1
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Hong ZH, Zhu L, Gao LL, Zhu Z, Su T, Krall L, Wu XN, Bock R, Wu GZ. Chloroplast precursor protein preClpD overaccumulation triggers multilevel reprogramming of gene expression and a heat shock-like response. Nat Commun 2025; 16:3777. [PMID: 40263324 PMCID: PMC12015282 DOI: 10.1038/s41467-025-59043-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 04/07/2025] [Indexed: 04/24/2025] Open
Abstract
Thousands of nucleus-encoded chloroplast proteins are synthesized as precursors on cytosolic ribosomes and posttranslationally imported into chloroplasts. Cytosolic accumulation of unfolded chloroplast precursor proteins (e.g., under stress conditions) is hazardous to the cell. The global cellular responses and regulatory pathways involved in triggering appropriate responses are largely unknown. Here, by inducible and constitutive overexpression of ClpD-GFP to result in precursor protein overaccumulation, we present a comprehensive picture of multilevel reprogramming of gene expression in response to chloroplast precursor overaccumulation stress (cPOS), reveal a critical role of translational activation in the expression of cytosolic chaperones (heat-shock proteins, HSPs), and demonstrate that chloroplast-derived reactive oxygen species act as retrograde signal for the transcriptional activation of small HSPs. Furthermore, we reveal an important role of the chaperone ClpB1/HOT1 in maintaining cellular proteostasis upon cPOS. Together, our observations uncover a cytosolic heat shock-like response to cPOS and provide insights into the underlying molecular mechanisms.
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Affiliation(s)
- Zheng-Hui Hong
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Liyu Zhu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Lin-Lin Gao
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhe Zhu
- School of Life Sciences, Yunnan University, Kunming, Yunnan Province, China
| | - Tong Su
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Leonard Krall
- School of Life Sciences, Yunnan University, Kunming, Yunnan Province, China
| | - Xu-Na Wu
- School of Life Sciences, Yunnan University, Kunming, Yunnan Province, China
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Guo-Zhang Wu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
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2
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Parres-Gold J, Levine M, Emert B, Stuart A, Elowitz MB. Contextual computation by competitive protein dimerization networks. Cell 2025; 188:1984-2002.e17. [PMID: 39978343 PMCID: PMC11973712 DOI: 10.1016/j.cell.2025.01.036] [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: 12/16/2023] [Revised: 12/03/2024] [Accepted: 01/27/2025] [Indexed: 02/22/2025]
Abstract
Many biological signaling pathways employ proteins that competitively dimerize in diverse combinations. These dimerization networks can perform biochemical computations in which the concentrations of monomer inputs determine the concentrations of dimer outputs. Despite their prevalence, little is known about the range of input-output computations that dimerization networks can perform and how it depends on network size and connectivity. Using a systematic computational approach, we demonstrate that even small dimerization networks of 3-6 monomers are expressive, performing diverse multi-input computations. Further, dimerization networks are versatile, performing different computations when their protein components are expressed at different levels, such as in different cell types. Remarkably, individual networks with random interaction affinities, when large enough, can perform nearly all potential one-input network computations merely by tuning their monomer expression levels. Thus, even the simple process of competitive dimerization provides a powerful architecture for multi-input, cell-type-specific signal processing.
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Affiliation(s)
- Jacob Parres-Gold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Matthew Levine
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Benjamin Emert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Andrew Stuart
- Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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3
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Wang JY, Wang Q, Peng YX, Jiang LG, Lu ZZ, Zheng LM, Li XH, Liu J, Long JC, Liu JH, He Y. ZmSSRP1 facilitates the progression of RNA polymerase II and is essential for kernel development in maize. THE PLANT CELL 2025; 37:koaf071. [PMID: 40166832 PMCID: PMC11983281 DOI: 10.1093/plcell/koaf071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Accepted: 03/02/2025] [Indexed: 04/02/2025]
Abstract
Transcript elongation controlled by RNA polymerase II (RNAP II) represents a key regulatory event in numerous cellular processes. However, the precise mechanisms underlying the regulation of RNAP II distribution and progression in plants remain largely elusive. Here, we positionally cloned the causal mutation in the defective kernel 59 (dek59) maize (Zea mays) mutant and demonstrated that Dek59 encodes Structure-Specific Recognition Protein 1 (ZmSSRP1), a subunit of the FAcilitates Chromatin Transcription (FACT) complex that regulates RNAP II. Using genome-wide mapping assays, we determined that ZmSSRP1-binding sites co-localize with those of RNAP II phosphorylated at its serine 2 residue (Ser2P) and are highly enriched within actively transcribed genes. Mutation of ZmSSRP1 resulted in Ser2P accumulation around the +1 nucleosome of genes, affecting gene expression in a gene length-dependent manner. The reduced amount of RNAP II in the dek59 mutant was rescued to wild-type-like levels by inhibiting the proteasome, indicating that arrested RNAP II degradation is proteasome-dependent. These findings reveal the indispensable role of ZmSSRP1 in regulating RNAP II-mediated transcription, which is critical for the proper expression of thousands of genes during maize seed development.
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Affiliation(s)
- Jin-Yu Wang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Wang
- State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Ye-Xiang Peng
- State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Lu-Guang Jiang
- State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Zi-Zheng Lu
- State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Lei-Ming Zheng
- State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Xiao-Han Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Juan Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jin-Cheng Long
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jing-Han Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan He
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
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4
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Fakih Z, Germain H. Implication of ribosomal protein in abiotic and biotic stress. PLANTA 2025; 261:85. [PMID: 40067484 DOI: 10.1007/s00425-025-04665-6] [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: 07/25/2024] [Accepted: 03/03/2025] [Indexed: 03/29/2025]
Abstract
MAIN CONCLUSION This review article explores the intricate role, and regulation of ribosomal protein in response to stress, particularly emphasizing their pivotal role to ameliorate abiotic and biotic stress conditions in crop plants. Plants must coordinate ribosomes production to balance cellular protein synthesis in response to environmental variations and pathogens invasion. Over the past decade, research has revealed ribosome subgroups respond to adverse conditions, suggesting that this tight coordination may be grounded in the induction of ribosome variants resulting in differential translation outcomes. Furthermore, an increasing snumber of studies on plant ribosomes have made it possible to explore the stress-regulated expression pattern of ribosomal protein large subunit (RPL) and ribosomal protein small subunit (RPS) genes. In this perspective, we reviewed the literature linking ribosome heterogeneity to plants' abiotic and biotic stress responses to offer an overview on the expression and biological function of ribosomal components including specialized translation of individual transcripts and its implications for the regulation and expression of important gene regulatory networks, along with phenotypic analysis in ribosomal gene mutations in physiologic and pathologic processes. We also highlight recent advances in understanding the molecular mechanisms behind the transcriptional regulation of ribosomal genes linked to stress events. This review may serve as the foundation of novel strategies to customize cultivars tolerant to challenging environments without the yield penalty.
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Affiliation(s)
- Zainab Fakih
- Department of Chemistry, Biochemistry and Physics and Groupe de Recherche en Biologie Végétale, Université du Québec À Trois-Rivières, Trois-Rivières, Québec, G9A 5H9, Canada
| | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics and Groupe de Recherche en Biologie Végétale, Université du Québec À Trois-Rivières, Trois-Rivières, Québec, G9A 5H9, Canada.
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5
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Mou R, Niu R, Yang R, Xu G. Engineering crop performance with upstream open reading frames. TRENDS IN PLANT SCIENCE 2025; 30:311-323. [PMID: 39472218 DOI: 10.1016/j.tplants.2024.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Revised: 10/07/2024] [Accepted: 10/10/2024] [Indexed: 03/08/2025]
Abstract
Plants intricately regulate the expression of protein-coding genes at multiple stages - including mRNA transcription, translation, decay, and protein degradation - to control growth, development, and responses to environmental challenges. Recent research highlights the importance of translational reprogramming as a pivotal mechanism in regulating gene expression across diverse physiological scenarios. This regulatory mechanism bears practical implications, particularly in bolstering crop productivity by manipulating RNA regulatory elements (RREs) to modulate heterologous gene expression through transgene and endogenous gene expression through gene editing. Here, we elucidate the potential of upstream open reading frames (uORFs), a prominent and stringent class of RREs, in optimizing crop performance, exemplifying the efficacy of translational control in enhancing agricultural yields.
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Affiliation(s)
- Rui Mou
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Ruixia Niu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Ruoying Yang
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guoyong Xu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; RNA Institute, Wuhan University, Wuhan, Hubei 430072, China.
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6
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Dutta P, Mäkinen K. Mapping and quantification of potato virus A RNA genomes within viral particles and polysomes in infected plant cells. J Virol Methods 2025; 332:115066. [PMID: 39549925 DOI: 10.1016/j.jviromet.2024.115066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 11/12/2024] [Accepted: 11/13/2024] [Indexed: 11/18/2024]
Abstract
Potato virus A belongs to the genus Potyvirus, a group of single-stranded positive sense RNA viruses infecting crops worldwide. To initiate infection in a host, its genome takes part in different activities, viz., translation, replication, encapsidation during the infection cycle. Extensive research has been carried out to scrutinize the stages of potyviral infection cycle and decipher the strategies it employs to cause disease. Nonetheless, the amount of viral RNA taking part in translation and virion formation, at a given time point, is missing. In this study, we quantified the percentage of viral RNA that exists as virions and those that associates with host polysome, relative to total viral RNA in infected plant tissue. We employed a revised version of immuno-capture reverse transcription PCR and polysome profiling to address our queries. We tested three different coating antibody concentrations and further optimized the immuno-capture reverse transcription PCR protocol to address its limitation of binding and retaining viral particles. Our results indicate that most of the viral RNA (69 %) exists as encapsidated genomes, while 3 % of total viral RNA associates with host polysomes. These findings are crucial for correct interpretation of quantitative translational studies in which correlation must be made between the number of polysome-associated transcripts and the amount of protein synthesized.
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Affiliation(s)
- Pinky Dutta
- Viikki Plants Science Centre and Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Finland
| | - Kristiina Mäkinen
- Viikki Plants Science Centre and Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Finland.
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7
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Renziehausen T, Chaudhury R, Hartman S, Mustroph A, Schmidt-Schippers RR. A mechanistic integration of hypoxia signaling with energy, redox, and hormonal cues. PLANT PHYSIOLOGY 2024; 197:kiae596. [PMID: 39530170 DOI: 10.1093/plphys/kiae596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 10/25/2024] [Accepted: 10/25/2024] [Indexed: 11/16/2024]
Abstract
Oxygen deficiency (hypoxia) occurs naturally in many developing plant tissues but can become a major threat during acute flooding stress. Consequently, plants as aerobic organisms must rapidly acclimate to hypoxia and the associated energy crisis to ensure cellular and ultimately organismal survival. In plants, oxygen sensing is tightly linked with oxygen-controlled protein stability of group VII ETHYLENE-RESPONSE FACTORs (ERFVII), which, when stabilized under hypoxia, act as key transcriptional regulators of hypoxia-responsive genes (HRGs). Multiple signaling pathways feed into hypoxia signaling to fine-tune cellular decision-making under stress. First, ATP shortage upon hypoxia directly affects the energy status and adjusts anaerobic metabolism. Secondly, altered redox homeostasis leads to reactive oxygen and nitrogen species (ROS and RNS) accumulation, evoking signaling and oxidative stress acclimation. Finally, the phytohormone ethylene promotes hypoxia signaling to improve acute stress acclimation, while hypoxia signaling in turn can alter ethylene, auxin, abscisic acid, salicylic acid, and jasmonate signaling to guide development and stress responses. In this Update, we summarize the current knowledge on how energy, redox, and hormone signaling pathways are induced under hypoxia and subsequently integrated at the molecular level to ensure stress-tailored cellular responses. We show that some HRGs are responsive to changes in redox, energy, and ethylene independently of the oxygen status, and we propose an updated HRG list that is more representative for hypoxia marker gene expression. We discuss the synergistic effects of hypoxia, energy, redox, and hormone signaling and their phenotypic consequences in the context of both environmental and developmental hypoxia.
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Affiliation(s)
- Tilo Renziehausen
- Plant Biotechnology, Faculty of Biology, University of Bielefeld, 33615 Bielefeld, Germany
- Center for Biotechnology, University of Bielefeld, 33615 Bielefeld, Germany
| | - Rim Chaudhury
- Plant Environmental Signalling and Development, Faculty of Biology, University of Freiburg, Freiburg 79104, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg 79104, Germany
| | - Sjon Hartman
- Plant Environmental Signalling and Development, Faculty of Biology, University of Freiburg, Freiburg 79104, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg 79104, Germany
| | - Angelika Mustroph
- Department of Plant Physiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Romy R Schmidt-Schippers
- Plant Biotechnology, Faculty of Biology, University of Bielefeld, 33615 Bielefeld, Germany
- Center for Biotechnology, University of Bielefeld, 33615 Bielefeld, Germany
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8
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van Veen H, Triozzi PM, Loreti E. Metabolic strategies in hypoxic plants. PLANT PHYSIOLOGY 2024; 197:kiae564. [PMID: 39446413 DOI: 10.1093/plphys/kiae564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 10/04/2024] [Indexed: 12/25/2024]
Abstract
Complex multicellular organisms have evolved in an oxygen-enriched atmosphere. Oxygen is therefore essential for all aerobic organisms, including plants, for energy production through cellular respiration. However, plants can experience hypoxia following extreme flooding events and also under aerated conditions in proliferative organs or tissues characterized by high oxygen consumption. When oxygen availability is compromised, plants adopt different strategies to cope with hypoxia and limited aeration. A common feature among different plant species is the activation of an anaerobic fermentative metabolism to provide ATP to maintain cellular homeostasis under hypoxia. Fermentation also requires many sugar substrates, which is not always feasible, and alternative metabolic strategies are thus needed. Recent findings have also shown that the hypoxic metabolism is also active in specific organs or tissues of the plant under aerated conditions. Here, we describe the regulatory mechanisms that control the metabolic strategies of plants and how they enable them to thrive despite challenging conditions. A comprehensive mechanistic understanding of the genetic and physiological components underlying hypoxic metabolism should help to provide opportunities to improve plant resilience under the current climate change scenario.
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Affiliation(s)
- Hans van Veen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747AG Groningen, The Netherlands
| | - Paolo Maria Triozzi
- PlantLab, Institute of Plant Sciences, Sant'Anna School of Advanced Studies, 56010 Pisa, Italy
| | - Elena Loreti
- Institute of Agricultural Biology and Biotechnology, CNR, National Research Council, 56124 Pisa, Italy
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9
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Gibbs DJ, Theodoulou FL, Bailey-Serres J. Primed to persevere: Hypoxia regulation from epigenome to protein accumulation in plants. PLANT PHYSIOLOGY 2024; 197:kiae584. [PMID: 39479777 DOI: 10.1093/plphys/kiae584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Accepted: 08/31/2024] [Indexed: 12/24/2024]
Abstract
Plant cells regularly encounter hypoxia (low-oxygen conditions) as part of normal growth and development, or in response to environmental stresses such as flooding. In recent years, our understanding of the multi-layered control of hypoxia-responsive gene expression has greatly increased. In this Update, we take a broad look at the epigenetic, transcriptional, translational, and post-translational mechanisms that regulate responses to low-oxygen levels. We highlight how a network of post-translational modifications (including phosphorylation), secondary messengers, transcriptional cascades, and retrograde signals from the mitochondria and endoplasmic reticulum (ER) feed into the control of transcription factor activity and hypoxia-responsive gene transcription. We discuss epigenetic mechanisms regulating the response to reduced oxygen availability, through focussing on active and repressive chromatin modifications and DNA methylation. We also describe current knowledge of the co- and post-transcriptional mechanisms that tightly regulate mRNA translation to coordinate effective gene expression under hypoxia. Finally, we present a series of outstanding questions in the field and consider how new insights into the molecular workings of the hypoxia-triggered regulatory hierarchy could pave the way for developing flood-resilient crops.
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Affiliation(s)
- Daniel J Gibbs
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | | | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
- Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, the Netherlands
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10
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Wang C, Tang Y, Zhou C, Li S, Chen J, Sun Z. RNA-seq and Ribosome Profiling Reveal the Translational Landscape of Rice in Response to Rice Stripe Virus Infection. Viruses 2024; 16:1866. [PMID: 39772176 PMCID: PMC11680141 DOI: 10.3390/v16121866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Revised: 11/26/2024] [Accepted: 11/28/2024] [Indexed: 01/11/2025] Open
Abstract
Rice is a crucial staple food for over half the global population, and viral infections pose significant threats to rice yields. This study focuses on the Rice Stripe Virus (RSV), which is known to drastically reduce rice productivity. We employed RNA-seq and ribosome profiling to analyze the transcriptional and translational responses of RSV-infected rice seedlings. Our results reveal that translational reprogramming is a critical aspect of the plant's defense mechanism, operating independently of transcriptional changes. Notably, less than half of the differentially expressed genes showed concordance between transcription and translation. Furthermore, RSV infection led to significant alterations in translational efficiency for numerous genes, suggesting that the virus selectively manipulates translation to enhance its pathogenicity. Our findings underscore the necessity of examining both transcriptional and translational landscapes to fully understand plant responses to viral infections.
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Affiliation(s)
- Chen Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (C.W.); (Y.T.); (C.Z.); (S.L.)
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA, Key Laboratory of Green Plant Protection of Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yao Tang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (C.W.); (Y.T.); (C.Z.); (S.L.)
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA, Key Laboratory of Green Plant Protection of Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Changmei Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (C.W.); (Y.T.); (C.Z.); (S.L.)
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA, Key Laboratory of Green Plant Protection of Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Shanshan Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (C.W.); (Y.T.); (C.Z.); (S.L.)
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA, Key Laboratory of Green Plant Protection of Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jianping Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (C.W.); (Y.T.); (C.Z.); (S.L.)
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA, Key Laboratory of Green Plant Protection of Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zongtao Sun
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (C.W.); (Y.T.); (C.Z.); (S.L.)
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11
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Batelli G, Ruggiero A, Esposito S, Venezia A, Lupini A, Nurcato R, Costa A, Palombieri S, Vitiello A, Mauceri A, Cammareri M, Sunseri F, Grandillo S, Granell A, Abenavoli MR, Grillo S. Combined salt and low nitrate stress conditions lead to morphophysiological changes and tissue-specific transcriptome reprogramming in tomato. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:108976. [PMID: 39094482 DOI: 10.1016/j.plaphy.2024.108976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024]
Abstract
Despite intense research towards the understanding of abiotic stress adaptation in tomato, the physiological adjustments and transcriptome modulation induced by combined salt and low nitrate (low N) conditions remain largely unknown. Here, three traditional tomato genotypes were grown under long-term single and combined stresses throughout a complete growth cycle. Physiological, molecular, and growth measurements showed extensive morphophysiological modifications under combined stress compared to the control, and single stress conditions, resulting in the highest penalty in yield and fruit size. The mRNA sequencing performed on both roots and leaves of genotype TRPO0040 indicated that the transcriptomic signature in leaves under combined stress conditions largely overlapped that of the low N treatment, whereas root transcriptomes were highly sensitive to salt stress. Differentially expressed genes were functionally interpreted using GO and KEGG enrichment analysis, which confirmed the stress and the tissue-specific changes. We also disclosed a set of genes underlying the specific response to combined conditions, including ribosome components and nitrate transporters, in leaves, and several genes involved in transport and response to stress in roots. Altogether, our results provide a comprehensive understanding of above- and below-ground physiological and molecular responses of tomato to salt stress and low N treatment, alone or in combination.
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Affiliation(s)
- Giorgia Batelli
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici (CNR-IBBR), Portici, 80055, Italy
| | - Alessandra Ruggiero
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici (CNR-IBBR), Portici, 80055, Italy
| | - Salvatore Esposito
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici (CNR-IBBR), Portici, 80055, Italy
| | - Accursio Venezia
- Research Centre for Vegetable and Ornamental Crops, Council for Agricultural Research and Economics (CREA-OF), 84098, Pontecagnano Faiano, Italy
| | - Antonio Lupini
- Department of Agraria, University Mediterranea of Reggio Calabria, Reggio Calabria, Italy
| | - Roberta Nurcato
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici (CNR-IBBR), Portici, 80055, Italy
| | - Antonello Costa
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici (CNR-IBBR), Portici, 80055, Italy
| | - Samuela Palombieri
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici (CNR-IBBR), Portici, 80055, Italy
| | - Antonella Vitiello
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici (CNR-IBBR), Portici, 80055, Italy
| | - Antonio Mauceri
- Department of Agraria, University Mediterranea of Reggio Calabria, Reggio Calabria, Italy
| | - Maria Cammareri
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici (CNR-IBBR), Portici, 80055, Italy
| | - Francesco Sunseri
- Department of Agraria, University Mediterranea of Reggio Calabria, Reggio Calabria, Italy
| | - Silvana Grandillo
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici (CNR-IBBR), Portici, 80055, Italy
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Maria Rosa Abenavoli
- Department of Agraria, University Mediterranea of Reggio Calabria, Reggio Calabria, Italy.
| | - Stefania Grillo
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici (CNR-IBBR), Portici, 80055, Italy.
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12
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Zhang J, Jin H, Chen Y, Jiang Y, Gu L, Lin G, Lin C, Wang Q. The eukaryotic translation initiation factor eIF4E regulates flowering and circadian rhythm in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 120:123-138. [PMID: 39145515 DOI: 10.1111/tpj.16975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 08/16/2024]
Abstract
Translation initiation is a critical, rate-limiting step in protein synthesis. The eukaryotic translation initiation factor 4E (eIF4E) plays an essential role in this process. However, the mechanisms by which eIF4E-dependent translation initiation regulates plant growth and development remain not fully understood. In this study, we found that Arabidopsis eIF4E proteins are distributed in both the nucleus and cytoplasm, with only the cytoplasmic eIF4E being involved in the control of photoperiodic flowering. Genome-wide translation profiling using Ribo-tag sequencing reveals that eIF4E may regulate plant flowering by maintaining the homeostatic translation of components in the photoperiodic flowering pathway. eIF4E not only regulates the translation of flowering genes such as FLOWERING LOCUS T (FT) and FLOWERING LOCUS D (FLD) but also influences the translation of circadian genes like CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and PSEUDO-RESPONSE REGULATOR 9 (PRR9). Consistently, our results show that the eIF4E modulates the rhythmic oscillation of the circadian clock. Together, our study provides mechanistic insights into how the protein translation regulates multiple developmental processes in Arabidopsis, including the circadian clock and photoperiodic flowering.
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Affiliation(s)
- Jing Zhang
- College of Life Sciences, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huanhuan Jin
- College of Life Sciences, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yadi Chen
- College of Life Sciences, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yonghong Jiang
- College of Life Sciences, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lianfeng Gu
- College of Life Sciences, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guifang Lin
- College of Life Sciences, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chentao Lin
- College of Life Sciences, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qin Wang
- College of Life Sciences, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
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13
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Ting MKY, Gao Y, Barahimipour R, Ghandour R, Liu J, Martinez-Seidel F, Smirnova J, Gotsmann VL, Fischer A, Haydon MJ, Willmund F, Zoschke R. Optimization of ribosome profiling in plants including structural analysis of rRNA fragments. PLANT METHODS 2024; 20:143. [PMID: 39285473 PMCID: PMC11406806 DOI: 10.1186/s13007-024-01267-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 09/02/2024] [Indexed: 09/19/2024]
Abstract
BACKGROUND Ribosome profiling (or Ribo-seq) is a technique that provides genome-wide information on the translational landscape (translatome). Across different plant studies, variable methodological setups have been described which raises questions about the general comparability of data that were generated from diverging methodologies. Furthermore, a common problem when performing Ribo-seq are abundant rRNA fragments that are wastefully incorporated into the libraries and dramatically reduce sequencing depth. To remove these rRNA contaminants, it is common to perform preliminary trials to identify these fragments because they are thought to vary depending on nuclease treatment, tissue source, and plant species. RESULTS Here, we compile valuable insights gathered over years of generating Ribo-seq datasets from different species and experimental setups. We highlight which technical steps are important for maintaining cross experiment comparability and describe a highly efficient approach for rRNA removal. Furthermore, we provide evidence that many rRNA fragments are structurally preserved over diverse nuclease regimes, as well as across plant species. Using a recently published cryo-electron microscopy (cryo-EM) structure of the tobacco 80S ribosome, we show that the most abundant rRNA fragments are spatially derived from the solvent-exposed surface of the ribosome. CONCLUSION The guidelines presented here shall aid newcomers in establishing ribosome profiling in new plant species and provide insights that will help in customizing the methodology for individual research goals.
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Affiliation(s)
- Michael K Y Ting
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
- School of BioSciences, University of Melbourne, VIC, Melbourne, 3010, Australia.
| | - Yang Gao
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Rouhollah Barahimipour
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Rabea Ghandour
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Jinghan Liu
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Federico Martinez-Seidel
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Julia Smirnova
- Charité Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany
| | - Vincent Leon Gotsmann
- Technical University Kaiserslautern, Paul-Ehrlich-Str. 23, 67663, Kaiserslautern, Germany
| | - Axel Fischer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Michael J Haydon
- School of BioSciences, University of Melbourne, VIC, Melbourne, 3010, Australia
| | - Felix Willmund
- Technical University Kaiserslautern, Paul-Ehrlich-Str. 23, 67663, Kaiserslautern, Germany
- Universität Marburg, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
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14
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Lin S, Shen ZY, Wang MD, Zhou XM, Xu T, Jiao XH, Wang LL, Guo XJ, Wu P. Lnc557 promotes Bombyx mori nucleopolyhedrovirus replication by interacting with BmELAVL1 to enhance its stability and expression. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 204:106046. [PMID: 39277373 DOI: 10.1016/j.pestbp.2024.106046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/06/2024] [Accepted: 07/23/2024] [Indexed: 09/17/2024]
Abstract
Bombyx mori nucleopolyhedrovirus (BmNPV) is a major pathogen that threatens the growth and sustainability of the sericultural industry. Currently, accumulated studies showed that long non-coding RNAs (lncRNAs) play important roles in the genesis and progression of various viruses and host-pathogens interactions. However, the functions and regulatory mechanisms of lncRNAs in insect-virus interaction are still limited. In this study, transcriptome sequencing and ribosome profiling sequencing (Ribo-seq) were performed in the BmNPV-infected midgut and control tissue, and a total of 9 differentially expressed (DE) lncRNAs and 27 small ORFs (sORFs) with micropeptide coding potential were identified. Among them, lncRNA XR_001139971.3 (lnc557) is verified to be significantly up-regulated upon BmNPV infection and may have the potential to encode a small peptide (ORF-674). The subcellular localization experiment showed that lnc557 was expressed in the cytoplasm. Overexpression of lnc557 promotes BmNPV replication and vice versa. By combining RNA pull-down, mass spectrometry, protein truncation and RNA immunoprecipitation (RIP) assays, we confirmed that lnc557 can bind to the RRM-5 domain of BmELAVL1 protein. Subsequently, we found that lnc557 could promote the expression of BmELAVL1 by enhancing the stability of BmELAVL1. Further, enhancing the expression of BmELAVL1 can promote the proliferation of BmNPV, while knockdown shows the opposite effect. Our data suggest that lnc557-mediated BmELAVL1 expression enhancement could play a positive role in BmNPV replication, which will provide a new insight into the molecular mechanism of interaction between Bombyx mori and virus.
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Affiliation(s)
- Su Lin
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Zhen-Yu Shen
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Meng-Dong Wang
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Xue-Min Zhou
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Tao Xu
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Xin-Hao Jiao
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Lu-Lai Wang
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Xi-Jie Guo
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Ping Wu
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China.
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15
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Lohmann J, Herzog O, Rosenzweig K, Weingartner M. Thermal adaptation in plants: understanding the dynamics of translation factors and condensates. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4258-4273. [PMID: 38630631 DOI: 10.1093/jxb/erae171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/16/2024] [Indexed: 04/19/2024]
Abstract
Plants, as sessile organisms, face the crucial challenge of adjusting growth and development with ever-changing environmental conditions. Protein synthesis is the fundamental process that enables growth of all organisms. Since elevated temperature presents a substantial threat to protein stability and function, immediate adjustments of protein synthesis rates are necessary to circumvent accumulation of proteotoxic stress and to ensure survival. This review provides an overview of the mechanisms that control translation under high-temperature stress by the modification of components of the translation machinery in plants, and compares them to yeast and metazoa. Recent research also suggests an important role for cytoplasmic biomolecular condensates, named stress granules, in these processes. Current understanding of the role of stress granules in translational regulation and of the molecular processes associated with translation that might occur within stress granules is also discussed.
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Affiliation(s)
- Julia Lohmann
- Institute of Plant Sciences and Microbiology, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - Oliver Herzog
- Institute of Plant Sciences and Microbiology, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - Kristina Rosenzweig
- Institute of Plant Sciences and Microbiology, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - Magdalena Weingartner
- Institute of Plant Sciences and Microbiology, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
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16
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Hou M, Fan W, Zhong D, Dai X, Wang Q, Liu W, Li S. Ribosome Pausing Negatively Regulates Protein Translation in Maize Seedlings during Dark-to-Light Transitions. Int J Mol Sci 2024; 25:7985. [PMID: 39063227 PMCID: PMC11277263 DOI: 10.3390/ijms25147985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Regulation of translation is a crucial step in gene expression. Developmental signals and environmental stimuli dynamically regulate translation via upstream small open reading frames (uORFs) and ribosome pausing. Recent studies have revealed many plant genes that are specifically regulated by uORF translation following changes in growth conditions, but ribosome-pausing events are less well understood. In this study, we performed ribosome profiling (Ribo-seq) of etiolated maize (Zea mays) seedlings exposed to light for different durations, revealing hundreds of genes specifically regulated at the translation level during the early period of light exposure. We identified over 400 ribosome-pausing events in the dark that were rapidly released after illumination. These results suggested that ribosome pausing negatively regulates translation from specific genes, a conclusion that was supported by a non-targeted proteomics analysis. Importantly, we identified a conserved nucleotide motif downstream of the pausing sites. Our results elucidate the role of ribosome pausing in the control of gene expression in plants; the identification of the cis-element at the pausing sites provides insight into the mechanisms behind translation regulation and potential targets for artificial control of plant translation.
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Affiliation(s)
- Mingming Hou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (M.H.); (W.F.); (Q.W.)
| | - Wei Fan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (M.H.); (W.F.); (Q.W.)
| | - Deyi Zhong
- Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China;
| | - Xing Dai
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China;
| | - Quan Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (M.H.); (W.F.); (Q.W.)
| | - Wanfei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (M.H.); (W.F.); (Q.W.)
| | - Shengben Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (M.H.); (W.F.); (Q.W.)
- Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China;
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17
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Sainz MM, Sotelo-Silveira M, Filippi CV, Zardo S. Legume-rhizobia symbiosis: Translatome analysis. Genet Mol Biol 2024; 47Suppl 1:e20230284. [PMID: 38954532 PMCID: PMC11223499 DOI: 10.1590/1678-4685-gmb-2023-0284] [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: 10/03/2023] [Accepted: 03/31/2024] [Indexed: 07/04/2024] Open
Abstract
Leguminous plants can establish endosymbiotic relationships with nitrogen-fixing soil rhizobacteria. Bacterial infection and nodule organogenesis are two independent but highly coordinated genetic programs that are active during this interaction. These genetic programs can be regulated along all the stages of gene expression. Most of the studies, for both eukaryotes and prokaryotes, focused on the transcriptional regulation level determining the abundance of mRNAs. However, it has been demonstrated that mRNA levels only sometimes correlate with the abundance or activity of the coded proteins. For this reason, in the past two decades, interest in the role of translational control of gene expression has increased, since the subset of mRNA being actively translated outperforms the information gained only by the transcriptome. In the case of legume-rhizobia interactions, the study of the translatome still needs to be explored further. Therefore, this review aims to discuss the methodologies for analyzing polysome-associated mRNAs at the genome-scale and their contribution to studying translational control to understand the complexity of this symbiotic interaction. Moreover, the Dual RNA-seq approach is discussed for its relevance in the context of a symbiotic nodule, where intricate multi-species gene expression networks occur.
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Affiliation(s)
- María Martha Sainz
- Universidad de la República, Facultad de Agronomía, Departamento
de Biología Vegetal, Laboratorio de Bioquímica, Montevideo, Uruguay
| | - Mariana Sotelo-Silveira
- Universidad de la República, Facultad de Agronomía, Departamento
de Biología Vegetal, Laboratorio de Bioquímica, Montevideo, Uruguay
| | - Carla V. Filippi
- Universidad de la República, Facultad de Agronomía, Departamento
de Biología Vegetal, Laboratorio de Bioquímica, Montevideo, Uruguay
| | - Sofía Zardo
- Universidad de la República, Facultad de Agronomía, Departamento
de Biología Vegetal, Laboratorio de Bioquímica, Montevideo, Uruguay
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18
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Zhu S, Yuan S, Niu R, Zhou Y, Wang Z, Xu G. RNAirport: a deep neural network-based database characterizing representative gene models in plants. J Genet Genomics 2024; 51:652-664. [PMID: 38518981 DOI: 10.1016/j.jgg.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 03/24/2024]
Abstract
A 5'-leader, known initially as the 5'-untranslated region, contains multiple isoforms due to alternative splicing (aS) and alternative transcription start site (aTSS). Therefore, a representative 5'-leader is demanded to examine the embedded RNA regulatory elements in controlling translation efficiency. Here, we develop a ranking algorithm and a deep-learning model to annotate representative 5'-leaders for five plant species. We rank the intra-sample and inter-sample frequency of aS-mediated transcript isoforms using the Kruskal-Wallis test-based algorithm and identify the representative aS-5'-leader. To further assign a representative 5'-end, we train the deep-learning model 5'leaderP to learn aTSS-mediated 5'-end distribution patterns from cap-analysis gene expression data. The model accurately predicts the 5'-end, confirmed experimentally in Arabidopsis and rice. The representative 5'-leader-contained gene models and 5'leaderP can be accessed at RNAirport (http://www.rnairport.com/leader5P/). The Stage 1 annotation of 5'-leader records 5'-leader diversity and will pave the way to Ribo-Seq open-reading frame annotation, identical to the project recently initiated by human GENCODE.
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Affiliation(s)
- Sitao Zhu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Shu Yuan
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Ruixia Niu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Yulu Zhou
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Zhao Wang
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guoyong Xu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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19
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Banaś K, Aksmann A, Płachno BJ, Kapusta M, Marciniak P, Ronowski R. Individual architecture and photosynthetic performance of the submerged form of Drosera intermedia Hayne. BMC PLANT BIOLOGY 2024; 24:449. [PMID: 38783181 PMCID: PMC11112915 DOI: 10.1186/s12870-024-05155-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
Drosera intermedia grows in acidic bogs in parts of valleys that are flooded in winter, and that often dry out in summer. It is also described as the sundew of the most heavily hydrated habitats in peatlands, and it is often found in water and even underwater. This sundew is the only one that can tolerate long periods of submersion, and more importantly produces a typical submerged form that can live in such conditions for many years. Submerged habitats are occupied by D. intermedia relatively frequently. The aim of the study was to determine the environmental conditions and architecture of individuals in the submerged form of D. intermedia. The features of the morphological and anatomical structure and chlorophyll a fluorescence of this form that were measured were compared with analogous ones in individuals that occurred in emerged and peatland habitats. The submerged form occurred to a depth of 20 cm. Compared to the other forms, its habitat had the highest pH (4.71-4.92; Me = 4.71), the highest temperature and substrate hydration, and above all, the lowest photosynthetically active radiation (PAR; 20.4-59.4%). This form differed from the other forms in almost all of the features of the plant's architecture. It is particularly noteworthy that it had the largest main axis height among all of the forms, which exceeded 18 cm. The number of living leaves in a rosette was notable (18.1 ± 8.1), while the number of dead leaves was very low (6.9 ± 3.8). The most significant differences were in the shape of its submerged leaves, in which the length of the leaf blade was the lowest of all of the forms (0.493 ± 0.15 mm; p < 0.001) and usually the widest. The stem cross-sectional area was noticeably smaller in the submerged form than in the other forms, the xylem was less developed and collaterally closed vascular bundles occurred. Our analysis of the parameters of chlorophyll fluorescence in vivo revealed that the maximum quantum yield of the primary photochemistry of photosystem II is the highest for the submerged form (Me = 0.681), the same as the maximum quantum yield of the electron transport (Me φE0 = 0.183). The efficiency of energy use per one active reaction center of photosystem II (RC) was the lowest in the submerged form (Me = 2.978), same as the fraction of energy trapped by one active RC (Me = 1.976) and the non-photochemical energy dissipation (DI0/RC; Me = 0.916). The ET0/RC parameter, associated with the efficiency of the energy utilization for electron transport by one RC, in the submerged plant reached the highest value (Me = 0.489). The submerged form of D. intermedia clearly differed from the emerged and peatland forms in its plant architecture. The submerged plants had a thinner leaf blade and less developed xylem than the other forms, however, their stems were much longer. The relatively high photosynthetic efficiency of the submerged forms suggests that most of the trapped energy is utilized to drive photosynthesis with a minimum energy loss, which may be a mechanism to compensate for the relatively small size of the leaf blade.
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Affiliation(s)
- Krzysztof Banaś
- Department of Plant Ecology, Faculty of Biology, University of Gdansk, 59 Wita Stwosza St., Gdańsk, PL, 80-308, Poland.
| | - Anna Aksmann
- Department of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Gdansk, 59 Wita Stwosza St., Gdańsk, 80-308, Poland
| | - Bartosz J Płachno
- Department of Plant Cytology and Embryology, Faculty of Biology, Institute of Botany, Jagiellonian University in Kraków, 9 Gronostajowa St., Kraków, 30-387, Poland
| | - Małgorzata Kapusta
- Bioimaging Laboratory, Faculty of Biology, University of Gdansk, 59 Wita Stwosza St., Gdańsk, 80-308, Poland
| | - Paweł Marciniak
- Department of Plant Ecology, Faculty of Biology, University of Gdansk, 59 Wita Stwosza St., Gdańsk, PL, 80-308, Poland
| | - Rafał Ronowski
- Department of Plant Ecology, Faculty of Biology, University of Gdansk, 59 Wita Stwosza St., Gdańsk, PL, 80-308, Poland
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20
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Wu J, Zhou M, Cheng Y, Chen X, Yan S, Deng S. Genome-Wide Analysis of C/S1-bZIP Subfamilies in Populus tomentosa and Unraveling the Role of PtobZIP55/21 in Response to Low Energy. Int J Mol Sci 2024; 25:5163. [PMID: 38791204 PMCID: PMC11120861 DOI: 10.3390/ijms25105163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/26/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
C/S1 basic leucine zipper (bZIP) transcription factors are essential for plant survival under energy deficiency. However, studies on the responses of C/S1-bZIPs to low energy in woody plants have not yet been reported. In this study, members of C/S1-bZIP subfamilies in Populus tomentosa were systematically analyzed using bioinformatic approaches. Four C-bZIPs and 10 S1-bZIPs were identified, and their protein properties, phylogenetic relationships, gene structures, conserved motifs, and uORFs were systematically investigated. In yeast two-hybrid assays, direct physical interactions between C-bZIP and S1-bZIP members were observed, highlighting their potential functional synergy. Moreover, expression profile analyses revealed that low energy induced transcription levels of most C/S1-bZIP members, with bZIP55 and bZIP21 (a homolog of bZIP55) exhibiting particularly significant upregulation. When the expression of bZIP55 and bZIP21 was co-suppressed using artificial microRNA mediated gene silencing in transgenic poplars, root growth was promoted. Further analyses revealed that bZIP55/21 negatively regulated the root development of P. tomentosa in response to low energy. These findings provide insights into the molecular mechanisms by which C/S1-bZIPs regulate poplar growth and development in response to energy deprivation.
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Affiliation(s)
| | | | | | | | | | - Shurong Deng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (J.W.); (M.Z.); (Y.C.); (X.C.); (S.Y.)
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21
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Wu HYL, Jen J, Hsu PY. What, where, and how: Regulation of translation and the translational landscape in plants. THE PLANT CELL 2024; 36:1540-1564. [PMID: 37437121 PMCID: PMC11062462 DOI: 10.1093/plcell/koad197] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/14/2023]
Abstract
Translation is a crucial step in gene expression and plays a vital role in regulating various aspects of plant development and environmental responses. It is a dynamic and complex program that involves interactions between mRNAs, transfer RNAs, and the ribosome machinery through both cis- and trans-regulation while integrating internal and external signals. Translational control can act in a global (transcriptome-wide) or mRNA-specific manner. Recent advances in genome-wide techniques, particularly ribosome profiling and proteomics, have led to numerous exciting discoveries in both global and mRNA-specific translation. In this review, we aim to provide a "primer" that introduces readers to this fascinating yet complex cellular process and provide a big picture of how essential components connect within the network. We begin with an overview of mRNA translation, followed by a discussion of the experimental approaches and recent findings in the field, focusing on unannotated translation events and translational control through cis-regulatory elements on mRNAs and trans-acting factors, as well as signaling networks through 3 conserved translational regulators TOR, SnRK1, and GCN2. Finally, we briefly touch on the spatial regulation of mRNAs in translational control. Here, we focus on cytosolic mRNAs; translation in organelles and viruses is not covered in this review.
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Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Joey Jen
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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22
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Wu TY, Li YR, Chang KJ, Fang JC, Urano D, Liu MJ. Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes. Genome Res 2024; 34:272-285. [PMID: 38479836 PMCID: PMC10984385 DOI: 10.1101/gr.278100.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
mRNA translation relies on identifying translation initiation sites (TISs) in mRNAs. Alternative TISs are prevalent across plant transcriptomes, but the mechanisms for their recognition are unclear. Using ribosome profiling and machine learning, we developed models for predicting alternative TISs in the tomato (Solanum lycopersicum). Distinct feature sets were predictive of AUG and nonAUG TISs in 5' untranslated regions and coding sequences, including a novel CU-rich sequence that promoted plant TIS activity, a translational enhancer found across dicots and monocots, and humans and viruses. Our results elucidate the mechanistic and evolutionary basis of TIS recognition, whereby cis-regulatory RNA signatures affect start site selection. The TIS prediction model provides global estimates of TISs to discover neglected protein-coding genes across plant genomes. The prevalence of cis-regulatory signatures across plant species, humans, and viruses suggests their broad and critical roles in reprogramming the translational landscape.
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Affiliation(s)
- Ting-Ying Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Ya-Ru Li
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Kai-Jyun Chang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Jhen-Cheng Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Daisuke Urano
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Ming-Jung Liu
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan;
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
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23
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Kempa M, Mikołajczak K, Ogrodowicz P, Pniewski T, Krajewski P, Kuczyńska A. The impact of multiple abiotic stresses on ns-LTP2.8 gene transcript and ns-LTP2.8 protein accumulation in germinating barley (Hordeum vulgare L.) embryos. PLoS One 2024; 19:e0299400. [PMID: 38502680 PMCID: PMC10950244 DOI: 10.1371/journal.pone.0299400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/09/2024] [Indexed: 03/21/2024] Open
Abstract
Abiotic stresses occur more often in combination than alone under regular field conditions limiting in more severe way crop production. Stress recognition in plants primarily occurs in the plasma membrane, modification of which is necessary to maintain homeostasis in response to it. It is known that lipid transport proteins (ns-LTPs) participate in modification of the lipidome of cell membranes. Representative of this group, ns-LTP2.8, may be involved in the reaction to abiotic stress of germinating barley plants by mediating the intracellular transport of hydrophobic particles, such as lipids, helping to maintain homeostasis. The ns-LTP2.8 protein was selected for analysis due to its ability to transport not only linear hydrophobic molecules but also compounds with a more complex spatial structure. Moreover, ns-LTP2.8 has been qualified as a member of pathogenesis-related proteins, which makes it particularly important in relation to its high allergenic potential. This paper demonstrates for the first time the influence of various abiotic stresses acting separately as well as in their combinations on the change in the ns-LTP2.8 transcript, ns-LTP2.8 protein and total soluble protein content in the embryonal axes of germinating spring barley genotypes with different ns-LTP2.8 allelic forms and stress tolerance. Tissue localization of ns-LTP2.8 transcript as well as ns-LTP2.8 protein were also examined. Although the impact of abiotic stresses on the regulation of gene transcription and translation processes remains not fully recognized, in this work we managed to demonstrate different impact on applied stresses on the fundamental cellular processes in very little studied tissue of the embryonal axis of barley.
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Affiliation(s)
- Michał Kempa
- Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Piotr Ogrodowicz
- Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Tomasz Pniewski
- Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Anetta Kuczyńska
- Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
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24
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Gotsmann VL, Ting MKY, Haase N, Rudorf S, Zoschke R, Willmund F. Utilizing high-resolution ribosome profiling for the global investigation of gene expression in Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1614-1634. [PMID: 38047591 DOI: 10.1111/tpj.16577] [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: 06/29/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
Ribosome profiling (Ribo-seq) is a powerful method for the deep analysis of translation mechanisms and regulatory circuits during gene expression. Extraction and sequencing of ribosome-protected fragments (RPFs) and parallel RNA-seq yields genome-wide insight into translational dynamics and post-transcriptional control of gene expression. Here, we provide details on the Ribo-seq method and the subsequent analysis with the unicellular model alga Chlamydomonas reinhardtii (Chlamydomonas) for generating high-resolution data covering more than 10 000 different transcripts. Detailed analysis of the ribosomal offsets on transcripts uncovers presumable transition states during translocation of elongating ribosomes within the 5' and 3' sections of transcripts and characteristics of eukaryotic translation termination, which are fundamentally distinct for chloroplast translation. In chloroplasts, a heterogeneous RPF size distribution along the coding sequence indicates specific regulatory phases during protein synthesis. For example, local accumulation of small RPFs correlates with local slowdown of psbA translation, possibly uncovering an uncharacterized regulatory step during PsbA/D1 synthesis. Further analyses of RPF distribution along specific cytosolic transcripts revealed characteristic patterns of translation elongation exemplified for the major light-harvesting complex proteins, LHCs. By providing high-quality datasets for all subcellular genomes and attaching our data to the Chlamydomonas reference genome, we aim to make ribosome profiles easily accessible for the broad research community. The data can be browsed without advanced bioinformatic background knowledge for translation output levels of specific genes and their splice variants and for monitoring genome annotation.
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Affiliation(s)
- Vincent Leon Gotsmann
- Molecular Genetics of Eukaryotes, RPTU Kaiserslautern-Landau, Paul-Ehrlich-Str. 23, 67663, Kaiserslautern, Germany
| | - Michael Kien Yin Ting
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Nadin Haase
- Institute of Cell Biology and Biophysics, Leibniz University Hanover, Herrenhäuser-Str. 2, 30419, Hanover, Germany
| | - Sophia Rudorf
- Institute of Cell Biology and Biophysics, Leibniz University Hanover, Herrenhäuser-Str. 2, 30419, Hanover, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, RPTU Kaiserslautern-Landau, Paul-Ehrlich-Str. 23, 67663, Kaiserslautern, Germany
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25
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Dawane A, Deshpande S, Vijayaraghavreddy P, Vemanna RS. Polysome-bound mRNAs and translational mechanisms regulate drought tolerance in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108513. [PMID: 38513519 DOI: 10.1016/j.plaphy.2024.108513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/23/2024]
Abstract
Plants evolved several acquired tolerance traits for drought stress adaptation to maintain the cellular homeostasis. Drought stress at the anthesis stage in rice affects productivity due to the inefficiency of protein synthesis machinery. The effect of translational mechanisms on different pathways involved in cellular tolerance plays an important role. We report differential responses of translation-associated mechanisms in rice using polysome bound mRNA sequencing at anthesis stage drought stress in resistant Apo and sensitive IR64 genotypes. Apo maintained higher polysomes with 60 S-to-40 S and polysome-to-monosome ratios which directly correlate with protein levels under stress. IR64 has less protein levels under stress due to defective translation machinery and reduced water potential. Many polysome-bound long non-coding RNAs (lncRNA) were identified in both genotypes under drought, influencing translation. Apo had higher levels of N6-Methyladenosine (m6A) mRNA modifications that contributed for sustained translation. Translation machinery in Apo could maintain higher levels of photosynthetic machinery-associated proteins in drought stress, which maintain gas exchange, photosynthesis and yield under stress. The protein stability and ribosome biogenesis mechanisms favoured improved translation in Apo. The phytohormone signalling and transcriptional responses were severely affected in IR64. Our results demonstrate that, the higher translation ability of Apo favours maintenance of photosynthesis and physiological responses that are required for drought stress adaptation.
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Affiliation(s)
- Akashata Dawane
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Haryana, 121 001, India
| | - Sanjay Deshpande
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Haryana, 121 001, India
| | | | - Ramu S Vemanna
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Haryana, 121 001, India.
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26
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Chen Y, Wang W, Yang Z, Peng H, Ni Z, Sun Q, Guo W. Innovative computational tools provide new insights into the polyploid wheat genome. ABIOTECH 2024; 5:52-70. [PMID: 38576428 PMCID: PMC10987449 DOI: 10.1007/s42994-023-00131-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/14/2023] [Indexed: 04/06/2024]
Abstract
Bread wheat (Triticum aestivum) is an important crop and serves as a significant source of protein and calories for humans, worldwide. Nevertheless, its large and allopolyploid genome poses constraints on genetic improvement. The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more challenging. Recently, we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat genome. Here, we summarize the methodological innovations and applications of these tools and databases. A series of step-by-step examples illustrates how these tools can be utilized for dissecting wheat germplasm resources and unveiling functional genes associated with important agronomic traits. Furthermore, we outline future perspectives on new advanced tools and databases, taking into consideration the unique features of bread wheat, to accelerate genomic-assisted wheat breeding.
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Affiliation(s)
- Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Wenxi Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Zhengzhao Yang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
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27
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Wang J, Li Y, Li M, Zhang W, Lu Y, Hua K, Ling X, Chen T, Guo D, Yang Y, Zheng Z, Liu Q, Zhang B. Translatome and Transcriptome Analyses Reveal the Mechanism that Underlies the Enhancement of Salt Stress by the Small Peptide Ospep5 in Plants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4277-4291. [PMID: 38288993 DOI: 10.1021/acs.jafc.3c08528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Salt stress significantly impedes plant growth and the crop yield. This study utilized de novo transcriptome assembly and ribosome profiling to explore mRNA translation's role in rice salt tolerance. We identified unrecognized translated open reading frames (ORFs), including 42 upstream transcripts and 86 unannotated transcripts. A noteworthy discovery was the role of a small ORF, Ospep5, in conferring salt tolerance. Overexpression of Ospep5 in plants increased salt tolerance, while its absence led to heightened sensitivity. This hypothesis was corroborated by the findings that exogenous application of the synthetic small peptide Ospep5 bolstered salt tolerance in both rice and Arabidopsis. We found that the mechanism underpinning the Ospep5-mediated salt tolerance involves the maintenance of intracellular Na+/K+ homeostasis, facilitated by upregulation of high-affinity potassium transporters (HKT) and Na+/H+ exchangers (SOS1). Furthermore, a comprehensive multiomics approach, particularly ribosome profiling, is instrumental in uncovering unannotated ORFs and elucidating their functions in plant stress responses.
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Affiliation(s)
- Jinyan Wang
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Yang Li
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Mingyue Li
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Wenting Zhang
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yaping Lu
- Experimental center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Kai Hua
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Xitie Ling
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Tianzi Chen
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Dongshu Guo
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Yuwen Yang
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Zhongbing Zheng
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Qing Liu
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
- College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Baolong Zhang
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
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28
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Wu HYL, Ai Q, Teixeira RT, Nguyen PHT, Song G, Montes C, Elmore JM, Walley JW, Hsu PY. Improved super-resolution ribosome profiling reveals prevalent translation of upstream ORFs and small ORFs in Arabidopsis. THE PLANT CELL 2024; 36:510-539. [PMID: 38000896 PMCID: PMC10896292 DOI: 10.1093/plcell/koad290] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/26/2023]
Abstract
A crucial step in functional genomics is identifying actively translated ORFs and linking them to biological functions. The challenge lies in identifying short ORFs, as their identification is greatly influenced by data quality and depth. Here, we improved the coverage of super-resolution Ribo-seq in Arabidopsis (Arabidopsis thaliana), revealing uncharacterized translation events for nuclear, chloroplastic, and mitochondrial genes. Assisted by a transcriptome assembly, we identified 7,751 unconventional translation events, comprising 6,996 upstream ORFs (uORFs) and 209 downstream ORFs on annotated protein-coding genes, as well as 546 ORFs in presumed noncoding RNAs. Proteomic data confirmed the production of stable proteins from some of these unannotated translation events. We present evidence of active translation from primary transcripts of trans-acting small interfering RNAs (TAS1-4) and microRNAs (pri-MIR163 and pri-MIR169) and periodic ribosome stalling supporting cotranslational decay. Additionally, we developed a method for identifying extremely short uORFs, including 370 minimum uORFs (AUG-stop), and 2,921 tiny uORFs (2 to 10 amino acids) and 681 uORFs that overlap with each other. Remarkably, these short uORFs exhibit strong translational repression as do longer uORFs. We also systematically discovered 594 uORFs regulated by alternative splicing, suggesting widespread isoform-specific translational control. Finally, these prevalent uORFs are associated with numerous important pathways. In summary, our improved Arabidopsis translational landscape provides valuable resources to study gene expression regulation.
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Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Qiaoyun Ai
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Rita Teresa Teixeira
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Phong H T Nguyen
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Gaoyuan Song
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Christian Montes
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - J Mitch Elmore
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Justin W Walley
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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29
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Kreisz P, Hellens AM, Fröschel C, Krischke M, Maag D, Feil R, Wildenhain T, Draken J, Braune G, Erdelitsch L, Cecchino L, Wagner TC, Ache P, Mueller MJ, Becker D, Lunn JE, Hanson J, Beveridge CA, Fichtner F, Barbier FF, Weiste C. S 1 basic leucine zipper transcription factors shape plant architecture by controlling C/N partitioning to apical and lateral organs. Proc Natl Acad Sci U S A 2024; 121:e2313343121. [PMID: 38315839 PMCID: PMC10873608 DOI: 10.1073/pnas.2313343121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/21/2023] [Indexed: 02/07/2024] Open
Abstract
Plants tightly control growth of their lateral organs, which led to the concept of apical dominance. However, outgrowth of the dormant lateral primordia is sensitive to the plant's nutritional status, resulting in an immense plasticity in plant architecture. While the impact of hormonal regulation on apical dominance is well characterized, the prime importance of sugar signaling to unleash lateral organ formation has just recently emerged. Here, we aimed to identify transcriptional regulators, which control the trade-off between growth of apical versus lateral organs. Making use of locally inducible gain-of-function as well as single and higher-order loss-of-function approaches of the sugar-responsive S1-basic-leucine-zipper (S1-bZIP) transcription factors, we disclosed their largely redundant function in establishing apical growth dominance. Consistently, comprehensive phenotypical and analytical studies of S1-bZIP mutants show a clear shift of sugar and organic nitrogen (N) allocation from apical to lateral organs, coinciding with strong lateral organ outgrowth. Tissue-specific transcriptomics reveal specific clade III SWEET sugar transporters, crucial for long-distance sugar transport to apical sinks and the glutaminase GLUTAMINE AMIDO-TRANSFERASE 1_2.1, involved in N homeostasis, as direct S1-bZIP targets, linking the architectural and metabolic mutant phenotypes to downstream gene regulation. Based on these results, we propose that S1-bZIPs control carbohydrate (C) partitioning from source leaves to apical organs and tune systemic N supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.
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Affiliation(s)
- Philipp Kreisz
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Alicia M. Hellens
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
| | - Christian Fröschel
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Markus Krischke
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Daniel Maag
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Regina Feil
- Group System Regulation, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm14476, Germany
| | - Theresa Wildenhain
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Jan Draken
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Gabriel Braune
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Leon Erdelitsch
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Laura Cecchino
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Tobias C. Wagner
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Peter Ache
- Department of Molecular Plant Physiology and Biophysics, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Martin J. Mueller
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - Dirk Becker
- Department of Molecular Plant Physiology and Biophysics, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
| | - John E. Lunn
- Group System Regulation, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm14476, Germany
| | - Johannes Hanson
- Department of Plant Physiology, Umeå Plant Science Center, Umeå University, UmeåSE-901 87, Sweden
| | - Christine A. Beveridge
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
| | - Franziska Fichtner
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- Department of Plant Biochemistry, Institute for Plant Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Francois F. Barbier
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
- Institute for Plant Sciences of Montpellier, University of Montpellier, CNRS, INRAe, Institut Agro, Montpellier34060, France
| | - Christoph Weiste
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg97082, Germany
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30
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Smith AB, Ganguly DR, Moore M, Bowerman AF, Janapala Y, Shirokikh NE, Pogson BJ, Crisp PA. Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:818-839. [PMID: 37947266 PMCID: PMC10952913 DOI: 10.1111/tpj.16531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
Transcript stability is an important determinant of its abundance and, consequently, translational output. Transcript destabilisation can be rapid and is well suited for modulating the cellular response. However, it is unclear the extent to which RNA stability is altered under changing environmental conditions in plants. We previously hypothesised that recovery-induced transcript destabilisation facilitated a phenomenon of rapid recovery gene downregulation (RRGD) in Arabidopsis thaliana (Arabidopsis) following light stress, based on mathematical calculations to account for ongoing transcription. Here, we test this hypothesis and investigate processes regulating transcript abundance and fate by quantifying changes in transcription, stability and translation before, during and after light stress. We adapt syringe infiltration to apply a transcriptional inhibitor to soil-grown plants in combination with stress treatments. Compared with measurements in juvenile plants and cell culture, we find reduced stability across a range of transcripts encoding proteins involved in RNA binding and processing. We also observe light-induced destabilisation of transcripts, followed by their stabilisation during recovery. We propose that this destabilisation facilitates RRGD, possibly in combination with transcriptional shut-off that was confirmed for HSP101, ROF1 and GOLS1. We also show that translation remains highly dynamic over the course of light stress and recovery, with a bias towards transcript-specific increases in ribosome association, independent of changes in total transcript abundance, after 30 min of light stress. Taken together, we provide evidence for the combinatorial regulation of transcription and stability that occurs to coordinate translation during light stress and recovery in Arabidopsis.
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Affiliation(s)
- Aaron B. Smith
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Diep R. Ganguly
- CSIRO Synthetic Biology Future Science PlatformCanberraAustralian Capital Territory2601Australia
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Marten Moore
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Andrew F. Bowerman
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Yoshika Janapala
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityClaytonVictoria3800Australia
| | - Nikolay E. Shirokikh
- The John Curtin School of Medical Research, The Shine‐Dalgarno Centre for RNA InnovationThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Barry J. Pogson
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Peter A. Crisp
- School of Agriculture and Food SciencesThe University of QueenslandBrisbaneQueensland4072Australia
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Wang S, Huang T, Xie Z, Wan L, Ren H, Wu T, Xie L, Luo S, Li M, Xie Z, Fan Q, Huang J, Zeng T, Zhang Y, Zhang M, Wei Y. Transcriptomic and Translatomic Analyses Reveal Insights into the Signaling Pathways of the Innate Immune Response in the Spleens of SPF Chickens Infected with Avian Reovirus. Viruses 2023; 15:2346. [PMID: 38140587 PMCID: PMC10747248 DOI: 10.3390/v15122346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Avian reovirus (ARV) infection is prevalent in farmed poultry and causes viral arthritis and severe immunosuppression. The spleen plays a very important part in protecting hosts against infectious pathogens. In this research, transcriptome and translatome sequencing technology were combined to investigate the mechanisms of transcriptional and translational regulation in the spleen after ARV infection. On a genome-wide scale, ARV infection can significantly reduce the translation efficiency (TE) of splenic genes. Differentially expressed translational efficiency genes (DTEGs) were identified, including 15 upregulated DTEGs and 396 downregulated DTEGs. These DTEGs were mainly enriched in immune regulation signaling pathways, which indicates that ARV infection reduces the innate immune response in the spleen. In addition, combined analyses revealed that the innate immune response involves the effects of transcriptional and translational regulation. Moreover, we discovered the key gene IL4I1, the most significantly upregulated gene at both the transcriptional and translational levels. Further studies in DF1 cells showed that overexpression of IL4I1 could inhibit the replication of ARV, while inhibiting the expression of endogenous IL4I1 with siRNA promoted the replication of ARV. Overexpression of IL4I1 significantly downregulated the mRNA expression of IFN-β, LGP2, TBK1 and NF-κB; however, the expression of these genes was significantly upregulated after inhibition of IL4I1, suggesting that IL4I1 may be a negative feedback effect of innate immune signaling pathways. In addition, there may be an interaction between IL4I1 and ARV σA protein, and we speculate that the IL4I1 protein plays a regulatory role by interacting with the σA protein. This study not only provides a new perspective on the regulatory mechanisms of the innate immune response after ARV infection but also enriches the knowledge of the host defense mechanisms against ARV invasion and the outcome of ARV evasion of the host's innate immune response.
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Affiliation(s)
- Sheng Wang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530000, China; (S.W.); (L.W.); (H.R.); (L.X.); (S.L.); (M.L.); (Z.X.); (Q.F.); (J.H.); (T.Z.); (Y.Z.); (M.Z.); (Y.W.)
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning 530000, China
| | - Tengda Huang
- Division of Liver Surgery, Department of General Surgery, Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China;
| | - Zhixun Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530000, China; (S.W.); (L.W.); (H.R.); (L.X.); (S.L.); (M.L.); (Z.X.); (Q.F.); (J.H.); (T.Z.); (Y.Z.); (M.Z.); (Y.W.)
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning 530000, China
| | - Lijun Wan
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530000, China; (S.W.); (L.W.); (H.R.); (L.X.); (S.L.); (M.L.); (Z.X.); (Q.F.); (J.H.); (T.Z.); (Y.Z.); (M.Z.); (Y.W.)
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning 530000, China
| | - Hongyu Ren
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530000, China; (S.W.); (L.W.); (H.R.); (L.X.); (S.L.); (M.L.); (Z.X.); (Q.F.); (J.H.); (T.Z.); (Y.Z.); (M.Z.); (Y.W.)
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning 530000, China
| | - Tian Wu
- NHC Key Laboratory of Transplant Engineering and Immunology, Regenerative Medicine Research Center, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital of Sichuan University, Chengdu 610041, China;
| | - Liji Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530000, China; (S.W.); (L.W.); (H.R.); (L.X.); (S.L.); (M.L.); (Z.X.); (Q.F.); (J.H.); (T.Z.); (Y.Z.); (M.Z.); (Y.W.)
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning 530000, China
| | - Sisi Luo
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530000, China; (S.W.); (L.W.); (H.R.); (L.X.); (S.L.); (M.L.); (Z.X.); (Q.F.); (J.H.); (T.Z.); (Y.Z.); (M.Z.); (Y.W.)
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning 530000, China
| | - Meng Li
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530000, China; (S.W.); (L.W.); (H.R.); (L.X.); (S.L.); (M.L.); (Z.X.); (Q.F.); (J.H.); (T.Z.); (Y.Z.); (M.Z.); (Y.W.)
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning 530000, China
| | - Zhiqin Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530000, China; (S.W.); (L.W.); (H.R.); (L.X.); (S.L.); (M.L.); (Z.X.); (Q.F.); (J.H.); (T.Z.); (Y.Z.); (M.Z.); (Y.W.)
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning 530000, China
| | - Qing Fan
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530000, China; (S.W.); (L.W.); (H.R.); (L.X.); (S.L.); (M.L.); (Z.X.); (Q.F.); (J.H.); (T.Z.); (Y.Z.); (M.Z.); (Y.W.)
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning 530000, China
| | - Jiaoling Huang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530000, China; (S.W.); (L.W.); (H.R.); (L.X.); (S.L.); (M.L.); (Z.X.); (Q.F.); (J.H.); (T.Z.); (Y.Z.); (M.Z.); (Y.W.)
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning 530000, China
| | - Tingting Zeng
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530000, China; (S.W.); (L.W.); (H.R.); (L.X.); (S.L.); (M.L.); (Z.X.); (Q.F.); (J.H.); (T.Z.); (Y.Z.); (M.Z.); (Y.W.)
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning 530000, China
| | - Yanfang Zhang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530000, China; (S.W.); (L.W.); (H.R.); (L.X.); (S.L.); (M.L.); (Z.X.); (Q.F.); (J.H.); (T.Z.); (Y.Z.); (M.Z.); (Y.W.)
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning 530000, China
| | - Minxiu Zhang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530000, China; (S.W.); (L.W.); (H.R.); (L.X.); (S.L.); (M.L.); (Z.X.); (Q.F.); (J.H.); (T.Z.); (Y.Z.); (M.Z.); (Y.W.)
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning 530000, China
| | - You Wei
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530000, China; (S.W.); (L.W.); (H.R.); (L.X.); (S.L.); (M.L.); (Z.X.); (Q.F.); (J.H.); (T.Z.); (Y.Z.); (M.Z.); (Y.W.)
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning 530000, China
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Siodmak A, Martinez-Seidel F, Rayapuram N, Bazin J, Alhoraibi H, Gentry-Torfer D, Tabassum N, Sheikh AH, Kise J, Blilou I, Crespi M, Kopka J, Hirt H. Dynamics of ribosome composition and ribosomal protein phosphorylation in immune signaling in Arabidopsis thaliana. Nucleic Acids Res 2023; 51:11876-11892. [PMID: 37823590 PMCID: PMC10681734 DOI: 10.1093/nar/gkad827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
In plants, the detection of microbe-associated molecular patterns (MAMPs) induces primary innate immunity by the activation of mitogen-activated protein kinases (MAPKs). We show here that the MAMP-activated MAPK MPK6 not only modulates defense through transcriptional regulation but also via the ribosomal protein translation machinery. To understand the effects of MPK6 on ribosomes and their constituent ribosomal proteins (RPs), polysomes, monosomes and the phosphorylation status of the RPs, MAMP-treated WT and mpk6 mutant plants were analysed. MAMP-activation induced rapid changes in RP composition of monosomes, polysomes and in the 60S ribosomal subunit in an MPK6-specific manner. Phosphoproteome analysis showed that MAMP-activation of MPK6 regulates the phosphorylation status of the P-stalk ribosomal proteins by phosphorylation of RPP0 and the concomitant dephosphorylation of RPP1 and RPP2. These events coincide with a significant decrease in the abundance of ribosome-bound RPP0s, RPP1s and RPP3s in polysomes. The P-stalk is essential in regulating protein translation by recruiting elongation factors. Accordingly, we found that RPP0C mutant plants are compromised in basal resistance to Pseudomonas syringae infection. These data suggest that MAMP-induced defense also involves MPK6-induced regulation of P-stalk proteins, highlighting a new role of ribosomal regulation in plant innate immunity.
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Affiliation(s)
- Anna Siodmak
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Federico Martinez-Seidel
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Naganand Rayapuram
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Jeremie Bazin
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Hanna Alhoraibi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21551 Jeddah, Saudi Arabia
| | - Dione Gentry-Torfer
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Naheed Tabassum
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Arsheed H Sheikh
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - José Kenyi González Kise
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ikram Blilou
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Martin Crespi
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Joachim Kopka
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Heribert Hirt
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria
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An Y, Wang Z, Liu B, Cao Y, Chen L. Translational Landscape of Medicago truncatula Seedlings under Salt Stress. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16657-16668. [PMID: 37880959 DOI: 10.1021/acs.jafc.3c03922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
The expression of plant genes under salt stress at the transcriptional level has been extensively studied. However, less attention has been paid to gene translation regulation under salt stress. In this study, Ribo-seq and RNA-seq analyses were conducted in Medicago truncatula seedlings grown under normal and salt stress conditions. The results showed that salt stress significantly altered the gene expression at the transcriptional and translational levels, with 2755 genes showing significant changes only at the translational level. Salt stress significantly inhibited the gene translation efficiency. Small ORFs (including uORFs in the 5'UTR, dORFs in 3'UTRs, and sORFs in lncRNAs) were identified throughout the genome of M. truncatula. The efficiency of gene translation was simultaneously regulated by the uORFs, dORFs, and miRNAs. In summary, our results provide valuable information about translatomic resources and new insights into plant responses to salt stress.
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Affiliation(s)
- Yixin An
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Ziqi Wang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Baijian Liu
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Yuwei Cao
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Lin Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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34
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Suhorukova AV, Sobolev DS, Milovskaya IG, Fadeev VS, Goldenkova-Pavlova IV, Tyurin AA. A Molecular Orchestration of Plant Translation under Abiotic Stress. Cells 2023; 12:2445. [PMID: 37887289 PMCID: PMC10605726 DOI: 10.3390/cells12202445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/12/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
The complexities of translational strategies make this stage of implementing genetic information one of the most challenging to comprehend and, simultaneously, perhaps the most engaging. It is evident that this diverse range of strategies results not only from a long evolutionary history, but is also of paramount importance for refining gene expression and metabolic modulation. This notion is particularly accurate for organisms that predominantly exhibit biochemical and physiological reactions with a lack of behavioural ones. Plants are a group of organisms that exhibit such features. Addressing unfavourable environmental conditions plays a pivotal role in plant physiology. This is particularly evident with the changing conditions of global warming and the irrevocable loss or depletion of natural ecosystems. In conceptual terms, the plant response to abiotic stress comprises a set of elaborate and intricate strategies. This is influenced by a range of abiotic factors that cause stressful conditions, and molecular genetic mechanisms that fine-tune metabolic pathways allowing the plant organism to overcome non-standard and non-optimal conditions. This review aims to focus on the current state of the art in the field of translational regulation in plants under abiotic stress conditions. Different regulatory elements and patterns are being assessed chronologically. We deem it important to focus on significant high-performance techniques for studying the genetic information dynamics during the translation phase.
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Li N, Duan Y, Ye Q, Ma Y, Ma R, Zhao L, Zhu S, Yu F, Qi S, Wang Y. The Arabidopsis eIF4E1 regulates NRT1.1-mediated nitrate signaling at both translational and transcriptional levels. THE NEW PHYTOLOGIST 2023; 240:338-353. [PMID: 37424317 DOI: 10.1111/nph.19129] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/18/2023] [Indexed: 07/11/2023]
Abstract
Identifying new nitrate regulatory genes and illustrating their mechanisms in modulating nitrate signaling are of great significance for achieving the high yield and nitrogen use efficiency (NUE) of crops. Here, we screened a mutant with defects in nitrate response and mapped the mutation to the gene eIF4E1 in Arabidopsis. Our results showed that eIF4E1 regulated nitrate signaling and metabolism. Ribo-seq and polysome profiling analysis revealed that eIF4E1 modulated the amount of some nitrogen (N)-related mRNAs being translated, especially the mRNA of NRT1.1 was reduced in the eif4e1 mutant. RNA-Seq results enriched some N-related genes, supporting that eIF4E1 is involved in nitrate regulation. The genetic analysis indicated that eIF4E1 worked upstream of NRT1.1 in nitrate signaling. In addition, an eIF4E1-interacting protein GEMIN2 was identified and found to be involved in nitrate signaling. Further investigation showed that overexpression of eIF4E1 promoted plant growth and enhanced yield and NUE. These results demonstrate that eIF4E1 regulates nitrate signaling by modulating NRT1.1 at both translational and transcriptional levels, laying the foundation for future research on the regulation of mineral nutrition at the translational level.
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Affiliation(s)
- Na Li
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yawen Duan
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Qing Ye
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yuhan Ma
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Rongjie Ma
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Lufei Zhao
- Agricultural Science and Engineering School, Liaocheng University, Liaocheng, Shandong, 252000, China
| | - Sirui Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan, 410082, China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan, 410082, China
| | - Shengdong Qi
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yong Wang
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
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Fang JC, Liu MJ. Translation initiation at AUG and non-AUG triplets in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111822. [PMID: 37574140 DOI: 10.1016/j.plantsci.2023.111822] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 07/22/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023]
Abstract
In plants and other eukaryotes, precise selection of translation initiation site (TIS) on mRNAs shapes the proteome in response to cellular events or environmental cues. The canonical translation of mRNAs initiates at a 5' proximal AUG codon in a favorable context. However, the coding and non-coding regions of plant genomes contain numerous unannotated alternative AUG and non-AUG TISs. Determining how and why these unexpected and prevalent TISs are activated in plants has emerged as an exciting research area. In this review, we focus on the selection of plant TISs and highlight studies that revealed previously unannotated TISs used in vivo via comparative genomics and genome-wide profiling of ribosome positioning and protein N-terminal ends. The biological signatures of non-AUG TIS-initiated open reading frames (ORFs) in plants are also discussed. We describe what is understood about cis-regulatory RNA elements and trans-acting eukaryotic initiation factors (eIFs) in the site selection for translation initiation by featuring the findings in plants along with supporting findings in non-plant species. The prevalent, unannotated TISs provide a hidden reservoir of ORFs that likely help reshape plant proteomes in response to developmental or environmental cues. These findings underscore the importance of understanding the mechanistic basis of TIS selection to functionally annotate plant genomes, especially for crops with large genomes.
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Affiliation(s)
- Jhen-Cheng Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Ming-Jung Liu
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan; Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan.
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Vélez-Bermúdez IC, Chou SJ, Chen AP, Lin WD, Schmidt W. Protocol to measure ribosome density along mRNA transcripts of Arabidopsis thaliana tissues using Ribo-seq. STAR Protoc 2023; 4:102520. [PMID: 37597190 PMCID: PMC10469065 DOI: 10.1016/j.xpro.2023.102520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/26/2023] [Accepted: 07/27/2023] [Indexed: 08/21/2023] Open
Abstract
Ribosome profiling (Ribo-seq) measures ribosome density along messenger RNA (mRNA) transcripts and is used to estimate the "translational fitness" of a given mRNA in response to environmental or developmental cues with high resolution. Here, we describe a protocol for Ribo-seq in plants adapted for the model plant Arabidopsis thaliana. We describe steps for lysis and nucleolytic digestion and ribosome footprinting. We then detail library construction, sequencing, and data analysis.
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Affiliation(s)
| | - Shu-Jen Chou
- Institute of Plant and Microbial Biology, Genomic Technology Core, Academia Sinica, Taipei 11529, Taiwan
| | - Ai-Ping Chen
- Institute of Plant and Microbial Biology, Genomic Technology Core, Academia Sinica, Taipei 11529, Taiwan
| | - Wen-Dar Lin
- Institute of Plant and Microbial Biology, Bioinformatics Core Lab, Academia Sinica, Taipei 11529, Taiwan
| | - Wolfgang Schmidt
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan.
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38
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Zhu W, Li H, Dong P, Ni X, Fan M, Yang Y, Xu S, Xu Y, Qian Y, Chen Z, Lü P. Low temperature-induced regulatory network rewiring via WRKY regulators during banana peel browning. PLANT PHYSIOLOGY 2023; 193:855-873. [PMID: 37279567 PMCID: PMC10469544 DOI: 10.1093/plphys/kiad322] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/08/2023]
Abstract
Banana (Musa spp.) fruits, as typical tropical fruits, are cold sensitive, and lower temperatures can disrupt cellular compartmentalization and lead to severe browning. How tropical fruits respond to low temperature compared to the cold response mechanisms of model plants remains unknown. Here, we systematically characterized the changes in chromatin accessibility, histone modifications, distal cis-regulatory elements, transcription factor binding, and gene expression levels in banana peels in response to low temperature. Dynamic patterns of cold-induced transcripts were generally accompanied by concordant chromatin accessibility and histone modification changes. These upregulated genes were enriched for WRKY binding sites in their promoters and/or active enhancers. Compared to banana peel at room temperature, large amounts of banana WRKYs were specifically induced by cold and mediated enhancer-promoter interactions regulating critical browning pathways, including phospholipid degradation, oxidation, and cold tolerance. This hypothesis was supported by DNA affinity purification sequencing, luciferase reporter assays, and transient expression assay. Together, our findings highlight widespread transcriptional reprogramming via WRKYs during banana peel browning at low temperature and provide an extensive resource for studying gene regulation in tropical plants in response to cold stress, as well as potential targets for improving cold tolerance and shelf life of tropical fruits.
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Affiliation(s)
- Wenjun Zhu
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hua Li
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Pengfei Dong
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xueting Ni
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Minlei Fan
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yingjie Yang
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shiyao Xu
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanbing Xu
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yangwen Qian
- WIMI Biotechnology Co., Ltd., Changzhou 213000, China
| | - Zhuo Chen
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peitao Lü
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Cheng H, Li L, Dong J, Wang S, Wu S, Rao S, Li L, Cheng S, Li L. Transcriptome and physiological determination reveal the effects of selenite on the growth and selenium metabolism in mung bean sprouts. Food Res Int 2023; 169:112880. [PMID: 37254328 DOI: 10.1016/j.foodres.2023.112880] [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: 07/24/2022] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 06/01/2023]
Abstract
Selenium (Se) biofortification of crops has been studied to substantially improve the Se content in human dietary food intake. In the present study, Vigna radiata (mung bean) seeds were soaked in different concentrations of sodium selenite (Na2SeO3). Low concentration of selenite is conducive to seed germination and growth, and can increase the fresh weight (FW) and dry weight (DW) of sprouts. The concentration of Na2SeO3 lower than 50 mg/kg resulted in noticeable elongation in the stem and marginal elongation in root. Mung bean seeds soaked with 80 mg/kg Na2SeO3 accounted for 93.77% of organic Se after growing for about 5 days. Transcriptome data revealed that Se treatment enhances starch and sugar metabolism, along with the up-regulation of ribosomal protein and DNA synthesis related genes. Further analysis indicated that the mung bean seeds absorbed Na2SeO3 through PHT1.1 and NIP2. Se (IV) was transformed into Se (VI) and transported to stems, leaves and roots through cotyledons during the germination of bean sprouts. SULTR3;3 may play an important role in the transit process. Se (VI) or Se (IV) transported to the leaves was catalytically transformed into SeCys through SiR and CS, and SeCys is further converted to MeSeCys through SMT. Most SeCys were transformed into SeHCys through CBL, transported to plastids, and finally transformed into SeMet through Met Synthase.
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Affiliation(s)
- Hua Cheng
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, China; College of Biology and Agricultural Resources, Huanggang Normal University, Hubei Huanggang 438000, China
| | - Lei Li
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, China
| | - Jingzhou Dong
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, China
| | - Shiyan Wang
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, China
| | - Shuai Wu
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, China
| | - Shen Rao
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, China
| | - Li Li
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, China
| | - Shuiyuan Cheng
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, China
| | - Linling Li
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, China; College of Biology and Agricultural Resources, Huanggang Normal University, Hubei Huanggang 438000, China.
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40
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Jian H, Wen S, Liu R, Zhang W, Li Z, Chen W, Zhou Y, Khassanov V, Mahmoud AMA, Wang J, Lyu D. Dynamic Translational Landscape Revealed by Genome-Wide Ribosome Profiling under Drought and Heat Stress in Potato. PLANTS (BASEL, SWITZERLAND) 2023; 12:2232. [PMID: 37375858 DOI: 10.3390/plants12122232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
The yield and quality of potatoes, an important staple crop, are seriously threatened by high temperature and drought stress. In order to deal with this adverse environment, plants have evolved a series of response mechanisms. However, the molecular mechanism of potato's response to environmental changes at the translational level is still unclear. In this study, we performed transcriptome- and ribosome-profiling assays with potato seedlings growing under normal, drought, and high-temperature conditions to reveal the dynamic translational landscapes for the first time. The translational efficiency was significantly affected by drought and heat stress in potato. A relatively high correlation (0.88 and 0.82 for drought and heat stress, respectively) of the fold changes of gene expression was observed between the transcriptional level and translational level globally based on the ribosome-profiling and RNA-seq data. However, only 41.58% and 27.69% of the different expressed genes were shared by transcription and translation in drought and heat stress, respectively, suggesting that the transcription or translation process can be changed independently. In total, the translational efficiency of 151 (83 and 68 for drought and heat, respectively) genes was significantly changed. In addition, sequence features, including GC content, sequence length, and normalized minimal free energy, significantly affected the translational efficiencies of genes. In addition, 28,490 upstream open reading frames (uORFs) were detected on 6463 genes, with an average of 4.4 uORFs per gene and a median length of 100 bp. These uORFs significantly affected the translational efficiency of downstream major open reading frames (mORFs). These results provide new information and directions for analyzing the molecular regulatory network of potato seedlings in response to drought and heat stress.
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Affiliation(s)
- Hongju Jian
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
| | - Shiqi Wen
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Rongrong Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Wenzhe Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Ziyan Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Weixi Chen
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yonghong Zhou
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
| | - Vadim Khassanov
- Department of Plant Protection and Quarantine, Faculty of Agronomy, S. Seifullin Kazakh Agrotechnical University, Zhenis Avenue, 010011 Astana, Kazakhstan
| | - Ahmed M A Mahmoud
- Department of Vegetable Crops, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Jichun Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
| | - Dianqiu Lyu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
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Jung H, Park HJ, Jo SH, Lee A, Lee HJ, Kim HS, Jung C, Cho HS. Nuclear OsFKBP20-1b maintains SR34 stability and promotes the splicing of retained introns upon ABA exposure in rice. THE NEW PHYTOLOGIST 2023; 238:2476-2494. [PMID: 36942934 DOI: 10.1111/nph.18892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/16/2023] [Indexed: 05/19/2023]
Abstract
Alternative splicing (AS) is a critical means by which plants respond to changes in the environment, but few splicing factors contributing to AS have been reported and functionally characterized in rice (Oryza sativa L.). Here, we explored the function and molecular mechanism of the spliceosome-associated protein OsFKBP20-1b during AS. We determined the AS landscape of wild-type and osfkbp20-1b knockout plants upon abscisic acid (ABA) treatment by transcriptome deep sequencing. To capture the dynamics of translating intron-containing mRNAs, we blocked transcription with cordycepin and performed polysome profiling. We also analyzed whether OsFKBP20-1b and the splicing factors OsSR34 and OsSR45 function together in AS using protoplast transfection assays. We show that OsFKBP20-1b interacts with OsSR34 and regulates its stability, suggesting a role as a chaperone-like protein in the spliceosome. OsFKBP20-1b facilitates the splicing of mRNAs with retained introns after ABA treatment; some of these mRNAs are translatable and encode functional transcriptional regulators of stress-responsive genes. In addition, interacting proteins, OsSR34 and OsSR45, regulate the splicing of the same retained introns as OsFKBP20-1b after ABA treatment. Our findings reveal that spliceosome-associated immunophilin functions in alternative RNA splicing in rice by positively regulating the splicing of retained introns to limit ABA response.
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Affiliation(s)
- Haemyeong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, South Korea
| | - Hyun Ji Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea
| | - Seung Hee Jo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, South Korea
| | - Areum Lee
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, South Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea
- Department of Functional Genomics, KRIBB School of Bioscience, UST, Daejeon, 34113, South Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, South Korea
| | - Choonkyun Jung
- Department of International Agricultural Technology and Crop Biotechnology Institute/Green Bio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- Department of Agriculture, Forestry, and Bioresources and Integrated Major in Global Smart Farm, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, South Korea
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Guo Y, Chen Y, Wang Y, Wu X, Zhang X, Mao W, Yu H, Guo K, Xu J, Ma L, Guo W, Hu Z, Xin M, Yao Y, Ni Z, Sun Q, Peng H. The translational landscape of bread wheat during grain development. THE PLANT CELL 2023; 35:1848-1867. [PMID: 36905284 PMCID: PMC10226598 DOI: 10.1093/plcell/koad075] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 02/09/2023] [Accepted: 02/19/2023] [Indexed: 05/30/2023]
Abstract
The dynamics of gene expression in crop grains has typically been investigated at the transcriptional level. However, this approach neglects translational regulation, a widespread mechanism that rapidly modulates gene expression to increase the plasticity of organisms. Here, we performed ribosome profiling and polysome profiling to obtain a comprehensive translatome data set of developing bread wheat (Triticum aestivum) grains. We further investigated the genome-wide translational dynamics during grain development, revealing that the translation of many functional genes is modulated in a stage-specific manner. The unbalanced translation between subgenomes is pervasive, which increases the expression flexibility of allohexaploid wheat. In addition, we uncovered widespread previously unannotated translation events, including upstream open reading frames (uORFs), downstream open reading frames (dORFs), and open reading frames (ORFs) in long noncoding RNAs, and characterized the temporal expression dynamics of small ORFs. We demonstrated that uORFs act as cis-regulatory elements that can repress or even enhance the translation of mRNAs. Gene translation may be combinatorially modulated by uORFs, dORFs, and microRNAs. In summary, our study presents a translatomic resource that provides a comprehensive and detailed overview of the translational regulation in developing bread wheat grains. This resource will facilitate future crop improvements for optimal yield and quality.
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Affiliation(s)
- Yiwen Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yongfa Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiaojia Wu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiaoyu Zhang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weiwei Mao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Hongjian Yu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Kai Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jin Xu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Liang Ma
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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43
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Zhu XT, Zhou R, Che J, Zheng YY, Tahir Ul Qamar M, Feng JW, Zhang J, Gao J, Chen LL. Ribosome profiling reveals the translational landscape and allele-specific translational efficiency in rice. PLANT COMMUNICATIONS 2023; 4:100457. [PMID: 36199246 PMCID: PMC10030323 DOI: 10.1016/j.xplc.2022.100457] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/23/2022] [Accepted: 10/01/2022] [Indexed: 05/04/2023]
Abstract
Translational regulation is a critical step in the process of gene expression and governs the synthesis of proteins from mRNAs. Many studies have revealed translational regulation in plants in response to various environmental stimuli. However, there have been no studies documenting the comprehensive landscape of translational regulation and allele-specific translational efficiency in multiple plant tissues, especially those of rice, a main staple crop that feeds nearly half of the world's population. Here we used RNA sequencing and ribosome profiling data to analyze the transcriptome and translatome of an elite hybrid rice, Shanyou 63 (SY63), and its parental varieties Zhenshan 97 and Minghui 63. The results revealed that gene expression patterns varied more among tissues than among varieties at the transcriptional and translational levels. We identified 3392 upstream open reading frames (uORFs), and the uORF-containing genes were enriched in transcription factors. Only 668 of 13 492 long non-coding RNAs could be translated into peptides. Finally, we discovered numerous genes with allele-specific translational efficiency in SY63 and demonstrated that some cis-regulatory elements may contribute to allelic divergence in translational efficiency. Overall, these findings may improve our understanding of translational regulation in rice and provide information for molecular breeding research.
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Affiliation(s)
- Xi-Tong Zhu
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Run Zhou
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian Che
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Yu Zheng
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Muhammad Tahir Ul Qamar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jia-Wu Feng
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianwei Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Junxiang Gao
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China.
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44
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Son S, Park SR. Plant translational reprogramming for stress resilience. FRONTIERS IN PLANT SCIENCE 2023; 14:1151587. [PMID: 36909402 PMCID: PMC9998923 DOI: 10.3389/fpls.2023.1151587] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Organisms regulate gene expression to produce essential proteins for numerous biological processes, from growth and development to stress responses. Transcription and translation are the major processes of gene expression. Plants evolved various transcription factors and transcriptome reprogramming mechanisms to dramatically modulate transcription in response to environmental cues. However, even the genome-wide modulation of a gene's transcripts will not have a meaningful effect if the transcripts are not properly biosynthesized into proteins. Therefore, protein translation must also be carefully controlled. Biotic and abiotic stresses threaten global crop production, and these stresses are seriously deteriorating due to climate change. Several studies have demonstrated improved plant resistance to various stresses through modulation of protein translation regulation, which requires a deep understanding of translational control in response to environmental stresses. Here, we highlight the translation mechanisms modulated by biotic, hypoxia, heat, and drought stresses, which are becoming more serious due to climate change. This review provides a strategy to improve stress tolerance in crops by modulating translational regulation.
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45
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Zhen Z, Dongying F, Yue S, Lipeng Z, Jingjing L, Minying L, Yuanyuan X, Juan H, Shiren S, Yi R, Bin H, Chao M. Translational profile of coding and non-coding RNAs revealed by genome wide profiling of ribosome footprints in grapevine. FRONTIERS IN PLANT SCIENCE 2023; 14:1097846. [PMID: 36844052 PMCID: PMC9944039 DOI: 10.3389/fpls.2023.1097846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Translation is a crucial process during plant growth and morphogenesis. In grapevine (Vitis vinifera L.), many transcripts can be detected by RNA sequencing; however, their translational regulation is still largely unknown, and a great number of translation products have not yet been identified. Here, ribosome footprint sequencing was carried out to reveal the translational profile of RNAs in grapevine. A total of 8291 detected transcripts were divided into four parts, including the coding, untranslated regions (UTR), intron, and intergenic regions, and the 26 nt ribosome-protected fragments (RPFs) showed a 3 nt periodic distribution. Furthermore, the predicted proteins were identified and classified by GO analysis. More importantly, 7 heat shock-binding proteins were found to be involved in molecular chaperone DNA J families participating in abiotic stress responses. These 7 proteins have different expression patterns in grape tissues; one of them was significantly upregulated by heat stress according to bioinformatics research and was identified as DNA JA6. The subcellular localization results showed that VvDNA JA6 and VvHSP70 were both localized on the cell membrane. Therefore, we speculate that DNA JA6 may interact with HSP70. In addition, overexpression of VvDNA JA6 and VvHSP70, reduced the malondialdehyde (MDA) content, improved the antioxidant enzyme activity of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD), increased the content of proline, an osmolyte substance, and affected the expression of the high-temperature marker genes VvHsfB1, VvHsfB2A, VvHsfC and VvHSP100. In summary, our study proved that VvDNA JA6 and the heat shock protein VvHSP70 play a positive role in the response to heat stress. This study lays a foundation for further exploring the balance between gene expression and protein translation in grapevine under heat stress.
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Affiliation(s)
- Zhang Zhen
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Fan Dongying
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Song Yue
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhang Lipeng
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Liu Jingjing
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Liu Minying
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xu Yuanyuan
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - He Juan
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Song Shiren
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Ren Yi
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Han Bin
- Changli Research Institute of Fruit Trees, Hebei Academy of Agricultural and Forestry Sciences, Changli, Hebei, China
| | - Ma Chao
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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Ryczek N, Łyś A, Makałowska I. The Functional Meaning of 5'UTR in Protein-Coding Genes. Int J Mol Sci 2023; 24:2976. [PMID: 36769304 PMCID: PMC9917990 DOI: 10.3390/ijms24032976] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
As it is well known, messenger RNA has many regulatory regions along its sequence length. One of them is the 5' untranslated region (5'UTR), which itself contains many regulatory elements such as upstream ORFs (uORFs), internal ribosome entry sites (IRESs), microRNA binding sites, and structural components involved in the regulation of mRNA stability, pre-mRNA splicing, and translation initiation. Activation of the alternative, more upstream transcription start site leads to an extension of 5'UTR. One of the consequences of 5'UTRs extension may be head-to-head gene overlap. This review describes elements in 5'UTR of protein-coding transcripts and the functional significance of protein-coding genes 5' overlap with implications for transcription, translation, and disease.
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Affiliation(s)
| | | | - Izabela Makałowska
- Institute of Human Biology and Evolution, Adam Mickiewicz University in Poznań, Uniwersytetu Ponańskiego 6, 61-614 Poznań, Poland
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47
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Zhou Y, Niu R, Tang Z, Mou R, Wang Z, Zhu S, Yang H, Ding P, Xu G. Plant HEM1 specifies a condensation domain to control immune gene translation. NATURE PLANTS 2023; 9:289-301. [PMID: 36797349 DOI: 10.1038/s41477-023-01355-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Translational reprogramming is a fundamental layer of immune regulation, but how such a global regulatory mechanism operates remains largely unknown. Here we perform a genetic screen and identify Arabidopsis HEM1 as a global translational regulator of plant immunity. The loss of HEM1 causes exaggerated cell death to restrict bacterial growth during effector-triggered immunity (ETI). By improving ribosome footprinting, we reveal that the hem1 mutant increases the translation efficiency of pro-death immune genes. We show that HEM1 contains a plant-specific low-complexity domain (LCD) absent from animal homologues. This LCD endows HEM1 with the capability of phase separation in vitro and in vivo. During ETI, HEM1 interacts and condensates with the translation machinery; this activity is promoted by the LCD. CRISPR removal of this LCD causes more ETI cell death. Our results suggest that HEM1 condensation constitutes a brake mechanism of immune activation by controlling the tissue health and disease resistance trade-off during ETI.
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Affiliation(s)
- Yulu Zhou
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, China
| | - Ruixia Niu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, China
| | - Zhijuan Tang
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, China
| | - Rui Mou
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, China
| | - Zhao Wang
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, China
| | - Sitao Zhu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, China
| | - Hongchun Yang
- School of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Pingtao Ding
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Guoyong Xu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
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48
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Cytosolic and mitochondrial ribosomal proteins mediate the locust phase transition via divergence of translational profiles. Proc Natl Acad Sci U S A 2023; 120:e2216851120. [PMID: 36701367 PMCID: PMC9945961 DOI: 10.1073/pnas.2216851120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The phase transition from solitary to gregarious locusts is crucial in outbreaks of locust plague, which threaten agricultural yield and food security. Research on the regulatory mechanisms of phase transition in locusts has focused primarily on the transcriptional or posttranslational level. However, the translational regulation of phase transition is unexplored. Here, we show a phase-dependent pattern at the translation level, which exhibits different polysome profiles between gregarious and solitary locusts. The gregarious locusts exhibit significant increases in 60S and polyribosomes, while solitary locusts possess higher peaks of the monoribosome and a specific "halfmer." The polysome profiles, a molecular phenotype, respond to changes in population density. In gregarious locusts, ten genes involved in the cytosolic ribosome pathway exhibited increased translational efficiency (TE). In solitary locusts, five genes from the mitochondrial ribosome pathway displayed increased TE. The high expression of large ribosomal protein 7 at the translational level promotes accumulation of the free 60S ribosomal subunit in gregarious locusts, while solitary locusts employ mitochondrial small ribosomal protein 18c to induce the assembly of mitochondrial ribosomes, causing divergence of the translational profiles and behavioral transition. This study reveals the translational regulatory mechanism of locust phase transition, in which the locusts employ divergent ribosome pathways to cope with changes in population density.
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Erokhina TN, Ryazantsev DY, Zavriev SK, Morozov SY. Regulatory miPEP Open Reading Frames Contained in the Primary Transcripts of microRNAs. Int J Mol Sci 2023; 24:ijms24032114. [PMID: 36768436 PMCID: PMC9917039 DOI: 10.3390/ijms24032114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
This review aims to consider retrospectively the available data on the coding properties of pri-microRNAs and the regulatory functions of their open reading frames (ORFs) and the encoded peptides (miPEPs). Studies identifying miPEPs and analyzing the fine molecular mechanisms of their functional activities are reviewed together with a brief description of the methods to identify pri-miRNA ORFs and the encoded protein products. Generally, miPEPs have been identified in many plant species of several families and in a few animal species. Importantly, molecular mechanisms of the miPEP action are often quite different between flowering plants and metazoan species. Requirement for the additional studies in these directions is highlighted by alternative findings concerning negative or positive regulation of pri-miRNA/miRNA expression by miPEPs in plants and animals. Additionally, the question of how miPEPs are distributed in non-flowering plant taxa is very important for understanding the evolutionary origin of such micropeptides. Evidently, further extensive studies are needed to explore the functions of miPEPs and the corresponding ORFs and to understand the full set of their roles in eukaryotic organisms. Thus, we address the most recent integrative views of different genomic, physiological, and molecular aspects concerning the expression of miPEPs and their possible fine functions.
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Affiliation(s)
- Tatiana N. Erokhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Dmitriy Y. Ryazantsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Sergey K. Zavriev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Sergey Y. Morozov
- Belozersky Institute of Physico-Chemical Biology and Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence:
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50
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Liu Q, Peng X, Shen M, Qian Q, Xing J, Li C, Gregory R. Ribo-uORF: a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling. Nucleic Acids Res 2023; 51:D248-D261. [PMID: 36440758 PMCID: PMC9825487 DOI: 10.1093/nar/gkac1094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/27/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Upstream open reading frames (uORFs) are typically defined as translation sites located within the 5' untranslated region upstream of the main protein coding sequence (CDS) of messenger RNAs (mRNAs). Although uORFs are prevalent in eukaryotic mRNAs and modulate the translation of downstream CDSs, a comprehensive resource for uORFs is currently lacking. We developed Ribo-uORF (http://rnainformatics.org.cn/RiboUORF) to serve as a comprehensive functional resource for uORF analysis based on ribosome profiling (Ribo-seq) data. Ribo-uORF currently supports six species: human, mouse, rat, zebrafish, fruit fly, and worm. Ribo-uORF includes 501 554 actively translated uORFs and 107 914 upstream translation initiation sites (uTIS), which were identified from 1495 Ribo-seq and 77 quantitative translation initiation sequencing (QTI-seq) datasets, respectively. We also developed mRNAbrowse to visualize items such as uORFs, cis-regulatory elements, genetic variations, eQTLs, GWAS-based associations, RNA modifications, and RNA editing. Ribo-uORF provides a very intuitive web interface for conveniently browsing, searching, and visualizing uORF data. Finally, uORFscan and UTR5var were developed in Ribo-uORF to precisely identify uORFs and analyze the influence of genetic mutations on uORFs using user-uploaded datasets. Ribo-uORF should greatly facilitate studies of uORFs and their roles in mRNA translation and posttranscriptional control of gene expression.
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Affiliation(s)
- Qi Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Guangzhou 510640, China
| | - Xin Peng
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Guangzhou 510640, China
| | - Mengyuan Shen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Guangzhou 510640, China
| | - Qian Qian
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Guangzhou 510640, China
| | - Junlian Xing
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Guangzhou 510640, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Guangzhou 510640, China
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
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