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Nagle MF, Yuan J, Kaur D, Ma C, Peremyslova E, Jiang Y, Zahl B, Niño de Rivera A, Muchero W, Fuxin L, Strauss SH. GWAS identifies candidate genes controlling adventitious rooting in Populus trichocarpa. HORTICULTURE RESEARCH 2023; 10:uhad125. [PMID: 37560019 PMCID: PMC10407606 DOI: 10.1093/hr/uhad125] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 06/05/2023] [Indexed: 08/11/2023]
Abstract
Adventitious rooting (AR) is critical to the propagation, breeding, and genetic engineering of trees. The capacity for plants to undergo this process is highly heritable and of a polygenic nature; however, the basis of its genetic variation is largely uncharacterized. To identify genetic regulators of AR, we performed a genome-wide association study (GWAS) using 1148 genotypes of Populus trichocarpa. GWASs are often limited by the abilities of researchers to collect precise phenotype data on a high-throughput scale; to help overcome this limitation, we developed a computer vision system to measure an array of traits related to adventitious root development in poplar, including temporal measures of lateral and basal root length and area. GWAS was performed using multiple methods and significance thresholds to handle non-normal phenotype statistics and to gain statistical power. These analyses yielded a total of 277 unique associations, suggesting that genes that control rooting include regulators of hormone signaling, cell division and structure, reactive oxygen species signaling, and other processes with known roles in root development. Numerous genes with uncharacterized functions and/or cryptic roles were also identified. These candidates provide targets for functional analysis, including physiological and epistatic analyses, to better characterize the complex polygenic regulation of AR.
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Affiliation(s)
- Michael F Nagle
- Department of Forest Ecosystems and Society, Oregon State University, 3180 SW Jefferson Way, Corvallis, OR, 97331, United States
| | - Jialin Yuan
- Department of Electrical Engineering and Computer Science, Oregon State University, 110 SW Park Terrace, Corvallis, OR, 97331, United States
| | - Damanpreet Kaur
- Department of Electrical Engineering and Computer Science, Oregon State University, 110 SW Park Terrace, Corvallis, OR, 97331, United States
| | - Cathleen Ma
- Department of Forest Ecosystems and Society, Oregon State University, 3180 SW Jefferson Way, Corvallis, OR, 97331, United States
| | - Ekaterina Peremyslova
- Department of Forest Ecosystems and Society, Oregon State University, 3180 SW Jefferson Way, Corvallis, OR, 97331, United States
| | - Yuan Jiang
- Statistics Department, Oregon State University, 103 SW Memorial Place, Corvallis, OR, 97331, United States
| | - Bahiya Zahl
- Department of Forest Ecosystems and Society, Oregon State University, 3180 SW Jefferson Way, Corvallis, OR, 97331, United States
| | - Alexa Niño de Rivera
- Department of Forest Ecosystems and Society, Oregon State University, 3180 SW Jefferson Way, Corvallis, OR, 97331, United States
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, United States
- Bredesen Center for Interdisciplinary Research, University of Tennessee, 821 Volunteer Blvd., Knoxville, TN, 37996, United States
| | - Li Fuxin
- Department of Electrical Engineering and Computer Science, Oregon State University, 110 SW Park Terrace, Corvallis, OR, 97331, United States
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, 3180 SW Jefferson Way, Corvallis, OR, 97331, United States
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Sousa-Baena MS, Onyenedum JG. Bouncing back stronger: Diversity, structure, and molecular regulation of gelatinous fiber development. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102198. [PMID: 35286861 DOI: 10.1016/j.pbi.2022.102198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 01/18/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Gelatinous fibers (G-fibers) are specialized contractile cells found in a diversity of vascular plant tissues, where they provide mechanical support and/or facilitate plant mobility. G-fibers are distinct from typical fibers by the presence of an innermost thickened G-layer, comprised mainly of axially oriented cellulose microfibrils. Despite the disparate developmental origins-tension wood fibers from the vascular cambium or primary phloem fibers from the procambium-G-fiber development, composition, and molecular signatures are remarkably similar; however, important distinctions do exist. Here, we synthesize current knowledge of the phylogenetic diversity, compositional makeup, and the molecular profiles that characterize G-fiber development and highlight open questions for future investigation.
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Affiliation(s)
- Mariane S Sousa-Baena
- School of Integrative Plant Sciences, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, USA.
| | - Joyce G Onyenedum
- School of Integrative Plant Sciences, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, USA
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3
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Differential Expression of Arabinogalactan in Response to Inclination in Stem of Pinus radiata Seedlings. PLANTS 2022; 11:plants11091190. [PMID: 35567191 PMCID: PMC9104628 DOI: 10.3390/plants11091190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/23/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022]
Abstract
Arabinogalactan proteins (AGPs) are members of a family of proteins that play important roles in cell wall dynamics. AGPs from inclined pines were determined using JIM7, LM2, and LM6 antibodies, showing a higher concentration in one side of the stem. The accumulation of AGPs in xylem and cell wall tissues is enhanced in response to loss of tree stem verticality. The differential gene expression of AGPs indicates that these proteins could be involved in the early response to inclination and also trigger signals such as lignin accumulation, as well as thicken cell wall and lamella media to restore stem vertical growth. A subfamily member of AGPs, which is Fasciclin-like has been described in angiosperm species as inducing tension wood and in some gymnosperms. A search for gene sequences of this subfamily was performed on an RNA-seq library, where 12 sequences were identified containing one or two fasciclin I domains (FAS), named PrFLA1 to PrFLA12. Four of these sequences were phylogenetically classified in group A, where PrFLA1 and PrFLA4 are differentially expressed in tilted pine trees.
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Ma Y, MacMillan CP, de Vries L, Mansfield SD, Hao P, Ratcliffe J, Bacic A, Johnson KL. FLA11 and FLA12 glycoproteins fine-tune stem secondary wall properties in response to mechanical stresses. THE NEW PHYTOLOGIST 2022; 233:1750-1767. [PMID: 34862967 PMCID: PMC9302641 DOI: 10.1111/nph.17898] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/20/2021] [Indexed: 05/19/2023]
Abstract
Secondary cell walls (SCWs) in stem xylem vessel and fibre cells enable plants to withstand the enormous compressive forces associated with upright growth. It remains unclear if xylem vessel and fibre cells can directly sense mechanical stimuli and modify their SCW during development. We provide evidence that Arabidopsis SCW-specific Fasciclin-Like Arabinogalactan-proteins 11 (FLA11) and 12 (FLA12) are possible cell surface sensors regulating SCW development in response to mechanical stimuli. Plants overexpressing FLA11 (OE-FLA11) showed earlier SCW development compared to the wild-type (WT) and altered SCW properties that phenocopy WT plants under compression stress. By contrast, OE-FLA12 stems showed higher cellulose content compared to WT plants, similar to plants experiencing tensile stress. fla11, OE-FLA11, fla12, and OE-FLA12 plants showed altered SCW responses to mechanical stress compared to the WT. Quantitative polymerase chain reaction (qPCR) and RNA-seq analysis revealed the up-regulation of genes and pathways involved in stress responses and SCW synthesis and regulation. Analysis of OE-FLA11 nst1 nst3 plants suggests that FLA11 regulation of SCWs is reliant on classical transcriptional networks. Our data support the involvement of FLA11 and FLA12 in SCW sensing complexes to fine-tune both the initiation of SCW development and the balance of lignin and cellulose synthesis/deposition in SCWs during development and in response to mechanical stimuli.
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Affiliation(s)
- Yingxuan Ma
- School of BioSciencesUniversity of MelbourneParkvilleVic.3052Australia
- Department of Animal, Plant and Soil ScienceLa Trobe Institute for Agriculture & FoodLa Trobe UniversityAgriBio BuildingBundooraVic.3086Australia
| | - Colleen P. MacMillan
- Agriculture and FoodCSIROCSIRO Black Mountain Science and Innovation ParkCanberraACT2601Australia
| | - Lisanne de Vries
- Department of Wood ScienceUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
| | - Shawn D. Mansfield
- Department of Wood ScienceUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
| | - Pengfei Hao
- Department of Animal, Plant and Soil ScienceLa Trobe Institute for Agriculture & FoodLa Trobe UniversityAgriBio BuildingBundooraVic.3086Australia
| | - Julian Ratcliffe
- Department of Animal, Plant and Soil ScienceLa Trobe Institute for Agriculture & FoodLa Trobe UniversityAgriBio BuildingBundooraVic.3086Australia
| | - Antony Bacic
- Department of Animal, Plant and Soil ScienceLa Trobe Institute for Agriculture & FoodLa Trobe UniversityAgriBio BuildingBundooraVic.3086Australia
- College of Forestry and BiotechnologySino‐Australia Plant Cell Wall Research CentreZhejiang Agriculture and Forestry UniversityLin'anHangzhou311300China
| | - Kim L. Johnson
- Department of Animal, Plant and Soil ScienceLa Trobe Institute for Agriculture & FoodLa Trobe UniversityAgriBio BuildingBundooraVic.3086Australia
- College of Forestry and BiotechnologySino‐Australia Plant Cell Wall Research CentreZhejiang Agriculture and Forestry UniversityLin'anHangzhou311300China
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Xiao Y, Ling J, Yi F, Ma W, Lu N, Zhu T, Wang J, Zhao K, Yun H. Transcriptomic, Proteomic, and Metabolic Profiles of Catalpa bungei Tension Wood Reveal New Insight Into Lignin Biosynthesis Involving Transcription Factor Regulation. FRONTIERS IN PLANT SCIENCE 2021; 12:704262. [PMID: 34868103 PMCID: PMC8634757 DOI: 10.3389/fpls.2021.704262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Lignin is a complex polymer in plant cell walls whose proportion is second only to that of cellulose and plays an important role in the mechanical properties of wood and stress resistance of plants. Here, we induced tension wood (TW) formation in Catalpa bungei by artificial bending and analyzed the lignin metabolism of the TW. LC-MS analysis showed that a significantly higher content of coniferyl aldehyde was observed in the TW cell wall than in the opposite wood (OW) and normal wood (NW) cell walls. TW had significantly lower contents of coniferyl alcohol than OW and NW. Raman spectroscopy results indicated that TW had lower total lignin than OW and NW. The transcription and translation levels of most of the differentially expressed genes (DEGs) involved in lignin monomer biosynthesis indicated upregulation in TW/OW and TW/NW. We found no significant difference in the transcription levels of three collision gases (CADs) between TW and OW or between NW, but their translation levels were significantly downregulated in TW, suggesting post-transcriptional control for CAD. We predicted and analyzed transcription factors that could target DEGs involved in lignin monomer biosynthesis in TW. Based on the analysis of the relationships of targeting and coexpression, we found that NAC (evm.model.group1.695) could potentially target 4CLs and CCoAOMT, that HD-Zip (evm.model.group7.1157) had potential targeting relationships with CCoAOMT, F5H, and CCR, and that their expression levels were significantly positive. It is speculated that the upregulation of NAC and HD-ZIP transcription factors activates the expression of downstream target genes, which leads to a significant increase in coniferyl aldehyde in TW. However, the decrease in total lignin in TW may be caused by the significant downregulation of CAD translation and the significant decrease in precursors (coniferyl alcohol). Whether the expression of CAD genes is regulated by post-transcriptional control and affects TW lignin metabolism needs further study.
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Affiliation(s)
- Yao Xiao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Juanjuan Ling
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Fei Yi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Tianqing Zhu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Kun Zhao
- Luoyang Academy of Agriculture and Forestry Sciences, Luoyang, China
| | - Huiling Yun
- Xiaolongshan Research Institute of Forest Science and Technology, Tianshui, China
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6
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Liu B, Liu J, Yu J, Wang Z, Sun Y, Li S, Lin YCJ, Chiang VL, Li W, Wang JP. Transcriptional reprogramming of xylem cell wall biosynthesis in tension wood. PLANT PHYSIOLOGY 2021; 186:250-269. [PMID: 33793955 PMCID: PMC8154086 DOI: 10.1093/plphys/kiab038] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/04/2021] [Indexed: 05/02/2023]
Abstract
Tension wood (TW) is a specialized xylem tissue developed under mechanical/tension stress in angiosperm trees. TW development involves transregulation of secondary cell wall genes, which leads to altered wood properties for stress adaptation. We induced TW in the stems of black cottonwood (Populus trichocarpa, Nisqually-1) and identified two significantly repressed transcription factor (TF) genes: class B3 heat-shock TF (HSFB3-1) and MYB092. Transcriptomic analysis and chromatin immunoprecipitation (ChIP) were used to identify direct TF-DNA interactions in P. trichocarpa xylem protoplasts overexpressing the TFs. This analysis established a transcriptional regulatory network in which PtrHSFB3-1 and PtrMYB092 directly activate 8 and 11 monolignol genes, respectively. The TF-DNA interactions were verified for their specificity and transactivator roles in 35 independent CRISPR-based biallelic mutants and overexpression transgenic lines of PtrHSFB3-1 and PtrMYB092 in P. trichocarpa. The gene-edited trees (mimicking the repressed PtrHSFB3-1 and PtrMYB092 under tension stress) have stem wood composition resembling that of TW during normal growth and under tension stress (i.e., low lignin and high cellulose), whereas the overexpressors showed an opposite effect (high lignin and low cellulose). Individual overexpression of the TFs impeded lignin reduction under tension stress and restored high levels of lignin biosynthesis in the TW. This study offers biological insights to further uncover how metabolism, growth, and stress adaptation are coordinately regulated in trees.
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Affiliation(s)
- Baoguang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Forestry, Beihua University, Jilin 132013, China
| | - Juan Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jing Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Zhifeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Ying-Chung Jimmy Lin
- Department of Life Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
- Author for communication:
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Allelign Ashagre H, Zaltzman D, Idan-Molakandov A, Romano H, Tzfadia O, Harpaz-Saad S. FASCICLIN-LIKE 18 Is a New Player Regulating Root Elongation in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:645286. [PMID: 33897736 PMCID: PMC8058476 DOI: 10.3389/fpls.2021.645286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/19/2021] [Indexed: 05/26/2023]
Abstract
The plasticity of root development represents a key trait that enables plants to adapt to diverse environmental cues. The pattern of cell wall deposition, alongside other parameters, affects the extent, and direction of root growth. In this study, we report that FASCICLIN-LIKE ARABINOGALACTAN PROTEIN 18 (FLA18) plays a role during root elongation in Arabidopsis thaliana. Using root-specific co-expression analysis, we identified FLA18 to be co-expressed with a sub-set of genes required for root elongation. FLA18 encodes for a putative extra-cellular arabinogalactan protein from the FLA-gene family. Two independent T-DNA insertion lines, named fla18-1 and fla18-2, display short and swollen lateral roots (LRs) when grown on sensitizing condition of high-sucrose containing medium. Unlike fla4/salt overly sensitive 5 (sos5), previously shown to display short and swollen primary root (PR) and LRs under these conditions, the PR of the fla18 mutants is slightly longer compared to the wild-type. Overexpression of the FLA18 CDS complemented the fla18 root phenotype. Genetic interaction between either of the fla18 alleles and sos5 reveals a more severe perturbation of anisotropic growth in both PR and LRs, as compared to the single mutants and the wild-type under restrictive conditions of high sucrose or high-salt containing medium. Additionally, under salt-stress conditions, fla18sos5 had a small, chlorotic shoot phenotype, that was not observed in any of the single mutants or the wild type. As previously shown for sos5, the fla18-1 and fla18-1sos5 root-elongation phenotype is suppressed by abscisic acid (ABA) and display hypersensitivity to the ABA synthesis inhibitor, Fluridon. Last, similar to other cell wall mutants, fla18 root elongation is hypersensitive to the cellulose synthase inhibitor, Isoxaben. Altogether, the presented data assign a new role for FLA18 in the regulation of root elongation. Future studies of the unique vs. redundant roles of FLA proteins during root elongation is anticipated to shed a new light on the regulation of root architecture during plant adaptation to different growth conditions.
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Affiliation(s)
- Hewot Allelign Ashagre
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Zaltzman
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anat Idan-Molakandov
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hila Romano
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Oren Tzfadia
- Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Institute for Tropical Medicine, Antwerp, Belgium
| | - Smadar Harpaz-Saad
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Jerusalem, Israel
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Petrova N, Nazipova A, Gorshkov O, Mokshina N, Patova O, Gorshkova T. Gene Expression Patterns for Proteins With Lectin Domains in Flax Stem Tissues Are Related to Deposition of Distinct Cell Wall Types. FRONTIERS IN PLANT SCIENCE 2021; 12:634594. [PMID: 33995436 PMCID: PMC8121149 DOI: 10.3389/fpls.2021.634594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/16/2021] [Indexed: 05/10/2023]
Abstract
The genomes of higher plants encode a variety of proteins with lectin domains that are able to specifically recognize certain carbohydrates. Plants are enriched in a variety of potentially complementary glycans, many of which are located in the cell wall. We performed a genome-wide search for flax proteins with lectin domains and compared the expression of the encoding genes in different stem tissues that have distinct cell wall types with different sets of major polysaccharides. Over 400 genes encoding proteins with lectin domains that belong to different families were revealed in the flax genome; three quarters of these genes were expressed in stem tissues. Hierarchical clustering of the data for all expressed lectins grouped the analyzed samples according to their characteristic cell wall type. Most lectins differentially expressed in tissues with primary, secondary, and tertiary cell walls were predicted to localize at the plasma membrane or cell wall. These lectins were from different families and had various architectural types. Three out of four flax genes for proteins with jacalin-like domains were highly upregulated in bast fibers at the stage of tertiary cell wall deposition. The dynamic changes in transcript level of many genes for lectins from various families were detected in stem tissue over the course of gravitropic response induced by plant gravistimulation. The data obtained in this study indicate a large number of lectin-mediated events in plants and provide insight into the proteins that take part in tissue specialization and reaction to abiotic stress.
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Affiliation(s)
- Natalia Petrova
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - Alsu Nazipova
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - Oleg Gorshkov
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - Natalia Mokshina
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - Olga Patova
- Institute of Physiology, FRC Komi Science Centre of Ural Branch of Russian Academy of Sciences, Syktyvkar, Russia
| | - Tatyana Gorshkova
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
- *Correspondence: Tatyana Gorshkova,
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Liu E, MacMillan CP, Shafee T, Ma Y, Ratcliffe J, van de Meene A, Bacic A, Humphries J, Johnson KL. Fasciclin-Like Arabinogalactan-Protein 16 (FLA16) Is Required for Stem Development in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:615392. [PMID: 33362841 PMCID: PMC7758453 DOI: 10.3389/fpls.2020.615392] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/23/2020] [Indexed: 05/19/2023]
Abstract
The predominant Fascilin 1 (FAS1)-containing proteins in plants belong to the Fasciclin-Like Arabinogalactan-protein (FLA) family of extracellular glycoproteins. In addition to FAS1 domains, these multi-domain FLA proteins contain glycomotif regions predicted to direct addition of large arabinogalactan (AG) glycans and many contain signal sequences for addition of a glycosylphosphatidylinositol (GPI)-anchor to tether them to the plasma membrane. FLAs are proposed to play both structural and signaling functions by forming a range of interactions in the plant extracellular matrix, similar to FAS1-containing proteins in animals. FLA group B members contain two FAS1 domains and are not predicted to be GPI-anchored. None of the group B members have been functionally characterized or their sub-cellular location resolved, limiting understanding of their function. We investigated the group B FLA16 in Arabidopsis that is predominantly expressed in inflorescence tissues. FLA16 is the most highly expressed FLA in the stem after Group A members FLA11 and FLA12 that are stem specific. A FLA16-YFP fusion protein driven by the endogenous putative FLA16 promoter in wild type background showed expression in cells with secondary cell walls, and FLA16 displayed characteristics of cell wall glycoproteins with moderate glycosylation. Investigation of a fla16 mutant showed loss of FLA16 leads to reduced stem length and altered biomechanical properties, likely as a result of reduced levels of cellulose. Immuno-labeling indicated support for FLA16 location to the plasma-membrane and (apoplastic) cell wall of interfascicular stem fiber cells. Together these results indicate FLA16, a two-FAS1 domain FLAs, plays a role in plant secondary cell wall synthesis and function.
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Affiliation(s)
- Edgar Liu
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Colleen P. MacMillan
- CSIRO, Agriculture and Food, CSIRO Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Thomas Shafee
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Yingxuan Ma
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Julian Ratcliffe
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | | | - Antony Bacic
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
| | - John Humphries
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Kim L. Johnson
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
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10
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Xiao Y, Yi F, Ling J, Yang G, Lu N, Jia Z, Wang J, Zhao K, Wang J, Ma W. Genome-wide analysis of lncRNA and mRNA expression and endogenous hormone regulation during tension wood formation in Catalpa bungei. BMC Genomics 2020; 21:609. [PMID: 32891118 PMCID: PMC7487903 DOI: 10.1186/s12864-020-07044-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/01/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Phytohormones are the key factors regulating vascular development in plants, and they are also involved in tension wood (TW) formation. Although the theory of hormone distribution in TW formation is widely supported, the effects of endogenous hormones on TW formation have not yet been assessed. In this study, TW formation was induced in Catalpa bungei by artificial bending. The phytohormone content of TW, opposite wood (OW) and normal wood (NW) was determined using liquid chromatography-mass spectrometry (LC-MS), and transcriptome sequencing was performed. The hormone content and related gene expression data were comprehensively analyzed. RESULTS The results of analyses of the plant hormone contents indicated significantly higher levels of cis-zeatin (cZ), indoleacetic acid (IAA) and abscisic acid (ABA) in TW than in OW. Genes involved in the IAA and ABA synthesis pathways, such as ALDH (evm. MODEL group5.1511) and UGT (evm. MODEL scaffold36.20), were significantly upregulated in TW. and the expression levels of ARF (evm. MODEL group5.1332), A-ARR (evm. MODEL group0.1600), and TCH4 (evm. MODEL group2.745), which participate in IAA, cZ and Brassinolide (BR) signal transduction, were significantly increased in TW. In particular, ARF expression may be regulated by long noncoding RNAs (lncRNAs) and the HD-ZIP transcription factor ATHB-15. CONCLUSIONS We constructed a multiple hormone-mediated network of C. bungei TW formation based on hormone levels and transcriptional expression profiles were identified during TW formation.
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Affiliation(s)
- Yao Xiao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Fei Yi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Juanjuan Ling
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Guijuan Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Na Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Zirui Jia
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Junchen Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Kun Zhao
- Luoyang Academy of Agriculture and Forestry Science, Luoyang, 471002, Henan Province, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China.
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11
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Xiao Y, Yi F, Ling J, Wang Z, Zhao K, Lu N, Qu G, Kong L, Ma W, Wang J. Transcriptomics and Proteomics Reveal the Cellulose and Pectin Metabolic Processes in the Tension Wood (Non-G-Layer) of Catalpa bungei. Int J Mol Sci 2020; 21:E1686. [PMID: 32121503 PMCID: PMC7084593 DOI: 10.3390/ijms21051686] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/23/2022] Open
Abstract
: Catalpa bungei is an economically important tree with high-quality wood and highly valuable to the study of wood formation. In this work, the xylem microstructure of C. bungei tension wood (TW) was observed, and we performed transcriptomics, proteomics and Raman spectroscopy of TW, opposite wood (OW) and normal wood (NW). The results showed that there was no obvious gelatinous layer (G-layer) in the TW of C. bungei and that the secondary wall deposition in the TW was reduced compared with that in the OW and NW. We found that most of the differentially expressed mRNAs and proteins were involved in carbohydrate polysaccharide synthesis. Raman spectroscopy results indicated that the cellulose and pectin content and pectin methylation in the TW were lower than those in the OW and NW, and many genes and proteins involved in the metabolic pathways of cellulose and pectin, such as galacturonosyltransferase (GAUT), polygalacturonase (PG), endoglucanase (CLE) and β-glucosidase (BGLU) genes, were significantly upregulated in TW. In addition, we found that the MYB2 transcription factor may regulate the pectin degradation genes PG1 and PG3, and ARF, ERF, SBP and MYB1 may be the key transcription factors regulating the synthesis and decomposition of cellulose. In contrast to previous studies on TW with a G-layer, our results revealed a change in metabolism in TW without a G-layer, and we inferred that the change in the pectin type, esterification and cellulose characteristics in the TW of C. bungei may contribute to high tensile stress. These results will enrich the understanding of the mechanism of TW formation.
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Affiliation(s)
- Yao Xiao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Y.X.); (F.Y.); (J.L.); (Z.W.); (N.L.); (W.M.)
| | - Fei Yi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Y.X.); (F.Y.); (J.L.); (Z.W.); (N.L.); (W.M.)
| | - Juanjuan Ling
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Y.X.); (F.Y.); (J.L.); (Z.W.); (N.L.); (W.M.)
| | - Zhi Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Y.X.); (F.Y.); (J.L.); (Z.W.); (N.L.); (W.M.)
| | - Kun Zhao
- Luoyang Academy of Agriculture and Forestry Science, Luoyang 471002, China;
| | - Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Y.X.); (F.Y.); (J.L.); (Z.W.); (N.L.); (W.M.)
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China;
| | - Lisheng Kong
- Department of Biology, Centre for Forest Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P5C2, Canada;
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Y.X.); (F.Y.); (J.L.); (Z.W.); (N.L.); (W.M.)
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Y.X.); (F.Y.); (J.L.); (Z.W.); (N.L.); (W.M.)
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12
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Tobias LM, Spokevicius AV, McFarlane HE, Bossinger G. The Cytoskeleton and Its Role in Determining Cellulose Microfibril Angle in Secondary Cell Walls of Woody Tree Species. PLANTS (BASEL, SWITZERLAND) 2020; 9:E90. [PMID: 31936868 PMCID: PMC7020502 DOI: 10.3390/plants9010090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 12/28/2022]
Abstract
Recent advances in our understanding of the molecular control of secondary cell wall (SCW) formation have shed light on molecular mechanisms that underpin domestication traits related to wood formation. One such trait is the cellulose microfibril angle (MFA), an important wood quality determinant that varies along tree developmental phases and in response to gravitational stimulus. The cytoskeleton, mainly composed of microtubules and actin filaments, collectively contribute to plant growth and development by participating in several cellular processes, including cellulose deposition. Studies in Arabidopsis have significantly aided our understanding of the roles of microtubules in xylem cell development during which correct SCW deposition and patterning are essential to provide structural support and allow for water transport. In contrast, studies relating to SCW formation in xylary elements performed in woody trees remain elusive. In combination, the data reviewed here suggest that the cytoskeleton plays important roles in determining the exact sites of cellulose deposition, overall SCW patterning and more specifically, the alignment and orientation of cellulose microfibrils. By relating the reviewed evidence to the process of wood formation, we present a model of microtubule participation in determining MFA in woody trees forming reaction wood (RW).
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Affiliation(s)
- Larissa Machado Tobias
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria 3363, Australia; (A.V.S.); (G.B.)
| | - Antanas V. Spokevicius
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria 3363, Australia; (A.V.S.); (G.B.)
| | - Heather E. McFarlane
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Gerd Bossinger
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria 3363, Australia; (A.V.S.); (G.B.)
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13
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Molecular Changes Concomitant with Vascular System Development in Mature Galls Induced by Root-Knot Nematodes in the Model Tree Host Populus tremula × P. alba. Int J Mol Sci 2020; 21:ijms21020406. [PMID: 31936440 PMCID: PMC7013992 DOI: 10.3390/ijms21020406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 12/22/2022] Open
Abstract
One of the most striking features occurring in the root-knot nematode Meloidogyne incognita induced galls is the reorganization of the vascular tissues. During the interaction of the model tree species Populus and M. incognita, a pronounced xylem proliferation was previously described in mature galls. To better characterise changes in expression of genes possibly involved in the induction and the formation of the de novo developed vascular tissues occurring in poplar galls, a comparative transcript profiling of 21-day-old galls versus uninfected root of poplar was performed. Genes coding for transcription factors associated with procambium maintenance and vascular differentiation were shown to be differentially regulated, together with genes partaking in phytohormones biosynthesis and signalling. Specific signatures of transcripts associated to primary cell wall biosynthesis and remodelling, as well as secondary cell wall formation (cellulose, xylan and lignin) were revealed in the galls. Ultimately, we show that molecules derived from the monolignol and salicylic acid pathways and related to secondary cell wall deposition accumulate in mature galls.
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14
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Costa M, Pereira AM, Pinto SC, Silva J, Pereira LG, Coimbra S. In silico and expression analyses of fasciclin-like arabinogalactan proteins reveal functional conservation during embryo and seed development. PLANT REPRODUCTION 2019; 32:353-370. [PMID: 31501923 PMCID: PMC6820600 DOI: 10.1007/s00497-019-00376-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 08/29/2019] [Indexed: 05/31/2023]
Abstract
KEY MESSAGE The fasciclin-like arabinogalactan proteins organization into four groups is conserved and may be related to specific roles in developmental processes across angiosperms. Fasciclin-like arabinogalactan proteins (FLAs) are a subclass of arabinogalactan proteins (AGPs), which contain fasciclin-like domains in addition to typical AGP domains. FLAs are present across all embryophytes, and despite their low overall sequence similarity, conserved regions that define the fasciclin functional domain (FAS) have been identified, suggesting that the cell adhesion property is also conserved. FLAs in Arabidopsis have been organized into four subgroups according to the number and distribution of functional domains. Recent studies associated FLAs with cell wall-related processes where domain organization seemed to be related to functional roles. In Arabidopsis, FLAs containing a single FAS domain were found to be important for the integrity and elasticity of the plant cell wall matrix, and FLAs with two FAS domains and two AGP domains were found to be involved in maintaining proper cell expansion under salt stress conditions. The main purpose of the present work was to elucidate the expression pattern of selected FLA genes during embryo and seed development using RT-qPCR. AtFLA8 and AtFLA10, two Arabidopsis genes that stood out in previous microarray studies of embryo development, were further examined using promoter-driven gene reporter analyses. We also studied the expression of cork oak FLA genes and found that their expression partially parallels the expression patterns of the putative AtFLA orthologs. We propose that the functional organization of FLAs is conserved and may be related to fundamental aspects of embryogenesis and seed development across angiosperms. Phylogenetic studies were performed, and we show that the same basic four-subgroup organization described for Arabidopsis FLA gene classification is valid for most Arabidopsis FLA orthologs of several plant species, namely poplar, corn and cork oak.
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Affiliation(s)
- Mário Costa
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Ana Marta Pereira
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Milan, Italy
| | - Sara Cristina Pinto
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Jessy Silva
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Luís Gustavo Pereira
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- GreenUPorto Sustainable Agrifood Production Research Centre, Porto, Portugal
| | - Sílvia Coimbra
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal.
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15
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Rey MD, Castillejo MÁ, Sánchez-Lucas R, Guerrero-Sanchez VM, López-Hidalgo C, Romero-Rodríguez C, Valero-Galván J, Sghaier-Hammami B, Simova-Stoilova L, Echevarría-Zomeño S, Jorge I, Gómez-Gálvez I, Papa ME, Carvalho K, Rodríguez de Francisco LE, Maldonado-Alconada AM, Valledor L, Jorrín-Novo JV. Proteomics, Holm Oak ( Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other? Int J Mol Sci 2019; 20:ijms20030692. [PMID: 30736277 PMCID: PMC6386906 DOI: 10.3390/ijms20030692] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 02/07/2023] Open
Abstract
Proteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as Quercus, Pines, Poplars, and Eucalyptus. This review assesses the potential and limitations of the proteomics approaches and is focused on Quercus ilex as a model species and other forest tree species. Proteomics has been used with Q. ilex since 2003 with the main aim of examining natural variability, developmental processes, and responses to biotic and abiotic stresses as in other species of the genus Quercus or Pinus. As with the progress in techniques in proteomics in other plant species, the research in Q. ilex moved from 2-DE based strategy to the latest gel-free shotgun workflows. Experimental design, protein extraction, mass spectrometric analysis, confidence levels of qualitative and quantitative proteomics data, and their interpretation are a true challenge with relation to forest tree species due to their extreme orphan and recalcitrant (non-orthodox) nature. Implementing a systems biology approach, it is time to validate proteomics data using complementary techniques and integrate it with the -omics and classical approaches. The full potential of the protein field in plant research is quite far from being entirely exploited. However, despite the methodological limitations present in proteomics, there is no doubt that this discipline has contributed to deeper knowledge of plant biology and, currently, is increasingly employed for translational purposes.
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Affiliation(s)
- María-Dolores Rey
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - María Ángeles Castillejo
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Rosa Sánchez-Lucas
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Victor M Guerrero-Sanchez
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Cristina López-Hidalgo
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Cristina Romero-Rodríguez
- Departamento de Fitoquímica, Dirección de Investigación de la Facultad de Ciencias Químicas de la Universidad Nacional de Asunción, Asunción 1001-1925, Paraguay.
| | - José Valero-Galván
- Department of Chemical and Biological Science, Biomedicine Science Institute, Autonomous University of Ciudad Juárez, Anillo Envolvente del Pronaf y Estocolmo s/n, Ciudad Juarez 32310, Mexico.
| | - Besma Sghaier-Hammami
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Lyudmila Simova-Stoilova
- Plant Molecular Biology Department, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl 21, 1113 Sofia, Bulgaria.
| | - Sira Echevarría-Zomeño
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Inmaculada Jorge
- Department of Vascular Biology and Inflammation (BVI), Spanish National Centre for Cardiovascular Research, Melchor Fernández Almagro 3, 28029 Madrid, Spain.
| | - Isabel Gómez-Gálvez
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - María Eugenia Papa
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Kamilla Carvalho
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | | | - Ana María Maldonado-Alconada
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Luis Valledor
- Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, Santiago Gascón Building, 2nd Floor (Office 2.9), 33006 Oviedo, Spain.
| | - Jesús V Jorrín-Novo
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
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16
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Seyfferth C, Wessels B, Jokipii-Lukkari S, Sundberg B, Delhomme N, Felten J, Tuominen H. Ethylene-Related Gene Expression Networks in Wood Formation. FRONTIERS IN PLANT SCIENCE 2018; 9:272. [PMID: 29593753 PMCID: PMC5861219 DOI: 10.3389/fpls.2018.00272] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/16/2018] [Indexed: 05/27/2023]
Abstract
Thickening of tree stems is the result of secondary growth, accomplished by the meristematic activity of the vascular cambium. Secondary growth of the stem entails developmental cascades resulting in the formation of secondary phloem outwards and secondary xylem (i.e., wood) inwards of the stem. Signaling and transcriptional reprogramming by the phytohormone ethylene modifies cambial growth and cell differentiation, but the molecular link between ethylene and secondary growth remains unknown. We addressed this shortcoming by analyzing expression profiles and co-expression networks of ethylene pathway genes using the AspWood transcriptome database which covers all stages of secondary growth in aspen (Populus tremula) stems. ACC synthase expression suggests that the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) is synthesized during xylem expansion and xylem cell maturation. Ethylene-mediated transcriptional reprogramming occurs during all stages of secondary growth, as deduced from AspWood expression profiles of ethylene-responsive genes. A network centrality analysis of the AspWood dataset identified EIN3D and 11 ERFs as hubs. No overlap was found between the co-expressed genes of the EIN3 and ERF hubs, suggesting target diversification and hence independent roles for these transcription factor families during normal wood formation. The EIN3D hub was part of a large co-expression gene module, which contained 16 transcription factors, among them several new candidates that have not been earlier connected to wood formation and a VND-INTERACTING 2 (VNI2) homolog. We experimentally demonstrated Populus EIN3D function in ethylene signaling in Arabidopsis thaliana. The ERF hubs ERF118 and ERF119 were connected on the basis of their expression pattern and gene co-expression module composition to xylem cell expansion and secondary cell wall formation, respectively. We hereby establish data resources for ethylene-responsive genes and potential targets for EIN3D and ERF transcription factors in Populus stem tissues, which can help to understand the range of ethylene targeted biological processes during secondary growth.
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Affiliation(s)
- Carolin Seyfferth
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Bernard Wessels
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Soile Jokipii-Lukkari
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Björn Sundberg
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Nicolas Delhomme
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Judith Felten
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Hannele Tuominen
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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