1
|
Kong S, Zhu M, Scarpin MR, Pan D, Jia L, Martinez RE, Alamos S, Vadde BVL, Garcia HG, Qian SB, Brunkard JO, Roeder AHK. DRMY1 promotes robust morphogenesis by sustaining the translation of cytokinin signaling inhibitor proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.07.536060. [PMID: 37066395 PMCID: PMC10104159 DOI: 10.1101/2023.04.07.536060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Robustness is the invariant development of phenotype despite environmental changes and genetic perturbations. In the Arabidopsis flower bud, four sepals robustly initiate and grow to constant size to enclose and protect the inner floral organs. We previously characterized the mutant development related myb-like1 ( drmy1 ), where 3-5 sepals initiate variably and grow to different sizes, compromising their protective function. The molecular mechanism underlying this loss of robustness was unclear. Here, we show that drmy1 has reduced TARGET OF RAPAMYCIN (TOR) activity, ribosomal content, and translation. Translation reduction decreases the protein level of ARABIDOPSIS RESPONSE REGULATOR7 (ARR7) and ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 (AHP6), two cytokinin signaling inhibitors that are normally rapidly produced before sepal initiation. The resultant upregulation of cytokinin signaling disrupts robust auxin patterning and sepal initiation. Our work shows that the homeostasis of translation, a ubiquitous cellular process, is crucial for the robust spatiotemporal patterning of organogenesis.
Collapse
|
2
|
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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [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.
Collapse
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
| |
Collapse
|
3
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
4
|
Dasgupta A, Urquidi Camacho RA, Enganti R, Cho SK, Tucker LL, Torreverde JS, Abraham PE, von Arnim AG. A phosphorylation-deficient ribosomal protein eS6 is largely functional in Arabidopsis thaliana, rescuing mutant defects from global translation and gene expression to photosynthesis and growth. PLANT DIRECT 2024; 8:e566. [PMID: 38250458 PMCID: PMC10799217 DOI: 10.1002/pld3.566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/04/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024]
Abstract
The eukaryote-specific ribosomal protein of the small subunit eS6 is phosphorylated through the target of rapamycin (TOR) kinase pathway. Although this phosphorylation event responds dynamically to environmental conditions and has been studied for over 50 years, its biochemical and physiological significance remains controversial and poorly understood. Here, we report data from Arabidopsis thaliana, which indicate that plants expressing only a phospho-deficient isoform of eS6 grow essentially normally under laboratory conditions. The eS6z (RPS6A) paralog of eS6 functionally rescued a double mutant in both rps6a and rps6b genes when expressed at approximately twice the wild-type dosage. A mutant isoform of eS6z lacking the major six phosphorylatable serine and threonine residues in its carboxyl-terminal tail also rescued the lethality, rosette growth, and polyribosome loading of the double mutant. This isoform also complemented many mutant phenotypes of rps6 that were newly characterized here, including photosynthetic efficiency, and most of the gene expression defects that were measured by transcriptomics and proteomics. However, compared with plants rescued with a phospho-enabled version of eS6z, the phospho-deficient seedlings retained a mild pointed-leaf phenotype, root growth was reduced, and certain cell cycle-related mRNAs and ribosome biogenesis proteins were misexpressed. The residual defects of the phospho-deficient seedlings could be understood as an incomplete rescue of the rps6 mutant defects. There was little or no evidence for gain-of-function defects. As previously published, the phospho-deficient eS6z also rescued the rps6a and rps6b single mutants; however, phosphorylation of the eS6y (RPS6B) paralog remained lower than predicted, further underscoring that plants can tolerate phospho-deficiency of eS6 well. Our data also yield new insights into how plants cope with mutations in essential, duplicated ribosomal protein isoforms.
Collapse
Affiliation(s)
- Anwesha Dasgupta
- Department of Biochemistry & Cellular and Molecular BiologyThe University of TennesseeKnoxvilleTennesseeUSA
| | | | - Ramya Enganti
- Department of Biochemistry & Cellular and Molecular BiologyThe University of TennesseeKnoxvilleTennesseeUSA
| | - Sung Ki Cho
- Department of Biochemistry & Cellular and Molecular BiologyThe University of TennesseeKnoxvilleTennesseeUSA
| | - Lindsey L. Tucker
- Department of Biochemistry & Cellular and Molecular BiologyThe University of TennesseeKnoxvilleTennesseeUSA
| | - John S. Torreverde
- Department of Biochemistry & Cellular and Molecular BiologyThe University of TennesseeKnoxvilleTennesseeUSA
| | - Paul E. Abraham
- Graduate School of Genome Science and TechnologyThe University of TennesseeKnoxvilleTennesseeUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Albrecht G. von Arnim
- Department of Biochemistry & Cellular and Molecular BiologyThe University of TennesseeKnoxvilleTennesseeUSA
- Graduate School of Genome Science and TechnologyThe University of TennesseeKnoxvilleTennesseeUSA
| |
Collapse
|
5
|
Sherlock ME, Baquero Galvis L, Vicens Q, Kieft JS, Jagannathan S. Principles, mechanisms, and biological implications of translation termination-reinitiation. RNA (NEW YORK, N.Y.) 2023; 29:865-884. [PMID: 37024263 PMCID: PMC10275272 DOI: 10.1261/rna.079375.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/28/2023] [Indexed: 06/11/2023]
Abstract
The gene expression pathway from DNA sequence to functional protein is not as straightforward as simple depictions of the central dogma might suggest. Each step is highly regulated, with complex and only partially understood molecular mechanisms at play. Translation is one step where the "one gene-one protein" paradigm breaks down, as often a single mature eukaryotic mRNA leads to more than one protein product. One way this occurs is through translation reinitiation, in which a ribosome starts making protein from one initiation site, translates until it terminates at a stop codon, but then escapes normal recycling steps and subsequently reinitiates at a different downstream site. This process is now recognized as both important and widespread, but we are only beginning to understand the interplay of factors involved in termination, recycling, and initiation that cause reinitiation events. There appear to be several ways to subvert recycling to achieve productive reinitiation, different types of stresses or signals that trigger this process, and the mechanism may depend in part on where the event occurs in the body of an mRNA. This perspective reviews the unique characteristics and mechanisms of reinitiation events, highlights the similarities and differences between three major scenarios of reinitiation, and raises outstanding questions that are promising avenues for future research.
Collapse
Affiliation(s)
- Madeline E Sherlock
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Laura Baquero Galvis
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Sujatha Jagannathan
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| |
Collapse
|
6
|
Ma Q, Wang Y, Li S, Wen J, Zhu L, Yan K, Du Y, Li S, Yan L, Xie Z, Lyu Y, Shen F, Li Q. Ribosome footprint profiling enables elucidating the systemic regulation of fatty acid accumulation in Acer truncatum. BMC Biol 2023; 21:68. [PMID: 37013569 PMCID: PMC10071632 DOI: 10.1186/s12915-023-01564-8] [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: 11/18/2022] [Accepted: 03/14/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND The accumulation of fatty acids in plants covers a wide range of functions in plant physiology and thereby affects adaptations and characteristics of species. As the famous woody oilseed crop, Acer truncatum accumulates unsaturated fatty acids and could serve as the model to understand the regulation and trait formation in oil-accumulation crops. Here, we performed Ribosome footprint profiling combing with a multi-omics strategy towards vital time points during seed development, and finally constructed systematic profiling from transcription to proteomes. Additionally, we characterized the small open reading frames (ORFs) and revealed that the translational efficiencies of focused genes were highly influenced by their sequence features. RESULTS The comprehensive multi-omics analysis of lipid metabolism was conducted in A. truncatum. We applied the Ribo-seq and RNA-seq techniques, and the analyses of transcriptional and translational profiles of seeds collected at 85 and 115 DAF were compared. Key members of biosynthesis-related structural genes (LACS, FAD2, FAD3, and KCS) were characterized fully. More meaningfully, the regulators (MYB, ABI, bZIP, and Dof) were identified and revealed to affect lipid biosynthesis via post-translational regulations. The translational features results showed that translation efficiency tended to be lower for the genes with a translated uORF than for the genes with a non-translated uORF. They provide new insights into the global mechanisms underlying the developmental regulation of lipid metabolism. CONCLUSIONS We performed Ribosome footprint profiling combing with a multi-omics strategy in A. truncatum seed development, which provides an example of the use of Ribosome footprint profiling in deciphering the complex regulation network and will be useful for elucidating the metabolism of A. truncatum seed oil and the regulatory mechanisms.
Collapse
Affiliation(s)
- Qiuyue Ma
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Yuxiao Wang
- Nanjing Forestry University, Nanjing, 210037, China
| | - Shushun Li
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Jing Wen
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Lu Zhu
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Kunyuan Yan
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Yiming Du
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China
| | - Shuxian Li
- Nanjing Forestry University, Nanjing, 210037, China
| | - Liping Yan
- Shandong Academy of Forestry Sciences, Jinan, 250014, China
| | - Zhijun Xie
- Xiangyang Forestry Science and Technology Extension Station, Xiangyang, 441000, China
| | - Yunzhou Lyu
- Jiangsu Academy of Forestry, Nanjing, 211153, China.
| | - Fei Shen
- Institute of Biology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100197, China.
| | - Qianzhong Li
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Nanjing, Nanjing, 210014, China.
| |
Collapse
|
7
|
Corydon TJ, Schulz H, Richter P, Strauch SM, Böhmer M, Ricciardi DA, Wehland M, Krüger M, Erzinger GS, Lebert M, Infanger M, Wise PM, Grimm D. Current Knowledge about the Impact of Microgravity on Gene Regulation. Cells 2023; 12:cells12071043. [PMID: 37048115 PMCID: PMC10093652 DOI: 10.3390/cells12071043] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/24/2023] [Accepted: 03/25/2023] [Indexed: 03/31/2023] Open
Abstract
Microgravity (µg) has a massive impact on the health of space explorers. Microgravity changes the proliferation, differentiation, and growth of cells. As crewed spaceflights into deep space are being planned along with the commercialization of space travelling, researchers have focused on gene regulation in cells and organisms exposed to real (r-) and simulated (s-) µg. In particular, cancer and metastasis research benefits from the findings obtained under µg conditions. Gene regulation is a key factor in a cell or an organism’s ability to sustain life and respond to environmental changes. It is a universal process to control the amount, location, and timing in which genes are expressed. In this review, we provide an overview of µg-induced changes in the numerous mechanisms involved in gene regulation, including regulatory proteins, microRNAs, and the chemical modification of DNA. In particular, we discuss the current knowledge about the impact of microgravity on gene regulation in different types of bacteria, protists, fungi, animals, humans, and cells with a focus on the brain, eye, endothelium, immune system, cartilage, muscle, bone, and various cancers as well as recent findings in plants. Importantly, the obtained data clearly imply that µg experiments can support translational medicine on Earth.
Collapse
Affiliation(s)
- Thomas J. Corydon
- Department of Biomedicine, Aarhus University, Hoegh Guldbergs Gade 10, 8000 Aarhus, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Blvd. 99, 8200 Aarhus, Denmark
- Correspondence: ; Tel.: +45-28-992-179
| | - Herbert Schulz
- Department of Microgravity and Translational Regenerative Medicine, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Clinic for Plastic, Aesthetic and Hand Surgery, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Leipziger Straße 44, 39120 Magdeburg, Germany
- Research Group ‘Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt-und Schwerelosigkeitsbedingungen’ (MARS), Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Peter Richter
- Gravitational Biology Group, Department of Biology, Friedrich-Alexander University, 91058 Erlangen, Germany
| | - Sebastian M. Strauch
- Postgraduate Program in Health and Environment, University of Joinville Region, Joinville 89219-710, SC, Brazil
| | - Maik Böhmer
- Institute for Molecular Biosciences, Johann Wolfgang Goethe Universität, 60438 Frankfurt am Main, Germany
| | - Dario A. Ricciardi
- Institute for Molecular Biosciences, Johann Wolfgang Goethe Universität, 60438 Frankfurt am Main, Germany
| | - Markus Wehland
- Department of Microgravity and Translational Regenerative Medicine, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Clinic for Plastic, Aesthetic and Hand Surgery, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Leipziger Straße 44, 39120 Magdeburg, Germany
- Research Group ‘Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt-und Schwerelosigkeitsbedingungen’ (MARS), Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Marcus Krüger
- Department of Microgravity and Translational Regenerative Medicine, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Research Group ‘Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt-und Schwerelosigkeitsbedingungen’ (MARS), Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Gilmar S. Erzinger
- Postgraduate Program in Health and Environment, University of Joinville Region, Joinville 89219-710, SC, Brazil
| | - Michael Lebert
- Gravitational Biology Group, Department of Biology, Friedrich-Alexander University, 91058 Erlangen, Germany
| | - Manfred Infanger
- Department of Microgravity and Translational Regenerative Medicine, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Clinic for Plastic, Aesthetic and Hand Surgery, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Leipziger Straße 44, 39120 Magdeburg, Germany
- Research Group ‘Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt-und Schwerelosigkeitsbedingungen’ (MARS), Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Petra M. Wise
- Department of Microgravity and Translational Regenerative Medicine, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Research Group ‘Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt-und Schwerelosigkeitsbedingungen’ (MARS), Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- The Saban Research Institute, Children’s Hospital Los Angeles, University of Southern California, 4650 Sunset Blvd, Los Angeles, CA 90027, USA
| | - Daniela Grimm
- Department of Biomedicine, Aarhus University, Hoegh Guldbergs Gade 10, 8000 Aarhus, Denmark
- Department of Microgravity and Translational Regenerative Medicine, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Clinic for Plastic, Aesthetic and Hand Surgery, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Leipziger Straße 44, 39120 Magdeburg, Germany
- Research Group ‘Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt-und Schwerelosigkeitsbedingungen’ (MARS), Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
| |
Collapse
|
8
|
Maruta T. How does light facilitate vitamin C biosynthesis in leaves? Biosci Biotechnol Biochem 2022; 86:1173-1182. [PMID: 35746883 DOI: 10.1093/bbb/zbac096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/14/2022] [Indexed: 11/14/2022]
Abstract
Plants store ascorbate in high concentrations, particularly in their leaves. Ascorbate is an excellent antioxidant that acts as an indispensable photoprotectant. The D-mannose/L-galactose pathway is responsible for ascorbate biosynthesis in plants. Light facilitates ascorbate biosynthesis in a light intensity-dependent manner to enhance ascorbate pool size in leaves, and photosynthesis is required for this process. Light- and photosynthesis-dependent activation of the rate-limiting enzyme GDP-L-galactose phosphorylase (GGP) plays a critical role in ascorbate pool size regulation. In addition, the tight regulation of ascorbate biosynthesis by ascorbate itself has been proposed. Ascorbate represses GGP translation in a dose-dependent manner through the upstream open reading frame in the 5'-untranslated regions of the gene, which may compete with the light-dependent activation of ascorbate biosynthesis. This review focuses on ascorbate biosynthesis based on past and latest findings and critically discusses how light activates this process.
Collapse
Affiliation(s)
- Takanori Maruta
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu, Matsue, Shimane, Japan
| |
Collapse
|
9
|
Translational regulation in pathogenic and beneficial plant-microbe interactions. Biochem J 2021; 478:2775-2788. [PMID: 34297042 DOI: 10.1042/bcj20210066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/17/2022]
Abstract
Plants are surrounded by a vast diversity of microorganisms. Limiting pathogenic microorganisms is crucial for plant survival. On the other hand, the interaction of plants with beneficial microorganisms promotes their growth or allows them to overcome nutrient deficiencies. Balancing the number and nature of these interactions is crucial for plant growth and development, and thus, for crop productivity in agriculture. Plants use sophisticated mechanisms to recognize pathogenic and beneficial microorganisms and genetic programs related to immunity or symbiosis. Although most research has focused on characterizing changes in the transcriptome during plant-microbe interactions, the application of techniques such as Translating Ribosome Affinity Purification (TRAP) and Ribosome profiling allowed examining the dynamic association of RNAs to the translational machinery, highlighting the importance of the translational level of control of gene expression in both pathogenic and beneficial interactions. These studies revealed that the transcriptional and the translational responses are not always correlated, and that translational control operates at cell-specific level. In addition, translational control is governed by cis-elements present in the 5'mRNA leader of regulated mRNAs, e.g. upstream open reading frames (uORFs) and sequence-specific motifs. In this review, we summarize and discuss the recent advances made in the field of translational control during pathogenic and beneficial plant-microbe interactions.
Collapse
|
10
|
Hata T, Satoh S, Takada N, Matsuo M, Obokata J. Kozak Sequence Acts as a Negative Regulator for De Novo Transcription Initiation of Newborn Coding Sequences in the Plant Genome. Mol Biol Evol 2021; 38:2791-2803. [PMID: 33705557 PMCID: PMC8233501 DOI: 10.1093/molbev/msab069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The manner in which newborn coding sequences and their transcriptional competency emerge during the process of gene evolution remains unclear. Here, we experimentally simulated eukaryotic gene origination processes by mimicking horizontal gene transfer events in the plant genome. We mapped the precise position of the transcription start sites (TSSs) of hundreds of newly introduced promoterless firefly luciferase (LUC) coding sequences in the genome of Arabidopsis thaliana cultured cells. The systematic characterization of the LUC-TSSs revealed that 80% of them occurred under the influence of endogenous promoters, while the remainder underwent de novo activation in the intergenic regions, starting from pyrimidine-purine dinucleotides. These de novo TSSs obeyed unexpected rules; they predominantly occurred ∼100 bp upstream of the LUC inserts and did not overlap with Kozak-containing putative open reading frames (ORFs). These features were the output of the immediate responses to the sequence insertions, rather than a bias in the screening of the LUC gene function. Regarding the wild-type genic TSSs, they appeared to have evolved to lack any ORFs in their vicinities. Therefore, the repulsion by the de novo TSSs of Kozak-containing ORFs described above might be the first selection gate for the occurrence and evolution of TSSs in the plant genome. Based on these results, we characterized the de novo type of TSS identified in the plant genome and discuss its significance in genome evolution.
Collapse
Affiliation(s)
- Takayuki Hata
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto, Japan
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka, Japan
| | - Soichirou Satoh
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto, Japan
| | - Naoto Takada
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto, Japan
| | - Mitsuhiro Matsuo
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka, Japan
| | - Junichi Obokata
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka, Japan
| |
Collapse
|
11
|
Lin L, Cao J, Du A, An Q, Chen X, Yuan S, Batool W, Shabbir A, Zhang D, Wang Z, Norvienyeku J. eIF3k Domain-Containing Protein Regulates Conidiogenesis, Appressorium Turgor, Virulence, Stress Tolerance, and Physiological and Pathogenic Development of Magnaporthe oryzae Oryzae. FRONTIERS IN PLANT SCIENCE 2021; 12:748120. [PMID: 34733303 PMCID: PMC8558559 DOI: 10.3389/fpls.2021.748120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/22/2021] [Indexed: 05/05/2023]
Abstract
The eukaryotic translation initiation factor 3 (eIF3) complex consists of essential and non-essential sub-complexes. Non-essential eIF3 complex subunits, such as eIF3e, eIF3j, eIF3k, and eIF3l, modulate stress tolerance and enhance the lifespan of Neurospora crassa and Caenorhabditis elegans. However, there is limited knowledge of the role of the non-essential eIF3 sub-complex in the pathophysiological development of plant fungal pathogens. Here, we deployed genetic and biochemical techniques to explore the influence of a hypothetical protein containing eIF3k domain in Magnaporthe oryzae Oryzae (MoOeIF3k) on reproduction, hyphae morphogenesis, stress tolerance, and pathogenesis. Also, the targeted disruption of MoOeIF3k suppressed vegetative growth and asexual sporulation in ΔMoOeif3k strains significantly. We demonstrated that MoOeIF3k promotes the initiation and development of the rice blast disease by positively regulating the mobilization and degradation of glycogen, appressorium integrity, host penetration, and colonization during host-pathogen interaction. For the first time, we demonstrated that the eIF3k subunit supports the survival of the blast fungus by suppressing vegetative growth and possibly regulating the conversions and utilization of stored cellular energy reserves under starvation conditions. We also observed that the deletion of MoOeIF3k accelerated ribosomal RNA (rRNA) generation in the ΔMoOeif3k strains with a corresponding increase in total protein output. In summary, this study unravels the pathophysiological significance of eIF3k filamentous fungi. The findings also underscored the need to systematically evaluate the individual subunits of the non-essential eIF3 sub-complex during host-pathogen interaction. Further studies are required to unravel the influence of synergetic coordination between translation and transcriptional regulatory machinery on the pathogenesis of filamentous fungi pathogens.
Collapse
Affiliation(s)
- Lili Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiaying Cao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Anqiang Du
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiuli An
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaomin Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuangshuang Yuan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wajjiha Batool
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ammarah Shabbir
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dongmei Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Oceanography, Minjiang University, Fuzhou, China
- Zonghua Wang,
| | - Justice Norvienyeku
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
- *Correspondence: Justice Norvienyeku,
| |
Collapse
|
12
|
Urquidi-Camacho RA, Lokdarshi A, von Arnim AG. Translational gene regulation in plants: A green new deal. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1597. [PMID: 32367681 PMCID: PMC9258721 DOI: 10.1002/wrna.1597] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 01/09/2023]
Abstract
The molecular machinery for protein synthesis is profoundly similar between plants and other eukaryotes. Mechanisms of translational gene regulation are embedded into the broader network of RNA-level processes including RNA quality control and RNA turnover. However, over eons of their separate history, plants acquired new components, dropped others, and generally evolved an alternate way of making the parts list of protein synthesis work. Research over the past 5 years has unveiled how plants utilize translational control to defend themselves against viruses, regulate translation in response to metabolites, and reversibly adjust translation to a wide variety of environmental parameters. Moreover, during seed and pollen development plants make use of RNA granules and other translational controls to underpin developmental transitions between quiescent and metabolically active stages. The economics of resource allocation over the daily light-dark cycle also include controls over cellular protein synthesis. Important new insights into translational control on cytosolic ribosomes continue to emerge from studies of translational control mechanisms in viruses. Finally, sketches of coherent signaling pathways that connect external stimuli with a translational response are emerging, anchored in part around TOR and GCN2 kinase signaling networks. These again reveal some mechanisms that are familiar and others that are different from other eukaryotes, motivating deeper studies on translational control in plants. This article is categorized under: Translation > Translation Regulation RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
Affiliation(s)
- Ricardo A. Urquidi-Camacho
- UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996
| | - Ansul Lokdarshi
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Albrecht G von Arnim
- Department of Biochemistry & Cellular and Molecular Biology and UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996
| |
Collapse
|
13
|
Xing S, Chen K, Zhu H, Zhang R, Zhang H, Li B, Gao C. Fine-tuning sugar content in strawberry. Genome Biol 2020; 21:230. [PMID: 32883370 PMCID: PMC7470447 DOI: 10.1186/s13059-020-02146-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/17/2020] [Indexed: 01/30/2023] Open
Abstract
Fine-tuning quantitative traits for continuous subtle phenotypes is highly advantageous. We engineer the highly conserved upstream open reading frame (uORF) of FvebZIPs1.1 in strawberry (Fragaria vesca), using base editor A3A-PBE. Seven novel alleles are generated. Sugar content of the homozygous T1 mutant lines is 33.9-83.6% higher than that of the wild-type. We also recover a series of transgene-free mutants with 35 novel genotypes containing a continuum of sugar content. All the novel genotypes could be immediately fixed in subsequent generations by asexual reproduction. Genome editing coupled with asexual reproduction offers tremendous opportunities for quantitative trait improvement.
Collapse
Affiliation(s)
- Sinian Xing
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Haocheng Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Rui Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Huawei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Bingbing Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
14
|
Wolf DA, Lin Y, Duan H, Cheng Y. eIF-Three to Tango: emerging functions of translation initiation factor eIF3 in protein synthesis and disease. J Mol Cell Biol 2020; 12:403-409. [PMID: 32279082 PMCID: PMC7333474 DOI: 10.1093/jmcb/mjaa018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/20/2020] [Accepted: 02/17/2020] [Indexed: 12/12/2022] Open
Abstract
Studies over the past three years have substantially expanded the involvements of eukaryotic initiation factor 3 (eIF3) in messenger RNA (mRNA) translation. It now appears that this multi-subunit complex is involved in every possible form of mRNA translation, controlling every step of protein synthesis from initiation to elongation, termination, and quality control in positive as well as negative fashion. Through the study of eIF3, we are beginning to appreciate protein synthesis as a highly integrated process coordinating protein production with protein folding, subcellular targeting, and degradation. At the same time, eIF3 subunits appear to have specific functions that probably vary between different tissues and individual cells. Considering the broad functions of eIF3 in protein homeostasis, it comes as little surprise that eIF3 is increasingly implicated in major human diseases and first attempts at therapeutically targeting eIF3 have been undertaken. Much remains to be learned, however, about subunit- and tissue-specific functions of eIF3 in protein synthesis and disease and their regulation by environmental conditions and post-translational modifications.
Collapse
Affiliation(s)
- Dieter A Wolf
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research & Innovation Center for Cell Stress Signaling, Xiamen University, Xiamen 361102, China
| | - Yingying Lin
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research & Innovation Center for Cell Stress Signaling, Xiamen University, Xiamen 361102, China
| | - Haoran Duan
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research & Innovation Center for Cell Stress Signaling, Xiamen University, Xiamen 361102, China
| | - Yabin Cheng
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research & Innovation Center for Cell Stress Signaling, Xiamen University, Xiamen 361102, China
| |
Collapse
|
15
|
Lokdarshi A, Papdi C, Pettkó-Szandtner A, Dorokhov S, Scheres B, Magyar Z, von Arnim AG, Bögre L, Horváth BM. ErbB-3 BINDING PROTEIN 1 Regulates Translation and Counteracts RETINOBLASTOMA RELATED to Maintain the Root Meristem. PLANT PHYSIOLOGY 2020; 182:919-932. [PMID: 31818906 PMCID: PMC6997692 DOI: 10.1104/pp.19.00805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/22/2019] [Indexed: 05/09/2023]
Abstract
The ErbB-3 BINDING PROTEIN 1 (EBP1) drives growth, but the mechanism of how it acts in plants is little understood. Here, we show that EBP1 expression and protein abundance in Arabidopsis (Arabidopsis thaliana) are predominantly confined to meristematic cells and are induced by sucrose and partially dependent on TARGET OF RAPAMYCIN (TOR) kinase activity. Consistent with being downstream of TOR, silencing of EBP1 restrains, while overexpression promotes, root growth, mostly under sucrose-limiting conditions. Inducible overexpression of RETINOBLASTOMA RELATED (RBR), a sugar-dependent transcriptional repressor of cell proliferation, depletes meristematic activity and causes precocious differentiation, which is attenuated by EBP1. To understand the molecular mechanism, we searched for EBP1- and RBR-interacting proteins by affinity purification and mass spectrometry. In line with the double-stranded RNA-binding activity of EBP1 in human (Homo sapiens) cells, the overwhelming majority of EBP1 interactors are part of ribonucleoprotein complexes regulating many aspects of protein synthesis, including ribosome biogenesis and mRNA translation. We confirmed that EBP1 associates with ribosomes and that EBP1 silencing hinders ribosomal RNA processing. We revealed that RBR also interacts with a set of EBP1-associated nucleolar proteins as well as factors that function in protein translation. This suggests EBP1 and RBR act antagonistically on common processes that determine the capacity for translation to tune meristematic activity in relation to available resources.
Collapse
Affiliation(s)
- Ansul Lokdarshi
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Csaba Papdi
- Department of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham Hill, Egham TW20 0EX, United Kingdom
| | - Aladár Pettkó-Szandtner
- Laboratory of Proteomics Research, Biological Research Centre, POB 521, H-6701 Szeged, Hungary
| | - Stefan Dorokhov
- Department of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham Hill, Egham TW20 0EX, United Kingdom
| | - Ben Scheres
- Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Zoltán Magyar
- Institute of Plant Biology, Biological Research Centre, POB 521, H-6701 Szeged, Hungary
| | - Albrecht G von Arnim
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
- UT-ORNL Graduate School of Genome Science and Technology, Knoxville, Tennessee 37996
| | - László Bögre
- Department of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham Hill, Egham TW20 0EX, United Kingdom
| | - Beatrix M Horváth
- Department of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham Hill, Egham TW20 0EX, United Kingdom
- Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
16
|
Raabe K, Honys D, Michailidis C. The role of eukaryotic initiation factor 3 in plant translation regulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 145:75-83. [PMID: 31665669 DOI: 10.1016/j.plaphy.2019.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/07/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Regulation of translation represents a critical step in the regulation of gene expression. In plants, the translation regulation plays an important role at all stages of development and, during stress responses, functions as a fast and flexible tool which not only modulates the global translation rate but also controls the production of specific proteins. Regulation of translation is mostly focused on the initiation phase. There, one of essential initiation factors is the large multisubunit protein complex of eukaryotic translation initiation factor 3 (eIF3). In all eukaryotes, the general eIF3 function is to scaffold the formation of the translation initiation complex and to enhance the accuracy of scanning mechanism for start codon selection. Over the past decades, additional eIF3 functions were described as necessary for development in various eukaryotic organisms, including plants. The importance of the eIF3 complex lies not only at the global level of initiation event, but also in the precise translation regulation of specific transcripts. This review gathers the available information on functions of the plant eIF3 complex.
Collapse
Affiliation(s)
- Karel Raabe
- Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojová 263, 165 02, Praha 6, Czech Republic
| | - David Honys
- Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojová 263, 165 02, Praha 6, Czech Republic
| | - Christos Michailidis
- Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojová 263, 165 02, Praha 6, Czech Republic.
| |
Collapse
|
17
|
Wu HYL, Song G, Walley JW, Hsu PY. The Tomato Translational Landscape Revealed by Transcriptome Assembly and Ribosome Profiling. PLANT PHYSIOLOGY 2019; 181:367-380. [PMID: 31248964 PMCID: PMC6716236 DOI: 10.1104/pp.19.00541] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/10/2019] [Indexed: 05/14/2023]
Abstract
Recent applications of translational control in Arabidopsis (Arabidopsis thaliana) highlight the potential power of manipulating mRNA translation for crop improvement. However, to what extent translational regulation is conserved between Arabidopsis and other species is largely unknown, and the translatome of most crops remains poorly studied. Here, we combined de novo transcriptome assembly and ribosome profiling to study global mRNA translation in tomato (Solanum lycopersicum) roots. Exploiting features corresponding to active translation, we discovered widespread unannotated translation events, including 1,329 upstream open reading frames (uORFs) within the 5' untranslated regions of annotated coding genes and 354 small ORFs (sORFs) among unannotated transcripts. uORFs may repress translation of their downstream main ORFs, whereas sORFs may encode signaling peptides. Besides evolutionarily conserved sORFs, we uncovered 96 Solanaceae-specific sORFs, revealing the importance of studying translatomes directly in crops. Proteomic analysis confirmed that some of the unannotated ORFs generate stable proteins in planta. In addition to defining the translatome, our results reveal the global regulation by uORFs and microRNAs. Despite diverging over 100 million years ago, many translational features are well conserved between Arabidopsis and tomato. Thus, our approach provides a high-throughput method to discover unannotated ORFs, elucidates evolutionarily conserved and unique translational features, and identifies regulatory mechanisms hidden in a crop genome.
Collapse
Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| |
Collapse
|
18
|
Chen K, Guo T, Li XM, Zhang YM, Yang YB, Ye WW, Dong NQ, Shi CL, Kan Y, Xiang YH, Zhang H, Li YC, Gao JP, Huang X, Zhao Q, Han B, Shan JX, Lin HX. Translational Regulation of Plant Response to High Temperature by a Dual-Function tRNA His Guanylyltransferase in Rice. MOLECULAR PLANT 2019; 12:1123-1142. [PMID: 31075443 DOI: 10.1016/j.molp.2019.04.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 04/11/2019] [Accepted: 04/29/2019] [Indexed: 05/23/2023]
Abstract
As sessile organisms, plants have evolved numerous strategies to acclimate to changes in environmental temperature. However, the molecular basis of this acclimation remains largely unclear. In this study we identified a tRNAHis guanylyltransferase, AET1, which contributes to the modification of pre-tRNAHis and is required for normal growth under high-temperature conditions in rice. Interestingly, AET1 possibly interacts with both RACK1A and eIF3h in the endoplasmic reticulum. Notably, AET1 can directly bind to OsARF mRNAs including the uORFs of OsARF19 and OsARF23, indicating that AET1 is associated with translation regulation. Furthermore, polysome profiling assays suggest that the translational status remains unaffected in the aet1 mutant, but that the translational efficiency of OsARF19 and OsARF23 is reduced; moreover, OsARF23 protein levels are obviously decreased in the aet1 mutant under high temperature, implying that AET1 regulates auxin signaling in response to high temperature. Our findings provide new insights into the molecular mechanisms whereby AET1 regulates the environmental temperature response in rice by playing a dual role in tRNA modification and translational control.
Collapse
Affiliation(s)
- Ke Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Xin-Min Li
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Yi-Min Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Bing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Chuan-Lin Shi
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Kan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - You-Huang Xiang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hai Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ya-Chao Li
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ji-Ping Gao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Xuehui Huang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Qiang Zhao
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Bin Han
- University of the Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China.
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| |
Collapse
|
19
|
Salomé PA, Merchant SS. A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism. THE PLANT CELL 2019; 31:1682-1707. [PMID: 31189738 PMCID: PMC6713297 DOI: 10.1105/tpc.18.00952] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/20/2019] [Accepted: 06/08/2019] [Indexed: 05/13/2023]
Abstract
The unicellular alga Chlamydomonas reinhardtii is a classical reference organism for studying photosynthesis, chloroplast biology, cell cycle control, and cilia structure and function. It is also an emerging model for studying sensory cilia, the production of high-value bioproducts, and in situ structural determination. Much of the early appeal of Chlamydomonas was rooted in its promise as a genetic system, but like other classic model organisms, this rise to prominence predated the discovery of the structure of DNA, whole-genome sequences, and molecular techniques for gene manipulation. The haploid genome of C. reinhardtii facilitates genetic analyses and offers many of the advantages of microbial systems applied to a photosynthetic organism. C. reinhardtii has contributed to our understanding of chloroplast-based photosynthesis and cilia biology. Despite pervasive transgene silencing, technological advances have allowed researchers to address outstanding lines of inquiry in algal research. The most thoroughly studied unicellular alga, C. reinhardtii, is the current standard for algal research, and although genome editing is still far from efficient and routine, it nevertheless serves as a template for other algae. We present a historical retrospective of the rise of C. reinhardtii to illuminate its past and present. We also present resources for current and future scientists who may wish to expand their studies to the realm of microalgae.
Collapse
Affiliation(s)
- Patrice A Salomé
- University of California, Los Angeles, Department of Chemistry and Biochemistry, Los Angeles, CA 90095
| | - Sabeeha S Merchant
- University of California, Los Angeles, Department of Chemistry and Biochemistry, Los Angeles, CA 90095
- University of California, Berkeley, Departments of Plant and Microbial Biology and Molecular and Cell Biology, Berkeley, CA 94720
| |
Collapse
|
20
|
Transcripts from downstream alternative transcription start sites evade uORF-mediated inhibition of gene expression in Arabidopsis. Proc Natl Acad Sci U S A 2018; 115:7831-7836. [PMID: 29915080 PMCID: PMC6064979 DOI: 10.1073/pnas.1804971115] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The upstream ORFs (uORFs) in the 5′UTRs of mRNA often function as repressors of main ORF translation or triggers of nonsense-mediated mRNA decay. In this study, we report on transcription start site (TSS) selection when etiolated Arabidopsis seedlings are exposed to blue light, and reveal that transcription from uORF-avoiding TSSs is induced throughout the genome. It is possible that transcripts arising from TSSs downstream of uORFs evade uORF-mediated inhibition of gene expression. Thus, uORF-avoiding transcription starts are an important mechanism of gene expression regulation during a plant’s response to environmental changes. Plants adapt to alterations in light conditions by controlling their gene expression profiles. Expression of light-inducible genes is transcriptionally induced by transcription factors such as HY5. However, few detailed analyses have been carried out on the control of transcription start sites (TSSs). Of the various wavelengths of light, it is blue light (BL) that regulates physiological responses such as hypocotyl elongation and flowering time. To understand how gene expression is controlled not only by transcript abundance but also by TSS selection, we examined genome-wide TSS profiles in Arabidopsis seedlings after exposure to BL irradiation following initial growth in the dark. Thousands of genes use multiple TSSs, and some transcripts have upstream ORFs (uORFs) that take precedence over the main ORF (mORF) encoding proteins. The uORFs often function as translation inhibitors of the mORF or as triggers of nonsense-mediated mRNA decay (NMD). Transcription from TSSs located downstream of the uORFs in 220 genes is enhanced by BL exposure. This type of regulation is found in HY5 and HYH, major regulators of light-dependent gene expression. Translation efficiencies of the genes showing enhanced usage of these TSSs increased upon BL exposure. We also show that transcripts from TSSs upstream of uORFs in 45 of the 220 genes, including HY5, accumulated in a mutant of NMD. These results suggest that BL controls gene expression not only by enhancing transcriptions but also by choosing the TSS, and transcripts from downstream TSSs evade uORF-mediated inhibition to ensure high expression of light-regulated genes.
Collapse
|
21
|
Hong S, Liu Y, Xiong H, Cai D, Fan Q. Eukaryotic translation initiation factor 3H suppression inhibits osteocarcinoma cell growth and tumorigenesis. Exp Ther Med 2018; 15:4925-4931. [PMID: 29805516 PMCID: PMC5952081 DOI: 10.3892/etm.2018.6031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 03/07/2018] [Indexed: 01/09/2023] Open
Abstract
Eukaryotic translation initiation factor 3H subunit (EIF3H) is a member of the EIF3 family and exhibits a central role in translation initiation in higher eukaryotes. Although EIF3H expression is upregulated in numerous tumour types, its potential role in human osteosarcoma (OS) has not yet been investigated. In the present study, it was demonstrated that EIF3H mRNA expression was upregulated in the human OS cell lines Saos-2 and U2OS. A recombinant lentivirus harbouring short hairpin RNA targeting EIF3H was constructed and successfully infected human OS Saos-2 and U2OS cells, resulting in 95% downregulated EIF3H expression compared with the respective control groups. Knockdown of EIF3H significantly inhibited the proliferation and colony formation of OS cells in vitro, and tumour growth in nude mice in vivo. Flow cytometry analysis revealed cell cycle arrest and promotion of apoptosis in OS cells with EIF3H knocked down. In conclusion, the results strongly suggested that EIF3H is a critical factor mediating the growth of OS cells and may represent a novel therapeutic target.
Collapse
Affiliation(s)
- Song Hong
- Department of Orthopedics, Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou 563003, P.R. China
| | - Yi Liu
- Department of Orthopedics, Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou 563003, P.R. China
| | - Huazhang Xiong
- Department of Orthopedics, Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou 563003, P.R. China
| | - Dongfeng Cai
- Department of Orthopedics, Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou 563003, P.R. China
| | - Qinghong Fan
- Department of Orthopedics, Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou 563003, P.R. China
| |
Collapse
|
22
|
Gunišová S, Hronová V, Mohammad MP, Hinnebusch AG, Valášek LS. Please do not recycle! Translation reinitiation in microbes and higher eukaryotes. FEMS Microbiol Rev 2018; 42:165-192. [PMID: 29281028 PMCID: PMC5972666 DOI: 10.1093/femsre/fux059] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 12/20/2017] [Indexed: 12/14/2022] Open
Abstract
Protein production must be strictly controlled at its beginning and end to synthesize a polypeptide that faithfully copies genetic information carried in the encoding mRNA. In contrast to viruses and prokaryotes, the majority of mRNAs in eukaryotes contain only one coding sequence, resulting in production of a single protein. There are, however, many exceptional mRNAs that either carry short open reading frames upstream of the main coding sequence (uORFs) or even contain multiple long ORFs. A wide variety of mechanisms have evolved in microbes and higher eukaryotes to prevent recycling of some or all translational components upon termination of the first translated ORF in such mRNAs and thereby enable subsequent translation of the next uORF or downstream coding sequence. These specialized reinitiation mechanisms are often regulated to couple translation of the downstream ORF to various stimuli. Here we review all known instances of both short uORF-mediated and long ORF-mediated reinitiation and present our current understanding of the underlying molecular mechanisms of these intriguing modes of translational control.
Collapse
Affiliation(s)
- Stanislava Gunišová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
| | - Vladislava Hronová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
| | - Mahabub Pasha Mohammad
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
| |
Collapse
|
23
|
Schepetilnikov M, Ryabova LA. Recent Discoveries on the Role of TOR (Target of Rapamycin) Signaling in Translation in Plants. PLANT PHYSIOLOGY 2018; 176:1095-1105. [PMID: 29122989 PMCID: PMC5813564 DOI: 10.1104/pp.17.01243] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/09/2017] [Indexed: 05/18/2023]
Abstract
TOR signaling regulates plant translation via a specific translation initiation mechanism: reinitiation.
Collapse
Affiliation(s)
- Mikhail Schepetilnikov
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Lyubov A Ryabova
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, 67084 Strasbourg, France
| |
Collapse
|
24
|
Valášek LS, Zeman J, Wagner S, Beznosková P, Pavlíková Z, Mohammad MP, Hronová V, Herrmannová A, Hashem Y, Gunišová S. Embraced by eIF3: structural and functional insights into the roles of eIF3 across the translation cycle. Nucleic Acids Res 2017; 45:10948-10968. [PMID: 28981723 PMCID: PMC5737393 DOI: 10.1093/nar/gkx805] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/31/2017] [Indexed: 12/31/2022] Open
Abstract
Protein synthesis is mediated via numerous molecules including the ribosome, mRNA, tRNAs, as well as translation initiation, elongation and release factors. Some of these factors play several roles throughout the entire process to ensure proper assembly of the preinitiation complex on the right mRNA, accurate selection of the initiation codon, errorless production of the encoded polypeptide and its proper termination. Perhaps, the most intriguing of these multitasking factors is the eukaryotic initiation factor eIF3. Recent evidence strongly suggests that this factor, which coordinates the progress of most of the initiation steps, does not come off the initiation complex upon subunit joining, but instead it remains bound to 80S ribosomes and gradually falls off during the first few elongation cycles to: (1) promote resumption of scanning on the same mRNA molecule for reinitiation downstream—in case of translation of upstream ORFs short enough to preserve eIF3 bound; or (2) come back during termination on long ORFs to fine tune its fidelity or, if signaled, promote programmed stop codon readthrough. Here, we unite recent structural views of the eIF3–40S complex and discus all known eIF3 roles to provide a broad picture of the eIF3’s impact on translational control in eukaryotic cells.
Collapse
Affiliation(s)
- Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Jakub Zeman
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Susan Wagner
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Petra Beznosková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Zuzana Pavlíková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Mahabub Pasha Mohammad
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Vladislava Hronová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Anna Herrmannová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Yaser Hashem
- CNRS, Architecture et Réactivité de l'ARN UPR9002, Université de Strasbourg, 67084 Strasbourg, France
| | - Stanislava Gunišová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| |
Collapse
|
25
|
Hsu PY, Benfey PN. Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants. Proteomics 2017; 18:e1700038. [PMID: 28759167 DOI: 10.1002/pmic.201700038] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/26/2017] [Indexed: 12/18/2022]
Abstract
Peptides encoded by small open reading frames (sORFs, usually <100 codons) play critical regulatory roles in plant development and environmental responses. Despite their importance, only a small number of these peptides have been identified and characterized. Genomic studies have revealed that many plant genomes contain thousands of possible sORFs, which could potentially encode small peptides. The challenge is to distinguish translated sORFs from nontranslated ones. Here, we highlight advances in methodologies for identifying these hidden sORFs in plant genomes, including ribosome profiling and proteomics. We also examine the evidence for new peptides arising from sORFs and discuss their functions in plant development, environmental responses, and translational control.
Collapse
Affiliation(s)
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC, USA.,Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| |
Collapse
|
26
|
Zhang L, Liu X, Gaikwad K, Kou X, Wang F, Tian X, Xin M, Ni Z, Sun Q, Peng H, Vierling E. Mutations in eIF5B Confer Thermosensitive and Pleiotropic Phenotypes via Translation Defects in Arabidopsis thaliana. THE PLANT CELL 2017; 29:1952-1969. [PMID: 28808135 PMCID: PMC5590492 DOI: 10.1105/tpc.16.00808] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 06/16/2017] [Accepted: 08/09/2017] [Indexed: 05/19/2023]
Abstract
The conserved eukaryotic translation initiation factor 5B, eIF5B, is a GTPase that acts late in translation initiation. We found that an Arabidopsis thaliana mutant sensitive to hot temperatures 3 (hot3-1), which behaves as the wild type in the absence of stress but is unable to acclimate to high temperature, carries a missense mutation in the eIF5B1 gene (At1g76810), producing a temperature sensitive protein. A more severe, T-DNA insertion allele (hot3-2) causes pleiotropic developmental phenotypes. Surprisingly, Arabidopsis has three other eIF5B genes that do not substitute for eIF5B1; two of these appear to be in the process of pseudogenization. Polysome profiling and RNA-seq analysis of hot3-1 plants show delayed recovery of polysomes after heat stress and reduced translational efficiency (TE) of a subset of stress protective proteins, demonstrating the critical role of translational control early in heat acclimation. Plants carrying the severe hot3-2 allele show decreased TE of auxin-regulated, ribosome-related, and electron transport genes, even under optimal growth conditions. The hot3-2 data suggest that disrupting specific eIF5B interactions on the ribosome can, directly or indirectly, differentially affect translation. Thus, modulating eIF5B interactions could be another mechanism of gene-specific translational control.
Collapse
Affiliation(s)
- Liyuan Zhang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P.R. China
| | - Xinye Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P.R. China
| | - Kishor Gaikwad
- National Research Centre on Plant Biotechnology, New Delhi 110012, India
| | - Xiaoxia Kou
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P.R. China
| | - Fei Wang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P.R. China
| | - Xuejun Tian
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P.R. China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P.R. China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P.R. China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P.R. China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P.R. China
| | - Elizabeth Vierling
- University of Massachusetts Amherst, Biochemistry and Molecular Biology, Amherst, Massachusetts 01003
| |
Collapse
|
27
|
Merchante C, Stepanova AN, Alonso JM. Translation regulation in plants: an interesting past, an exciting present and a promising future. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:628-653. [PMID: 28244193 DOI: 10.1111/tpj.13520] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/17/2017] [Accepted: 02/21/2017] [Indexed: 05/19/2023]
Abstract
Changes in gene expression are at the core of most biological processes, from cell differentiation to organ development, including the adaptation of the whole organism to the ever-changing environment. Although the central role of transcriptional regulation is solidly established and the general mechanisms involved in this type of regulation are relatively well understood, it is clear that regulation at a translational level also plays an essential role in modulating gene expression. Despite the large number of examples illustrating the critical role played by translational regulation in determining the expression levels of a gene, our understanding of the molecular mechanisms behind such types of regulation has been slow to emerge. With the recent development of high-throughput approaches to map and quantify different critical parameters affecting translation, such as RNA structure, protein-RNA interactions and ribosome occupancy at the genome level, a renewed enthusiasm toward studying translation regulation is warranted. The use of these new powerful technologies in well-established and uncharacterized translation-dependent processes holds the promise to decipher the likely complex and diverse, but also fascinating, mechanisms behind the regulation of translation.
Collapse
Affiliation(s)
- Catharina Merchante
- Departamento de Biologia Molecular y Bioquimica, Universidad de Malaga-Instituto de Hortofruticultura Subtropical y Mediterranea, IHSM-UMA-CSIC, Malaga, Andalucía, Spain
| | - Anna N Stepanova
- Department of Plant and Microbial Biology, Genetics Graduate Program, North Carolina State University, Raleigh, NC, 27607, USA
| | - Jose M Alonso
- Department of Plant and Microbial Biology, Genetics Graduate Program, North Carolina State University, Raleigh, NC, 27607, USA
| |
Collapse
|
28
|
Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis. Proc Natl Acad Sci U S A 2016; 113:E7126-E7135. [PMID: 27791167 DOI: 10.1073/pnas.1614788113] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Because ribosomes decode mRNA every 3 nt, the periodic property of ribosome footprints could be used to identify novel translated ORFs. However, due to the limited resolution of existing methods, the 3-nt periodicity is observed mostly in a global analysis, but not in individual transcripts. Here, we report a protocol applied to Arabidopsis that maps over 90% of the footprints to the main reading frame and thus offers super-resolution profiles for individual transcripts to precisely define translated regions. The resulting data not only support many annotated and predicted noncanonical translation events but also uncover small ORFs in annotated noncoding RNAs and pseudogenes. A substantial number of these unannotated ORFs are evolutionarily conserved, and some produce stable proteins. Thus, our study provides a valuable resource for plant genomics and an efficient optimization strategy for ribosome profiling in other organisms.
Collapse
|
29
|
Wang W, Xu M, Liu X, Tu J. The Rice Eukaryotic Translation Initiation Factor 3 Subunit e (OseIF3e) Influences Organ Size and Pollen Maturation. FRONTIERS IN PLANT SCIENCE 2016; 7:1399. [PMID: 27703462 PMCID: PMC5028392 DOI: 10.3389/fpls.2016.01399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/02/2016] [Indexed: 05/24/2023]
Abstract
Eukaryotic translation initiation factor 3 (eIF3) is a large protein complex that participates in most translation initiation processes. While eIF3 has been well characterized, less is known about the roles of individual eIF3 subunits, particularly in plants. Here, we identified and characterized OseIF3e in rice (Oryza sativa L.). OseIF3e was constitutively expressed in various tissues, but most strongly in vigorously growing organs. Transgenic OseIF3e-silenced rice plants showed inhibited growth in seedling and vegetative stages. Repression of OseIF3e led to defects in pollen maturation but did not affect pollen mitosis. In rice, eIF3e interacted with eIF3 subunits b, d, e, f, h, and k, and with eIF6, forming homo- and heterodimers to initiate translation. Furthermore, OseIF3e was shown by yeast two-hybrid assay to specifically bind to inhibitors of cyclin-dependent kinases 1, 5, and 6. This interaction was mediated by the sequence of amino acid residues at positions 118-138, which included a conserved motif (IGPEQIETLYQFAKF). These results suggested although OseIF3e is not a "functional core" subunit of eIF3, it still plays crucial roles in rice growth and development, in combination with other factors. We proposed a pathway by which OseIF3e influence organ size and pollen maturation in rice, providing an opportunity to optimize plant architecture for crop breeding.
Collapse
|
30
|
A Transcript-Specific eIF3 Complex Mediates Global Translational Control of Energy Metabolism. Cell Rep 2016; 16:1891-902. [PMID: 27477275 DOI: 10.1016/j.celrep.2016.07.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 05/19/2016] [Accepted: 07/03/2016] [Indexed: 01/20/2023] Open
Abstract
The multi-subunit eukaryotic translation initiation factor eIF3 is thought to assist in the recruitment of ribosomes to mRNA. The expression of eIF3 subunits is frequently disrupted in human cancers, but the specific roles of individual subunits in mRNA translation and cancer remain elusive. Using global transcriptomic, proteomic, and metabolomic profiling, we found a striking failure of Schizosaccharomyces pombe cells lacking eIF3e and eIF3d to synthesize components of the mitochondrial electron transport chain, leading to a defect in respiration, endogenous oxidative stress, and premature aging. Energy balance was maintained, however, by a switch to glycolysis with increased glucose uptake, upregulation of glycolytic enzymes, and strict dependence on a fermentable carbon source. This metabolic regulatory function appears to be conserved in human cells where eIF3e binds metabolic mRNAs and promotes their translation. Thus, via its eIF3d-eIF3e module, eIF3 orchestrates an mRNA-specific translational mechanism controlling energy metabolism that may be disrupted in cancer.
Collapse
|
31
|
Missra A, Ernest B, Lohoff T, Jia Q, Satterlee J, Ke K, von Arnim AG. The Circadian Clock Modulates Global Daily Cycles of mRNA Ribosome Loading. THE PLANT CELL 2015; 27:2582-99. [PMID: 26392078 PMCID: PMC4815098 DOI: 10.1105/tpc.15.00546] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/02/2015] [Indexed: 05/03/2023]
Abstract
Circadian control of gene expression is well characterized at the transcriptional level, but little is known about diel or circadian control of translation. Genome-wide translation state profiling of mRNAs in Arabidopsis thaliana seedlings grown in long day was performed to estimate ribosome loading per mRNA. The experiments revealed extensive translational regulation of key biological processes. Notably, translation of mRNAs for ribosomal proteins and mitochondrial respiration peaked at night. Central clock mRNAs are among those subject to fluctuations in ribosome loading. There was no consistent phase relationship between peak translation states and peak transcript levels. The overlay of distinct transcriptional and translational cycles can be expected to alter the waveform of the protein synthesis rate. Plants that constitutively overexpress the clock gene CCA1 showed phase shifts in peak translation, with a 6-h delay from midnight to dawn or from noon to evening being particularly common. Moreover, cycles of ribosome loading that were detected under continuous light in the wild type collapsed in the CCA1 overexpressor. Finally, at the transcript level, the CCA1-ox strain adopted a global pattern of transcript abundance that was broadly correlated with the light-dark environment. Altogether, these data demonstrate that gene-specific diel cycles of ribosome loading are controlled in part by the circadian clock.
Collapse
Affiliation(s)
- Anamika Missra
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840
| | - Ben Ernest
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996-0840
| | - Tim Lohoff
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840 Molekulare Zellphysiologie, Fakultät Biologie, Universität Bielefeld, D-33615 Bielefeld, Germany
| | - Qidong Jia
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996-0840
| | - James Satterlee
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840
| | - Kenneth Ke
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840
| | - Albrecht G von Arnim
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840 Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996-0840
| |
Collapse
|
32
|
Basbouss-Serhal I, Soubigou-Taconnat L, Bailly C, Leymarie J. Germination Potential of Dormant and Nondormant Arabidopsis Seeds Is Driven by Distinct Recruitment of Messenger RNAs to Polysomes. PLANT PHYSIOLOGY 2015; 168:1049-65. [PMID: 26019300 PMCID: PMC4741348 DOI: 10.1104/pp.15.00510] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 05/21/2015] [Indexed: 05/19/2023]
Abstract
Dormancy is a complex evolutionary trait that temporally prevents seed germination, thus allowing seedling growth at a favorable season. High-throughput analyses of transcriptomes have led to significant progress in understanding the molecular regulation of this process, but the role of posttranscriptional mechanisms has received little attention. In this work, we have studied the dynamics of messenger RNA association with polysomes and compared the transcriptome with the translatome in dormant and nondormant seeds of Arabidopsis (Arabidopsis thaliana) during their imbibition at 25 °C in darkness, a temperature preventing germination of dormant seeds only. DNA microarray analysis revealed that 4,670 and 7,028 transcripts were differentially abundant in dormant and nondormant seeds in the transcriptome and the translatome, respectively. We show that there is no correlation between transcriptome and translatome and that germination regulation is also largely translational, implying a selective and dynamic recruitment of messenger RNAs to polysomes in both dormant and nondormant seeds. The study of 5' untranslated region features revealed that GC content and the number of upstream open reading frames could play a role in selective translation occurring during germination. Gene Ontology clustering showed that the functions of polysome-associated transcripts differed between dormant and nondormant seeds and revealed actors in seed dormancy and germination. In conclusion, our results demonstrate the essential role of selective polysome loading in this biological process.
Collapse
Affiliation(s)
- Isabelle Basbouss-Serhal
- Sorbonne Universités, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, F-75005 Paris, France (I.B.-S., C.B., J.L.);Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., C.B., J.L.); andUnité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165, Institut National de la Recherche Agronomique, 91057 Evry, France (L.S.-T.)
| | - Ludivine Soubigou-Taconnat
- Sorbonne Universités, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, F-75005 Paris, France (I.B.-S., C.B., J.L.);Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., C.B., J.L.); andUnité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165, Institut National de la Recherche Agronomique, 91057 Evry, France (L.S.-T.)
| | - Christophe Bailly
- Sorbonne Universités, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, F-75005 Paris, France (I.B.-S., C.B., J.L.);Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., C.B., J.L.); andUnité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165, Institut National de la Recherche Agronomique, 91057 Evry, France (L.S.-T.)
| | - Juliette Leymarie
- Sorbonne Universités, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, F-75005 Paris, France (I.B.-S., C.B., J.L.);Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., C.B., J.L.); andUnité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165, Institut National de la Recherche Agronomique, 91057 Evry, France (L.S.-T.)
| |
Collapse
|
33
|
Browning KS, Bailey-Serres J. Mechanism of cytoplasmic mRNA translation. THE ARABIDOPSIS BOOK 2015; 13:e0176. [PMID: 26019692 PMCID: PMC4441251 DOI: 10.1199/tab.0176] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein synthesis is a fundamental process in gene expression that depends upon the abundance and accessibility of the mRNA transcript as well as the activity of many protein and RNA-protein complexes. Here we focus on the intricate mechanics of mRNA translation in the cytoplasm of higher plants. This chapter includes an inventory of the plant translational apparatus and a detailed review of the translational processes of initiation, elongation, and termination. The majority of mechanistic studies of cytoplasmic translation have been carried out in yeast and mammalian systems. The factors and mechanisms of translation are for the most part conserved across eukaryotes; however, some distinctions are known to exist in plants. A comprehensive understanding of the complex translational apparatus and its regulation in plants is warranted, as the modulation of protein production is critical to development, environmental plasticity and biomass yield in diverse ecosystems and agricultural settings.
Collapse
Affiliation(s)
- Karen S. Browning
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas at Austin, Austin TX 78712-0165
- Both authors contributed equally to this work
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences and Center for Plant Cell Biology, University of California, Riverside, CA, 92521 USA
- Both authors contributed equally to this work
| |
Collapse
|
34
|
Peng HY, Qi YP, Lee J, Yang LT, Guo P, Jiang HX, Chen LS. Proteomic analysis of Citrus sinensis roots and leaves in response to long-term magnesium-deficiency. BMC Genomics 2015; 16:253. [PMID: 25887480 PMCID: PMC4383213 DOI: 10.1186/s12864-015-1462-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 03/09/2015] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Magnesium (Mg)-deficiency is frequently observed in Citrus plantations and is responsible for the loss of productivity and poor fruit quality. Knowledge on the effects of Mg-deficiency on upstream targets is scarce. Seedlings of 'Xuegan' [Citrus sinensis (L.) Osbeck] were irrigated with Mg-deficient (0 mM MgSO4) or Mg-sufficient (1 mM MgSO4) nutrient solution for 16 weeks. Thereafter, we first investigated the proteomic responses of C. sinensis roots and leaves to Mg-deficiency using two-dimensional electrophoresis (2-DE) in order to (a) enrich our understanding of the molecular mechanisms of plants to deal with Mg-deficiency and (b) understand the molecular mechanisms by which Mg-deficiency lead to a decrease in photosynthesis. RESULTS Fifty-nine upregulated and 31 downregulated protein spots were isolated in Mg-deficient leaves, while only 19 upregulated and 12 downregulated protein spots in Mg-deficient roots. Many Mg-deficiency-responsive proteins were involved in carbohydrate and energy metabolism, followed by protein metabolism, stress responses, nucleic acid metabolism, cell wall and cytoskeleton metabolism, lipid metabolism and cell transport. The larger changes in leaf proteome versus root one in response to Mg-deficiency was further supported by our observation that total soluble protein concentration was decreased by Mg-deficiency in leaves, but unaffected in roots. Mg-deficiency had decreased levels of proteins [i.e. ribulose-1,5-bisphosphate carboxylase (Rubisco), rubisco activase, oxygen evolving enhancer protein 1, photosynthetic electron transfer-like protein, ferredoxin-NADP reductase (FNR), aldolase] involved in photosynthesis, thus decreasing leaf photosynthesis. To cope with Mg-deficiency, C. sinensis leaves and roots might respond adaptively to Mg-deficiency through: improving leaf respiration and lowering root respiration, but increasing (decreasing) the levels of proteins related to ATP synthase in roots (leaves); enhancing the levels of proteins involved in reactive oxygen species (ROS) scavenging and other stress-responsive proteins; accelerating proteolytic cleavage of proteins by proteases, protein transport and amino acid metabolism; and upregulating the levels of proteins involved in cell wall and cytoskeleton metabolism. CONCLUSIONS Our results demonstrated that proteomics were more affected by long-term Mg-deficiency in leaves than in roots, and that the adaptive responses differed between roots and leaves when exposed to long-term Mg-deficiency. Mg-deficiency decreased the levels of many proteins involved in photosynthesis, thus decreasing leaf photosynthesis.
Collapse
Affiliation(s)
- Hao-Yang Peng
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Institute of Horticultural Plant Physiology, Biochemistry, and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Yi-Ping Qi
- Institute of Materia Medica, Fujian Academy of Medical Sciences, Fuzhou, 350001, China.
| | - Jinwook Lee
- Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, ROK.
| | - Lin-Tong Yang
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Institute of Horticultural Plant Physiology, Biochemistry, and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Peng Guo
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Institute of Horticultural Plant Physiology, Biochemistry, and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Huan-Xin Jiang
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Institute of Horticultural Plant Physiology, Biochemistry, and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Li-Song Chen
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Institute of Horticultural Plant Physiology, Biochemistry, and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Fujian Key Laboratory for Plant Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- The Higher Educational Key Laboratory of Fujian Province for Soil Ecosystem Health and Regulation, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
35
|
Laing WA, Martínez-Sánchez M, Wright MA, Bulley SM, Brewster D, Dare AP, Rassam M, Wang D, Storey R, Macknight RC, Hellens RP. An upstream open reading frame is essential for feedback regulation of ascorbate biosynthesis in Arabidopsis. THE PLANT CELL 2015; 27:772-86. [PMID: 25724639 PMCID: PMC4558653 DOI: 10.1105/tpc.114.133777] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 01/18/2015] [Accepted: 02/11/2015] [Indexed: 05/18/2023]
Abstract
Ascorbate (vitamin C) is an essential antioxidant and enzyme cofactor in both plants and animals. Ascorbate concentration is tightly regulated in plants, partly to respond to stress. Here, we demonstrate that ascorbate concentrations are determined via the posttranscriptional repression of GDP-l-galactose phosphorylase (GGP), a major control enzyme in the ascorbate biosynthesis pathway. This regulation requires a cis-acting upstream open reading frame (uORF) that represses the translation of the downstream GGP open reading frame under high ascorbate concentration. Disruption of this uORF stops the ascorbate feedback regulation of translation and results in increased ascorbate concentrations in leaves. The uORF is predicted to initiate at a noncanonical codon (ACG rather than AUG) and encode a 60- to 65-residue peptide. Analysis of ribosome protection data from Arabidopsis thaliana showed colocation of high levels of ribosomes with both the uORF and the main coding sequence of GGP. Together, our data indicate that the noncanonical uORF is translated and encodes a peptide that functions in the ascorbate inhibition of translation. This posttranslational regulation of ascorbate is likely an ancient mechanism of control as the uORF is conserved in GGP genes from mosses to angiosperms.
Collapse
Affiliation(s)
- William A Laing
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand
| | | | - Michele A Wright
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand
| | - Sean M Bulley
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand
| | - Di Brewster
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand
| | - Andrew P Dare
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand
| | - Maysoon Rassam
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand
| | - Daisy Wang
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand
| | - Roy Storey
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand
| | - Richard C Macknight
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
| | - Roger P Hellens
- The New Zealand Institute for Plant and Food Research, Auckland 1142, New Zealand Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
| |
Collapse
|
36
|
Benina M, Ribeiro DM, Gechev TS, Mueller-Roeber B, Schippers JHM. A cell type-specific view on the translation of mRNAs from ROS-responsive genes upon paraquat treatment of Arabidopsis thaliana leaves. PLANT, CELL & ENVIRONMENT 2015; 38:349-63. [PMID: 24738758 DOI: 10.1111/pce.12355] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 03/21/2014] [Accepted: 03/24/2014] [Indexed: 05/10/2023]
Abstract
Oxidative stress causes dramatic changes in the expression levels of many genes. The formation of a functional protein through successful mRNA translation is central to a coordinated cellular response. To what extent the response towards reactive oxygen species (ROS) is regulated at the translational level is poorly understood. Here we analysed leaf- and tissue-specific translatomes using a set of transgenic Arabidopsis thaliana lines expressing a FLAG-tagged ribosomal protein to immunopurify polysome-bound mRNAs before and after oxidative stress. We determined transcript levels of 171 ROS-responsive genes upon paraquat treatment, which causes formation of superoxide radicals, at the whole-organ level. Furthermore, the translation of mRNAs was determined for five cell types: mesophyll, bundle sheath, phloem companion, epidermal and guard cells. Mesophyll and bundle sheath cells showed the strongest response to paraquat treatment. Interestingly, several ROS-responsive transcription factors displayed cell type-specific translation patterns, while others were translated in all cell types. In part, cell type-specific translation could be explained by the length of the 5'-untranslated region (5'-UTR) and the presence of upstream open reading frames (uORFs). Our analysis reveals insights into the translational regulation of ROS-responsive genes, which is important to understanding cell-specific responses and functions during oxidative stress.
Collapse
Affiliation(s)
- Maria Benina
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000, Plovdiv, Bulgaria; Institute of Molecular Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | | | | | | | | |
Collapse
|
37
|
Kakehi JI, Kawano E, Yoshimoto K, Cai Q, Imai A, Takahashi T. Mutations in ribosomal proteins, RPL4 and RACK1, suppress the phenotype of a thermospermine-deficient mutant of Arabidopsis thaliana. PLoS One 2015; 10:e0117309. [PMID: 25625317 PMCID: PMC4308196 DOI: 10.1371/journal.pone.0117309] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/22/2014] [Indexed: 11/18/2022] Open
Abstract
Thermospermine acts in negative regulation of xylem differentiation and its deficient mutant of Arabidopsis thaliana, acaulis5 (acl5), shows excessive xylem formation and severe dwarfism. Studies of two dominant suppressors of acl5, sac51-d and sac52-d, have revealed that SAC51 and SAC52 encode a transcription factor and a ribosomal protein L10 (RPL10), respectively, and these mutations enhance translation of the SAC51 mRNA, which contains conserved upstream open reading frames in the 5’ leader. Here we report identification of SAC53 and SAC56 responsible for additional suppressors of acl5. sac53-d is a semi-dominant allele of the gene encoding a receptor for activated C kinase 1 (RACK1) homolog, a component of the 40S ribosomal subunit. sac56-d represents a semi-dominant allele of the gene for RPL4. We show that the GUS reporter activity driven by the CaMV 35S promoter plus the SAC51 5’ leader is reduced in acl5 and restored by sac52-d, sac53-d, and sac56-d as well as thermospermine. Furthermore, the SAC51 mRNA, which may be a target of nonsense-mediated mRNA decay, was found to be stabilized in these ribosomal mutants and by thermospermine. These ribosomal proteins are suggested to act in the control of uORF-mediated translation repression of SAC51, which is derepressed by thermospermine.
Collapse
Affiliation(s)
- Jun-Ichi Kakehi
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Eri Kawano
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Kaori Yoshimoto
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Qingqing Cai
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Akihiro Imai
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Taku Takahashi
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
- * E-mail:
| |
Collapse
|
38
|
Juntawong P, Hummel M, Bazin J, Bailey-Serres J. Ribosome profiling: a tool for quantitative evaluation of dynamics in mRNA translation. Methods Mol Biol 2015; 1284:139-73. [PMID: 25757771 DOI: 10.1007/978-1-4939-2444-8_7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Translational regulation is important for plant growth, metabolism, and acclimation to environmental challenges. Ribosome profiling involves the nuclease digestion of mRNAs associated with ribosomes and mapping of the generated ribosome-protected footprints to transcripts. This is useful for investigation of translational regulation. Here we present a detailed method to generate, purify, and high-throughput-sequence ribosome footprints from Arabidopsis thaliana using two different isolation methods, namely, conventional differential centrifugation and the translating ribosome affinity purification (TRAP) technology. These methodologies provide researchers with an opportunity to quantitatively assess with high-resolution the translational activity of individual mRNAs by determination of the position and number of ribosomes in the corresponding mRNA. The results can provide insights into the translation of upstream open reading frames, alternatively spliced transcripts, short open reading frames, and other aspects of translation.
Collapse
Affiliation(s)
- Piyada Juntawong
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | | | | | | |
Collapse
|
39
|
Nolte C, Staiger D. RNA around the clock - regulation at the RNA level in biological timing. FRONTIERS IN PLANT SCIENCE 2015; 6:311. [PMID: 25999975 PMCID: PMC4419606 DOI: 10.3389/fpls.2015.00311] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/19/2015] [Indexed: 05/21/2023]
Abstract
The circadian timing system in plants synchronizes their physiological functions with the environment. This is achieved by a global control of gene expression programs with a considerable part of the transcriptome undergoing 24-h oscillations in steady-state abundance. These circadian oscillations are driven by a set of core clock proteins that generate their own 24-h rhythm through periodic feedback on their own transcription. Additionally, post-transcriptional events are instrumental for oscillations of core clock genes and genes in clock output. Here we provide an update on molecular events at the RNA level that contribute to the 24-h rhythm of the core clock proteins and shape the circadian transcriptome. We focus on the circadian system of the model plant Arabidopsis thaliana but also discuss selected regulatory principles in other organisms.
Collapse
Affiliation(s)
| | - Dorothee Staiger
- *Correspondence: Dorothee Staiger, Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Universitaetsstrasse 25, Bielefeld D-33615, Germany
| |
Collapse
|
40
|
Hu Q, Merchante C, Stepanova AN, Alonso JM, Heber S. A Stacking-Based Approach to Identify Translated Upstream Open Reading Frames in Arabidopsis Thaliana. BIOINFORMATICS RESEARCH AND APPLICATIONS 2015. [DOI: 10.1007/978-3-319-19048-8_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
41
|
Retzer K, Butt H, Korbei B, Luschnig C. The far side of auxin signaling: fundamental cellular activities and their contribution to a defined growth response in plants. PROTOPLASMA 2014; 251:731-46. [PMID: 24221297 PMCID: PMC4059964 DOI: 10.1007/s00709-013-0572-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 10/15/2013] [Indexed: 05/04/2023]
Abstract
Recent years have provided us with spectacular insights into the biology of the plant hormone auxin, leaving the impression of a highly versatile molecule involved in virtually every aspect of plant development. A combination of genetics, biochemistry, and cell biology has established auxin signaling pathways, leading to the identification of two distinct modes of auxin perception and downstream regulatory cascades. Major targets of these signaling modules are components of the polar auxin transport machinery, mediating directional distribution of the phytohormone throughout the plant body, and decisively affecting plant development. Alterations in auxin transport, metabolism, or signaling that occur as a result of intrinsic as well as environmental stimuli, control adjustments in morphogenetic programs, giving rise to defined growth responses attributed to the activity of the phytohormone. Some of the results obtained from the analysis of auxin, however, do not fit coherently into a picture of highly specific signaling events, but rather suggest mutual interactions between auxin and fundamental cellular pathways, like the control of intracellular protein sorting or translation. Crosstalk between auxin and these basic determinants of cellular activity and how they might shape auxin effects in the control of morphogenesis are the subject of this review.
Collapse
Affiliation(s)
- Katarzyna Retzer
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, BOKU, Wien Muthgasse 18, 1190 Wien, Austria
| | - Haroon Butt
- Department of Biological Sciences, Forman Christian College, Ferozepur Road, Lahore, 54600 Pakistan
| | - Barbara Korbei
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, BOKU, Wien Muthgasse 18, 1190 Wien, Austria
| | - Christian Luschnig
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, BOKU, Wien Muthgasse 18, 1190 Wien, Austria
| |
Collapse
|
42
|
Henriques R, Bögre L, Horváth B, Magyar Z. Balancing act: matching growth with environment by the TOR signalling pathway. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2691-701. [PMID: 24567496 DOI: 10.1093/jxb/eru049] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
One of the most fundamental aspects of growth in plants is its plasticity in relation to fluctuating environmental conditions. Growth of meristematic cells relies predominantly on protein synthesis, one of the most energy-consuming activities in cells, and thus is tightly regulated in accordance with the available nutrient and energy supplies. The Target of Rapamycin (TOR) signalling pathway takes a central position in this regulation. The core of the TOR signalling pathway is conserved throughout evolution, and can be traced back to the last eukaryotic common ancestor. In plants, a single complex constitutes the TOR signalling pathway. Manipulating the components of the TOR complex in Arabidopsis highlighted its common role as a major regulator of protein synthesis and metabolism, that is also involved in other biological functions such as cell-wall integrity, regulation of cell proliferation, and cell size. TOR, as an integral part of the auxin signalling pathway, connects hormonal and nutrient pathways. Downstream of TOR, S6 kinase and the ribosomal S6 protein have been shown to mediate several of these responses, although there is evidence of other complex non-linear TOR signalling pathway structures.
Collapse
Affiliation(s)
- Rossana Henriques
- Center for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Parc de Recerca UAB, Edifici CRAG, Campus UAB, Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
| | - László Bögre
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey TW20 0EX, UK
| | - Beátrix Horváth
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey TW20 0EX, UK
| | - Zoltán Magyar
- Institute of Plant Biology, Biological Research Centre, Temesvári kru. 62, POB 521, H-6701, Szeged, Hungary
| |
Collapse
|
43
|
Zhou F, Roy B, Dunlap JR, Enganti R, von Arnim AG. Translational control of Arabidopsis meristem stability and organogenesis by the eukaryotic translation factor eIF3h. PLoS One 2014; 9:e95396. [PMID: 24736281 PMCID: PMC3988188 DOI: 10.1371/journal.pone.0095396] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Accepted: 03/25/2014] [Indexed: 11/18/2022] Open
Abstract
Essentially all aboveground plant tissues develop from the stem cells in the primary shoot apical meristem. Proliferation of the stem cell population in the Arabidopsis shoot apical meristem is tightly controlled by a feedback loop formed primarily by the homeodomain transcription factor WUSCHEL (WUS) and the CLAVATA ligand-receptor system. In this study, it is shown that mutation of a translation initiation factor, eIF3h, causes a tendency to develop a strikingly enlarged shoot apical meristem with elevated and ectopic expression of WUS and CLAVATA3 (CLV3). Many of the mRNAs that function in apical meristem maintenance possess upstream open reading frames (uORFs), translational attenuators that render translation partially dependent on eIF3h. Specifically, the mRNA for the receptor kinase, CLV1, is undertranslated in the eif3h mutant as shown by transient and transgenic expression assays. Concordant phenotypic observations include defects in organ polarity and in translation of another uORF-containing mRNA, ASYMMETRIC LEAVES 1 (AS1), in eif3h. In summary, the expression of developmental regulatory mRNAs is attenuated by uORFs, and this attenuation is balanced in part by the translation initiation factor, eIF3h. Thus, translational control plays a key role in Arabidopsis stem cell regulation and organogenesis.
Collapse
Affiliation(s)
- Fujun Zhou
- Genome Science and Technology Program, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Bijoyita Roy
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - John R. Dunlap
- Division of Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Ramya Enganti
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Albrecht G. von Arnim
- Genome Science and Technology Program, The University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| |
Collapse
|
44
|
von Arnim AG, Jia Q, Vaughn JN. Regulation of plant translation by upstream open reading frames. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 214:1-12. [PMID: 24268158 DOI: 10.1016/j.plantsci.2013.09.006] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 09/08/2013] [Accepted: 09/10/2013] [Indexed: 05/08/2023]
Abstract
We review the evidence that upstream open reading frames (uORFs) function as RNA sequence elements for post-transcriptional control of gene expression, specifically translation. uORFs are highly abundant in the genomes of angiosperms. Their negative effect on translation is often attenuated by ribosomal translation reinitiation, a process whose molecular biochemistry is still being investigated. Certain uORFs render translation responsive to small molecules, thus offering a path for metabolic control of gene expression in evolution and synthetic biology. In some cases, uORFs form modular logic gates in signal transduction. uORFs thus provide eukaryotes with a functionality analogous to, or comparable to, riboswitches and attenuators in prokaryotes. uORFs exist in many genes regulating development and point toward translational control of development. While many uORFs appear to be poorly conserved, and the number of genes with conserved-peptide uORFs is modest, many mRNAs have a conserved pattern of uORFs. Evolutionarily, the gain and loss of uORFs may be a widespread mechanism that diversifies gene expression patterns. Last but not least, this review includes a dedicated uORF database for Arabidopsis.
Collapse
Affiliation(s)
- Albrecht G von Arnim
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840, USA; Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996-0840, USA.
| | | | | |
Collapse
|
45
|
Wu SH. Gene expression regulation in photomorphogenesis from the perspective of the central dogma. ANNUAL REVIEW OF PLANT BIOLOGY 2014; 65:311-33. [PMID: 24779996 DOI: 10.1146/annurev-arplant-050213-040337] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Depending on the environment a young seedling encounters, the developmental program following seed germination could be skotomorphogenesis in the dark or photomorphogenesis in the light. Light signals are interpreted by a repertoire of photoreceptors followed by sophisticated gene expression networks, eventually resulting in developmental changes. The expression and functions of photoreceptors and key signaling molecules are highly coordinated and regulated at multiple levels of the central dogma in molecular biology. Light activates gene expression through the actions of positive transcriptional regulators and the relaxation of chromatin by histone acetylation. Small regulatory RNAs help attenuate the expression of light-responsive genes. Alternative splicing, protein phosphorylation/dephosphorylation, the formation of diverse transcriptional complexes, and selective protein degradation all contribute to proteome diversity and change the functions of individual proteins.
Collapse
Affiliation(s)
- Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan;
| |
Collapse
|
46
|
Missra A, von Arnim AG. Analysis of mRNA translation states in Arabidopsis over the diurnal cycle by polysome microarray. Methods Mol Biol 2014; 1158:157-74. [PMID: 24792050 DOI: 10.1007/978-1-4939-0700-7_10] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Gene regulation at the level of translation occurs in response to environmental perturbation and is increasingly recognized as a factor affecting plant development. Despite extensive knowledge of transcriptional control, very little is known about translational regulation of genes in response to the daily light/dark cycles. Here we describe the experimental layout designed to address how the translation states of genes change at various times during a diurnal cycle in Arabidopsis thaliana seedlings. We have adopted a strategy combining sucrose-gradient profiling of ribosomes and high-throughput microarray analysis of the ribosome-associated mRNA to investigate the translational landscape of the Arabidopsis genome. This is a powerful technique that can be easily extended to study translation regulation in different genetic backgrounds and under various environmental conditions.
Collapse
Affiliation(s)
- Anamika Missra
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, 37996-0840, USA,
| | | |
Collapse
|
47
|
Tiruneh BS, Kim BH, Gallie DR, Roy B, von Arnim AG. The global translation profile in a ribosomal protein mutant resembles that of an eIF3 mutant. BMC Biol 2013; 11:123. [PMID: 24377433 PMCID: PMC3901033 DOI: 10.1186/1741-7007-11-123] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/17/2013] [Indexed: 01/15/2023] Open
Abstract
Background Genome-wide assays performed in Arabidopsis and other organisms have revealed that the translation status of mRNAs responds dramatically to different environmental stresses and genetic lesions in the translation apparatus. To identify additional features of the global landscape of translational control, we used microarray analysis of polysomal as well as non-polysomal mRNAs to examine the defects in translation in a poly(A) binding protein mutant, pab2 pab8, as well as in a mutant of a large ribosomal subunit protein, rpl24b/shortvalve1. Results The mutation of RPL24B stimulated the ribosome occupancy of mRNAs for nuclear encoded ribosomal proteins. Detailed analysis yielded new insights into the translational regulon containing the ribosomal protein mRNAs. First, the ribosome occupancy defects in the rpl24b mutant partially overlapped with those in a previously analyzed initiation factor mutant, eif3h. Second, a group of mRNAs with incomplete coding sequences appeared to be uncoupled from the regulon, since their dependence on RPL24B differed from regular mRNAs. Third, different sister paralogs of the ribosomal proteins differed in their translation state in the wild-type. Some sister paralogs also differed in their response to the rpl24b mutation. In contrast to rpl24b, the pab2 pab8 mutant revealed few gene specific translational defects, but a group of seed storage protein mRNAs were stimulated in their ribosome occupancy. In the course of this work, while optimizing the statistical analysis of ribosome occupancy data, we collected 12 biological replicates of translation states from wild-type seedlings. We defined 20% of mRNAs as having a high variance in their translation state. Many of these mRNAs were functionally associated with responses to the environment, suggesting that subtle variation in the environmental conditions is sensed by plants and transduced to affect the translational efficiency of hundreds of mRNAs. Conclusions These data represent the first genome-wide analysis of translation in a eukaryote defective in the large ribosomal subunit. RPL24 and eIF3h play similar but non-identical roles in eukaryotic translation. The data also shed light on the fine structure of the regulon of ribosomal protein mRNAs.
Collapse
Affiliation(s)
| | | | | | | | - Albrecht G von Arnim
- Department of Biochemistry, Cellular and Molecular Biology, M407 Walters Life Sciences, The University of Tennessee, Knoxville, TN 37996-0840, USA.
| |
Collapse
|
48
|
Smith MD, Gu Y, Querol-Audí J, Vogan JM, Nitido A, Cate JHD. Human-like eukaryotic translation initiation factor 3 from Neurospora crassa. PLoS One 2013; 8:e78715. [PMID: 24250809 PMCID: PMC3826745 DOI: 10.1371/journal.pone.0078715] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 09/22/2013] [Indexed: 02/05/2023] Open
Abstract
Eukaryotic translation initiation factor 3 (eIF3) is a key regulator of translation initiation, but its in vivo assembly and molecular functions remain unclear. Here we show that eIF3 from Neurospora crassa is structurally and compositionally similar to human eIF3. N. crassa eIF3 forms a stable 12-subunit complex linked genetically and biochemically to the 13th subunit, eIF3j, which in humans modulates mRNA start codon selection. Based on N. crassa genetic analysis, most subunits in eIF3 are essential. Subunits that can be deleted (e, h, k and l) map to the right side of the eIF3 complex, suggesting that they may coordinately regulate eIF3 function. Consistent with this model, subunits eIF3k and eIF3l are incorporated into the eIF3 complex as a pair, and their insertion depends on the presence of subunit eIF3h, a key regulator of vertebrate development. Comparisons to other eIF3 complexes suggest that eIF3 assembles around an eIF3a and eIF3c dimer, which may explain the coordinated regulation of human eIF3 levels. Taken together, these results show that Neurospora crassa eIF3 provides a tractable system for probing the structure and function of human-like eIF3 in the context of living cells.
Collapse
Affiliation(s)
- M. Duane Smith
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Yu Gu
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Jordi Querol-Audí
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Jacob M. Vogan
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Adam Nitido
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Jamie H. D. Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Department of Chemistry, University of California, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
| |
Collapse
|
49
|
Liu MJ, Wu SH, Wu JF, Lin WD, Wu YC, Tsai TY, Tsai HL, Wu SH. Translational landscape of photomorphogenic Arabidopsis. THE PLANT CELL 2013; 25:3699-710. [PMID: 24179124 PMCID: PMC3877810 DOI: 10.1105/tpc.113.114769] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 09/27/2013] [Accepted: 10/11/2013] [Indexed: 05/19/2023]
Abstract
Translational control plays a vital role in regulating gene expression. To decipher the molecular basis of translational regulation in photomorphogenic Arabidopsis thaliana, we adopted a ribosome profiling method to map the genome-wide positions of translating ribosomes in Arabidopsis etiolated seedlings in the dark and after light exposure. We found that, in Arabidopsis, a translating ribosome protects an ~30-nucleotide region and moves in three-nucleotide periodicity, characteristics also observed in Saccharomyces cerevisiae and mammals. Light enhanced the translation of genes involved in the organization and function of chloroplasts. Upstream open reading frames initiated by ATG but not CTG mediated translational repression of the downstream main open reading frame. Also, we observed widespread translational repression of microRNA target genes in both light- and dark-grown Arabidopsis seedlings. This genome-wide characterization of transcripts undergoing translation at the nucleotide-resolution level reveals that a combination of multiple translational mechanisms orchestrates and fine-tunes the translation of diverse transcripts in plants with environmental responsiveness.
Collapse
Affiliation(s)
- Ming-Jung Liu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Szu-Hsien Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology and Department of Life Sciences, National Chung-Hsing University, Taichung 402, Taiwan
| | - Jing-Fen Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Wen-Dar Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Chen Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Tsung-Ying Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Huang-Lung Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology and Department of Life Sciences, National Chung-Hsing University, Taichung 402, Taiwan
- Address correspondence to
| |
Collapse
|
50
|
Kim Y, Lee G, Jeon E, Sohn EJ, Lee Y, Kang H, Lee DW, Kim DH, Hwang I. The immediate upstream region of the 5'-UTR from the AUG start codon has a pronounced effect on the translational efficiency in Arabidopsis thaliana. Nucleic Acids Res 2013; 42:485-98. [PMID: 24084084 PMCID: PMC3874180 DOI: 10.1093/nar/gkt864] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The nucleotide sequence around the translational initiation site is an important cis-acting element for post-transcriptional regulation. However, it has not been fully understood how the sequence context at the 5′-untranslated region (5′-UTR) affects the translational efficiency of individual mRNAs. In this study, we provide evidence that the 5′-UTRs of Arabidopsis genes showing a great difference in the nucleotide sequence vary greatly in translational efficiency with more than a 200-fold difference. Of the four types of nucleotides, the A residue was the most favourable nucleotide from positions −1 to −21 of the 5′-UTRs in Arabidopsis genes. In particular, the A residue in the 5′-UTR from positions −1 to −5 was required for a high-level translational efficiency. In contrast, the T residue in the 5′-UTR from positions −1 to −5 was the least favourable nucleotide in translational efficiency. Furthermore, the effect of the sequence context in the −1 to −21 region of the 5′-UTR was conserved in different plant species. Based on these observations, we propose that the sequence context immediately upstream of the AUG initiation codon plays a crucial role in determining the translational efficiency of plant genes.
Collapse
Affiliation(s)
- Younghyun Kim
- Department of Life Sciences, School of Bioscience and Bioengineering and Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, Korea
| | | | | | | | | | | | | | | | | |
Collapse
|