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Qi M, Wang S, Li N, Li L, Zhang Y, Xue J, Wang J, Wu R, Lian N. Genome-wide analysis of TPX2 gene family in Populus trichocarpa and its specific response genes under various abiotic stresses. FRONTIERS IN PLANT SCIENCE 2023; 14:1159181. [PMID: 36993860 PMCID: PMC10040543 DOI: 10.3389/fpls.2023.1159181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 02/22/2023] [Indexed: 06/19/2023]
Abstract
Microtubules are essential for regulating cell morphogenesis, plant growth, and the response of plants to abiotic stresses. TPX2 proteins are the main players determining the spatiotemporally dynamic nature of the MTs. However, how TPX2 members respond to abiotic stresses in poplar remains largely unknown. Herein, 19 TPX2 family members were identified from the poplar genome and analyzed the structural characteristics as well as gene expression patterns. All TPX2 members had the conserved structural characteristics, but exhibited different expression profiles in different tissues, indicating their varying roles during plant growth. Additionally, several light, hormone, and abiotic stress responsive cis-acting regulatory elements were detected on the promoters of PtTPX2 genes. Furthermore, expression analysis in various tissues of Populus trichocarpa showed that the PtTPX2 genes responded differently to heat, drought and salt stress. In summary, these results provide a comprehensive analysis for the TPX2 gene family in poplar and an effective contribution to revealing the mechanisms of PtTPX2 in the regulatory network of abiotic stress.
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Affiliation(s)
- Meng Qi
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shengjie Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Na Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lingfeng Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yue Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jingyi Xue
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jingyi Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Na Lian
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, China
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In silico analysis of key regulatory networks related to microfibril angle in Populus trichocarpa Hook. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01238-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
AbstractDissection of regulatory network that control wood structure is highly challenging in functional genomics. Nevertheless, due to the availability of genomic, transcriptomic and proteomic sequences, a large amount of information is available for use in achieving this goal. MicroRNAs, which compose a class of small non-coding RNA molecules that inhibit protein translation by targeting mRNA cleavage sites and thus regulate a wide variety of developmental and physiological processes in plants, are important parts of this regulatory network. These findings and the availability of sequence information have made it possible to carry out an in silico analysis to predict and annotate miRNAs and their target genes associated with an important factor affecting wood rigidity, microfibril angle (MFA), throughout the Populus trichocarpa Hook. genome. Our computational approach revealed miRNAs and their targets via ESTs, sequences putatively associated with microfibril angle. In total, 250 miRNAs were identified as RNA molecules with roles in the silencing and post-transcriptional regulation of the expression of nine genes. We found SHY2, IAA4 (ATAUX2–11), BZIP60, AP2, MYB15, ABI3, MYB17, LAF1 and MYB28 as important nodes in a network with possible role in MFA determination. Other co-expressed genes putatively involved in this regulatory system were also identified by construction of a co-expression network. The candidate genes from this study may help unravel the regulatory networks putatively linked to microfibril angle.
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Byrt CS, Munns R, Burton RA, Gilliham M, Wege S. Root cell wall solutions for crop plants in saline soils. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 269:47-55. [PMID: 29606216 DOI: 10.1016/j.plantsci.2017.12.012] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/28/2017] [Accepted: 12/27/2017] [Indexed: 05/05/2023]
Abstract
The root growth of most crop plants is inhibited by soil salinity. Roots respond by modulating metabolism, gene expression and protein activity, which results in changes in cell wall composition, transport processes, cell size and shape, and root architecture. Here, we focus on the effects of salt stress on cell wall modifying enzymes, cellulose microfibril orientation and non-cellulosic polysaccharide deposition in root elongation zones, as important determinants of inhibition of root elongation, and highlight cell wall changes linked to tolerance to salt stressed and water limited roots. Salt stress induces changes in the wall composition of specific root cell types, including the increased deposition of lignin and suberin in endodermal and exodermal cells. These changes can benefit the plant by preventing water loss and altering ion transport pathways. We suggest that binding of Na+ ions to cell wall components might influence the passage of Na+ and that Na+ can influence the binding of other ions and hinder the function of pectin during cell growth. Naturally occurring differences in cell wall structure may provide new resources for breeding crops that are more salt tolerant.
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Affiliation(s)
- Caitlin S Byrt
- Plant Transport and Signalling Group, Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia. http://twitter.com/BotanicGeek
| | - Rana Munns
- ARC Centre of Excellence in Plant Energy Biology, and School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Rachel A Burton
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Matthew Gilliham
- Plant Transport and Signalling Group, Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Stefanie Wege
- Plant Transport and Signalling Group, Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
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Liu Y, Visetsouk M, Mynlieff M, Qin H, Lechtreck KF, Yang P. H +- and Na +- elicited rapid changes of the microtubule cytoskeleton in the biflagellated green alga Chlamydomonas. eLife 2017; 6:26002. [PMID: 28875932 PMCID: PMC5779235 DOI: 10.7554/elife.26002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 09/05/2017] [Indexed: 12/27/2022] Open
Abstract
Although microtubules are known for dynamic instability, the dynamicity is considered to be tightly controlled to support a variety of cellular processes. Yet diverse evidence suggests that this is not applicable to Chlamydomonas, a biflagellate fresh water green alga, but intense autofluorescence from photosynthesis pigments has hindered the investigation. By expressing a bright fluorescent reporter protein at the endogenous level, we demonstrate in real time discreet sweeping changes in algal microtubules elicited by rises of intracellular H+ and Na+. These results from this model organism with characteristics of animal and plant cells provide novel explanations regarding how pH may drive cellular processes; how plants may respond to, and perhaps sense stresses; and how organisms with a similar sensitive cytoskeleton may be susceptible to environmental changes.
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Affiliation(s)
- Yi Liu
- Department of Biological Sciences, Marquette University, Milwaukee, United States
| | - Mike Visetsouk
- Department of Biological Sciences, Marquette University, Milwaukee, United States
| | - Michelle Mynlieff
- Department of Biological Sciences, Marquette University, Milwaukee, United States
| | - Hongmin Qin
- Department of Biology, Texas A&M University, College Station, United States
| | - Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athen, United States
| | - Pinfen Yang
- Department of Biological Sciences, Marquette University, Milwaukee, United States
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Stecker KE, Minkoff BB, Sussman MR. Phosphoproteomic Analyses Reveal Early Signaling Events in the Osmotic Stress Response. PLANT PHYSIOLOGY 2014; 165:1171-1187. [PMID: 24808101 PMCID: PMC4081330 DOI: 10.1104/pp.114.238816] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/29/2014] [Indexed: 05/18/2023]
Abstract
Elucidating how plants sense and respond to water loss is important for identifying genetic and chemical interventions that may help sustain crop yields in water-limiting environments. Currently, the molecular mechanisms involved in the initial perception and response to dehydration are not well understood. Modern mass spectrometric methods for quantifying changes in the phosphoproteome provide an opportunity to identify key phosphorylation events involved in this process. Here, we have used both untargeted and targeted isotope-assisted mass spectrometric methods of phosphopeptide quantitation to characterize proteins in Arabidopsis (Arabidopsis thaliana) whose degree of phosphorylation is rapidly altered by hyperosmotic treatment. Thus, protein phosphorylation events responsive to 5 min of 0.3 m mannitol treatment were first identified using 15N metabolic labeling and untargeted mass spectrometry with a high-resolution ion-trap instrument. The results from these discovery experiments were then validated using targeted Selected Reaction Monitoring mass spectrometry with a triple quadrupole. Targeted Selected Reaction Monitoring experiments were conducted with plants treated under nine different environmental perturbations to determine whether the phosphorylation changes were specific for osmosignaling or involved cross talk with other signaling pathways. The results indicate that regulatory proteins such as members of the mitogen-activated protein kinase family are specifically phosphorylated in response to osmotic stress. Proteins involved in 5' messenger RNA decapping and phosphatidylinositol 3,5-bisphosphate synthesis were also identified as targets of dehydration-induced phosphoregulation. The results of these experiments demonstrate the utility of targeted phosphoproteomic analysis in understanding protein regulation networks and provide new insight into cellular processes involved in the osmotic stress response.
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Affiliation(s)
- Kelly E Stecker
- Department of Biochemistry and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
| | - Benjamin B Minkoff
- Department of Biochemistry and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
| | - Michael R Sussman
- Department of Biochemistry and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
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Sasidharan R, Keuskamp DH, Kooke R, Voesenek LACJ, Pierik R. Interactions between auxin, microtubules and XTHs mediate green shade- induced petiole elongation in arabidopsis. PLoS One 2014; 9:e90587. [PMID: 24594664 PMCID: PMC3942468 DOI: 10.1371/journal.pone.0090587] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 02/03/2014] [Indexed: 01/06/2023] Open
Abstract
Plants are highly attuned to translating environmental changes to appropriate modifications in growth. Such phenotypic plasticity is observed in dense vegetations, where shading by neighboring plants, triggers rapid unidirectional shoot growth (shade avoidance), such as petiole elongation, which is partly under the control of auxin. This growth is fuelled by cellular expansion requiring cell-wall modification by proteins such as xyloglucan endotransglucosylase/hydrolases (XTHs). Cortical microtubules (cMTs) are highly dynamic cytoskeletal structures that are also implicated in growth regulation. The objective of this study was to investigate the tripartite interaction between auxin, cMTs and XTHs in shade avoidance. Our results indicate a role for cMTs to control rapid petiole elongation in Arabidopsis during shade avoidance. Genetic and pharmacological perturbation of cMTs obliterated shade-induced growth and led to a reduction in XTH activity as well. Furthermore, the cMT disruption repressed the shade-induced expression of a specific set of XTHs. These XTHs were also regulated by the hormone auxin, an important regulator of plant developmental plasticity and also of several shade avoidance responses. Accordingly, the effect of cMT disruption on the shade enhanced XTH expression could be rescued by auxin application. Based on the results we hypothesize that cMTs can mediate petiole elongation during shade avoidance by regulating the expression of cell wall modifying proteins via control of auxin distribution.
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Affiliation(s)
- Rashmi Sasidharan
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Diederik H Keuskamp
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands; Environmental Sciences, Wageningen University, Wageningen, The Netherlands
| | - Rik Kooke
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands; Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - Laurentius A C J Voesenek
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Ronald Pierik
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
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Yip YY, Yeap YYC, Bogoyevitch MA, Ng DCH. cAMP-dependent protein kinase and c-Jun N-terminal kinase mediate stathmin phosphorylation for the maintenance of interphase microtubules during osmotic stress. J Biol Chem 2013; 289:2157-69. [PMID: 24302736 DOI: 10.1074/jbc.m113.470682] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Dynamic microtubule changes after a cell stress challenge are required for cell survival and adaptation. Stathmin (STMN), a cytoplasmic microtubule-destabilizing phosphoprotein, regulates interphase microtubules during cell stress, but the signaling mechanisms involved are poorly defined. In this study ectopic expression of single alanine-substituted phospho-resistant mutants demonstrated that STMN Ser-38 and Ser-63 phosphorylation were specifically required to maintain interphase microtubules during hyperosmotic stress. STMN was phosphorylated on Ser-38 and Ser-63 in response to hyperosmolarity, heat shock, and arsenite treatment but rapidly dephosphorylated after oxidative stress treatment. Two-dimensional PAGE and Phos-tag gel analysis of stress-stimulated STMN phospho-isoforms revealed rapid STMN Ser-38 phosphorylation followed by subsequent Ser-25 and Ser-63 phosphorylation. Previously, we delineated stress-stimulated JNK targeting of STMN. Here, we identified cAMP-dependent protein kinase (PKA) signaling as responsible for stress-induced STMN Ser-63 phosphorylation. Increased cAMP levels induced by cholera toxin triggered potent STMN Ser-63 phosphorylation. Osmotic stress stimulated an increase in PKA activity and elevated STMN Ser-63 and CREB (cAMP-response element-binding protein) Ser-133 phosphorylation that was substantially attenuated by pretreatment with H-89, a PKA inhibitor. Interestingly, PKA activity and subsequent phosphorylation of STMN were augmented in the absence of JNK activation, indicating JNK and PKA pathway cross-talk during stress regulation of STMN. Taken together our study indicates that JNK- and PKA-mediated STMN Ser-38 and Ser-63 phosphorylation are required to preserve interphase microtubules in response to hyperosmotic stress.
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Affiliation(s)
- Yan Y Yip
- From the Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
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Liu K, Sun J, Yao L, Yuan Y. Transcriptome analysis reveals critical genes and key pathways for early cotton fiber elongation in Ligon lintless-1 mutant. Genomics 2012; 100:42-50. [PMID: 22576057 DOI: 10.1016/j.ygeno.2012.04.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 04/24/2012] [Accepted: 04/26/2012] [Indexed: 12/13/2022]
Abstract
Fiber length is a key determinant of cotton yield and quality. Using a monogenic dominant cotton mutant Ligon lintless-1 with extremely short fibers, we employed microarray technology and quantitative real time PCR to compare transcriptomes of Li(1) and the normal wild-type TM-1, the results showed that only a few genes differentially expressed in 0 days postanthesis (DPA) ovules and 3 DPA fibers, whereas 577 transcripts differentially expressed in 6 DPA fibers. 6 DPA is probably a key phase determining fiber elongation. Gene ontology analyses showed such processes as response to stimulus, signal transduction, and lipid metabolism were readjusted by the mutant gene. Pathway studio analysis indicated that auxin signaling and sugar signaling pathways play major roles in modulation of early fiber elongation. This work provides new insight into the mechanisms of fiber development, and offers novel genes as potential objects for genetic manipulation to achieve improvement of fiber properties.
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Affiliation(s)
- Kang Liu
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
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Bogdanov AA, Zinovkin RA, Zamyatnin AA. RNA editing: breaking the dogma. BIOCHEMISTRY (MOSCOW) 2011; 76:867-8. [DOI: 10.1134/s0006297911080013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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