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Requena JM. The Leishmania ribosome: more than passive mRNA translating machinery. Trends Biochem Sci 2024:S0968-0004(24)00151-8. [PMID: 38897854 DOI: 10.1016/j.tibs.2024.06.008] [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: 06/10/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
While the central dogma of molecular biology describes how genetic information flows, gene expression is also affected by epigenetic and epitranscriptomic processes. A recent report by Rajan et al. demonstrates how pseudouridylation of a Leishmania ribosomal rRNA affects the expression of particular proteins: an example of epitranslatomic control.
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Affiliation(s)
- Jose M Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain.
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2
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He J, Wang A, Zhao Q, Zou Y, Zhang Z, Sha N, Hou G, Zhou B, Yang Y, Chen T, Zhao Y, Jiang Y. RNAi screens identify HES4 as a regulator of redox balance supporting pyrimidine synthesis and tumor growth. Nat Struct Mol Biol 2024:10.1038/s41594-024-01309-3. [PMID: 38769389 DOI: 10.1038/s41594-024-01309-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/08/2024] [Indexed: 05/22/2024]
Abstract
NADH/NAD+ redox balance is pivotal for cellular metabolism. Systematic identification of NAD(H) redox regulators, although currently lacking, would help uncover unknown effectors critically implicated in the coordination of growth metabolism. In this study, we performed a genome-scale RNA interference (RNAi) screen to globally survey the genes involved in redox modulation and identified the HES family bHLH transcription factor HES4 as a negative regulator of NADH/NAD+ ratio. Functionally, HES4 is shown to be crucial for maintaining mitochondrial electron transport chain (ETC) activity and pyrimidine synthesis. More specifically, HES4 directly represses transcription of SLC44A2 and SDS, thereby inhibiting mitochondrial choline oxidation and cytosolic serine deamination, respectively, which, in turn, ensures coenzyme Q reduction capacity for DHODH-mediated UMP synthesis and serine-derived dTMP production. Accordingly, inhibition of choline oxidation preserves mitochondrial serine catabolism and ETC-coupled redox balance. Furthermore, HES4 protein stability is enhanced under EGFR activation, and increased HES4 levels facilitate EGFR-driven tumor growth and predict poor prognosis of lung adenocarcinoma. These findings illustrate an unidentified mechanism, underlying pyrimidine biosynthesis in the intersection between serine and choline catabolism, and underscore the physiological importance of HES4 in tumor metabolism.
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Affiliation(s)
- Jing He
- Department of Liver Surgery and Shanghai Cancer Institute, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Aoxue Wang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- Research Unit of New Techniques for Live-Cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China
| | - Qin Zhao
- Department of Liver Surgery and Shanghai Cancer Institute, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yejun Zou
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- Research Unit of New Techniques for Live-Cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhuo Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- Research Unit of New Techniques for Live-Cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China
| | - Nannan Sha
- Department of Liver Surgery and Shanghai Cancer Institute, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guofang Hou
- Department of Liver Surgery and Shanghai Cancer Institute, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bei Zhou
- Department of Liver Surgery and Shanghai Cancer Institute, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Tao Chen
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- Research Unit of New Techniques for Live-Cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China.
| | - Yuhui Jiang
- Department of Liver Surgery and Shanghai Cancer Institute, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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3
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Solari CA, Ortolá Martínez MC, Fernandez JM, Bates C, Cueto G, Valacco MP, Morales-Polanco F, Moreno S, Rossi S, Ashe MP, Portela P. Riboproteome remodeling during quiescence exit in Saccharomyces cerevisiae. iScience 2024; 27:108727. [PMID: 38235324 PMCID: PMC10792236 DOI: 10.1016/j.isci.2023.108727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/15/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
The quiescent state is the prevalent mode of cellular life in most cells. Saccharomyces cerevisiae is a useful model for studying the molecular basis of the cell cycle, quiescence, and aging. Previous studies indicate that heterogeneous ribosomes show a specialized translation function to adjust the cellular proteome upon a specific stimulus. Using nano LC-MS/MS, we identified 69 of the 79 ribosomal proteins (RPs) that constitute the eukaryotic 80S ribosome during quiescence. Our study shows that the riboproteome is composed of 444 accessory proteins comprising cellular functions such as translation, protein folding, amino acid and glucose metabolism, cellular responses to oxidative stress, and protein degradation. Furthermore, the stoichiometry of both RPs and accessory proteins on ribosome particles is different depending on growth conditions and among monosome and polysome fractions. Deficiency of different RPs resulted in defects of translational capacity, suggesting that ribosome composition can result in changes in translational activity during quiescence.
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Affiliation(s)
- Clara A. Solari
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - María Clara Ortolá Martínez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Juan M. Fernandez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Christian Bates
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Gerardo Cueto
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Instituto IEGEBA (CONICET-UBA), Buenos Aires, Argentina
| | - María Pía Valacco
- CEQUIBIEM- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Fabián Morales-Polanco
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Silvia Moreno
- CEQUIBIEM- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Silvia Rossi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Mark P. Ashe
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Paula Portela
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
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4
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Ugajin N, Imami K, Takada H, Ishihama Y, Chiba S, Mishima Y. Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development. RNA (NEW YORK, N.Y.) 2023; 29:1910-1927. [PMID: 37751929 PMCID: PMC10653392 DOI: 10.1261/rna.079633.123] [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: 02/12/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
The ribosome is a translational apparatus that comprises about 80 ribosomal proteins and four rRNAs. Recent studies reported that ribosome ubiquitination is crucial for translational regulation and ribosome-associated quality control (RQC). However, little is known about the dynamics of ribosome ubiquitination under complex biological processes of multicellular organisms. To explore ribosome ubiquitination during animal development, we generated a zebrafish strain that expresses a FLAG-tagged ribosomal protein Rpl36/eL36 from its endogenous locus. We examined ribosome ubiquitination during zebrafish development by combining affinity purification of ribosomes from rpl36-FLAG zebrafish embryos with immunoblotting analysis. Our findings showed that the ubiquitination of ribosomal proteins dynamically changed as development proceeded. We also showed that during zebrafish development, the ribosome was ubiquitinated by Znf598, an E3 ubiquitin ligase that activates RQC. Ribosomal protein Rps10/eS10 was found to be a key ubiquitinated protein during development. Furthermore, we showed that Rps10/eS10 ubiquitination-site mutations reduced the overall ubiquitination pattern of the ribosome. These results demonstrate the complexity and dynamics of ribosome ubiquitination during zebrafish development.
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Affiliation(s)
- Nozomi Ugajin
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Koshi Imami
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiraku Takada
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shinobu Chiba
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Yuichiro Mishima
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
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5
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Rao A, Lyu B, Jahan I, Lubertozzi A, Zhou G, Tedeschi F, Jankowsky E, Kang J, Carstens B, Poss KD, Baskin K, Goldman JA. The translation initiation factor homolog eif4e1c regulates cardiomyocyte metabolism and proliferation during heart regeneration. Development 2023; 150:dev201376. [PMID: 37306388 PMCID: PMC10281269 DOI: 10.1242/dev.201376] [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: 10/19/2022] [Accepted: 04/28/2023] [Indexed: 05/25/2023]
Abstract
The eIF4E family of translation initiation factors bind 5' methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability, yet other related eIF4E families exist and are utilized in specific contexts or tissues. Here, we describe a family called Eif4e1c, for which we find roles during heart development and regeneration in zebrafish. The Eif4e1c family is present in all aquatic vertebrates but is lost in all terrestrial species. A core group of amino acids shared over 500 million years of evolution forms an interface along the protein surface, suggesting that Eif4e1c functions in a novel pathway. Deletion of eif4e1c in zebrafish caused growth deficits and impaired survival in juveniles. Mutants surviving to adulthood had fewer cardiomyocytes and reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although eif4e1c is broadly expressed, its disruption had most notable impact on the heart and at juvenile stages. Our findings reveal context-dependent requirements for translation initiation regulators during heart regeneration.
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Affiliation(s)
- Anupama Rao
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Baken Lyu
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Ishrat Jahan
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Anna Lubertozzi
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Gao Zhou
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Frank Tedeschi
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Eckhard Jankowsky
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Bryan Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kenneth D. Poss
- Department of Cell Biology, Duke Regeneration Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kedryn Baskin
- Department of Cell Biology and Physiology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Joseph Aaron Goldman
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
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6
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Jonsson WO, Borowik AK, Pranay A, Kinter MT, Mirek ET, Levy JL, Snyder EM, Miller BF, Anthony TG. Kinetic proteomics identifies targeted changes in liver metabolism and the ribo-interactome by dietary sulfur amino acid restriction. GeroScience 2023; 45:2425-2441. [PMID: 36976488 PMCID: PMC10651627 DOI: 10.1007/s11357-023-00758-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/19/2023] [Indexed: 03/29/2023] Open
Abstract
Dietary sulfur amino acid restriction (SAAR) protects against diet-induced obesity, extends healthspan, and coincides with an overall reduction in hepatic protein synthesis. To explore the underpinnings of SAAR-induced slowed growth and its impact on liver metabolism and proteostasis, we resolved changes in hepatic mRNA and protein abundances and compared synthesis rates of individual liver proteins. To achieve this, adult male mice were provided deuterium-labeled drinking water while freely consuming either a regular-fat or high-fat diet that was SAA restricted. Livers from these mice and their respective dietary controls were used to conduct transcriptomic, proteomic, and kinetic proteomic analyses. We found that remodeling of the transcriptome by SAAR was largely agnostic to dietary fat content. Shared signatures included activation of the integrated stress response alongside alterations in metabolic processes impacting lipids, fatty acids, and amino acids. Changes to the proteome correlated poorly with the transcriptome, and yet, functional clustering of kinetic proteomic changes in the liver during SAAR revealed that the management of fatty acids and amino acids were altered to support central metabolism and redox balance. Dietary SAAR also strongly influenced the synthesis rates of ribosomal proteins and ribosome-interacting proteins regardless of dietary fat. Taken together, dietary SAAR alters the transcriptome and proteome in the liver to safely manage increased fatty acid flux and energy use and couples this with targeted changes in the ribo-interactome to support proteostasis and slowed growth.
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Affiliation(s)
- William O Jonsson
- Department of Nutritional Sciences and the New Jersey Institute for Food, Nutrition and Health, Rutgers University, 59 Dudley Road - Foran Hall, Room 166, New Brunswick, NJ, 08901, USA
| | - Agnieszka K Borowik
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Atul Pranay
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Michael T Kinter
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Emily T Mirek
- Department of Nutritional Sciences and the New Jersey Institute for Food, Nutrition and Health, Rutgers University, 59 Dudley Road - Foran Hall, Room 166, New Brunswick, NJ, 08901, USA
| | - Jordan L Levy
- Department of Nutritional Sciences and the New Jersey Institute for Food, Nutrition and Health, Rutgers University, 59 Dudley Road - Foran Hall, Room 166, New Brunswick, NJ, 08901, USA
| | - Elizabeth M Snyder
- Department of Animal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Benjamin F Miller
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Oklahoma City VA, Oklahoma City, OK, USA
| | - Tracy G Anthony
- Department of Nutritional Sciences and the New Jersey Institute for Food, Nutrition and Health, Rutgers University, 59 Dudley Road - Foran Hall, Room 166, New Brunswick, NJ, 08901, USA.
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7
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Gu X, Zhang F, Xie X, Cheng Y, Xu X. Effects of N and P addition on nutrient and stoichiometry of rhizosphere and non-rhizosphere soils of alfalfa in alkaline soil. Sci Rep 2023; 13:12119. [PMID: 37495627 PMCID: PMC10372058 DOI: 10.1038/s41598-023-39030-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Nitrogen (N) and phosphorus (P) are important nutrients for plant growth and development. Soil alkalization is one of the main obstacles limiting the sustainable development of agriculture. Northern Ningxia is located in the arid and semi-arid region, with serious soil alkalinization. Alfalfa has the advantages of strong saline-alkali tolerance, high yield, high quality, and wide adaptability. It is an important forage for the comprehensive improvement and rational utilization of saline-alkali land and has great significance for solving land resource shortages, improving the ecological environment, and ensuring food security. It is important to study soil organic carbon (SOC), total N (TN), total P (TP), and stoichiometry of the rhizosphere and non-rhizosphere of alfalfa in alkaline soils. Therefore, N and P were added to the alkaline alfalfa field in the Yinchuan Plain of Hetao Basin in our experiment. Six treatments were set up, i.e., N-free (WN), medium N (MN) for 90 kg/hm2, high N (HN) for 180 kg/hm2, P-free (WP), medium P (MP) for 135 kg/hm2, and high P (HP) for 270 kg/hm2. The results are as follows: The N addition promotes SOC and TN but inhibits TP, and P addition promotes SOC and TP but inhibits TN of three soil layers. The N addition decreases C/N but increases C/P and N/P, while the P addition increases C/N but decreases C/P and N/P of three soil layers. The SOC, TN, TP, C/N, C/P, and N/P under HN and HP treatment reach the significance level (P < 0.05). Appropriate additions of N and P can improve rhizosphere and non-rhizosphere nutrients and stoichiometric structure, facilitating absorption and utilization by alfalfa and improve the production potential of alfalfa in alkaline soil.
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Affiliation(s)
- Xudong Gu
- College of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Fengju Zhang
- College of Ecology and Environment, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Xiaowei Xie
- College of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Yunlong Cheng
- College of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Xing Xu
- College of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China.
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8
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Matsuura-Suzuki E, Toh H, Iwasaki S. Human-rabbit Hybrid Translation System to Explore the Function of Modified Ribosomes. Bio Protoc 2023; 13:e4714. [PMID: 37456340 PMCID: PMC10339341 DOI: 10.21769/bioprotoc.4714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/15/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
In vitro translation systems are a useful biochemical tool to research translational regulation. Although the preparation of translation-competent cell extracts from mammals has often been a challenge, the commercially available rabbit reticulocyte lysate (RRL) is an exception. However, its valid use, investigating the mechanism of translation machinery such as ribosomes in RRL, presents an analytic hurdle. To overcome this issue, the hybrid translation system, which is based on the supplementation of purified human ribosomes into ribosome-depleted RRL, has been developed. Here, we describe the step-by-step protocol of this system to study translation driven by ribosomes lacking post-translational modifications of the ribosomal protein. Moreover, we combined this approach with a previously developed reporter mRNA to assess the processivity of translation elongation. This protocol could be used to study the potency of heterologous ribosomes.
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Affiliation(s)
- Eriko Matsuura-Suzuki
- 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
| | - 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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9
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Slavov N. Single-cell proteomics: quantifying post-transcriptional regulation during development with mass-spectrometry. Development 2023; 150:dev201492. [PMID: 37387573 PMCID: PMC10323229 DOI: 10.1242/dev.201492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Many developmental processes are regulated post-transcriptionally. Such post-transcriptional regulatory mechanisms can now be analyzed by robust single-cell mass spectrometry methods that allow accurate quantification of proteins and their modification in single cells. These methods can enable quantitative exploration of protein synthesis and degradation mechanisms that contribute to developmental cell fate specification. Furthermore, they may support functional analysis of protein conformations and activities in single cells, and thus link protein functions to developmental processes. This Spotlight provides an accessible introduction to single-cell mass spectrometry methods and suggests initial biological questions that are ripe for investigation.
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Affiliation(s)
- Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
- Parallel Squared Technology Institute, Watertown, MA 02472, USA
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10
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Meng-Lin K, Ung CY, Zhang C, Weiskittel TM, Wisniewski P, Zhang Z, Tan SH, Yeo KS, Zhu S, Correia C, Li H. SPIN-AI: A Deep Learning Model That Identifies Spatially Predictive Genes. Biomolecules 2023; 13:895. [PMID: 37371475 PMCID: PMC10296445 DOI: 10.3390/biom13060895] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Spatially resolved sequencing technologies help us dissect how cells are organized in space. Several available computational approaches focus on the identification of spatially variable genes (SVGs), genes whose expression patterns vary in space. The detection of SVGs is analogous to the identification of differentially expressed genes and permits us to understand how genes and associated molecular processes are spatially distributed within cellular niches. However, the expression activities of SVGs fail to encode all information inherent in the spatial distribution of cells. Here, we devised a deep learning model, Spatially Informed Artificial Intelligence (SPIN-AI), to identify spatially predictive genes (SPGs), whose expression can predict how cells are organized in space. We used SPIN-AI on spatial transcriptomic data from squamous cell carcinoma (SCC) as a proof of concept. Our results demonstrate that SPGs not only recapitulate the biology of SCC but also identify genes distinct from SVGs. Moreover, we found a substantial number of ribosomal genes that were SPGs but not SVGs. Since SPGs possess the capability to predict spatial cellular organization, we reason that SPGs capture more biologically relevant information for a given cellular niche than SVGs. Thus, SPIN-AI has broad applications for detecting SPGs and uncovering which biological processes play important roles in governing cellular organization.
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Affiliation(s)
- Kevin Meng-Lin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
| | - Choong-Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
| | - Taylor M. Weiskittel
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
| | - Philip Wisniewski
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
| | - Zhuofei Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
| | - Shyang-Hong Tan
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
| | - Kok-Siong Yeo
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (K.-S.Y.); (S.Z.)
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (K.-S.Y.); (S.Z.)
| | - Cristina Correia
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
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11
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Anisimova AS, Kolyupanova NM, Makarova NE, Egorov AA, Kulakovskiy IV, Dmitriev SE. Human Tissues Exhibit Diverse Composition of Translation Machinery. Int J Mol Sci 2023; 24:ijms24098361. [PMID: 37176068 PMCID: PMC10179197 DOI: 10.3390/ijms24098361] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/26/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
While protein synthesis is vital for the majority of cell types of the human body, diversely differentiated cells require specific translation regulation. This suggests the specialization of translation machinery across tissues and organs. Using transcriptomic data from GTEx, FANTOM, and Gene Atlas, we systematically explored the abundance of transcripts encoding translation factors and aminoacyl-tRNA synthetases (ARSases) in human tissues. We revised a few known and identified several novel translation-related genes exhibiting strict tissue-specific expression. The proteins they encode include eEF1A1, eEF1A2, PABPC1L, PABPC3, eIF1B, eIF4E1B, eIF4ENIF1, and eIF5AL1. Furthermore, our analysis revealed a pervasive tissue-specific relative abundance of translation machinery components (e.g., PABP and eRF3 paralogs, eIF2B and eIF3 subunits, eIF5MPs, and some ARSases), suggesting presumptive variance in the composition of translation initiation, elongation, and termination complexes. These conclusions were largely confirmed by the analysis of proteomic data. Finally, we paid attention to sexual dimorphism in the repertoire of translation factors encoded in sex chromosomes (eIF1A, eIF2γ, and DDX3), and identified the testis and brain as organs with the most diverged expression of translation-associated genes.
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Affiliation(s)
- Aleksandra S Anisimova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Natalia M Kolyupanova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Nadezhda E Makarova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Artyom A Egorov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Ivan V Kulakovskiy
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 117971 Moscow, Russia
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Laboratory of Regulatory Genomics, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
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12
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Wang YX, Lin SR, Xu LZ, Ye YY, Qi PZ, Wang WF, Buttino I, Li HF, Guo BY. Comparative transcriptomic analysis revealed changes in multiple signaling pathways involved in protein degradation in the digestive gland of Mytilus coruscus during high-temperatures. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 46:101060. [PMID: 36731219 DOI: 10.1016/j.cbd.2023.101060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/28/2023]
Abstract
As a result of global warming, the Mytilus coruscus living attached in the intertidal zone experience extreme and fluctuating changes in temperature, and extreme temperature changes are causing mass mortality of intertidal species. This study explores the transcriptional response of M. coruscus at different temperatures (18 °C, 26 °C, and 33 °C) and different times (0, 12, and 24 h) of action by analyzing the potential temperature of the intertidal zone. In response to high temperatures, several signaling pathways in M. coruscus, ribosome, endocytosis, endoplasmic reticulum stress, protein degradation, and lysosomes, interact to counter the adverse effects of high temperatures on protein homeostasis. Increased expression of key genes, including heat shock proteins (Hsp70, Hsp20, and Hsp110), Lysosome-associated membrane glycoprotein (LAMP), endoplasmic reticulum chaperone (BiP), and baculoviral IAP repeat-containing protein 7 (BIRC7), may further mitigate the effects of heat stress and delay mortality in M. coruscus. These results reveal changes in multiple signaling pathways involved in protein degradation during high-temperature stress, which will contribute to our overall understanding of the molecular mechanisms underlying the response of M. coruscus to high-temperature stress.
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Affiliation(s)
- Yu-Xia Wang
- National Engineering Research Center for Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Shuang-Rui Lin
- National Engineering Research Center for Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Le-Zhong Xu
- National Engineering Research Center for Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Ying-Ying Ye
- National Engineering Research Center for Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Peng-Zhi Qi
- National Engineering Research Center for Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Wei-Feng Wang
- National Engineering Research Center for Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Isabella Buttino
- Italian Institute for Environmental Protection and Research ISPRA, Via del Cedro n.38, 57122 Livorno, Italy
| | - Hong-Fei Li
- National Engineering Research Center for Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China.
| | - Bao-Ying Guo
- National Engineering Research Center for Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China.
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13
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Lignieres L, Legros V, Khelil M, Senecaut N, Lauber MA, Camadro JM, Chevreux G. Capillary liquid chromatography coupled with mass spectrometry for analysis of nanogram protein quantities on a wide-pore superficially porous particle column in top-down proteomics. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1214:123566. [PMID: 36516651 DOI: 10.1016/j.jchromb.2022.123566] [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: 10/06/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
In top-down proteomics experiments, intact protein ions are subjected to gas-phase fragmentation for MS analysis without prior digestion. This approach is used to characterize post-translational modifications and clipped forms of proteins, avoids several "inference" problems associated with bottom-up proteomics, and is well suited to the study of proteoforms. In the past decade, top-down proteomics has progressed rapidly, taking advantage of MS instrumentation improvements and the efforts of pioneering groups working to improve sample handling and data processing. The potential of this technology has been established through its successful use in a number of important biological studies. However, many challenges remain to be addressed like improving protein separation capabilities such that it might become possible to expand the dynamic range of whole proteome analysis, address co-elution and convoluted mass spectral data, and aid final data processing from peak identification to quantification. In this study, we investigated the use of a wide-pore silica-based superficially porous media with a high coverage phenyl bonding, commercially packed into customized capillary columns for the purpose of top-down proteomics. Protein samples of increasing complexity were tested, namely subunit digests of a monoclonal antibody, components of purified histones and proteins extracted from eukaryotic ribosomes. High quality mass spectra were obtained from only 100 ng of protein sample while using difluoroacetic acid as an ion pairing agent to improve peak shape and chromatographic resolution. A peak width at half height of about 15 s for a 45 min gradient time was observed on a complex mixture giving an estimated peak capacity close to 100. Most importantly, efficient separations were obtained for highly diverse proteins and there was no need to make method specific adjustments, suggesting this is a highly versatile and easy-to-use setup for top-down proteomics.
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Affiliation(s)
- Laurent Lignieres
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Véronique Legros
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Manel Khelil
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Nicolas Senecaut
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Matthew A Lauber
- Waters Corporation, 34, Maple Street, Milford, MA 01757-3696, United States
| | | | - Guillaume Chevreux
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France.
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14
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Wang X, Zhu J, Zhang D, Liu G. Ribosomal control in RNA virus-infected cells. Front Microbiol 2022; 13:1026887. [PMID: 36419416 PMCID: PMC9677555 DOI: 10.3389/fmicb.2022.1026887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022] Open
Abstract
Viruses are strictly intracellular parasites requiring host cellular functions to complete their reproduction cycle involving virus infection of host cell, viral genome replication, viral protein translation, and virion release. Ribosomes are protein synthesis factories in cells, and viruses need to manipulate ribosomes to complete their protein synthesis. Viruses use translation initiation factors through their own RNA structures or cap structures, thereby inducing ribosomes to synthesize viral proteins. Viruses also affect ribosome production and the assembly of mature ribosomes, and regulate the recognition of mRNA by ribosomes, thereby promoting viral protein synthesis and inhibiting the synthesis of host antiviral immune proteins. Here, we review the remarkable mechanisms used by RNA viruses to regulate ribosomes, in particular, the mechanisms by which RNA viruses induce the formation of specific heterogeneous ribosomes required for viral protein translation. This review provides valuable insights into the control of viral infection and diseases from the perspective of viral protein synthesis.
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15
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Buchanan IM, Smith TM, Gerber AP, Seibt J. Are there roles for heterogeneous ribosomes during sleep in the rodent brain? Front Mol Biosci 2022; 9:1008921. [PMID: 36275625 PMCID: PMC9582285 DOI: 10.3389/fmolb.2022.1008921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
The regulation of mRNA translation plays an essential role in neurons, contributing to important brain functions, such as brain plasticity and memory formation. Translation is conducted by ribosomes, which at their core consist of ribosomal proteins (RPs) and ribosomal RNAs. While translation can be regulated at diverse levels through global or mRNA-specific means, recent evidence suggests that ribosomes with distinct configurations are involved in the translation of different subsets of mRNAs. However, whether and how such proclaimed ribosome heterogeneity could be connected to neuronal functions remains largely unresolved. Here, we postulate that the existence of heterologous ribosomes within neurons, especially at discrete synapses, subserve brain plasticity. This hypothesis is supported by recent studies in rodents showing that heterogeneous RP expression occurs in dendrites, the compartment of neurons where synapses are made. We further propose that sleep, which is fundamental for brain plasticity and memory formation, has a particular role in the formation of heterologous ribosomes, specialised in the translation of mRNAs specific for synaptic plasticity. This aspect of our hypothesis is supported by recent studies showing increased translation and changes in RP expression during sleep after learning. Thus, certain RPs are regulated by sleep, and could support different sleep functions, in particular brain plasticity. Future experiments investigating cell-specific heterogeneity in RPs across the sleep-wake cycle and in response to different behaviour would help address this question.
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Affiliation(s)
- Isla M. Buchanan
- Integrated Master Programme in Biochemistry, University of Surrey, Guildford, United Kingdom
| | - Trevor M. Smith
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- Surrey Sleep Research Centre, University of Surrey, Guildford, United Kingdom
| | - André P. Gerber
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- *Correspondence: André P. Gerber, ; Julie Seibt,
| | - Julie Seibt
- Surrey Sleep Research Centre, University of Surrey, Guildford, United Kingdom
- *Correspondence: André P. Gerber, ; Julie Seibt,
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16
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Engineering Ribosomes to Alleviate Abiotic Stress in Plants: A Perspective. PLANTS 2022; 11:plants11162097. [PMID: 36015400 PMCID: PMC9415564 DOI: 10.3390/plants11162097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022]
Abstract
As the centerpiece of the biomass production process, ribosome activity is highly coordinated with environmental cues. Findings revealing ribosome subgroups responsive to adverse conditions suggest this tight coordination may be grounded in the induction of variant ribosome compositions and the differential translation outcomes they might produce. In this perspective, we go through the literature linking ribosome heterogeneity to plants’ abiotic stress response. Once unraveled, this crosstalk may serve as the foundation of novel strategies to custom cultivars tolerant to challenging environments without the yield penalty.
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17
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Temaj G, Saha S, Dragusha S, Ejupi V, Buttari B, Profumo E, Beqa L, Saso L. Ribosomopathies and cancer: pharmacological implications. Expert Rev Clin Pharmacol 2022; 15:729-746. [PMID: 35787725 DOI: 10.1080/17512433.2022.2098110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The ribosome is a ribonucleoprotein organelle responsible for protein synthesis, and its biogenesis is a highly coordinated process that involves many macromolecular components. Any acquired or inherited impairment in ribosome biogenesis or ribosomopathies is associated with the development of different cancers and rare genetic diseases. Interference with multiple steps of protein synthesis has been shown to promote tumor cell death. AREAS COVERED We discuss the current insights about impaired ribosome biogenesis and their secondary consequences on protein synthesis, transcriptional and translational responses, proteotoxic stress, and other metabolic pathways associated with cancer and rare diseases. Studies investigating the modulation of different therapeutic chemical entities targeting cancer in in vitro and in vivo models have also been detailed. EXPERT OPINION Despite the association between inherited mutations affecting ribosome biogenesis and cancer biology, the development of therapeutics targeting the essential cellular machinery has only started to emerge. New chemical entities should be designed to modulate different checkpoints (translating oncoproteins, dysregulation of specific ribosome-assembly machinery, ribosomal stress, and rewiring ribosomal functions). Although safe and effective therapies are lacking, consideration should also be given to using existing drugs alone or in combination for long-term safety, with known risks for feasibility in clinical trials and synergistic effects.
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Affiliation(s)
| | - Sarmistha Saha
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | | | - Valon Ejupi
- College UBT, Faculty of Pharmacy, Prishtina, Kosovo
| | - Brigitta Buttari
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | - Elisabetta Profumo
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | - Lule Beqa
- College UBT, Faculty of Pharmacy, Prishtina, Kosovo
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", Sapienza University of Rome, Italy
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18
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Matsuura-Suzuki E, Shimazu T, Takahashi M, Kotoshiba K, Suzuki T, Kashiwagi K, Sohtome Y, Akakabe M, Sodeoka M, Dohmae N, Ito T, Shinkai Y, Iwasaki S. METTL18-mediated histidine methylation of RPL3 modulates translation elongation for proteostasis maintenance. eLife 2022; 11:e72780. [PMID: 35674491 PMCID: PMC9177149 DOI: 10.7554/elife.72780] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 05/26/2022] [Indexed: 12/24/2022] Open
Abstract
Protein methylation occurs predominantly on lysine and arginine residues, but histidine also serves as a methylation substrate. However, a limited number of enzymes responsible for this modification have been reported. Moreover, the biological role of histidine methylation has remained poorly understood to date. Here, we report that human METTL18 is a histidine methyltransferase for the ribosomal protein RPL3 and that the modification specifically slows ribosome traversal on Tyr codons, allowing the proper folding of synthesized proteins. By performing an in vitro methylation assay with a methyl donor analog and quantitative mass spectrometry, we found that His245 of RPL3 is methylated at the τ-N position by METTL18. Structural comparison of the modified and unmodified ribosomes showed stoichiometric modification and suggested a role in translation reactions. Indeed, genome-wide ribosome profiling and an in vitro translation assay revealed that translation elongation at Tyr codons was suppressed by RPL3 methylation. Because the slower elongation provides enough time for nascent protein folding, RPL3 methylation protects cells from the cellular aggregation of Tyr-rich proteins. Our results reveal histidine methylation as an example of a ribosome modification that ensures proteome integrity in cells.
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Affiliation(s)
- Eriko Matsuura-Suzuki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering ResearchSaitamaJapan
| | - Tadahiro Shimazu
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering ResearchSaitamaJapan
| | - Mari Takahashi
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics ResearchYokohamaJapan
| | - Kaoru Kotoshiba
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering ResearchSaitamaJapan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource ScienceSaitamaJapan
| | - Kazuhiro Kashiwagi
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics ResearchYokohamaJapan
| | - Yoshihiro Sohtome
- RIKEN Center for Sustainable Resource ScienceSaitamaJapan
- Synthetic Organic Chemistry Lab, RIKEN Cluster for Pioneering ResearchSaitamaJapan
| | - Mai Akakabe
- Synthetic Organic Chemistry Lab, RIKEN Cluster for Pioneering ResearchSaitamaJapan
| | - Mikiko Sodeoka
- RIKEN Center for Sustainable Resource ScienceSaitamaJapan
- Synthetic Organic Chemistry Lab, RIKEN Cluster for Pioneering ResearchSaitamaJapan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource ScienceSaitamaJapan
| | - Takuhiro Ito
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics ResearchYokohamaJapan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering ResearchSaitamaJapan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering ResearchSaitamaJapan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of TokyoChibaJapan
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19
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Bartolec TK, Hamey JJ, Keller A, Chavez JD, Bruce JE, Wilkins MR. Differential Proteome and Interactome Analysis Reveal the Basis of Pleiotropy Associated With the Histidine Methyltransferase Hpm1p. Mol Cell Proteomics 2022; 21:100249. [PMID: 35609787 PMCID: PMC9234706 DOI: 10.1016/j.mcpro.2022.100249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/28/2022] [Accepted: 05/19/2022] [Indexed: 10/31/2022] Open
Abstract
The methylation of histidine is a post-translational modification whose function is poorly understood. Methyltransferase histidine protein methyltransferase 1 (Hpm1p) monomethylates H243 in the ribosomal protein Rpl3p and represents the only known histidine methyltransferase in Saccharomyces cerevisiae. Interestingly, the hpm1 deletion strain is highly pleiotropic, with many extraribosomal phenotypes including improved growth rates in alternative carbon sources. Here, we investigate how the loss of histidine methyltransferase Hpm1p results in diverse phenotypes, through use of targeted mass spectrometry (MS), growth assays, quantitative proteomics, and differential crosslinking MS. We confirmed the localization and stoichiometry of the H243 methylation site, found unreported sensitivities of Δhpm1 yeast to nonribosomal stressors, and identified differentially abundant proteins upon hpm1 knockout with clear links to the coordination of sugar metabolism. We adapted the emerging technique of quantitative large-scale stable isotope labeling of amino acids in cell culture crosslinking MS for yeast, which resulted in the identification of 1267 unique in vivo lysine-lysine crosslinks. By reproducibly monitoring over 350 of these in WT and Δhpm1, we detected changes to protein structure or protein-protein interactions in the ribosome, membrane proteins, chromatin, and mitochondria. Importantly, these occurred independently of changes in protein abundance and could explain a number of phenotypes of Δhpm1, not addressed by expression analysis. Further to this, some phenotypes were predicted solely from changes in protein structure or interactions and could be validated by orthogonal techniques. Taken together, these studies reveal a broad role for Hpm1p in yeast and illustrate how crosslinking MS will be an essential tool for understanding complex phenotypes.
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Affiliation(s)
- Tara K Bartolec
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Randwick, New South Wales, Australia
| | - Joshua J Hamey
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Randwick, New South Wales, Australia
| | - Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Randwick, New South Wales, Australia.
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20
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Fan W, Eklund E, Sherman RM, Liu H, Pitts S, Ford B, Rajeshkumar NV, Laiho M. Widespread genetic heterogeneity of human ribosomal RNA genes. RNA (NEW YORK, N.Y.) 2022; 28:478-492. [PMID: 35110373 PMCID: PMC8925967 DOI: 10.1261/rna.078925.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/28/2021] [Indexed: 05/28/2023]
Abstract
Polymorphism drives survival under stress and provides adaptability. Genetic polymorphism of ribosomal RNA (rRNA) genes derives from internal repeat variation of this multicopy gene, and from interindividual variation. A considerable amount of rRNA sequence heterogeneity has been proposed but has been challenging to estimate given the scarcity of accurate reference sequences. We identified four rDNA copies on chromosome 21 (GRCh38) with 99% similarity to recently introduced reference sequence KY962518.1. We customized a GATK bioinformatics pipeline using the four rDNA loci, spanning a total 145 kb, for variant calling and used high-coverage whole-genome sequencing (WGS) data from the 1000 Genomes Project to analyze variants in 2504 individuals from 26 populations. We identified a total of 3791 variant positions. The variants positioned nonrandomly on the rRNA gene. Invariant regions included the promoter, early 5' ETS, most of 18S, 5.8S, ITS1, and large areas of the intragenic spacer. A total of 470 variant positions were observed on 28S rRNA. The majority of the 28S rRNA variants were located on highly flexible human-expanded rRNA helical folds ES7L and ES27L, suggesting that these represent positions of diversity and are potentially under continuous evolution. Several variants were validated based on RNA-seq analyses. Population analyses showed remarkable ancestry-linked genetic variance and the presence of both high penetrance and frequent variants in the 5' ETS, ITS2, and 28S regions segregating according to the continental populations. These findings provide a genetic view of rRNA gene array heterogeneity and raise the need to functionally assess how the 28S rRNA variants affect ribosome functions.
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Affiliation(s)
- Wenjun Fan
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Eetu Eklund
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Rachel M Sherman
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Hester Liu
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Stephanie Pitts
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Brittany Ford
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - N V Rajeshkumar
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Marikki Laiho
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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21
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Surya A, Sarinay-Cenik E. Cell autonomous and non-autonomous consequences of deviations in translation machinery on organism growth and the connecting signalling pathways. Open Biol 2022; 12:210308. [PMID: 35472285 PMCID: PMC9042575 DOI: 10.1098/rsob.210308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/31/2022] [Indexed: 01/09/2023] Open
Abstract
Translation machinery is responsible for the production of cellular proteins; thus, cells devote the majority of their resources to ribosome biogenesis and protein synthesis. Single-copy loss of function in the translation machinery components results in rare ribosomopathy disorders, such as Diamond-Blackfan anaemia in humans and similar developmental defects in various model organisms. Somatic copy number alterations of translation machinery components are also observed in specific tumours. The organism-wide response to haploinsufficient loss-of-function mutations in ribosomal proteins or translation machinery components is complex: variations in translation machinery lead to reduced ribosome biogenesis, protein translation and altered protein homeostasis and cellular signalling pathways. Cells are affected both autonomously and non-autonomously by changes in translation machinery or ribosome biogenesis through cell-cell interactions and secreted hormones. We first briefly introduce the model organisms where mutants or knockdowns of protein synthesis and ribosome biogenesis are characterized. Next, we specifically describe observations in Caenorhabditis elegans and Drosophila melanogaster, where insufficient protein synthesis in a subset of cells triggers cell non-autonomous growth or apoptosis responses that affect nearby cells and tissues. We then cover the characterized signalling pathways that interact with ribosome biogenesis/protein synthesis machinery with an emphasis on their respective functions during organism development.
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Affiliation(s)
- Agustian Surya
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Elif Sarinay-Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
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22
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Yang YM, Karbstein K. The chaperone Tsr2 regulates Rps26 release and reincorporation from mature ribosomes to enable a reversible, ribosome-mediated response to stress. SCIENCE ADVANCES 2022; 8:eabl4386. [PMID: 35213229 PMCID: PMC8880767 DOI: 10.1126/sciadv.abl4386] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/13/2022] [Indexed: 05/04/2023]
Abstract
Although ribosome assembly is quality controlled to maintain protein homeostasis, different ribosome populations have been described. How these form, especially under stress conditions that affect energy levels and stop the energy-intensive production of ribosomes, remains unknown. Here, we demonstrate how a physiologically relevant ribosome population arises during high Na+, sorbitol, or pH stress via dissociation of Rps26 from fully assembled ribosomes to enable a translational response to these stresses. The chaperone Tsr2 releases Rps26 in the presence of high Na+ or pH in vitro and is required for Rps26 release in vivo. Moreover, Tsr2 stores free Rps26 and promotes reincorporation of the protein, thereby repairing the subunit after the Na+ stress subsides. Our data implicate a residue in Rps26 involved in Diamond Blackfan Anemia in mediating the effects of Na+. These data demonstrate how different ribosome populations can arise rapidly, without major energy input and without bypass of quality control mechanisms.
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Affiliation(s)
- Yoon-Mo Yang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Katrin Karbstein
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
- HHMI Faculty Scholar, Chevy Chase, MD 20815, USA
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23
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Engineering and functional analysis of yeast with a monotypic 40S ribosome subunit. Proc Natl Acad Sci U S A 2022; 119:2114445119. [PMID: 35105807 PMCID: PMC8833219 DOI: 10.1073/pnas.2114445119] [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] [Accepted: 12/21/2021] [Indexed: 01/21/2023] Open
Abstract
Ribosomes are not monolithic but dynamic machines composed of heterogeneous ribosomal protein (RP) paralogs with elusive functions. Isolation and characterization of monotypic ribosomes with homogeneous RP paralog compositions represent ideal approaches to understand the role of pervasive RP paralogs in customizing translation abilities but are largely hurdled by the complexity of the cellular ribosome pool (e.g., in Saccharomyces cerevisiae, 59 RP paralog pairs allow >1017 potential RP combinations). Here, we engineered a yeast with monotypic 40S ribosomes, including both defined and homogenous RP paralogs, and further functional studies revealed that duplicated RP paralogs impart robustness and phenotypic plasticity (such as paromomycin tolerance) through both gene dose amplification and paralog-specific regulation, paving a way for the study of monotypic ribosomes. Emerging evidence reveals that ribosomes are not monolithic but dynamic machines with heterogeneous protein compositions that can reshape ribosomal translational abilities and cellular adaptation to environmental changes. Duplications of ribosomal protein (RP) genes are ubiquitous among organisms and are believed to affect cell function through paralog-specific regulation (e.g., by generating heterogeneous ribosomes) and/or gene dose amplification. However, direct evaluations of their impacts on cell function remain elusive due to the highly heterogeneous cellular RP pool. Here, we engineered a yeast with homogeneous 40S RP paralog compositions, designated homo-40S, by deleting the entire set of alternative duplicated genes encoding yeast 40S RP paralogs. Homo-40S displayed mild growth defects along with high sensitivity to the translation inhibitor paromomycin and a significantly increased stop codon readthrough. Moreover, doubling of the remaining RP paralogous genes in homo-40S rescued these phenotypes markedly, although not fully, compared to the wild-type phenotype, indicating that the dose of 40S RP genes together with the heterogeneity of the contents was vital for maintaining normal translational functionalities and growth robustness. Additional experiments revealed that homo-40S improved paromomycin tolerance via acquisition of bypass mutations or evolved to be diploid to generate fast-growing derivatives, highlighting the mutational robustness of engineered yeast to accommodate environmental and genetic changes. In summary, our work demonstrated that duplicated RP paralogs impart robustness and phenotypic plasticity through both gene dose amplification and paralog-specific regulation, paving the way for the direct study of ribosome biology through monotypic ribosomes with a homogeneous composition of specific RP paralogs.
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24
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Joo M, Yeom JH, Choi Y, Jun H, Song W, Kim HL, Lee K, Shin E. Specialised ribosomes as versatile regulators of gene expression. RNA Biol 2022; 19:1103-1114. [PMID: 36255182 PMCID: PMC9586635 DOI: 10.1080/15476286.2022.2135299] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The ribosome has long been thought to be a homogeneous cellular machine that constitutively and globally synthesises proteins from mRNA. However, recent studies have revealed that ribosomes are highly heterogeneous, dynamic macromolecular complexes with specialised roles in translational regulation in many organisms across the kingdoms. In this review, we summarise the current understanding of ribosome heterogeneity and the specialised functions of heterogeneous ribosomes. We also discuss specialised translation systems that utilise orthogonal ribosomes.
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Affiliation(s)
- Minju Joo
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Ji-Hyun Yeom
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Younkyung Choi
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hyeon Jun
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Wooseok Song
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hyun-Lee Kim
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Eunkyoung Shin
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
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25
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Martinez-Seidel F, Hsieh YC, Walther D, Kopka J, Pereira Firmino AA. [Formula: see text]: ComplexOme-Structural Network Interpreter used to study spatial enrichment in metazoan ribosomes. BMC Bioinformatics 2021; 22:605. [PMID: 34930116 PMCID: PMC8686616 DOI: 10.1186/s12859-021-04510-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 12/01/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Upon environmental stimuli, ribosomes are surmised to undergo compositional rearrangements due to abundance changes among proteins assembled into the complex, leading to modulated structural and functional characteristics. Here, we present the ComplexOme-Structural Network Interpreter ([Formula: see text]), a computational method to allow testing whether ribosomal proteins (rProteins) that exhibit abundance changes under specific conditions are spatially confined to particular regions within the large ribosomal complex. RESULTS [Formula: see text] translates experimentally determined structures into graphs, with nodes representing proteins and edges the spatial proximity between them. In its first implementation, [Formula: see text] considers rProteins and ignores rRNA and other objects. Spatial regions are defined using a random walk with restart methodology, followed by a procedure to obtain a minimum set of regions that cover all proteins in the complex. Structural coherence is achieved by applying weights to the edges reflecting the physical proximity between purportedly contacting proteins. The weighting probabilistically guides the random-walk path trajectory. Parameter tuning during region selection provides the option to tailor the method to specific biological questions by yielding regions of different sizes with minimum overlaps. In addition, other graph community detection algorithms may be used for the [Formula: see text] workflow, considering that they yield different sized, non-overlapping regions. All tested algorithms result in the same node kernels under equivalent regions. Based on the defined regions, available abundance change information of proteins is mapped onto the graph and subsequently tested for enrichment in any of the defined spatial regions. We applied [Formula: see text] to the cytosolic ribosome structures of Saccharomyces cerevisiae, Oryctolagus cuniculus, and Triticum aestivum using datasets with available quantitative protein abundance change information. We found that in yeast, substoichiometric rProteins depleted from translating polysomes are significantly constrained to a ribosomal region close to the tRNA entry and exit sites. CONCLUSIONS [Formula: see text] offers a computational method to partition multi-protein complexes into structural regions and a statistical approach to test for spatial enrichments of any given subsets of proteins. [Formula: see text] is applicable to any multi-protein complex given appropriate structural and abundance-change data. [Formula: see text] is publicly available as a GitHub repository https://github.com/MSeidelFed/COSNet_i and can be installed using the python installer pip.
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Affiliation(s)
- Federico Martinez-Seidel
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- School of BioSciences, University of Melbourne, Parkville, VC 3010 Australia
| | - Yin-Chen Hsieh
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Institute for Arctic and Marine Biology, UiT Arctic University of Norway, 9037 Tromsø, Norway
| | - Dirk Walther
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Joachim Kopka
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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26
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Zou Q, Yang L, Shi R, Qi Y, Zhang X, Qi H. Proteostasis regulated by testis-specific ribosomal protein RPL39L maintains mouse spermatogenesis. iScience 2021; 24:103396. [PMID: 34825148 PMCID: PMC8605100 DOI: 10.1016/j.isci.2021.103396] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 01/03/2023] Open
Abstract
Maintaining proteostasis is important for animal development. How proteostasis influences spermatogenesis that generates male gametes, spermatozoa, is not clear. We show that testis-specific paralog of ribosomal large subunit protein RPL39, RPL39L, is required for mouse spermatogenesis. Deletion of Rpl39l in mouse caused reduced proliferation of spermatogonial stem cells, malformed sperm mitochondria and flagella, leading to sub-fertility in males. Biochemical analyses revealed that lack of RPL39L deteriorated protein synthesis and protein quality control in spermatogenic cells, partly due to reduced biogenesis of ribosomal subunits and ribosome homeostasis. RPL39/RPL39L is likely assembled into ribosomes via H/ACA domain containing NOP10 complex early in ribosome biogenesis pathway. Furthermore, Rpl39l null mice exhibited compromised regenerative spermatogenesis after chemical insult and early degenerative spermatogenesis in aging mice. These data demonstrate that maintaining proteostasis is important for spermatogenesis, of which ribosome homeostasis maintained by ribosomal proteins coordinates translation machinery to the regulation of cellular growth. Rpl39l deletion causes reduced spermatogenesis and subfertility in male mice SSC proliferation, mitochondria and sperm flagella compromised in Rpl39l–/– mice Rpl39l deletion affects ribosomal LSU formation and protein quality control Aberrant proteostasis affects spermatogenesis and regeneration
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Affiliation(s)
- Qianxing Zou
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lele Yang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China
| | - Ruona Shi
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Department of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Yuling Qi
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou 510630, China
| | - Xiaofei Zhang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou 510630, China
| | - Huayu Qi
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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27
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Jansson MD, Häfner SJ, Altinel K, Tehler D, Krogh N, Jakobsen E, Andersen JV, Andersen KL, Schoof EM, Ménard P, Nielsen H, Lund AH. Regulation of translation by site-specific ribosomal RNA methylation. Nat Struct Mol Biol 2021; 28:889-899. [PMID: 34759377 DOI: 10.1038/s41594-021-00669-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/03/2021] [Indexed: 11/09/2022]
Abstract
Ribosomes are complex ribozymes that interpret genetic information by translating messenger RNA (mRNA) into proteins. Natural variation in ribosome composition has been documented in several organisms and can arise from several different sources. A key question is whether specific control over ribosome heterogeneity represents a mechanism by which translation can be regulated. We used RiboMeth-seq to demonstrate that differential 2'-O-methylation of ribosomal RNA (rRNA) represents a considerable source of ribosome heterogeneity in human cells, and that modification levels at distinct sites can change dynamically in response to upstream signaling pathways, such as MYC oncogene expression. Ablation of one prominent methylation resulted in altered translation of select mRNAs and corresponding changes in cellular phenotypes. Thus, differential rRNA 2'-O-methylation can give rise to ribosomes with specialized function. This suggests a broader mechanism where the specific regulation of rRNA modification patterns fine tunes translation.
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Affiliation(s)
- Martin D Jansson
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
| | - Sophia J Häfner
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Kübra Altinel
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Disa Tehler
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Emil Jakobsen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Jens V Andersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Kasper L Andersen
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Erwin M Schoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Patrice Ménard
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Anders H Lund
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
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28
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Georgeson J, Schwartz S. The ribosome epitranscriptome: inert-or a platform for functional plasticity? RNA (NEW YORK, N.Y.) 2021; 27:1293-1301. [PMID: 34312287 PMCID: PMC8522695 DOI: 10.1261/rna.078859.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A universal property of all rRNAs explored to date is the prevalence of post-transcriptional ("epitranscriptional") modifications, which expand the chemical and topological properties of the four standard nucleosides. Are these modifications an inert, constitutive part of the ribosome? Or could they, in part, also regulate the structure or function of the ribosome? In this review, we summarize emerging evidence that rRNA modifications are more heterogeneous than previously thought, and that they can also vary from one condition to another, such as in the context of a cellular response or a developmental trajectory. We discuss the implications of these results and key open questions on the path toward connecting such heterogeneity with function.
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Affiliation(s)
- Joseph Georgeson
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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29
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Fusco CM, Desch K, Dörrbaum AR, Wang M, Staab A, Chan ICW, Vail E, Villeri V, Langer JD, Schuman EM. Neuronal ribosomes exhibit dynamic and context-dependent exchange of ribosomal proteins. Nat Commun 2021; 12:6127. [PMID: 34675203 PMCID: PMC8531293 DOI: 10.1038/s41467-021-26365-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022] Open
Abstract
Owing to their morphological complexity and dense network connections, neurons modify their proteomes locally, using mRNAs and ribosomes present in the neuropil (tissue enriched for dendrites and axons). Although ribosome biogenesis largely takes place in the nucleus and perinuclear region, neuronal ribosomal protein (RP) mRNAs have been frequently detected remotely, in dendrites and axons. Here, using imaging and ribosome profiling, we directly detected the RP mRNAs and their translation in the neuropil. Combining brief metabolic labeling with mass spectrometry, we found that a group of RPs rapidly associated with translating ribosomes in the cytoplasm and that this incorporation was independent of canonical ribosome biogenesis. Moreover, the incorporation probability of some RPs was regulated by location (neurites vs. cell bodies) and changes in the cellular environment (following oxidative stress). Our results suggest new mechanisms for the local activation, repair and/or specialization of the translational machinery within neuronal processes, potentially allowing neuronal synapses a rapid means to regulate local protein synthesis.
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Affiliation(s)
- Claudia M. Fusco
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Kristina Desch
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Aline R. Dörrbaum
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,Present Address: MOS, Center for Mass Spectrometry and Optical Spectroscopy, Mannheim, Germany
| | - Mantian Wang
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,grid.508836.0Present Address: Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - Anja Staab
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Ivy C. W. Chan
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,grid.424247.30000 0004 0438 0426Present Address: German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Eleanor Vail
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Veronica Villeri
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,grid.412041.20000 0001 2106 639XPresent Address: Department of Neuroscience, University of Bordeaux, Bordeaux, France
| | - Julian D. Langer
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,grid.419494.50000 0001 1018 9466Max Planck Institute for Biophysics, Frankfurt, Germany
| | - Erin M. Schuman
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
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30
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Masuda K, Kasahara K, Narumi R, Shimojo M, Shimizu Y. Versatile and multiplexed mass spectrometry-based absolute quantification with cell-free-synthesized internal standard peptides. J Proteomics 2021; 251:104393. [PMID: 34678518 DOI: 10.1016/j.jprot.2021.104393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/04/2021] [Accepted: 10/04/2021] [Indexed: 10/20/2022]
Abstract
Preparation of stable isotope-labeled internal standard peptides is crucial for mass spectrometry (MS)-based targeted proteomics. Herein, we developed versatile and multiplexed absolute protein quantification method using MS. A previously developed method based on the cell-free peptide synthesis system, termed MS-based quantification by isotope-labeled cell-free products (MS-QBiC), was improved for multiple peptide synthesis in one-pot reaction. We pluralized the quantification tags used for the quantification of synthesized peptides and thus, made it possible to use cell-free synthesized isotope-labeled peptides as mixtures for the absolute quantification. The improved multiplexed MS-QBiC method was proved to be applied to clarify ribosomal proteins stoichiometry in the ribosomal subunit, one of the largest cellular complexes. The study demonstrates that the developed method enables the preparation of several dozens and even several hundreds of internal standard peptides within a few days for quantification of multiple proteins with only a single-run of MS analysis. SIGNIFICANCE: The developed method can be applied for the preparation of internal standard peptides without limiting the number of peptides to be synthesized, which may result in more practical screening of quantitatively reliable peptides, one of the fundamental steps in the reliable absolute quantification using MS. Furthermore, the method is highly versatile for proteome analysis of any organisms or species without any cDNA or SIL peptide libraries. The quantification can be finished in a few days including design and preparation of appropriate SIL peptides using small-scale batch cell-free reactions, which has a potential to be a part of the standard methodology in a field of quantitative proteomics.
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Affiliation(s)
- Keiko Masuda
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Keiko Kasahara
- Department of Surgery, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan; Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Ryohei Narumi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Masaru Shimojo
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan.
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31
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Perez JD, Fusco CM, Schuman EM. A Functional Dissection of the mRNA and Locally Synthesized Protein Population in Neuronal Dendrites and Axons. Annu Rev Genet 2021; 55:183-207. [PMID: 34460296 DOI: 10.1146/annurev-genet-030321-054851] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Neurons are characterized by a complex morphology that enables the generation of subcellular compartments with unique biochemical and biophysical properties, such as dendrites, axons, and synapses. To sustain these different compartments and carry a wide array of elaborate operations, neurons express a diverse repertoire of gene products. Extensive regulation at both the messenger RNA (mRNA) and protein levels allows for the differentiation of subcellular compartments as well as numerous forms of plasticity in response to variable stimuli. Among the multiple mechanisms that control cellular functions, mRNA translation is manipulated by neurons to regulate where and when a protein emerges. Interestingly, transcriptomic and translatomic profiles of both dendrites and axons have revealed that the mRNA population only partially predicts the local protein population and that this relation significantly varies between different gene groups. Here, we describe the space that local translation occupies within the large molecular and regulatory complexity of neurons, in contrast to other modes of regulation. We then discuss the specialized organization of mRNAs within different neuronal compartments, as revealed by profiles of the local transcriptome. Finally, we discuss the features and functional implications of both locally correlated-and anticorrelated-mRNA-protein relations both under baseline conditions and during synaptic plasticity. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Julio D Perez
- Max Planck Institute for Brain Research, 60438 Frankfurt, Germany;
| | - Claudia M Fusco
- Max Planck Institute for Brain Research, 60438 Frankfurt, Germany;
| | - Erin M Schuman
- Max Planck Institute for Brain Research, 60438 Frankfurt, Germany;
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32
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Gay DM, Lund AH, Jansson MD. Translational control through ribosome heterogeneity and functional specialization. Trends Biochem Sci 2021; 47:66-81. [PMID: 34312084 DOI: 10.1016/j.tibs.2021.07.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/18/2021] [Accepted: 07/01/2021] [Indexed: 12/31/2022]
Abstract
The conceptual origins of ribosome specialization can be traced back to the earliest days of molecular biology. Yet, this field has only recently begun to gather momentum, with numerous studies identifying distinct heterogeneous ribosome populations across multiple species and model systems. It is proposed that some of these compositionally distinct ribosomes may be functionally specialized and able to regulate the translation of specific mRNAs. Identification and functional characterization of specialized ribosomes has the potential to elucidate a novel layer of gene expression control, at the level of translation, where the ribosome itself is a key regulatory player. In this review, we discuss different sources of ribosome heterogeneity, evidence for ribosome specialization, and also the future directions of this exciting field.
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Affiliation(s)
- David M Gay
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anders H Lund
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Martin D Jansson
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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33
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Wei HH, Fan XJ, Hu Y, Tian XX, Guo M, Mao MW, Fang ZY, Wu P, Gao SX, Peng C, Yang Y, Wang Z. A systematic survey of PRMT interactomes reveals the key roles of arginine methylation in the global control of RNA splicing and translation. Sci Bull (Beijing) 2021; 66:1342-1357. [PMID: 36654156 DOI: 10.1016/j.scib.2021.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/13/2020] [Accepted: 12/30/2020] [Indexed: 01/20/2023]
Abstract
Thousands of proteins undergo arginine methylation, a widespread post-translational modification catalyzed by several protein arginine methyltransferases (PRMTs). However, global understanding of their biological functions is limited due to the lack of a complete picture of the catalytic network for each PRMT. Here, we systematically identified interacting proteins for all human PRMTs and demonstrated their functional importance in mRNA splicing and translation. We demonstrated significant overlapping of interactomes of human PRMTs with the known methylarginine-containing proteins. Different PRMTs are functionally redundant with a high degree of overlap in their substrates and high similarities between their putative methylation motifs. Importantly, RNA-binding proteins involved in regulating RNA splicing and translation contain highly enriched arginine methylation regions. Moreover, inhibition of PRMTs globally alternates alternative splicing (AS) and suppresses translation. In particular, ribosomal proteins are extensively modified with methylarginine, and mutations in their methylation sites suppress ribosome assembly, translation, and eventually cell growth. Collectively, our study provides a global view of different PRMT networks and uncovers critical functions of arginine methylation in regulating mRNA splicing and translation.
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Affiliation(s)
- Huan-Huan Wei
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Xiao-Juan Fan
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yue Hu
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiao-Xu Tian
- National Facility for Protein Science in Shanghai, Zhang-Jiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Meng Guo
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710000, China
| | - Miao-Wei Mao
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhao-Yuan Fang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ping Wu
- National Facility for Protein Science in Shanghai, Zhang-Jiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Shuai-Xin Gao
- National Facility for Protein Science in Shanghai, Zhang-Jiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhang-Jiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yun Yang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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34
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Mitochondrial Regulation of the 26S Proteasome. Cell Rep 2021; 32:108059. [PMID: 32846138 DOI: 10.1016/j.celrep.2020.108059] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/18/2020] [Accepted: 07/31/2020] [Indexed: 12/26/2022] Open
Abstract
The proteasome is the main proteolytic system for targeted protein degradation in the cell and is fine-tuned according to cellular needs. Here, we demonstrate that mitochondrial dysfunction and concomitant metabolic reprogramming of the tricarboxylic acid (TCA) cycle reduce the assembly and activity of the 26S proteasome. Both mitochondrial mutations in respiratory complex I and treatment with the anti-diabetic drug metformin impair 26S proteasome activity. Defective 26S assembly is reversible and can be overcome by supplementation of aspartate or pyruvate. This metabolic regulation of 26S activity involves specific regulation of proteasome assembly factors via the mTORC1 pathway. Of note, reducing 26S activity by metformin confers increased resistance toward the proteasome inhibitor bortezomib, which is reversible upon pyruvate supplementation. Our study uncovers unexpected consequences of defective mitochondrial metabolism for proteasomal protein degradation in the cell, which has important pathophysiological and therapeutic implications.
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35
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Lashkevich KA, Dmitriev SE. mRNA Targeting, Transport and Local Translation in Eukaryotic Cells: From the Classical View to a Diversity of New Concepts. Mol Biol 2021; 55:507-537. [PMID: 34092811 PMCID: PMC8164833 DOI: 10.1134/s0026893321030080] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 02/26/2021] [Accepted: 03/12/2021] [Indexed: 12/28/2022]
Abstract
Spatial organization of protein biosynthesis in the eukaryotic cell has been studied for more than fifty years, thus many facts have already been included in textbooks. According to the classical view, mRNA transcripts encoding secreted and transmembrane proteins are translated by ribosomes associated with endoplasmic reticulum membranes, while soluble cytoplasmic proteins are synthesized on free polysomes. However, in the last few years, new data has emerged, revealing selective translation of mRNA on mitochondria and plastids, in proximity to peroxisomes and endosomes, in various granules and at the cytoskeleton (actin network, vimentin intermediate filaments, microtubules and centrosomes). There are also long-standing debates about the possibility of protein synthesis in the nucleus. Localized translation can be determined by targeting signals in the synthesized protein, nucleotide sequences in the mRNA itself, or both. With RNA-binding proteins, many transcripts can be assembled into specific RNA condensates and form RNP particles, which may be transported by molecular motors to the sites of active translation, form granules and provoke liquid-liquid phase separation in the cytoplasm, both under normal conditions and during cell stress. The translation of some mRNAs occurs in specialized "translation factories," assemblysomes, transperons and other structures necessary for the correct folding of proteins, interaction with functional partners and formation of oligomeric complexes. Intracellular localization of mRNA has a significant impact on the efficiency of its translation and presumably determines its response to cellular stress. Compartmentalization of mRNAs and the translation machinery also plays an important role in viral infections. Many viruses provoke the formation of specific intracellular structures, virus factories, for the production of their proteins. Here we review the current concepts of the molecular mechanisms of transport, selective localization and local translation of cellular and viral mRNAs, their effects on protein targeting and topogenesis, and on the regulation of protein biosynthesis in different compartments of the eukaryotic cell. Special attention is paid to new systems biology approaches, providing new cues to the study of localized translation.
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Affiliation(s)
- Kseniya A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119234 Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Moscow State University, 119234 Moscow, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119234 Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Moscow State University, 119234 Moscow, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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36
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Slc1a3-2A-CreERT2 mice reveal unique features of Bergmann glia and augment a growing collection of Cre drivers and effectors in the 129S4 genetic background. Sci Rep 2021; 11:5412. [PMID: 33686166 PMCID: PMC7940647 DOI: 10.1038/s41598-021-84887-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 02/22/2021] [Indexed: 12/26/2022] Open
Abstract
Genetic variation is a primary determinant of phenotypic diversity. In laboratory mice, genetic variation can be a serious experimental confounder, and thus minimized through inbreeding. However, generalizations of results obtained with inbred strains must be made with caution, especially when working with complex phenotypes and disease models. Here we compared behavioral characteristics of C57Bl/6—the strain most widely used in biomedical research—with those of 129S4. In contrast to 129S4, C57Bl/6 demonstrated high within-strain and intra-litter behavioral hyperactivity. Although high consistency would be advantageous, the majority of disease models and transgenic tools are in C57Bl/6. We recently established six Cre driver lines and two Cre effector lines in 129S4. To augment this collection, we genetically engineered a Cre line to study astrocytes in 129S4. It was validated with two Cre effector lines: calcium indicator gCaMP5g-tdTomato and RiboTag—a tool widely used to study cell type-specific translatomes. These reporters are in different genomic loci, and in both the Cre was functional and astrocyte-specific. We found that calcium signals lasted longer and had a higher amplitude in cortical compared to hippocampal astrocytes, genes linked to a single neurodegenerative disease have highly divergent expression patterns, and that ribosome proteins are non-uniformly expressed across brain regions and cell types.
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37
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Xu Y, Li X, Liang W, Liu M. Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in the Phytopathogenic Fungus Botrytis cinerea. Front Microbiol 2020; 11:585614. [PMID: 33329453 PMCID: PMC7728723 DOI: 10.3389/fmicb.2020.585614] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/09/2020] [Indexed: 12/21/2022] Open
Abstract
Posttranslational modifications (PTMs) of the whole proteome have become a hot topic in the research field of epigenetics, and an increasing number of PTM types have been identified and shown to play significant roles in different cellular processes. Protein lysine 2-hydroxyisobutyrylation (Khib) is a newly detected PTM, and the 2-hydroxyisobutyrylome has been identified in several species. Botrytis cinerea is recognized as one of the most destructive pathogens due to its broad host distribution and very large economic losses; thus the many aspects of its pathogenesis have been continuously studied. However, distribution and function of Khib in this phytopathogenic fungus are not clear. In this study, a proteome-wide analysis of Khib in B. cinerea was performed, and 5,398 Khib sites on 1,181 proteins were identified. Bioinformatics analysis showed that the 2-hydroxyisobutyrylome in B. cinerea contains both conserved proteins and novel proteins when compared with Khib proteins in other species. Functional classification, functional enrichment and protein interaction network analyses showed that Khib proteins are widely distributed in cellular compartments and involved in diverse cellular processes. Significantly, 37 proteins involved in different aspects of regulating the pathogenicity of B. cinerea were detected as Khib proteins. Our results provide a comprehensive view of the 2-hydroxyisobutyrylome and lay a foundation for further studying the regulatory mechanism of Khib in both B. cinerea and other plant pathogens.
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Affiliation(s)
- Yang Xu
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Xiaoxia Li
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Wenxing Liang
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Mengjie Liu
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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38
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Dong HJ, Zhang R, Kuang Y, Wang XJ. Selective regulation in ribosome biogenesis and protein production for efficient viral translation. Arch Microbiol 2020; 203:1021-1032. [PMID: 33124672 PMCID: PMC7594972 DOI: 10.1007/s00203-020-02094-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/18/2020] [Accepted: 10/13/2020] [Indexed: 11/25/2022]
Abstract
As intracellular parasites, viruses depend heavily on host cell structures and their functions to complete their life cycle and produce new viral particles. Viruses utilize or modulate cellular translational machinery to achieve efficient replication; the role of ribosome biogenesis and protein synthesis in viral replication particularly highlights the importance of the ribosome quantity and/or quality in controlling viral protein synthesis. Recently reported studies have demonstrated that ribosome biogenesis factors (RBFs) and ribosomal proteins (RPs) act as multifaceted regulators in selective translation of viral transcripts. Here we summarize the recent literature on RBFs and RPs and their association with subcellular redistribution, post-translational modification, enzyme catalysis, and direct interaction with viral proteins. The advances described in this literature establish a rationale for targeting ribosome production and function in the design of the next generation of antiviral agents.
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Affiliation(s)
- Hui-Jun Dong
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Rui Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
| | - Yu Kuang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
| | - Xiao-Jia Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
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39
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Skariah G, Todd PK. Translational control in aging and neurodegeneration. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1628. [PMID: 32954679 DOI: 10.1002/wrna.1628] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/19/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]
Abstract
Protein metabolism plays central roles in age-related decline and neurodegeneration. While a large body of research has explored age-related changes in protein degradation, alterations in the efficiency and fidelity of protein synthesis with aging are less well understood. Age-associated changes occur in both the protein synthetic machinery (ribosomal proteins and rRNA) and within regulatory factors controlling translation. At the same time, many of the interventions that prolong lifespan do so in part by pre-emptively decreasing protein synthesis rates to allow better harmonization to age-related declines in protein catabolism. Here we review the roles of translation regulation in aging, with a specific focus on factors implicated in age-related neurodegeneration. We discuss how emerging technologies such as ribosome profiling and superior mass spectrometric approaches are illuminating age-dependent mRNA-specific changes in translation rates across tissues to reveal a critical interplay between catabolic and anabolic pathways that likely contribute to functional decline. These new findings point to nodes in posttranscriptional gene regulation that both contribute to aging and offer targets for therapy. This article is categorized under: Translation > Translation Regulation Translation > Ribosome Biogenesis Translation > Translation Mechanisms.
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Affiliation(s)
- Geena Skariah
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
- Ann Arbor VA Healthcare System, Department of Veterans Affairs, Ann Arbor, Michigan, USA
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40
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Schneider K, Venn B, Mühlhaus T. TMEA: A Thermodynamically Motivated Framework for Functional Characterization of Biological Responses to System Acclimation. ENTROPY 2020; 22:e22091030. [PMID: 33286800 PMCID: PMC7597090 DOI: 10.3390/e22091030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/07/2020] [Accepted: 09/11/2020] [Indexed: 12/16/2022]
Abstract
The objective of gene set enrichment analysis (GSEA) in modern biological studies is to identify functional profiles in huge sets of biomolecules generated by high-throughput measurements of genes, transcripts, metabolites, and proteins. GSEA is based on a two-stage process using classical statistical analysis to score the input data and subsequent testing for overrepresentation of the enrichment score within a given functional coherent set. However, enrichment scores computed by different methods are merely statistically motivated and often elusive to direct biological interpretation. Here, we propose a novel approach, called Thermodynamically Motivated Enrichment Analysis (TMEA), to account for the energy investment in biological relevant processes. Therefore, TMEA is based on surprisal analysis, which offers a thermodynamic-free energy-based representation of the biological steady state and of the biological change. The contribution of each biomolecule underlying the changes in free energy is used in a Monte Carlo resampling procedure resulting in a functional characterization directly coupled to the thermodynamic characterization of biological responses to system perturbations. To illustrate the utility of our method on real experimental data, we benchmark our approach on plant acclimation to high light and compare the performance of TMEA with the most frequently used method for GSEA.
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41
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Petelski AA, Slavov N. Analyzing Ribosome Remodeling in Health and Disease. Proteomics 2020; 20:e2000039. [PMID: 32820594 PMCID: PMC7501214 DOI: 10.1002/pmic.202000039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/01/2020] [Indexed: 12/24/2022]
Abstract
Increasing evidence suggests that ribosomes actively regulate protein synthesis. However, much of this evidence is indirect, leaving this layer of gene regulation largely unexplored, in part due to methodological limitations. Indeed, evidence is reviewed demonstrating that commonly used methods, such as transcriptomics, are inadequate because the variability in mRNAs coding for ribosomal proteins (RP) does not necessarily correspond to RP variability. Thus protein remodeling of ribosomes should be investigated by methods that allow direct quantification of RPs, ideally of isolated ribosomes. Such methods are reviewed, focusing on mass spectrometry and emphasizing method-specific biases and approaches to control these biases. It is argued that using multiple complementary methods can help reduce the danger of interpreting reproducible systematic biases as evidence for ribosome remodeling.
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Affiliation(s)
- Aleksandra A Petelski
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
- Barnett Institute, Northeastern University, Boston, MA, 02115, USA
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
- Barnett Institute, Northeastern University, Boston, MA, 02115, USA
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
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42
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Buoso E, Masi M, Long A, Chiappini C, Travelli C, Govoni S, Racchi M. Ribosomes as a nexus between translation and cancer progression: Focus on ribosomal Receptor for Activated C Kinase 1 (RACK1) in breast cancer. Br J Pharmacol 2020; 179:2813-2828. [PMID: 32726469 DOI: 10.1111/bph.15218] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/30/2020] [Accepted: 07/16/2020] [Indexed: 12/19/2022] Open
Abstract
Ribosomes coordinate spatiotemporal control of gene expression, contributing to the acquisition and maintenance of cancer phenotype. The link between ribosomes and cancer is found in the roles of individual ribosomal proteins in tumorigenesis and cancer progression, including the ribosomal protein, receptor for activated C kinase 1 (RACK1). RACK1 regulates cancer cell invasion and is localized in spreading initiation centres, structural adhesion complexes containing RNA binding proteins and poly-adenylated mRNAs that suggest a local translation process. As RACK1 is a ribosomal protein directly involved in translation and in breast cancer progression, we propose a new molecular mechanism for breast cancer cell migration and invasion, which considers the molecular differences between epithelial and mesenchymal cell profiles in order to characterize and provide novel targets for therapeutic strategies. Hence, we provide an analysis on how ribosomes translate cancer progression with a final focus on the ribosomal protein RACK1 in breast cancer.
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Affiliation(s)
- Erica Buoso
- Department of Drug Sciences, University of Pavia, Pavia, Italy
| | - Mirco Masi
- Department of Drug Sciences, University of Pavia, Pavia, Italy.,Scuola Universitaria Superiore IUSS Pavia, Pavia, Italy
| | - Aideen Long
- Department of Clinical Medicine, Institute of Molecular Medicine, Trinity College, Dublin, Ireland
| | | | | | - Stefano Govoni
- Department of Drug Sciences, University of Pavia, Pavia, Italy
| | - Marco Racchi
- Department of Drug Sciences, University of Pavia, Pavia, Italy
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43
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Abstract
Many organisms, including bacteria, code for multiple paralogues of some ribosomal protein subunits. The relative contribution of these alternative subunits to ribosome function and protein synthesis is unknown and controversial. Many studies on alternative ribosomes have been confounded by isolation of alternative and canonical ribosomes from different strains or growth conditions, potentially confounding results. Here, we show that one form of alternative ribosome from Mycobacterium smegmatis has a distinct translational profile compared with canonical ribosomes purified from an identical cellular context. We also identify a role for alternative ribosomes in iron homeostasis. Given the prevalence of alternative ribosomal genes in diverse organisms, our study suggests that alternative ribosomes may represent a further layer of regulation of gene translation. Alternative ribosome subunit proteins are prevalent in the genomes of diverse bacterial species, but their functional significance is controversial. Attempts to study microbial ribosomal heterogeneity have mostly relied on comparing wild-type strains with mutants in which subunits have been deleted, but this approach does not allow direct comparison of alternate ribosome isoforms isolated from identical cellular contexts. Here, by simultaneously purifying canonical and alternative RpsR ribosomes from Mycobacterium smegmatis, we show that alternative ribosomes have distinct translational features compared with their canonical counterparts. Both alternative and canonical ribosomes actively take part in protein synthesis, although they translate a subset of genes with differential efficiency as measured by ribosome profiling. We also show that alternative ribosomes have a relative defect in initiation complex formation. Furthermore, a strain of M. smegmatis in which the alternative ribosome protein operon is deleted grows poorly in iron-depleted medium, uncovering a role for alternative ribosomes in iron homeostasis. Our work confirms the distinct and nonredundant contribution of alternative bacterial ribosomes for adaptation to hostile environments.
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44
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Buccitelli C, Selbach M. mRNAs, proteins and the emerging principles of gene expression control. Nat Rev Genet 2020; 21:630-644. [PMID: 32709985 DOI: 10.1038/s41576-020-0258-4] [Citation(s) in RCA: 488] [Impact Index Per Article: 122.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2020] [Indexed: 12/15/2022]
Abstract
Gene expression involves transcription, translation and the turnover of mRNAs and proteins. The degree to which protein abundances scale with mRNA levels and the implications in cases where this dependency breaks down remain an intensely debated topic. Here we review recent mRNA-protein correlation studies in the light of the quantitative parameters of the gene expression pathway, contextual confounders and buffering mechanisms. Although protein and mRNA levels typically show reasonable correlation, we describe how transcriptomics and proteomics provide useful non-redundant readouts. Integrating both types of data can reveal exciting biology and is an essential step in refining our understanding of the principles of gene expression control.
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Affiliation(s)
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany. .,Charité - Universitätsmedizin Berlin, Berlin, Germany.
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45
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Lilleorg S, Reier K, Volõnkin P, Remme J, Liiv A. Phenotypic effects of paralogous ribosomal proteins bL31A and bL31B in E. coli. Sci Rep 2020; 10:11682. [PMID: 32669635 PMCID: PMC7363858 DOI: 10.1038/s41598-020-68582-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 06/24/2020] [Indexed: 02/07/2023] Open
Abstract
Ribosomes are essential macromolecular complexes conducting protein biosynthesis in all domains of life. Cells can have heterogeneous ribosomes, i.e. ribosomes with various ribosomal RNA and ribosomal protein (r-protein) composition. However, the functional importance of heterogeneous ribosomes has remained elusive. One of the possible sources for ribosome heterogeneity is provided by paralogous r-proteins. In E. coli, ribosomal protein bL31 has two paralogs: bL31A encoded by rpmE and bL31B encoded by ykgM. This study investigates phenotypic effects of these ribosomal protein paralogs using bacterial strains expressing only bL31A or bL31B. We show that bL31A confers higher fitness to E. coli under lower temperatures. In addition, bL31A and bL31B have different effects on translation reading frame maintenance and apparent translation processivity in vivo as demonstrated by dual luciferase assay. In general, this study demonstrates that ribosomal protein paralog composition (bL31A versus bL31B) can affect cell growth and translation outcome.
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Affiliation(s)
- Silva Lilleorg
- Institute of Molecular and Cell Biology, University of Tartu, Riia street 23B, 51010, Tartu, Estonia
| | - Kaspar Reier
- Institute of Molecular and Cell Biology, University of Tartu, Riia street 23B, 51010, Tartu, Estonia
| | - Pavel Volõnkin
- Institute of Molecular and Cell Biology, University of Tartu, Riia street 23B, 51010, Tartu, Estonia
| | - Jaanus Remme
- Institute of Molecular and Cell Biology, University of Tartu, Riia street 23B, 51010, Tartu, Estonia
| | - Aivar Liiv
- Institute of Molecular and Cell Biology, University of Tartu, Riia street 23B, 51010, Tartu, Estonia.
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46
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Zhu X, Zhang W, Guo J, Zhang X, Li L, Wang T, Yan J, Zhang F, Hou B, Gao N, Gao GF, Zhou X. Noc4L-Mediated Ribosome Biogenesis Controls Activation of Regulatory and Conventional T Cells. Cell Rep 2020; 27:1205-1220.e4. [PMID: 31018134 DOI: 10.1016/j.celrep.2019.03.083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 02/12/2019] [Accepted: 03/22/2019] [Indexed: 12/21/2022] Open
Abstract
Regulatory T cell (Treg) activation is crucial for maintaining self-tolerance, but the translational regulation of this process is still poorly understood. Although ribosome biogenesis is considered a housekeeping process, emerging evidence supports the hypothesis that ribosome biogenesis can selectively regulate protein synthesis by tuning translation. Here, we focused on the ribosome biogenesis factor Noc4L, based on the observations that Noc4L is highly expressed in activated Tregs. Conditional Noc4L knockout in Tregs resulted in a lethal autoimmune phenotype resembling Treg-deficient scurfy mice. Interestingly, the Noc4L defect did not globally affect overall protein translation in Tregs but was selectively detrimental to the expression of mRNAs related to Treg activation. These results demonstrate the critical role of Noc4L-mediated ribosome biogenesis in controlling the activation of Tregs and maintaining immune tolerance.
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Affiliation(s)
- Xueping Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Jie Guo
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Xuejie Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liping Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinghua Yan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Fuping Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baidong Hou
- University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Ning Gao
- School of Life Sciences, Peking University, Beijing 100871, China
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.
| | - Xuyu Zhou
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.
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47
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Yu R, Campbell K, Pereira R, Björkeroth J, Qi Q, Vorontsov E, Sihlbom C, Nielsen J. Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast. Nat Commun 2020; 11:1881. [PMID: 32312967 PMCID: PMC7171132 DOI: 10.1038/s41467-020-15749-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 03/25/2020] [Indexed: 12/22/2022] Open
Abstract
Cells maintain reserves in their metabolic and translational capacities as a strategy to quickly respond to changing environments. Here we quantify these reserves by stepwise reducing nitrogen availability in yeast steady-state chemostat cultures, imposing severe restrictions on total cellular protein and transcript content. Combining multi-omics analysis with metabolic modeling, we find that seven metabolic superpathways maintain >50% metabolic capacity in reserve, with glucose metabolism maintaining >80% reserve capacity. Cells maintain >50% reserve in translational capacity for 2490 out of 3361 expressed genes (74%), with a disproportionately large reserve dedicated to translating metabolic proteins. Finally, ribosome reserves contain up to 30% sub-stoichiometric ribosomal proteins, with activation of reserve translational capacity associated with selective upregulation of 17 ribosomal proteins. Together, our dataset provides a quantitative link between yeast physiology and cellular economics, which could be leveraged in future cell engineering through targeted proteome streamlining. Cells maintain reserves in their metabolic and translational capacities enabling fast response to changing environments. Here, the authors quantify reserves in yeast by stepwise reduction in nitrogen availability and a combination of multi-omic analysis and metabolic modelling.
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Affiliation(s)
- Rosemary Yu
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Kate Campbell
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Rui Pereira
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Johan Björkeroth
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Qi Qi
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Egor Vorontsov
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, SE-413 90, Gothenburg, Sweden
| | - Carina Sihlbom
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, SE-413 90, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark. .,BioInnovation Institute, Ole Måløes Vej 3, DK-2200, Copenhagen N, Denmark.
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48
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Wang X, Meul T, Meiners S. Exploring the proteasome system: A novel concept of proteasome inhibition and regulation. Pharmacol Ther 2020; 211:107526. [PMID: 32173559 DOI: 10.1016/j.pharmthera.2020.107526] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/08/2020] [Indexed: 12/13/2022]
Abstract
The proteasome is a well-identified therapeutic target for cancer treatment. It acts as the main protein degradation system in the cell and degrades key mediators of cell growth, survival and function. The term "proteasome" embraces a whole family of distinct complexes, which share a common proteolytic core, the 20S proteasome, but differ by their attached proteasome activators. Each of these proteasome complexes plays specific roles in the control of cellular function. In addition, distinct proteasome interacting proteins regulate proteasome activity in subcellular compartments and in response to cellular signals. Proteasome activators and regulators may thus serve as building blocks to fine-tune proteasome function in the cell according to cellular needs. Inhibitors of the proteasome, e.g. the FDA approved drugs Velcade™, Kyprolis™, Ninlaro™, inactivate the catalytic 20S core and effectively block protein degradation of all proteasome complexes in the cell resulting in inhibition of cell growth and induction of apoptosis. Efficacy of these inhibitors, however, is hampered by their pronounced cytotoxic side-effects as well as by the emerging development of resistance to catalytic proteasome inhibitors. Targeted inhibition of distinct buiding blocks of the proteasome system, i.e. proteasome activators or regulators, represents an alternative strategy to overcome these limitations. In this review, we stress the importance of the diversity of the proteasome complexes constituting an entire proteasome system. Our building block concept provides a rationale for the defined targeting of distinct proteasome super-complexes in disease. We thereby aim to stimulate the development of innovative therapeutic approaches beyond broad catalytic proteasome inhibition.
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Affiliation(s)
- Xinyuan Wang
- Comprehensive Pneumology Center (CPC), University Hospital of the Ludwig-Maximilians-University (LMU) and Helmholtz Zentrum München, German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Thomas Meul
- Comprehensive Pneumology Center (CPC), University Hospital of the Ludwig-Maximilians-University (LMU) and Helmholtz Zentrum München, German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Silke Meiners
- Comprehensive Pneumology Center (CPC), University Hospital of the Ludwig-Maximilians-University (LMU) and Helmholtz Zentrum München, German Center for Lung Research (DZL), 81377 Munich, Germany.
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49
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Taggart JC, Zauber H, Selbach M, Li GW, McShane E. Keeping the Proportions of Protein Complex Components in Check. Cell Syst 2020; 10:125-132. [PMID: 32105631 PMCID: PMC7195860 DOI: 10.1016/j.cels.2020.01.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/17/2020] [Accepted: 01/29/2020] [Indexed: 02/07/2023]
Abstract
How do cells maintain relative proportions of protein complex components? Advances in quantitative, genome-wide measurements have begun to shed light onto the roles of protein synthesis and degradation in establishing the precise proportions in living cells: on the one hand, ribosome profiling studies indicate that proteins are already produced in the correct relative proportions. On the other hand, proteomic studies found that many complexes contain subunits that are made in excess and subsequently degraded. Here, we discuss these seemingly contradictory findings, emerging principles, and remaining open questions. We conclude that establishing precise protein levels involves both coordinated synthesis and post-translational fine-tuning via protein degradation.
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Affiliation(s)
| | - Henrik Zauber
- Proteome dynamics, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Matthias Selbach
- Proteome dynamics, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany.
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Erik McShane
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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50
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Ford D. Ribosomal heterogeneity - A new inroad for pharmacological innovation. Biochem Pharmacol 2020; 175:113874. [PMID: 32105657 DOI: 10.1016/j.bcp.2020.113874] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 02/20/2020] [Indexed: 12/13/2022]
Abstract
The paradigm of ribosome usage in protein translation has shifted from a stance proposed as scientists began to unpick the genetic code that each mRNA was partnered by its own, unique ribosome to a rapid reversal of this view that ribosomes are completely interchangeable and simply recruited to mRNAs from a completely homogenous cellular pool. Evidence that the ribosomal proteome, ribosomal gene transcriptome and ribosome protein and RNA modifications differ between cells and tissues points to the fact that ribosomes are heterogeneous in their composition and have a degree of specialisation in their function. It has also been posited that the tissue-specificity of ribosome diseases provides an indication of functional ribosome heterogeneity, but there are substantial caveats to this interpretation. Only now have proteomic technologies developed to a level enabling accurate stoichiometric comparison of the abundance of specific ribosomal proteins in actively translating ribosomes and to measure protein in non-denatured ribosomes. This poises the field for the provocation that ribosome heterogeneity offers a novel and powerful inroad for the pharmacological targeting of disease. Such ribosome-targeted treatments may extend beyond specific ribosomopathies through strategies such as targeting features of ribosomes that are unique to diseased cells, particularly cancer cells, or to activated immune cells, as well as augmenting the action of other drugs through weakening the production of new proteins in target tissues. We may also be able to harness the potential power in ribosome diversity and specialism to better tune synthetic biology for the production of pharmaceutical proteins.
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Affiliation(s)
- Dianne Ford
- Northumbria University, Northumberland Building, Northumberland Road, Newcastle upon Tyne, NE1 8ST, United Kingdom.
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