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Li S, Xu J, Cao Y, Wu J, Liu Q, Zhang D. Genome-Wide Analyses of CCHC Family Genes and Their Expression Profiles under Drought Stress in Rose ( Rosa chinensis). Int J Mol Sci 2024; 25:8983. [PMID: 39201669 PMCID: PMC11354476 DOI: 10.3390/ijms25168983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 09/03/2024] Open
Abstract
CCHC-type zinc finger proteins (CCHC-ZFPs), ubiquitous across plant species, are integral to their growth, development, hormonal regulation, and stress adaptation. Roses (Rosa sp.), as one of the most significant and extensively cultivated ornamentals, account for more than 30% of the global cut-flower market. Despite its significance, the CCHC gene family in roses (Rosa sp.) remains unexplored. This investigation identified and categorized 41 CCHC gene members located on seven chromosomes of rose into 14 subfamilies through motif distribution and phylogenetic analyses involving ten additional plant species, including Ginkgo biloba, Ostreococcus lucimarinus, Arabidopsis thaliana, and others. This study revealed that dispersed duplication likely plays a crucial role in the diversification of the CCHC genes, with the Ka/Ks ratio suggesting a history of strong purifying selection. Promoter analysis highlighted a rich presence of cis-acting regulatory elements linked to both abiotic and biotic stress responses. Differential expression analysis under drought conditions grouped the 41 CCHC gene members into five distinct clusters, with those in group 4 exhibiting pronounced regulation in roots and leaves under severe drought. Furthermore, virus-induced gene silencing (VIGS) of the RcCCHC25 member from group 4 compromised drought resilience in rose foliage. This comprehensive analysis lays the groundwork for further investigations into the functional dynamics of the CCHC gene family in rose physiology and stress responses.
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Affiliation(s)
- Shijie Li
- School of Landscape Architecture, Beijing University of Agriculture, Beinong Road 7, Huilongguan, Changping District, Beijing 102206, China; (S.L.); (J.X.); (Y.C.); (J.W.)
| | - Jun Xu
- School of Landscape Architecture, Beijing University of Agriculture, Beinong Road 7, Huilongguan, Changping District, Beijing 102206, China; (S.L.); (J.X.); (Y.C.); (J.W.)
| | - Yong Cao
- School of Landscape Architecture, Beijing University of Agriculture, Beinong Road 7, Huilongguan, Changping District, Beijing 102206, China; (S.L.); (J.X.); (Y.C.); (J.W.)
| | - Jie Wu
- School of Landscape Architecture, Beijing University of Agriculture, Beinong Road 7, Huilongguan, Changping District, Beijing 102206, China; (S.L.); (J.X.); (Y.C.); (J.W.)
| | - Qing Liu
- CSIRO Agriculture and Food, Black Mountain, Canberra, ACT 2601, Australia;
| | - Deqiang Zhang
- School of Landscape Architecture, Beijing University of Agriculture, Beinong Road 7, Huilongguan, Changping District, Beijing 102206, China; (S.L.); (J.X.); (Y.C.); (J.W.)
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Radkova M, Revalska M, Zhiponova M, Iantcheva A. Evaluation of the role of Medicago truncatula Zn finger CCHC type protein after heterologous expression in Arabidopsis thaliana. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.2006786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Mariana Radkova
- Functional Genetics Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Miglena Revalska
- Functional Genetics Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Miroslava Zhiponova
- Department of Plant Physiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Anelia Iantcheva
- Functional Genetics Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
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Ma L, Cheng K, Li J, Deng Z, Zhang C, Zhu H. Roles of Plant Glycine-Rich RNA-Binding Proteins in Development and Stress Responses. Int J Mol Sci 2021; 22:ijms22115849. [PMID: 34072567 PMCID: PMC8198583 DOI: 10.3390/ijms22115849] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 01/02/2023] Open
Abstract
In recent years, much progress has been made in elucidating the functional roles of plant glycine-rich RNA-binding proteins (GR-RBPs) during development and stress responses. Canonical GR-RBPs contain an RNA recognition motif (RRM) or a cold-shock domain (CSD) at the N-terminus and a glycine-rich domain at the C-terminus, which have been associated with several different RNA processes, such as alternative splicing, mRNA export and RNA editing. However, many aspects of GR-RBP function, the targeting of their RNAs, interacting proteins and the consequences of the RNA target process are not well understood. Here, we discuss recent findings in the field, newly defined roles for GR-RBPs and the actions of GR-RBPs on target RNA metabolism.
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Affiliation(s)
- Liqun Ma
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
| | - Ke Cheng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
| | - Zhiqi Deng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
| | - Chunjiao Zhang
- Supervision, Inspection & Testing Center of Agricultural Products Quality, Ministry of Agriculture and Rural Affairs, Beijing 100083, China;
| | - Hongliang Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
- Correspondence:
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Pleiotropic roles of cold shock proteins with special emphasis on unexplored cold shock protein member of Plasmodium falciparum. Malar J 2020; 19:382. [PMID: 33109193 PMCID: PMC7592540 DOI: 10.1186/s12936-020-03448-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
The cold shock domain (CSD) forms the hallmark of the cold shock protein family that provides the characteristic feature of binding with nucleic acids. While much of the information is available on bacterial, plants and human cold shock proteins, their existence and functions in the malaria parasite remains undefined. In the present review, the available information on functions of well-characterized cold shock protein members in different organisms has been collected and an attempt was made to identify the presence and role of cold shock proteins in malaria parasite. A single Plasmodium falciparum cold shock protein (PfCoSP) was found in P. falciparum which is reported to be essential for parasite survival. Essentiality of PfCoSP underscores its importance in malaria parasite life cycle. In silico tools were used to predict the features of PfCoSP and to identify its homologues in bacteria, plants, humans, and other Plasmodium species. Modelled structures of PfCoSP and its homologues in Plasmodium species were compared with human cold shock protein 'YBOX-1' (Y-box binding protein 1) that provide important insights into their functioning. PfCoSP model was subjected to docking with B-form DNA and RNA to reveal a number of residues crucial for their interaction. Transcriptome analysis and motifs identified in PfCoSP implicate its role in controlling gene expression at gametocyte, ookinete and asexual blood stages of malaria parasite. Overall, this review emphasizes the functional diversity of the cold shock protein family by discussing their known roles in gene expression regulation, cold acclimation, developmental processes like flowering transition, and flower and seed development, and probable function in gametocytogenesis in case of malaria parasite. This enables readers to view the cold shock protein family comprehensively.
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Harrington SA, Backhaus AE, Fox S, Rogers C, Borrill P, Uauy C, Richardson A. A heat-shock inducible system for flexible gene expression in cereals. PLANT METHODS 2020; 16:137. [PMID: 33072173 PMCID: PMC7557097 DOI: 10.1186/s13007-020-00677-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Functional characterisation of genes using transgenic methods is increasingly common in cereal crops. Yet standard methods of gene over-expression can lead to undesirable developmental phenotypes, or even embryo lethality, due to ectopic gene expression. Inducible expression systems allow the study of such genes by preventing their expression until treatment with the specific inducer. When combined with the Cre-Lox recombination system, inducible promoters can be used to initiate constitutive expression of a gene of interest. Yet while these systems are well established in dicot model plants, like Arabidopsis thaliana, they have not yet been implemented in grasses. RESULTS Here we present an irreversible heat-shock inducible system developed using Golden Gate-compatible components which utilises Cre recombinase to drive constitutive gene expression in barley and wheat. We show that a heat shock treatment of 38 °C is sufficient to activate the construct and drive expression of the gene of interest. Modulating the duration of heat shock controls the density of induced cells. Short durations of heat shock cause activation of the construct in isolated single cells, while longer durations lead to global construct activation. The system can be successfully activated in multiple tissues and at multiple developmental stages and shows no activation at standard growth temperatures (~ 20 °C). CONCLUSIONS This system provides an adaptable framework for use in gene functional characterisation in cereal crops. The developed vectors can be easily adapted for specific genes of interest within the Golden Gate cloning system. By using an environmental signal to induce activation of the construct, the system avoids pitfalls associated with consistent and complete application of chemical inducers. As with any inducible system, care must be taken to ensure that the expected construct activation has indeed taken place.
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Affiliation(s)
| | | | - Samantha Fox
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Christian Rogers
- ENSA, Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR UK
| | - Philippa Borrill
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Annis Richardson
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF UK
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Lou L, Ding L, Wang T, Xiang Y. Emerging Roles of RNA-Binding Proteins in Seed Development and Performance. Int J Mol Sci 2020; 21:ijms21186822. [PMID: 32957608 PMCID: PMC7555721 DOI: 10.3390/ijms21186822] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/10/2020] [Accepted: 09/10/2020] [Indexed: 02/01/2023] Open
Abstract
Seed development, dormancy, and germination are key physiological events that are not only important for seed generation, survival, and dispersal, but also contribute to agricultural production. RNA-binding proteins (RBPs) directly interact with target mRNAs and fine-tune mRNA metabolism by governing post-transcriptional regulation, including RNA processing, intron splicing, nuclear export, trafficking, stability/decay, and translational control. Recent studies have functionally characterized increasing numbers of diverse RBPs and shown that they participate in seed development and performance, providing significant insight into the role of RBP-mRNA interactions in seed processes. In this review, we discuss recent research progress on newly defined RBPs that have crucial roles in RNA metabolism and affect seed development, dormancy, and germination.
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Hussain Q, Shi J, Scheben A, Zhan J, Wang X, Liu G, Yan G, King GJ, Edwards D, Wang H. Genetic and signalling pathways of dry fruit size: targets for genome editing-based crop improvement. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1124-1140. [PMID: 31850661 PMCID: PMC7152616 DOI: 10.1111/pbi.13318] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/20/2019] [Accepted: 12/08/2019] [Indexed: 05/24/2023]
Abstract
Fruit is seed-bearing structures specific to angiosperm that form from the gynoecium after flowering. Fruit size is an important fitness character for plant evolution and an agronomical trait for crop domestication/improvement. Despite the functional and economic importance of fruit size, the underlying genes and mechanisms are poorly understood, especially for dry fruit types. Improving our understanding of the genomic basis for fruit size opens the potential to apply gene-editing technology such as CRISPR/Cas to modulate fruit size in a range of species. This review examines the genes involved in the regulation of fruit size and identifies their genetic/signalling pathways, including the phytohormones, transcription and elongation factors, ubiquitin-proteasome and microRNA pathways, G-protein and receptor kinases signalling, arabinogalactan and RNA-binding proteins. Interestingly, different plant taxa have conserved functions for various fruit size regulators, suggesting that common genome edits across species may have similar outcomes. Many fruit size regulators identified to date are pleiotropic and affect other organs such as seeds, flowers and leaves, indicating a coordinated regulation. The relationships between fruit size and fruit number/seed number per fruit/seed size, as well as future research questions, are also discussed.
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Affiliation(s)
- Quaid Hussain
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
| | - Jiaqin Shi
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
| | - Armin Scheben
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | - Jiepeng Zhan
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
| | - Guihua Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
| | - Guijun Yan
- UWA School of Agriculture and EnvironmentThe UWA Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Graham J. King
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreNSWAustralia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
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8
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Budkina KS, Zlobin NE, Kononova SV, Ovchinnikov LP, Babakov AV. Cold Shock Domain Proteins: Structure and Interaction with Nucleic Acids. BIOCHEMISTRY (MOSCOW) 2020; 85:S1-S19. [DOI: 10.1134/s0006297920140011] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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9
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Devani RS, Chirmade T, Sinha S, Bendahmane A, Dholakia BB, Banerjee AK, Banerjee J. Flower bud proteome reveals modulation of sex-biased proteins potentially associated with sex expression and modification in dioecious Coccinia grandis. BMC PLANT BIOLOGY 2019; 19:330. [PMID: 31337343 PMCID: PMC6651928 DOI: 10.1186/s12870-019-1937-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/11/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND Dioecy is an important sexual system wherein, male and female flowers are borne on separate unisexual plants. Knowledge of sex-related differences can enhance our understanding in molecular and developmental processes leading to unisexual flower development. Coccinia grandis is a dioecious species belonging to Cucurbitaceae, a family well-known for diverse sexual forms. Male and female plants have 22A + XY and 22A + XX chromosomes, respectively. Previously, we have reported a gynomonoecious form (22A + XX) of C. grandis bearing morphologically hermaphrodite flowers (GyM-H) and female flowers (GyM-F). Also, we have showed that foliar spray of AgNO3 on female plant induces morphologically hermaphrodite bud development (Ag-H) despite the absence of Y-chromosome. RESULTS To identify sex-related differences, total proteomes from male, female, GyM-H and Ag-H flower buds at early and middle stages of development were analysed by label-free proteomics. Protein search against the cucumber protein sequences (Phytozome) as well as in silico translated C. grandis flower bud transcriptome database, resulted in the identification of 2426 and 3385 proteins (FDR ≤ 1%), respectively. The latter database was chosen for further analysis as it led to the detection of higher number of proteins. Identified proteins were annotated using BLAST2GO pipeline. SWATH-MS-based comparative abundance analysis between Female_Early_vs_Male_Early, Ag_Early_vs_Female_Early, GyM-H_Middle_vs_Male_Middle and Ag_Middle_vs_ Male_Middle led to the identification of 650, 1108, 905 and 805 differentially expressed proteins, respectively, at fold change ≥1.5 and P ≤ 0.05. Ethylene biosynthesis-related candidates as highlighted in protein interaction network were upregulated in female buds compared to male buds. AgNO3 treatment on female plant induced proteins related to pollen development in Ag-H buds. Additionally, a few proteins governing pollen germination and tube growth were highly enriched in male buds compared to Ag-H and GyM-H buds. CONCLUSION Overall, current proteomic analysis provides insights in the identification of key proteins governing dioecy and unisexual flower development in cucurbitaceae, the second largest horticultural family in terms of economic importance. Also, our results suggest that the ethylene-mediated stamen inhibition might be conserved in dioecious C. grandis similar to its monoecious cucurbit relatives. Further, male-biased proteins associated with pollen germination and tube growth identified here can help in understanding pollen fertility.
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Affiliation(s)
- Ravi Suresh Devani
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune, 411008 India
- IPS2, INRA, CNRS, University Paris Sud, University of Evry, University of Paris Diderot, University of Paris Saclay, Batiment 630, 91405 Orsay, France
| | - Tejas Chirmade
- Biochemical Science Division National Chemical laboratory (CSIR-NCL), Pune, 411008 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Sangram Sinha
- Department of Botany, Tripura University, Suryamaninagar, Tripura 799022 India
| | - Abdelhafid Bendahmane
- IPS2, INRA, CNRS, University Paris Sud, University of Evry, University of Paris Diderot, University of Paris Saclay, Batiment 630, 91405 Orsay, France
| | - Bhushan B. Dholakia
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune, 411008 India
- Biochemical Science Division National Chemical laboratory (CSIR-NCL), Pune, 411008 India
- Department of Molecular Biology & Bioinformatics, Tripura University, Suryamaninagar, Tripura 799022 India
| | - Anjan Kumar Banerjee
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune, 411008 India
| | - Jayeeta Banerjee
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune, 411008 India
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Genome-wide identification and expression analysis of glycine-rich RNA-binding protein family in sweet potato wild relative Ipomoea trifida. Gene 2018; 686:177-186. [PMID: 30453066 DOI: 10.1016/j.gene.2018.11.044] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 10/08/2018] [Accepted: 11/15/2018] [Indexed: 01/31/2023]
Abstract
Glycine-rich RNA-binding proteins (GRPs) contain RNA recognition motif (RRM) and glycine-rich domains at the N- or C-terminus, respectively, and they participate in varied physiological and biochemical processes, as well as environmental stresses. Sweet potato from the genus Ipomoea is one of the most important crops. However, the role of the GRP gene family in Ipomoea plant species has not been reported yet. At the same time, the genome of sweet potato remains to be elucidated, but the genome of I. trifida which is most probably the progenitor of the sweet potato was released recently. In this regard, we carried out genome-wide analysis of GRP family members in I. trifida. Here, we identified nine GRP genes in I. trifida and investigated their motif distribution, promoters and gene structure. Subsequently, we performed phylogenetic analysis with the GRP genes from I. trifida, Arabidopsis thaliana, Zea mays L. and Oryza sativa to investigate their phylogenetic relationship. Moreover, we studied the expression patterns of ItGRPs in the roots, stems, young and mature leaves and flowers and found that ItGRP genes were tissue-specific. Meanwhile, the expression profiles under four abiotic stress conditions, including heat, cold, salt and drought stress treatments, revealed that some genes were markedly up-regulated or down-regulated. Taken together, our findings will provide reference to studies on the function of GRP genes in the development and stress response of I. trifida.
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11
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Deng Y, Hu Z, Chai Z, Tang YZ. Cloning and Partial Characterization of a Cold Shock Domain-Containing Protein Gene from the Dinoflagellate Scrippsiella trochoidea. J Eukaryot Microbiol 2018; 66:393-403. [PMID: 30099808 DOI: 10.1111/jeu.12681] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 07/17/2018] [Accepted: 08/03/2018] [Indexed: 11/30/2022]
Abstract
CSPs, cold shock domain (CSD) containing proteins, are demonstrated to be involved in low temperature responses and various cellular processes under normal growth conditions. Here, we used the cosmopolitan, toxic, and resting cyst-producing dinoflagellate Scrippsiella trochoidea as a representative harmful algal bloom-forming dinoflagellate to investigate the expression patterns of CSP in vegetative cells in response to temperature shocks and in resting cysts, with an objective to probe the possible function of CSP in dinoflagellates. The full-length cDNA of a CSP gene from S. trochoidea (StCSP) was obtained which has a solely N-terminal CSD with conserved nucleic acids binding motifs. The qPCR results together indicated StCSP expression was not modulated by temperature at the transcriptional level and implied this gene may not be associated with temperature stress responses in S. trochoidea as the gene's name implies. However, we observed significantly higher StCSP transcripts in resting cysts (newly formed and maintained in dormancy for different periods of time) than that observed in vegetative cells (at exponential and stationary stages), indicating StCSP is actively expressed during dormancy of S. trochoidea. Taking together our recent transcriptomic work on S. trochoidea into consideration, we postulate that StCSP may play roles during encystment and cyst dormancy of the species.
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Affiliation(s)
- Yunyan Deng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhaoyang Chai
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
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12
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Campos NA, Panis B, Carpentier SC. Somatic Embryogenesis in Coffee: The Evolution of Biotechnology and the Integration of Omics Technologies Offer Great Opportunities. FRONTIERS IN PLANT SCIENCE 2017; 8:1460. [PMID: 28871271 PMCID: PMC5566963 DOI: 10.3389/fpls.2017.01460] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/07/2017] [Indexed: 05/22/2023]
Abstract
One of the most important crops cultivated around the world is coffee. There are two main cultivated species, Coffea arabica and C. canephora. Both species are difficult to improve through conventional breeding, taking at least 20 years to produce a new cultivar. Biotechnological tools such as genetic transformation, micropropagation and somatic embryogenesis (SE) have been extensively studied in order to provide practical results for coffee improvement. While genetic transformation got many attention in the past and is booming with the CRISPR technology, micropropagation and SE are still the major bottle neck and urgently need more attention. The methodologies to induce SE and the further development of the embryos are genotype-dependent, what leads to an almost empirical development of specific protocols for each cultivar or clone. This is a serious limitation and excludes a general comprehensive understanding of the process as a whole. The aim of this review is to provide an overview of which achievements and molecular insights have been gained in (coffee) somatic embryogenesis and encourage researchers to invest further in the in vitro technology and combine it with the latest omics techniques (genomics, transcriptomics, proteomics, metabolomics, and phenomics). We conclude that the evolution of biotechnology and the integration of omics technologies offer great opportunities to (i) optimize the production process of SE and the subsequent conversion into rooted plantlets and (ii) to screen for possible somaclonal variation. However, currently the usage of the latest biotechnology did not pass the stage beyond proof of potential and needs to further improve.
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Affiliation(s)
| | | | - Sebastien C. Carpentier
- Department of Biosystems, KU LeuvenLeuven, Belgium
- Facility for Systems Biology Based Mass Spectrometry, KU LeuvenLeuven, Belgium
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13
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Li C, Sako Y, Imai A, Nishiyama T, Thompson K, Kubo M, Hiwatashi Y, Kabeya Y, Karlson D, Wu SH, Ishikawa M, Murata T, Benfey PN, Sato Y, Tamada Y, Hasebe M. A Lin28 homologue reprograms differentiated cells to stem cells in the moss Physcomitrella patens. Nat Commun 2017; 8:14242. [PMID: 28128346 PMCID: PMC5290140 DOI: 10.1038/ncomms14242] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 12/12/2016] [Indexed: 12/21/2022] Open
Abstract
Both land plants and metazoa have the capacity to reprogram differentiated cells to stem cells. Here we show that the moss Physcomitrella patens Cold-Shock Domain Protein 1 (PpCSP1) regulates reprogramming of differentiated leaf cells to chloronema apical stem cells and shares conserved domains with the induced pluripotent stem cell factor Lin28 in mammals. PpCSP1 accumulates in the reprogramming cells and is maintained throughout the reprogramming process and in the resultant stem cells. Expression of PpCSP1 is negatively regulated by its 3′-untranslated region (3′-UTR). Removal of the 3′-UTR stabilizes PpCSP1 transcripts, results in accumulation of PpCSP1 protein and enhances reprogramming. A quadruple deletion mutant of PpCSP1 and three closely related PpCSP genes exhibits attenuated reprogramming indicating that the PpCSP genes function redundantly in cellular reprogramming. Taken together, these data demonstrate a positive role of PpCSP1 in reprogramming, which is similar to the function of mammalian Lin28. Land plants and metazoans are both able to reprogram differentiated cells to stem cells under certain circumstances. Here the authors show that the moss CSP1 protein, which shares conserved domains with the mammalian pluripotent stem cell factor Lin28, promotes reprogramming of leaf cells to apical stem cells.
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Affiliation(s)
- Chen Li
- National Institute for Basic Biology, Division of Evolutionary Biology, Okazaki 444-8585, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585, Japan
| | - Yusuke Sako
- National Institute for Basic Biology, Division of Evolutionary Biology, Okazaki 444-8585, Japan.,ERATO, Hasebe Reprogramming Evolution Project, Japan Science and Technology Agency, Okazaki 444-8585, Japan
| | - Akihiro Imai
- National Institute for Basic Biology, Division of Evolutionary Biology, Okazaki 444-8585, Japan.,ERATO, Hasebe Reprogramming Evolution Project, Japan Science and Technology Agency, Okazaki 444-8585, Japan
| | - Tomoaki Nishiyama
- ERATO, Hasebe Reprogramming Evolution Project, Japan Science and Technology Agency, Okazaki 444-8585, Japan.,Advanced Science Research Center, Institute for Gene Research, Kanazawa University, Kanazawa 920-0934, Japan
| | - Kari Thompson
- National Institute for Basic Biology, Division of Evolutionary Biology, Okazaki 444-8585, Japan.,ERATO, Hasebe Reprogramming Evolution Project, Japan Science and Technology Agency, Okazaki 444-8585, Japan.,Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia 26506, USA
| | - Minoru Kubo
- National Institute for Basic Biology, Division of Evolutionary Biology, Okazaki 444-8585, Japan.,ERATO, Hasebe Reprogramming Evolution Project, Japan Science and Technology Agency, Okazaki 444-8585, Japan
| | - Yuji Hiwatashi
- National Institute for Basic Biology, Division of Evolutionary Biology, Okazaki 444-8585, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585, Japan
| | - Yukiko Kabeya
- National Institute for Basic Biology, Division of Evolutionary Biology, Okazaki 444-8585, Japan
| | - Dale Karlson
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia 26506, USA
| | - Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Masaki Ishikawa
- National Institute for Basic Biology, Division of Evolutionary Biology, Okazaki 444-8585, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585, Japan
| | - Takashi Murata
- National Institute for Basic Biology, Division of Evolutionary Biology, Okazaki 444-8585, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585, Japan
| | - Philip N Benfey
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, North Carolina 27708, USA
| | - Yoshikatsu Sato
- National Institute for Basic Biology, Division of Evolutionary Biology, Okazaki 444-8585, Japan.,ERATO, Hasebe Reprogramming Evolution Project, Japan Science and Technology Agency, Okazaki 444-8585, Japan
| | - Yosuke Tamada
- National Institute for Basic Biology, Division of Evolutionary Biology, Okazaki 444-8585, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585, Japan
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Division of Evolutionary Biology, Okazaki 444-8585, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585, Japan.,ERATO, Hasebe Reprogramming Evolution Project, Japan Science and Technology Agency, Okazaki 444-8585, Japan
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14
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Campos NA, Paiva LV, Panis B, Carpentier SC. The proteome profile of embryogenic cell suspensions of Coffea arabica L. Proteomics 2016; 16:1001-5. [PMID: 27001127 DOI: 10.1002/pmic.201500399] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/03/2015] [Accepted: 01/11/2016] [Indexed: 12/28/2022]
Abstract
Somatic embryogenesis, is a process by which new viable embryos are produced from somatic tissues. Somatic embryogenesis is not only a useful biotechnological tool for the massive clonal propagation and genetic engineering but it also allows to obtain fundamental knowledge about the molecular changes that take place during embryogenesis. We present the proteome profile of two embryogenic cell suspensions. We identified 1052 non-redundant proteins. We present their known GO annotations and show two protein networks sharing the GO annotations related to stress and embryogenic capacity via the free program Cytoscape. To our knowledge these results give the first high-throughput proteome description of embryogenic cell suspensions and provide new information about somatic embryos for the whole plant community. The published proteome is a first step toward understanding somatic embryogenesis in coffee and toward a better annotation of proteins in an important non-model crop. All data are available via ProteomeXchange with identifier PXD002963.
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Affiliation(s)
| | - Luciano V Paiva
- Chemical Department, Federal University of Lavras, Minas Gerais, Brazil
| | - Bart Panis
- Bioversity International, Leuven, Belgium
| | - Sebastien C Carpentier
- Biosystems Department, KULeuven, Leuven, Belgium.,SYBIOMA: Facility for SYstems BIOlogy based MAss spectrometry, Leuven, Belgium
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15
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Characterization of Two Dinoflagellate Cold Shock Domain Proteins. mSphere 2016; 1:mSphere00034-15. [PMID: 27303711 PMCID: PMC4863620 DOI: 10.1128/msphere.00034-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/05/2015] [Indexed: 01/16/2023] Open
Abstract
Dinoflagellate transcriptomes contain cold shock domain proteins as the major component of the proteins annotated as transcription factors. We show here that the major family of cold shock domain proteins in the dinoflagellate Lingulodinium do not bind specific sequences, suggesting that transcriptional control is not a predominant mechanism for regulating gene expression in this group of protists. Roughly two-thirds of the proteins annotated as transcription factors in dinoflagellate transcriptomes are cold shock domain-containing proteins (CSPs), an uncommon condition in eukaryotic organisms. However, no functional analysis has ever been reported for a dinoflagellate CSP, and so it is not known if they do in fact act as transcription factors. We describe here some of the properties of two CSPs from the dinoflagellate Lingulodinium polyedrum, LpCSP1 and LpCSP2, which contain a glycine-rich C-terminal domain and an N-terminal cold shock domain phylogenetically related to those in bacteria. However, neither of the two LpCSPs act like the bacterial CSP, since they do not functionally complement the Escherichia coli quadruple cold shock domain protein mutant BX04, and cold shock does not induce LpCSP1 and LpCSP2 to detectable levels, based on two-dimensional gel electrophoresis. Both CSPs bind to RNA and single-stranded DNA in a nonspecific manner in electrophoretic mobility shift assays, and both proteins also bind double-stranded DNA nonspecifically, albeit more weakly. These CSPs are thus unlikely to act alone as sequence-specific transcription factors. IMPORTANCE Dinoflagellate transcriptomes contain cold shock domain proteins as the major component of the proteins annotated as transcription factors. We show here that the major family of cold shock domain proteins in the dinoflagellate Lingulodinium do not bind specific sequences, suggesting that transcriptional control is not a predominant mechanism for regulating gene expression in this group of protists.
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16
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Choi MJ, Park YR, Park SJ, Kang H. Stress-responsive expression patterns and functional characterization of cold shock domain proteins in cabbage (Brassica rapa) under abiotic stress conditions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 96:132-40. [PMID: 26263516 DOI: 10.1016/j.plaphy.2015.07.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/24/2015] [Accepted: 07/27/2015] [Indexed: 05/24/2023]
Abstract
Although the functional roles of cold shock domain proteins (CSDPs) have been demonstrated during the growth, development, and stress adaptation of Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and wheat (Triticum aestivum), the functions of CSDPs in other plants species, including cabbage (Brassica rapa), are largely unknown. To gain insight into the roles of CSDPs in cabbage under stress conditions, the genes encoding CSDPs in cabbage were isolated, and the functional roles of CSDPs in response to environmental stresses were analyzed. Real-time RT-PCR analysis revealed that the levels of BrCSDP transcripts increased during cold, salt, or drought stress, as well as upon ABA treatment. Among the five BrCSDP genes found in the cabbage genome, one CSDP (BRU12051), named BrCSDP3, was unique in that it is localized to the chloroplast as well as to the nucleus. Ectopic expression of BrCSDP3 in Arabidopsis resulted in accelerated seed germination and better seedling growth compared to the wild-type plants under high salt or dehydration stress conditions, and in response to ABA treatment. BrCSDP3 did not affect the splicing of intron-containing genes and processing of rRNAs in the chloroplast. BrCSDP3 had the ability to complement RNA chaperone-deficient Escherichia coli mutant cells under low temperatures as well as DNA- and RNA-melting abilities, suggesting that it possesses RNA chaperone activity. Taken together, these results suggest that BrCSDP3, harboring RNA chaperone activity, plays a role as a positive regulator in seed germination and seedling growth under stress conditions.
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Affiliation(s)
- Min Ji Choi
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, South Korea
| | - Ye Rin Park
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, South Korea
| | - Su Jung Park
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, South Korea
| | - Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, South Korea.
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17
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Zhang J, Zhao Y, Xiao H, Zheng Y, Yue B. Genome-wide identification, evolution, and expression analysis of RNA-binding glycine-rich protein family in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:1020-1031. [PMID: 24783971 DOI: 10.1111/jipb.12210] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Accepted: 04/25/2014] [Indexed: 06/03/2023]
Abstract
The RNA-binding glycine-rich protein (RB-GRP) family is characterized by the presence of a glycine-rich domain arranged in (Gly)n-X repeats and an RNA-recognition motif (RRM). RB-GRPs participate in varied physiological and biochemical processes especially in the stress response of plants. In this study, a total of 23 RB-GRPs distributed on 10 chromosomes were identified in maize (Zea mays L.), and they were divided into four subgroups according to their conserved domain architecture. Five pairs of paralogs were identified, while none of them was located on the same chromosomal region, suggesting that segmental duplication is predominant in the duplication events of the RB-GRPs in maize. Comparative analysis of RB-GRPs in maize, Arabidopsis (Arabidopsis thaliana L.), rice (Oryza sativa L.), and wheat (Triticum aestivum) revealed that two exclusive subgroups were only identified in maize. Expression of eight ZmRB-GRPs was significantly regulated by at least two kinds of stresses. In addition, cis-elements predicted in the promoter regions of the ZmRB-GRPs also indicated that these ZmRB-GRPs would be involved in stress response of maize. The preliminary genome-wide analysis of the RB-GRPs in maize would provide useful information for further study on the function of the ZmRB-GRPs.
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Affiliation(s)
- Jianhua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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18
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Mani A, Gupta DK. Single-stranded nucleic acid binding in Arabidopsis thaliana cold shock protein is cold shock domain dependent. J Biomol Struct Dyn 2014; 33:861-8. [DOI: 10.1080/07391102.2014.907747] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Ashutosh Mani
- Center of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Allahabad 211002, India
| | - Dwijendra K. Gupta
- Center of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Allahabad 211002, India
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19
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Juntawong P, Sorenson R, Bailey-Serres J. Cold shock protein 1 chaperones mRNAs during translation in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:1016-28. [PMID: 23551487 DOI: 10.1111/tpj.12187] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 03/20/2013] [Accepted: 03/25/2013] [Indexed: 05/11/2023]
Abstract
RNA binding proteins (RBPs) function post-transcriptionally to fine-tune gene regulation. Arabidopsis thaliana has four Gly-rich, zinc finger-containing RBPs called cold shock proteins 1-4 (CSP1-CSP4), that possess an evolutionary conserved cold shock domain. Here, we determined that CSP1 associates with polyribosomes (polysomes) via an RNA-mediated interaction. Both the abundance and polysomal co-fractionation of CSP1 was enhanced in the cold (4°C), but did not influence global levels of polysomes, which were minimally perturbed by above freezing cold temperatures. Using a polyclonal antiserum, CSP1 was co-immunopurified with several hundred transcripts from rosettes of plants cultivated at 23°C or transferred to 4°C for 12 h. CSP1-associated mRNAs were characterized by G+C-rich 5' untranslated regions and gene ontologies related to cellular respiration, mRNA binding and translation. The majority of the CSP1-associated mRNAs were constitutively expressed and stable in the cold. CSP1 abundance was correlated with improved translation of ribosomal protein mRNAs during cold stress and improved maintenance of homeostasis and translation of mRNAs under water-deficit stress. In summary, CSP1 selectively chaperones mRNAs, providing translational enhancement during stress.
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Affiliation(s)
- Piyada Juntawong
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521, USA
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20
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AtCSP1 regulates germination timing promoted by low temperature. FEBS Lett 2013; 587:2186-92. [PMID: 23732703 DOI: 10.1016/j.febslet.2013.05.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 05/07/2013] [Accepted: 05/08/2013] [Indexed: 11/22/2022]
Abstract
An Arabidopsis gene trap line (GT606), which disrupted the AtCSP1 gene, exhibited an early germination phenotype that was affected by stratification treatment. Comparative analysis of GUS expression in seeds at the early germination stage, with or without stratification, demonstrated that AtCSP1 expression was affected by cold temperature. Evaluation of germination assays with varying concentrations of ABA or NaCl revealed a reduced sensitivity of the atcsp1 mutant to both ABA and NaCl. Taken together, these data support the hypothesis that AtCSP1 affects early stages of seed germination subsequent to stratification treatment of seeds.
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21
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Sasaki K, Kim MH, Imai R. Arabidopsis COLD SHOCK DOMAIN PROTEIN 2 is a negative regulator of cold acclimation. THE NEW PHYTOLOGIST 2013; 198:95-102. [PMID: 23323758 DOI: 10.1111/nph.12118] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 11/27/2012] [Indexed: 06/01/2023]
Abstract
Bacterial cold shock proteins (CSPs) act as RNA chaperones that destabilize mRNA secondary structures at low temperatures. Bacterial CSPs are composed solely of a nucleic acid-binding domain termed the cold shock domain (CSD). Plant CSD proteins contain an auxiliary domain in addition to the CSD but also show RNA chaperone activity. However, their biological functions are poorly understood. We examined Arabidopsis COLD SHOCK DOMAIN PROTEIN 2 (AtCSP2) using overexpressing and mutant lines. A double mutant, with reduced AtCSP2 and no AtCSP4, showed higher freezing tolerance than the wild-type when cold-acclimated. The increase in freezing tolerance was associated with up-regulation of CBF transcription factors and their downstream genes. By contrast, overexpression of AtCSP2 resulted in decreased freezing tolerance when cold-acclimated. In addition, late flowering and shorter siliques were observed in the overexpressing lines. AtCSP2 negatively regulates freezing tolerance and is partially redundant with its closest paralog, AtCSP4.
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Affiliation(s)
- Kentaro Sasaki
- Hokkaido Agriculture Research Center, National Agriculture and Food Research Organization, Hitsujigaoka 1, Toyohira-ku, Sapporo, 062-8555, Japan
- Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, 060-8589, Japan
| | - Myung-Hee Kim
- Hokkaido Agriculture Research Center, National Agriculture and Food Research Organization, Hitsujigaoka 1, Toyohira-ku, Sapporo, 062-8555, Japan
| | - Ryozo Imai
- Hokkaido Agriculture Research Center, National Agriculture and Food Research Organization, Hitsujigaoka 1, Toyohira-ku, Sapporo, 062-8555, Japan
- Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, 060-8589, Japan
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22
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Ryzhova NN, Filiushin MA, Artem’eva AM, Berdnikova MV, Taranov VV, Babakov AV, Kochieva EZ. Identification and nucleotide polymorphisms in Brassica rapa genes coding cold-shock domain proteins. Mol Biol 2013. [DOI: 10.1134/s0026893312060143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Kang H, Park SJ, Kwak KJ. Plant RNA chaperones in stress response. TRENDS IN PLANT SCIENCE 2013; 18:100-6. [PMID: 22947615 DOI: 10.1016/j.tplants.2012.08.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 08/02/2012] [Accepted: 08/13/2012] [Indexed: 05/18/2023]
Abstract
Post-transcriptional regulation of RNA metabolism is a key regulatory process in diverse cellular processes, including the stress response of plants, during which a variety of RNA-binding proteins (RBPs) function as central regulators in cells. RNA chaperones are RBPs found in all living organisms and function by providing assistance to the correct folding of RNA molecules during RNA metabolism. Although our understanding of the role of RNA chaperones in plants is far less advanced than in bacteria, viruses, and animals, recent progress in functional characterization and determination of RNA chaperone activity of several RBPs has shed new light on the emerging roles of RNA chaperones during the stress response of plants.
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Affiliation(s)
- Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757, Korea.
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24
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Yang Y, Karlson D. Effects of mutations in the Arabidopsis Cold Shock Domain Protein 3 (AtCSP3) gene on leaf cell expansion. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:4861-73. [PMID: 22888122 PMCID: PMC3427997 DOI: 10.1093/jxb/ers160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The cold shock domain is among the most evolutionarily conserved nucleic acid binding domains from prokaryotes to higher eukaryotes, including plants. Although eukaryotic cold shock domain proteins have been extensively studied as transcriptional and post-transcriptional regulators during various developmental processes, their functional roles in plants remains poorly understood. In this study, AtCSP3 (At2g17870), which is one of four Arabidopsis thaliana c old s hock domain proteins (AtCSPs), was functionally characterized. Quantitative RT-PCR analysis confirmed high expression of AtCSP3 in reproductive and meristematic tissues. A homozygous atcsp3 loss-of-function mutant exhibits an overall reduced seedling size, stunted and orbicular rosette leaves, reduced petiole length, and curled leaf blades. Palisade mesophyll cells are smaller and more circular in atcsp3 leaves. Cell size analysis indicated that the reduced size of the circular mesophyll cells appears to be generated by a reduction of cell length along the leaf-length axis, resulting in an orbicular leaf shape. It was also determined that leaf cell expansion is impaired for lateral leaf development in the atcsp3 loss-of-function mutant, but leaf cell proliferation is not affected. AtCSP3 loss-of-function resulted in a dramatic reduction of LNG1 transcript, a gene that is involved in two-dimensional leaf polarity regulation. Transient subcellular localization of AtCSP3 in onion epidermal cells confirmed a nucleocytoplasmic localization pattern. Collectively, these data suggest that AtCSP3 is functionally linked to the regulation of leaf length by affecting LNG1 transcript accumulation during leaf development. A putative function of AtCSP3 as an RNA binding protein is also discussed in relation to leaf development.
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Affiliation(s)
- Yongil Yang
- Division of Plant and Soil Sciences, West Virginia UniversityMorgantown, WV 26506-6108, USA
- Present address: Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Dale Karlson
- Division of Plant and Soil Sciences, West Virginia UniversityMorgantown, WV 26506-6108, USA
- Present address and to whom correspondence should be sent: Monsanto Company, 110 TW Alexander Drive, RTP, NC 27709,USA. E-mail:
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25
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Nakaminami K, Matsui A, Shinozaki K, Seki M. RNA regulation in plant abiotic stress responses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:149-53. [PMID: 21840431 DOI: 10.1016/j.bbagrm.2011.07.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 07/27/2011] [Accepted: 07/29/2011] [Indexed: 01/01/2023]
Abstract
RNA regulatory processes such as transcription, degradation and stabilization control are the major mechanisms that determine the levels of mRNAs in plants. Transcriptional and post-transcriptional regulations of RNAs are drastically altered during plant stress responses. As a result of these molecular processes, plants are capable of adjusting to changing environmental conditions. Understanding the role of these mechanisms in plant stress responses is important and necessary for the engineering of stress-tolerant plants. Recent studies in the area of RNA regulation have increased our understanding of how plants respond to environmental stresses. This review highlights recent progress in RNA regulatory processes that are involved in plant stress responses, such as small RNAs, alternative splicing, RNA granules and RNA-binding proteins. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.
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