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Méndez-Gómez M, Sierra-Cacho D, Jiménez-Morales E, Guzmán P. Modulation of early gene expression responses to water deprivation stress by the E3 ubiquitin ligase ATL80: implications for retrograde signaling interplay. BMC PLANT BIOLOGY 2024; 24:180. [PMID: 38459432 PMCID: PMC10921668 DOI: 10.1186/s12870-024-04872-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/28/2024] [Indexed: 03/10/2024]
Abstract
BACKGROUND Primary response genes play a pivotal role in translating short-lived stress signals into sustained adaptive responses. In this study, we investigated the involvement of ATL80, an E3 ubiquitin ligase, in the dynamics of gene expression following water deprivation stress. We observed that ATL80 is rapidly activated within minutes of water deprivation stress perception, reaching peak expression around 60 min before gradually declining. ATL80, despite its post-translational regulation role, emerged as a key player in modulating early gene expression responses to water deprivation stress. RESULTS The impact of ATL80 on gene expression was assessed using a time-course microarray analysis (0, 15, 30, 60, and 120 min), revealing a burst of differentially expressed genes, many of which were associated with various stress responses. In addition, the diversity of early modulation of gene expression in response to water deprivation stress was significantly abolished in the atl80 mutant compared to wild-type plants. A subset of 73 genes that exhibited a similar expression pattern to ATL80 was identified. Among them, several are linked to stress responses, including ERF/AP2 and WRKY transcription factors, calcium signaling genes, MAP kinases, and signaling peptides. Promoter analysis predicts enrichment of binding sites for CAMTA1 and CAMTA5, which are known regulators of rapid stress responses. Furthermore, we have identified a group of differentially expressed ERF/AP2 transcription factors, proteins associated with folding and refolding, as well as pinpointed core module genes which are known to play roles in retrograde signaling pathways that cross-referenced with the early ATL80 transcriptome. CONCLUSIONS Based on these findings, we propose that ATL80 may target one or more components within the retrograde signaling pathways for degradation. In essence, ATL80 serves as a bridge connecting these signaling pathways and effectively functions as an alarm signal.
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Affiliation(s)
- Manuel Méndez-Gómez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, 36824, Gto, México
| | - Daniel Sierra-Cacho
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, 36824, Gto, México
| | - Estela Jiménez-Morales
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, 36824, Gto, México
| | - Plinio Guzmán
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, 36824, Gto, México.
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Li P, Zhang Y, Zhao C, Jiang M. Evolution of the Tóxicos en Levadura 63 (TL63) gene family in plants and functional characterization of Arabidopsis thaliana TL63 under oxidative stress. PLANTA 2023; 258:87. [PMID: 37750983 DOI: 10.1007/s00425-023-04243-8] [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: 07/09/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023]
Abstract
MAIN CONCLUSION TL63 orthologs were angiosperm specific and had undergone motifs loss and gain, and increased purifying selection. AtTL63 was involved in the response of yeast and Arabidopsis plants to oxidative stress. The Tóxicos en Levadura (TL) family, a class of E3 ubiquitin ligases with typical RING-H2 type zinc finger structure, plays a pivotal role in mediating physiological processes and responding to stress in plants. However, the evolution and function of TL63 remain unclear. In this study, TL63 homologs were dated roughly back to the origin of land plants and confirmed to have subjected to the gain and loss of motifs and increased purifying selection. Phylogenetic analysis displayed that 279 TL63s could be divided into four main clades (Clade A-D). Notably, the ancestral tandem TL40/41 cluster contributed to the expansion of modern Brassicaceae TL40/41. The substitution rate tests revealed that the TL63 lineage was evidently different from other lineages. The codon usage index exhibited that monocotyledons preferred to use not A3s and T3s, but C3s, G3s, CAI, CBI and Fop. Sequence analysis showed that the TL63 homologs had conserved TM and GLD motifs and RING-H2 domain whose key amino acid residues accounted for the high average abundance. Particularly, Arabidopsis thaliana TL63 (AtTL63) was located in the nuclei, cell membranes and peroxisomes and expressed universally and significantly throughout A. thaliana development. Under H2O2 treatment, low or moderate expression of the AtTL63 held beneficial effects on the growth and viability of yeast cells and the mutation or overexpression of the AtTL63 positively affected the growth of A. thaliana plants. In brief, this study could supply useful insight into the evolution of the plant TL63s and the AtTL63 functions under oxidative stress.
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Affiliation(s)
- Peng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yuxin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Changling Zhao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.
| | - Min Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
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Seiml-Buchinger V, Reifschneider E, Bittner A, Baier M. Ascorbate peroxidase postcold regulation of chloroplast NADPH dehydrogenase activity controls cold memory. PLANT PHYSIOLOGY 2022; 190:1997-2016. [PMID: 35946757 PMCID: PMC9614503 DOI: 10.1093/plphys/kiac355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Exposure of Arabidopsis (Arabidopsis thaliana) to 4°C imprints a cold memory that modulates gene expression in response to a second (triggering) stress stimulus applied several days later. Comparison of plastid transcriptomes of cold-primed and control plants directly before they were exposed to the triggering stimulus showed downregulation of several subunits of chloroplast NADPH dehydrogenase (NDH) and regulatory subunits of ATP synthase. NDH is, like proton gradient 5 (PGR5)-PGR5-like1 (PGRL1), a thylakoid-embedded, ferredoxin-dependent plastoquinone reductase that protects photosystem I and stabilizes ATP synthesis by cyclic electron transport (CET). Like PGRL1A and PGRL1B transcript levels, ndhA and ndhD transcript levels decreased during the 24-h long priming cold treatment. PGRL1 transcript levels were quickly reset in the postcold phase, but expression of ndhA remained low. The transcript abundances of other ndh genes decreased within the next days. Comparison of thylakoid-bound ascorbate peroxidase (tAPX)-free and transiently tAPX-overexpressing or tAPX-downregulating Arabidopsis lines demonstrated that ndh expression is suppressed by postcold induction of tAPX. Four days after cold priming, when tAPX protein accumulation was maximal, NDH activity was almost fully lost. Lack of the NdhH-folding chaperonin Crr27 (Cpn60β4), but not lack of the NDH activity modulating subunits NdhM, NdhO, or photosynthetic NDH subcomplex B2 (PnsB2), strengthened priming regulation of zinc finger of A. thaliana 10, which is a nuclear-localized target gene of the tAPX-dependent cold-priming pathway. We conclude that cold-priming modifies chloroplast-to-nucleus stress signaling by tAPX-mediated suppression of NDH-dependent CET and that plastid-encoded NdhH, which controls subcomplex A assembly, is of special importance for memory stabilization.
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Affiliation(s)
- Victoria Seiml-Buchinger
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Berlin 14195,Germany
| | - Elena Reifschneider
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Berlin 14195,Germany
| | - Andras Bittner
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Berlin 14195,Germany
| | - Margarete Baier
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Berlin 14195,Germany
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Association mapping of autumn-seeded rye (Secale cereale L.) reveals genetic linkages between genes controlling winter hardiness and plant development. Sci Rep 2022; 12:5793. [PMID: 35388069 PMCID: PMC8986816 DOI: 10.1038/s41598-022-09582-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 03/25/2022] [Indexed: 12/23/2022] Open
Abstract
Winter field survival (WFS) in autumn-seeded winter cereals is a complex trait associated with low temperature tolerance (LTT), prostrate growth habit (PGH), and final leaf number (FLN). WFS and the three sub-traits were analyzed by a genome-wide association study of 96 rye (Secale cereal L.) genotypes of different origins and winter-hardiness levels. A total of 10,244 single nucleotide polymorphism (SNP) markers were identified by genotyping by sequencing and 259 marker-trait-associations (MTAs; p < 0.01) were revealed by association mapping. The ten most significant SNPs (p < 1.49e−04) associated with WFS corresponded to nine strong candidate genes: Inducer of CBF Expression 1 (ICE1), Cold-regulated 413-Plasma Membrane Protein 1 (COR413-PM1), Ice Recrystallization Inhibition Protein 1 (IRIP1), Jasmonate-resistant 1 (JAR1), BIPP2C1-like protein phosphatase, Chloroplast Unusual Positioning Protein-1 (CHUP1), FRIGIDA-like 4 (FRL4-like) protein, Chalcone Synthase 2 (CHS2), and Phenylalanine Ammonia-lyase 8 (PAL8). Seven of the candidate genes were also significant for one or several of the sub-traits supporting the hypothesis that WFS, LTT, FLN, and PGH are genetically interlinked. The winter-hardy rye genotypes generally carried additional allele variants for the strong candidate genes, which suggested allele diversity was a major contributor to cold acclimation efficiency and consistent high WFS under varying field conditions.
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Bittner A, Hause B, Baier M. Cold-priming causes dampening of oxylipin biosynthesis and signalling during the early cold- and light-triggering response of Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7163-7179. [PMID: 34185054 PMCID: PMC8547158 DOI: 10.1093/jxb/erab314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/27/2021] [Indexed: 05/21/2023]
Abstract
Cold-priming uncouples cold and light regulation of otherwise tightly co-regulated genes. In this study, we focused on the early regulatory processes in Arabidopsis within the first 2 h in cold and in high light after a 5-d lag-phase at 20 °C and 24 h cold-priming at 4 °C. Priming quickly modified gene expression in a trigger-specific manner. In the early stress-response phase during cold and high-light triggering, it reduced the regulatory amplitudes of many up- and down-regulated genes. A third of the priming-regulated genes were jasmonate-sensitive, including the full set of genes required for oxylipin biosynthesis. Analysis of wild-type and mutant plants based on qPCR demonstrated that biosynthesis of the jasmonic acid (JA) precursor 12-oxo phytenoic acid (OPDA) relative to the availability of JA dampened the response of the genes for oxylipin biosynthesis. In oxylipin biosynthetic mutants, cold-priming more strongly affected genes involved in the biosynthesis of OPDA than in its conversion to JA. In addition, priming-dependent dampening of the triggering response was more linked to OPDA than to regulation of the JA concentration. Spray application of OPDA prior to triggering counteracted the priming effect. Regulation of the oxylipin hub was controlled by modulation of the oxylipin-sensitivity of the genes for OPDA biosynthesis, but it was insensitive to priming-induced accumulation of thylakoid ascorbate peroxidase, thus identifying a parallel-acting cold-priming pathway.
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Affiliation(s)
- Andras Bittner
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Königin-Luise-Straße 12–16, 14195 Berlin, Germany
| | - Bettina Hause
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Margarete Baier
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Königin-Luise-Straße 12–16, 14195 Berlin, Germany
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Zhang X, Fan X, Wang Y, Xu D, Zhang J, Ye N. Exploring Core Response Mechanisms to Multiple Environmental Stressors Via A Genome-Wide Study in the Brown Alga Saccharina japonica (Laminariales, Phaeophyceae). JOURNAL OF PHYCOLOGY 2021; 57:345-354. [PMID: 33211355 DOI: 10.1111/jpy.13108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/22/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
Saccharina japonica is an important large brown alga and a major component of productive beds on the northwest coast of the Pacific Ocean. Abiotic stress response mechanisms are receiving considerable attention because global climate change is increasing their abiotic stress levels. However, our knowledge of how S. japonica broadly responds to stress is limited. In this study, we investigated the S. japonica responsive genes underlying acclimation to diverse stressors of acidification, high light, high temperature, hypersalinity, and hyposalinity and identified 408 core genes constantly and differentially expressed in response to all stressors. Our results confirm that stressors had strong effects on genes participating in photosynthesis, amino acid metabolism, carbohydrate metabolism, halogen metabolism, and reactive oxygen species defense. These findings will improve our understanding of brown algal response mechanisms linked to environmental stress and provide a list of candidate genes for improving algal stress tolerance in light of environmental stress in future studies.
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Affiliation(s)
- Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China
| | - Yitao Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China
| | - Jian Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China
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7
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Schulze WX, Altenbuchinger M, He M, Kränzlein M, Zörb C. Proteome profiling of repeated drought stress reveals genotype-specific responses and memory effects in maize. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 159:67-79. [PMID: 33341081 DOI: 10.1016/j.plaphy.2020.12.009] [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: 10/09/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Drought has become a major stress for agricultural productivity in temperate regions, such as central Europe. Thus, information on how crop plants respond to drought is important to develop tolerant hybrids and to ensure yield stability. Posttranscriptional regulation through changed protein abundances is an important mechanism of short-term response to stress events that has not yet been widely exploited in breeding strategies. Here, we investigated the response to repeated drought exposure of a tolerant and a sensitive maize hybrid in order to understand general protein abundance changes induced by singular drought or repeated drought events. In general, drought affected protein abundance of multiple pathways in the plant. We identified starch metabolism, aquaporin abundance, PSII proteins and histones as strongly associated with typical drought-induced phenotypes such as increased membrane leakage, osmolality or effects on stomatal conductance and assimilation rate. In addition, we found a strong effect of drought on nutrient assimilation, especially the sulfur metabolism. In general, pre-experience of mild drought before exposure to a more severe drought resulted in visible adaptations resulting in dampened phenotypes as well as lower magnitude of protein abundance changes.
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Affiliation(s)
- Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany.
| | - Michael Altenbuchinger
- Research Group Computational Biology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Mingjie He
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Markus Kränzlein
- Institute of Crop Sciences, University of Hohenheim, 70593, Stuttgart, Germany
| | - Christian Zörb
- Institute of Crop Sciences, University of Hohenheim, 70593, Stuttgart, Germany
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Castañeda V, González EM, Wienkoop S. Phloem Sap Proteins Are Part of a Core Stress Responsive Proteome Involved in Drought Stress Adjustment. FRONTIERS IN PLANT SCIENCE 2021; 12:625224. [PMID: 33603764 PMCID: PMC7884324 DOI: 10.3389/fpls.2021.625224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/08/2021] [Indexed: 05/08/2023]
Abstract
During moderate drought stress, plants can adjust by changes in the protein profiles of the different organs. Plants transport and modulate extracellular stimuli local and systemically through commonly induced inter- and intracellular reactions. However, most proteins are frequently considered, cell and organelle specific. Hence, while signaling molecules and peptides can travel systemically throughout the whole plant, it is not clear, whether protein isoforms may exist ubiquitously across organs, and what function those may have during drought regulation. By applying shotgun proteomics, we extracted a core proteome of 92 identical protein isoforms, shared ubiquitously amongst several Medicago truncatula tissues, including roots, phloem sap, petioles, and leaves. We investigated their relative distribution across the different tissues and their response to moderate drought stress. In addition, we functionally compared this plant core stress responsive proteome with the organ-specific proteomes. Our study revealed plant ubiquitous protein isoforms, mainly related to redox homeostasis and signaling and involved in protein interaction networks across the whole plant. Furthermore, about 90% of these identified core protein isoforms were significantly involved in drought stress response, indicating a crucial role of the core stress responsive proteome (CSRP) in the plant organ cross-communication, important for a long-distance stress-responsive network. Besides, the data allowed for a comprehensive characterization of the phloem proteome, revealing new insights into its function. For instance, CSRP protein levels involved in stress and redox are relatively more abundant in the phloem compared to the other tissues already under control conditions. This suggests a major role of the phloem in stress protection and antioxidant activity enabling the plants metabolic maintenance and rapid response upon moderate stress. We anticipate our study to be a starting point for future investigations of the role of the core plant proteome. Under an evolutionary perspective, CSRP would enable communication of different cells with each other and the environment being crucial for coordinated stress response of multicellular organisms.
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Affiliation(s)
- Veronica Castañeda
- Department of Sciences, Institute for Multidisciplinary Research in Applied Biology, Universidad Pública de Navarra, Pamplona, Spain
| | - Esther M. González
- Department of Sciences, Institute for Multidisciplinary Research in Applied Biology, Universidad Pública de Navarra, Pamplona, Spain
- Esther M. González,
| | - Stefanie Wienkoop
- Unit of Molecular Systems Biology, Department of Functional and Evolution Ecology, University of Vienna, Vienna, Austria
- *Correspondence: Stefanie Wienkoop,
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FMO1 Is Involved in Excess Light Stress-Induced Signal Transduction and Cell Death Signaling. Cells 2020; 9:cells9102163. [PMID: 32987853 PMCID: PMC7600522 DOI: 10.3390/cells9102163] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
Because of their sessile nature, plants evolved integrated defense and acclimation mechanisms to simultaneously cope with adverse biotic and abiotic conditions. Among these are systemic acquired resistance (SAR) and systemic acquired acclimation (SAA). Growing evidence suggests that SAR and SAA activate similar cellular mechanisms and employ common signaling pathways for the induction of acclimatory and defense responses. It is therefore possible to consider these processes together, rather than separately, as a common systemic acquired acclimation and resistance (SAAR) mechanism. Arabidopsis thaliana flavin-dependent monooxygenase 1 (FMO1) was previously described as a regulator of plant resistance in response to pathogens as an important component of SAR. In the current study, we investigated its role in SAA, induced by a partial exposure of Arabidopsis rosette to local excess light stress. We demonstrate here that FMO1 expression is induced in leaves directly exposed to excess light stress as well as in systemic leaves remaining in low light. We also show that FMO1 is required for the systemic induction of ASCORBATE PEROXIDASE 2 (APX2) and ZINC-FINGER OF ARABIDOPSIS 10 (ZAT10) expression and spread of the reactive oxygen species (ROS) systemic signal in response to a local application of excess light treatment. Additionally, our results demonstrate that FMO1 is involved in the regulation of excess light-triggered systemic cell death, which is under control of LESION SIMULATING DISEASE 1 (LSD1). Our study indicates therefore that FMO1 plays an important role in triggering SAA response, supporting the hypothesis that SAA and SAR are tightly connected and use the same signaling pathways.
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Cohen SP, Leach JE. High temperature-induced plant disease susceptibility: more than the sum of its parts. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:235-241. [PMID: 32321671 DOI: 10.1016/j.pbi.2020.02.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/25/2020] [Accepted: 02/28/2020] [Indexed: 05/20/2023]
Abstract
Higher temperatures associated with climate change often increase the severity of plant diseases. An understanding of how plants respond to pathogens during high temperature stress is required for crop improvement, but the molecular mechanisms underlying this response are largely unknown. Mechanistic research has primarily focused on plant responses during either single stresses or heat-induced loss of single gene resistance. Transcriptome analyses of plant responses to a single stress compared to combined-stresses reveal significant differences showing that single-stress response studies are inadequate for determining the mechanisms of high temperature-induced disease susceptibility. To combat plant disease in light of climate change, future research will require comprehensive study designs and analyses.
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Affiliation(s)
- Stephen P Cohen
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523-1177, United States; Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, United States
| | - Jan E Leach
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523-1177, United States.
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Tiwari B, Habermann K, Arif MA, Weil HL, Garcia-Molina A, Kleine T, Mühlhaus T, Frank W. Identification of small RNAs during cold acclimation in Arabidopsis thaliana. BMC PLANT BIOLOGY 2020; 20:298. [PMID: 32600430 PMCID: PMC7325139 DOI: 10.1186/s12870-020-02511-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/22/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Cold stress causes dynamic changes in gene expression that are partially caused by small non-coding RNAs since they regulate protein coding transcripts and act in epigenetic gene silencing pathways. Thus, a detailed analysis of transcriptional changes of small RNAs (sRNAs) belonging to all known sRNA classes such as microRNAs (miRNA) and small interfering RNA (siRNAs) in response to cold contributes to an understanding of cold-related transcriptome changes. RESULT We subjected A. thaliana plants to cold acclimation conditions (4 °C) and analyzed the sRNA transcriptomes after 3 h, 6 h and 2 d. We found 93 cold responsive differentially expressed miRNAs and only 14 of these were previously shown to be cold responsive. We performed miRNA target prediction for all differentially expressed miRNAs and a GO analysis revealed the overrepresentation of miRNA-targeted transcripts that code for proteins acting in transcriptional regulation. We also identified a large number of differentially expressed cis- and trans-nat-siRNAs, as well as sRNAs that are derived from long non-coding RNAs. By combining the results of sRNA and mRNA profiling with miRNA target predictions and publicly available information on transcription factors, we reconstructed a cold-specific, miRNA and transcription factor dependent gene regulatory network. We verified the validity of links in the network by testing its ability to predict target gene expression under cold acclimation. CONCLUSION In A. thaliana, miRNAs and sRNAs derived from cis- and trans-NAT gene pairs and sRNAs derived from lncRNAs play an important role in regulating gene expression in cold acclimation conditions. This study provides a fundamental database to deepen our knowledge and understanding of regulatory networks in cold acclimation.
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Affiliation(s)
- Bhavika Tiwari
- Department of Biology I, Plant Molecular Cell Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Kristin Habermann
- Department of Biology I, Plant Molecular Cell Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - M. Asif Arif
- Department of Biology I, Plant Molecular Cell Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Heinrich Lukas Weil
- Computational Systems Biology, Technische Universität Kaiserslautern, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany
| | - Antoni Garcia-Molina
- Department of Biology I, Plant Molecular Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Department of Biology I, Plant Molecular Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, Technische Universität Kaiserslautern, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany
| | - Wolfgang Frank
- Department of Biology I, Plant Molecular Cell Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
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12
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Bittner A, van Buer J, Baier M. Cold priming uncouples light- and cold-regulation of gene expression in Arabidopsis thaliana. BMC PLANT BIOLOGY 2020; 20:281. [PMID: 32552683 PMCID: PMC7301481 DOI: 10.1186/s12870-020-02487-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 06/10/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND The majority of stress-sensitive genes responds to cold and high light in the same direction, if plants face the stresses for the first time. As shown recently for a small selection of genes of the core environmental stress response cluster, pre-treatment of Arabidopsis thaliana with a 24 h long 4 °C cold stimulus modifies cold regulation of gene expression for up to a week at 20 °C, although the primary cold effects are reverted within the first 24 h. Such memory-based regulation is called priming. Here, we analyse the effect of 24 h cold priming on cold regulation of gene expression on a transcriptome-wide scale and investigate if and how cold priming affects light regulation of gene expression. RESULTS Cold-priming affected cold and excess light regulation of a small subset of genes. In contrast to the strong gene co-regulation observed upon cold and light stress in non-primed plants, most priming-sensitive genes were regulated in a stressor-specific manner in cold-primed plant. Furthermore, almost as much genes were inversely regulated as co-regulated by a 24 h long 4 °C cold treatment and exposure to heat-filtered high light (800 μmol quanta m- 2 s- 1). Gene ontology enrichment analysis revealed that cold priming preferentially supports expression of genes involved in the defence against plant pathogens upon cold triggering. The regulation took place on the cost of the expression of genes involved in growth regulation and transport. On the contrary, cold priming resulted in stronger expression of genes regulating metabolism and development and weaker expression of defence genes in response to high light triggering. qPCR with independently cultivated and treated replicates confirmed the trends observed in the RNASeq guide experiment. CONCLUSION A 24 h long priming cold stimulus activates a several days lasting stress memory that controls cold and light regulation of gene expression and adjusts growth and defence regulation in a stressor-specific manner.
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Affiliation(s)
- Andras Bittner
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Königin-Luise-Straße 12-16, 14195 Berlin, Germany
| | - Jörn van Buer
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Königin-Luise-Straße 12-16, 14195 Berlin, Germany
| | - Margarete Baier
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Königin-Luise-Straße 12-16, 14195 Berlin, Germany
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13
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Mohl JE, Fetcher N, Stunz E, Tang J, Moody ML. Comparative transcriptomics of an arctic foundation species, tussock cottongrass (Eriophorum vaginatum), during an extreme heat event. Sci Rep 2020; 10:8990. [PMID: 32488082 PMCID: PMC7265556 DOI: 10.1038/s41598-020-65693-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 05/05/2020] [Indexed: 11/25/2022] Open
Abstract
Tussock cottongrass (Eriophorum vaginatum) is a foundation species for much of the arctic moist acidic tundra, which is currently experiencing extreme effects of climate change. The Arctic is facing higher summer temperatures and extreme weather events are becoming more common. We used Illumina RNA-Seq to analyse cDNA libraries for differential expression of genes from leaves of ecologically well-characterized ecotypes of tussock cottongrass found along a latitudinal gradient in the Alaskan Arctic and transplanted into a common garden. Plant sampling was performed on a typical summer day and during an extreme heat event. We obtained a de novo assembly that contained 423,353 unigenes. There were 363 unigenes up-regulated and 1,117 down-regulated among all ecotypes examined during the extreme heat event. Of these, 26 HSP unigenes had >log2-fold up-regulation. Several TFs associated with heat stress in previous studies were identified that had >log2-fold up- or down-regulation during the extreme heat event (e.g., DREB, NAC). There was consistent variation in DEGs among ecotypes, but not specifically related to whether plants originated from taiga or tundra ecosystems. As the climate changes it is essential to determine ecotypic diversity at the genomic level, especially for widespread species that impact ecosystem function.
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Affiliation(s)
- Jonathon E Mohl
- Bioinformatics Program, University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Ned Fetcher
- Institute for Environmental Science and Sustainability, Wilkes University, Wilkes-Barre, PA, 18766, USA
| | - Elizabeth Stunz
- Biological Sciences, University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Jianwu Tang
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Michael L Moody
- Biological Sciences, University of Texas at El Paso, El Paso, TX, 79968, USA.
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14
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Brown AJP, Larcombe DE, Pradhan A. Thoughts on the evolution of Core Environmental Responses in yeasts. Fungal Biol 2020; 124:475-481. [PMID: 32389310 PMCID: PMC7232023 DOI: 10.1016/j.funbio.2020.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 12/18/2022]
Abstract
The model yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe, display Core Environmental Responses (CERs) that include the induction of a core set of stress genes in response to diverse environmental stresses. CERs underlie the phenomenon of stress cross-protection, whereby exposure to one type of stress can provide protection against subsequent exposure to a second type of stress. CERs have probably arisen through the accumulation, over evolutionary time, of protective anticipatory responses (“adaptive prediction”). CERs have been observed in other evolutionarily divergent fungi but, interestingly, not in the pathogenic yeast, Candida albicans. We argue that this is because we have not looked in the right place. In response to specific host inputs, C. albicans does activate anticipatory responses that protect it against impending attack from the immune system. Therefore, we suggest that C. albicans has evolved a CER that reflects the environmental challenges it faces in host niches. We review Core Environmental Responses (CERs) in domesticated and pathogenic yeasts. CERs probably evolved through the accumulation of protective anticipatory responses. Evolutionarily diverse yeasts display CERs, but the pathogen, Candida albicans, does not. C. albicans has evolved an alternative CER that protects against immune clearance. This has implications for the investigation of CERs in other fungi.
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Affiliation(s)
- Alistair J P Brown
- MRC Centre for Medical Mycology, University of Exeter, Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
| | - Daniel E Larcombe
- MRC Centre for Medical Mycology, University of Exeter, Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Arnab Pradhan
- MRC Centre for Medical Mycology, University of Exeter, Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
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15
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Dossa K, Mmadi MA, Zhou R, Zhang T, Su R, Zhang Y, Wang L, You J, Zhang X. Depicting the Core Transcriptome Modulating Multiple Abiotic Stresses Responses in Sesame ( Sesamum indicum L.). Int J Mol Sci 2019; 20:ijms20163930. [PMID: 31412539 PMCID: PMC6721054 DOI: 10.3390/ijms20163930] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/26/2019] [Accepted: 08/10/2019] [Indexed: 01/21/2023] Open
Abstract
Sesame is a source of a healthy vegetable oil, attracting a growing interest worldwide. Abiotic stresses have devastating effects on sesame yield; hence, studies have been performed to understand sesame molecular responses to abiotic stresses, but the core abiotic stress-responsive genes (CARG) that the plant reuses in response to an array of environmental stresses are unknown. We performed a meta-analysis of 72 RNA-Seq datasets from drought, waterlogging, salt and osmotic stresses and identified 543 genes constantly and differentially expressed in response to all stresses, representing the sesame CARG. Weighted gene co-expression network analysis of the CARG revealed three functional modules controlled by key transcription factors. Except for salt stress, the modules were positively correlated with the abiotic stresses. Network topology of the modules showed several hub genes predicted to play prominent functions. As proof of concept, we generated over-expressing Arabidopsis lines with hub and non-hub genes. Transgenic plants performed better under drought, waterlogging, and osmotic stresses than the wild-type plants but did not tolerate the salt treatment. As expected, the hub gene was significantly more potent than the non-hub gene. Overall, we discovered several novel candidate genes, which will fuel investigations on plant responses to multiple abiotic stresses.
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Affiliation(s)
- Komivi Dossa
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
| | - Marie A Mmadi
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Rong Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Tianyuan Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruqi Su
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Yujuan Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Linhai Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Jun You
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
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16
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Ahn H, Jo K, Jeong D, Pak M, Hur J, Jung W, Kim S. PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation. FRONTIERS IN PLANT SCIENCE 2019; 10:698. [PMID: 31258543 PMCID: PMC6587906 DOI: 10.3389/fpls.2019.00698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Transcription factor (TF) has a significant influence on the state of a cell by regulating multiple down-stream genes. Thus, experimental and computational biologists have made great efforts to construct TF gene networks for regulatory interactions between TFs and their target genes. Now, an important research question is how to utilize TF networks to investigate the response of a plant to stress at the transcription control level using time-series transcriptome data. In this article, we present a new computational network, PropaNet, to investigate dynamics of TF networks from time-series transcriptome data using two state-of-the-art network analysis techniques, influence maximization and network propagation. PropaNet uses the influence maximization technique to produce a ranked list of TFs, in the order of TF that explains differentially expressed genes (DEGs) better at each time point. Then, a network propagation technique is used to select a group of TFs that explains DEGs best as a whole. For the analysis of Arabidopsis time series datasets from AtGenExpress, we used PlantRegMap as a template TF network and performed PropaNet analysis to investigate transcriptional dynamics of Arabidopsis under cold and heat stress. The time varying TF networks showed that Arabidopsis responded to cold and heat stress quite differently. For cold stress, bHLH and bZIP type TFs were the first responding TFs and the cold signal influenced histone variants, various genes involved in cell architecture, osmosis and restructuring of cells. However, the consequences of plants under heat stress were up-regulation of genes related to accelerating differentiation and starting re-differentiation. In terms of energy metabolism, plants under heat stress show elevated metabolic process and resulting in an exhausted status. We believe that PropaNet will be useful for the construction of condition-specific time-varying TF network for time-series data analysis in response to stress. PropaNet is available at http://biohealth.snu.ac.kr/software/PropaNet.
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Affiliation(s)
- Hongryul Ahn
- Bioinformatics Institute, Seoul National University, Seoul, South Korea
| | - Kyuri Jo
- Bioinformatics Institute, Seoul National University, Seoul, South Korea
| | - Dabin Jeong
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Minwoo Pak
- Department of Computer Science and Engineering, Seoul National University, Seoul, South Korea
| | - Jihye Hur
- Department of Crop Science, Konkuk University, Seoul, South Korea
| | - Woosuk Jung
- Department of Crop Science, Konkuk University, Seoul, South Korea
| | - Sun Kim
- Bioinformatics Institute, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
- Department of Computer Science and Engineering, Seoul National University, Seoul, South Korea
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17
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Mayer KS, Chen X, Sanders D, Chen J, Jiang J, Nguyen P, Scalf M, Smith LM, Zhong X. HDA9-PWR-HOS15 Is a Core Histone Deacetylase Complex Regulating Transcription and Development. PLANT PHYSIOLOGY 2019; 180:342-355. [PMID: 30765479 PMCID: PMC6501109 DOI: 10.1104/pp.18.01156] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/31/2019] [Indexed: 05/19/2023]
Abstract
Histone deacetylases remove acetyl groups from histone proteins and play important roles in many genomic processes. How histone deacetylases perform specialized molecular and biological functions in plants is poorly understood. Here, we identify HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 15 (HOS15) as a core member of the Arabidopsis (Arabidopsis thaliana) HISTONE DEACETYLASE9-POWERDRESS (HDA9-PWR) complex. HOS15 immunoprecipitates with both HDA9 and PWR. Mutation of HOS15 induces histone hyperacetylation and methylation changes similar to hda9 and pwr mutants. HOS15, HDA9, and PWR are coexpressed in all organs, and mutant combinations display remarkable phenotypic resemblance and nonadditivity for organogenesis and developmental phase transitions. Ninety percent of HOS15-regulated genes are also controlled by HDA9 and PWR HDA9 binds to and directly represses 92 genes, many of which are responsive to biotic and abiotic stimuli, including a family of ethylene response factor genes. Additionally, HOS15 regulates HDA9 nuclear accumulation and chromatin association. Collectively, this study establishes that HOS15 forms a core complex with HDA9 and PWR to control gene expression and plant development.
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Affiliation(s)
- Kevin S Mayer
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Xiangsong Chen
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Dean Sanders
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jiani Chen
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jianjun Jiang
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Phu Nguyen
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Xuehua Zhong
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53706
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18
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Cohen SP, Leach JE. Abiotic and biotic stresses induce a core transcriptome response in rice. Sci Rep 2019; 9:6273. [PMID: 31000746 PMCID: PMC6472405 DOI: 10.1038/s41598-019-42731-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 04/04/2019] [Indexed: 11/26/2022] Open
Abstract
Environmental stresses greatly limit crop yield. With the increase in extreme weather events due to climate change and the constant pressure of diseases and pests, there is an urgent need to develop crop varieties that can tolerate multiple stresses. However, our knowledge of how plants broadly respond to stress is limited. Here, we explore the rice core stress response via meta-analysis of publicly available rice transcriptome data. Our results confirm that rice universally down-regulates photosynthesis in response to both abiotic and biotic stress. Rice also generally up-regulates hormone-responsive genes during stress response, most notably genes in the abscisic acid, jasmonic acid and salicylic acid pathways. We identified several promoter motifs that are likely involved in stress-responsive regulatory mechanisms in rice. With this work, we provide a list of candidate genes to study for improving rice stress tolerance in light of environmental stresses. This work also serves as a proof of concept to show that meta-analysis of diverse transcriptome data is a valid approach to develop robust hypotheses for how plants respond to stress.
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Affiliation(s)
- Stephen P Cohen
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, CO, 80523-1177, Fort Collins, USA.,Cell and Molecular Biology Graduate Program, Colorado State University, CO, 80523-1005, Fort Collins, USA
| | - Jan E Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, CO, 80523-1177, Fort Collins, USA.
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19
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Cui F, Brosché M, Shapiguzov A, He XQ, Vainonen JP, Leppälä J, Trotta A, Kangasjärvi S, Salojärvi J, Kangasjärvi J, Overmyer K. Interaction of methyl viologen-induced chloroplast and mitochondrial signalling in Arabidopsis. Free Radic Biol Med 2019; 134:555-566. [PMID: 30738155 DOI: 10.1016/j.freeradbiomed.2019.02.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 01/20/2023]
Abstract
Reactive oxygen species (ROS) are key signalling intermediates in plant metabolism, defence, and stress adaptation. In plants, both the chloroplast and mitochondria are centres of metabolic control and ROS production, which coordinate stress responses in other cell compartments. The herbicide and experimental tool, methyl viologen (MV) induces ROS generation in the chloroplast under illumination, but is also toxic in non-photosynthetic organisms. We used MV to probe plant ROS signalling in compartments other than the chloroplast. Taking a genetic approach in the model plant Arabidopsis (Arabidopsis thaliana), we used natural variation, QTL mapping, and mutant studies with MV in the light, but also under dark conditions, when the chloroplast electron transport is inactive. These studies revealed a light-independent MV-induced ROS-signalling pathway, suggesting mitochondrial involvement. Mitochondrial Mn SUPEROXIDE DISMUTASE was required for ROS-tolerance and the effect of MV was enhanced by exogenous sugar, providing further evidence for the role of mitochondria. Mutant and hormone feeding assays revealed roles for stress hormones in organellar ROS-responses. The radical-induced cell death1 mutant, which is tolerant to MV-induced ROS and exhibits altered mitochondrial signalling, was used to probe interactions between organelles. Our studies suggest that mitochondria are involved in the response to ROS induced by MV in plants.
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Affiliation(s)
- Fuqiang Cui
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, P.O Box 65 (Viikinkaari 1), FI-00014, Helsinki, Finland
| | - Mikael Brosché
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, P.O Box 65 (Viikinkaari 1), FI-00014, Helsinki, Finland; Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia
| | - Alexey Shapiguzov
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, P.O Box 65 (Viikinkaari 1), FI-00014, Helsinki, Finland; Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276, Moscow, Russia
| | - Xin-Qiang He
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, P.O Box 65 (Viikinkaari 1), FI-00014, Helsinki, Finland; College of Life Sciences, Peking University, Beijing, 100871, China
| | - Julia P Vainonen
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, P.O Box 65 (Viikinkaari 1), FI-00014, Helsinki, Finland
| | - Johanna Leppälä
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, P.O Box 65 (Viikinkaari 1), FI-00014, Helsinki, Finland
| | - Andrea Trotta
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Saijaliisa Kangasjärvi
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, P.O Box 65 (Viikinkaari 1), FI-00014, Helsinki, Finland; School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Jaakko Kangasjärvi
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, P.O Box 65 (Viikinkaari 1), FI-00014, Helsinki, Finland
| | - Kirk Overmyer
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, P.O Box 65 (Viikinkaari 1), FI-00014, Helsinki, Finland.
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20
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van Buer J, Prescher A, Baier M. Cold-priming of chloroplast ROS signalling is developmentally regulated and is locally controlled at the thylakoid membrane. Sci Rep 2019; 9:3022. [PMID: 30816299 PMCID: PMC6395587 DOI: 10.1038/s41598-019-39838-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/29/2019] [Indexed: 12/31/2022] Open
Abstract
24 h exposure to 4 °C primes Arabidopsis thaliana in the pre-bolting rosette stage for several days against full cold activation of the ROS responsive genes ZAT10 and BAP1 and causes stronger cold-induction of pleiotropically stress-regulated genes. Transient over-expression of thylakoid ascorbate peroxidase (tAPX) at 20 °C mimicked and tAPX transcript silencing antagonized cold-priming of ZAT10 expression. The tAPX effect could not be replaced by over-expression of stromal ascorbate peroxidase (sAPX) demonstrating that priming is specific to regulation of tAPX availability and, consequently, regulated locally at the thylakoid membrane. Arabidopsis acquired cold primability in the early rosette stage between 2 and 4 weeks. During further rosette development, primability was widely maintained in the oldest leaves. Later formed and later maturing leaves were not primable demonstrating that priming is stronger regulated with plant age than with leaf age. In 4-week-old plants, which were strongest primable, the memory was fully erasable and lost seven days after priming. In summary, we conclude that cold-priming of chloroplast-to-nucleus ROS signalling by transient post-stress induction of tAPX transcription is a strategy to modify cell signalling for some time without affecting the alertness for activation of cold acclimation responses.
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Affiliation(s)
- Jörn van Buer
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Königin-Luise-Straße 12-16, 14195, Berlin, Germany
| | - Andreas Prescher
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Königin-Luise-Straße 12-16, 14195, Berlin, Germany
| | - Margarete Baier
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Königin-Luise-Straße 12-16, 14195, Berlin, Germany.
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21
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Theune ML, Bloss U, Brand LH, Ladwig F, Wanke D. Phylogenetic Analyses and GAGA-Motif Binding Studies of BBR/BPC Proteins Lend to Clues in GAGA-Motif Recognition and a Regulatory Role in Brassinosteroid Signaling. FRONTIERS IN PLANT SCIENCE 2019; 10:466. [PMID: 31057577 PMCID: PMC6477699 DOI: 10.3389/fpls.2019.00466] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 03/28/2019] [Indexed: 05/21/2023]
Abstract
Plant GAGA-motif binding factors are encoded by the BARLEY B RECOMBINANT / BASIC PENTACYSTEINE (BBR/BPC) family, which fulfill indispensable functions in growth and development. BBR/BPC proteins control flower development, size of the stem cell niche and seed development through transcriptional regulation of homeotic transcription factor genes. They are responsible for the context dependent recruitment of Polycomb repressive complexes (PRC) or other repressive proteins to GAGA-motifs, which are contained in Polycomb repressive DNA-elements (PREs). Hallmark of the protein family is the highly conserved BPC domain, which is required for DNA binding. Here we study the evolution and diversification of the BBR/BPC family and its DNA-binding domain. Our analyses supports a further division of the family into four main groups (I-IV) and several subgroups, to resolve a strict monophyletic descent of the BPC domain. We prove a polyphyletic origin for group III proteins, which evolved from group I and II members through extensive loss of domains in the N-terminus. Conserved motif searches lend to the identification of a WAR/KHGTN consensus and a TIR/K motif at the very C-terminus of the BPC-domain. We could show by DPI-ELISA that this signature is required for DNA-binding in AtBPC1. Additional binding studies with AtBPC1, AtBPC6 and mutated oligonucleotides consolidated the binding to GAGA tetramers. To validate these findings, we used previously published ChIP-seq data from GFP-BPC6. We uncovered that many genes of the brassinosteroid signaling pathway are targeted by AtBPC6. Consistently, bpc6, bpc4 bpc6, and lhp1 bpc4 bpc4 mutants display brassinosteroid-dependent root growth phenotypes. Both, a function in brassinosteroid signaling and our phylogenetic data supports a link between BBR/BPC diversification in the land plant lineage and the complexity of flower and seed plant evolution.
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Affiliation(s)
- Marius L. Theune
- Molecular Plant Biology, Saarland University, Saarbrücken, Germany
| | - Ulrich Bloss
- ZMBP-Plant Physiology, Tübingen University, Tübingen, Germany
| | - Luise H. Brand
- ZMBP-Plant Physiology, Tübingen University, Tübingen, Germany
| | | | - Dierk Wanke
- Molecular Plant Biology, Saarland University, Saarbrücken, Germany
- ZMBP-Plant Physiology, Tübingen University, Tübingen, Germany
- *Correspondence: Dierk Wanke,
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22
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Buckner E, Madison I, Chou H, Matthiadis A, Melvin CE, Sozzani R, Williams C, Long TA. Automated Imaging, Tracking, and Analytics Pipeline for Differentiating Environmental Effects on Root Meristematic Cell Division. FRONTIERS IN PLANT SCIENCE 2019; 10:1487. [PMID: 31803217 PMCID: PMC6877711 DOI: 10.3389/fpls.2019.01487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 10/28/2019] [Indexed: 05/04/2023]
Abstract
Exposure of plants to abiotic stresses, whether individually or in combination, triggers dynamic changes to gene regulation. These responses induce distinct changes in phenotypic characteristics, enabling the plant to adapt to changing environments. For example, iron deficiency and heat stress have been shown to alter root development by reducing primary root growth and reducing cell proliferation, respectively. Currently, identifying the dynamic temporal coordination of genetic responses to combined abiotic stresses remains a bottleneck. This is, in part, due to an inability to isolate specific intervals in developmental time where differential activity in plant stress responses plays a critical role. Here, we observed that iron deficiency, in combination with temporary heat stress, suppresses the expression of iron deficiency-responsive pPYE::LUC (POPEYE::luciferase) and pBTS::LUC (BRUTUS::luciferase) reporter genes. Moreover, root growth was suppressed less under combined iron deficiency and heat stress than under either single stress condition. To further explore the interaction between pathways, we also created a computer vision pipeline to extract, analyze, and compare high-dimensional dynamic spatial and temporal cellular data in response to heat and iron deficiency stress conditions at high temporal resolution. Specifically, we used fluorescence light sheet microscopy to image Arabidopsis thaliana roots expressing CYCB1;1:GFP, a marker for cell entry into mitosis, every 20 min for 24 h exposed to either iron sufficiency, iron deficiency, heat stress, or combined iron deficiency and heat stress. Our pipeline extracted spatiotemporal metrics from these time-course data. These metrics showed that the persistency and timing of CYCB1;1:GFP signal were uniquely different under combined iron deficiency and heat stress conditions versus the single stress conditions. These metrics also indicated that the spatiotemporal characteristics of the CYCB1;1:GFP signal under combined stress were more dissimilar to the control response than the response seen under iron deficiency for the majority of the 24-h experiment. Moreover, the combined stress response was less dissimilar to the control than the response seen under heat stress. This indicated that pathways activated when the plant is exposed to both iron deficiency and heat stress affected CYCB1;1:GFP spatiotemporal function antagonistically.
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Affiliation(s)
- Eli Buckner
- Electrical and Computer Engineering Department, North Carolina State University, Raleigh, NC, United States
| | - Imani Madison
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, United States
| | - Hsuan Chou
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, United States
| | - Anna Matthiadis
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, United States
| | - Charles E. Melvin
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, United States
| | - Rosangela Sozzani
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, United States
| | - Cranos Williams
- Electrical and Computer Engineering Department, North Carolina State University, Raleigh, NC, United States
- *Correspondence: Cranos Williams, ; Terri A. Long,
| | - Terri A. Long
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, United States
- *Correspondence: Cranos Williams, ; Terri A. Long,
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23
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Pucker B, Brockington SF. Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes. BMC Genomics 2018; 19:980. [PMID: 30594132 PMCID: PMC6310983 DOI: 10.1186/s12864-018-5360-z] [Citation(s) in RCA: 30] [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: 10/11/2018] [Accepted: 12/10/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Most eukaryotic genes comprise exons and introns thus requiring the precise removal of introns from pre-mRNAs to enable protein biosynthesis. U2 and U12 spliceosomes catalyze this step by recognizing motifs on the transcript in order to remove the introns. A process which is dependent on precise definition of exon-intron borders by splice sites, which are consequently highly conserved across species. Only very few combinations of terminal dinucleotides are frequently observed at intron ends, dominated by the canonical GT-AG splice sites on the DNA level. RESULTS Here we investigate the occurrence of diverse combinations of dinucleotides at predicted splice sites. Analyzing 121 plant genome sequences based on their annotation revealed strong splice site conservation across species, annotation errors, and true biological divergence from canonical splice sites. The frequency of non-canonical splice sites clearly correlates with their divergence from canonical ones indicating either an accumulation of probably neutral mutations, or evolution towards canonical splice sites. Strong conservation across multiple species and non-random accumulation of substitutions in splice sites indicate a functional relevance of non-canonical splice sites. The average composition of splice sites across all investigated species is 98.7% for GT-AG, 1.2% for GC-AG, 0.06% for AT-AC, and 0.09% for minor non-canonical splice sites. RNA-Seq data sets of 35 species were incorporated to validate non-canonical splice site predictions through gaps in sequencing reads alignments and to demonstrate the expression of affected genes. CONCLUSION We conclude that bona fide non-canonical splice sites are present and appear to be functionally relevant in most plant genomes, although at low abundance.
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Affiliation(s)
- Boas Pucker
- Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Samuel F. Brockington
- Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, UK
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24
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Khan MA, Castro-Guerrero NA, McInturf SA, Nguyen NT, Dame AN, Wang J, Bindbeutel RK, Joshi T, Jurisson SS, Nusinow DA, Mendoza-Cozatl DG. Changes in iron availability in Arabidopsis are rapidly sensed in the leaf vasculature and impaired sensing leads to opposite transcriptional programs in leaves and roots. PLANT, CELL & ENVIRONMENT 2018; 41:2263-2276. [PMID: 29520929 DOI: 10.1111/pce.13192] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 03/04/2018] [Accepted: 03/05/2018] [Indexed: 05/18/2023]
Abstract
The OLIGOPEPTIDE TRANSPORTER 3 (OPT3) has recently been identified as a component of the systemic network mediating iron (Fe) deficiency responses in Arabidopsis. Reduced expression of OPT3 induces an over accumulation of Fe in roots and leaves, due in part by an elevated expression of the IRON-REGULATED TRANSPORTER 1. Here we show however, that opt3 leaves display a transcriptional program consistent with an Fe overload, suggesting that Fe excess is properly sensed in opt3 leaves and that the OPT3-mediated shoot-to-root signaling is critical to prevent a systemic Fe overload. We also took advantage of the tissue-specific localization of OPT3, together with other Fe-responsive genes, to determine the timing and location of early transcriptional events during Fe limitation and resupply. Our results show that the leaf vasculature responds more rapidly than roots to both Fe deprivation and resupply, suggesting that the leaf vasculature is within the first tissues that sense and respond to changes in Fe availability. Our data highlight the importance of the leaf vasculature in Fe homeostasis by sensing changes in apoplastic levels of Fe coming through the xylem and relaying this information back to roots via the phloem to regulate Fe uptake at the root level.
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Affiliation(s)
- Mather A Khan
- Division of Plant Sciences, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Norma A Castro-Guerrero
- Division of Plant Sciences, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Samuel A McInturf
- Division of Plant Sciences, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Nga T Nguyen
- Division of Plant Sciences, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Ashley N Dame
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Jiaojiao Wang
- Department of Computer Science; C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | | | - Trupti Joshi
- Department of Computer Science; C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- Department of Molecular Microbiology and Immunology and Office of Research, School of Medicine; Informatics Institute, University of Missouri, Columbia, MO, 65211, USA
| | - Silvia S Jurisson
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, USA
| | | | - David G Mendoza-Cozatl
- Division of Plant Sciences, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
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25
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Alberto D, Couée I, Pateyron S, Sulmon C, Gouesbet G. Low doses of triazine xenobiotics mobilize ABA and cytokinin regulations in a stress- and low-energy-dependent manner. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:8-22. [PMID: 30080643 DOI: 10.1016/j.plantsci.2018.04.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/25/2018] [Accepted: 04/28/2018] [Indexed: 06/08/2023]
Abstract
The extent of residual contaminations of pesticides through drift, run-off and leaching is a potential threat to non-target plant communities. Arabidopsis thaliana responds to low doses of the herbicide atrazine, and of its degradation products, desethylatrazine and hydroxyatrazine, not only in the long term, but also under conditions of short-term exposure. In order to investigate underlying molecular mechanisms of low-dose responses and to decipher commonalities and specificities between different chemical treatments, parallel transcriptomic studies of the early effects of the atrazine-desethylatrazine-hydroxyatrazine chemical series were undertaken using whole-genome microarrays. All of the triazines under study produced coordinated and specific changes in gene expression. Hydroxyatrazine-responsive genes were mainly linked to root development, whereas atrazine and desethylatrazine mostly affected molecular signaling networks implicated in stress and hormone responses. Analysis of signaling-related genes, promoter sites and shared-function interaction networks highlighted the involvement of energy-, stress-, abscisic acid- and cytokinin-regulated processes, and emphasized the importance of cold-, heat- and drought-related signaling in the perception of low doses of triazines. These links between low-dose xenobiotic impacts and stress-hormone crosstalk pathways give novel insights into plant-pesticide interactions and plant-pollution interactions that are essential for toxicity evaluation in the context of environmental risk assessment.
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Affiliation(s)
- Diana Alberto
- Université de Rennes 1 / Centre National de la Recherche Scientifique, UMR 6553 ECOBIO, Rennes, F-35000, France
| | - Ivan Couée
- Université de Rennes 1 / Centre National de la Recherche Scientifique, UMR 6553 ECOBIO, Rennes, F-35000, France
| | - Stéphanie Pateyron
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay, France
| | - Cécile Sulmon
- Université de Rennes 1 / Centre National de la Recherche Scientifique, UMR 6553 ECOBIO, Rennes, F-35000, France
| | - Gwenola Gouesbet
- Université de Rennes 1 / Centre National de la Recherche Scientifique, UMR 6553 ECOBIO, Rennes, F-35000, France.
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26
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Cho SM, Lee H, Jo H, Lee H, Kang Y, Park H, Lee J. Comparative transcriptome analysis of field- and chamber-grown samples of Colobanthus quitensis (Kunth) Bartl, an Antarctic flowering plant. Sci Rep 2018; 8:11049. [PMID: 30038328 PMCID: PMC6056519 DOI: 10.1038/s41598-018-29335-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 07/09/2018] [Indexed: 11/09/2022] Open
Abstract
Colobanthus quitensis is one of the two vascular plants inhabiting the Antarctic. In natural habitats, it grows in the form of a cushion or mats, commonly observed in high latitudes or alpine vegetation. Although this species has been investigated over many years to study its geographical distribution and physiological adaptations to climate change, very limited genetic information is available. The high-throughput sequencing with a de novo assembly analysis yielded 47,070 contigs with blast-hits. Through the functional classification and enrichment analysis, we identified that photosynthesis and phenylpropanoid pathway genes show differential expression depending on the habitat environment. We found that the known 'plant core environmental stress response (PCESR)' genes were abundantly expressed in Antarctic samples, and confirmed that their expression is mainly induced by low-temperature. In addition, we suggest that differential expression of thermomorphogenesis-related genes may contribute to phenotypic plasticity of the plant, for instance, displaying a cushion-like phenotype to adapt to harsh environments.
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Affiliation(s)
- Sung Mi Cho
- Unit of Polar Genomics, Korea Polar Research Institute, KIOST, Incheon, 21990, Republic of Korea
| | - Hyoungseok Lee
- Unit of Polar Genomics, Korea Polar Research Institute, KIOST, Incheon, 21990, Republic of Korea.,Polar Science, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Hojin Jo
- Unit of Polar Genomics, Korea Polar Research Institute, KIOST, Incheon, 21990, Republic of Korea.,Polar Science, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Horim Lee
- Department of Biotechnology, Duksung Women's University, Seoul, 01369, Republic of Korea
| | - Yoonjee Kang
- Unit of Polar Genomics, Korea Polar Research Institute, KIOST, Incheon, 21990, Republic of Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, KIOST, Incheon, 21990, Republic of Korea.,Polar Science, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Jungeun Lee
- Unit of Polar Genomics, Korea Polar Research Institute, KIOST, Incheon, 21990, Republic of Korea. .,Polar Science, University of Science and Technology, Incheon, 21990, Republic of Korea.
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27
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Gairola S, Al Shaer KI, Al Harthi EK, Mosa KA. Strengthening desert plant biotechnology research in the United Arab Emirates: a viewpoint. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:521-533. [PMID: 30042610 PMCID: PMC6041242 DOI: 10.1007/s12298-018-0551-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 02/19/2018] [Accepted: 05/08/2018] [Indexed: 05/09/2023]
Abstract
The biotechnology of desert plants is a vast subject. The main applications in this broad field of study comprises of plant tissue culture, genetic engineering, molecular markers and others. Biotechnology applications have the potential to address biodiversity conservation as well as agricultural, medicinal, and environmental issues. There is a need to increase our knowledge of the genetic diversity through the use of molecular genetics and biotechnological approaches in desert plants in the Arabian Gulf region including those in the United Arab Emirates (UAE). This article provides a prospective research for the study of UAE desert plant diversity through DNA fingerprinting as well as understanding the mechanisms of both abiotic stress resistance (including salinity, drought and heat stresses) and biotic stress resistance (including disease and insect resistance). Special attention is given to the desert halophytes and their utilization to alleviate the salinity stress, which is one of the major challenges in agriculture. In addition, symbioses with microorganisms are thought to be hypothesized as important components of desert plant survival under stressful environmental conditions. Thus, factors shaping the diversity and functionality of plant microbiomes in desert ecosystems are also emphasized in this article. It is important to establish a critical mass for biotechnology research and applications while strengthening the channels for collaboration among research/academic institutions in the area of desert plant biotechnology.
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Affiliation(s)
- Sanjay Gairola
- Sharjah Seed Bank and Herbarium, Sharjah Research Academy, University City, Sharjah, P. Box 60999, Sharjah, UAE
| | - Khawla I. Al Shaer
- Plant Molecular Biology and Biotechnology Laboratory, Sharjah Research Academy, University City, Sharjah, P. Box 60999, Sharjah, UAE
| | - Eman K. Al Harthi
- Plant Molecular Biology and Biotechnology Laboratory, Sharjah Research Academy, University City, Sharjah, P. Box 60999, Sharjah, UAE
| | - Kareem A. Mosa
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
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28
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Shen PC, Hour AL, Liu LYD. Microarray meta-analysis to explore abiotic stress-specific gene expression patterns in Arabidopsis. BOTANICAL STUDIES 2017; 58:22. [PMID: 28510204 PMCID: PMC5432924 DOI: 10.1186/s40529-017-0176-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/05/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND Abiotic stresses are the major limiting factors that affect plant growth, development, yield and final quality. Deciphering the underlying mechanisms of plants' adaptations to stresses using few datasets might overlook the different aspects of stress tolerance in plants, which might be simultaneously and consequently operated in the system. Fortunately, the accumulated microarray expression data offer an opportunity to infer abiotic stress-specific gene expression patterns through meta-analysis. In this study, we propose to combine microarray gene expression data under control, cold, drought, heat, and salt conditions and determined modules (gene sets) of genes highly associated with each other according to the observed expression data. RESULTS By analyzing the expression variations of the Eigen genes from different conditions, we had identified two, three, and five gene modules as cold-, heat-, and salt-specific modules, respectively. Most of the cold- or heat-specific modules were differentially expressed to a particular degree in shoot samples, while most of the salt-specific modules were differentially expressed to a particular degree in root samples. A gene ontology (GO) analysis on the stress-specific modules suggested that the gene modules exclusively enriched stress-related GO terms and that different genes under the same GO terms may be alternatively disturbed in different conditions. The gene regulatory events for two genes, DREB1A and DEAR1, in the cold-specific gene module had also been validated, as evidenced through the literature search. CONCLUSIONS Our protocols study the specificity of the gene modules that were specifically activated under a particular type of abiotic stress. The biplot can also assist to visualize the stress-specific gene modules. In conclusion, our approach has the potential to further elucidate mechanisms in plants and beneficial for future experiments design under different abiotic stresses.
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Affiliation(s)
- Po-chih Shen
- Biometrics Division, Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Ai-ling Hour
- Department of Life Science, Fu-Jen Catholic University, Xinbei, Taiwan
| | - Li-yu Daisy Liu
- Biometrics Division, Department of Agronomy, National Taiwan University, Taipei, Taiwan
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29
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Vie AK, Najafi J, Winge P, Cattan E, Wrzaczek M, Kangasjärvi J, Miller G, Brembu T, Bones AM. The IDA-LIKE peptides IDL6 and IDL7 are negative modulators of stress responses in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3557-3571. [PMID: 28586470 PMCID: PMC5853212 DOI: 10.1093/jxb/erx168] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/04/2017] [Indexed: 05/13/2023]
Abstract
Small signalling peptides have emerged as important cell to cell messengers in plant development and stress responses. However, only a few of the predicted peptides have been functionally characterized. Here, we present functional characterization of two members of the IDA-LIKE (IDL) peptide family in Arabidopsis thaliana, IDL6 and IDL7. Localization studies suggest that the peptides require a signal peptide and C-terminal processing to be correctly transported out of the cell. Both IDL6 and IDL7 appear to be unstable transcripts under post-transcriptional regulation. Treatment of plants with synthetic IDL6 and IDL7 peptides resulted in down-regulation of a broad range of stress-responsive genes, including early stress-responsive transcripts, dominated by a large group of ZINC FINGER PROTEIN (ZFP) genes, WRKY genes, and genes encoding calcium-dependent proteins. IDL7 expression was rapidly induced by hydrogen peroxide, and idl7 and idl6 idl7 double mutants displayed reduced cell death upon exposure to extracellular reactive oxygen species (ROS). Co-treatment of the bacterial elicitor flg22 with IDL7 peptide attenuated the rapid ROS burst induced by treatment with flg22 alone. Taken together, our results suggest that IDL7, and possibly IDL6, act as negative modulators of stress-induced ROS signalling in Arabidopsis.
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Affiliation(s)
- Ane Kjersti Vie
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Javad Najafi
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Per Winge
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ester Cattan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Michael Wrzaczek
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Finland
| | - Jaakko Kangasjärvi
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Finland
- Distinguished Scientist Fellowship Program, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Gad Miller
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Tore Brembu
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Atle M Bones
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
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30
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Song J, Liu Q, Hu B, Wu W. Photoreceptor PhyB Involved in Arabidopsis Temperature Perception and Heat-Tolerance Formation. Int J Mol Sci 2017; 18:ijms18061194. [PMID: 28587227 PMCID: PMC5486017 DOI: 10.3390/ijms18061194] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 01/02/2023] Open
Abstract
The influence of temperature on plants is essential. However, our knowledge on the intricate regulation process underlying heat stress (HS) response in plants is limited. Recently, information about thermal sensors in vivo has begun to emerge. In this study, another primary environmental stimulus, light, was verified once again to work with temperature synergistically on plants, through the modulation of numerous biological processes. With the application of transcriptomic analysis, a substantial number of heat-responsive genes were detected involved in both light- and phytohormone-mediated pathways in Arabidopsis. During this process, phytoreceptor phyB acts as a molecular switch to turn on or turn off several other genes HS response, under different light conditions. Furthermore, a morphological study showed the afunction of phyB enhanced plants thermal tolerance, confirming the important role of this phytochrome in temperature perception and response in plants. This study adds data to the picture of light and temperature signaling cross-talk in plants, which is important for the exploration of complicated HS responses or light-mediated mechanisms. Furthermore, based on its influence on Arabidopsis thermal response in both morphological and physiological levels, phyB is a photoreceptor, as revealed before, as well as an essential thermal sensor in plants.
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Affiliation(s)
- Junyi Song
- College of Science, National University of Defense Technology, Changsha 410073, China.
| | - Qijun Liu
- College of Science, National University of Defense Technology, Changsha 410073, China.
| | - Biru Hu
- College of Science, National University of Defense Technology, Changsha 410073, China.
| | - Wenjian Wu
- College of Science, National University of Defense Technology, Changsha 410073, China.
- State Key Lab of Nuclear, Biological and Chemical Protection for Civilian, Beijing 102205, China.
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31
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Choi WG, Miller G, Wallace I, Harper J, Mittler R, Gilroy S. Orchestrating rapid long-distance signaling in plants with Ca 2+ , ROS and electrical signals. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:698-707. [PMID: 28112437 PMCID: PMC5677518 DOI: 10.1111/tpj.13492] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/15/2017] [Accepted: 01/17/2017] [Indexed: 05/18/2023]
Abstract
Plants show a rapid systemic response to a wide range of environmental stresses, where the signals from the site of stimulus perception are transmitted to distal organs to elicit plant-wide responses. A wide range of signaling molecules are trafficked through the plant, but a trio of potentially interacting messengers, reactive oxygen species (ROS), Ca2+ and electrical signaling ('trio signaling') appear to form a network supporting rapid signal transmission. The molecular components underlying this rapid communication are beginning to be identified, such as the ROS producing NAPDH oxidase RBOHD, the ion channel two pore channel 1 (TPC1), and glutamate receptor-like channels GLR3.3 and GLR3.6. The plant cell wall presents a plant-specific route for possible propagation of signals from cell to cell. However, the degree to which the cell wall limits information exchange between cells via transfer of small molecules through an extracellular route, or whether it provides an environment to facilitate transmission of regulators such as ROS or H+ remains to be determined. Similarly, the role of plasmodesmata as both conduits and gatekeepers for the propagation of rapid cell-to-cell signaling remains a key open question. Regardless of how signals move from cell to cell, they help prepare distant parts of the plant for impending challenges from specific biotic or abiotic stresses.
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Affiliation(s)
- Won-Gyu Choi
- Department of Biochemistry and Molecular Biology, University of Nevada, 1664 North Virginia Street, Reno, NV 89557, USA
- For correspondence ( or )
| | - Gad Miller
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, The Gonda Medical Diagnostic Research Building (204), Room 211, Ramat-Gan 52900, Israel
| | - Ian Wallace
- Department of Biochemistry and Molecular Biology, University of Nevada, 1664 North Virginia Street, Reno, NV 89557, USA
| | - Jeffrey Harper
- Department of Biochemistry and Molecular Biology, University of Nevada, 1664 North Virginia Street, Reno, NV 89557, USA
- For correspondence ( or )
| | - Ron Mittler
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA
| | - Simon Gilroy
- Department of Botany, University of Wisconsin, Birge Hall, 430 Lincoln Drive, Madison, WI 53706, USA
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32
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An JP, Li R, Qu FJ, You CX, Wang XF, Hao YJ. Ectopic expression of an apple cytochrome P450 gene MdCYPM1 negatively regulates plant photomorphogenesis and stress response in Arabidopsis. Biochem Biophys Res Commun 2017; 483:1-9. [PMID: 28073698 DOI: 10.1016/j.bbrc.2017.01.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 11/29/2022]
Abstract
Cytochrome P450s play an important role in plant growth and are involved in multiple stresses response. However, little is known about the functions of cytochrome P450s in apple. Here, a Malus × domestica cytochrome P450 monooxygenase 1 gene, MdCYPM1, was identified and subsequently cloned from apple 'Gala' (Malus × domestica). To verify the functions of MdCYPM1, we generated transgenic Arabidopsis plants expressing the apple MdCYPM1 gene under the control of the Cauliflower mosaic virus 35S promoter. Four transgenic lines (#3, #5, #7 and #8) were selected for further study. The transgenic plants exhibited a series of skotomorphogenesis phenotypes relative to wild-type controls, such as reduction of the chlorophyll, anthocyanins content and hypocotyls elongation. In addition, overexpression of MdCYPM1 influenced auxin transport and flowering time in transgenic Arabidopsis. Furthermore, MdCYPM1 expression was induced by salt and mannitol treatments, and the transgenic plants were negatively regulated by salinity and osmotic stresses during germination. These results suggest that MdCYPM1 plays a vital role in plant growth and development.
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Affiliation(s)
- Jian-Ping An
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Rui Li
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Feng-Jia Qu
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Chun-Xiang You
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Xiao-Fei Wang
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
| | - Yu-Jin Hao
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
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Yadav BS, Lahav T, Reuveni E, Chamovitz DA, Freilich S. Multidimensional patterns of metabolic response in abiotic stress-induced growth of Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2016; 92:689-699. [PMID: 27633976 DOI: 10.1007/s11103-016-0539-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 08/29/2016] [Indexed: 05/11/2023]
Abstract
Contextualization of specific transcriptional responses of Arabidopsis within the stress-tissue-time perspective provides a simplified representation of the cellular transcriptional response pathways to abiotic stress, while reducing the dimensions in gene-oriented response description. Crops resistant to abiotic stresses are a long-term goal of many research programs, thus understanding the progression of stress responses is of great interest. We reanalyzed the AtGenExpress transcription dataset to go beyond gene-level characterization, and to contextualize the discrete information into (1) a process-level signature of stress-specific, time-specific, and tissue-specific responses and (2) identify patterns of response progression across a time axis. To gain a functional perspective, ∼1000 pathways associated with the differentially-expressed genes were characterized across all experiments. We find that the global response of pathways to stress is multi-dimensional and does not obviously cluster according to stress, time or tissue. The early response to abiotic stress typically involves induction of genes involved in transcription, hormone synthesis and signaling modules; a later response typically involves metabolism of amino acids and secondary metabolites. By linking specific primary and secondary response pathways, we outline possible stress-associated routes of response progression. The contextualization of specific processes within stress-tissue-time perspective provides a simplified representation of cellular response while reducing the dimensions in gene-oriented response description. Such simplified representation allows finding stress-specific markers based on process-combinations pointing whether a stress-specific response was invoked as well as provide a reference point for the conductance of comparative inter-plant study of stress response, bypassing the need in detailed orthologous mapping.
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Affiliation(s)
- Brijesh S Yadav
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Lahav
- Newe-Ya'ar Research Center, Institute of Plant Sciences, Agricultural Research Organization, PO Box 1021, 30095, Ramat Yishay, Israel
| | - Eli Reuveni
- Newe-Ya'ar Research Center, Institute of Plant Sciences, Agricultural Research Organization, PO Box 1021, 30095, Ramat Yishay, Israel
| | - Daniel A Chamovitz
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Shiri Freilich
- Newe-Ya'ar Research Center, Institute of Plant Sciences, Agricultural Research Organization, PO Box 1021, 30095, Ramat Yishay, Israel.
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Markiewicz-Potoczny M, Lydall D. Costs, benefits and redundant mechanisms of adaption to chronic low-dose stress in yeast. Cell Cycle 2016; 15:2732-41. [PMID: 27628486 PMCID: PMC5053569 DOI: 10.1080/15384101.2016.1218104] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
All organisms live in changeable, stressful environments. It has been reported that exposure to low-dose stresses or poisons can improve fitness. However, examining the effects of chronic low-dose chemical exposure is challenging. To address this issue we used temperature sensitive mutations affecting the yeast cell division cycle to induce low-dose stress for 40 generation times, or more. We examined cdc13-1 mutants, defective in telomere function, and cdc15-2 mutants, defective in mitotic kinase activity. We found that each stress induced similar adaptive responses. Stress-exposed cells became resistant to higher levels of stress but less fit, in comparison with unstressed cells, in conditions of low stress. The costs and benefits of adaptation to chronic stress were reversible. In the cdc13-1 context we tested the effects of Rad9, a central player in the response to telomere defects, Exo1, a nuclease that degrades defective telomeres, and Msn2 and Msn4, 2 transcription factors that contribute to the environmental stress response. We also observed, as expected, that Rad9 and Exo1 modulated the response of cells to stress. In addition we observed that adaptation to stress could still occur in these contexts, with associated costs and benefits. We conclude that functionally redundant cellular networks control the adaptive responses to low dose chronic stress. Our data suggests that if organisms adapt to low dose stress it is helpful if stress continues or increases but harmful should stress levels reduce.
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Affiliation(s)
- Marta Markiewicz-Potoczny
- a Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Newcastle upon Tyne , UK
| | - David Lydall
- a Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Newcastle upon Tyne , UK
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Ben Daniel BH, Cattan E, Wachtel C, Avrahami D, Glick Y, Malichy A, Gerber D, Miller G. Identification of novel transcriptional regulators of Zat12 using comprehensive yeast one-hybrid screens. PHYSIOLOGIA PLANTARUM 2016; 157:422-441. [PMID: 26923089 DOI: 10.1111/ppl.12439] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/22/2016] [Accepted: 01/28/2016] [Indexed: 06/05/2023]
Abstract
To appropriately acclimate to environmental stresses, plants have to rapidly activate a specific transcriptional program. Yet, the identity and function of many of the transcriptional regulators that mediate early responses to abiotic stress stimuli is still unknown. In this work we employed the promoter of the multi-stress-responsive zinc-finger protein Zat12 in yeast one-hybrid (Y1H) screens to identify early abiotic stress-responsive transcriptional regulators. Analysis of Zat12 promoter fragments fused to luciferase underlined an approximately 200 bp fragment responsive to NaCl and to reactive oxygen species (ROS). Using these segments and others as baits against Y1H control or stress Arabidopsis prey libraries, we identified 15 potential Zat12 transcriptional regulators. Among the prominent proteins identified were known transcription factors including bZIP29 and ANAC91 as well as unknown function proteins such as a homolog of the human USB1, a U6 small nuclear RNA (snRNA) processing protein, and dormancy/auxin-associated family protein 2 (DRM2). Altered expression of Zat12 during high light stress in the knockout mutants further indicated the involvement of these proteins in the regulation of Zat12. Using a state of the art microfluidic approach we showed that AtUSB1 and DRM2 can specifically bind dsDNA and were able to identify the preferred DNA-binding motif of all four proteins. Overall, the proteins identified in this work provide an important start point for charting the earliest signaling network of Zat12 and of other genes required for acclimation to abiotic stresses.
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Affiliation(s)
- Bat-Hen Ben Daniel
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Esther Cattan
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Chaim Wachtel
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Dorit Avrahami
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- The Nanotechnology Institute, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Yair Glick
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- The Nanotechnology Institute, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Asaf Malichy
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- The Nanotechnology Institute, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Doron Gerber
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- The Nanotechnology Institute, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Gad Miller
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
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Willems P, Mhamdi A, Stael S, Storme V, Kerchev P, Noctor G, Gevaert K, Van Breusegem F. The ROS Wheel: Refining ROS Transcriptional Footprints. PLANT PHYSIOLOGY 2016; 171:1720-33. [PMID: 27246095 PMCID: PMC4936575 DOI: 10.1104/pp.16.00420] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 05/30/2016] [Indexed: 05/19/2023]
Abstract
In the last decade, microarray studies have delivered extensive inventories of transcriptome-wide changes in messenger RNA levels provoked by various types of oxidative stress in Arabidopsis (Arabidopsis thaliana). Previous cross-study comparisons indicated how different types of reactive oxygen species (ROS) and their subcellular accumulation sites are able to reshape the transcriptome in specific manners. However, these analyses often employed simplistic statistical frameworks that are not compatible with large-scale analyses. Here, we reanalyzed a total of 79 Affymetrix ATH1 microarray studies of redox homeostasis perturbation experiments. To create hierarchy in such a high number of transcriptomic data sets, all transcriptional profiles were clustered on the overlap extent of their differentially expressed transcripts. Subsequently, meta-analysis determined a single magnitude of differential expression across studies and identified common transcriptional footprints per cluster. The resulting transcriptional footprints revealed the regulation of various metabolic pathways and gene families. The RESPIRATORY BURST OXIDASE HOMOLOG F-mediated respiratory burst had a major impact and was a converging point among several studies. Conversely, the timing of the oxidative stress response was a determining factor in shaping different transcriptome footprints. Our study emphasizes the need to interpret transcriptomic data sets in a systematic context, where initial, specific stress triggers can converge to common, aspecific transcriptional changes. We believe that these refined transcriptional footprints provide a valuable resource for assessing the involvement of ROS in biological processes in plants.
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Affiliation(s)
- Patrick Willems
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Medical Biotechnology Center, VIB, 9000 Ghent, Belgium (P.W., S.S., K.G.);Department of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W., S.S., K.G.);Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (A.M., G.N.); andUnité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (A.M., G.N.)
| | - Amna Mhamdi
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Medical Biotechnology Center, VIB, 9000 Ghent, Belgium (P.W., S.S., K.G.);Department of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W., S.S., K.G.);Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (A.M., G.N.); andUnité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (A.M., G.N.)
| | - Simon Stael
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Medical Biotechnology Center, VIB, 9000 Ghent, Belgium (P.W., S.S., K.G.);Department of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W., S.S., K.G.);Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (A.M., G.N.); andUnité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (A.M., G.N.)
| | - Veronique Storme
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Medical Biotechnology Center, VIB, 9000 Ghent, Belgium (P.W., S.S., K.G.);Department of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W., S.S., K.G.);Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (A.M., G.N.); andUnité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (A.M., G.N.)
| | - Pavel Kerchev
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Medical Biotechnology Center, VIB, 9000 Ghent, Belgium (P.W., S.S., K.G.);Department of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W., S.S., K.G.);Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (A.M., G.N.); andUnité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (A.M., G.N.)
| | - Graham Noctor
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Medical Biotechnology Center, VIB, 9000 Ghent, Belgium (P.W., S.S., K.G.);Department of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W., S.S., K.G.);Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (A.M., G.N.); andUnité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (A.M., G.N.)
| | - Kris Gevaert
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Medical Biotechnology Center, VIB, 9000 Ghent, Belgium (P.W., S.S., K.G.);Department of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W., S.S., K.G.);Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (A.M., G.N.); andUnité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (A.M., G.N.)
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Medical Biotechnology Center, VIB, 9000 Ghent, Belgium (P.W., S.S., K.G.);Department of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W., S.S., K.G.);Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (A.M., G.N.); andUnité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (A.M., G.N.)
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Rabara RC, Tripathi P, Reese RN, Rushton DL, Alexander D, Timko MP, Shen QJ, Rushton PJ. Tobacco drought stress responses reveal new targets for Solanaceae crop improvement. BMC Genomics 2015; 16:484. [PMID: 26123791 PMCID: PMC4485875 DOI: 10.1186/s12864-015-1575-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 04/24/2015] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The Solanaceae are an economically important family of plants that include tobacco (Nicotiana tabacum L.), tomato, and potato. Drought is a major cause of crop losses. RESULTS We have identified major changes in physiology, metabolites, mRNA levels, and promoter activities during the tobacco response to drought. We have classified these as potential components of core responses that may be common to many plant species or responses that may be family/species-specific features of the drought stress response in tobacco or the Solanaceae. In tobacco the largest increase in any metabolite was a striking 70-fold increase in 4-hydroxy-2-oxoglutaric acid (KHG) in roots that appears to be tobacco/Solanaceae specific. KHG is poorly characterized in plants but is broken down to pyruvate and glyoxylate after the E. coli SOS response to facilitate the resumption of respiration. A similar process in tobacco would represent a mechanism to restart respiration upon water availability after drought. At the mRNA level, transcription factor gene induction by drought also showed both core and species/family specific responses. Many Group IX Subgroup 3 AP2/ERF transcription factors in tobacco appear to play roles in nicotine biosynthesis as a response to herbivory, whereas their counterparts in legume species appear to play roles in drought responses. We observed apparent Solanaceae-specific drought induction of several Group IId WRKY genes. One of these, NtWRKY69, showed ABA-independent drought stress-inducible promoter activity that moved into the leaf through the vascular tissue and then eventually into the surrounding leaf cells. CONCLUSIONS We propose components of a core metabolic response to drought stress in plants and also show that some major responses to drought stress at the metabolome and transcriptome levels are family specific. We therefore propose that the observed family-specific changes in metabolism are regulated, at least in part, by family-specific changes in transcription factor activity. We also present a list of potential targets for the improvement of Solanaceae drought responses.
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Affiliation(s)
- Roel C Rabara
- Texas A&M AgriLife Research and Extension Center, Dallas, Texas, 75252, USA.
| | - Prateek Tripathi
- Molecular and Computational Biology Section, Dana & David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA.
| | - R Neil Reese
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA.
| | - Deena L Rushton
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA.
| | | | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, Virginia, 22904, USA.
| | - Qingxi J Shen
- School of Life Sciences, University of Nevada, Las Vegas, 89154, USA.
| | - Paul J Rushton
- Texas A&M AgriLife Research and Extension Center, Dallas, Texas, 75252, USA.
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Fang H, Meng Q, Xu J, Tang H, Tang S, Zhang H, Huang J. Knock-down of stress inducible OsSRFP1 encoding an E3 ubiquitin ligase with transcriptional activation activity confers abiotic stress tolerance through enhancing antioxidant protection in rice. PLANT MOLECULAR BIOLOGY 2015; 87:441-58. [PMID: 25667045 DOI: 10.1007/s11103-015-0294-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 01/23/2015] [Indexed: 05/08/2023]
Abstract
E3 ubiquitin ligases are involved in a variety of physiological processes. This study demonstrated the function of a previously unknown rice RING finger E3 ligase, Oryza sativa Stress-related RING Finger Protein 1 (OsSRFP1) in stress responses in rice. OsSRFP1 was ubiquitously expressed in various rice organs, with the higher expression levels in roots, panicles and culm nodes. The transcript of OsSRFP1 was induced by cold, dehydration, salt, H2O2 and abscisic acid treatments. Interestingly, the OsSRFP1-overexpressing plants were less tolerant to salt, cold and oxidative stresses than wild type plants; while the RNA interference silencing of OsSRFP1 plants were more tolerant than wild type without yield penalty. Compared with the wild type, amounts of free proline and activities of antioxidant enzymes were increased in the RNAi plants but decreased in the overexpression plants under cold stress, which were inversely correlated with the malondialdehyde and hydrogen peroxide (H2O2) levels in the tested lines. Microarray analysis showed that expression of numerous genes involving in ROS homeostasis was altered in the OsSRFP1-overexpressing plants under normal and cold conditions. In vitro ubiquitination assays showed that OsSRFP1 possessed E3 ubiquitin ligase activity and the intact RING domain was essential for the activity. Moreover, OsSRFP1 might function in transcriptional regulation with nuclear localization. Taken together, our results demonstrate that OsSRFP1 may have dual functions in post-translational and transcriptional regulations in modulating abiotic stress responses in rice, at least in part, by negatively regulating antioxidant enzymes-mediated reactive oxygen species removal.
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Affiliation(s)
- Huimin Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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Oelze ML, Muthuramalingam M, Vogel MO, Dietz KJ. The link between transcript regulation and de novo protein synthesis in the retrograde high light acclimation response of Arabidopsis thaliana. BMC Genomics 2014; 15:320. [PMID: 24884362 PMCID: PMC4034770 DOI: 10.1186/1471-2164-15-320] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/24/2014] [Indexed: 11/10/2022] Open
Abstract
Background Efficient light acclimation of photosynthetic cells is a basic and important property of plants. The process of acclimation depends on transformation of retrograde signals in gene expression, transcript accumulation and de novo protein synthesis. While signalling cues, transcriptomes and some involved players have been characterized, an integrated view is only slowly emerging, and information on the translational level is missing. Transfer of low (8 μmol quanta.m-2.s-1) or normal light (80 μmol quanta.m-2.s-1) acclimated 30 d old Arabidopsis thaliana plants to high light (800 μmol quanta.m-2.s-1) triggers retrograde signals. Using this established approach, we sought to link transcriptome data with de novo synthesized proteins by in vivo labelling with 35S methionine and proteome composition. Results De novo synthesized protein and proteome patterns could reliably be matched with newly annotated master gels. Each molecular level could be quantified for a set of 41 proteins. Among the proteins preferentially synthesized in plants transferred to high light were enzymes including carbonic anhydrase, fructose-1,6-bisphosphate aldolase, O-acetyl serine thiol lyase, and chaperones, while low rates upon transfer to high light were measured for e.g. dehydroascorbate reductase, glyceraldehyde-3-phosphate dehydrogenase and CuZn superoxide dismutase, and opposite responses between 10-fold and 100-fold light increment for e.g. glutamine synthetase and phosphoglycerate kinase. Conclusions The results prove the hypothesis that transcript abundance is poorly linked to de novo protein synthesis due to profound regulation at the level of translation. This vertical systems biology approach enables to quantitatively and kinetically link the molecular levels for scrutinizing signal processing and response generation.
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Affiliation(s)
| | | | | | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Faculty of Biology - W5-134, University of Bielefeld, 33501 Bielefeld, Germany.
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