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Whiting JR, Booker TR, Rougeux C, Lind BM, Singh P, Lu M, Huang K, Whitlock MC, Aitken SN, Andrew RL, Borevitz JO, Bruhl JJ, Collins TL, Fischer MC, Hodgins KA, Holliday JA, Ingvarsson PK, Janes JK, Khandaker M, Koenig D, Kreiner JM, Kremer A, Lascoux M, Leroy T, Milesi P, Murray KD, Pyhäjärvi T, Rellstab C, Rieseberg LH, Roux F, Stinchcombe JR, Telford IRH, Todesco M, Tyrmi JS, Wang B, Weigel D, Willi Y, Wright SI, Zhou L, Yeaman S. The genetic architecture of repeated local adaptation to climate in distantly related plants. Nat Ecol Evol 2024:10.1038/s41559-024-02514-5. [PMID: 39187610 DOI: 10.1038/s41559-024-02514-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 07/22/2024] [Indexed: 08/28/2024]
Abstract
Closely related species often use the same genes to adapt to similar environments. However, we know little about why such genes possess increased adaptive potential and whether this is conserved across deeper evolutionary lineages. Adaptation to climate presents a natural laboratory to test these ideas, as even distantly related species must contend with similar stresses. Here, we re-analyse genomic data from thousands of individuals from 25 plant species as diverged as lodgepole pine and Arabidopsis (~300 Myr). We test for genetic repeatability based on within-species associations between allele frequencies in genes and variation in 21 climate variables. Our results demonstrate significant statistical evidence for genetic repeatability across deep time that is not expected under randomness, identifying a suite of 108 gene families (orthogroups) and gene functions that repeatedly drive local adaptation to climate. This set includes many orthogroups with well-known functions in abiotic stress response. Using gene co-expression networks to quantify pleiotropy, we find that orthogroups with stronger evidence for repeatability exhibit greater network centrality and broader expression across tissues (higher pleiotropy), contrary to the 'cost of complexity' theory. These gene families may be important in helping wild and crop species cope with future climate change, representing important candidates for future study.
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Affiliation(s)
- James R Whiting
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
| | - Tom R Booker
- Department of Zoology, Faculty of Science, University of British Columbia, Vancouver, British Colombia, Canada
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Clément Rougeux
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Brandon M Lind
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pooja Singh
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Mengmeng Lu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael C Whitlock
- Department of Zoology, Faculty of Science, University of British Columbia, Vancouver, British Colombia, Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rose L Andrew
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Justin O Borevitz
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jeremy J Bruhl
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Timothy L Collins
- Department of Planning and Environment, Queanbeyan, New South Wales, Australia
- Department of Climate Change, Energy, the Environment and Water, Queanbeyan, New South Wales, Australia
| | - Martin C Fischer
- ETH Zurich: Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, USA
| | - Pär K Ingvarsson
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jasmine K Janes
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
- Department of Ecosystem Science and Management, University of Northern British Columbia, Prince George, British Columbia, Canada
- Species Survival Commission, Orchid Specialist Group, IUCN North America, Washington, DC, USA
| | - Momena Khandaker
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Daniel Koenig
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Julia M Kreiner
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Antoine Kremer
- UMR BIOGECO, INRAE, Université de Bordeaux; 69 Route d'Arcachon, Cestas, France
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thibault Leroy
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Pascal Milesi
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kevin D Murray
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Tanja Pyhäjärvi
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | | | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fabrice Roux
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - John R Stinchcombe
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Ian R H Telford
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Marco Todesco
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada
| | - Jaakko S Tyrmi
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Baosheng Wang
- South China National Botanical Garden, Guangzhou, China
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Yvonne Willi
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Stephen I Wright
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Lecong Zhou
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, USA
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
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Prakash V, Sharma V, Devendran R, Prajapati R, Ahmad B, Kumar R. A transition from enemies to allies: how viruses improve drought resilience in plants. STRESS BIOLOGY 2024; 4:33. [PMID: 38981936 PMCID: PMC11233480 DOI: 10.1007/s44154-024-00172-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/03/2024] [Indexed: 07/11/2024]
Abstract
Global crop production is severely affected by environmental factors such as drought, salinity, cold, flood etc. Among these stresses, drought is one of the major abiotic stresses reducing crop productivity. It is expected that drought conditions will further increase because of the increasing global temperature. In general, viruses are seen as a pathogen affecting the crop productivity. However, several researches are showing that viruses can induce drought tolerance in plants. This review explores the mechanisms underlying the interplay between viral infections and the drought response mechanisms in plants. We tried to address the molecular pathways and physiological changes induced by viruses that confer drought tolerance, including alterations in hormone signaling, antioxidant defenses, scavenging the reactive oxygen species, role of RNA silencing and miRNA pathway, change in the expression of several genes including heat shock proteins, cellulose synthase etc. Furthermore, we discuss various viruses implicated in providing drought tolerance and examine the range of plant species exhibiting this phenomenon. By applying current knowledge and identifying gaps in understanding, this review aims to provide valuable insights into the complex dynamics of virus-induced drought tolerance in plants, paving the way for future research directions and practical applications in sustainable agriculture.
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Affiliation(s)
- Ved Prakash
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
| | - Veerendra Sharma
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | - Ramgopal Prajapati
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Bilal Ahmad
- Division of Biology, Kansas State University, Manhattan, KS, USA
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Liu Y, Xiao W, Wang F, Wang Y, Dong Y, Nie W, Tan C, An S, Chang E, Jiang Z, Wang J, Jia Z. Adaptive divergence, historical population dynamics, and simulation of suitable distributions for Picea Meyeri and P. Mongolica at the whole-genome level. BMC PLANT BIOLOGY 2024; 24:479. [PMID: 38816690 PMCID: PMC11137980 DOI: 10.1186/s12870-024-05166-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/17/2024] [Indexed: 06/01/2024]
Abstract
The taxonomic classification of Picea meyeri and P. mongolica has long been controversial. To investigate the genetic relatedness, evolutionary history, and population history dynamics of these species, genotyping-by-sequencing (GBS) technology was utilized to acquire whole-genome single nucleotide polymorphism (SNP) markers, which were subsequently used to assess population structure, population dynamics, and adaptive differentiation. Phylogenetic and population structural analyses at the genomic level indicated that although the ancestor of P. mongolica was a hybrid of P. meyeri and P. koraiensis, P. mongolica is an independent Picea species. Additionally, P. mongolica is more closely related to P. meyeri than to P. koraiensis, which is consistent with its geographic distribution. There were up to eight instances of interspecific and intraspecific gene flow between P. meyeri and P. mongolica. The P. meyeri and P. mongolica effective population sizes generally decreased, and Maxent modeling revealed that from the Last Glacial Maximum (LGM) to the present, their habitat areas decreased initially and then increased. However, under future climate scenarios, the habitat areas of both species were projected to decrease, especially under high-emission scenarios, which would place P. mongolica at risk of extinction and in urgent need of protection. Local adaptation has promoted differentiation between P. meyeri and P. mongolica. Genotype‒environment association analysis revealed 96,543 SNPs associated with environmental factors, mainly related to plant adaptations to moisture and temperature. Selective sweeps revealed that the selected genes among P. meyeri, P. mongolica and P. koraiensis are primarily associated in vascular plants with flowering, fruit development, and stress resistance. This research enhances our understanding of Picea species classification and provides a basis for future genetic improvement and species conservation efforts.
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Affiliation(s)
- Yifu Liu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, 100091, China
| | - Wenfa Xiao
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, 100091, China
| | - Fude Wang
- Heilongjiang Forestry Research Institute, Harbin, 150080, China
| | - Ya Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yao Dong
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, 100091, China
| | - Wen Nie
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, 100091, China
| | - Cancan Tan
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, 100091, China
| | - Sanping An
- Research Institute of Forestry of Xiaolong Mountain, Gansu Provincial Key Laboratory of Secondary Forest Cultivation, Tianshui, 741022, China
| | - Ermei Chang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Zeping Jiang
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, 100091, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Zirui Jia
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
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Božić M, Ignjatović Micić D, Delić N, Nikolić A. Maize miRNAs and their putative target genes involved in chilling stress response in 5-day old seedlings. BMC Genomics 2024; 25:479. [PMID: 38750515 PMCID: PMC11094857 DOI: 10.1186/s12864-024-10403-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/09/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND In the context of early sowing of maize as a promising adaptation strategy that could significantly reduce the negative effects of climate change, an in-depth understanding of mechanisms underlying plant response to low-temperature stress is demanded. Although microRNAs (miRNAs) have been recognized as key regulators of plant stress response, research on their role in chilling tolerance of maize during early seedling stages is scarce. Therefore, it is of great significance to explore chilling-responsive miRNAs, reveal their expression patterns and associated target genes, as well as to examine the possible functions of the conserved and novel miRNAs. In this study, the role of miRNAs was examined in 5d-old maize seedlings of one tolerant and one sensitive inbred line exposed to chilling (10/8 °C) stress for 6 h and 24 h, by applying high throughput sequencing. RESULTS A total of 145 annotated known miRNAs belonging to 30 families and 876 potentially novel miRNAs were identified. Differential expression (DE) analysis between control and stress conditions identified 98 common miRNAs for both genotypes at one time point and eight miRNAs at both time points. Target prediction and enrichment analysis showed that the DE zma-miR396, zma-miR156, zma-miR319, and zma-miR159 miRNAs modulate growth and development. Furthermore, it was found that several other DE miRNAs were involved in abiotic stress response: antioxidative mechanisms (zma-miR398), signal transduction (zma-miR156, zma-miR167, zma-miR169) and regulation of water content (zma-miR164, zma-miR394, zma-miR396). The results underline the zma-miRNAs involvement in the modulation of their target genes expression as an important aspect of the plant's survival strategy and acclimation to chilling stress conditions. CONCLUSIONS To our understanding, this is the first study on miRNAs in 5-d old seedlings' response to chilling stress, providing data on the role of known and novel miRNAs post-transcriptional regulation of expressed genes and contributing a possible platform for further network and functional analysis.
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Affiliation(s)
- Manja Božić
- Laboratory for Molecular Genetics and Physiology, Research and Development Department, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Dragana Ignjatović Micić
- Laboratory for Molecular Genetics and Physiology, Research and Development Department, Maize Research Institute Zemun Polje, Belgrade, Serbia.
| | - Nenad Delić
- Laboratory for Molecular Genetics and Physiology, Research and Development Department, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Ana Nikolić
- Laboratory for Molecular Genetics and Physiology, Research and Development Department, Maize Research Institute Zemun Polje, Belgrade, Serbia
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da Silva Filho JLB, Pestana RKN, da Silva Júnior WJ, Coelho Filho MA, Ferreira CF, de Oliveira EJ, Kido EA. Exploiting DNA methylation in cassava under water deficit for crop improvement. PLoS One 2024; 19:e0296254. [PMID: 38386677 PMCID: PMC10883565 DOI: 10.1371/journal.pone.0296254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/08/2023] [Indexed: 02/24/2024] Open
Abstract
DNA methylation plays a key role in the development and plant responses to biotic and abiotic stresses. This work aimed to evaluate the DNA methylation in contrasting cassava genotypes for water deficit tolerance. The varieties BRS Formosa (bitter) and BRS Dourada (sweet) were grown under greenhouse conditions for 50 days, and afterwards, irrigation was suspended. The stressed (water deficit) and non-stressed plants (negative control) consisted the treatments with five plants per variety. The DNA samples of each variety and treatment provided 12 MethylRAD-Seq libraries (two cassava varieties, two treatments, and three replicates). The sequenced data revealed methylated sites covering 18 to 21% of the Manihot esculenta Crantz genome, depending on the variety and the treatment. The CCGG methylated sites mapped mostly in intergenic regions, exons, and introns, while the CCNGG sites mapped mostly intergenic, upstream, introns, and exons regions. In both cases, methylated sites in UTRs were less detected. The differentially methylated sites analysis indicated distinct methylation profiles since only 12% of the sites (CCGG and CCNGG) were methylated in both varieties. Enriched gene ontology terms highlighted the immediate response of the bitter variety to stress, while the sweet variety appears to suffer more potential stress-damages. The predicted protein-protein interaction networks reinforced such profiles. Additionally, the genomes of the BRS varieties uncovered SNPs/INDELs events covering genes stood out by the interactomes. Our data can be useful in deciphering the roles of DNA methylation in cassava drought-tolerance responses and adaptation to abiotic stresses.
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Affiliation(s)
| | | | - Wilson José da Silva Júnior
- Laboratório de Genética Molecular de Plantas, Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
| | | | | | | | - Ederson Akio Kido
- Laboratório de Genética Molecular de Plantas, Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
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Yang X, Ji C, Liu X, Wei Z, Pang Q, Zhang A. Arabidopsis nucleoporin NUP96 mediates plant salt tolerance by modulating the transcription of salt-responsive genes. PLANTA 2023; 259:34. [PMID: 38160450 DOI: 10.1007/s00425-023-04312-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
MAIN CONCLUSION Physiological and molecular tests show that NUP96 plays an important role in the plant response to salt stress, resulting from the reprogramming of transcriptomic profiles, which are likely to be mediated by the influence on the nuclear/cytosol shuttling of the key regulators of salt tolerance. As a key component of the nuclear pore complex (NPC), nucleoporin 96 (NUP96) is critical for modulating plant development and interactions with environmental factors, but whether NUP96 is involved in the salt response is still unknown. Here, we analyzed the role of Arabidopsis NUP96 under salt stress. The loss-of-function mutant nup96 exhibited salt sensitivity in terms of rosette growth and root elongation, and showed attenuated capacity in maintaining ion and ROS homeostasis, which could be compensated for by the overexpression of NUP96. RNA sequencing revealed that many salt-responsive genes were misregulated after NUP96 mutation, and especially NUP96 is required for the expression of a large portion of salt-induced genes. This is likely correlated with the activity in facilitating nuclear/cytosol transport of the underlying regulators in salt tolerance such as the transcription factor ATAP2, targeted by eight downregulated genes in nup96 under salt stress. Our results illustrate that NUP96 plays an important role in the salt response, probably by regulating the nucleocytoplasmic shuttling of key mRNAs or proteins associated with plant salt responsiveness.
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Affiliation(s)
- Xiaomin Yang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Chengcheng Ji
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Xinxin Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Zhaoxin Wei
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Qiuying Pang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
| | - Aiqin Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
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Luklová M, Novák J, Kopecká R, Kameniarová M, Gibasová V, Brzobohatý B, Černý M. Phytochromes and Their Role in Diurnal Variations of ROS Metabolism and Plant Proteome. Int J Mol Sci 2022; 23:14134. [PMID: 36430613 PMCID: PMC9695588 DOI: 10.3390/ijms232214134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/12/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022] Open
Abstract
Plants are sessile organisms forced to adapt to environmental variations recurring in a day-night cycle. Extensive research has uncovered the transcriptional control of plants' inner clock and has revealed at least some part of the intricate and elaborate regulatory mechanisms that govern plant diel responses and provide adaptation to the ever-changing environment. Here, we analyzed the proteome of the Arabidopsis thaliana mutant genotypes collected in the middle of the day and the middle of the night, including four mutants in the phytochrome (phyA, phyB, phyC, and phyD) and the circadian clock protein LHY. Our approach provided a novel insight into the diel regulations, identifying 640 significant changes in the night-day protein abundance. The comparison with previous studies confirmed that a large portion of identified proteins was a known target of diurnal regulation. However, more than 300 were novel oscillations hidden under standard growth chamber conditions or not manifested in the wild type. Our results indicated a prominent role for ROS metabolism and phytohormone cytokinin in the observed regulations, and the consecutive analyses confirmed that. The cytokinin signaling significantly increased at night, and in the mutants, the hydrogen peroxide content was lower, and the night-day variation seemed to be lost in the phyD genotype. Furthermore, regulations in the lhy and phyB mutants were partially similar to those found in the catalase mutant cat2, indicating shared ROS-mediated signaling pathways. Our data also shed light on the role of the relatively poorly characterized Phytochrome D, pointing to its connection to glutathione metabolism and the regulation of glutathione S-transferases.
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Affiliation(s)
| | | | | | | | | | | | - Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
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Jin L, Zhang G, Yang G, Dong J. Identification of the Karyopherin Superfamily in Maize and Its Functional Cues in Plant Development. Int J Mol Sci 2022; 23:ijms232214103. [PMID: 36430578 PMCID: PMC9699179 DOI: 10.3390/ijms232214103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/06/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022] Open
Abstract
Appropriate nucleo-cytoplasmic partitioning of proteins is a vital regulatory mechanism in phytohormone signaling and plant development. However, how this is achieved remains incompletely understood. The Karyopherin (KAP) superfamily is critical for separating the biological processes in the nucleus from those in the cytoplasm. The KAP superfamily is divided into Importin α (IMPα) and Importin β (IMPβ) families and includes the core components in mediating nucleocytoplasmic transport. Recent reports suggest the KAPs play crucial regulatory roles in Arabidopsis development and stress response by regulating the nucleo-cytoplasmic transport of members in hormone signaling. However, the KAP members and their associated molecular mechanisms are still poorly understood in maize. Therefore, we first identified seven IMPα and twenty-seven IMPβ genes in the maize genome and described their evolution traits and the recognition rules for substrates with nuclear localization signals (NLSs) or nuclear export signals (NESs) in plants. Next, we searched for the protein interaction partners of the ZmKAPs and selected the ones with Arabidopsis orthologs functioning in auxin biosynthesis, transport, and signaling to predict their potential function. Finally, we found that several ZmKAPs share similar expression patterns with their interacting proteins, implying their function in root development. Overall, this article focuses on the Karyopherin superfamily in maize and starts with this entry point by systematically comprehending the KAP-mediated nucleo-cytoplasmic transport process in plants, and then predicts the function of the ZmKAPs during maize development, with a perspective on a closely associated regulatory mechanism between the nucleo-cytoplasmic transport and the phytohormone network.
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Affiliation(s)
- Lu Jin
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Guobin Zhang
- College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Guixiao Yang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Jiaqiang Dong
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
- Correspondence:
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9
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Chang YN, Wang Z, Ren Z, Wang CH, Wang P, Zhu JK, Li X, Duan CG. NUCLEAR PORE ANCHOR and EARLY IN SHORT DAYS 4 negatively regulate abscisic acid signaling by inhibiting Snf1-related protein kinase2 activity and stability in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2060-2074. [PMID: 35984097 DOI: 10.1111/jipb.13349] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Abscisic acid (ABA) is a key regulator of plant responses to abiotic stresses, such as drought. Abscisic acid receptors and coreceptors perceive ABA to activate Snf1-related protein kinase2s (SnRK2s) that phosphorylate downstream effectors, thereby activating ABA signaling and the stress response. As stress responses come with fitness penalties for plants, it is crucial to tightly control SnRK2 kinase activity to restrict ABA signaling. However, how SnRK2 kinases are inactivated remains elusive. Here, we show that NUCLEAR PORE ANCHOR (NUA), a nuclear pore complex (NPC) component, negatively regulates ABA-mediated inhibition of seed germination and post-germination growth, and drought tolerance in Arabidopsis thaliana. The role of NUA in response to ABA depends on SnRK2.2 and SnRK2.3 for seed germination and on SnRK2.6 for drought. NUA does not directly inhibit the phosphorylation of these SnRK2s or affects their abundance. However, the NUA-interacting protein EARLY IN SHORT DAYS 4 (ESD4), a SUMO protease, negatively regulates ABA signaling by directly interacting with and inhibiting SnRK2 phosphorylation and protein levels. More importantly, we demonstrated that SnRK2.6 can be SUMOylated in vitro, and ESD4 inhibits its SUMOylation. Taken together, we identified NUA and ESD4 as SnRK2 kinase inhibitors that block SnRK2 activity, and reveal a mechanism whereby NUA and ESD4 negatively regulate plant responses to ABA and drought stress possibly through SUMOylation-dependent regulation of SnRK2s.
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Affiliation(s)
- Ya-Nan Chang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, the Chinese Academy of Science, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhijuan Wang
- National Key Laboratory of Crop Genetic and Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ziyin Ren
- National Key Laboratory of Crop Genetic and Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chun-Han Wang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, the Chinese Academy of Science, Shanghai, 201602, China
| | - Pengcheng Wang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, the Chinese Academy of Science, Shanghai, 201602, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, the Chinese Academy of Science, Shanghai, 201602, China
- Department of Horticulture and Architecture Landscape, Purdue University, West Lafayette, IN 47907, USA
| | - Xia Li
- National Key Laboratory of Crop Genetic and Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, the Chinese Academy of Science, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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10
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Qin Z, Wu YN, Sun TT, Ma T, Xu M, Pang C, Li SW, Li S. Arabidopsis RAN GTPases are critical for mitosis during male and female gametogenesis. FEBS Lett 2022; 596:1892-1903. [PMID: 35680649 DOI: 10.1002/1873-3468.14422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 11/09/2022]
Abstract
The development of male and female gametophytes is a prerequisite for successful propagation of angiosperms. The small GTPases RAN play fundamental roles in numerous cellular processes. Although RAN GTPases have been characterized in plants, their roles in cellular processes are far from understood. We report here that RAN GTPases in Arabidopsis are critical for gametophytic development. RAN1 loss-of-function showed no defects in gametophytic development likely due to redundancy. However, the expression of a dominant negative or constitutively active RAN1 resulted in gametophytic lethality. Genetic interference of RAN GTPases caused the arrest of pollen mitosis I and of mitosis of functional megaspores, implying a key role of properly regulated RAN activity in mitosis during gametophytic development.
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Affiliation(s)
- Zheng Qin
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tian'jin, China
| | - Ya-Nan Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Tian-Tian Sun
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Ting Ma
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Meng Xu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Chen Pang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Shan-Wei Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Sha Li
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tian'jin, China.,State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
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11
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Yang Z, Du H, Sun J, Xing X, Kong Y, Li W, Li X, Zhang C. A Nodule-Localized Small Heat Shock Protein GmHSP17.1 Confers Nodule Development and Nitrogen Fixation in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:838718. [PMID: 35356122 PMCID: PMC8959767 DOI: 10.3389/fpls.2022.838718] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Small heat shock proteins (sHSPs) are ubiquitous proteins present in all organisms. The sHSPs are not only upregulated under heat shock as well as other stresses but also are expressed in unstressed cells, indicating quite diverse functions of sHSPs. However, there is little known about the role of sHSPs in nodulation and nitrogen fixation in soybean. In this study, we cloned a candidate protein of sHSP, GmHSP17.1, from proteome of nodule and analyzed its function in soybean nodulation. We found that GmHSP17.1 was a cytosolic protein and preferentially expressed during nodule development. An overexpression of GmHSP17.1 in composite transgenic plants showed increases in nodule number, fresh weight, nodule size, area of infection cells, and nitrogenase activity, and subsequently promoted the content of nitrogen and growth of soybean plants. While GmHSP17.1 RNA interference (RNAi) lines showed significantly impaired nodule development and nitrogen fixation efficiency. Through liquid chromatography-tandem mass spectrometry (LC-MS/MS), GmRIP1 was identified as the first potential target of GmHSP17.1, and was shown to be specifically expressed in soybean nodules. The interaction between GmHSP17.1 and GmRIP1 was further confirmed by yeast-two hybrid (Y2H), bimolecular fluorescence complementation (BiFC) in vivo and pull-down assay in vitro. Furthermore, peroxidase activity was markedly increased in GmHSP17.1 overexpressed nodules and decreased in RNAi lines. As a result, the reactive oxygen species (ROS) content greatly decreased in GmHSP17.1 overexpression lines and increased in suppression lines. Taken together, we conclude that GmHSP17.1 plays an important role in soybean nodulation through interacting with GmRIP1. Our results provide foundation for studying the mechanism of nitrogen fixation and for the genetics improvement of legume plants.
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Affiliation(s)
- Zhanwu Yang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Hui Du
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Jingyi Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xinzhu Xing
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Youbin Kong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Wenlong Li
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xihuan Li
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Caiying Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
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12
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Yang Z, Du H, Xing X, Li W, Kong Y, Li X, Zhang C. A small heat shock protein, GmHSP17.9, from nodule confers symbiotic nitrogen fixation and seed yield in soybean. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:103-115. [PMID: 34487637 PMCID: PMC8710831 DOI: 10.1111/pbi.13698] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 08/11/2021] [Accepted: 08/26/2021] [Indexed: 05/27/2023]
Abstract
Legume-rhizobia symbiosis enables biological nitrogen fixation to improve crop production for sustainable agriculture. Small heat shock proteins (sHSPs) are involved in multiple environmental stresses and plant development processes. However, the role of sHSPs in nodule development in soybean remains largely unknown. In the present study, we identified a nodule-localized sHSP, called GmHSP17.9, in soybean, which was markedly up-regulated during nodule development. GmHSP17.9 was specifically expressed in the infected regions of the nodules. GmHSP17.9 overexpression and RNAi in transgenic composite plants and loss of function in CRISPR-Cas9 gene-editing mutant plants in soybean resulted in remarkable alterations in nodule number, nodule fresh weight, nitrogenase activity, contents of poly β-hydroxybutyrate bodies (PHBs), ureide and total nitrogen content, which caused significant changes in plant growth and seed yield. GmHSP17.9 was also found to act as a chaperone for its interacting partner, GmNOD100, a sucrose synthase in soybean nodules which was also preferentially expressed in the infected zone of nodules, similar to GmHSP17.9. Functional analysis of GmNOD100 in composite transgenic plants revealed that GmNOD100 played an essential role in soybean nodulation. The hsp17.9 lines showed markedly more reduced sucrose synthase activity, lower contents of UDP-glucose and acetyl coenzyme A (acetyl-CoA), and decreased activity of succinic dehydrogenase (SDH) in the tricarboxylic acid (TCA) cycle in nodules due to the missing interaction with GmNOD100. Our findings reveal an important role and an unprecedented molecular mechanism of sHSPs in nodule development and nitrogen fixation in soybean.
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Affiliation(s)
- Zhanwu Yang
- North China Key Laboratory for Germplasm Resources of Education MinistryCollege of AgronomyHebei Agricultural UniversityBaodingChina
| | - Hui Du
- North China Key Laboratory for Germplasm Resources of Education MinistryCollege of AgronomyHebei Agricultural UniversityBaodingChina
| | - Xinzhu Xing
- North China Key Laboratory for Germplasm Resources of Education MinistryCollege of AgronomyHebei Agricultural UniversityBaodingChina
| | - Wenlong Li
- North China Key Laboratory for Germplasm Resources of Education MinistryCollege of AgronomyHebei Agricultural UniversityBaodingChina
| | - Youbin Kong
- North China Key Laboratory for Germplasm Resources of Education MinistryCollege of AgronomyHebei Agricultural UniversityBaodingChina
| | - Xihuan Li
- North China Key Laboratory for Germplasm Resources of Education MinistryCollege of AgronomyHebei Agricultural UniversityBaodingChina
| | - Caiying Zhang
- North China Key Laboratory for Germplasm Resources of Education MinistryCollege of AgronomyHebei Agricultural UniversityBaodingChina
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13
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Rodriguez MC, Mehta D, Tan M, Uhrig RG. Quantitative Proteome and PTMome Analysis of Arabidopsis thaliana Root Responses to Persistent Osmotic and Salinity Stress. PLANT & CELL PHYSIOLOGY 2021; 62:1012-1029. [PMID: 34059891 DOI: 10.1093/pcp/pcab076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/12/2021] [Accepted: 05/31/2021] [Indexed: 06/12/2023]
Abstract
Abiotic stresses such as drought result in large annual economic losses around the world. As sessile organisms, plants cannot escape the environmental stresses they encounter but instead must adapt to survive. Studies investigating plant responses to osmotic and/or salt stress have largely focused on short-term systemic responses, leaving our understanding of intermediate to longer-term adaptation (24 h to d) lacking. In addition to protein abundance and phosphorylation changes, evidence suggests reversible lysine acetylation may also be important for abiotic stress responses. Therefore, to characterize the protein-level effects of osmotic and salt stress, we undertook a label-free proteomic analysis of Arabidopsis thaliana roots exposed to 300 mM mannitol and 150 mM NaCl for 24 h. We assessed protein phosphorylation, lysine acetylation and changes in protein abundance, detecting significant changes in 245, 35 and 107 total proteins, respectively. Comparison with available transcriptome data indicates that transcriptome- and proteome-level changes occur in parallel, while post-translational modifications (PTMs) do not. Further, we find significant changes in PTMs, and protein abundance involve different proteins from the same networks, indicating a multifaceted regulatory approach to prolonged osmotic and salt stress. In particular, we find extensive protein-level changes involving sulfur metabolism under both osmotic and salt conditions as well as changes in protein kinases and transcription factors that may represent new targets for drought stress signaling. Collectively, we find that protein-level changes continue to occur in plant roots 24 h from the onset of osmotic and salt stress and that these changes differ across multiple proteome levels.
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Affiliation(s)
- Maria C Rodriguez
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
- These authors contributed equally to the work
| | - Devang Mehta
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
- These authors contributed equally to the work
| | - Maryalle Tan
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
| | - Richard G Uhrig
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
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14
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Xiong F, Groot EP, Zhang Y, Li S. Functions of plant importin β proteins beyond nucleocytoplasmic transport. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6140-6149. [PMID: 34089597 DOI: 10.1093/jxb/erab263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/04/2021] [Indexed: 06/12/2023]
Abstract
In eukaryotic cells, nuclear activities are isolated from other cellular functions by the nuclear envelope. Because the nuclear envelope provides a diffusion barrier for macromolecules, a complex nuclear transport machinery has evolved that is highly conserved from yeast to plants and mammals. Among those components, the importin β family is the most important one. In this review, we summarize recent findings on the biological function of importin β family members, including development, reproduction, abiotic stress responses, and plant immunity. In addition to the traditional nuclear transport function, we highlight the new molecular functions of importin β, including protein turnover, miRNA regulation, and signaling. Taken together, our review will provide a systematic view of this versatile protein family in plants.
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Affiliation(s)
- Feng Xiong
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Edwin P Groot
- Sino-German Joint Research Center for Agricultural Biology, State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Yan Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Sha Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
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15
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Wang Z, Wang M, Yang C, Zhao L, Qin G, Peng L, Zheng Q, Nie W, Song CP, Shi H, Zhu JK, Zhao C. SWO1 modulates cell wall integrity under salt stress by interacting with importin ɑ in Arabidopsis. STRESS BIOLOGY 2021; 1:9. [PMID: 37676567 PMCID: PMC10442049 DOI: 10.1007/s44154-021-00010-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/24/2021] [Indexed: 09/08/2023]
Abstract
Maintenance of cell wall integrity is of great importance not only for plant growth and development, but also for the adaptation of plants to adverse environments. However, how the cell wall integrity is modulated under salt stress is still poorly understood. Here, we report that a nuclear-localized Agenet domain-containing protein SWO1 (SWOLLEN 1) is required for the maintenance of cell wall integrity in Arabidopsis under salt stress. Mutation in SWO1 gene results in swollen root tips, disordered root cell morphology, and root elongation inhibition under salt stress. The swo1 mutant accumulates less cellulose and pectin but more lignin under high salinity. RNA-seq and ChIP-seq assays reveal that SWO1 binds to the promoter of several cell wall-related genes and regulates their expression under saline conditions. Further study indicates that SWO1 interacts with importin ɑ IMPA1 and IMPA2, which are required for the import of nuclear-localized proteins. The impa1 impa2 double mutant also exhibits root growth inhibition under salt stress and mutations of these two genes aggravate the salt-hypersensitive phenotype of the swo1 mutant. Taken together, our data suggest that SWO1 functions together with importin ɑ to regulate the expression of cell wall-related genes, which enables plants to maintain cell wall integrity under high salinity.
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Affiliation(s)
- Zhidan Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mugui Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Changhong Yang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lun Zhao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guochen Qin
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Li Peng
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Qijie Zheng
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wenfeng Nie
- Department of Horticulture, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Chun-Peng Song
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Chunzhao Zhao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China.
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16
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Jha DK, Chanwala J, Sandeep IS, Dey N. Comprehensive identification and expression analysis of GRAS gene family under abiotic stress and phytohormone treatments in Pearl millet. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:1039-1052. [PMID: 34266539 DOI: 10.1071/fp21051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
Pearl millet is an important C4 cereal plant that possesses enormous capacity to survive under extreme climatic conditions. It serves as a major food source for people in arid and semiarid regions of south-east Asia and Africa. GRAS is an important transcription factor gene family of plant that play a critical role in regulating developmental processes, stress responses and phytohormonal signalling. In the present study, we have identified a total number of 57 GRAS members in pearl millet. Phylogenetic analysis clustered all the PgGRAS genes into eight groups (GroupI-GroupVIII). Motif analysis has shown that all the PgGRAS proteins had conserved GRAS domains and gene structure analysis revealed a high structural diversity among PgGRAS genes. Expression patterns of PgGRAS genes in different tissues (leaf, stem and root) and under various abiotic stress (drought, heat and salinity) were determined. Further, expression analysis was also carried out in response to various hormones (SA, MeJA, GA and ABA). The results provide a clear understanding of GRAS transcription factor family in pearl millet, and lay a good foundation for the functional characterisation of GRAS genes in pearl millet.
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Affiliation(s)
- Deepak Kumar Jha
- Department of Gene Function and Regulation, Institute of Life Sciences, Chandrasekharpur,Bhubaneswar, Odisha, India
| | - Jeky Chanwala
- Department of Gene Function and Regulation, Institute of Life Sciences, Chandrasekharpur,Bhubaneswar, Odisha, India; and Regional Centre for Biotechnology, Faridabad, 121001 Haryana, India
| | - I Sriram Sandeep
- Department of Gene Function and Regulation, Institute of Life Sciences, Chandrasekharpur,Bhubaneswar, Odisha, India
| | - Nrisingha Dey
- Department of Gene Function and Regulation, Institute of Life Sciences, Chandrasekharpur,Bhubaneswar, Odisha, India; and Corresponding author. ,
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17
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Dikaya V, El Arbi N, Rojas-Murcia N, Nardeli SM, Goretti D, Schmid M. Insights into the role of alternative splicing in plant temperature response. JOURNAL OF EXPERIMENTAL BOTANY 2021:erab234. [PMID: 34105719 DOI: 10.1093/jxb/erab234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Indexed: 05/21/2023]
Abstract
Alternative splicing occurs in all eukaryotic organisms. Since the first description of multiexon genes and the splicing machinery, the field has expanded rapidly, especially in animals and yeast. However, our knowledge about splicing in plants is still quite fragmented. Though eukaryotes show some similarity in the composition and dynamics of the splicing machinery, observations of unique plant traits are only starting to emerge. For instance, plant alternative splicing is closely linked to their ability to perceive various environmental stimuli. Due to their sessile lifestyle, temperature is a central source of information allowing plants to adjust their development to match current growth conditions. Hence, seasonal temperature fluctuations and day-night cycles can strongly influence plant morphology across developmental stages. Here we discuss the available data about temperature-dependent alternative splicing in plants. Given its fragmented state it is not always possible to fit specific observations into a coherent picture, yet it is sufficient to estimate the complexity of this field and the need of further research. Better understanding of alternative splicing as a part of plant temperature response and adaptation may also prove to be a powerful tool for both, fundamental and applied sciences.
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Affiliation(s)
- Varvara Dikaya
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Nabila El Arbi
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Nelson Rojas-Murcia
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Sarah Muniz Nardeli
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Daniela Goretti
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Markus Schmid
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, People's Republic of China
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18
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Xu F, Jia M, Li X, Tang Y, Jiang K, Bao J, Gu Y. Exportin-4 coordinates nuclear shuttling of TOPLESS family transcription corepressors to regulate plant immunity. THE PLANT CELL 2021; 33:697-713. [PMID: 33955481 PMCID: PMC8136914 DOI: 10.1093/plcell/koaa047] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/07/2020] [Indexed: 05/03/2023]
Abstract
The regulated nucleocytoplasmic exchange of macromolecules is essential for the eukaryotic cell. However, nuclear transport pathways defined by different nuclear transport receptors (NTRs), including importins and exportins, and their significance in activating distinct stress responses are poorly understood in plants. Here, we exploited a CRISPR/Cas9-based genetic screen to search for modifiers of CONSTITUTIVE EXPRESSION OF PATHOGENESIS-RELATED GENE 5 (cpr5), an Arabidopsis thaliana nucleoporin mutant that activates autoimmune responses that partially mimic effector-triggered immunity (ETI). We identified an NTR gene, Exportin-4 (XPO4), as a genetic interactor of CPR5. The xpo4 cpr5 double mutant activates catastrophic immune responses, which leads to seedling lethality. By leveraging the newly developed proximity-labeling proteomics, we profiled XPO4 substrates and identified TOPLESS (TPL) and TPL-related (TPR) transcription corepressors as XPO4-specific cargo. TPL/TPRs target negative regulators of immunity and are redundantly required for ETI induction. We found that loss-of-XPO4 promotes the nuclear accumulation of TPL/TPRs in the presence of elevated salicylic acid (SA), which contributes to the SA-mediated defense amplification and potentiates immune induction in the cpr5 mutant. We showed that TPL and TPRs are required for the enhanced immune activation observed in xpo4 cpr5 but not for the cpr5 single-mutant phenotype, underscoring the functional interplay between XPO4 and TPL/TPRs and its importance in cpr5-dependent immune induction. We propose that XPO4 coordinates the nuclear accumulation of TPL/TPRs, which plays a role in regulating SA-mediated defense feedback to modulate immune strength downstream of CPR5 during ETI induction.
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Affiliation(s)
- Feifei Xu
- Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute of Nuclear Agricultural Sciences, Key Laboratory for Nuclear Agricultural Sciences of Zhejiang Province and Ministry of Agriculture and Rural Affairs, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Min Jia
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Xin Li
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Yu Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Keni Jiang
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Jinsong Bao
- Institute of Nuclear Agricultural Sciences, Key Laboratory for Nuclear Agricultural Sciences of Zhejiang Province and Ministry of Agriculture and Rural Affairs, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
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19
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Cambiagno DA, Giudicatti AJ, Arce AL, Gagliardi D, Li L, Yuan W, Lundberg DS, Weigel D, Manavella PA. HASTY modulates miRNA biogenesis by linking pri-miRNA transcription and processing. MOLECULAR PLANT 2021; 14:426-439. [PMID: 33385584 DOI: 10.1016/j.molp.2020.12.019] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/29/2020] [Accepted: 12/28/2020] [Indexed: 05/23/2023]
Abstract
Post-transcriptional gene silencing mediated by microRNAs (miRNAs) modulates numerous developmental and stress response pathways. For the last two decades, HASTY (HST), the ortholog of human EXPORTIN 5, was considered to be a candidate protein that exports plant miRNAs from the nucleus to the cytoplasm. Here, we report that HST functions in the miRNA pathway independent of its cargo-exporting activity in Arabidopsis. We found that Arabidopsis mutants with impaired HST shuttling exhibit normal subcellular distribution of miRNAs. Interestingly, protein-protein interaction and microscopy assays showed that HST directly interacts with the microprocessor core component DCL1 through its N-terminal domain. Moreover, mass spectrometry analysis revealed that HST also interacts independently of its N-terminal domain with the mediator complex subunit MED37. Further experiments revealed that HST could act as a scaffold to facilitate the recruitment of DCL1 to genomic MIRNA loci by stabilizing the DCL1-MED37 complex, which in turn promotes the transcription and proper processing of primary miRNA transcripts (pri-miRNAs). Taken together, these results suggest that HST is likely associated with the formation of the miRNA biogenesis complex at MIRNA genes, promoting the transcription and processing of pri-miRNAs rather than the direct export of processed miRNAs from the nucleus.
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Affiliation(s)
- Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Delfina Gagliardi
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Lei Li
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Wei Yuan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Derek S Lundberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
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20
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Manchikatla PK, Kalavikatte D, Mallikarjuna BP, Palakurthi R, Khan AW, Jha UC, Bajaj P, Singam P, Chitikineni A, Varshney RK, Thudi M. MutMap Approach Enables Rapid Identification of Candidate Genes and Development of Markers Associated With Early Flowering and Enhanced Seed Size in Chickpea ( Cicer arietinum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:688694. [PMID: 34326857 PMCID: PMC8313520 DOI: 10.3389/fpls.2021.688694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/02/2021] [Indexed: 05/16/2023]
Abstract
Globally terminal drought is one of the major constraints to chickpea (Cicer arietinum L.) production. Early flowering genotypes escape terminal drought, and the increase in seed size compensates for yield losses arising from terminal drought. A MutMap population for early flowering and large seed size was developed by crossing the mutant line ICC4958-M3-2828 with wild-type ICC 4958. Based on the phenotyping of MutMap population, extreme bulks for days to flowering and 100-seed weight were sequenced using Hi-Seq2500 at 10X coverage. On aligning 47.41 million filtered reads to the CDC Frontier reference genome, 31.41 million reads were mapped and 332,395 single nucleotide polymorphisms (SNPs) were called. A reference genome assembly for ICC 4958 was developed replacing these SNPs in particular positions of the CDC Frontier genome. SNPs specific for each mutant bulk ranged from 3,993 to 5,771. We report a single unique genomic region on Ca6 (between 9.76 and 12.96 Mb) harboring 31, 22, 17, and 32 SNPs with a peak of SNP index = 1 for low bulk for flowering time, high bulk for flowering time, high bulk for 100-seed weight, and low bulk for 100-seed weight, respectively. Among these, 22 SNPs are present in 20 candidate genes and had a moderate allelic impact on the genes. Two markers, Ca6EF10509893 for early flowering and Ca6HSDW10099486 for 100-seed weight, were developed and validated using the candidate SNPs. Thus, the associated genes, candidate SNPs, and markers developed in this study are useful for breeding chickpea varieties that mitigate yield losses under drought stress.
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Affiliation(s)
- Praveen Kumar Manchikatla
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Danamma Kalavikatte
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Bingi Pujari Mallikarjuna
- Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, Regional Research Centre, Dharwad, India
| | - Ramesh Palakurthi
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Aamir W. Khan
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Uday Chand Jha
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Prasad Bajaj
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prashant Singam
- Department of Genetics, Osmania University, Hyderabad, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
- *Correspondence: Rajeev K. Varshney, ;
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
- Mahendar Thudi,
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21
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Wolff H, Jakoby M, Stephan L, Koebke E, Hülskamp M. Heat Stress-Dependent Association of Membrane Trafficking Proteins With mRNPs Is Selective. FRONTIERS IN PLANT SCIENCE 2021; 12:670499. [PMID: 34249042 PMCID: PMC8264791 DOI: 10.3389/fpls.2021.670499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/27/2021] [Indexed: 05/03/2023]
Abstract
The Arabidopsis AAA ATPase SKD1 is essential for ESCRT-dependent endosomal sorting by mediating the disassembly of the ESCRTIII complex in an ATP-dependent manner. In this study, we show that SKD1 localizes to messenger ribonucleoprotein complexes upon heat stress. Consistent with this, the interactome of SKD1 revealed differential interactions under normal and stress conditions and included membrane transport proteins as well as proteins associated with RNA metabolism. Localization studies with selected interactome proteins revealed that not only RNA associated proteins but also several ESCRTIII and membrane trafficking proteins were recruited to messenger ribonucleoprotein granules after heat stress.
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Affiliation(s)
- Heike Wolff
- Cluster of Excellence on Plant Sciences (CEPLAS), Botanical Institute, Cologne University, Cologne, Germany
| | - Marc Jakoby
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Lisa Stephan
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Eva Koebke
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Martin Hülskamp
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
- *Correspondence: Martin Hülskamp
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22
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Lüdke D, Rohmann PFW, Wiermer M. Nucleocytoplasmic Communication in Healthy and Diseased Plant Tissues. FRONTIERS IN PLANT SCIENCE 2021; 12:719453. [PMID: 34394173 PMCID: PMC8357054 DOI: 10.3389/fpls.2021.719453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/09/2021] [Indexed: 05/16/2023]
Abstract
The double membrane of the nuclear envelope (NE) constitutes a selective compartment barrier that separates nuclear from cytoplasmic processes. Plant viability and responses to a changing environment depend on the spatial communication between both compartments. This communication is based on the bidirectional exchange of proteins and RNAs and is regulated by a sophisticated transport machinery. Macromolecular traffic across the NE depends on nuclear transport receptors (NTRs) that mediate nuclear import (i.e. importins) or export (i.e. exportins), as well as on nuclear pore complexes (NPCs) that are composed of nucleoporin proteins (NUPs) and span the NE. In this review, we provide an overview of plant NPC- and NTR-directed cargo transport and we consider transport independent functions of NPCs and NE-associated proteins in regulating plant developmental processes and responses to environmental stresses.
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Affiliation(s)
- Daniel Lüdke
- Molecular Biology of Plant-Microbe Interactions Research Group, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, Göttingen, Germany
| | - Philipp F. W. Rohmann
- Molecular Biology of Plant-Microbe Interactions Research Group, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, Göttingen, Germany
| | - Marcel Wiermer
- Molecular Biology of Plant-Microbe Interactions Research Group, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, Göttingen, Germany
- Molecular Biology of Plant-Microbe Interactions Research Group, Göttingen Center for Molecular Biosciences, University of Göttingen, Göttingen, Germany
- *Correspondence: Marcel Wiermer,
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23
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Li X, Gu Y. Structural and functional insight into the nuclear pore complex and nuclear transport receptors in plant stress signaling. CURRENT OPINION IN PLANT BIOLOGY 2020; 58:60-68. [PMID: 33217650 DOI: 10.1016/j.pbi.2020.10.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/13/2020] [Indexed: 06/11/2023]
Abstract
Nuclear pore complexes (NPC) are highly conserved mega protein complexes that penetrate the double-layered nuclear membrane and form channels to allow bi-directional transport of macromolecules between the nucleus and the cytosol. Non-passive nucleocytoplasmic transport also requires nuclear transport receptors (NTR), which bind cargo molecules and shuttle them across the NPC. The NPC and NTRs constitute two fundamental layers of regulatory mechanisms that together determine the selective nuclear translocation of signal molecules and play essential roles in activating the precise response of a cell to environmental stimuli. Here we discuss recent findings in the NPC made by advanced structural biology approaches, and dissect distinct functions of different NPC components and NTRs in plants' responses to various biotic and abiotic stresses.
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Affiliation(s)
- Xin Li
- Department of Plant and Microbial Biology, University of California, Berkeley, USA; Innovative Genomics Institute, University of California, Berkeley, USA
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, USA; Innovative Genomics Institute, University of California, Berkeley, USA.
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24
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Oh TR, Yu SG, Yang HW, Kim JH, Kim WT. AtKPNB1, an Arabidopsis importin-β protein, is downstream of the RING E3 ubiquitin ligase AtAIRP1 in the ABA-mediated drought stress response. PLANTA 2020; 252:93. [PMID: 33106936 DOI: 10.1007/s00425-020-03500-4] [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: 07/29/2020] [Accepted: 10/15/2020] [Indexed: 05/20/2023]
Abstract
AtKPNB1, an Arabidopsis importin-β protein, was regulated by AtAIRP1 E3 ubiquitin ligase, which intensified the ABA-mediated drought stress response. As an early step in the abscisic acid (ABA)-mediated drought response, the ABA signal is transduced into the nucleus, and thus the nuclear transport system is crucially involved in the drought stress response. AtKPNB1, an importin-β protein, which is a core component of nuclear transport, was previously reported to be a negative factor in the ABA-mediated drought stress response (Luo et al. Luo et al., Plant J 75:377-389, 2013). Here, we report that AtAIPR1, an Arabidopsis RING-type E3 ubiquitin (Ub) ligase, interacted with and ubiquitinated AtKPNB1. A null mutation of AtKPNB1 suppressed the ABA-insensitive germination phenotype of atairp1 mutant seedlings as compared to that of the wild-type plants. Furthermore, the ABA-insensitive stomatal closure and drought-susceptible phenotypes of atairp1 were rescued in atairp1atkpnb1 double mutant progeny, indicating that AtKPNB1 functions downstream of AtAIRP1. These data suggest that AtAIRP1 regulates the ABA-mediated drought response in Arabidopsis via ubiquitination of AtKPNB1.
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Affiliation(s)
- Tae Rin Oh
- Department of Systems Biology, Division of Life Science, Yonsei University, Seoul, 03722, Korea
- Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Seong Gwan Yu
- Department of Systems Biology, Division of Life Science, Yonsei University, Seoul, 03722, Korea
- Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Hee Woong Yang
- Department of Systems Biology, Division of Life Science, Yonsei University, Seoul, 03722, Korea
- Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Jong Hum Kim
- Department of Systems Biology, Division of Life Science, Yonsei University, Seoul, 03722, Korea
- Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Korea
- Present address: Department of Energy, Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Woo Taek Kim
- Department of Systems Biology, Division of Life Science, Yonsei University, Seoul, 03722, Korea.
- Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Korea.
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25
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Zhang C, An N, Jia P, Zhang W, Liang J, Zhang X, Zhou H, Ma W, Han M, Xing L, Ren X. Genomic identification and expression analysis of nuclear pore proteins in Malus domestica. Sci Rep 2020; 10:17426. [PMID: 33060661 PMCID: PMC7566457 DOI: 10.1038/s41598-020-74171-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/15/2020] [Indexed: 11/09/2022] Open
Abstract
The nuclear pore complex (NPC), comprised of individual nucleoporin (Nup) proteins, controls nucleo-cytoplasmic transport of RNA and protein, and is important for regulating plant growth and development. However, there are no reports on this complex in fruit tree species. In this study, we identified 38 apple Nups and named them based on the known Arabidopsis thaliana homologs. We also completed bioinformatics analyses of the intron and exon structural data for apple Nups. The proteins encoded by the apple Nups lacked a universally conserved domain. Moreover, a phylogenetic analysis separated the apple and A. thaliana Nups into three groups. The phylogenetic tree indicated that MdNup54 and MdNup62 are most closely related to genes in other Rosaceae species. To characterize the 38 candidate Malus domestica Nups, we measured their stage-specific expression levels. Our tests revealed these proteins were differentially expressed among diverse tissues. We analyzed the expression levels of seven apple Nups in response to an indole-3-acetic acid (IAA) treatment. The phytohormone treatment significantly inhibited apple flowering. A qRT-PCR analysis proved that an IAA treatment significantly inhibited the expression of these seven genes. A preliminary study regarding two members of the Nup62 subcomplex, MdNup54 and MdNup62, confirmed these two proteins can interact with each other. A yeast two-hybrid assay verified that MdNup54 can interact with MdKNAT4 and MdKNAT6. On the basis of the study results, we identified apple NPC and predicted its structure and function. The data generated in this investigation provide important reference material for follow-up research.
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Affiliation(s)
- Chenguang Zhang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Na An
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Peng Jia
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Wei Zhang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Jiayan Liang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Xu Zhang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Hua Zhou
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Wenchun Ma
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, Yangling, China.
| | - Libo Xing
- College of Horticulture, Northwest A&F University, Yangling, China.
| | - Xiaolin Ren
- College of Horticulture, Northwest A&F University, Yangling, China.
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26
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Wang Z, Ren Z, Cheng C, Wang T, Ji H, Zhao Y, Deng Z, Zhi L, Lu J, Wu X, Xu S, Cao M, Zhao H, Liu L, Zhu J, Li X. Counteraction of ABA-Mediated Inhibition of Seed Germination and Seedling Establishment by ABA Signaling Terminator in Arabidopsis. MOLECULAR PLANT 2020; 13:1284-1297. [PMID: 32619606 DOI: 10.1016/j.molp.2020.06.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 06/02/2020] [Accepted: 06/26/2020] [Indexed: 05/07/2023]
Abstract
Seed germination and seedling establishment are important for the reproductive success of plants, but seeds and seedlings typically encounter constantly changing environmental conditions. By inhibiting seed germination and post-germinative growth through the PYR1/PYL/RCAR ABA receptors and PP2C co-receptors, the phytohormone abscisic acid (ABA) prevents premature germination and seedling growth under unfavorable conditions. However, little is known about how the ABA-mediated inhibition of seed germination and seedling establishment is thwarted. Here, we report that ABA Signaling Terminator (ABT), a WD40 protein, efficiently switches off ABA signaling and is critical for seed germination and seedling establishment. ABT is induced by ABA in a PYR1/PYL/RCAR-PP2C-dependent manner. Overexpression of ABT promotes seed germination and seedling greening in the presence of ABA, whereas knockout of ABT has the opposite effect. We found that ABT interacts with the PYR1/PYL/RCAR and PP2C proteins, interferes with the interaction between PYR1/PYL4 and ABI1/ABI2, and hampers the inhibition of ABI1/ABI2 by ABA-bound PYR1/PYL4, thereby terminating ABA signaling. Taken together, our results reveal a core mechanism of ABA signaling termination that is critical for seed germination and seedling establishment in Arabidopsis.
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Affiliation(s)
- Zhijuan Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Ziyin Ren
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Chunhong Cheng
- Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Tao Wang
- Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, P.R. China
| | - Hongtao Ji
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Yang Zhao
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai Institutes for Biological Sciences, Shanghai 200032, P.R. China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Zhiping Deng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 3210021, P.R. China
| | - Liya Zhi
- Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, P.R. China
| | - Jingjing Lu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Xinying Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Shimin Xu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Mengmeng Cao
- Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, P.R. China
| | - Hongtao Zhao
- Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, P.R. China
| | - Liu Liu
- Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Jiankang Zhu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai Institutes for Biological Sciences, Shanghai 200032, P.R. China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China.
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27
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Hu SF, Wei WL, Hong SF, Fang RY, Wu HY, Lin PC, Sanobar N, Wang HP, Sulistio M, Wu CT, Lo HF, Lin SS. Investigation of the effects of P1 on HC-pro-mediated gene silencing suppression through genetics and omics approaches. BOTANICAL STUDIES 2020; 61:22. [PMID: 32748085 PMCID: PMC7399735 DOI: 10.1186/s40529-020-00299-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/16/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Posttranscriptional gene silencing (PTGS) is one of the most important mechanisms for plants during viral infection. However, viruses have also developed viral suppressors to negatively control PTGS by inhibiting microRNA (miRNA) and short-interfering RNA (siRNA) regulation in plants. The first identified viral suppressor, P1/HC-Pro, is a fusion protein that was translated from potyviral RNA. Upon infecting plants, the P1 protein itself is released from HC-Pro by the self-cleaving activity of P1. P1 has an unknown function in enhancing HC-Pro-mediated PTGS suppression. We performed proteomics to identify P1-interacting proteins. We also performed transcriptomics that were generated from Col-0 and various P1/HC-Pro-related transgenic plants to identify novel genes. The results showed several novel genes were identified through the comparative network analysis that might be involved in P1/HC-Pro-mediated PTGS suppression. RESULTS First, we demonstrated that P1 enhances HC-Pro function and that the mechanism might work through P1 binding to VERNALIZATION INDEPENDENCE 3/SUPERKILLER 8 (VIP3/SKI8), a subunit of the exosome, to interfere with the 5'-fragment of the PTGS-cleaved RNA degradation product. Second, the AGO1 was specifically posttranslationally degraded in transgenic Arabidopsis expressing P1/HC-Pro of turnip mosaic virus (TuMV) (P1/HCTu plant). Third, the comparative network highlighted potentially critical genes in PTGS, including miRNA targets, calcium signaling, hormone (JA, ET, and ABA) signaling, and defense response. CONCLUSION Through these genetic and omics approaches, we revealed an overall perspective to identify many critical genes involved in PTGS. These new findings significantly impact in our understanding of P1/HC-Pro-mediated PTGS suppression.
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Affiliation(s)
- Sin-Fen Hu
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Wei-Lun Wei
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Syuan-Fei Hong
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Ru-Ying Fang
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Hsin-Yi Wu
- Instrumentation Center, National Taiwan University, Taipei, 106, Taiwan
| | - Pin-Chun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Neda Sanobar
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Hsin-Ping Wang
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 106, Taiwan
| | - Margo Sulistio
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 106, Taiwan
| | - Chun-Ta Wu
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 106, Taiwan
| | - Hsiao-Feng Lo
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 106, Taiwan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan.
- Center of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.
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28
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Nielsen E. The Small GTPase Superfamily in Plants: A Conserved Regulatory Module with Novel Functions. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:247-272. [PMID: 32442390 DOI: 10.1146/annurev-arplant-112619-025827] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Small GTP-binding proteins represent a highly conserved signaling module in eukaryotes that regulates diverse cellular processes such as signal transduction, cytoskeletal organization and cell polarity, cell proliferation and differentiation, intracellular membrane trafficking and transport vesicle formation, and nucleocytoplasmic transport. These proteins function as molecular switches that cycle between active and inactive states, and this cycle is linked to GTP binding and hydrolysis. In this review, the roles of the plant complement of small GTP-binding proteins in these cellular processes are described, as well as accessory proteins that control their activity, and current understanding of the functions of individual members of these families in plants-with a focus on the model organism Arabidopsis-is presented. Some potential novel roles of these GTPases in plants, relative to their established roles in yeast and/or animal systems, are also discussed.
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Affiliation(s)
- Erik Nielsen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
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29
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Genome-Wide Identification, Expression Profile and Evolution Analysis of Karyopherin β Gene Family in Solanum tuberosum Group Phureja DM1-3 Reveals Its Roles in Abiotic Stresses. Int J Mol Sci 2020; 21:ijms21030931. [PMID: 32023817 PMCID: PMC7037939 DOI: 10.3390/ijms21030931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/19/2020] [Accepted: 01/28/2020] [Indexed: 12/17/2022] Open
Abstract
In eukaryotic cells, nucleocytoplasmic trafficking of macromolecules is largely mediated by Karyopherin β/Importin (KPNβ or Impβ) nuclear transport factors, and they import and export cargo proteins or RNAs via the nuclear pores across the nuclear envelope, consequently effecting the cellular signal cascades in response to pathogen attack and environmental cues. Although achievements on understanding the roles of several KPNβs have been obtained from model plant Arabidopsis thaliana, comprehensive analysis of potato KPNβ gene family is yet to be elucidated. In our genome-wide identifications, a total of 13 StKPNβ (Solanum tuberosum KPNβ) genes were found in the genome of the doubled monoploid S. tuberosum Group Phureja DM1-3. Sequence alignment and conserved domain analysis suggested the presence of importin-β N-terminal domain (IBN_N, PF08310) or Exporin1-like domain (XpoI, PF08389) at N-terminus and HEAT motif at the C-terminal portion in most StKPNβs. Phylogenetic analysis indicated that members of StKPNβ could be classified into 16 subgroups in accordance with their homology to human KPNβs, which was also supported by exon-intron structure, consensus motifs, and domain compositions. RNA-Seq analysis and quantitative real-time PCR experiments revealed that, except StKPNβ3d and StKPNβ4, almost all StKPNβs were ubiquitously expressed in all tissues analyzed, whereas transcriptional levels of several StKPNβs were increased upon biotic/abiotic stress or phytohormone treatments, reflecting their potential roles in plant growth, development or stress responses. Furthermore, we demonstrated that silencing of StKPNβ3a, a SA- and H2O2-inducible KPNβ genes led to increased susceptibility to environmental challenges, implying its crucial roles in plant adaption to abiotic stresses. Overall, our results provide molecular insights into StKPNβ gene family, which will serve as a strong foundation for further functional characterization and will facilitate potato breeding programs.
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Wang Z, Liu L, Cheng C, Ren Z, Xu S, Li X. GAI Functions in the Plant Response to Dehydration Stress in Arabidopsis thaliana. Int J Mol Sci 2020; 21:ijms21030819. [PMID: 32012796 PMCID: PMC7037545 DOI: 10.3390/ijms21030819] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 12/15/2022] Open
Abstract
DELLA (GAI/RGA/RGL1/RGL2/RGL3) proteins are key negative regulators in GA (gibberellin) signaling and are involved in regulating plant growth as a response to environmental stresses. It has been shown that the DELLA protein PROCERA (PRO) in tomato promotes drought tolerance, but its molecular mechanism remains unknown. Here, we showed that the gai-1 (gibberellin insensitive 1) mutant (generated from the gai-1 (Ler) allele (with a 17 amino acid deletion within the DELLA domain of GAI) by backcrossing gai-1 (Ler) with Col-0 three times), the gain-of-function mutant of GAI (GA INSENSITIVE) in Arabidopsis, increases drought tolerance. The stomatal density of the gai-1 mutant was increased but its stomatal aperture was decreased under abscisic acid (ABA) treatment conditions, suggesting that the drought tolerance of the gai-1 mutant is a complex trait. We further tested the interactions between DELLA proteins and ABF2 (abscisic acid (ABA)-responsive element (ABRE)-binding transcription factors) and found that there was a strong interaction between DELLA proteins and ABF2. Our results provide new insight into DELLA proteins and their role in drought stress tolerance.
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Affiliation(s)
- Zhijuan Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.W.); (Z.R.)
| | - Liu Liu
- The State Key Laboratory of Plant Cell & Chromosome Engineering, Center for Agricultural Research Resources, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, China; (L.L.); (C.C.)
- Graduate University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Chunhong Cheng
- The State Key Laboratory of Plant Cell & Chromosome Engineering, Center for Agricultural Research Resources, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, China; (L.L.); (C.C.)
- Graduate University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Ziyin Ren
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.W.); (Z.R.)
| | - Shimin Xu
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.W.); (Z.R.)
| | - Xia Li
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.W.); (Z.R.)
- Correspondence: ; Tel.: +86-027-87856637
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Duarte GT, Volkova PY, Geras'kin SA. The response profile to chronic radiation exposure based on the transcriptome analysis of Scots pine from Chernobyl affected zone. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 250:618-626. [PMID: 31035144 DOI: 10.1016/j.envpol.2019.04.064] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/27/2019] [Accepted: 04/13/2019] [Indexed: 06/09/2023]
Abstract
Radioactive contamination of the natural areas is one of the most long-lasting anthropogenic impacts on the environment. Scots pine (Pinus sylvestris L.) is a promising organism for radiation-related research because of its high radiosensitivity, but the genome size of Pinacea species has imposed obstacles for high-throughput studies so far. In this work, we conducted the analysis of the de novo assembled transcriptome of Scots pine populations growing in the Chernobyl-affected zone, which is still today contaminated with radionuclides because of the accident at the nuclear power plant in 1986. The transcriptome profiles indicate a clear pattern of adaptive stress response, which seems to be dose-dependent. The transcriptional response indicates a continuous modulation of the cellular redox system, enhanced expression of chaperones and histones, along with the control of ions balance. Interestingly, the activity of transposable element families is inversely correlated to the exposure levels to radiation. These adaptive responses, which are triggered by radiation doses 30 times lower than the one accepted as a safe for biota species by international regulations, suggest that the environmental management in radiation protection should be reviewed.
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Affiliation(s)
- Gustavo T Duarte
- Russian Institute of Radiology and Agroecology, 249032, Obninsk, Russia; Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Polina Yu Volkova
- Russian Institute of Radiology and Agroecology, 249032, Obninsk, Russia
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Gu Y. The nuclear pore complex: a strategic platform for regulating cell signaling. THE NEW PHYTOLOGIST 2018; 219:25-30. [PMID: 28858378 DOI: 10.1111/nph.14756] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/13/2017] [Indexed: 05/22/2023]
Abstract
Contents Summary 25 I Introduction 25 II. Structural organization of the NPC 26 III. The role of NPCs in immune signaling 26 IV. The role of NPCs in hormone signaling 28 V. Conclusions 29 Acknowledgements 29 References 29 SUMMARY: Nuclear pore complexes (NPCs) are fundamental components of the eukaryotic cell. They perforate the nuclear envelope and serve as highly selective transport gates that enable bi-directional macromolecule exchange between the nucleus and cytoplasm. Recent studies illustrate that the NPC is not a static structural channel but a flexible environment and strategic player during nuclear signaling. The constitutional and conformational dynamics of the NPC allow it to tailor nucleocytoplasmic transport activities and define specific signaling output in response to various cellular and environmental cues. In this Insight, we review the roles of NPC constituents in immune activation and hormone signaling in plants, and discuss the possible role of the NPC as a legitimate platform for regulating cell signaling.
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Affiliation(s)
- Yangnan Gu
- Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, 100084, China
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
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Luo Y, Qiu Y, Na R, Meerja F, Lu QS, Yang C, Tian L. A Golden Gate and Gateway double-compatible vector system for high throughput functional analysis of genes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 271:117-126. [PMID: 29650149 DOI: 10.1016/j.plantsci.2018.03.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/20/2018] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
Abstract
A major research topic nowadays is to study and understand the functions of the increasing number of predicted genes that have been discovered through the complete genome sequencing of many plant species. With the aim of developing tools for rapid and convenient gene function analysis, we have developed a set of "pGate" vectors based on the principle of Golden gate and Gateway cloning approaches. These vectors combine the positive aspects of both Golden gate and Gateway cloning strategies. pGate vectors can not only be used as Golden gate recipient vectors to assemble multiple DNA fragments in a pre-defined order, but they can also work as an entry vector to transfer the assembled DNA fragment(s) to a large number of already-existing, functionally diverse, Gateway compatible destination vectors without adding additional nucleotides during cloning. We show the pGate vectors are effective and convenient in several major aspects of gene function analyses, including BiFC (Bimolecular fluorescence complementation) to analyze protein-protein interaction, amiRNA (artificial microRNA) candidate screening and as assembly of CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeats, CRISPR-associated protein-9 nuclease) system elements together for genome editing. The pGate system is a practical and flexible tool which can facilitate plant gene function research.
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Affiliation(s)
- Yanjie Luo
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V4T3, Canada
| | - Yang Qiu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V4T3, Canada; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ren Na
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Farida Meerja
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V4T3, Canada; Department of Biology, Western University, London, ON, N6A5B7, Canada
| | - Qing Shi Lu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V4T3, Canada
| | - Chunyan Yang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Lining Tian
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V4T3, Canada.
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Transcriptome profiling during mangrove viviparity in response to abscisic acid. Sci Rep 2018; 8:770. [PMID: 29335506 PMCID: PMC5768736 DOI: 10.1038/s41598-018-19236-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 12/27/2017] [Indexed: 01/21/2023] Open
Abstract
Mangrove plants adapt to coastal tidal mudflats with specially evolved viviparity seed development. However, very little is known about the genetic and molecular mechanisms of mangrove viviparity. Here, we tested a hypothesis that plant hormone abscisic acid (ABA) plays a significant role in precocious germination of viviparous Kandelia obovata seeds by exogenous applications. Through transcriptome analysis of ABA treated seeds, it was found that ABA repressed mangrove fruit growth and development, and there were thousands of genes differentially expressed. As a result, dynamics of the pathways were dramatically altered. In particular, "Plant hormone signal transduction" and "MAPK signaling pathway" were represented significantly. Among differentially expressed genes, some key genes of ABA signal transduction were induced, while ABA biosynthesis genes were repressed. Take ABI1 and ABI2, key negative regulators in ABA signal pathway, as examples, homologous alignment and a phylogenetic tree in various species showed that ABI1 and ABI2 are highly conserved among various species. The functional similarity of these genes was confirmed by transgenic work in Arabidopsis. Taken together, ABA inhibited mangrove viviparity, but mangroves developed a mechanism to prevent accidently increase of ABA in the harsh environment for maintaining viviparous reproductive strategy.
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A Class II small heat shock protein OsHsp18.0 plays positive roles in both biotic and abiotic defense responses in rice. Sci Rep 2017; 7:11333. [PMID: 28900229 PMCID: PMC5595972 DOI: 10.1038/s41598-017-11882-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 08/31/2017] [Indexed: 11/08/2022] Open
Abstract
Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastating diseases of rice. However, the molecular mechanism underpinning the Xoo resistance of rice is still not fully understood. Here, we report that a class II small heat shock protein gene, OsHsp18.0, whose expression was differentially induced between a resistant and a susceptible variety in response to Xoo infection, plays positive roles in both biotic and abiotic resistance. The molecular chaperone activity of OsHsp18.0 was confirmed by a bacterium-expressed glutathione S-transferase fusion protein. Overexpression of OsHsp18.0 in a susceptible rice variety significantly enhanced its resistance to multiple Xoo strains, whereas silencing of OsHsp18.0 in a resistant variety drastically increased its susceptibility. The enhanced Xoo resistance in OsHsp18.0-overexpressing lines was positively correlated with the sensitized salicylic acid-dependent defense responses. In addition to disease resistance, the OsHsp18.0 overexpressing and silencing lines exhibited enhanced and reduced tolerance, respectively, to heat and salt treatments. The subcellular localization study revealed that the green fluorescent protein-OsHsp18.0 was enriched on the nuclear envelope, suggesting a potential role of OsHsp18.0 in the nucleo-cytoplasmic trafficking. Together, our results reveal that the rice OsHsp18.0 is a positive regulator in both biotic and abiotic defense responses.
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Yang Y, Wang W, Chu Z, Zhu JK, Zhang H. Roles of Nuclear Pores and Nucleo-cytoplasmic Trafficking in Plant Stress Responses. FRONTIERS IN PLANT SCIENCE 2017; 8:574. [PMID: 28446921 PMCID: PMC5388774 DOI: 10.3389/fpls.2017.00574] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 03/30/2017] [Indexed: 05/29/2023]
Abstract
The nuclear pore complex (NPC) is a large protein complex that controls the exchange of components between the nucleus and the cytoplasm. In plants, the NPC family components play critical roles not only in essential growth and developmental processes, but also in plant responses to various environmental stress conditions. The involvement of NPC components in plant stress responses is mainly attributed to different mechanisms including control of mRNA/protein nucleo-cytoplasmic trafficking and transcriptional gene regulation. This mini review summarizes current knowledge of the NPC-mediated plant stress responses and provides an overview of the underlying molecular mechanisms.
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Affiliation(s)
- Yu Yang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Wei Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical GardenShanghai, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of SciencesShanghai, China
| | - Zhaoqing Chu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical GardenShanghai, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of SciencesShanghai, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
- Department of Horticulture and Landscape Architecture, Purdue University, West LafayetteIN, USA
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
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AlShareef S, Ling Y, Butt H, Mariappan KG, Benhamed M, Mahfouz MM. Herboxidiene triggers splicing repression and abiotic stress responses in plants. BMC Genomics 2017; 18:260. [PMID: 28347276 PMCID: PMC5369228 DOI: 10.1186/s12864-017-3656-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/22/2017] [Indexed: 12/28/2022] Open
Abstract
Background Constitutive and alternative splicing of pre-mRNAs from multiexonic genes controls the diversity of the proteome; these precisely regulated processes also fine-tune responses to cues related to growth, development, and stresses. Small-molecule inhibitors that perturb splicing provide invaluable tools for use as chemical probes to uncover the molecular underpinnings of splicing regulation and as potential anticancer compounds. Results Here, we show that herboxidiene (GEX1A) inhibits both constitutive and alternative splicing. Moreover, GEX1A activates genome-wide transcriptional patterns involved in abiotic stress responses in plants. GEX1A treatment -activated ABA-inducible promoters, and led to stomatal closure. Interestingly, GEX1A and pladienolide B (PB) elicited similar cellular changes, including alterations in the patterns of transcription and splicing, suggesting that these compounds might target the same spliceosome complex in plant cells. Conclusions Our study establishes GEX1A as a potent splicing inhibitor in plants that can be used to probe the assembly, dynamics, and molecular functions of the spliceosome and to study the interplay between splicing stress and abiotic stresses, as well as having potential biotechnological applications. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3656-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sahar AlShareef
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Yu Ling
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Kiruthiga G Mariappan
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Moussa Benhamed
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
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Ling Y, Alshareef S, Butt H, Lozano-Juste J, Li L, Galal AA, Moustafa A, Momin AA, Tashkandi M, Richardson DN, Fujii H, Arold S, Rodriguez PL, Duque P, Mahfouz MM. Pre-mRNA splicing repression triggers abiotic stress signaling in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:291-309. [PMID: 27664942 DOI: 10.1111/tpj.13383] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 09/15/2016] [Accepted: 09/21/2016] [Indexed: 05/24/2023]
Abstract
Alternative splicing (AS) of precursor RNAs enhances transcriptome plasticity and proteome diversity in response to diverse growth and stress cues. Recent work has shown that AS is pervasive across plant species, with more than 60% of intron-containing genes producing different isoforms. Mammalian cell-based assays have discovered various inhibitors of AS. Here, we show that the macrolide pladienolide B (PB) inhibits constitutive splicing and AS in plants. Also, our RNA sequencing (RNA-seq) data revealed that PB mimics abiotic stress signals including salt, drought and abscisic acid (ABA). PB activates the abiotic stress- and ABA-responsive reporters RD29A::LUC and MAPKKK18::uidA in Arabidopsis thaliana and mimics the effects of ABA on stomatal aperture. Genome-wide analysis of AS by RNA-seq revealed that PB perturbs the splicing machinery and leads to a striking increase in intron retention and a reduction in other forms of AS. Interestingly, PB treatment activates the ABA signaling pathway by inhibiting the splicing of clade A PP2C phosphatases while still maintaining to some extent the splicing of ABA-activated SnRK2 kinases. Taken together, our data establish PB as an inhibitor and modulator of splicing and a mimic of abiotic stress signals in plants. Thus, PB reveals the molecular underpinnings of the interplay between stress responses, ABA signaling and post-transcriptional regulation in plants.
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Affiliation(s)
- Yu Ling
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Sahar Alshareef
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Jorge Lozano-Juste
- Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, ES-46022, Valencia, Spain
| | - Lixin Li
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Aya A Galal
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo, 11835, Egypt
| | - Ahmed Moustafa
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo, 11835, Egypt
| | - Afaque A Momin
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Manal Tashkandi
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Dale N Richardson
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Hiroaki Fujii
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014, Turku, Finland
| | - Stefan Arold
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Pedro L Rodriguez
- Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, ES-46022, Valencia, Spain
| | - Paula Duque
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
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The Small G Protein AtRAN1 Regulates Vegetative Growth and Stress Tolerance in Arabidopsis thaliana. PLoS One 2016; 11:e0154787. [PMID: 27258048 PMCID: PMC4892486 DOI: 10.1371/journal.pone.0154787] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 04/19/2016] [Indexed: 12/02/2022] Open
Abstract
The evolutionarily conserved small G-protein Ran plays important role in nuclear translocation of proteins, cell cycle regulation, and nuclear envelope maintenance in mammalian cells and yeast. Arabidopsis Ran proteins are encoded by a family of four genes and are highly conserved at the protein level. However, their biological functions are poorly understood. We report here that AtRAN1 plays an important role in vegetative growth and the molecular improvement of stress tolerance in Arabidopsis. AtRAN1 overexpression promoted vegetative growth and enhanced abiotic tolerance, while the atran1 atran3 double mutant showed higher freezing sensitivity than WT. The AtRAN1 gene is ubiquitously expressed in plants, and the expression levels are higher in the buds, flowers and siliques. Subcellular localization results showed that AtRAN1 is mainly localized in the nucleus, with some present in the cytoplasm. AtRAN1 could maintain cell division and cell cycle progression and promote the formation of an intact nuclear envelope, especially under freezing conditions.
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Bhardwaj J, Gangwar I, Panzade G, Shankar R, Yadav SK. Global De Novo Protein-Protein Interactome Elucidates Interactions of Drought-Responsive Proteins in Horse Gram (Macrotyloma uniflorum). J Proteome Res 2016; 15:1794-809. [PMID: 27161830 DOI: 10.1021/acs.jproteome.5b01114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Inspired by the availability of de novo transcriptome of horse gram (Macrotyloma uniflorum) and recent developments in systems biology studies, the first ever global protein-protein interactome (PPI) map was constructed for this highly drought-tolerant legume. Large-scale studies of PPIs and the constructed database would provide rationale behind the interplay at cascading translational levels for drought stress-adaptive mechanisms in horse gram. Using a bidirectional approach (interolog and domain-based), a high-confidence interactome map and database for horse gram was constructed. Available transcriptomic information for shoot and root tissues of a sensitive (M-191; genotype 1) and a drought-tolerant (M-249; genotype 2) genotype of horse gram was utilized to draw comparative PPI subnetworks under drought stress. High-confidence 6804 interactions were predicted among 1812 proteins covering about one-fourth of the horse gram proteome. The highest number of interactions (33.86%) in horse gram interactome matched with Arabidopsis PPI data. The top five hub nodes mostly included ubiquitin and heat-shock-related proteins. Higher numbers of PPIs were found to be responsive in shoot tissue (416) and root tissue (2228) of genotype 2 compared with shoot tissue (136) and root tissue (579) of genotype 1. Characterization of PPIs using gene ontology analysis revealed that kinase and transferase activities involved in signal transduction, cellular processes, nucleocytoplasmic transport, protein ubiquitination, and localization of molecules were most responsive to drought stress. Hence, these could be framed in stress adaptive mechanisms of horse gram. Being the first legume global PPI map, it would provide new insights into gene and protein regulatory networks for drought stress tolerance mechanisms in horse gram. Information compiled in the form of database (MauPIR) will provide the much needed high-confidence systems biology information for horse gram genes, proteins, and involved processes. This information would ease the effort and increase the efficacy for similar studies on other legumes. Public access is available at http://14.139.59.221/MauPIR/ .
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Affiliation(s)
| | | | | | | | - Sudesh Kumar Yadav
- Center of Innovative and Applied Bioprocessing (CIAB) , Mohali 160071, Punjab, India
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Li W, Wang T, Zhang Y, Li Y. Overexpression of soybean miR172c confers tolerance to water deficit and salt stress, but increases ABA sensitivity in transgenic Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:175-94. [PMID: 26466661 DOI: 10.1093/jxb/erv450] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
MiRNAs play crucial roles in many aspects of plant development and the response to the environment. The miR172 family has been shown to participate in the control of flowering time and the response to abiotic stress. This family regulates the expression of APETALA2 (AP2)-like transcription factors in Arabidopsis. In the present study, soybean (Glycine max L. Merr.) miR172c, a member of the miR172 family, and its target gene were investigated for abiotic stress responses in transgenic Arabidopsis. gma-miR172c was induced by abscisic acid (ABA) treatments and abiotic stresses, including salt and water deficit. 5'-RACE (5'-rapid amplification of cDNA ends) assays indicated that miR172c directed Glyma01g39520 mRNA cleavage in soybeans. Overexpression of gma-miR172c in Arabidopsis resulted in reduced leaf water loss and increased survival rate under stress conditions. Meanwhile, the root length, germination rate, and cotyledon greening of transgenic plants were improved during both high salt and water deficit conditions. In addition, transgenic plants exhibited hypersensitivity to ABA during both the seed germination and post-germination seedling growth stages. Stress-related physiological indicators and the expression of stress/ABA-responsive genes were affected by abiotic treatments. The overexpression of gma-miR172c in Arabidopsis promoted earlier flowering compared with the wild type through modulation of the expression of flowering genes, such as FT and LFY during long days, especially under drought conditions. Glyma01g39520 weakened ABA sensitivity and reduced the tolerance to drought stress in the snz mutant of Arabidopsis by reducing the expression of ABI3 and ABI5. Overall, the present results demonstrate that gma-miR172c confers water deficit and salt tolerance but increased ABA sensitivity by regulating Glyma01g39520, which also accelerates flowering under abiotic stresses.
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Affiliation(s)
- Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Education Ministry (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, 150030, China
| | - Tao Wang
- Key Laboratory of Soybean Biology in Chinese Education Ministry (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, 150030, China
| | - Yuhang Zhang
- Key Laboratory of Soybean Biology in Chinese Education Ministry (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, 150030, China
| | - Yongguang Li
- Key Laboratory of Soybean Biology in Chinese Education Ministry (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, 150030, China
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Herud O, Weijers D, Lau S, Jürgens G. Auxin responsiveness of the MONOPTEROS-BODENLOS module in primary root initiation critically depends on the nuclear import kinetics of the Aux/IAA inhibitor BODENLOS. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:269-77. [PMID: 26714008 DOI: 10.1111/tpj.13108] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/07/2015] [Accepted: 12/14/2015] [Indexed: 05/28/2023]
Abstract
Primary root formation in early embryogenesis of Arabidopsis thaliana is initiated with the specification of a single cell called hypophysis. This initial step requires the auxin-dependent release of the transcription factor MONOPTEROS (MP, also known as ARF5) from its inhibition by the Aux/IAA protein BODENLOS (BDL, also known as IAA12). Auxin-insensitive bdl mutant embryos and mp loss-of-function embryos fail to specify the hypophysis, giving rise to rootless seedlings. A suppressor screen of rootless bdl mutant seedlings yielded a mutation in the nuclear import receptor IMPORTIN-ALPHA 6 (IMPα6) that promoted primary root formation through rescue of the embryonic hypophysis defects, without causing additional phenotypic changes. Aux/IAA proteins are continually synthesized and degraded, which is essential for rapid transcriptional responses to changing auxin concentrations. Nuclear translocation of bdl:3×GFP was slowed down in impα6 mutants as measured by fluorescence recovery after photobleaching (FRAP) analysis, which correlated with the reduced inhibition of MP by bdl in transient expression assays in impα6 knock-down protoplasts. The MP-BDL module acts like an auxin-triggered genetic switch because MP activates its own expression as well as the expression of its inhibitor BDL. Using an established simulation model, we determined that the reduced nuclear translocation rate of BDL in impα6 mutant embryos rendered the auxin-triggered switch unstable, impairing the fast response to changes in auxin concentration. Our results suggest that the instability of the inhibitor BDL necessitates a fast nuclear uptake in order to reach the critical threshold level required for auxin responsiveness of the MP-BDL module in primary root initiation.
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Affiliation(s)
- Ole Herud
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Dolf Weijers
- Department of Developmental Genetics, Center for Plant Molecular Biology, University of Tübingen, Tübingen, 72076, Germany
| | - Steffen Lau
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Gerd Jürgens
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
- Department of Developmental Genetics, Center for Plant Molecular Biology, University of Tübingen, Tübingen, 72076, Germany
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43
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Hedayati V, Mousavi A, Razavi K, Cultrera N, Alagna F, Mariotti R, Hosseini-Mazinani M, Baldoni L. Polymorphisms in the AOX2 gene are associated with the rooting ability of olive cuttings. PLANT CELL REPORTS 2015; 34:1151-64. [PMID: 25749737 DOI: 10.1007/s00299-015-1774-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 02/11/2015] [Accepted: 02/17/2015] [Indexed: 05/05/2023]
Abstract
Different rooting ability candidate genes were tested on an olive cross progeny. Our results demonstrated that only the AOX2 gene was strongly induced. OeAOX2 was fully characterised and correlated to phenotypical traits. The formation of adventitious roots is a key step in the vegetative propagation of trees crop species, and this ability is under strict genetic control. While numerous studies have been carried out to identify genes controlling adventitious root formation, only a few loci have been characterised. In this work, candidate genes that were putatively involved in rooting ability were identified in olive (Olea europaea L.) by similarity with orthologs identified in other plant species. The mRNA levels of these genes were analysed by real-time PCR during root induction in high- (HR) and low-rooting (LR) individuals. Interestingly, alternative oxidase 2 (AOX2), which was previously reported to be a functional marker for rooting in olive cuttings, showed a strong induction in HR individuals. From the OeAOX2 full-length gene, alleles and effective polymorphisms were distinguished and analysed in the cross progeny, which were segregated based on rooting. The results revealed a possible correlation between two single nucleotide polymorphisms of OeAOX2 gene and rooting ability.
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Affiliation(s)
- Vahideh Hedayati
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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44
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Liu P, Zhang H, Yu B, Xiong L, Xia Y. Proteomic identification of early salicylate- and flg22-responsive redox-sensitive proteins in Arabidopsis. Sci Rep 2015; 5:8625. [PMID: 25720653 PMCID: PMC4342551 DOI: 10.1038/srep08625] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 01/27/2015] [Indexed: 12/04/2022] Open
Abstract
Accumulation of reactive oxygen species (ROS) is one of the early defense responses against pathogen infection in plants. The mechanism about the initial and direct regulation of the defense signaling pathway by ROS remains elusive. Perturbation of cellular redox homeostasis by ROS is believed to alter functions of redox-sensitive proteins through their oxidative modifications. Here we report an OxiTRAQ-based proteomic study in identifying proteins whose cysteines underwent oxidative modifications in Arabidopsis cells during the early response to salicylate or flg22, two defense pathway elicitors that are known to disturb cellular redox homeostasis. Among the salicylate- and/or flg22-responsive redox-sensitive proteins are those involved in transcriptional regulation, chromatin remodeling, RNA processing, post-translational modifications, and nucleocytoplasmic shuttling. The identification of the salicylate-/flg22-responsive redox-sensitive proteins provides a foundation from which further study can be conducted toward understanding biological significance of their oxidative modifications during the plant defense response.
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Affiliation(s)
- Pei Liu
- 1] Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong [2] Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Huoming Zhang
- Biosciences Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Boying Yu
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Liming Xiong
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Yiji Xia
- 1] Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong [2] Partner State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, Hong Kong
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45
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El-Maarouf-Bouteau H, Sajjad Y, Bazin J, Langlade N, Cristescu SM, Balzergue S, Baudouin E, Bailly C. Reactive oxygen species, abscisic acid and ethylene interact to regulate sunflower seed germination. PLANT, CELL & ENVIRONMENT 2015; 38:364-74. [PMID: 24811898 DOI: 10.1111/pce.12371] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 04/24/2014] [Accepted: 04/27/2014] [Indexed: 05/06/2023]
Abstract
Sunflower (Helianthus annuus L.) seed dormancy is regulated by reactive oxygen species (ROS) and can be alleviated by incubating dormant embryos in the presence of methylviologen (MV), a ROS-generating compound. Ethylene alleviates sunflower seed dormancy whereas abscisic acid (ABA) represses germination. The purposes of this study were to identify the molecular basis of ROS effect on seed germination and to investigate their possible relationship with hormone signalling pathways. Ethylene treatment provoked ROS generation in embryonic axis whereas ABA had no effect on their production. The beneficial effect of ethylene on germination was lowered in the presence of antioxidant compounds, and MV suppressed the inhibitory effect of ABA. MV treatment did not alter significantly ethylene nor ABA production during seed imbibition. Microarray analysis showed that MV treatment triggered differential expression of 120 probe sets (59 more abundant and 61 less abundant genes), and most of the identified transcripts were related to cell signalling components. Many transcripts less represented in MV-treated seeds were involved in ABA signalling, thus suggesting an interaction between ROS and ABA signalling pathways at the transcriptional level. Altogether, these results shed new light on the crosstalk between ROS and plant hormones in seed germination.
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46
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Kimura M, Imamoto N. Biological significance of the importin-β family-dependent nucleocytoplasmic transport pathways. Traffic 2014; 15:727-48. [PMID: 24766099 DOI: 10.1111/tra.12174] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/22/2014] [Accepted: 04/22/2014] [Indexed: 12/19/2022]
Abstract
Importin-β family proteins (Imp-βs) are nucleocytoplasmic transport receptors (NTRs) that import and export proteins and RNAs through the nuclear pores. The family consists of 14-20 members depending on the biological species, and each member transports a specific group of cargoes. Thus, the Imp-βs mediate multiple, parallel transport pathways that can be regulated separately. In fact, the spatiotemporally differential expressions and the functional regulations of Imp-βs have been reported. Additionally, the biological significance of each pathway has been characterized by linking the function of a member of Imp-βs to a cellular consequence. Connecting these concepts, the regulation of the transport pathways conceivably induces alterations in the cellular physiological states. However, few studies have linked the regulation of an importin-β family NTR to an induced cellular response and the corresponding cargoes, despite the significance of this linkage in comprehending the biological relevance of the transport pathways. This review of recent reports on the regulation and biological functions of the Imp-βs highlights the significance of the transport pathways in physiological contexts and points out the possibility that the identification of yet unknown specific cargoes will reinforce the importance of transport regulation.
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Affiliation(s)
- Makoto Kimura
- Cellular Dynamics Laboratory, RIKEN, Hirosawa 2-1, Wako, Saitama, 351-0198, Japan
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47
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Paul P, Simm S, Mirus O, Scharf KD, Fragkostefanakis S, Schleiff E. The complexity of vesicle transport factors in plants examined by orthology search. PLoS One 2014; 9:e97745. [PMID: 24844592 PMCID: PMC4028247 DOI: 10.1371/journal.pone.0097745] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 04/24/2014] [Indexed: 11/18/2022] Open
Abstract
Vesicle transport is a central process to ensure protein and lipid distribution in eukaryotic cells. The current knowledge on the molecular components and mechanisms of this process is majorly based on studies in Saccharomyces cerevisiae and Arabidopsis thaliana, which revealed 240 different proteinaceous factors either experimentally proven or predicted to be involved in vesicle transport. In here, we performed an orthologue search using two different algorithms to identify the components of the secretory pathway in yeast and 14 plant genomes by using the 'core-set' of 240 factors as bait. We identified 4021 orthologues and (co-)orthologues in the discussed plant species accounting for components of COP-II, COP-I, Clathrin Coated Vesicles, Retromers and ESCRTs, Rab GTPases, Tethering factors and SNAREs. In plants, we observed a significantly higher number of (co-)orthologues than yeast, while only 8 tethering factors from yeast seem to be absent in the analyzed plant genomes. To link the identified (co-)orthologues to vesicle transport, the domain architecture of the proteins from yeast, genetic model plant A. thaliana and agriculturally relevant crop Solanum lycopersicum has been inspected. For the orthologous groups containing (co-)orthologues from yeast, A. thaliana and S. lycopersicum, we observed the same domain architecture for 79% (416/527) of the (co-)orthologues, which documents a very high conservation of this process. Further, publically available tissue-specific expression profiles for a subset of (co-)orthologues found in A. thaliana and S. lycopersicum suggest that some (co-)orthologues are involved in tissue-specific functions. Inspection of localization of the (co-)orthologues based on available proteome data or localization predictions lead to the assignment of plastid- as well as mitochondrial localized (co-)orthologues of vesicle transport factors and the relevance of this is discussed.
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Affiliation(s)
- Puneet Paul
- Department of Biosciences Molecular Cell Biology of Plants
| | - Stefan Simm
- Department of Biosciences Molecular Cell Biology of Plants
| | - Oliver Mirus
- Department of Biosciences Molecular Cell Biology of Plants
| | | | | | - Enrico Schleiff
- Department of Biosciences Molecular Cell Biology of Plants
- Cluster of Excellence Frankfurt
- Center of Membrane Proteomics; Goethe University Frankfurt, Frankfurt/Main, Germany
- * E-mail:
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48
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Xie M, Wu D, Duan G, Wang L, He R, Li X, Tang D, Zhao X, Liu X. AtWNK9 is regulated by ABA and dehydration and is involved in drought tolerance in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 77:73-83. [PMID: 24561249 DOI: 10.1016/j.plaphy.2014.01.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 01/30/2014] [Indexed: 06/03/2023]
Abstract
WNK (with no lysine [K]) kinases play important regulatory roles in flowering, as well as salt and osmotic stress tolerance in plants. Here, we report that AtWNK9, a member of the Arabidopsis WNK gene family, was induced by exogenous abscisic acid (ABA) treatment and dehydration stress. Overexpression of AtWNK9 from the cauliflower mosaic virus 35S promoter in Arabidopsis resulted in increased sensitivity to ABA, strong inhibition of primary root elongation, increased proline accumulation, reduced stomatal aperture, and a reduced rate of water loss. In addition, plant survival under drought stress was improved compared to wild type. In contrast, a mutant with a T-DNA insertion in AtWNK9 showed reduced ABA sensitivity and an increased rate of water loss; further, it showed increased susceptibility to drought stress. The transcription of a number of ABA signaling components, including ABI1, ERA1, ABI3, and ABF3, was up-regulated in AtWNK9 transgenic plants and down-regulated in the wnk9 mutant in response to ABA. Some ABA-responsive and biosynthetic genes, as well as other drought-related genes, were altered at various levels in AtWNK9 transgenic plants and wnk9 mutants under dehydration stress. Overall, these findings suggest that AtWNK9 plays a positive role in ABA signaling and improves drought tolerance in transgenic Arabidopsis.
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Affiliation(s)
- Minmin Xie
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Dan Wu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Guifang Duan
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Liqun Wang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Reqing He
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Xiushan Li
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Dongying Tang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Xiaoying Zhao
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China.
| | - Xuanming Liu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China; State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China.
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49
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Tamura K, Hara-Nishimura I. Functional insights of nucleocytoplasmic transport in plants. FRONTIERS IN PLANT SCIENCE 2014; 5:118. [PMID: 24765097 PMCID: PMC3980095 DOI: 10.3389/fpls.2014.00118] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 03/12/2014] [Indexed: 05/19/2023]
Abstract
Plant nucleocytoplasmic transport beyond the nuclear envelope is important not only for basic cellular functions but also for growth, development, hormonal signaling, and responses to environmental stimuli. Key components of this transport system include nuclear transport receptors and nucleoporins. The functional and physical interactions between receptors and the nuclear pore in the nuclear membrane are indispensable for nucleocytoplasmic transport. Recently, several groups have reported various plant mutants that are deficient in factors involved in nucleocytoplasmic transport. Here, we summarize the current state of knowledge about nucleocytoplasmic transport in plants, and we review the plant-specific regulation and roles of this process in plants.
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Affiliation(s)
| | - Ikuko Hara-Nishimura
- *Correspondence: Ikuko Hara-Nishimura, Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan e-mail:
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50
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Luo Y, Wang Z, Tian L, Li X. The function of importin β1 is conserved in eukaryotes but the substrates may vary in organisms. PLANT SIGNALING & BEHAVIOR 2013; 8:25106. [PMID: 23733071 PMCID: PMC3999071 DOI: 10.4161/psb.25106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 05/21/2013] [Indexed: 06/02/2023]
Abstract
Importin β1 is the nuclear-cytoplasmic transport receptor in eukaryotic cells. Its main function is to transport NLS (nuclear localization signal)-containing proteins from cytoplasm to nucleus. Our recent study found that AtKPNB1, a homolog of the human KPNB1, is an essential component of the classical nuclear import of the NLS-containing proteins in Arabidopsis and modulates plant development and ABA-mediated stress response. Human KPNB1 can also directly transport the nuclear proteins, such as ribosomal protein RPS7e, without the intervention of importin α proteins. However, we found that AtKPNB1 does not directly recognize and import the human RPS7e homologous proteins AtRPS7A, AtRPS7B and AtRPS7C into the nucleus like human KPNB1. These findings suggest that the importin β1 protein has the conserved function in translocating nuclear proteins to the nucleus, but their specific cargos may vary in different organisms.
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Affiliation(s)
- Yanjie Luo
- The State Key Laboratory of Plant Cell & Chromosome Engineering; Center of Agricultural Research Resources; Institute of Genetics and Developmental Biology
- Gradulate University of Chinese Academy of Sciences; Beijing, PR China
| | - Zhijuan Wang
- The State Key Laboratory of Plant Cell & Chromosome Engineering; Center of Agricultural Research Resources; Institute of Genetics and Developmental Biology
| | - Lining Tian
- Southern Crop Protection and Food Research Centre; Agriculture and Agri-Food Canada; London, ON Canada
- Department of Biology; Western University; London, ON Canada
| | - Xia Li
- The State Key Laboratory of Plant Cell & Chromosome Engineering; Center of Agricultural Research Resources; Institute of Genetics and Developmental Biology
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