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Wang L, Li H, Lei Z, Jeong DH, Cho J. The CARBON CATABOLITE REPRESSION 4A-mediated RNA deadenylation pathway acts on the transposon RNAs that are not regulated by small RNAs. THE NEW PHYTOLOGIST 2024; 241:1636-1645. [PMID: 38009859 DOI: 10.1111/nph.19435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
Transposable elements (TEs) are mobile genetic elements that can impair the host genome stability and integrity. It has been well documented that activated transposons in plants are suppressed by small interfering (si) RNAs. However, transposon repression by the cytoplasmic RNA surveillance system is unknown. Here, we show that mRNA deadenylation is critical for controlling transposons in Arabidopsis. Trimming of poly(A) tail is a rate-limiting step that precedes the RNA decay and is primarily mediated by the CARBON CATABOLITE REPRESSION 4 (CCR4)-NEGATIVE ON TATA-LESS (NOT) complex. We found that the loss of CCR4a leads to strong derepression and mobilization of TEs in Arabidopsis. Intriguingly, CCR4a regulates a largely distinct set of TEs from those controlled by RNA-dependent RNA Polymerase 6 (RDR6), a key enzyme that produces cytoplasmic siRNAs. This indicates that the cytoplasmic RNA quality control mechanism targets the TEs that are poorly recognized by the previously well-characterized RDR6-mediated pathway, and thereby augments the host genome stability. Our study suggests a hitherto unknown mechanism for transposon repression mediated by RNA deadenylation and unveils a complex nature of the host's strategy to maintain the genome integrity.
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Affiliation(s)
- Ling Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Hui Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Zhen Lei
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Dong-Hoon Jeong
- Department of Life Science, Hallym University, Chuncheon, 24252, Korea
- Multidisciplinary Genome Institute, Hallym University, Chuncheon, 24252, Korea
| | - Jungnam Cho
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
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2
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Wang L, Liu L, Zhao J, Li C, Wu H, Zhao H, Wu Q. Granule-bound starch synthase in plants: Towards an understanding of their evolution, regulatory mechanisms, applications, and perspectives. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111843. [PMID: 37648115 DOI: 10.1016/j.plantsci.2023.111843] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/01/2023]
Abstract
Amylose content (AC) is a significant quality trait in starchy crops, affecting their processing and application by the food and non-food industries. Therefore, fine-tuning AC in these crops has become a focus for breeders. Granule-bound starch synthase (GBSS) is the core enzyme that directly determines the AC levels. Several excellent reviews have summarized key progress in various aspects of GBSS research in recent years, but they mostly focus on cereals. Herein, we provide an in-depth review of GBSS research in monocots and dicots, focusing on the molecular characteristics, evolutionary relationships, expression patterns, molecular regulation mechanisms, and applications. We also discuss future challenges and directions for controlling AC in starchy crops, and found simultaneously increasing both the PTST and GBSS gene expression levels may be an effective strategy to increase amylose content.
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Affiliation(s)
- Lei Wang
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Linling Liu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Jiali Zhao
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Chenglei Li
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Huala Wu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Haixia Zhao
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Qi Wu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China.
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3
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Zheng J, Sun L, Wang D, He L, Du W, Guo S, Wang L. Roles of a CCR4-NOT complex component GmNOT4-1 in regulating soybean nodulation. FRONTIERS IN PLANT SCIENCE 2023; 14:1172354. [PMID: 37342147 PMCID: PMC10277652 DOI: 10.3389/fpls.2023.1172354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/02/2023] [Indexed: 06/22/2023]
Abstract
Legume-rhizobial symbiotic nitrogen fixation is the most efficient nitrogen assimilation system in the ecosystem. In the special interaction between organ-root nodules, legumes supply rhizobial carbohydrates for their proliferation, while rhizobials provide host plants with absorbable nitrogen. Nodule initiation and formation require a complex molecular dialogue between legumes and rhizobia, which involves the accurate regulation of a series of legume genes. The CCR4-NOT complex is a conserved multi-subunit complex with functions regulating gene expression in many cellular processes. However, the functions of the CCR4-NOT complex in rhizobia-host interactions remain unclear. In this study, we identified seven members of the NOT4 family in soybean and further classified them into three subgroups. Bioinformatic analysis showed that NOT4s shared relatively conserved motifs and gene structures in each subgroup, while there were significant differences between NOT4s in the different subgroups. Expression profile analysis indicated that NOT4s may be involved in nodulation in soybean, as most of them were induced by Rhizobium infection and highly expressed in nodules. We further selected GmNOT4-1 to clarify the biological function of these genes in soybean nodulation. Interestingly, we found that either GmNOT4-1 overexpression or down-regulation of GmNOT4-1 by RNAi or CRISPR/Cas9 gene editing would suppress the number of nodules in soybean. Intriguingly, alterations in the expression of GmNOT4-1 repressed the expression of genes in the Nod factor signaling pathway. This research provides new insight into the function of the CCR4-NOT family in legumes and reveals GmNOT4-1 to be a potent gene for regulating symbiotic nodulation.
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Affiliation(s)
- Jiangtao Zheng
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Lili Sun
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Dongmei Wang
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Lin He
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Weijun Du
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Shujin Guo
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Lixiang Wang
- College of Agronomy, Shanxi Agricultural University, Taigu, China
- State Key Laboratory of Crop Stress Adaptation Improvement, School of Life Sciences, Henan University, Kaifeng, China
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4
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Transcriptome Analysis Reveals a Comprehensive Virus Resistance Response Mechanism in Pecan Infected by a Novel Badnavirus Pecan Virus. Int J Mol Sci 2022; 23:ijms232113576. [PMID: 36362365 PMCID: PMC9655656 DOI: 10.3390/ijms232113576] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/31/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Pecan leaf-variegated plant, which was infected with a novel badnavirus named pecan mosaic virus (PMV) detected by small RNA deep sequencing, is a vital model plant for studying the molecular mechanism of retaining green or chlorosis of virus-infected leaves. In this report, PMV infection in pecan leaves induced PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI). PMV infection suppressed the expressions of key genes of fatty acid, oleic acid (C18:1), and very-long-chain fatty acids (VLCFA) biosynthesis, indicating that fatty acids-derived signaling was one of the important defense pathways in response to PMV infection in pecan. PMV infection in pecans enhanced the expressions of pathogenesis-related protein 1 (PR1). However, the transcripts of phenylalanine ammonia-lyase (PAL) and isochorismate synthase (ICS) were downregulated, indicating that salicylic acid (SA) biosynthesis was blocked in pecan infected with PMV. Meanwhile, disruption of auxin signaling affected the activation of the jasmonic acid (JA) pathway. Thus, C18:1 and JA signals are involved in response to PMV infection in pecan. In PMV-infected yellow leaves, damaged chloroplast structure and activation of mitogen-activated protein kinase 3 (MPK3) inhibited photosynthesis. Cytokinin and SA biosynthesis was blocked, leading to plants losing immune responses and systemic acquired resistance (SAR). The repression of photosynthesis and the induction of sink metabolism in the infected tissue led to dramatic changes in carbohydrate partitioning. On the contrary, the green leaves of PMV infection in pecan plants had whole cell tissue structure and chloroplast clustering, establishing a strong antiviral immunity system. Cytokinin biosynthesis and signaling transductions were remarkably strengthened, activating plant immune responses. Meanwhile, cytokinin accumulation in green leaves induced partial SA biosynthesis and gained comparatively higher SAR compared to that of yellow leaves. Disturbance of the ribosome biogenesis might enhance the resistance to PMV infection in pecan and lead to leaves staying green.
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5
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Schwenk P, Hiltbrunner A. Phytochrome A Mediates the Disassembly of Processing Bodies in Far-Red Light. FRONTIERS IN PLANT SCIENCE 2022; 13:828529. [PMID: 35283917 PMCID: PMC8905148 DOI: 10.3389/fpls.2022.828529] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/18/2022] [Indexed: 05/27/2023]
Abstract
Phytochromes are red- and far-red light receptors that control the growth and development of plants, enabling them to respond adequately to changing light conditions. It has been shown that halted mRNAs stored in RNA granules called processing bodies are released upon light perception and contribute to the adaptation to the light environment. However, the photophysiological background of this process is largely unknown. We found that light of different wavelengths can trigger the disassembly of processing bodies in a dose- and time-dependent manner. We show that phytochromes control this process in red- and far-red light and that cytoplasmic phytochrome A is sufficient and necessary for the far-red light-induced disassembly of processing bodies. This adds a novel, unexpected cytoplasmic function to the processes controlled by phytochrome A. Overall, our findings suggest a role of phytochromes in the control of translationally halted mRNAs that are stored in processing bodies. We expect our findings to facilitate understanding of how light and environmental cues control the assembly and disassembly of processing bodies, which could have broader implications for the regulation of non-membranous organelles in general.
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Affiliation(s)
- Philipp Schwenk
- Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Andreas Hiltbrunner
- Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
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6
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Krzyszton M, Kufel J. Analysis of mRNA-derived siRNAs in mutants of mRNA maturation and surveillance pathways in Arabidopsis thaliana. Sci Rep 2022; 12:1474. [PMID: 35087200 PMCID: PMC8795450 DOI: 10.1038/s41598-022-05574-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/14/2022] [Indexed: 02/05/2023] Open
Abstract
Defects in RNA maturation and RNA decay factors may generate substrates for the RNA interference machinery. This phenomenon was observed in plants where mutations in some RNA-related factors lead to the production of RNA-quality control small interfering RNAs and several mutants show enhanced silencing of reporter transgenes. To assess the potential of RNAi activation on endogenous transcripts, we sequenced small RNAs from a set of Arabidopsis thaliana mutants with defects in various RNA metabolism pathways. We observed a global production of siRNAs caused by inefficient pre-mRNA cleavage and polyadenylation leading to read-through transcription into downstream antisense genes. In addition, in the lsm1a lsm1b double mutant, we identified NIA1, SMXL5, and several miRNA-targeted mRNAs as producing siRNAs, a group of transcripts suggested being especially sensitive to deficiencies in RNA metabolism. However, in most cases, RNA metabolism perturbations do not lead to the widespread production of siRNA derived from mRNA molecules. This observation is contrary to multiple studies based on reporter transgenes and suggests that only a very high accumulation of defective mRNA species caused by specific mutations or substantial RNA processing defects trigger RNAi pathways.
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Affiliation(s)
- Michal Krzyszton
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Joanna Kufel
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
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7
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Hirayama T. PARN-like Proteins Regulate Gene Expression in Land Plant Mitochondria by Modulating mRNA Polyadenylation. Int J Mol Sci 2021; 22:ijms221910776. [PMID: 34639116 PMCID: PMC8509313 DOI: 10.3390/ijms221910776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/21/2021] [Accepted: 10/02/2021] [Indexed: 11/20/2022] Open
Abstract
Mitochondria have their own double-stranded DNA genomes and systems to regulate transcription, mRNA processing, and translation. These systems differ from those operating in the host cell, and among eukaryotes. In recent decades, studies have revealed several plant-specific features of mitochondrial gene regulation. The polyadenylation status of mRNA is critical for its stability and translation in mitochondria. In this short review, I focus on recent advances in understanding the mechanisms regulating mRNA polyadenylation in plant mitochondria, including the role of poly(A)-specific ribonuclease-like proteins (PARNs). Accumulating evidence suggests that plant mitochondria have unique regulatory systems for mRNA poly(A) status and that PARNs play pivotal roles in these systems.
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Affiliation(s)
- Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurahiki 710-0046, Okayama, Japan
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8
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Schwenk P, Sheerin DJ, Ponnu J, Staudt AM, Lesch KL, Lichtenberg E, Medzihradszky KF, Hoecker U, Klement E, Viczián A, Hiltbrunner A. Uncovering a novel function of the CCR4-NOT complex in phytochrome A-mediated light signalling in plants. eLife 2021; 10:63697. [PMID: 33783355 PMCID: PMC8009681 DOI: 10.7554/elife.63697] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/03/2021] [Indexed: 12/21/2022] Open
Abstract
Phytochromes are photoreceptors regulating growth and development in plants. Using the model plant Arabidopsis, we identified a novel signalling pathway downstream of the far-red light-sensing phytochrome, phyA, that depends on the highly conserved CCR4-NOT complex. CCR4-NOT is integral to RNA metabolism in yeast and animals, but its function in plants is largely unknown. NOT9B, an Arabidopsis homologue of human CNOT9, is a component of the CCR4-NOT complex, and acts as negative regulator of phyA-specific light signalling when bound to NOT1, the scaffold protein of the complex. Light-activated phyA interacts with and displaces NOT9B from NOT1, suggesting a potential mechanism for light signalling through CCR4-NOT. ARGONAUTE 1 and proteins involved in splicing associate with NOT9B and we show that NOT9B is required for specific phyA-dependent alternative splicing events. Furthermore, association with nuclear localised ARGONAUTE 1 raises the possibility that NOT9B and CCR4-NOT are involved in phyA-modulated gene expression. Place a seedling on a windowsill, and soon you will notice the fragile stem bending towards the glass to soak in the sun and optimize its growth. Plants can ‘sense’ light thanks to specialized photoreceptor molecules: for instance, the phytochrome A is responsible for detecting weak and ‘far-red’ light from the very edge of the visible spectrum. Once the phytochrome has been activated, this message is relayed to the rest of the plant through an intricate process that requires other molecules. The CCR4-NOT protein complex is vital for all plants, animals and fungi, suggesting that it was already present in early life forms. Here, Schwenk et al. examine whether CCR4-NOT could have acquired a new role in plants to help them respond to far-red light. Scanning the genetic information of the plant model Arabidopsis thaliana revealed that the gene encoding the NOT9 subunit of CCR4-NOT had been duplicated in plants during evolution. NOT9B, the protein that the new copy codes for, has a docking site that can attach to both phytochrome A and CCR4-NOT. When NOT9B binds phytochrome A, it is released from the CCR4-NOT complex: this could trigger a cascade of reactions that ultimately changes how A. thaliana responds to far-red light. Plants that had not enough or too much NOT9B were respectively more or less responsive to that type of light, showing that the duplication of the gene coding for this subunit had helped plants respond to certain types of light. The findings by Schwenk et al. illustrate how existing structures can be repurposed during evolution to carry new roles. They also provide a deeper understanding of how plants optimize their growth, a useful piece of information in a world where most people rely on crops as their main source of nutrients.
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Affiliation(s)
- Philipp Schwenk
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - David J Sheerin
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Jathish Ponnu
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Anne-Marie Staudt
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Klara L Lesch
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany.,Internal Medicine IV, Department of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Elisabeth Lichtenberg
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Ute Hoecker
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Eva Klement
- Laboratory of Proteomics Research, Biological Research Centre, Szeged, Hungary
| | - András Viczián
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
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9
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Li T, Yang H, Lu Y, Dong Q, Liu G, Chen F, Zhou Y. Comparative transcriptome analysis of differentially expressed genes related to the physiological changes of yellow-green leaf mutant of maize. PeerJ 2021; 9:e10567. [PMID: 33628629 PMCID: PMC7894110 DOI: 10.7717/peerj.10567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/23/2020] [Indexed: 11/20/2022] Open
Abstract
Chlorophylls, green pigments in chloroplasts, are essential for photosynthesis. Reduction in chlorophyll content may result in retarded growth, dwarfism, and sterility. In this study, a yellow-green leaf mutant of maize, indicative of abnormity in chlorophyll content, was identified. The physiological parameters of this mutant were measured. Next, global gene expression of this mutant was determined using transcriptome analysis and compared to that of wild-type maize plants. The yellow-green leaf mutant of maize was found to contain lower contents of chlorophyll a, chlorophyll b and carotenoid compounds. It contained fewer active PSII centers and displayed lower values of original chlorophyll fluorescence parameters than the wild-type plants. The real-time fluorescence yield, the electron transport rate, and the net photosynthetic rate of the mutant plants showed reduction as well. In contrast, the maximum photochemical quantum yield of PSII of the mutant plants was similar to that of the wild-type plants. Comparative transcriptome analysis of the mutant plants and wild-type plants led to the identification of differentially expressed 1,122 genes, of which 536 genes were up-regulated and 586 genes down-regulated in the mutant. Five genes in the chlorophyll metabolism pathway, nine genes in the tricarboxylic acid cycle and seven genes related to the conversion of sucrose to starch displayed down-regulated expression. In contrast, genes encoding a photosystem II reaction center PsbP family protein and the PGR5-like protein 1A (PGRL1A) exhibited increased transcript abundance.
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Affiliation(s)
- Tingchun Li
- Tobacco Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China.,Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Huaying Yang
- Tobacco Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yan Lu
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
| | - Qing Dong
- Tobacco Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Guihu Liu
- Tobacco Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Yingbing Zhou
- Tobacco Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
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10
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Fang JC, Tsai YC, Chou WL, Liu HY, Chang CC, Wu SJ, Lu CA. A CCR4-associated factor 1, OsCAF1B, confers tolerance of low-temperature stress to rice seedlings. PLANT MOLECULAR BIOLOGY 2021; 105:177-192. [PMID: 33025522 DOI: 10.1007/s11103-020-01079-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
Rice is an important crop in the world. However, little is known about rice mRNA deadenylation, which is an important regulation step of gene expression at the post-transcriptional level. The CCR4-NOT1 complex contains two key components, CCR4 and CAF1, which are the main cytoplasmic deadenylases in eukaryotic cells. Expression of OsCAF1B was tightly coupled with low-temperature exposure. In the present study, we investigated the function of OsCAF1B in rice by characterizing the molecular and physiological responses to cold stress in OsCAF1B overexpression lines and dominant-negative mutant lines. Our results demonstrate that OsCAF1B plays an important role in growth and development of rice seedlings at low temperatures. Rice is a tropical and subtropical crop that is sensitive to low temperature, and activates a complex gene regulatory network in response to cold stress. Poly(A) tail shortening, also termed deadenylation, is the rate-limiting step of mRNA degradation in eukaryotic cells. CCR4-associated factor 1 (CAF1) proteins are important enzymes for catalysis of mRNA deadenylation in eukaryotes. In the present study, the role of a rice cold-induced CAF1, OsCAF1B, in adaptation of rice plants to low-temperature stress was investigated. Expression of OsCAF1B was closely linked with low-temperature exposure. The increased survival percentage and reduced electrolyte leakage exhibited by OsCAF1B overexpression transgenic lines subjected to cold stress indicate that OsCAF1B plays a positive role in rice growth under low ambient temperature. The enhancement of cold tolerance by OsCAF1B in transgenic rice seedlings involved OsCAF1B deadenylase gene expression, and was associated with elevated expression of late-response cold-related transcription factor genes. In addition, the expression level of OsCAF1B was higher in a cold-tolerant japonica rice cultivar than in a cold-sensitive indica rice cultivar. The results reveal a hitherto undiscovered function of OsCAF1B deadenylase gene expression, which is required for adaptation to cold stress in rice.
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Affiliation(s)
- Jhen-Cheng Fang
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County, 320, Taiwan, ROC
| | - Yin-Chuan Tsai
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County, 320, Taiwan, ROC
| | - Wei-Lun Chou
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County, 320, Taiwan, ROC
| | - Hsin-Yi Liu
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County, 320, Taiwan, ROC
| | - Chun-Chen Chang
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County, 320, Taiwan, ROC
| | - Shaw-Jye Wu
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County, 320, Taiwan, ROC
| | - Chung-An Lu
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County, 320, Taiwan, ROC.
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11
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Joshna CR, Saha P, Atugala D, Chua G, Muench DG. Plant PUF RNA-binding proteins: A wealth of diversity for post-transcriptional gene regulation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 297:110505. [PMID: 32563454 DOI: 10.1016/j.plantsci.2020.110505] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 03/30/2020] [Accepted: 04/19/2020] [Indexed: 06/11/2023]
Abstract
PUF proteins are a conserved group of sequence-specific RNA-binding proteins that typically function to negatively regulate mRNA stability and translation. PUFs are well characterized at the molecular, structural and functional levels in Drosophila, Caenorhabditis elegans, budding yeast and human systems. Although usually encoded by small gene families, PUFs are over-represented in the plant genome, with up to 36 genes identified in a single species. PUF gene expansion in plants has resulted in extensive variability in gene expression patterns, diversity in predicted RNA-binding domain structure, and novel combinations of key amino acids involved in modular nucleotide binding. Reports on the characterization of plant PUF structure and function continue to expand, and include RNA target identification, subcellular distribution, crystal structure, and molecular mechanisms. Arabidopsis PUF mutant analysis has provided insight into biological function, and has identified roles related to development and environmental stress tolerance. The diversity of plant PUFs implies an extensive role for this family of proteins in post-transcriptional gene regulation. This diversity also holds the potential for providing novel RNA-binding domains that could be engineered to produce designer PUFs to alter the metabolism of target RNAs in the cell.
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Affiliation(s)
- Chris R Joshna
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N1N4, Canada
| | - Pritha Saha
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N1N4, Canada
| | - Dilini Atugala
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N1N4, Canada
| | - Gordon Chua
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N1N4, Canada
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N1N4, Canada.
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12
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Zhou HR, Lin RN, Huang HW, Li L, Cai T, Zhu JK, Chen S, He XJ. The CCR4-NOT complex component NOT1 regulates RNA-directed DNA methylation and transcriptional silencing by facilitating Pol IV-dependent siRNA production. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1503-1515. [PMID: 32412137 DOI: 10.1111/tpj.14818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/29/2020] [Accepted: 05/07/2020] [Indexed: 05/20/2023]
Abstract
Small interfering RNAs (siRNAs) are responsible for establishing and maintaining DNA methylation through the RNA-directed DNA methylation (RdDM) pathway in plants. Although siRNA biogenesis is well known, it is relatively unclear about how the process is regulated. By a forward genetic screen in Arabidopsis thaliana, we identified a mutant defective in NOT1 and demonstrated that NOT1 is required for transcriptional silencing at RdDM target genomic loci. We demonstrated that NOT1 is required for Pol IV-dependent siRNA accumulation and DNA methylation at a subset of RdDM target genomic loci. Furthermore, we revealed that NOT1 is a constituent of a multi-subunit CCR4-NOT deadenylase complex by immunoprecipitation combined with mass spectrometry and demonstrated that the CCR4-NOT components can function as a whole to mediate chromatin silencing. Therefore, our work establishes that the CCR4-NOT complex regulates the biogenesis of Pol IV-dependent siRNAs, and hence facilitates DNA methylation and transcriptional silencing in Arabidopsis.
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Affiliation(s)
- Hao-Ran Zhou
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Rong-Nan Lin
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Huan-Wei Huang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Tao Cai
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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13
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Pereira PA, Boavida LC, Santos MR, Becker JD. AtNOT1 is required for gametophyte development in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1289-1303. [PMID: 32369648 DOI: 10.1111/tpj.14801] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 04/15/2020] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
In flowering plants, pollen development is under a dynamic and well-orchestrated transcriptional control, characterized by an early phase with high transcript diversity and a late post-mitotic phase skewed to a cell-type-specific transcriptome. Such transcriptional changes require a balance between synthesis and degradation of mRNA transcripts, the latter being initiated by deadenylation. The CCR4-NOT complex is the main evolutionary conserved deadenylase complex in eukaryotes, and its function is essential during germline specification in animals. We hypothesized that the CCR4-NOT complex might play a central role in mRNA turnover during microgametogenesis in Arabidopsis. Disruption of NOT1 gene, which encodes the scaffold protein of the CCR4-NOT complex, showed abnormal seed set. Genetic analysis failed to recover homozygous progeny, and reciprocal crosses confirmed reduced transmission through the male and female gametophytes. Concordantly, not1 embryo sacs showed delayed development and defects in embryogenesis. not1 pollen grains exhibited abnormal male germ unit configurations and failed to germinate. Transcriptome analysis of pollen from not1/+ mutants revealed that lack of NOT1 leads to an extensive transcriptional deregulation during microgametogenesis. Therefore, our work establishes NOT1 as an important player during gametophyte development in Arabidopsis.
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Affiliation(s)
- Patrícia A Pereira
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras, 2780-156, Portugal
| | - Leonor C Boavida
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras, 2780-156, Portugal
| | - Mário R Santos
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras, 2780-156, Portugal
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras, 2780-156, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
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14
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Zhang Y, Liu C, Cheng H, Tian S, Liu Y, Wang S, Zhang H, Saqib M, Wei H, Wei Z. DNA methylation and its effects on gene expression during primary to secondary growth in poplar stems. BMC Genomics 2020; 21:498. [PMID: 32689934 PMCID: PMC7372836 DOI: 10.1186/s12864-020-06902-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/10/2020] [Indexed: 12/24/2022] Open
Abstract
Background As an important epigenetic mark, 5-methylcytosine (5mC) methylation is involved in many DNA-dependent biological processes and plays a role during development and differentiation of multicellular organisms. However, there is still a lack of knowledge about the dynamic aspects and the roles of global 5mC methylation in wood formation in tree trunks. In this study, we not only scrutinized single-base resolution methylomes of primary stems (PS), transitional stems (TS), and secondary stems (SS) of Populus trichocarpa using a high-throughput bisulfite sequencing technique, but also analyzed the effects of 5mC methylation on the expression of genes involved in wood formation. Results The overall average percentages of CG, CHG, and CHH methylation in poplar stems were ~ 53.6%, ~ 37.7%, and ~ 8.5%, respectively, and the differences of 5mC in genome-wide CG/CHG/CHH contexts among PS, TS, and SS were statistically significant (p < 0.05). The evident differences in CG, CHG, and CHH methylation contexts among 2 kb proximal promoters, gene bodies, and 2 kb downstream regions were observed among PS, TS, and SS. Further analysis revealed a perceptible global correlation between 5mC methylation levels of gene bodies and transcript levels but failed to reveal a correlation between 5mC methylation levels of proximal promoter regions and transcript levels. We identified 653 and 858 DMGs and 4978 and 4780 DEGs in PS vs TS and TS vs SS comparisons, respectively. Only 113 genes of 653 DMGs and 4978 DEGs, and 114 genes of 858 DMGs and 4780 DEG were common. Counterparts of some of these common genes in other species, including Arabidopsis thaliana, are known to be involved in secondary cell wall biosynthesis and hormone signaling. This indicates that methylation may directly modulate wood formation genes and indirectly attune hormone signaling genes, which in turn impact wood formation. Conclusions DNA methylation only marginally affects pathway genes or regulators involved in wood formation, suggesting that further studies of wood formation should lean towards the indirect effects of methylation. The information and data we provide here will be instrumental for understanding the roles of methylation in wood formation in tree species.
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Affiliation(s)
- Yang Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Cong Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - He Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Shuanghui Tian
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Yingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Shuang Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Huaxin Zhang
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China
| | - Muhammad Saqib
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Zhigang Wei
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.
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15
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Zhang ZJ, Gao Q, Fang XD, Ding ZH, Gao DM, Xu WY, Cao Q, Qiao JH, Yang YZ, Han C, Wang Y, Yuan X, Li D, Wang XB. CCR4, a RNA decay factor, is hijacked by a plant cytorhabdovirus phosphoprotein to facilitate virus replication. eLife 2020; 9:53753. [PMID: 32207684 PMCID: PMC7105381 DOI: 10.7554/elife.53753] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/21/2020] [Indexed: 12/14/2022] Open
Abstract
Carbon catabolite repression 4 (CCR4) is a conserved mRNA deadenylase regulating posttranscriptional gene expression. However, regulation of CCR4 in virus infections is less understood. Here, we characterized a pro-viral role of CCR4 in replication of a plant cytorhabdovirus, Barley yellow striate mosaic virus (BYSMV). The barley (Hordeum vulgare) CCR4 protein (HvCCR4) was identified to interact with the BYSMV phosphoprotein (P). The BYSMV P protein recruited HvCCR4 from processing bodies (PBs) into viroplasm-like bodies. Overexpression of HvCCR4 promoted BYSMV replication in plants. Conversely, knockdown of the small brown planthopper CCR4 inhibited viral accumulation in the insect vector. Biochemistry experiments revealed that HvCCR4 was recruited into N–RNA complexes by the BYSMV P protein and triggered turnover of N-bound cellular mRNAs, thereby releasing RNA-free N protein to bind viral genomic RNA for optimal viral replication. Our results demonstrate that the co-opted CCR4-mediated RNA decay facilitates cytorhabdovirus replication in plants and insects.
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Affiliation(s)
- Zhen-Jia Zhang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qiang Gao
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiao-Dong Fang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhi-Hang Ding
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Dong-Min Gao
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wen-Ya Xu
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qing Cao
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ji-Hui Qiao
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yi-Zhou Yang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chenggui Han
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Ying Wang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Xuefeng Yuan
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Shandong Province Key Laboratory of Agricultural Microbiology, Tai'an, China
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xian-Bing Wang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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16
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Fang JC, Liu HY, Tsai YC, Chou WL, Chang CC, Lu CA. A CCR4 Association Factor 1, OsCAF1B, Participates in the αAmy3 mRNA Poly(A) Tail Shortening and Plays a Role in Germination and Seedling Growth. PLANT & CELL PHYSIOLOGY 2020; 61:554-564. [PMID: 31782784 DOI: 10.1093/pcp/pcz221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
Poly(A) tail (PAT) shortening, also termed deadenylation, is the rate-limiting step of mRNA degradation in eukaryotic cells. The carbon catabolite repressor 4-associated factor 1s (CAF1s) were shown to be one of the major enzymes for catalyzing mRNA deadenylation in yeast and mammalian cells. However, the functions of CAF1 proteins in plants are poorly understood. Herein, a sugar-upregulated CAF1 gene, OsCAF1B, is investigated in rice. Using gain-of-function and dominant-negative mutation analysis, we show that overexpression of OsCAF1B resulted in an accelerated α-amylase gene (αAmy3) mRNA degradation phenomenon, while ectopic expression of a form of OsCAF1B that had lost its deadenylase activity resulted in a delayed αAmy3 mRNA degradation phenomenon in transgenic rice cells. The change in αAmy3 mRNA degradation in transgenic rice is associated with the altered lengths of the αAmy3 mRNA PAT, indicating that OsCAF1B acts as a negative regulator of αAmy3 mRNA stability in rice. Additionally, we found that overexpression of OsCAF1B retards seed germination and seedling growth. These findings indicate that OsCAF1B participates in sugar-induced αAmy3 mRNA degradation and deadenylation and acts a negative factor for germination and seedling development.
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Affiliation(s)
- Jhen-Cheng Fang
- Department of Life Sciences, National Central University, Taoyuan City, 320, Taiwan, ROC
| | - Hsin-Yi Liu
- Department of Life Sciences, National Central University, Taoyuan City, 320, Taiwan, ROC
| | - Yin-Chuan Tsai
- Department of Life Sciences, National Central University, Taoyuan City, 320, Taiwan, ROC
| | - Wei-Lun Chou
- Department of Life Sciences, National Central University, Taoyuan City, 320, Taiwan, ROC
| | - Chun-Chen Chang
- Department of Life Sciences, National Central University, Taoyuan City, 320, Taiwan, ROC
| | - Chung-An Lu
- Department of Life Sciences, National Central University, Taoyuan City, 320, Taiwan, ROC
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17
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Arae T, Morita K, Imahori R, Suzuki Y, Yasuda S, Sato T, Yamaguchi J, Chiba Y. Identification of Arabidopsis CCR4-NOT Complexes with Pumilio RNA-Binding Proteins, APUM5 and APUM2. PLANT & CELL PHYSIOLOGY 2019; 60:2015-2025. [PMID: 31093672 DOI: 10.1093/pcp/pcz089] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
CCR4/CAF1 are widely conserved deadenylases in eukaryotes. They form a large complex that includes NOT1 as a scaffold protein and various NOT proteins that are core components of multiple levels of gene expression control. The CCR4-NOT complex also contains several RNA-binding proteins as accessory proteins, which are required for target recognition by CCR4/CAF1 deadenylases. AtCCR4a/b, orthologs of human CCR4 in Arabidopsis, have various physiological effects. AtCCR4 isoforms are likely to have specific target mRNAs related to each physiological effect; however, AtCCR4 does not have RNA-binding capability. Therefore, identifying factors that interact with AtCCR4a/b is indispensable to understand its function as a regulator of gene expression, as well as the target mRNA recognition mechanism. Here, we identified putative components of the AtCCR4-NOT complex using co-immunoprecipitation in combination with mass spectrometry using FLAG-tagged AtCCR4b and subsequent verification with a yeast two-hybrid assay. Interestingly, four of 11 AtCAF1 isoforms interacted with both AtCCR4b and AtNOT1, whereas two isoforms interacted only with AtNOT1 in yeast two-hybrid assays. These results imply that Arabidopsis has multiple CCR4-NOT complexes with various combinations of deadenylases. We also revealed that the RNA-binding protein Arabidopsis Pumilio 5 and 2 interacted with AtCCR4a/b in the cytoplasm with a few foci.
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Affiliation(s)
- Toshihiro Arae
- Graduate School of Life Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Japan
| | - Kotone Morita
- Graduate School of Life Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Japan
| | - Riko Imahori
- School of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Japan
| | - Yuya Suzuki
- Graduate School of Life Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Japan
| | - Shigetaka Yasuda
- Graduate School of Life Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Japan
| | - Takeo Sato
- Graduate School of Life Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Japan
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Japan
| | - Junji Yamaguchi
- Graduate School of Life Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Japan
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Japan
| | - Yukako Chiba
- Graduate School of Life Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Japan
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Japan
- JST PRESTO, Kawaguchi, Japan
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18
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A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis. Nat Genet 2019; 51:627-635. [PMID: 30886426 PMCID: PMC6636631 DOI: 10.1038/s41588-019-0370-6] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 02/08/2019] [Indexed: 12/22/2022]
Abstract
Photosynthetic organisms provide food and energy for nearly all life on Earth, yet half of their protein-coding genes remain uncharacterized1,2. Characterization of these genes could be greatly accelerated by new genetic resources for unicellular organisms. Here, we generated a genome-wide, indexed library of mapped insertion mutants for the unicellular alga Chlamydomonas reinhardtii. The 62,389 mutants in the library, covering 83% of nuclear, protein-coding genes, are available to the community. Each mutant contains unique DNA barcodes, allowing the collection to be screened as a pool. We performed a genome-wide survey of genes required for photosynthesis, which identified 303 candidate genes. Characterization of one of these genes, the conserved predicted phosphatase-encoding gene CPL3, showed it is important for accumulation of multiple photosynthetic protein complexes. Notably, 21 of the 43 highest-confidence genes are novel, opening new opportunities for advances in our understanding of this biogeochemically fundamental process. This library will accelerate the characterization of thousands of genes in algae, plants and animals. Generation of a library of 62,389 mapped insertion mutants for the unicellular alga Chlamydomonas reinhardtii enables screening for genes required for photosynthesis and the identification of 303 candidate genes.
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19
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Nakaminami K, Seki M. RNA Regulation in Plant Cold Stress Response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1081:23-44. [PMID: 30288702 DOI: 10.1007/978-981-13-1244-1_2] [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] [Indexed: 12/19/2022]
Abstract
In addition to plants, all organisms react to environmental stimuli via the perception of signals and subsequently respond through alterations of gene expression. However, genes/mRNAs are usually not the functional unit themselves, and instead, resultant protein products with individual functions result in various acquired phenotypes. In order to fully characterize the adaptive responses of plants to environmental stimuli, it is essential to determine the level of proteins, in addition to the regulation of mRNA expression. This regulatory step, which is referred to as "mRNA posttranscriptional regulation," occurs subsequent to mRNA transcription and prior to translation. Although these RNA regulatory mechanisms have been well-studied in many organisms, including plants, it is not fully understood how plants respond to environmental stimuli, such as cold stress, via these RNA regulations.A recent study described several RNA regulatory factors in relation to environmental stress responses, including plant cold stress tolerance. In this chapter, the functions of RNA regulatory factors and comprehensive analyses related to the RNA regulations involved in cold stress response are summarized, such as mRNA maturation, including capping, splicing, polyadenylation of mRNA, and the quality control system of mRNA; mRNA degradation, including the decapping step; and mRNA stabilization. In addition, the putative roles of messenger ribonucleoprotein (mRNP) granules, such as processing bodies (PBs) and stress granules (SGs), which are cytoplasmic particles, are described in relation to RNA regulations under stress conditions. These RNA regulatory systems are important for adjusting or fine-tuning and determining the final levels of mRNAs and proteins in order to adapt or respond to environmental stresses. Collectively, these new areas of study revealed that plants possess precise novel regulatory mechanisms which specifically function in the response to cold stress.
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Affiliation(s)
- Kentaro Nakaminami
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- Plant Epigenome Regulation Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Saitama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST), Kawaguchi, Saitama, Japan
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20
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Catalá R, Carrasco-López C, Perea-Resa C, Hernández-Verdeja T, Salinas J. Emerging Roles of LSM Complexes in Posttranscriptional Regulation of Plant Response to Abiotic Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:167. [PMID: 30873189 PMCID: PMC6401655 DOI: 10.3389/fpls.2019.00167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/31/2019] [Indexed: 05/04/2023]
Abstract
It has long been assumed that the wide reprogramming of gene expression that modulates plant response to unfavorable environmental conditions is mainly controlled at the transcriptional level. A growing body of evidence, however, indicates that posttranscriptional regulatory mechanisms also play a relevant role in this control. Thus, the LSMs, a family of proteins involved in mRNA metabolism highly conserved in eukaryotes, have emerged as prominent regulators of plant tolerance to abiotic stress. Arabidopsis contains two main LSM ring-shaped heteroheptameric complexes, LSM1-7 and LSM2-8, with different subcellular localization and function. The LSM1-7 ring is part of the cytoplasmic decapping complex that regulates mRNA stability. On the other hand, the LSM2-8 complex accumulates in the nucleus to ensure appropriate levels of U6 snRNA and, therefore, correct pre-mRNA splicing. Recent studies reported unexpected results that led to a fundamental change in the assumed consideration that LSM complexes are mere components of the mRNA decapping and splicing cellular machineries. Indeed, these data have demonstrated that LSM1-7 and LSM2-8 rings operate in Arabidopsis by selecting specific RNA targets, depending on the environmental conditions. This specificity allows them to actively imposing particular gene expression patterns that fine-tune plant responses to abiotic stresses. In this review, we will summarize current and past knowledge on the role of LSM rings in modulating plant physiology, with special focus on their function in abiotic stress responses.
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21
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Beyond Transcription: Fine-Tuning of Circadian Timekeeping by Post-Transcriptional Regulation. Genes (Basel) 2018; 9:genes9120616. [PMID: 30544736 PMCID: PMC6315869 DOI: 10.3390/genes9120616] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/28/2022] Open
Abstract
The circadian clock is an important endogenous timekeeper, helping plants to prepare for the periodic changes of light and darkness in their environment. The clockwork of this molecular timer is made up of clock proteins that regulate transcription of their own genes with a 24 h rhythm. Furthermore, the rhythmically expressed clock proteins regulate time-of-day dependent transcription of downstream genes, causing messenger RNA (mRNA) oscillations of a large part of the transcriptome. On top of the transcriptional regulation by the clock, circadian rhythms in mRNAs rely in large parts on post-transcriptional regulation, including alternative pre-mRNA splicing, mRNA degradation, and translational control. Here, we present recent insights into the contribution of post-transcriptional regulation to core clock function and to regulation of circadian gene expression in Arabidopsis thaliana.
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22
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Tsuzuki M, Motomura K, Kumakura N, Takeda A. Interconnections between mRNA degradation and RDR-dependent siRNA production in mRNA turnover in plants. JOURNAL OF PLANT RESEARCH 2017; 130:211-226. [PMID: 28197782 DOI: 10.1007/s10265-017-0906-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 12/08/2016] [Indexed: 06/06/2023]
Abstract
Accumulation of an mRNA species is determined by the balance between the synthesis and the degradation of the mRNA. Individual mRNA molecules are selectively and actively degraded through RNA degradation pathways, which include 5'-3' mRNA degradation pathway, 3'-5' mRNA degradation pathway, and RNA-dependent RNA polymerase-mediated mRNA degradation pathway. Recent studies have revealed that these RNA degradation pathways compete with each other in mRNA turnover in plants and that plants have a hidden layer of non-coding small-interfering RNA production from a set of mRNAs. In this review, we summarize the current information about plant mRNA degradation pathways in mRNA turnover and discuss the potential roles of a novel class of the endogenous siRNAs derived from plant mRNAs.
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Affiliation(s)
- Masayuki Tsuzuki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kazuki Motomura
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Naoyoshi Kumakura
- Center for Sustainable Resource Science, RIKEN, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Atsushi Takeda
- Department of Biotechnology, Graduate School of Life Sciences, Ritsumeikan University, Shiga, 525-8577, Japan.
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23
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Ma L, Xue N, Fu X, Zhang H, Li G. Arabidopsis thaliana FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1) modulate starch synthesis in response to light and sugar. THE NEW PHYTOLOGIST 2017; 213:1682-1696. [PMID: 27859295 DOI: 10.1111/nph.14300] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/22/2016] [Indexed: 05/25/2023]
Abstract
In living organisms, daily light/dark cycles profoundly affect cellular processes. In plants, optimal growth and development, and adaptation to daily light-dark cycles, require starch synthesis and turnover. However, the underlying molecular mechanisms coordinating daily starch metabolism remain poorly understood. To explore the roles of Arabidopsis thaliana light signal transduction proteins FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1) in starch metabolism, the contents of starch and water-soluble polysaccharides, and the structure of starch granules were investigated in fhy3, far1 and fhy3 far1 mutant plants. Disruption of FHY3 or FAR1 reduced starch accumulation and altered starch granule structure in the fhy3-4, far1-2, and fhy3-4 far1-2 mutant plants. Furthermore, molecular and genetic evidence revealed that the gene encoding the starch-debranching enzyme ISOAMYLASE2 (ISA2) is a direct target of FHY3 and FAR1, and functions in light-induced starch synthesis. Our data establish the first molecular link between light signal transduction and starch synthesis, suggesting that the light-signaling proteins FHY3 and FAR1 influence starch synthesis and starch granule formation through transcriptional activation of ISA2.
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Affiliation(s)
- Lin Ma
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Na Xue
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiaoyu Fu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Haisen Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
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Chou WL, Chung YL, Fang JC, Lu CA. Novel interaction between CCR4 and CAF1 in rice CCR4-NOT deadenylase complex. PLANT MOLECULAR BIOLOGY 2017; 93:79-96. [PMID: 27714489 DOI: 10.1007/s11103-016-0548-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 09/28/2016] [Indexed: 06/06/2023]
Abstract
Rice is an important crop in the world. However, little is known about rice mRNA deadenylation, which is an important regulation step of gene expression at the post-transcriptional level. The CCR4-NOT1 complex contains two key components, CCR4 and CAF1, which are the main cytoplasmic deadenylases in eukaryotic cells. In yeast and humans, CCR4 can interact with CAF1 via its N-terminal LRR domain. However, no CCR4 protein containing N-terminal LRR motifs have been found in plants. In this manuscript, we demonstrate a novel pattern of interaction between OsCCR4 and OsCAF1 in the rice CCR4-NOT complex, and that OsCAF1 acts as a bridge between OsCCR4 and OsNOT1 in this complex. Our results revealed that the Mynd-like domain at the N-terminus of rice CCR4 proteins and the PXLXP motif at the rice CAF1 N-terminus play critical roles in OsCCR4-OsCAF1 interaction. Deadenylation, also called poly(A) tail shortening, is the first rate-limiting step in general cytoplasmic mRNA degradation in eukaryotic cells. Carbon catabolite repressor (CCR)4 and CCR4-associated factor (CAF)1 in the CCR4-NOT complex function in mRNA poly(A) tail shortening. CCR4s contain N-terminal leucine-rich repeat (LRR) motifs that interact with CAF1s in yeast, fruit fly and mammals. In silico analysis has not identified any plant CCR4 proteins that contain LRR motifs. Here, two rice CCR4 homologous genes, OsCCR4a and OsCCR4b, were identified. The isolated recombinant exonuclease-endonuclease-phosphatase domain of OsCCR4a and OsCCR4b exhibited 3'-5' exonuclease activity in vitro, and point mutation of a catalytic residue in this domain disrupted the deadenylase activity. Both OsCCR4a and OsCCR4b fluorescent fusion proteins were localized in the rice cytoplasm and nucleus, and both associated with processing bodies via their N-terminus. Binding analyses showed that OsCCR4a and OsCCR4b directly interacted with three rice CAF1 family members: OsCAF1A, OsCAF1G and OsCAF1H. The zf-MYND-like domain at the N terminus of rice CCR4 and the PXLXP motif of rice CAF1 play critical roles in OsCCR4-OsCAF1 interaction. OsCAF1 proteins, but not OsCCR4 proteins, can interact with the MIG4G domain of rice OsNOT1. Our studies thus reveal a hitherto undiscovered novel interaction pattern that connects OsCCR4 and OsCAF1 in the rice CCR4-NOT complex.
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Affiliation(s)
- Wei-Lun Chou
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC
| | - Yue-Lin Chung
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC
| | - Jhen-Cheng Fang
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC
| | - Chung-An Lu
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC.
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Kawa D, Testerink C. Regulation of mRNA decay in plant responses to salt and osmotic stress. Cell Mol Life Sci 2016; 74:1165-1176. [PMID: 27677492 PMCID: PMC5346435 DOI: 10.1007/s00018-016-2376-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/09/2016] [Accepted: 09/21/2016] [Indexed: 11/24/2022]
Abstract
Plant acclimation to environmental stresses requires fast signaling to initiate changes in developmental and metabolic responses. Regulation of gene expression by transcription factors and protein kinases acting upstream are important elements of responses to salt and drought. Gene expression can be also controlled at the post-transcriptional level. Recent analyses on mutants in mRNA metabolism factors suggest their contribution to stress signaling. Here we highlight the components of mRNA decay pathways that contribute to responses to osmotic and salt stress. We hypothesize that phosphorylation state of proteins involved in mRNA decapping affect their substrate specificity.
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Affiliation(s)
- Dorota Kawa
- Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Postbus 94215, 1090 GE, Amsterdam, The Netherlands
| | - Christa Testerink
- Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Postbus 94215, 1090 GE, Amsterdam, The Netherlands.
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26
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Chen XJ, Zhang XH, Hu LD, Zhang JQ, Jiang Y, Yang Y, Yan YB. DsCaf1 is involved in environmental stress response of Dunaliella salina. Int J Biol Macromol 2015; 82:369-74. [PMID: 26454106 DOI: 10.1016/j.ijbiomac.2015.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/02/2015] [Accepted: 10/06/2015] [Indexed: 10/22/2022]
Abstract
Regulation of mRNA fates can alter the gene-expression profile promptly and specifically. Deadenylation is a process of which the poly(A) tail is degraded by deadenylases. By regulating mRNA turnover, deadenylases are involved in various vital cellular processes including stress responses. However, it is unclear whether deadenylases play a role in the adaption/tolerance of extremophiles. In this research, we cloned the deadenylase caf1 from Dunaliella salina (dscaf1), a unicellular green alga with exceptional halotolerance. In silicon analysis indicated that compared with the mesophilic alga Chlamydomonas reinhardtii caf1, dscaf1 promoter contained more elements responsive to abiotic stresses. Dscaf1 had an extremely high expression level under hypersaline conditions. When the D. salina cells were subject to stress shock, a two-stage response was observed for dscaf1 expression. The mRNA level of dscaf1 had an immediate 2-4 fold increase and followed by an ∼10 fold increase after hyperosmotic, heat or UV treatment, while had an about 3 fold increase quickly followed by an abrupt decrease after hypoosmotic or cold shock. The dissimilarity in dscaf1 expression patterns suggested that DsCaf1 is a stress-responsive deadenylase with the ability to regulate fates of a specific group of mRNAs for a certain type of stress.
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Affiliation(s)
- Xiang-Jun Chen
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Key Laboratory of Bio-Resources and Eco-Environment of MOE, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Xin-Hang Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Li-Dan Hu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jia-Quan Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yan Jiang
- Key Laboratory of Bio-Resources and Eco-Environment of MOE, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of MOE, College of Life Science, Sichuan University, Chengdu 610064, China.
| | - Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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27
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Romanowski A, Yanovsky MJ. Circadian rhythms and post-transcriptional regulation in higher plants. FRONTIERS IN PLANT SCIENCE 2015; 6:437. [PMID: 26124767 PMCID: PMC4464108 DOI: 10.3389/fpls.2015.00437] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 05/28/2015] [Indexed: 05/06/2023]
Abstract
The circadian clock of plants allows them to cope with daily changes in their environment. This is accomplished by the rhythmic regulation of gene expression, in a process that involves many regulatory steps. One of the key steps involved at the RNA level is post-transcriptional regulation, which ensures a correct control on the different amounts and types of mRNA that will ultimately define the current physiological state of the plant cell. Recent advances in the study of the processes of regulation of pre-mRNA processing, RNA turn-over and surveillance, regulation of translation, function of lncRNAs, biogenesis and function of small RNAs, and the development of bioinformatics tools have helped to vastly expand our understanding of how this regulatory step performs its role. In this work we review the current progress in circadian regulation at the post-transcriptional level research in plants. It is the continuous interaction of all the information flow control post-transcriptional processes that allow a plant to precisely time and predict daily environmental changes.
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Affiliation(s)
| | - Marcelo J. Yanovsky
- *Correspondence: Marcelo J. Yanovsky, Laboratorio de Genómica Comparativa del Desarrollo Vegetal, Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina,
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