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Taguchi H, Niwa T. Reconstituted Cell-free Translation Systems for Exploring Protein Folding and Aggregation. J Mol Biol 2024; 436:168726. [PMID: 39074633 DOI: 10.1016/j.jmb.2024.168726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/18/2024] [Accepted: 07/24/2024] [Indexed: 07/31/2024]
Abstract
Protein folding is crucial for achieving functional three-dimensional structures. However, the process is often hampered by aggregate formation, necessitating the presence of chaperones and quality control systems within the cell to maintain protein homeostasis. Despite a long history of folding studies involving the denaturation and subsequent refolding of translation-completed purified proteins, numerous facets of cotranslational folding, wherein nascent polypeptides are synthesized by ribosomes and folded during translation, remain unexplored. Cell-free protein synthesis (CFPS) systems are invaluable tools for studying cotranslational folding, offering a platform not only for elucidating mechanisms but also for large-scale analyses to identify aggregation-prone proteins. This review provides an overview of the extensive use of CFPS in folding studies to date. In particular, we discuss a comprehensive aggregation formation assay of thousands of Escherichia coli proteins conducted under chaperone-free conditions using a reconstituted translation system, along with its derived studies.
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Affiliation(s)
- Hideki Taguchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, S2-19, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
| | - Tatsuya Niwa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, S2-19, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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2
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Tomuro K, Mito M, Toh H, Kawamoto N, Miyake T, Chow SYA, Doi M, Ikeuchi Y, Shichino Y, Iwasaki S. Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts. Nat Commun 2024; 15:7061. [PMID: 39187487 PMCID: PMC11347596 DOI: 10.1038/s41467-024-51258-0] [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: 07/09/2023] [Accepted: 08/02/2024] [Indexed: 08/28/2024] Open
Abstract
Ribosome profiling, which is based on deep sequencing of ribosome footprints, has served as a powerful tool for elucidating the regulatory mechanism of protein synthesis. However, the current method has substantial issues: contamination by rRNAs and the lack of appropriate methods to measure ribosome numbers in transcripts. Here, we overcome these hurdles through the development of "Ribo-FilterOut", which is based on the separation of footprints from ribosome subunits by ultrafiltration, and "Ribo-Calibration", which relies on external spike-ins of stoichiometrically defined mRNA-ribosome complexes. A combination of these approaches estimates the number of ribosomes on a transcript, the translation initiation rate, and the overall number of translation events before its decay, all in a genome-wide manner. Moreover, our method reveals the allocation of ribosomes under heat shock stress, during aging, and across cell types. Our strategy of modified ribosome profiling measures kinetic and stoichiometric parameters of cellular translation across the transcriptome.
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Grants
- JP20H05784 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP24H02307 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05782 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP24H02306 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05786 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP24H02307 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP21H05734 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP23H04268 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP23gm6910005 Japan Agency for Medical Research and Development (AMED)
- JP22fk0108570 Japan Agency for Medical Research and Development (AMED)
- JP23H02415 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23H00095 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21K15023 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23K05648 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP22K20765 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23K14173 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23KJ2178 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23KJ2175 MEXT | Japan Society for the Promotion of Science (JSPS)
- Pioneering Project MEXT | RIKEN
- RIKEN TRIP initiative "TRIP-AGIS" MEXT | RIKEN
- Pioneering Project MEXT | RIKEN
- JPMJBS2418 MEXT | Japan Science and Technology Agency (JST)
- JPMJFR226F MEXT | Japan Science and Technology Agency (JST)
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Affiliation(s)
- Kotaro Tomuro
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Hirotaka Toh
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Naohiro Kawamoto
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Takahito Miyake
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Siu Yu A Chow
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
| | - Masao Doi
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Institute for AI and Beyond, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan.
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3
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Ciccarelli M, Andréasson C. Protein Misfolding Releases Human HSF1 from HSP70 Latency Control. J Mol Biol 2024; 436:168740. [PMID: 39122169 DOI: 10.1016/j.jmb.2024.168740] [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: 05/20/2024] [Revised: 07/25/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
Heat shock factor 1 (HSF1) responds to stress to mount the heat shock response (HSR), a conserved transcriptional program that allows cells to maintain proteostasis by upregulating heat shock proteins (HSPs). The homeostatic stress regulation of HSF1 plays a key role in human physiology and health but its mechanism has remained difficult to pinpoint. Recent work in the budding yeast model has implicated stress-inducible chaperones of the HSP70 family as direct negative regulators of HSF1 activity. Here, we have investigated the latency control and activation of human HSF1 by HSP70 and misfolded proteins. Purified oligomeric HSF1-HSP70 (HSPA1A) complexes exhibited basal DNA binding activity that was inhibited by increasing the levels of HSP70 and, importantly, misfolded proteins reverted the inhibitory effect. Using site-specific UV photo-crosslinking, we monitored HSP70-HSF1 complexes in HEK293T cells. While HSF1 was bound by the substrate binding domain of HSP70 in unstressed cells, activation of HSF1 by heat shock as well as by inducing the misfolding of newly synthesized proteins resulted in release of HSF1 from the chaperone. Taken our results together, we conclude that latent HSF1 populate dynamic complexes with HSP70, which are sensitive to increased levels of misfolded proteins that compete for binding to the HSP70 substrate binding domain. Thus, human HSF1 is activated by various stress conditions that all titrate available HSP70.
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Affiliation(s)
- Michela Ciccarelli
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden.
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4
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Lohmann J, Herzog O, Rosenzweig K, Weingartner M. Thermal adaptation in plants: understanding the dynamics of translation factors and condensates. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4258-4273. [PMID: 38630631 DOI: 10.1093/jxb/erae171] [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: 12/15/2023] [Accepted: 04/16/2024] [Indexed: 04/19/2024]
Abstract
Plants, as sessile organisms, face the crucial challenge of adjusting growth and development with ever-changing environmental conditions. Protein synthesis is the fundamental process that enables growth of all organisms. Since elevated temperature presents a substantial threat to protein stability and function, immediate adjustments of protein synthesis rates are necessary to circumvent accumulation of proteotoxic stress and to ensure survival. This review provides an overview of the mechanisms that control translation under high-temperature stress by the modification of components of the translation machinery in plants, and compares them to yeast and metazoa. Recent research also suggests an important role for cytoplasmic biomolecular condensates, named stress granules, in these processes. Current understanding of the role of stress granules in translational regulation and of the molecular processes associated with translation that might occur within stress granules is also discussed.
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Affiliation(s)
- Julia Lohmann
- Institute of Plant Sciences and Microbiology, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - Oliver Herzog
- Institute of Plant Sciences and Microbiology, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - Kristina Rosenzweig
- Institute of Plant Sciences and Microbiology, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - Magdalena Weingartner
- Institute of Plant Sciences and Microbiology, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
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5
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Li X, Dan X, Liu J, Lv Q, Li X. Translation elongation factor-1α is pivotal for plant heat tolerance despite its pronounced heat-induced aggregation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108649. [PMID: 38653099 DOI: 10.1016/j.plaphy.2024.108649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024]
Abstract
The translation elongation factor 1α (EF1α) protein is a highly conserved G protein that is crucial for protein translation in all eukaryotic organisms. EF1α quickly became insoluble at temperatures 42 °C treatment for 2h in vitro, but generally remained soluble in vivo even after being exposed to temperatures as high as 45 °C for an extended period, which suggests that protective mechanisms exist for keeping EF1α soluble in plant cells under heat stress. EF1α had fast in vivo insolubilization when exposed to 45 °C, resulting in about 40% of the protein aggregating after 9 h. Given its established role in protein translation, heat-induced aggregation is most likely to impact the function of the elongation factor. Overexpression of constitutive mutants in both GTP-bound and GDP-bound forms of EF1α resulted in significantly decreased heat tolerance. These findings provide evidence to support the critical role of EF1α, a thermosensitive protein, in the heat tolerance of plants.
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Affiliation(s)
- Xifeng Li
- College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China; College of Life Sciences, China Jiliang University, Hangzhou, 310018, China.
| | - Xinya Dan
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Jia Liu
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Qiaoqiao Lv
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Xie Li
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
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6
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Chan C, Groisman EA. Chaperone Hsp70 helps Salmonella survive infection-relevant stress by reducing protein synthesis. PLoS Biol 2024; 22:e3002560. [PMID: 38574172 PMCID: PMC10994381 DOI: 10.1371/journal.pbio.3002560] [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: 12/03/2023] [Accepted: 02/23/2024] [Indexed: 04/06/2024] Open
Abstract
In all domains of life, Hsp70 chaperones preserve protein homeostasis by promoting protein folding and degradation and preventing protein aggregation. We now report that the Hsp70 from the bacterial pathogen Salmonella enterica serovar Typhimurium-termed DnaK-independently reduces protein synthesis in vitro and in S. Typhimurium facing cytoplasmic Mg2+ starvation, a condition encountered during infection. This reduction reflects a 3-fold increase in ribosome association with DnaK and a 30-fold decrease in ribosome association with trigger factor, the chaperone normally associated with translating ribosomes. Surprisingly, this reduction does not involve J-domain cochaperones, unlike previously known functions of DnaK. Removing the 74 C-terminal amino acids of the 638-residue long DnaK impeded DnaK association with ribosomes and reduction of protein synthesis, rendering S. Typhimurium defective in protein homeostasis during cytoplasmic Mg2+ starvation. DnaK-dependent reduction in protein synthesis is critical for survival against Mg2+ starvation because inhibiting protein synthesis in a dnaK-independent manner overcame the 10,000-fold loss in viability resulting from DnaK truncation. Our results indicate that DnaK protects bacteria from infection-relevant stresses by coordinating protein synthesis with protein folding capacity.
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Affiliation(s)
- Carissa Chan
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
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7
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Smith AB, Ganguly DR, Moore M, Bowerman AF, Janapala Y, Shirokikh NE, Pogson BJ, Crisp PA. Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:818-839. [PMID: 37947266 PMCID: PMC10952913 DOI: 10.1111/tpj.16531] [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: 03/22/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
Transcript stability is an important determinant of its abundance and, consequently, translational output. Transcript destabilisation can be rapid and is well suited for modulating the cellular response. However, it is unclear the extent to which RNA stability is altered under changing environmental conditions in plants. We previously hypothesised that recovery-induced transcript destabilisation facilitated a phenomenon of rapid recovery gene downregulation (RRGD) in Arabidopsis thaliana (Arabidopsis) following light stress, based on mathematical calculations to account for ongoing transcription. Here, we test this hypothesis and investigate processes regulating transcript abundance and fate by quantifying changes in transcription, stability and translation before, during and after light stress. We adapt syringe infiltration to apply a transcriptional inhibitor to soil-grown plants in combination with stress treatments. Compared with measurements in juvenile plants and cell culture, we find reduced stability across a range of transcripts encoding proteins involved in RNA binding and processing. We also observe light-induced destabilisation of transcripts, followed by their stabilisation during recovery. We propose that this destabilisation facilitates RRGD, possibly in combination with transcriptional shut-off that was confirmed for HSP101, ROF1 and GOLS1. We also show that translation remains highly dynamic over the course of light stress and recovery, with a bias towards transcript-specific increases in ribosome association, independent of changes in total transcript abundance, after 30 min of light stress. Taken together, we provide evidence for the combinatorial regulation of transcription and stability that occurs to coordinate translation during light stress and recovery in Arabidopsis.
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Affiliation(s)
- Aaron B. Smith
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Diep R. Ganguly
- CSIRO Synthetic Biology Future Science PlatformCanberraAustralian Capital Territory2601Australia
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Marten Moore
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Andrew F. Bowerman
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Yoshika Janapala
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityClaytonVictoria3800Australia
| | - Nikolay E. Shirokikh
- The John Curtin School of Medical Research, The Shine‐Dalgarno Centre for RNA InnovationThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Barry J. Pogson
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Peter A. Crisp
- School of Agriculture and Food SciencesThe University of QueenslandBrisbaneQueensland4072Australia
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8
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Che R, Liu Y, Yan S, Yang C, Sun Y, Liu C, Ma F. Elongation factor MdEF-Tu coordinates with heat shock protein MdHsp70 to enhance apple thermotolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1250-1263. [PMID: 37991990 DOI: 10.1111/tpj.16561] [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: 05/13/2023] [Revised: 10/08/2023] [Accepted: 11/13/2023] [Indexed: 11/24/2023]
Abstract
High-temperature stress results in protein misfolding/unfolding and subsequently promotes the accumulation of cytotoxic protein aggregates that can compromise cell survival. Heat shock proteins (HSPs) function as molecular chaperones that coordinate the refolding and degradation of aggregated proteins to mitigate the detrimental effects of high temperatures. However, the relationship between HSPs and protein aggregates in apples under high temperatures remains unclear. Here, we show that an apple (Malus domestica) chloroplast-localized, heat-sensitive elongation factor Tu (MdEF-Tu), positively regulates apple thermotolerance when it is overexpressed. Transgenic apple plants exhibited higher photosynthetic capacity and better integrity of chloroplasts during heat stress. Under high temperatures, MdEF-Tu formed insoluble aggregates accompanied by ubiquitination modifications. Furthermore, we identified a chaperone heat shock protein (MdHsp70), as an interacting protein of MdEF-Tu. Moreover, we observed obviously elevated MdHsp70 levels in 35S: MdEF-Tu apple plants that prevented the accumulation of ubiquitinated MdEF-Tu aggregates, which positively contributes to the thermotolerance of the transgenic plants. Overall, our results provide new insights into the molecular chaperone function of MdHsp70, which mediates the homeostasis of thermosensitive proteins under high temperatures.
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Affiliation(s)
- Runmin Che
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuerong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shengqi Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chao Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yubo Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Changhai Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Su D, Ding C, Qiu J, Yang G, Wang R, Liu Y, Tao J, Luo W, Weng G, Zhang T. Ribosome profiling: a powerful tool in oncological research. Biomark Res 2024; 12:11. [PMID: 38273337 PMCID: PMC10809610 DOI: 10.1186/s40364-024-00562-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
Neoplastic cells need to adapt their gene expression pattern to survive in an ever-changing or unfavorable tumor microenvironment. Protein synthesis (or mRNA translation), an essential part of gene expression, is dysregulated in cancer. The emergence of distinct translatomic technologies has revolutionized oncological studies to elucidate translational regulatory mechanisms. Ribosome profiling can provide adequate information on diverse aspects of translation by aiding in quantitatively analyzing the intensity of translating ribosome-protected fragments. Here, we review the primary currently used translatomics techniques and highlight their advantages and disadvantages as tools for translatomics studies. Subsequently, we clarified the areas in which ribosome profiling could be applied to better understand translational control. Finally, we summarized the latest advances in cancer studies using ribosome profiling to highlight the extensive application of this powerful and promising translatomic tool.
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Affiliation(s)
- Dan Su
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Chen Ding
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Jiangdong Qiu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Gang Yang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Ruobing Wang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Yueze Liu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Jinxin Tao
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Wenhao Luo
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Guihu Weng
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
| | - Taiping Zhang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China.
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China.
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10
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Black A, Williams TD, Soubigou F, Joshua IM, Zhou H, Lamoliatte F, Rousseau A. The ribosome-associated chaperone Zuo1 controls translation upon TORC1 inhibition. EMBO J 2023; 42:e113240. [PMID: 37984430 PMCID: PMC10711665 DOI: 10.15252/embj.2022113240] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/22/2023] Open
Abstract
Protein requirements of eukaryotic cells are ensured by proteostasis, which is mediated by tight control of TORC1 activity. Upon TORC1 inhibition, protein degradation is increased and protein synthesis is reduced through inhibition of translation initiation to maintain cell viability. Here, we show that the ribosome-associated complex (RAC)/Ssb chaperone system, composed of the HSP70 chaperone Ssb and its HSP40 co-chaperone Zuo1, is required to maintain proteostasis and cell viability under TORC1 inhibition in Saccharomyces cerevisiae. In the absence of Zuo1, translation does not decrease in response to the loss of TORC1 activity. A functional interaction between Zuo1 and Ssb is required for proper translational control and proteostasis maintenance upon TORC1 inhibition. Furthermore, we have shown that the rapid degradation of eIF4G following TORC1 inhibition is mediated by autophagy and is prevented in zuo1Δ cells, contributing to decreased survival in these conditions. We found that autophagy is defective in zuo1Δ cells, which impedes eIF4G degradation upon TORC1 inhibition. Our findings identify an essential role for RAC/Ssb in regulating translation in response to changes in TORC1 signalling.
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Affiliation(s)
- Ailsa Black
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeDundeeUK
| | - Thomas D Williams
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeDundeeUK
| | - Flavie Soubigou
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeDundeeUK
| | - Ifeoluwapo M Joshua
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeDundeeUK
| | - Houjiang Zhou
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeDundeeUK
| | - Frederic Lamoliatte
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeDundeeUK
| | - Adrien Rousseau
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeDundeeUK
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11
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Maiti S, Bhattacharya K, Wider D, Hany D, Panasenko O, Bernasconi L, Hulo N, Picard D. Hsf1 and the molecular chaperone Hsp90 support a 'rewiring stress response' leading to an adaptive cell size increase in chronic stress. eLife 2023; 12:RP88658. [PMID: 38059913 DOI: 10.7554/elife.88658] [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] [Indexed: 12/08/2023] Open
Abstract
Cells are exposed to a wide variety of internal and external stresses. Although many studies have focused on cellular responses to acute and severe stresses, little is known about how cellular systems adapt to sublethal chronic stresses. Using mammalian cells in culture, we discovered that they adapt to chronic mild stresses of up to two weeks, notably proteotoxic stresses such as heat, by increasing their size and translation, thereby scaling the amount of total protein. These adaptations render them more resilient to persistent and subsequent stresses. We demonstrate that Hsf1, well known for its role in acute stress responses, is required for the cell size increase, and that the molecular chaperone Hsp90 is essential for coupling the cell size increase to augmented translation. We term this translational reprogramming the 'rewiring stress response', and propose that this protective process of chronic stress adaptation contributes to the increase in size as cells get older, and that its failure promotes aging.
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Affiliation(s)
- Samarpan Maiti
- Département de Biologie Moléculaire et Cellulaire, Université de Genève, Genève, Switzerland
| | - Kaushik Bhattacharya
- Département de Biologie Moléculaire et Cellulaire, Université de Genève, Genève, Switzerland
| | - Diana Wider
- Département de Biologie Moléculaire et Cellulaire, Université de Genève, Genève, Switzerland
| | - Dina Hany
- Département de Biologie Moléculaire et Cellulaire, Université de Genève, Genève, Switzerland
- On leave from: Department of Pharmacology and Therapeutics, Faculty of Pharmacy, Pharos University in Alexandria, Alexandria, Egypt
| | - Olesya Panasenko
- BioCode: RNA to Proteins Core Facility, Département de Microbiologie et Médecine Moléculaire, Faculté de Médecine, Université de Genève, Genève, Switzerland
| | - Lilia Bernasconi
- Département de Biologie Moléculaire et Cellulaire, Université de Genève, Genève, Switzerland
| | - Nicolas Hulo
- Institute of Genetics and Genomics of Geneva, Université de Genève, Genève, Switzerland
| | - Didier Picard
- Département de Biologie Moléculaire et Cellulaire, Université de Genève, Genève, Switzerland
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12
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Li N, Duan Y, Ye Q, Ma Y, Ma R, Zhao L, Zhu S, Yu F, Qi S, Wang Y. The Arabidopsis eIF4E1 regulates NRT1.1-mediated nitrate signaling at both translational and transcriptional levels. THE NEW PHYTOLOGIST 2023; 240:338-353. [PMID: 37424317 DOI: 10.1111/nph.19129] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/18/2023] [Indexed: 07/11/2023]
Abstract
Identifying new nitrate regulatory genes and illustrating their mechanisms in modulating nitrate signaling are of great significance for achieving the high yield and nitrogen use efficiency (NUE) of crops. Here, we screened a mutant with defects in nitrate response and mapped the mutation to the gene eIF4E1 in Arabidopsis. Our results showed that eIF4E1 regulated nitrate signaling and metabolism. Ribo-seq and polysome profiling analysis revealed that eIF4E1 modulated the amount of some nitrogen (N)-related mRNAs being translated, especially the mRNA of NRT1.1 was reduced in the eif4e1 mutant. RNA-Seq results enriched some N-related genes, supporting that eIF4E1 is involved in nitrate regulation. The genetic analysis indicated that eIF4E1 worked upstream of NRT1.1 in nitrate signaling. In addition, an eIF4E1-interacting protein GEMIN2 was identified and found to be involved in nitrate signaling. Further investigation showed that overexpression of eIF4E1 promoted plant growth and enhanced yield and NUE. These results demonstrate that eIF4E1 regulates nitrate signaling by modulating NRT1.1 at both translational and transcriptional levels, laying the foundation for future research on the regulation of mineral nutrition at the translational level.
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Affiliation(s)
- Na Li
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yawen Duan
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Qing Ye
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yuhan Ma
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Rongjie Ma
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Lufei Zhao
- Agricultural Science and Engineering School, Liaocheng University, Liaocheng, Shandong, 252000, China
| | - Sirui Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan, 410082, China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan, 410082, China
| | - Shengdong Qi
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yong Wang
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
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13
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Höpfler M, Hegde RS. Control of mRNA fate by its encoded nascent polypeptide. Mol Cell 2023; 83:2840-2855. [PMID: 37595554 PMCID: PMC10501990 DOI: 10.1016/j.molcel.2023.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 08/20/2023]
Abstract
Cells tightly regulate mRNA processing, localization, and stability to ensure accurate gene expression in diverse cellular states and conditions. Most of these regulatory steps have traditionally been thought to occur before translation by the action of RNA-binding proteins. Several recent discoveries highlight multiple co-translational mechanisms that modulate mRNA translation, localization, processing, and stability. These mechanisms operate by recognition of the nascent protein, which is necessarily coupled to its encoding mRNA during translation. Hence, the distinctive sequence or structure of a particular nascent chain can recruit recognition factors with privileged access to the corresponding mRNA in an otherwise crowded cellular environment. Here, we draw on both well-established and recent examples to provide a conceptual framework for how cells exploit nascent protein recognition to direct mRNA fate. These mechanisms allow cells to dynamically and specifically regulate their transcriptomes in response to changes in cellular states to maintain protein homeostasis.
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14
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Alagar Boopathy L, Beadle E, Xiao A, Garcia-Bueno Rico A, Alecki C, Garcia de-Andres I, Edelmeier K, Lazzari L, Amiri M, Vera M. The ribosome quality control factor Asc1 determines the fate of HSP70 mRNA on and off the ribosome. Nucleic Acids Res 2023; 51:6370-6388. [PMID: 37158240 PMCID: PMC10325905 DOI: 10.1093/nar/gkad338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 05/10/2023] Open
Abstract
Cells survive harsh environmental conditions by potently upregulating molecular chaperones such as heat shock proteins (HSPs), particularly the inducible members of the HSP70 family. The life cycle of HSP70 mRNA in the cytoplasm is unique-it is translated during stress when most cellular mRNA translation is repressed and rapidly degraded upon recovery. Contrary to its 5' untranslated region's role in maximizing translation, we discovered that the HSP70 coding sequence (CDS) suppresses its translation via the ribosome quality control (RQC) mechanism. The CDS of the most inducible Saccharomyces cerevisiae HSP70 gene, SSA4, is uniquely enriched with low-frequency codons that promote ribosome stalling during heat stress. Stalled ribosomes are recognized by the RQC components Asc1p and Hel2p and two novel RQC components, the ribosomal proteins Rps28Ap and Rps19Bp. Surprisingly, RQC does not signal SSA4 mRNA degradation via No-Go-Decay. Instead, Asc1p destabilizes SSA4 mRNA during recovery from heat stress by a mechanism independent of ribosome binding and SSA4 codon optimality. Therefore, Asc1p operates in two pathways that converge to regulate the SSA4 mRNA life cycle during stress and recovery. Our research identifies Asc1p as a critical regulator of the stress response and RQC as the mechanism tuning HSP70 synthesis.
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Affiliation(s)
| | - Emma Beadle
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | - Alan RuoChen Xiao
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | | | - Celia Alecki
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | | | - Kyla Edelmeier
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | - Luca Lazzari
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | - Mehdi Amiri
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | - Maria Vera
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
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15
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Barros GC, Guerrero S, Silva GM. The central role of translation elongation in response to stress. Biochem Soc Trans 2023; 51:959-969. [PMID: 37318088 PMCID: PMC11160351 DOI: 10.1042/bst20220584] [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: 02/06/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023]
Abstract
Protein synthesis is essential to support homeostasis, and thus, must be highly regulated during cellular response to harmful environments. All stages of translation are susceptible to regulation under stress, however, the mechanisms involved in translation regulation beyond initiation have only begun to be elucidated. Methodological advances enabled critical discoveries on the control of translation elongation, highlighting its important role in translation repression and the synthesis of stress-response proteins. In this article, we discuss recent findings on mechanisms of elongation control mediated by ribosome pausing and collisions and the availability of tRNAs and elongation factors. We also discuss how elongation intersects with distinct modes of translation control, further supporting cellular viability and gene expression reprogramming. Finally, we highlight how several of these pathways are reversibly regulated, emphasizing the dynamics of translation control during stress-response progression. A comprehensive understanding of translation regulation under stress will produce fundamental knowledge of protein dynamics while opening new avenues and strategies to overcome dysregulated protein production and cellular sensitivity to stress.
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Affiliation(s)
| | | | - Gustavo M. Silva
- Department of Biology, Duke University, Durham, NC, USA
- Lead contact
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16
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Jian H, Wen S, Liu R, Zhang W, Li Z, Chen W, Zhou Y, Khassanov V, Mahmoud AMA, Wang J, Lyu D. Dynamic Translational Landscape Revealed by Genome-Wide Ribosome Profiling under Drought and Heat Stress in Potato. PLANTS (BASEL, SWITZERLAND) 2023; 12:2232. [PMID: 37375858 DOI: 10.3390/plants12122232] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
The yield and quality of potatoes, an important staple crop, are seriously threatened by high temperature and drought stress. In order to deal with this adverse environment, plants have evolved a series of response mechanisms. However, the molecular mechanism of potato's response to environmental changes at the translational level is still unclear. In this study, we performed transcriptome- and ribosome-profiling assays with potato seedlings growing under normal, drought, and high-temperature conditions to reveal the dynamic translational landscapes for the first time. The translational efficiency was significantly affected by drought and heat stress in potato. A relatively high correlation (0.88 and 0.82 for drought and heat stress, respectively) of the fold changes of gene expression was observed between the transcriptional level and translational level globally based on the ribosome-profiling and RNA-seq data. However, only 41.58% and 27.69% of the different expressed genes were shared by transcription and translation in drought and heat stress, respectively, suggesting that the transcription or translation process can be changed independently. In total, the translational efficiency of 151 (83 and 68 for drought and heat, respectively) genes was significantly changed. In addition, sequence features, including GC content, sequence length, and normalized minimal free energy, significantly affected the translational efficiencies of genes. In addition, 28,490 upstream open reading frames (uORFs) were detected on 6463 genes, with an average of 4.4 uORFs per gene and a median length of 100 bp. These uORFs significantly affected the translational efficiency of downstream major open reading frames (mORFs). These results provide new information and directions for analyzing the molecular regulatory network of potato seedlings in response to drought and heat stress.
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Affiliation(s)
- Hongju Jian
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
| | - Shiqi Wen
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Rongrong Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Wenzhe Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Ziyan Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Weixi Chen
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yonghong Zhou
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
| | - Vadim Khassanov
- Department of Plant Protection and Quarantine, Faculty of Agronomy, S. Seifullin Kazakh Agrotechnical University, Zhenis Avenue, 010011 Astana, Kazakhstan
| | - Ahmed M A Mahmoud
- Department of Vegetable Crops, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Jichun Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
| | - Dianqiu Lyu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
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17
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Knowles CM, Goich D, Bloom ALM, Kalem MC, Panepinto JC. Contributions of Ccr4 and Gcn2 to the Translational Response of C. neoformans to Host-Relevant Stressors and Integrated Stress Response Induction. mBio 2023; 14:e0019623. [PMID: 37017529 PMCID: PMC10127693 DOI: 10.1128/mbio.00196-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/06/2023] [Indexed: 04/06/2023] Open
Abstract
In response to the host environment, the human pathogen Cryptococcus neoformans must rapidly reprogram its translatome from one which promotes growth to one which is responsive to host stress. In this study, we investigate the two events which comprise translatome reprogramming: the removal of abundant, pro-growth mRNAs from the translating pool, and the regulated entry of stress-responsive mRNAs into the translating pool. Removal of pro-growth mRNAs from the translating pool is controlled primarily by two regulatory mechanisms, repression of translation initiation via Gcn2, and decay mediated by Ccr4. We determined that translatome reprogramming in response to oxidative stress requires both Gcn2 and Ccr4, whereas the response to temperature requires only Ccr4. Additionally, we assessed ribosome collision in response to host-relevant stress and found that collided ribosomes accumulated during temperature stress but not during oxidative stress. The phosphorylation of eIF2α that occurred as a result of translational stress led us to investigate the induction of the integrated stress response (ISR). We found that eIF2α phosphorylation varied in response to the type and magnitude of stress, yet all tested conditions induced translation of the ISR transcription factor Gcn4. However, Gcn4 translation did not necessarily result in canonical Gcn4-dependent transcription. Finally, we define the ISR regulon in response to oxidative stress. In conclusion, this study begins to reveal the translational regulation in response to host-relevant stressors in an environmental fungus which is capable of adapting to the environment inside the human host. IMPORTANCE Cryptococcus neoformans is a human pathogen capable of causing devastating infections. It must rapidly adapt to changing environments as it leaves its niche in the soil and enters the human lung. Previous work has demonstrated a need to reprogram gene expression at the level of translation to promote stress adaptation. In this work, we investigate the contributions and interplay of the major mechanisms that regulate entry of new mRNAs into the pool (translation initiation) and the clearance of unneeded mRNAs from the pool (mRNA decay). One result of this reprogramming is the induction of the integrated stress response (ISR) regulon. Surprisingly, all stresses tested led to the production of the ISR transcription factor Gcn4, but not necessarily to transcription of ISR target genes. Furthermore, stresses result in differential levels of ribosome collisions, but these are not necessarily predictive of initiation repression as has been suggested in the model yeast.
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Affiliation(s)
- Corey M. Knowles
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - David Goich
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Amanda L. M. Bloom
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Murat C. Kalem
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - John C. Panepinto
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
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18
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Tungalag S, Shinriki S, Hirayama M, Nagamachi A, Kanai A, Inaba T, Matsui H. Ribosome profiling analysis reveals the roles of DDX41 in translational regulation. Int J Hematol 2023; 117:876-888. [PMID: 36780110 DOI: 10.1007/s12185-023-03558-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/14/2023]
Abstract
DDX41 mutation has been observed in myeloid malignancies including myelodysplastic syndromes and acute myeloid leukemia, but the underlying causative mechanisms of these diseases have not been fully elucidated. The DDX41 protein is an ATP-dependent RNA helicase with roles in RNA metabolism. We previously showed that DDX41 is involved in ribosome biogenesis by promoting the processing of newly transcribed pre-ribosomal RNA. To build on this finding, in this study, we leveraged ribosome profiling technology to investigate the involvement of DDX41 in translation. We found that DDX41 knockdown resulted in both translationally increased and decreased transcripts. Both gene set enrichment analysis and gene ontology analysis indicated that ribosome-associated genes were translationally promoted after DDX41 knockdown, in part because these transcripts had significantly shorter transcript length and higher transcriptional and translational levels. In addition, we found that transcripts with 5'-terminal oligopyrimidine motifs tended to be translationally upregulated when the DDX41 level was low. Our data suggest that a translationally regulated feedback mechanism involving DDX41 may exist for ribosome biogenesis.
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Affiliation(s)
- Saruul Tungalag
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Satoru Shinriki
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Mayumi Hirayama
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan.,Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Akiko Nagamachi
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Akinori Kanai
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Toshiya Inaba
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Hirotaka Matsui
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan.
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19
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Li F, Fang J, Yu Y, Hao S, Zou Q, Zeng Q, Yang X. Reanalysis of ribosome profiling datasets reveals a function of rocaglamide A in perturbing the dynamics of translation elongation via eIF4A. Nat Commun 2023; 14:553. [PMID: 36725859 PMCID: PMC9891901 DOI: 10.1038/s41467-023-36290-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
The quickly accumulating ribosome profiling data is an insightful resource for studying the critical details of translation regulation under various biological contexts. Rocaglamide A (RocA), an antitumor heterotricyclic natural compound, has been shown to inhibit translation initiation of a large group of mRNA species by clamping eIF4A onto poly-purine motifs in the 5' UTRs. However, reanalysis of previous ribosome profiling datasets reveals an unexpected shift of the ribosome occupancy pattern, upon RocA treatment in various types of cells, during early translation elongation for a specific group of mRNA transcripts without poly-purine motifs over-represented in their 5' UTRs. Such perturbation of translation elongation dynamics can be attributed to the blockage of translating ribosomes due to the binding of eIF4A to the poly-purine sequence in coding regions. In summary, our study presents the complete dual modes of RocA in blocking translation initiation and elongation, which underlie the potent antitumor effect of RocA.
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Affiliation(s)
- Fajin Li
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China. .,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, 100084, China.
| | - Jianhuo Fang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Yifan Yu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Sijia Hao
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China.,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, 100084, China
| | - Qin Zou
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Qinglin Zeng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China. .,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, 100084, China.
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20
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Kalemkeridou M, Nanas I, Moutou K, Amiridis GS, Tsipourlianos A, Dovolou E, Mamuris Z, Giannoulis T. Genetic diversity and thermotolerance in Holstein cows: Pathway analysis and marker development using whole-genome sequencing. Reprod Domest Anim 2023; 58:146-157. [PMID: 36196498 DOI: 10.1111/rda.14274] [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: 09/09/2022] [Accepted: 10/02/2022] [Indexed: 01/07/2023]
Abstract
Heat stress causes extensive losses in the dairy sector, due to negative effects on milk production and reproduction. Cows have evolved a series of protective mechanisms, (physiological, biochemical, behavioural) to cope with the thermostressing environments, which have allowed the preservation of productive and reproductive potential of specific animals during summer; these animals are considered thermotolerant and could be used to design programs of selective breeding. These programs, targeting the generations of a population of heat-resistant animals, would increase the frequency of the desired phenotypes, tackling the financial losses on one hand and reducing the carbon footprints of the dairy sector on the other. The development of genomics techniques has enabled genome wide variant calling, to detect SNPs associated with the desired phenotypes. In this study, we used a comparative genomics approach to detect genetic variation associated with thermotolerance and to design molecular markers for characterizing the animals as tolerant/sensitive. A total of 40 cows from each group were split in four sequencing pools and a whole-genome sequencing approach was used. Results and conclusion: Genome-wide genetic variation between groups was characterized and enrichment analysis revealed specific pathways which participate in the adaptive mechanisms of thermotolerance, implicated into systemic and cellular responses, including the immune system functionality, Heat Stress and Unfolded Protein Response. The markers made a promising set of results, as specific SNPs in five genes encoding for Heat Shock Proteins were significantly associated with thermotolerance.
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Affiliation(s)
- Maria Kalemkeridou
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Ioannis Nanas
- Department of Obstetrics and Reproduction, Veterinary Faculty, University of Thessaly, Karditsa, Greece
| | - Katerina Moutou
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Georgios S Amiridis
- Department of Obstetrics and Reproduction, Veterinary Faculty, University of Thessaly, Karditsa, Greece
| | - Andreas Tsipourlianos
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleni Dovolou
- Department of Obstetrics and Reproduction, Veterinary Faculty, University of Thessaly, Karditsa, Greece.,Department of Animal Sciences, University of Thessaly, Larissa, Greece
| | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Themistoklis Giannoulis
- Department of Animal Sciences, University of Thessaly, Larissa, Greece.,Laboratory of Biology, Genetics and Bioinformatics, Department of Animal Science, University of Thessaly, Larissa, Greece
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21
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Timcheva K, Dufour S, Touat-Todeschini L, Burnard C, Carpentier MC, Chuffart F, Merret R, Helsmoortel M, Ferré S, Grézy A, Couté Y, Rousseaux S, Khochbin S, Vourc'h C, Bousquet-Antonelli C, Kiernan R, Seigneurin-Berny D, Verdel A. Chromatin-associated YTHDC1 coordinates heat-induced reprogramming of gene expression. Cell Rep 2022; 41:111784. [PMID: 36516773 DOI: 10.1016/j.celrep.2022.111784] [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: 02/15/2021] [Revised: 08/01/2022] [Accepted: 11/15/2022] [Indexed: 12/15/2022] Open
Abstract
Heat stress (HS) induces a cellular response leading to profound changes in gene expression. Here, we show that human YTHDC1, a reader of N6-methyladenosine (m6A) RNA modification, mostly associates to the chromatin fraction and that HS induces a redistribution of YTHDC1 across the genome, including to heat-induced heat shock protein (HSP) genes. YTHDC1 binding to m6A-modified HSP transcripts co-transcriptionally promotes expression of HSPs. In parallel, hundreds of the genes enriched in YTHDC1 during HS have their transcripts undergoing YTHDC1- and m6A-dependent intron retention. Later, YTHDC1 concentrates within nuclear stress bodies (nSBs) where it binds to m6A-modified SATIII non-coding RNAs, produced in an HSF1-dependent manner upon HS. These findings reveal that YTHDC1 plays a central role in a chromatin-associated m6A-based reprogramming of gene expression during HS. Furthermore, they support the model where the subsequent and temporary sequestration of YTHDC1 within nSBs calibrates the timing of this YTHDC1-dependent gene expression reprogramming.
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Affiliation(s)
- Kalina Timcheva
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Solenne Dufour
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Leila Touat-Todeschini
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Callum Burnard
- Gene Regulation Laboratory, Institut de Génétique Humaine, UMR9002, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Marie-Christine Carpentier
- University Perpignan Via Domitia, LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; CNRS LGDP-UMR5096, UPVD, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Florent Chuffart
- Epigenetic Regulations, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Rémy Merret
- University Perpignan Via Domitia, LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; CNRS LGDP-UMR5096, UPVD, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Marion Helsmoortel
- Gene Regulation Laboratory, Institut de Génétique Humaine, UMR9002, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Sabrina Ferré
- University Grenoble Alpes, Inserm, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Aude Grézy
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Yohann Couté
- University Grenoble Alpes, Inserm, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Sophie Rousseaux
- Epigenetic Regulations, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Saadi Khochbin
- Epigenetic Regulations, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Claire Vourc'h
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Cécile Bousquet-Antonelli
- University Perpignan Via Domitia, LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; CNRS LGDP-UMR5096, UPVD, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Rosemary Kiernan
- Gene Regulation Laboratory, Institut de Génétique Humaine, UMR9002, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Daphné Seigneurin-Berny
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France.
| | - André Verdel
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France.
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22
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The Thermal Stress Coping Network of the Nematode Caenorhabditis elegans. Int J Mol Sci 2022; 23:ijms232314907. [PMID: 36499234 PMCID: PMC9737000 DOI: 10.3390/ijms232314907] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/11/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022] Open
Abstract
Response to hyperthermia, highly conserved from bacteria to humans, involves transcriptional upregulation of genes involved in battling the cytotoxicity caused by misfolded and denatured proteins, with the aim of proteostasis restoration. C. elegans senses and responds to changes in growth temperature or noxious thermal stress by well-defined signaling pathways. Under adverse conditions, regulation of the heat shock response (HSR) in C. elegans is controlled by a single transcription factor, heat-shock factor 1 (HSF-1). HSR and HSF-1 in particular are proven to be central to survival under proteotoxic stress, with additional roles in normal physiological processes. For years, it was a common belief that upregulation of heat shock proteins (HSPs) by HSF-1 was the main and most important step toward thermotolerance. However, an ever-growing number of studies have shown that targets of HSF-1 involved in cytoskeletal and exoskeletal integrity preservation as well as other HSF-1 dependent and independent pathways are equally important. In this review, we follow the thermal stimulus from reception by the nematode nerve endings till the activation of cellular response programs. We analyze the different HSF-1 functions in HSR as well as all the recently discovered mechanisms that add to the knowledge of the heat stress coping network of C. elegans.
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23
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Winkenbach LP, Parker DM, Williams RTP, Nishimura EO. The ERM-1 membrane-binding domain directs erm-1 mRNA localization to the plasma membrane in the C. elegans embryo. Development 2022; 149:279335. [PMID: 36314842 PMCID: PMC9793419 DOI: 10.1242/dev.200930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
mRNA localization and transport are integral in regulating gene expression. In Caenorhabditis elegans embryos, the maternally inherited mRNA erm-1 (Ezrin/Radixin/Moesin) becomes concentrated in anterior blastomeres. erm-1 mRNA localizes within those blastomeres to the plasma membrane where the essential ERM-1 protein, a membrane-actin linker, is also found. We demonstrate that the localization of erm-1 mRNA to the plasma membrane is translation dependent and requires its encoded N-terminal, membrane-binding (FERM) domain. By perturbing translation through multiple methods, we found that erm-1 mRNA localization at the plasma membrane persisted only if the nascent peptide remained in complex with the translating mRNA. Indeed, re-coding the erm-1 mRNA coding sequence while preserving the encoded amino acid sequence did not disrupt erm-1 mRNA localization, corroborating that the information directing mRNA localization resides within its membrane-binding protein domain. A single-molecule inexpensive fluorescence in situ hybridization screen of 17 genes encoding similar membrane-binding domains identified three plasma membrane-localized mRNAs in the early embryo. Ten additional transcripts showed potential membrane localization later in development. These findings point to a translation-dependent pathway for localization of mRNAs encoding membrane-associated proteins.
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Affiliation(s)
- Lindsay P. Winkenbach
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Dylan M. Parker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA,Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80303, USA
| | - Robert T. P. Williams
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Erin Osborne Nishimura
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA,Author for correspondence ()
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24
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Hassell D, Denney A, Singer E, Benson A, Roth A, Ceglowski J, Steingesser M, McMurray M. Chaperone requirements for de novo folding of Saccharomyces cerevisiae septins. Mol Biol Cell 2022; 33:ar111. [PMID: 35947497 PMCID: PMC9635297 DOI: 10.1091/mbc.e22-07-0262] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/02/2022] [Indexed: 11/11/2022] Open
Abstract
Polymers of septin protein complexes play cytoskeletal roles in eukaryotic cells. The specific subunit composition within complexes controls functions and higher-order structural properties. All septins have globular GTPase domains. The other eukaryotic cytoskeletal NTPases strictly require assistance from molecular chaperones of the cytosol, particularly the cage-like chaperonins, to fold into oligomerization-competent conformations. We previously identified cytosolic chaperones that bind septins and influence the oligomerization ability of septins carrying mutations linked to human disease, but it was unknown to what extent wild-type septins require chaperone assistance for their native folding. Here we use a combination of in vivo and in vitro approaches to demonstrate chaperone requirements for de novo folding and complex assembly by budding yeast septins. Individually purified septins adopted nonnative conformations and formed nonnative homodimers. In chaperonin- or Hsp70-deficient cells, septins folded slower and were unable to assemble posttranslationally into native complexes. One septin, Cdc12, was so dependent on cotranslational chaperonin assistance that translation failed without it. Our findings point to distinct translation elongation rates for different septins as a possible mechanism to direct a stepwise, cotranslational assembly pathway in which general cytosolic chaperones act as key intermediaries.
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Affiliation(s)
- Daniel Hassell
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Ashley Denney
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Emily Singer
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Aleyna Benson
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Andrew Roth
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Julia Ceglowski
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Marc Steingesser
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Michael McMurray
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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25
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Elucidation of the interaction proteome of mitochondrial chaperone Hsp78 highlights its role in protein aggregation during heat stress. J Biol Chem 2022; 298:102494. [PMID: 36115461 PMCID: PMC9574514 DOI: 10.1016/j.jbc.2022.102494] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
Chaperones of the Hsp100/Clp family represent major components of protein homeostasis, conferring maintenance of protein activity under stress. The ClpB-type members of the family, present in bacteria, fungi, and plants, are able to resolubilize aggregated proteins. The mitochondrial member of the ClpB family in Saccharomyces cerevisiae is Hsp78. Although Hsp78 has been shown to contribute to proteostasis in elevated temperatures, the biochemical mechanisms underlying this mitochondria-specific thermotolerance are still largely unclear. To identify endogenous chaperone substrate proteins, here, we generated an Hsp78-ATPase mutant with stabilized substrate-binding behavior. We used two stable isotope labeling–based quantitative mass spectrometry approaches to analyze the role of Hsp78 during heat stress–induced mitochondrial protein aggregation and disaggregation on a proteomic level. We first identified the endogenous substrate spectrum of the Hsp78 chaperone, comprising a wide variety of proteins related to metabolic functions including energy production and protein synthesis, as well as other chaperones, indicating its crucial functions in mitochondrial stress resistance. We then compared these interaction data with aggregation and disaggregation processes in mitochondria under heat stress, which revealed specific aggregation-prone protein populations and demonstrated the direct quantitative impact of Hsp78 on stress-dependent protein solubility under different conditions. We conclude that Hsp78, together with its cofactors, represents a recovery system that protects major mitochondrial metabolic functions during heat stress as well as restores protein biogenesis capacity after the return to normal conditions.
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26
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Soto I, Couvillion M, Hansen KG, McShane E, Moran JC, Barrientos A, Churchman LS. Balanced mitochondrial and cytosolic translatomes underlie the biogenesis of human respiratory complexes. Genome Biol 2022; 23:170. [PMID: 35945592 PMCID: PMC9361522 DOI: 10.1186/s13059-022-02732-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 07/18/2022] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Oxidative phosphorylation (OXPHOS) complexes consist of nuclear and mitochondrial DNA-encoded subunits. Their biogenesis requires cross-compartment gene regulation to mitigate the accumulation of disproportionate subunits. To determine how human cells coordinate mitochondrial and nuclear gene expression processes, we tailored ribosome profiling for the unique features of the human mitoribosome. RESULTS We resolve features of mitochondrial translation initiation and identify a small ORF in the 3' UTR of MT-ND5. Analysis of ribosome footprints in five cell types reveals that average mitochondrial synthesis levels correspond precisely to cytosolic levels across OXPHOS complexes, and these average rates reflect the relative abundances of the complexes. Balanced mitochondrial and cytosolic synthesis does not rely on rapid feedback between the two translation systems, and imbalance caused by mitochondrial translation deficiency is associated with the induction of proteotoxicity pathways. CONCLUSIONS Based on our findings, we propose that human OXPHOS complexes are synthesized proportionally to each other, with mitonuclear balance relying on the regulation of OXPHOS subunit translation across cellular compartments, which may represent a proteostasis vulnerability.
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Affiliation(s)
- Iliana Soto
- Blavatnik Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Mary Couvillion
- Blavatnik Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Katja G Hansen
- Blavatnik Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Erik McShane
- Blavatnik Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - J Conor Moran
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - L Stirling Churchman
- Blavatnik Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
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27
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Ebner JN, Wyss MK, Ritz D, von Fumetti S. Effects of thermal acclimation on the proteome of the planarian Crenobia alpina from an alpine freshwater spring. J Exp Biol 2022; 225:276068. [PMID: 35875852 PMCID: PMC9440759 DOI: 10.1242/jeb.244218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2022]
Abstract
Species' acclimation capacity and their ability to maintain molecular homeostasis outside ideal temperature ranges will partly predict their success following climate change-induced thermal regime shifts. Theory predicts that ectothermic organisms from thermally stable environments have muted plasticity, and that these species may be particularly vulnerable to temperature increases. Whether such species retained or lost acclimation capacity remains largely unknown. We studied proteome changes in the planarian Crenobia alpina, a prominent member of cold-stable alpine habitats that is considered to be a cold-adapted stenotherm. We found that the species' critical thermal maximum (CTmax) is above its experienced habitat temperatures and that different populations exhibit differential CTmax acclimation capacity, whereby an alpine population showed reduced plasticity. In a separate experiment, we acclimated C. alpina individuals from the alpine population to 8, 11, 14 or 17°C over the course of 168 h and compared their comprehensively annotated proteomes. Network analyses of 3399 proteins and protein set enrichment showed that while the species' proteome is overall stable across these temperatures, protein sets functioning in oxidative stress response, mitochondria, protein synthesis and turnover are lower in abundance following warm acclimation. Proteins associated with an unfolded protein response, ciliogenesis, tissue damage repair, development and the innate immune system were higher in abundance following warm acclimation. Our findings suggest that this species has not suffered DNA decay (e.g. loss of heat-shock proteins) during evolution in a cold-stable environment and has retained plasticity in response to elevated temperatures, challenging the notion that stable environments necessarily result in muted plasticity. Summary: The proteome of an alpine Crenobia alpina population shows plasticity in response to acclimation to warmer temperatures.
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Affiliation(s)
- Joshua Niklas Ebner
- 1 Spring Ecology Research Group, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Mirjam Kathrin Wyss
- 1 Spring Ecology Research Group, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Danilo Ritz
- 2 Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Stefanie von Fumetti
- 1 Spring Ecology Research Group, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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28
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Pulse labeling reveals the tail end of protein folding by proteome profiling. Cell Rep 2022; 40:111096. [PMID: 35858568 PMCID: PMC9893312 DOI: 10.1016/j.celrep.2022.111096] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/18/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
Accurate and efficient folding of nascent protein sequences into their native states requires support from the protein homeostasis network. Herein we probe which newly translated proteins are thermo-sensitive, making them susceptible to misfolding and aggregation under heat stress using pulse-SILAC mass spectrometry. We find a distinct group of proteins that is highly sensitive to this perturbation when newly synthesized but not once matured. These proteins are abundant and highly structured. Notably, they display a tendency to form β sheet secondary structures, have more complex folding topology, and are enriched for chaperone-binding motifs, suggesting a higher demand for chaperone-assisted folding. These polypeptides are also more often components of stable protein complexes in comparison with other proteins. Combining these findings suggests the existence of a specific subset of proteins in the cell that is particularly vulnerable to misfolding and aggregation following synthesis before reaching the native state.
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29
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Xu B, Gao X, Li X, Jia Y, Li F, Zhang Z. Cell cycle arrest explains the observed bulk 3D genomic alterations in response to long-term heat shock in K562 cells. Genome Res 2022; 32:1285-1297. [PMID: 35835565 PMCID: PMC9341516 DOI: 10.1101/gr.276554.122] [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: 01/05/2022] [Accepted: 06/13/2022] [Indexed: 01/03/2023]
Abstract
Heat shock is a common environmental stress, although the response of the nucleus to it remains controversial in mammalian cells. Acute reaction and chronic adaptation to environmental stress may have distinct internal rewiring in the gene regulation networks. However, this difference remains largely unexplored. Here, we report that chromatin conformation and chromatin accessibility respond differently in short- and long-term heat shock in human K562 cells. We found that chromatin conformation in K562 cells was largely stable in response to short-term heat shock, whereas it showed clear and characteristic changes after long-term heat treatment with little alteration in chromatin accessibility during the whole process. We further show in silico and experimental evidence strongly suggesting that changes in chromatin conformation may largely stem from an accumulation of cells in the M stage of the cell cycle in response to heat shock. Our results represent a paradigm shift away from the controversial view of chromatin response to heat shock and emphasize the necessity of cell cycle analysis when interpreting bulk Hi-C data.
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Affiliation(s)
- Bingxiang Xu
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Chaoyang District, Beijing 100101, China;,School of Life Science, University of Chinese Academy of Sciences, Beijing 101408, China;,School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Xiaomeng Gao
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Chaoyang District, Beijing 100101, China;,School of Life Science, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Xiaoli Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Chaoyang District, Beijing 100101, China;,School of Life Science, University of Chinese Academy of Sciences, Beijing 101408, China;,Department of Cell Biology and Genetics, Core Facility of Developmental Biology, Chongqing Medical University, Chongqing 400016, China
| | - Yan Jia
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Chaoyang District, Beijing 100101, China
| | - Feifei Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Chaoyang District, Beijing 100101, China;,Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Zhihua Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Chaoyang District, Beijing 100101, China;,School of Life Science, University of Chinese Academy of Sciences, Beijing 101408, China
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30
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Rosenkranz RRE, Ullrich S, Löchli K, Simm S, Fragkostefanakis S. Relevance and Regulation of Alternative Splicing in Plant Heat Stress Response: Current Understanding and Future Directions. FRONTIERS IN PLANT SCIENCE 2022; 13:911277. [PMID: 35812973 PMCID: PMC9260394 DOI: 10.3389/fpls.2022.911277] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/26/2022] [Indexed: 05/26/2023]
Abstract
Alternative splicing (AS) is a major mechanism for gene expression in eukaryotes, increasing proteome diversity but also regulating transcriptome abundance. High temperatures have a strong impact on the splicing profile of many genes and therefore AS is considered as an integral part of heat stress response. While many studies have established a detailed description of the diversity of the RNAome under heat stress in different plant species and stress regimes, little is known on the underlying mechanisms that control this temperature-sensitive process. AS is mainly regulated by the activity of splicing regulators. Changes in the abundance of these proteins through transcription and AS, post-translational modifications and interactions with exonic and intronic cis-elements and core elements of the spliceosomes modulate the outcome of pre-mRNA splicing. As a major part of pre-mRNAs are spliced co-transcriptionally, the chromatin environment along with the RNA polymerase II elongation play a major role in the regulation of pre-mRNA splicing under heat stress conditions. Despite its importance, our understanding on the regulation of heat stress sensitive AS in plants is scarce. In this review, we summarize the current status of knowledge on the regulation of AS in plants under heat stress conditions. We discuss possible implications of different pathways based on results from non-plant systems to provide a perspective for researchers who aim to elucidate the molecular basis of AS under high temperatures.
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Affiliation(s)
| | - Sarah Ullrich
- Molecular Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Karin Löchli
- Molecular Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
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31
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Hernández-Elvira M, Sunnerhagen P. Post-transcriptional regulation during stress. FEMS Yeast Res 2022; 22:6585650. [PMID: 35561747 PMCID: PMC9246287 DOI: 10.1093/femsyr/foac025] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/25/2022] [Accepted: 05/10/2022] [Indexed: 11/12/2022] Open
Abstract
To remain competitive, cells exposed to stress of varying duration, rapidity of onset, and intensity, have to balance their expenditure on growth and proliferation versus stress protection. To a large degree dependent on the time scale of stress exposure, the different levels of gene expression control: transcriptional, post-transcriptional and post-translational, will be engaged in stress responses. The post-transcriptional level is appropriate for minute-scale responses to transient stress, and for recovery upon return to normal conditions. The turnover rate, translational activity, covalent modifications, and subcellular localisation of RNA species are regulated under stress by multiple cellular pathways. The interplay between these pathways is required to achieve the appropriate signalling intensity and prevent undue triggering of stress-activated pathways at low stress levels, avoid overshoot, and down-regulate the response in a timely fashion. As much of our understanding of post-transcriptional regulation has been gained in yeast, this review is written with a yeast bias, but attempts to generalise to other eukaryotes. It summarises aspects of how post-transcriptional events in eukaryotes mitigate short-term environmental stresses, and how different pathways interact to optimise the stress response under shifting external conditions.
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Affiliation(s)
- Mariana Hernández-Elvira
- Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, P.O. Box 462, S-405 30 Göteborg, Sweden
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, P.O. Box 462, S-405 30 Göteborg, Sweden
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32
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Guzikowski AR, Harvey AT, Zhang J, Zhu S, Begovich K, Cohn MH, Wilhelm JE, Zid BM. Differential translation elongation directs protein synthesis in response to acute glucose deprivation in yeast. RNA Biol 2022; 19:636-649. [PMID: 35491906 PMCID: PMC9067459 DOI: 10.1080/15476286.2022.2065784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Protein synthesis is energetically expensive and its rate is influenced by factors such as cell type and environment. Suppression of translation is a canonical response to stressful changes in the cellular environment. In particular, inhibition of the initiation step of translation has been highlighted as the key control step in stress-induced translational suppression as mechanisms that quickly suppress initiation are well-conserved. However, cells have evolved complex regulatory means to control translation apart from initiation. Here, we examine the role of the elongation step of translation in yeast subjected to acute glucose deprivation. The use of ribosome profiling and in vivo reporter assays demonstrated elongation rates slow progressively following glucose removal. We observed that ribosome distribution broadly shifts towards the downstream ends of transcripts after both acute and gradual glucose deprivation but not in response to other stressors. Additionally, on assessed mRNAs, a correlation existed between ribosome occupancy and protein production pre-stress but was lost after stress. These results indicate that stress-induced elongation regulation causes ribosomes to slow down and build up on a considerable proportion of the transcriptome in response to glucose withdrawal. Finally, we report ribosomes that built up along transcripts are competent to resume elongation and complete protein synthesis after readdition of glucose to starved cells. This suggests that yeast has evolved mechanisms to slow translation elongation in response to glucose starvation which do not preclude continuation of protein production from those ribosomes, thereby averting a need for new initiation events to take place to synthesize proteins. Abbreviations: AUG: start codon, bp: base pair(s), CDS: coding sequence, CHX: cycloheximide, eEF2: eukaryotic elongation factor 2, LTM: lactimidomycin, nt: nucleotide, PGK1: 3-phosphoglycerate kinase, ribosomal biogenesis: ribi, RO: ribosome occupancy, RPF: ribosome protected fragment, TE: translational efficiency
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Affiliation(s)
- Anna R. Guzikowski
- Division of Biological Sciences, University of California, San Diego, CA, USA
| | - Alex T. Harvey
- Department of Chemistry & Biochemistry, University of California, San Diego, CA, USA
| | - Jingxiao Zhang
- Department of Chemistry & Biochemistry, University of California, San Diego, CA, USA
| | - Shihui Zhu
- Department of Chemistry & Biochemistry, University of California, San Diego, CA, USA
| | - Kyle Begovich
- Division of Biological Sciences, University of California, San Diego, CA, USA
| | - Molly H. Cohn
- Department of Chemistry & Biochemistry, University of California, San Diego, CA, USA
| | - James E. Wilhelm
- Division of Biological Sciences, University of California, San Diego, CA, USA
| | - Brian M. Zid
- Department of Chemistry & Biochemistry, University of California, San Diego, CA, USA
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33
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Seely SM, Gagnon MG. Mechanisms of ribosome recycling in bacteria and mitochondria: a structural perspective. RNA Biol 2022; 19:662-677. [PMID: 35485608 PMCID: PMC9067457 DOI: 10.1080/15476286.2022.2067712] [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] [Indexed: 10/28/2022] Open
Abstract
In all living cells, the ribosome translates the genetic information carried by messenger RNAs (mRNAs) into proteins. The process of ribosome recycling, a key step during protein synthesis that ensures ribosomal subunits remain available for new rounds of translation, has been largely overlooked. Despite being essential to the survival of the cell, several mechanistic aspects of ribosome recycling remain unclear. In eubacteria and mitochondria, recycling of the ribosome into subunits requires the concerted action of the ribosome recycling factor (RRF) and elongation factor G (EF-G). Recently, the conserved protein HflX was identified in bacteria as an alternative factor that recycles the ribosome under stress growth conditions. The homologue of HflX, the GTP-binding protein 6 (GTPBP6), has a dual role in mitochondrial translation by facilitating ribosome recycling and biogenesis. In this review, mechanisms of ribosome recycling in eubacteria and mitochondria are described based on structural studies of ribosome complexes.
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Affiliation(s)
- Savannah M Seely
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1019, USA
| | - Matthieu G Gagnon
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1019, USA.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-1019, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1019, USA.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas 77555, USA
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34
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Filbeck S, Cerullo F, Pfeffer S, Joazeiro CAP. Ribosome-associated quality-control mechanisms from bacteria to humans. Mol Cell 2022; 82:1451-1466. [PMID: 35452614 PMCID: PMC9034055 DOI: 10.1016/j.molcel.2022.03.038] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022]
Abstract
Ribosome-associated quality-control (RQC) surveys incomplete nascent polypeptides produced by interrupted translation. Central players in RQC are the human ribosome- and tRNA-binding protein, NEMF, and its orthologs, yeast Rqc2 and bacterial RqcH, which sense large ribosomal subunits obstructed with nascent chains and then promote nascent-chain proteolysis. In canonical eukaryotic RQC, NEMF stabilizes the LTN1/Listerin E3 ligase binding to obstructed ribosomal subunits for nascent-chain ubiquitylation. Furthermore, NEMF orthologs across evolution modify nascent chains by mediating C-terminal, untemplated polypeptide elongation. In eukaryotes, this process exposes ribosome-buried nascent-chain lysines, the ubiquitin acceptor sites, to LTN1. Remarkably, in both bacteria and eukaryotes, C-terminal tails also have an extra-ribosomal function as degrons. Here, we discuss recent findings on RQC mechanisms and briefly review how ribosomal stalling is sensed upstream of RQC, including via ribosome collisions, from an evolutionary perspective. Because RQC defects impair cellular fitness and cause neurodegeneration, this knowledge provides a framework for pathway-related biology and disease studies.
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Affiliation(s)
- Sebastian Filbeck
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Federico Cerullo
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.
| | - Claudio A P Joazeiro
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Department of Molecular Medicine, Scripps Florida, Jupiter, FL 33458, USA.
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35
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Trösch R, Ries F, Westrich LD, Gao Y, Herkt C, Hoppstädter J, Heck-Roth J, Mustas M, Scheuring D, Choquet Y, Räschle M, Zoschke R, Willmund F. Fast and global reorganization of the chloroplast protein biogenesis network during heat acclimation. THE PLANT CELL 2022; 34:1075-1099. [PMID: 34958373 PMCID: PMC8894945 DOI: 10.1093/plcell/koab317] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/20/2021] [Indexed: 06/02/2023]
Abstract
Photosynthesis is a central determinant of plant biomass production, but its homeostasis is increasingly challenged by heat. Little is known about the sensitive regulatory principles involved in heat acclimation that underly the biogenesis and repair of chloroplast-encoded core subunits of photosynthetic complexes. Employing time-resolved ribosome and transcript profiling together with selective ribosome proteomics, we systematically deciphered these processes in chloroplasts of Chlamydomonas reinhardtii. We revealed protein biosynthesis and altered translation elongation as central processes for heat acclimation and showed that these principles are conserved between the alga and the flowering plant Nicotiana tabacum. Short-term heat exposure resulted in specific translational repression of chlorophyll a-containing core antenna proteins of photosystems I and II. Furthermore, translocation of ribosome nascent chain complexes to thylakoid membranes was affected, as reflected by the increased accumulation of stromal cpSRP54-bound ribosomes. The successful recovery of synthesizing these proteins under prolonged acclimation of nonlethal heat conditions was associated with specific changes of the co-translational protein interaction network, including increased ribosome association of chlorophyll biogenesis enzymes and acclimation factors responsible for complex assembly. We hypothesize that co-translational cofactor binding and targeting might be bottlenecks under heat but become optimized upon heat acclimation to sustain correct co-translational protein complex assembly.
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Affiliation(s)
- Raphael Trösch
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern 67663, Germany
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Fabian Ries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Lisa Désirée Westrich
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Yang Gao
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Claudia Herkt
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Julia Hoppstädter
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Johannes Heck-Roth
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Matthieu Mustas
- Biologie du Chloroplaste et Perception de la Lumieère Chez les Microalgues, Institut de Biologie Physico-Chimique, UMR CNRS/UPMC, Paris 7141, France
| | - David Scheuring
- Plant Pathology, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Yves Choquet
- Biologie du Chloroplaste et Perception de la Lumieère Chez les Microalgues, Institut de Biologie Physico-Chimique, UMR CNRS/UPMC, Paris 7141, France
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern 67663, Germany
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36
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Alagar Boopathy LR, Jacob-Tomas S, Alecki C, Vera M. Mechanisms tailoring the expression of heat shock proteins to proteostasis challenges. J Biol Chem 2022; 298:101796. [PMID: 35248532 PMCID: PMC9065632 DOI: 10.1016/j.jbc.2022.101796] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 12/14/2022] Open
Abstract
All cells possess an internal stress response to cope with environmental and pathophysiological challenges. Upon stress, cells reprogram their molecular functions to activate a survival mechanism known as the heat shock response, which mediates the rapid induction of molecular chaperones such as the heat shock proteins (HSPs). This potent production overcomes the general suppression of gene expression and results in high levels of HSPs to subsequently refold or degrade misfolded proteins. Once the damage or stress is repaired or removed, cells terminate the production of HSPs and resume regular functions. Thus, fulfillment of the stress response requires swift and robust coordination between stress response activation and completion that is determined by the status of the cell. In recent years, single-cell fluorescence microscopy techniques have begun to be used in unravelling HSP-gene expression pathways, from DNA transcription to mRNA degradation. In this review, we will address the molecular mechanisms in different organisms and cell types that coordinate the expression of HSPs with signaling networks that act to reprogram gene transcription, mRNA translation, and decay and ensure protein quality control.
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37
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Xie M, Yang L, Chen G, Wang Y, Xie Z, Wang H. RiboChat: a chat-style web interface for analysis and annotation of ribosome profiling data. Brief Bioinform 2022; 23:6511203. [DOI: 10.1093/bib/bbab559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/29/2021] [Accepted: 12/08/2021] [Indexed: 11/13/2022] Open
Abstract
Abstract
The increasing volume of ribosome profiling (Ribo-seq) data, computational complexity of its data processing and operational handicap of related analytical procedures present a daunting set of informatics challenges. These impose a substantial barrier to researchers particularly with no or limited bioinformatics expertise in analyzing and decoding translation information from Ribo-seq data, thus driving the need for a new research paradigm for data computation and information extraction. In this knowledge base, we herein present a novel interactive web platform, RiboChat (https://db.cngb.org/ribobench/chat.html), for direct analyzing and annotating Ribo-seq data in the form of a chat conversation. It consists of a user-friendly web interface and a backend cloud-computing service. When typing a data analysis question into the chat window, the object-text detection module will be run to recognize relevant keywords from the input text. Based on the features identified in the input, individual analytics modules are then scored to find the perfect-matching candidate. The corresponding analytics module will be further executed after checking the completion status of the uploading of datasets and configured parameters. Overall, RiboChat represents an important step forward in the emerging direction of next-generation data analytics and will enable the broad research community to conveniently decipher translation information embedded within Ribo-seq data.
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38
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Andreev DE, Baranov PV, Milogorodskii A, Rachinskii D. A deterministic model for non-monotone relationship between translation of upstream and downstream open reading frames. MATHEMATICAL MEDICINE AND BIOLOGY : A JOURNAL OF THE IMA 2021; 38:490-515. [PMID: 34718568 DOI: 10.1093/imammb/dqab015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 08/12/2021] [Accepted: 10/06/2021] [Indexed: 01/01/2023]
Abstract
Totally asymmetric simple exclusion process (TASEP) modelling was shown to offer a parsimonious explanation for the experimentally confirmed ability of a single upstream open reading frames (uORFs) to upregulate downstream translation during the integrated stress response. As revealed by numerical simulations, the model predicts that reducing the density of scanning ribosomes upstream of certain uORFs increases the flow of ribosomes downstream. To gain a better insight into the mechanism which ensures the non-monotone relation between the upstream and downstream flows, in this work, we propose a phenomenological deterministic model approximating the TASEP model of the translation process. We establish the existence of a stationary solution featuring the decreasing density along the uORF for the deterministic model. Further, we find an explicit non-monotone relation between the upstream ribosome density and the downstream flow for the stationary solution in the limit of increasing uORF length and increasingly leaky initiation. The stationary distribution of the TASEP model, the stationary solution of the deterministic model and the explicit limit are compared numerically.
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Affiliation(s)
- D E Andreev
- Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow, 119991, Russian Federation, and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
| | - P V Baranov
- University College Cork, College Road, Cork, T12 K8AF, Ireland, and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry (RAS), 16/10 Miklukho-Maklay str., Moscow, 117997, Russian Federation
| | - A Milogorodskii
- Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow, 119991, Russian Federation, and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
| | - D Rachinskii
- Department of Mathematical Sciences, The University of Texas at Dallas, 800 W. Campbell Rd, Richardson, TX 75080, USA
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39
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Fan X, Bao T, Yi H, Zhang Z, Zhang K, Liu X, Lin X, Zhang Z, Feng Z. Ribosome Profiling and RNA Sequencing Reveal Genome-Wide Cellular Translation and Transcription Regulation Under Osmotic Stress in Lactobacillus rhamnosus ATCC 53103. Front Microbiol 2021; 12:781454. [PMID: 34899662 PMCID: PMC8656396 DOI: 10.3389/fmicb.2021.781454] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/27/2021] [Indexed: 12/27/2022] Open
Abstract
To determine whether osmotic pressure affects the translation efficiency of Lactobacillus rhamnosus, the ribosome profiling assay was performed to analyze the changes in translation efficiency in L. rhamnosus ATCC 53103. Under osmotic stress, differentially expressed genes (DEGs) involved in fatty acid biosynthesis and metabolism, ribosome, and purine metabolism pathways were co-regulated with consistent expression direction at translation and transcription levels. DEGs involved in the biosynthesis of phenylalanine, tyrosine, and tryptophan, and the phosphotransferase system pathways also were co-regulated at translation and transcription levels, while they showed opposite expression direction at two levels. Moreover, DEGs involved in the two-component system, amino acid metabolism, and pyruvate metabolism pathways were only regulated at the transcription level. And DEGs involved in fructose and mannose metabolism were only regulated at the translation level. The translation efficiency of DEGs involved in the biosynthesis of amino acids was downregulated while in quorum sensing and PTS pathways was upregulated. In addition, the ribosome footprints accumulated in open reading frame regions resulted in impaired translation initiation and elongation under osmotic stress. In summary, L. rhamnosus ATCC 53103 could respond to osmotic stress by translation regulation and control the balance between survival and growth of cells by transcription and translation.
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Affiliation(s)
- Xuejing Fan
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Tianyu Bao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Huaxi Yi
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Zongcai Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Kenan Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xin Liu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xue Lin
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Zhen Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Zhen Feng
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China.,Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
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40
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Gao J, Shi H, Juhlin CC, Larsson C, Lui WO. Merkel cell polyomavirus T-antigens regulate DICER1 mRNA stability and translation through HSC70. iScience 2021; 24:103264. [PMID: 34761184 PMCID: PMC8567380 DOI: 10.1016/j.isci.2021.103264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/13/2021] [Accepted: 10/09/2021] [Indexed: 01/07/2023] Open
Abstract
Merkel cell carcinoma is an aggressive skin malignancy, mostly caused by Merkel cell polyomavirus (MCPyV). MCPyV T-antigens can induce mature microRNA expressions through the DnaJ domain, but its underlying mechanism is still unknown. Here, we report that the T-antigens induce protein expression and mRNA stability of DICER1, a key factor in microRNA biogenesis, through heat shock cognate 70 (HSC70). HSC70 directly interacts with the AU-rich elements (ARE) of DICER1 mRNA in both coding and 3′ untranslated region in the presence of MCPyV T-antigen. The T-antigen/HSC70 interaction could induce luciferase activity of synthetic ARE-containing reporter, as well as the stability of ARE-containing mRNAs, suggesting a broader role of MCPyV T-antigens in regulating multiple mRNAs via HSC70. These findings highlight a new role for the interaction of HSC70 and MCPyV T-antigens in mRNA regulation and an undescribed regulatory mechanism of DICER1 mRNA stability and translation through its direct interaction with HSC70. MCPyV T-antigen and HSC70 interaction regulates DICER1 expression HSC70 directly binds to ARE in the 3′UTR of DICER1 for expression regulation An unknown motif in DICER1 CDS is also required for its expression regulation by LT The LT-HSC70 interaction can regulate other ARE-containing mRNAs
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Affiliation(s)
- Jiwei Gao
- Department of Oncology-Pathology, Karolinska Institutet; BioClinicum, Karolinska University Hospital, 171 64 Solna, Sweden
| | - Hao Shi
- Department of Oncology-Pathology, Karolinska Institutet; BioClinicum, Karolinska University Hospital, 171 64 Solna, Sweden
| | - C Christofer Juhlin
- Department of Oncology-Pathology, Karolinska Institutet; BioClinicum, Karolinska University Hospital, 171 64 Solna, Sweden.,Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, 171 64 Solna, Sweden
| | - Catharina Larsson
- Department of Oncology-Pathology, Karolinska Institutet; BioClinicum, Karolinska University Hospital, 171 64 Solna, Sweden
| | - Weng-Onn Lui
- Department of Oncology-Pathology, Karolinska Institutet; BioClinicum, Karolinska University Hospital, 171 64 Solna, Sweden
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41
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Molecular Effects of Elongation Factor Ts and Trigger Factor on the Unfolding and Aggregation of Elongation Factor Tu Induced by the Prokaryotic Molecular Chaperone Hsp33. BIOLOGY 2021; 10:biology10111171. [PMID: 34827164 PMCID: PMC8614738 DOI: 10.3390/biology10111171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/13/2022]
Abstract
Simple Summary Proteins are versatile biological macromolecules involved in most biological processes. However, because of the highly labile nature of protein structures, protein quality control (PQC) to ensure proteostasis (i.e., protein homeostasis)is difficult. Therefore, proteins of a specialized class (i.e., molecular chaperones) are required that assist in proper folding and prevent aberrant folding of other proteins. Hsp33 was originally discovered as a holding chaperone that is overexpressed upon heat shock and activated by oxidation to prevent the misfolding of client proteins. Recently, an unfoldase/aggregase activity of Hsp33 was identified in its reduced state against a specific substrate, EF-Tu, which plays a key role in protein biosynthesis in cells. The present study demonstrates that EF-Tu unfolding/aggregation by Hsp33 can be accelerated by another molecular chaperone trigger factor. Given that the unfolded/aggregated EF-Tu is finally degraded by another chaperone, Lon protease, it is likely that a chaperone network dysregulating EF-Tu operates in heat shock to attenuate protein biosynthesis, which is harmful to cell survival under stressed conditions. Therefore, the apparently contradictory chaperone function (i.e., promotion of client misfolding) of Hsp33 can also be associated with the PQC processes to ensure proteostasis in cells. Abstract Hsp33, a prokaryotic redox-regulated holding chaperone, has been recently identified to be able to exhibit an unfoldase and aggregase activity against elongation factor Tu (EF-Tu) in its reduced state. In this study, we investigated the effect of elongation factor Ts (EF-Ts) and trigger factor (TF) on Hsp33-mediated EF-Tu unfolding and aggregation using gel filtration, light scattering, circular dichroism, and isothermal titration calorimetry. We found that EF-Tu unfolding and subsequent aggregation induced by Hsp33 were evident even in its complex state with EF-Ts, which enhanced EF-Tu stability. In addition, although TF alone had no substantial effect on the stability of EF-Tu, it markedly amplified the Hsp33-mediated EF-Tu unfolding and aggregation. Collectively, the present results constitute the first example of synergistic unfoldase/aggregase activity of molecular chaperones and suggest that the stability of EF-Tu is modulated by a sophisticated network of molecular chaperones to regulate protein biosynthesis in cells under stress conditions.
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42
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Srinivasan B, Samaddar S, Mylavarapu SVS, Clement JP, Banerjee S. Homeostatic scaling is driven by a translation-dependent degradation axis that recruits miRISC remodeling. PLoS Biol 2021; 19:e3001432. [PMID: 34813590 PMCID: PMC8610276 DOI: 10.1371/journal.pbio.3001432] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/30/2021] [Indexed: 01/17/2023] Open
Abstract
Homeostatic scaling in neurons has been attributed to the individual contribution of either translation or degradation; however, there remains limited insight toward understanding how the interplay between the two processes effectuates synaptic homeostasis. Here, we report that a codependence between protein synthesis and degradation mechanisms drives synaptic homeostasis, whereas abrogation of either prevents it. Coordination between the two processes is achieved through the formation of a tripartite complex between translation regulators, the 26S proteasome, and the miRNA-induced silencing complex (miRISC) components such as Argonaute, MOV10, and Trim32 on actively translating transcripts or polysomes. The components of this ternary complex directly interact with each other in an RNA-dependent manner. Disruption of polysomes abolishes this ternary interaction, suggesting that translating RNAs facilitate the combinatorial action of the proteasome and the translational apparatus. We identify that synaptic downscaling involves miRISC remodeling, which entails the mTORC1-dependent translation of Trim32, an E3 ligase, and the subsequent degradation of its target, MOV10 via the phosphorylation of p70 S6 kinase. We find that the E3 ligase Trim32 specifically polyubiquitinates MOV10 for its degradation during synaptic downscaling. MOV10 degradation alone is sufficient to invoke downscaling by enhancing Arc translation through its 3' UTR and causing the subsequent removal of postsynaptic AMPA receptors. Synaptic scaling was occluded when we depleted Trim32 and overexpressed MOV10 in neurons, suggesting that the Trim32-MOV10 axis is necessary for synaptic downscaling. We propose a mechanism that exploits a translation-driven protein degradation paradigm to invoke miRISC remodeling and induce homeostatic scaling during chronic network activity.
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Affiliation(s)
| | | | | | - James P. Clement
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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43
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Jobava R, Mao Y, Guan BJ, Hu D, Krokowski D, Chen CW, Shu XE, Chukwurah E, Wu J, Gao Z, Zagore LL, Merrick WC, Trifunovic A, Hsieh AC, Valadkhan S, Zhang Y, Qi X, Jankowsky E, Topisirovic I, Licatalosi DD, Qian SB, Hatzoglou M. Adaptive translational pausing is a hallmark of the cellular response to severe environmental stress. Mol Cell 2021; 81:4191-4208.e8. [PMID: 34686314 PMCID: PMC8559772 DOI: 10.1016/j.molcel.2021.09.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/27/2021] [Accepted: 09/28/2021] [Indexed: 12/12/2022]
Abstract
To survive, mammalian cells must adapt to environmental challenges. While the cellular response to mild stress has been widely studied, how cells respond to severe stress remains unclear. We show here that under severe hyperosmotic stress, cells enter a transient hibernation-like state in anticipation of recovery. We demonstrate this adaptive pausing response (APR) is a coordinated cellular response that limits ATP supply and consumption through mitochondrial fragmentation and widespread pausing of mRNA translation. This pausing is accomplished by ribosome stalling at translation initiation codons, which keeps mRNAs poised to resume translation upon recovery. We further show that recovery from severe stress involves ISR (integrated stress response) signaling that permits cell cycle progression, resumption of growth, and reversal of mitochondria fragmentation. Our findings indicate that cells can respond to severe stress via a hibernation-like mechanism that preserves vital elements of cellular function under harsh environmental conditions.
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Affiliation(s)
- Raul Jobava
- Department of Biochemistry, CWRU, Cleveland, OH 44106, USA; Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Bo-Jhih Guan
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Di Hu
- Department of Physiology & Biophysics, CWRU, Cleveland, OH 44106, USA
| | - Dawid Krokowski
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA; Department of Molecular Biology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Lublin 20-033, Poland
| | - Chien-Wen Chen
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Xin Erica Shu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Evelyn Chukwurah
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Jing Wu
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Zhaofeng Gao
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Leah L Zagore
- Department of Biochemistry, CWRU, Cleveland, OH 44106, USA; Center for RNA Science and Therapeutics, CWRU, Cleveland, OH 44106, USA
| | | | - Aleksandra Trifunovic
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Medical Faculty, University of Cologne, 50931 Cologne, Germany; Institute for Mitochondrial Diseases and Ageing, Medical Faculty and Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Andrew C Hsieh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Saba Valadkhan
- Department of Molecular Biology and Microbiology, CWRU, Cleveland, OH 44106, USA
| | - Youwei Zhang
- Department of Pharmacology, CWRU, Cleveland, OH 44106, USA
| | - Xin Qi
- Department of Physiology & Biophysics, CWRU, Cleveland, OH 44106, USA
| | - Eckhard Jankowsky
- Department of Biochemistry, CWRU, Cleveland, OH 44106, USA; Center for RNA Science and Therapeutics, CWRU, Cleveland, OH 44106, USA
| | - Ivan Topisirovic
- Gerald Bronfman Department of Oncology, Departments of Biochemistry and Experimental Medicine and Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC H3T 1E2, Canada
| | - Donny D Licatalosi
- Department of Biochemistry, CWRU, Cleveland, OH 44106, USA; Center for RNA Science and Therapeutics, CWRU, Cleveland, OH 44106, USA.
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA.
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44
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Abstract
Translation of the genetic information into proteins, performed by the ribosome, is a key cellular process in all organisms. Translation usually proceeds smoothly, but, unfortunately, undesirable events can lead to stalling of translating ribosomes. To rescue these faulty arrested ribosomes, bacterial cells possess three well-characterized quality control systems, tmRNA, ArfA, and ArfB. Recently, an additional ribosome rescue mechanism has been discovered in Bacillus subtilis. In contrast to the "canonical" systems targeting the 70S bacterial ribosome, this latter mechanism operates by first splitting the ribosome into the small (30S) and large (50S) subunits to then clearing the resultant jammed large subunit from the incomplete nascent polypeptide. Here, I will discuss the recent microbiological, biochemical, and structural data regarding functioning of this novel rescue system.
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Affiliation(s)
- Maxim S Svetlov
- Center for Biomolecular Sciences, Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
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45
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Fabbri L, Chakraborty A, Robert C, Vagner S. The plasticity of mRNA translation during cancer progression and therapy resistance. Nat Rev Cancer 2021; 21:558-577. [PMID: 34341537 DOI: 10.1038/s41568-021-00380-y] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/14/2021] [Indexed: 02/07/2023]
Abstract
Translational control of mRNAs during gene expression allows cells to promptly and dynamically adapt to a variety of stimuli, including in neoplasia in response to aberrant oncogenic signalling (for example, PI3K-AKT-mTOR, RAS-MAPK and MYC) and microenvironmental stress such as low oxygen and nutrient supply. Such translational rewiring allows rapid, specific changes in the cell proteome that shape specific cancer phenotypes to promote cancer onset, progression and resistance to anticancer therapies. In this Review, we illustrate the plasticity of mRNA translation. We first highlight the diverse mechanisms by which it is regulated, including by translation factors (for example, eukaryotic initiation factor 4F (eIF4F) and eIF2), RNA-binding proteins, tRNAs and ribosomal RNAs that are modulated in response to aberrant intracellular pathways or microenvironmental stress. We then describe how translational control can influence tumour behaviour by impacting on the phenotypic plasticity of cancer cells as well as on components of the tumour microenvironment. Finally, we highlight the role of mRNA translation in the cellular response to anticancer therapies and its promise as a key therapeutic target.
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Affiliation(s)
- Lucilla Fabbri
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Orsay, France
| | - Alina Chakraborty
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Orsay, France
| | - Caroline Robert
- INSERM U981, Gustave Roussy Cancer Campus, Villejuif, France
- Université Paris-Sud, Université Paris-Saclay, Kremlin-Bicêtre, France
- Dermato-Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Stéphan Vagner
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France.
- Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France.
- Equipe Labellisée Ligue Nationale Contre le Cancer, Orsay, France.
- Dermato-Oncology, Gustave Roussy Cancer Campus, Villejuif, France.
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46
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Padmanabhan PK, Ferreira GR, Zghidi-Abouzid O, Oliveira C, Dumas C, Mariz FC, Papadopoulou B. Genetic depletion of the RNA helicase DDX3 leads to impaired elongation of translating ribosomes triggering co-translational quality control of newly synthesized polypeptides. Nucleic Acids Res 2021; 49:9459-9478. [PMID: 34358325 PMCID: PMC8450092 DOI: 10.1093/nar/gkab667] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 11/29/2022] Open
Abstract
DDX3 is a multifaceted RNA helicase of the DEAD-box family that plays central roles in all aspects of RNA metabolism including translation initiation. Here, we provide evidence that the Leishmania DDX3 ortholog functions in post-initiation steps of translation. We show that genetic depletion of DDX3 slows down ribosome movement resulting in elongation-stalled ribosomes, impaired translation elongation and decreased de novo protein synthesis. We also demonstrate that the essential ribosome recycling factor Rli1/ABCE1 and termination factors eRF3 and GTPBP1 are less recruited to ribosomes upon DDX3 loss, suggesting that arrested ribosomes may be inefficiently dissociated and recycled. Furthermore, we show that prolonged ribosome stalling triggers co-translational ubiquitination of nascent polypeptide chains and a higher recruitment of E3 ubiquitin ligases and proteasome components to ribosomes of DDX3 knockout cells, which further supports that ribosomes are not elongating optimally. Impaired elongation of translating ribosomes also results in the accumulation of cytoplasmic protein aggregates, which implies that defects in translation overwhelm the normal quality controls. The partial recovery of translation by overexpressing Hsp70 supports this possibility. Collectively, these results suggest an important novel contribution of DDX3 to optimal elongation of translating ribosomes by preventing prolonged translation stalls and stimulating recycling of arrested ribosomes.
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Affiliation(s)
- Prasad Kottayil Padmanabhan
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Gabriel Reis Ferreira
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Ouafa Zghidi-Abouzid
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Camila Oliveira
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Carole Dumas
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Filipe Colaço Mariz
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Barbara Papadopoulou
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
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47
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Pagliuso DC, Bodas DM, Pasquinelli AE. Recovery from heat shock requires the microRNA pathway in Caenorhabditis elegans. PLoS Genet 2021; 17:e1009734. [PMID: 34351906 PMCID: PMC8370650 DOI: 10.1371/journal.pgen.1009734] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 08/17/2021] [Accepted: 07/22/2021] [Indexed: 12/16/2022] Open
Abstract
The heat shock response (HSR) is a highly conserved cellular process that promotes survival during stress. A hallmark of the HSR is the rapid induction of heat shock proteins (HSPs), such as HSP-70, by transcriptional activation. Once the stress is alleviated, HSPs return to near basal levels through incompletely understood mechanisms. Here, we show that the microRNA pathway acts during heat shock recovery in Caenorhabditis elegans. Depletion of the miRNA Argonaute, Argonaute Like Gene 1 (ALG-1), after an episode of heat shock resulted in decreased survival and perdurance of high hsp-70 levels. We present evidence that regulation of hsp-70 is dependent on miR-85 and sequences in the hsp-70 3’UTR that contain target sites for this miRNA. Regulation of hsp-70 by the miRNA pathway was found to be particularly important during recovery from HS, as animals that lacked miR-85 or its target sites in the hsp-70 3’UTR overexpressed HSP-70 and exhibited reduced viability. In summary, our findings show that down-regulation of hsp-70 by miR-85 after HS promotes survival, highlighting a previously unappreciated role for the miRNA pathway during recovery from stress. In the natural world, organisms constantly face stressful conditions such as oxidative stress, pathogen infection, starvation and heat stress. While many studies have focused on the cellular response to stress, less is known about how gene expression re-sets after the stress has been ameliorated. Here, we show that the microRNA pathway plays a critical role during the recovery phase after an episode of heat shock in the nematode, Caenorhabditis elegans. Elevated temperatures induce high expression of heat shock proteins (HSPs), including HSP-70, that provide protection from the damaging effects of high heat. We found that restoration of basal levels of HSP-70 after heat shock depends on Argonaute Like Gene 1 and miR-85. Moreover, loss of miRNA-mediated repression of HSP-70 results in compromised survival following heat shock. Our study draws attention to the recovery phase of the heat shock response and highlights an important role for the microRNA pathway in re-establishing gene expression programs needed for organismal viability post stress.
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Affiliation(s)
- Delaney C. Pagliuso
- Division of Biology, University of California, San Diego, La Jolla, California, United States of America
| | - Devavrat M. Bodas
- Division of Biology, University of California, San Diego, La Jolla, California, United States of America
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Amy E. Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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48
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Mateyak MK, He D, Sharma P, Kinzy TG. Mutational analysis reveals potential phosphorylation sites in eukaryotic elongation factor 1A that are important for its activity. FEBS Lett 2021; 595:2208-2220. [PMID: 34293820 PMCID: PMC9292714 DOI: 10.1002/1873-3468.14164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/11/2021] [Accepted: 07/13/2021] [Indexed: 11/25/2022]
Abstract
Previous studies have suggested that phosphorylation of translation elongation factor 1A (eEF1A) can alter its function, and large‐scale phospho‐proteomic analyses in Saccharomyces cerevisiae have identified 14 eEF1A residues phosphorylated under various conditions. Here, a series of eEF1A mutations at these proposed sites were created and the effects on eEF1A activity were analyzed. The eEF1A‐S53D and eEF1A‐T430D phosphomimetic mutant strains were inviable, while corresponding alanine mutants survived but displayed defects in growth and protein synthesis. The activity of an eEF1A‐S289D mutant was significantly reduced in the absence of the guanine nucleotide exchange factor eEF1Bα and could be restored by an exchange‐deficient form of the protein, suggesting that eEF1Bα promotes eEF1A activity by a mechanism other than nucleotide exchange. Our data show that several of the phosphorylation sites identified by high‐throughput analysis are critical for eEF1A function.
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Affiliation(s)
- Maria K Mateyak
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Dongming He
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Pragati Sharma
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Terri Goss Kinzy
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Illinois State University, Normal, IL, USA
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49
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Domnauer M, Zheng F, Li L, Zhang Y, Chang CE, Unruh JR, Conkright-Fincham J, McCroskey S, Florens L, Zhang Y, Seidel C, Fong B, Schilling B, Sharma R, Ramanathan A, Si K, Zhou C. Proteome plasticity in response to persistent environmental change. Mol Cell 2021; 81:3294-3309.e12. [PMID: 34293321 DOI: 10.1016/j.molcel.2021.06.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/28/2021] [Accepted: 06/22/2021] [Indexed: 01/17/2023]
Abstract
Temperature is a variable component of the environment, and all organisms must deal with or adapt to temperature change. Acute temperature change activates cellular stress responses, resulting in refolding or removal of damaged proteins. However, how organisms adapt to long-term temperature change remains largely unexplored. Here we report that budding yeast responds to long-term high temperature challenge by switching from chaperone induction to reduction of temperature-sensitive proteins and re-localizing a portion of its proteome. Surprisingly, we also find that many proteins adopt an alternative conformation. Using Fet3p as an example, we find that the temperature-dependent conformational difference is accompanied by distinct thermostability, subcellular localization, and, importantly, cellular functions. We postulate that, in addition to the known mechanisms of adaptation, conformational plasticity allows some polypeptides to acquire new biophysical properties and functions when environmental change endures.
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Affiliation(s)
- Matthew Domnauer
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; USC Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave., Los Angeles, CA 90191, USA
| | - Fan Zheng
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA
| | - Liying Li
- UCSF, 1550 Fourth St, RH490 San Francisco, CA 94158, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Catherine E Chang
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA
| | - Jay R Unruh
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | | | - Scott McCroskey
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Christopher Seidel
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Benjamin Fong
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA
| | - Birgit Schilling
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; USC Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave., Los Angeles, CA 90191, USA
| | - Rishi Sharma
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA
| | - Arvind Ramanathan
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; Institute for Stem Cell Science and Regenerative Medicine GKVK, Bengaluru, Karnataka 560065, India
| | - Kausik Si
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Chuankai Zhou
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; USC Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave., Los Angeles, CA 90191, USA.
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50
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Mundodi V, Choudhary S, Smith AD, Kadosh D. Global translational landscape of the Candida albicans morphological transition. G3-GENES GENOMES GENETICS 2021; 11:6046988. [PMID: 33585865 PMCID: PMC7849906 DOI: 10.1093/g3journal/jkaa043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/01/2020] [Indexed: 12/14/2022]
Abstract
Candida albicans, a major human fungal pathogen associated with high mortality and/or morbidity rates in a wide variety of immunocompromised individuals, undergoes a reversible morphological transition from yeast to filamentous cells that is required for virulence. While previous studies have identified and characterized global transcriptional mechanisms important for driving this transition, as well as other virulence properties, in C. albicans and other pathogens, considerably little is known about the role of genome-wide translational mechanisms. Using ribosome profiling, we report the first global translational profile associated with C. albicans morphogenesis. Strikingly, many genes involved in pathogenesis, filamentation, and the response to stress show reduced translational efficiency (TE). Several of these genes are known to be strongly induced at the transcriptional level, suggesting that a translational fine-tuning mechanism is in place. We also identify potential upstream open reading frames (uORFs), associated with genes involved in pathogenesis, and novel ORFs, several of which show altered TE during filamentation. Using a novel bioinformatics method for global analysis of ribosome pausing that will be applicable to a wide variety of genetic systems, we demonstrate an enrichment of ribosome pausing sites in C. albicans genes associated with protein synthesis and cell wall functions. Altogether, our results suggest that the C. albicans morphological transition, and most likely additional virulence processes in fungal pathogens, is associated with widespread global alterations in TE that do not simply reflect changes in transcript levels. These alterations affect the expression of many genes associated with processes essential for virulence and pathogenesis.
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Affiliation(s)
- Vasanthakrishna Mundodi
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Saket Choudhary
- Department of Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew D Smith
- Department of Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
| | - David Kadosh
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
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