and quantity of dye incorporated into the coacervates. Our work presents a simple design for enzyme-responsive coacervates and provides insights into the interactions between the enzyme and coacervates as a whole.
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Affiliation(s)
- Zhicheng Jin
- Department of NanoEngineering, University of California, San Diego, La Jolla 92093, California, United States
| | - Chuxuan Ling
- Department of NanoEngineering, University of California, San Diego, La Jolla 92093, California, United States
| | - Wonjun Yim
- Materials Science and Engineering Program, University of California, San Diego, La Jolla 92093, California, United States
| | - Yu-Ci Chang
- Materials Science and Engineering Program, University of California, San Diego, La Jolla 92093, California, United States
| | - Tengyu He
- Materials Science and Engineering Program, University of California, San Diego, La Jolla 92093, California, United States
| | - Ke Li
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore 138634, Republic of Singapore
| | - Jiajing Zhou
- Department of NanoEngineering, University of California, San Diego, La Jolla 92093, California, United States
| | - Yong Cheng
- Department of NanoEngineering, University of California, San Diego, La Jolla 92093, California, United States
| | - Yi Li
- Department of NanoEngineering, University of California, San Diego, La Jolla 92093, California, United States
| | - Justin Yeung
- Department of Bioengineering, University of California, San Diego, La Jolla 92093, California, United States
| | - Ruijia Wang
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla 92093, California, United States
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla 92093, California, United States
| | - Lubna Amer
- Materials Science and Engineering Program, University of California, San Diego, La Jolla 92093, California, United States
| | - Hedi Mattoussi
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee 32306, Florida, United States
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla 92093, California, United States
| | - Jesse V Jokerst
- Department of NanoEngineering, University of California, San Diego, La Jolla 92093, California, United States
- Materials Science and Engineering Program, University of California, San Diego, La Jolla 92093, California, United States
- Department of Radiology, University of California, San Diego, La Jolla 92093, California, United States
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4
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van Tartwijk FW, Kaminski CF. Protein Condensation, Cellular Organization, and Spatiotemporal Regulation of Cytoplasmic Properties. Adv Biol (Weinh) 2022; 6:e2101328. [PMID: 35796197 DOI: 10.1002/adbi.202101328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/15/2022] [Indexed: 01/28/2023]
Abstract
The cytoplasm is an aqueous, highly crowded solution of active macromolecules. Its properties influence the behavior of proteins, including their folding, motion, and interactions. In particular, proteins in the cytoplasm can interact to form phase-separated assemblies, so-called biomolecular condensates. The interplay between cytoplasmic properties and protein condensation is critical in a number of functional contexts and is the subject of this review. The authors first describe how cytoplasmic properties can affect protein behavior, in particular condensate formation, and then describe the functional implications of this interplay in three cellular contexts, which exemplify how protein self-organization can be adapted to support certain physiological phenotypes. The authors then describe the formation of RNA-protein condensates in highly polarized cells such as neurons, where condensates play a critical role in the regulation of local protein synthesis, and describe how different stressors trigger extensive reorganization of the cytoplasm, both through signaling pathways and through direct stress-induced changes in cytoplasmic properties. Finally, the authors describe changes in protein behavior and cytoplasmic properties that may occur in extremophiles, in particular organisms that have adapted to inhabit environments of extreme temperature, and discuss the implications and functional importance of these changes.
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Affiliation(s)
- Francesca W van Tartwijk
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
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5
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Vermeersch L, Cool L, Gorkovskiy A, Voordeckers K, Wenseleers T, Verstrepen KJ. Do microbes have a memory? History-dependent behavior in the adaptation to variable environments. Front Microbiol 2022; 13:1004488. [PMID: 36299722 PMCID: PMC9589428 DOI: 10.3389/fmicb.2022.1004488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/26/2022] [Indexed: 11/18/2022] Open
Abstract
Microbes are constantly confronted with changes and challenges in their environment. A proper response to these environmental cues is needed for optimal cellular functioning and fitness. Interestingly, past exposure to environmental cues can accelerate or boost the response when this condition returns, even in daughter cells that have not directly encountered the initial cue. Moreover, this behavior is mostly epigenetic and often goes hand in hand with strong heterogeneity in the strength and speed of the response between isogenic cells of the same population, which might function as a bet-hedging strategy. In this review, we discuss examples of history-dependent behavior (HDB) or “memory,” with a specific focus on HDB in fluctuating environments. In most examples discussed, the lag time before the response to an environmental change is used as an experimentally measurable proxy for HDB. We highlight different mechanisms already implicated in HDB, and by using HDB in fluctuating carbon conditions as a case study, we showcase how the metabolic state of a cell can be a key determining factor for HDB. Finally, we consider possible evolutionary causes and consequences of such HDB.
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Affiliation(s)
- Lieselotte Vermeersch
- VIB – KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Lloyd Cool
- VIB – KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - Anton Gorkovskiy
- VIB – KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Karin Voordeckers
- VIB – KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Tom Wenseleers
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - Kevin J. Verstrepen
- VIB – KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
- *Correspondence: Kevin J. Verstrepen,
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6
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Glauninger H, Wong Hickernell CJ, Bard JAM, Drummond DA. Stressful steps: Progress and challenges in understanding stress-induced mRNA condensation and accumulation in stress granules. Mol Cell 2022; 82:2544-2556. [PMID: 35662398 PMCID: PMC9308734 DOI: 10.1016/j.molcel.2022.05.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 03/14/2022] [Accepted: 05/11/2022] [Indexed: 01/11/2023]
Abstract
Stress-induced condensation of mRNA and protein into massive cytosolic clusters is conserved across eukaryotes. Known as stress granules when visible by imaging, these structures remarkably have no broadly accepted biological function, mechanism of formation or dispersal, or even molecular composition. As part of a larger surge of interest in biomolecular condensation, studies of stress granules and related RNA/protein condensates have increasingly probed the biochemical underpinnings of condensation. Here, we review open questions and recent advances, including the stages from initial condensate formation to accumulation in mature stress granules, mechanisms by which stress-induced condensates form and dissolve, and surprising twists in understanding the RNA components of stress granules and their role in condensation. We outline grand challenges in understanding stress-induced RNA condensation, centering on the unique and substantial barriers in the molecular study of cellular structures, such as stress granules, for which no biological function has been firmly established.
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Affiliation(s)
- Hendrik Glauninger
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60673, USA
| | | | - Jared A M Bard
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60673, USA
| | - D Allan Drummond
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60673, USA.
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7
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Alalam H, Zepeda-Martínez JA, Sunnerhagen P. Global SLAM-seq for accurate mRNA decay determination and identification of NMD targets. RNA 2022; 28:905-915. [PMID: 35296539 PMCID: PMC9074897 DOI: 10.1261/rna.079077.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Gene expression analysis requires accurate measurements of global RNA degradation rates, earlier problematic with methods disruptive to cell physiology. Recently, metabolic RNA labeling emerged as an efficient and minimally invasive technique applied in mammalian cells. Here, we have adapted SH-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) for a global mRNA stability study in yeast using 4-thiouracil pulse-chase labeling. We assign high-confidence half-life estimates for 67.5% of expressed ORFs, and measure a median half-life of 9.4 min. For mRNAs where half-life estimates exist in the literature, their ranking order was in good agreement with previous data, indicating that SLAM-seq efficiently classifies stable and unstable transcripts. We then leveraged our yeast protocol to identify targets of the nonsense-mediated decay (NMD) pathway by measuring the change in RNA half-lives, instead of steady-state RNA level changes. With SLAM-seq, we assign 580 transcripts as putative NMD targets, based on their measured half-lives in wild-type and upf3Δ mutants. We find 225 novel targets, and observe a strong agreement with previous reports of NMD targets, 61.2% of our candidates being identified in previous studies. This indicates that SLAM-seq is a simpler and more economic method for global quantification of mRNA half-lives. Our adaptation for yeast yielded global quantitative measures of the NMD effect on transcript half-lives, high correlation with RNA half-lives measured previously with more technically challenging protocols, and identification of novel NMD regulated transcripts that escaped prior detection.
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Affiliation(s)
- Hanna Alalam
- Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, S-405 30 Göteborg, Sweden
| | | | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, S-405 30 Göteborg, Sweden
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8
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Kocik RA, Gasch AP. Breadth and Specificity in Pleiotropic Protein Kinase A Activity and Environmental Responses. Front Cell Dev Biol 2022; 10:803392. [PMID: 35252178 PMCID: PMC8888911 DOI: 10.3389/fcell.2022.803392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Protein Kinase A (PKA) is an essential kinase that is conserved across eukaryotes and plays fundamental roles in a wide range of organismal processes, including growth control, learning and memory, cardiovascular health, and development. PKA mediates these responses through the direct phosphorylation of hundreds of proteins-however, which proteins are phosphorylated can vary widely across cell types and environmental cues, even within the same organism. A major question is how cells enact specificity and precision in PKA activity to mount the proper response, especially during environmental changes in which only a subset of PKA-controlled processes must respond. Research over the years has uncovered multiple strategies that cells use to modulate PKA activity and specificity. This review highlights recent advances in our understanding of PKA signaling control including subcellular targeting, phase separation, feedback control, and standing waves of allosteric regulation. We discuss how the complex inputs and outputs to the PKA network simultaneously pose challenges and solutions in signaling integration and insulation. PKA serves as a model for how the same regulatory factors can serve broad pleiotropic functions but maintain specificity in localized control.
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Affiliation(s)
- Rachel A Kocik
- Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI, United States.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States.,Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, United States
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9
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Agwunobi DO, Pei T, Bai R, Wang Z, Shi X, Zhang M, Yu Z, Liu J. miR-2a and miR-279 are functionally associated with cold tolerance in Dermacentor silvarum (Acari: Ixodidae). Comp Biochem Physiol Part D Genomics Proteomics 2022; 41:100946. [PMID: 34872025 DOI: 10.1016/j.cbd.2021.100946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/15/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022]
Abstract
Ticks are obligate blood-sucking ectoparasites that can attack mammals, birds, reptiles as well as amphibians. Dermacentor silvarum, an important vector of various pathogenic bacteria, viruses, and protozoans, is widely distributed in China. MicroRNAs (miRNAs) are ~22 nucleotide non-coding small RNA molecules, involved in the regulation of various physiological and cellular processes. Previous studies demonstrated the vital roles of miRNAs during the reproduction and development of ticks, whereas, the regulatory/functional roles of microRNAs during the cold response of ticks remain unexplored. Here, we identified and functionally explored D. silvarum miRNAs involved in cold response to gain further understanding of the molecular regulatory mechanisms underlying cold stress in ticks. The microRNA libraries of D. silvarum were established via high-throughput sequencing after exposure to different cold treatments. A total of 147 miRNAs, including 44 known miRNAs and 103 new miRNAs, were identified. The verification of six highly differentially expressed miRNAs (miR-2a, miR-5305, miR-7, miR-279, miR-993, and novel-3) via RT-qPCR were consistent with the high-throughput sequence results. miR-2a peaked by day 6 and miR-279 expression was lowest by day 3 after cold treatment. The potential target genes of miR-2a and miR-279 were the glycogen phosphorylase (GPase) gene and serine gene, respectively. After injecting D. silvarum ticks with miR-2a and miR-279 antagonists, their respective target genes were up-regulated and vice-versa after injection with the agonists. These results indicated that these two miRNAs and their target genes may be involved in the cold response of D. silvarum ticks.
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Affiliation(s)
- Desmond O Agwunobi
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Tingwei Pei
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Ruwei Bai
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Zihao Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xinyue Shi
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Miao Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China.
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China.
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10
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Jaquet V, Wallerich S, Voegeli S, Túrós D, Viloria EC, Becskei A. Determinants of the temperature adaptation of mRNA degradation. Nucleic Acids Res 2022; 50:1092-1110. [PMID: 35018460 PMCID: PMC8789057 DOI: 10.1093/nar/gkab1261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/04/2021] [Accepted: 12/09/2021] [Indexed: 12/26/2022] Open
Abstract
The rate of chemical reactions increases proportionally with temperature, but the interplay of biochemical reactions permits deviations from this relation and adaptation. The degradation of individual mRNAs in yeast increased to varying degrees with temperature. We examined how these variations are influenced by the translation and codon composition of mRNAs. We developed a method that revealed the existence of a neutral half-life above which mRNAs are stabilized by translation but below which they are destabilized. The proportion of these two mRNA subpopulations remained relatively constant under different conditions, even with slow cell growth due to nutrient limitation, but heat shock reduced the proportion of translationally stabilized mRNAs. At the same time, the degradation of these mRNAs was partially temperature-compensated through Upf1, the mediator of nonsense-mediated decay. Compensation was also promoted by some asparagine and serine codons, whereas tyrosine codons promote temperature sensitization. These codons play an important role in the degradation of mRNAs encoding key cell membrane and cell wall proteins, which promote cell integrity.
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Affiliation(s)
- Vincent Jaquet
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Sandrine Wallerich
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Sylvia Voegeli
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Demeter Túrós
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Eduardo C Viloria
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Attila Becskei
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
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11
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Singh A, Kandi AR, Jayaprakashappa D, Thuery G, Purohit DJ, Huelsmeier J, Singh R, Pothapragada SS, Ramaswami M, Bakthavachalu B. The Transcriptional Response to Oxidative Stress is Independent of Stress-Granule Formation. Mol Biol Cell 2022; 33:ar25. [PMID: 34985933 PMCID: PMC9250384 DOI: 10.1091/mbc.e21-08-0418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Cells respond to stress with translational arrest, robust transcriptional changes, and transcription-independent formation of mRNP assemblies termed stress granules (SGs). Despite considerable interest in the role of SGs in oxidative, unfolded-protein and viral stress responses, whether and how SGs contribute to stress-induced transcription has not been rigorously examined. To address this, we characterized transcriptional changes in Drosophila S2 cells induced by acute oxidative-stress and assessed how these were altered under conditions that disrupted SG assembly. Oxidative stress for 3-hours predominantly resulted in induction or upregulation of stress-responsive mRNAs whose levels peaked during recovery after stress cessation. The stress-transcriptome is enriched in mRNAs coding for chaperones, including HSP70s, small heat shock proteins, glutathione transferases, and several non-coding RNAs. Oxidative stress also induced cytoplasmic SGs that disassembled 3-hours after stress cessation. As expected, RNAi-mediated knockdown of the conserved G3BP1/Rasputin protein inhibited SG assembly. However, this disruption had no significant effect on the stress-induced transcriptional response or stress-induced translational arrest. Thus, SG assembly and stress-induced gene expression alterations appear to be driven by distinctive signaling processes. We suggest that while SG assembly represents a fast, transient mechanism, the transcriptional response enables a slower, longer-lasting mechanism for adaptation to and recovery from cell stress.
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Affiliation(s)
- Amanjot Singh
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India
| | - Arvind Reddy Kandi
- Tata Institute for Genetics and Society Centre at inStem, Bellary Road, Bangalore 560065, India
| | | | - Guillaume Thuery
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2 Ireland
| | - Devam J Purohit
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India
| | - Joern Huelsmeier
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2 Ireland
| | - Rashi Singh
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India
| | | | - Mani Ramaswami
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India.,Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2 Ireland
| | - Baskar Bakthavachalu
- Tata Institute for Genetics and Society Centre at inStem, Bellary Road, Bangalore 560065, India.,School of Basic Sciences, Indian Institute of Technology, Mandi 175005, India
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