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Zhang Y, Wang Y, Liu R, Fei Z, Fan X, Jiang J, Sun L, Meng X, Liu C. Antibody array-based proteome approach reveals proteins involved in grape seed development. PLANT PHYSIOLOGY 2024; 195:462-478. [PMID: 38395446 PMCID: PMC11060674 DOI: 10.1093/plphys/kiad682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 10/16/2023] [Indexed: 02/25/2024]
Abstract
Grape (Vitis vinifera) is one of the most widely cultivated fruits globally, primarily used for processing and fresh consumption. Seedless grapes are favored by consumers for their convenience, making the study of seedlessness a subject of great interest to scientists. To identify regulators involved in this process in grape, a monoclonal antibody (mAb)-array-based proteomics approach, which contains 21,120 mAbs, was employed for screening proteins/antigens differentially accumulated in grape during development. Differences in antigen signals were detected between seeded and seedless grapes revealing the differential accumulation of 2,587 proteins. After immunoblotting validation, 71 antigens were further immunoprecipitated and identified by mass spectrometry (MS). An in planta protein-protein interaction (PPI) network of those differentially accumulated proteins was established using mAb antibody by immunoprecipitation (IP)-MS, which reveals the alteration of pathways related to carbon metabolism and glycolysis. To validate our result, a seedless-related protein, DUF642 domain-containing protein (VvDUF642), which is functionally uncharacterized in grapes, was ectopically overexpressed in tomato (Solanum lycopersicum "MicroTom") and led to a reduction in seed production. PPI network indicated that VvDUF642 interacts with pectin acetylesterase (VvPAE) in grapes, which was validated by BiFC and Co-IP. As anticipated, overexpression of VvPAE substantially reduced seed production in tomato. Moreover, S. lycopersicum colourless non-ripening expression was altered in VvDUF642- and VvPAE-overexpressing plants. Taken together, we provided a high-throughput method for the identification of proteins involved in the seed formation process. Among those, VvDUF642 and VvPAE are potential targets for breeding seedless grapes and other important fruits in the future.
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Affiliation(s)
- Ying Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou 450009, China
- Chuxiong Yunguo Agriculture Technology Research Institute (Yunnan), Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Henan 450008, China
| | - Yiming Wang
- The Key Laboratory of Plant Immunity, Collage of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruitao Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou 450009, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853-1801, USA
| | - Xiucai Fan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou 450009, China
| | - Jianfu Jiang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou 450009, China
| | - Lei Sun
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou 450009, China
| | - Xun Meng
- School of Life Science, Northwest University, Xi’an, Shanxi 710069, China
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Chonghuai Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou 450009, China
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Wannitikul P, Wattana-Amorn P, Sathitnaitham S, Sakulkoo J, Suttangkakul A, Wonnapinij P, Bassel GW, Simister R, Gomez LD, Vuttipongchaikij S. Disruption of a DUF247 Containing Protein Alters Cell Wall Polysaccharides and Reduces Growth in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2023; 12:1977. [PMID: 37653894 PMCID: PMC10221614 DOI: 10.3390/plants12101977] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 09/02/2023]
Abstract
Plant cell wall biosynthesis is a complex process that requires proteins and enzymes from glycan synthesis to wall assembly. We show that disruption of At3g50120 (DUF247-1), a member of the DUF247 multigene family containing 28 genes in Arabidopsis, results in alterations to the structure and composition of cell wall polysaccharides and reduced growth and plant size. An ELISA using cell wall antibodies shows that the mutants also exhibit ~50% reductions in xyloglucan (XyG), glucuronoxylan (GX) and heteromannan (HM) epitopes in the NaOH fraction and ~50% increases in homogalacturonan (HG) epitopes in the CDTA fraction. Furthermore, the polymer sizes of XyGs and GXs are reduced with concomitant increases in short-chain polymers, while those of HGs and mHGs are slightly increased. Complementation using 35S:DUF247-1 partially recovers the XyG and HG content, but not those of GX and HM, suggesting that DUF247-1 is more closely associated with XyGs and HGs. DUF247-1 is expressed throughout Arabidopsis, particularly in vascular and developing tissues, and its disruption affects the expression of other gene members, indicating a regulatory control role within the gene family. Our results demonstrate that DUF247-1 is required for normal cell wall composition and structure and Arabidopsis growth.
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Affiliation(s)
- Pitchaporn Wannitikul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
| | - Pakorn Wattana-Amorn
- Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry, Department of Chemistry, Faculty of Science, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand;
| | - Sukhita Sathitnaitham
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
| | - Jenjira Sakulkoo
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
- Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
- Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - George W. Bassel
- School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK;
| | - Rachael Simister
- CNAP, Department of Biology, University of York, Heslington, York YO10 5DD, UK; (R.S.); (L.D.G.)
| | - Leonardo D. Gomez
- CNAP, Department of Biology, University of York, Heslington, York YO10 5DD, UK; (R.S.); (L.D.G.)
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
- Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
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Pineda-Hernández E, Cruz-Valderrama JE, Gómez-Maqueo X, Martínez-Barajas E, Gamboa-deBuen A. BIIDXI, a DUF642 Cell Wall Protein That Regulates Pectin Methyl Esterase Activity, Is Involved in Thermotolerance Processes in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2022; 11:3049. [PMID: 36432778 PMCID: PMC9694414 DOI: 10.3390/plants11223049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/29/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Plant cell wall remodeling is an important process during plant responses to heat stress. Pectins, a group of cell wall polysaccharides with a great diversity of complex chemical structures, are also involved in heat stress responses. Enzymatic activity of the pectin methyl esterases, which remove methyl groups from pectins in the cell wall, is regulated by DUF642 proteins, as described in different plants, including Arabidopsis thaliana and Oryza sativa. Our results demonstrated that heat stress altered the expression of the DUF642 gene, BIIDXI. There was an important decrease in BIIDXI expression during the first hour of HS, followed by an increase at 24 h. bdx-1 seedlings had less tolerance to heat stress but presented a normal heat stress response; HSFA2 and HSP22 expressions were highly increased, as they were in WT seedlings. Thermopriming triggered changes in pectin methyl esterase activity in WT seedlings, while no increases in PME activity were detected in bdx-1 seedlings at the same conditions. Taken together, our results suggest that BIIDXI is involved in thermotolerance via PME activation.
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Affiliation(s)
- Eduardo Pineda-Hernández
- Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico
| | - José Erik Cruz-Valderrama
- Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico
| | - Ximena Gómez-Maqueo
- Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico
| | - Eleazar Martínez-Barajas
- Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico
| | - Alicia Gamboa-deBuen
- Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico
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Zhu Y, Yuan G, Wang Y, An G, Li W, Liu J, Sun D. Mapping and functional verification of leaf yellowing genes in watermelon during whole growth period. FRONTIERS IN PLANT SCIENCE 2022; 13:1049114. [PMID: 36340411 PMCID: PMC9627507 DOI: 10.3389/fpls.2022.1049114] [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: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Increasing light energy utilization efficiency is an effective way to increase yield and improve quality of watermelon. Leaf is the main place for photosynthesis, and the color of leaf is directly related to the change of photosynthesis. In addition, leaf yellowing can be used as a marker trait to play an important role in watermelon hybrid breeding and improve seed breeding. It can not only be used to eliminate hybrids at seedling stage, but also be used to determine seed purity. In this study, transcriptome analysis was first carried out using the whole growth period leaf yellowing watermelon mutant w-yl and inbred line ZK, and identified 2,471 differentially expressed genes (DEGs) in the comparison group w-yl-vs-ZK. Among the top 20 terms of the gene ontology (GO) enrichment pathway, 17 terms were related to photosynthesis. KEGG pathway enrichment analysis showed that the most abundant pathway was photosynthesis-antenna proteins. The F2 population was constructed by conventional hybridization with the inbred line ZK. Genetic analysis showed that leaf yellowing of the mutant was controlled by a single recessive gene. The leaf yellowing gene of watermelon located between Ind14,179,011 and InD16,396,362 on chromosome 2 by using indel-specific PCR markers, with a region of 2.217 Mb. In the interval, it was found that five genes may have gene fragment deletion in w-yl, among which Cla97C02G036010, Cla97C02G036030, Cla97C02G036040, Cla97C02G036050 were the whole fragment loss, and Cla97C02G0360 was the C-terminal partial base loss. Gene function verification results showed that Cla97C02G036040, Cla97C02G036050 and Cla97C02G036060 may be the key factors leading to yellowing of w-yl leaves.
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Affiliation(s)
- Yingchun Zhu
- The Key Laboratory of Genetic Resource Evaluation and Application of Horticultural Crops (Fruit), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, China
| | - Gaopeng Yuan
- The Key Laboratory of Genetic Resource Evaluation and Application of Horticultural Crops (Fruit), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Yifan Wang
- The Key Laboratory of Genetic Resource Evaluation and Application of Horticultural Crops (Fruit), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Guolin An
- The Key Laboratory of Genetic Resource Evaluation and Application of Horticultural Crops (Fruit), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Weihua Li
- The Key Laboratory of Genetic Resource Evaluation and Application of Horticultural Crops (Fruit), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Junpu Liu
- The Key Laboratory of Genetic Resource Evaluation and Application of Horticultural Crops (Fruit), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, China
| | - Dexi Sun
- The Key Laboratory of Genetic Resource Evaluation and Application of Horticultural Crops (Fruit), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
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San Clemente H, Kolkas H, Canut H, Jamet E. Plant Cell Wall Proteomes: The Core of Conserved Protein Families and the Case of Non-Canonical Proteins. Int J Mol Sci 2022; 23:ijms23084273. [PMID: 35457091 PMCID: PMC9029284 DOI: 10.3390/ijms23084273] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/06/2022] [Accepted: 04/10/2022] [Indexed: 12/25/2022] Open
Abstract
Plant cell wall proteins (CWPs) play critical roles during plant development and in response to stresses. Proteomics has revealed their great diversity. With nearly 1000 identified CWPs, the Arabidopsis thaliana cell wall proteome is the best described to date and it covers the main plant organs and cell suspension cultures. Other monocot and dicot plants have been studied as well as bryophytes, such as Physcomitrella patens and Marchantia polymorpha. Although these proteomes were obtained using various flowcharts, they can be searched for the presence of members of a given protein family. Thereby, a core cell wall proteome which does not pretend to be exhaustive, yet could be defined. It comprises: (i) glycoside hydrolases and pectin methyl esterases, (ii) class III peroxidases, (iii) Asp, Ser and Cys proteases, (iv) non-specific lipid transfer proteins, (v) fasciclin arabinogalactan proteins, (vi) purple acid phosphatases and (vii) thaumatins. All the conserved CWP families could represent a set of house-keeping CWPs critical for either the maintenance of the basic cell wall functions, allowing immediate response to environmental stresses or both. Besides, the presence of non-canonical proteins devoid of a predicted signal peptide in cell wall proteomes is discussed in relation to the possible existence of alternative secretion pathways.
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6
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Plant Cell Wall Proteins and Development. Int J Mol Sci 2020; 21:ijms21082731. [PMID: 32326416 PMCID: PMC7215729 DOI: 10.3390/ijms21082731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 11/24/2022] Open
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Lai Y, Zhang D, Wang J, Wang J, Ren P, Yao L, Si E, Kong Y, Wang H. Integrative Transcriptomic and Proteomic Analyses of Molecular Mechanism Responding to Salt Stress during Seed Germination in Hulless Barley. Int J Mol Sci 2020; 21:ijms21010359. [PMID: 31935789 PMCID: PMC6981547 DOI: 10.3390/ijms21010359] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/03/2020] [Accepted: 01/03/2020] [Indexed: 12/19/2022] Open
Abstract
Hulless barley (Hordeum vulgare L. var. nudum) is one of the most important crops in the Qinghai-Tibet Plateau. Soil salinity seriously affects its cultivation. To investigate the mechanism of salt stress response during seed germination, two contrasting hulless barley genotypes were selected to first investigate the molecular mechanism of seed salinity response during the germination stage using RNA-sequencing and isobaric tags for relative and absolute quantitation technologies. Compared to the salt-sensitive landrace lk621, the salt-tolerant one lk573 germinated normally under salt stress. The changes in hormone contents also differed between lk621 and lk573. In lk573, 1597 differentially expressed genes (DEGs) and 171 differentially expressed proteins (DEPs) were specifically detected at 4 h after salt stress, and correspondingly, 2748 and 328 specifically detected at 16 h. Most specific DEGs in lk573 were involved in response to oxidative stress, biosynthetic process, protein localization, and vesicle-mediated transport, and most specific DEPs were assigned to an oxidation-reduction process, carbohydrate metabolic process, and protein phosphorylation. There were 96 genes specifically differentially expressed at both transcriptomic and proteomic levels in lk573. These results revealed the molecular mechanism of salt tolerance and provided candidate genes for further study and salt-tolerant improvement in hulless barley.
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Affiliation(s)
- Yong Lai
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (Y.L.); (D.Z.)
| | - Dangquan Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (Y.L.); (D.Z.)
| | - Jinmin Wang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Juncheng Wang
- Gansu Provincial Key Lab of Aridland Crop Science, Lanzhou 730070, China
| | - Panrong Ren
- Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lirong Yao
- Gansu Provincial Key Lab of Aridland Crop Science, Lanzhou 730070, China
| | - Erjing Si
- Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
| | - Yuhua Kong
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (Y.L.); (D.Z.)
- Correspondence: (Y.K.); (H.W.)
| | - Huajun Wang
- Gansu Provincial Key Lab of Aridland Crop Science, Lanzhou 730070, China
- Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
- Correspondence: (Y.K.); (H.W.)
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Mehdi C, Virginie L, Audrey G, Axelle B, Colette L, Hélène R, Elisabeth J, Fabienne G, Mathilde FA. Cell Wall Proteome of Wheat Grain Endosperm and Outer Layers at Two Key Stages of Early Development. Int J Mol Sci 2019; 21:ijms21010239. [PMID: 31905787 PMCID: PMC6981528 DOI: 10.3390/ijms21010239] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 12/29/2022] Open
Abstract
The cell wall is an important compartment in grain cells that fulfills both structural and functional roles. It has a dynamic structure that is constantly modified during development and in response to biotic and abiotic stresses. Non-structural cell wall proteins (CWPs) are key players in the remodeling of the cell wall during events that punctuate the plant life. Here, a subcellular and quantitative proteomic approach was carried out to identify CWPs possibly involved in changes in cell wall metabolism at two key stages of wheat grain development: the end of the cellularization step and the beginning of storage accumulation. Endosperm and outer layers of wheat grain were analyzed separately as they have different origins (maternal and seed) and functions in grains. Altogether, 734 proteins with predicted signal peptides were identified (CWPs). Functional annotation of CWPs pointed out a large number of proteins potentially involved in cell wall polysaccharide remodeling. In the grain outer layers, numerous proteins involved in cutin formation or lignin polymerization were found, while an unexpected abundance of proteins annotated as plant invertase/pectin methyl esterase inhibitors were identified in the endosperm. In addition, numerous CWPs were accumulating in the endosperm at the grain filling stage, thus revealing strong metabolic activities in the cell wall during endosperm cell differentiation, while protein accumulation was more intense at the earlier stage of development in outer layers. Altogether, our work gives important information on cell wall metabolism during early grain development in both parts of the grain, namely the endosperm and outer layers. The wheat cell wall proteome is the largest cell wall proteome of a monocot species found so far.
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Affiliation(s)
- Cherkaoui Mehdi
- INRAE, UR BIA, F-44316 Nantes, France; (C.M.); (L.V.); (G.A.); (B.A.); (L.C.); (R.H.); (G.F.)
| | - Lollier Virginie
- INRAE, UR BIA, F-44316 Nantes, France; (C.M.); (L.V.); (G.A.); (B.A.); (L.C.); (R.H.); (G.F.)
| | - Geairon Audrey
- INRAE, UR BIA, F-44316 Nantes, France; (C.M.); (L.V.); (G.A.); (B.A.); (L.C.); (R.H.); (G.F.)
| | - Bouder Axelle
- INRAE, UR BIA, F-44316 Nantes, France; (C.M.); (L.V.); (G.A.); (B.A.); (L.C.); (R.H.); (G.F.)
| | - Larré Colette
- INRAE, UR BIA, F-44316 Nantes, France; (C.M.); (L.V.); (G.A.); (B.A.); (L.C.); (R.H.); (G.F.)
| | - Rogniaux Hélène
- INRAE, UR BIA, F-44316 Nantes, France; (C.M.); (L.V.); (G.A.); (B.A.); (L.C.); (R.H.); (G.F.)
| | - Jamet Elisabeth
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 31326 Castanet Tolosan, France;
| | - Guillon Fabienne
- INRAE, UR BIA, F-44316 Nantes, France; (C.M.); (L.V.); (G.A.); (B.A.); (L.C.); (R.H.); (G.F.)
| | - Francin-Allami Mathilde
- INRAE, UR BIA, F-44316 Nantes, France; (C.M.); (L.V.); (G.A.); (B.A.); (L.C.); (R.H.); (G.F.)
- Correspondence:
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Sergeant K, Printz B, Guerriero G, Renaut J, Lutts S, Hausman JF. The Dynamics of the Cell Wall Proteome of Developing Alfalfa Stems. BIOLOGY 2019; 8:E60. [PMID: 31430995 PMCID: PMC6784106 DOI: 10.3390/biology8030060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/06/2019] [Accepted: 08/14/2019] [Indexed: 12/24/2022]
Abstract
In this study, the cell-wall-enriched subproteomes at three different heights of alfalfa stems were compared. Since these three heights correspond to different states in stem development, a view on the dynamics of the cell wall proteome during cell maturation is obtained. This study of cell wall protein-enriched fractions forms the basis for a description of the development process of the cell wall and the linking cell wall localized proteins with the evolution of cell wall composition and structure. The sequential extraction of cell wall proteins with CaCl2, EGTA, and LiCl-complemented buffers was combined with a gel-based proteome approach and multivariate analysis. Although the highest similarities were observed between the apical and intermediate stem regions, the proteome patterns are characteristic for each region. Proteins that bind carbohydrates and have proteolytic activity, as well as enzymes involved in glycan remobilization, accumulate in the basal stem region. Beta-amylase and ferritin likewise accumulate more in the basal stem segment. Therefore, remobilization of nutrients appears to be an important process in the oldest stem segment. The intermediate and apical regions are sites of cell wall polymer remodeling, as suggested by the high abundance of proteins involved in the remodeling of the cell wall, such as xyloglucan endoglucosylase, beta-galactosidase, or the BURP-domain containing polygalacturonase non-catalytic subunit. However, the most striking change between the different stem parts is the strong accumulation of a DUF642-conserved domain containing protein in the apical region of the stem, which suggests a particular role of this protein during the early development of stem tissues.
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Affiliation(s)
- Kjell Sergeant
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 4362 Esch/Alzette, Luxembourg.
| | - Bruno Printz
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 4362 Esch/Alzette, Luxembourg
- Groupe de Recherche en Physiologie végétale (GRPV), Université catholique de Louvain, Earth and Life Institute Agronomy (ELI-A), 1348 Louvain-la-Neuve, Belgium
| | - Gea Guerriero
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 4362 Esch/Alzette, Luxembourg
| | - Jenny Renaut
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 4362 Esch/Alzette, Luxembourg
| | - Stanley Lutts
- Groupe de Recherche en Physiologie végétale (GRPV), Université catholique de Louvain, Earth and Life Institute Agronomy (ELI-A), 1348 Louvain-la-Neuve, Belgium
| | - Jean-Francois Hausman
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 4362 Esch/Alzette, Luxembourg
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Cruz-Valderrama JE, Gómez-Maqueo X, Salazar-Iribe A, Zúñiga-Sánchez E, Hernández-Barrera A, Quezada-Rodríguez E, Gamboa-deBuen A. Overview of the Role of Cell Wall DUF642 Proteins in Plant Development. Int J Mol Sci 2019; 20:E3333. [PMID: 31284602 PMCID: PMC6651502 DOI: 10.3390/ijms20133333] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 02/06/2023] Open
Abstract
The DUF642 protein family is found exclusively in spermatophytes and is represented by 10 genes in Arabidopsis and in most of the 24 plant species analyzed to date. Even though the primary structure of DUF642 proteins is highly conserved in different spermatophyte species, studies of their expression patterns in Arabidopsis have shown that the spatial-temporal expression pattern for each gene is specific and consistent with the phenotypes of the mutant plants studied so far. Additionally, the regulation of DUF642 gene expression by hormones and environmental stimuli was specific for each gene, showing both up- and down-regulation depending of the analyzed tissue and the intensity or duration of the stimuli. These expression patterns suggest that the DUF642 genes are involved throughout the development and growth of plants. In general, changes in the expression patterns of DUF642 genes can be related to changes in pectin methyl esterase activity and/or to changes in the degree of methyl-esterified homogalacturonans during plant development in different cell types. Thus, the regulation of pectin methyl esterases mediated by DUF642 genes could contribute to the regulation of the cell wall properties during plant growth.
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Affiliation(s)
| | - Ximena Gómez-Maqueo
- Instituto de Ecología, Universidad Nacional Autónoma de México. Mexico City 04510, Mexico
| | - Alexis Salazar-Iribe
- Instituto de Ecología, Universidad Nacional Autónoma de México. Mexico City 04510, Mexico
| | - Esther Zúñiga-Sánchez
- Instituto de Ecología, Universidad Nacional Autónoma de México. Mexico City 04510, Mexico
| | | | - Elsa Quezada-Rodríguez
- Instituto de Ecología, Universidad Nacional Autónoma de México. Mexico City 04510, Mexico
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11
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Calderan-Rodrigues MJ, Guimarães Fonseca J, de Moraes FE, Vaz Setem L, Carmanhanis Begossi A, Labate CA. Plant Cell Wall Proteomics: A Focus on Monocot Species, Brachypodium distachyon, Saccharum spp. and Oryza sativa. Int J Mol Sci 2019; 20:E1975. [PMID: 31018495 PMCID: PMC6514655 DOI: 10.3390/ijms20081975] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 12/13/2022] Open
Abstract
Plant cell walls mostly comprise polysaccharides and proteins. The composition of monocots' primary cell walls differs from that of dicots walls with respect to the type of hemicelluloses, the reduction of pectin abundance and the presence of aromatic molecules. Cell wall proteins (CWPs) differ among plant species, and their distribution within functional classes varies according to cell types, organs, developmental stages and/or environmental conditions. In this review, we go deeper into the findings of cell wall proteomics in monocot species and make a comparative analysis of the CWPs identified, considering their predicted functions, the organs analyzed, the plant developmental stage and their possible use as targets for biofuel production. Arabidopsis thaliana CWPs were considered as a reference to allow comparisons among different monocots, i.e., Brachypodium distachyon, Saccharum spp. and Oryza sativa. Altogether, 1159 CWPs have been acknowledged, and specificities and similarities are discussed. In particular, a search for A. thaliana homologs of CWPs identified so far in monocots allows the definition of monocot CWPs characteristics. Finally, the analysis of monocot CWPs appears to be a powerful tool for identifying candidate proteins of interest for tailoring cell walls to increase biomass yield of transformation for second-generation biofuels production.
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Affiliation(s)
- Maria Juliana Calderan-Rodrigues
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
| | - Juliana Guimarães Fonseca
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
| | - Fabrício Edgar de Moraes
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
| | - Laís Vaz Setem
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
| | - Amanda Carmanhanis Begossi
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
| | - Carlos Alberto Labate
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
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12
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Durand TC, Cueff G, Godin B, Valot B, Clément G, Gaude T, Rajjou L. Combined Proteomic and Metabolomic Profiling of the Arabidopsis thaliana vps29 Mutant Reveals Pleiotropic Functions of the Retromer in Seed Development. Int J Mol Sci 2019; 20:E362. [PMID: 30654520 PMCID: PMC6359594 DOI: 10.3390/ijms20020362] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 12/25/2022] Open
Abstract
The retromer is a multiprotein complex conserved from yeast to humans, which is involved in intracellular protein trafficking and protein recycling. Selection of cargo proteins transported by the retromer depends on the core retromer subunit composed of the three vacuolar protein sorting (VPS) proteins, namely VPS26, VPS29, and VPS35. To gain a better knowledge of the importance of the plant retromer in protein sorting, we carried out a comparative proteomic and metabolomic analysis of Arabidopsis thaliana seeds from the wild-type and the null-retromer mutant vps29. Here, we report that the retromer mutant displays major alterations in the maturation of seed storage proteins and synthesis of lipid reserves, which are accompanied by severely impaired seed vigor and longevity. We also show that the lack of retromer components is counterbalanced by an increase in proteins involved in intracellular trafficking, notably members of the Ras-related proteins in brain (RAB) family proteins. Our study suggests that loss of the retromer stimulates energy metabolism, affects many metabolic pathways, including that of cell wall biogenesis, and triggers an osmotic stress response, underlining the importance of retromer function in seed biology.
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Affiliation(s)
- Thomas C Durand
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon I, CNRS, INRA, 69342 Lyon, France.
| | - Gwendal Cueff
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles cedex, France.
| | - Béatrice Godin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles cedex, France.
| | - Benoît Valot
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France.
| | - Gilles Clément
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles cedex, France.
| | - Thierry Gaude
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon I, CNRS, INRA, 69342 Lyon, France.
| | - Loïc Rajjou
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles cedex, France.
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13
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Salzano AM, Renzone G, Sobolev AP, Carbone V, Petriccione M, Capitani D, Vitale M, Novi G, Zambrano N, Pasquariello MS, Mannina L, Scaloni A. Unveiling Kiwifruit Metabolite and Protein Changes in the Course of Postharvest Cold Storage. FRONTIERS IN PLANT SCIENCE 2019; 10:71. [PMID: 30778366 PMCID: PMC6369206 DOI: 10.3389/fpls.2019.00071] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 01/17/2019] [Indexed: 05/07/2023]
Abstract
Actinidia deliciosa cv. Hayward fruit is renowned for its micro- and macronutrients, which vary in their levels during berry physiological development and postharvest processing. In this context, we have recently described metabolic pathways/molecular effectors in fruit outer endocarp characterizing the different stages of berry physiological maturation. Here, we report on the kiwifruit postharvest phase through an integrated approach consisting of pomological analysis combined with NMR/LC-UV/ESI-IT-MSn- and 2D-DIGE/nanoLC-ESI-LIT-MS/MS-based proteometabolomic measurements. Kiwifruit samples stored under conventional, cold-based postharvest conditions not involving the use of dedicated chemicals were sampled at four stages (from fruit harvest to pre-commercialization) and analyzed in comparison for pomological features, and outer endocarp metabolite and protein content. About 42 metabolites were quantified, together with corresponding proteomic changes. Proteomics showed that proteins associated with disease/defense, energy, protein destination/storage, cell structure and metabolism functions were affected at precise fruit postharvest times, providing a justification to corresponding pomological/metabolite content characteristics. Bioinformatic analysis of variably represented proteins revealed a central network of interacting species, modulating metabolite level variations during postharvest fruit storage. Kiwifruit allergens were also quantified, demonstrating in some cases their highest levels at the fruit pre-commercialization stage. By lining up kiwifruit postharvest processing to a proteometabolomic depiction, this study integrates previous observations on metabolite and protein content in postharvest berries treated with specific chemical additives, and provides a reference framework for further studies on the optimization of fruit storage before its commercialization.
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Affiliation(s)
- Anna Maria Salzano
- Proteomics & Mass Spectrometry Laboratory, Istituto per il Sistema Produzione Animale In Ambiente Mediterraneo, National Research Council, Naples, Italy
| | - Giovanni Renzone
- Proteomics & Mass Spectrometry Laboratory, Istituto per il Sistema Produzione Animale In Ambiente Mediterraneo, National Research Council, Naples, Italy
| | - Anatoly P. Sobolev
- Magnetic Resonance Laboratory “Annalaura Segre”, Institute of Chemical Methodologies, National Research Council, Monterotondo, Italy
| | - Virginia Carbone
- Institute of Food Sciences, National Research Council, Avellino, Italy
| | - Milena Petriccione
- Centro di Ricerca per Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Caserta, Italy
| | - Donatella Capitani
- Magnetic Resonance Laboratory “Annalaura Segre”, Institute of Chemical Methodologies, National Research Council, Monterotondo, Italy
| | - Monica Vitale
- Proteomics & Mass Spectrometry Laboratory, Istituto per il Sistema Produzione Animale In Ambiente Mediterraneo, National Research Council, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Gianfranco Novi
- Proteomics & Mass Spectrometry Laboratory, Istituto per il Sistema Produzione Animale In Ambiente Mediterraneo, National Research Council, Naples, Italy
| | - Nicola Zambrano
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
- Ceinge Biotecnologie Avanzate S. C. a R. L., Naples, Italy
| | - Maria Silvia Pasquariello
- Centro di Ricerca per Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Caserta, Italy
| | - Luisa Mannina
- Magnetic Resonance Laboratory “Annalaura Segre”, Institute of Chemical Methodologies, National Research Council, Monterotondo, Italy
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Rome, Italy
| | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, Istituto per il Sistema Produzione Animale In Ambiente Mediterraneo, National Research Council, Naples, Italy
- *Correspondence: Andrea Scaloni,
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14
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Salazar-Iribe A, Cruz-Valderrama JE, Jímenez-Durán K, Gómez-Maqueo X, Gamboa-deBuen A. BIIDXI, a DUF642 cell wall protein, is involved in hypocotyl growth via auxin efflux. JOURNAL OF PLANT PHYSIOLOGY 2018; 231:105-109. [PMID: 30253266 DOI: 10.1016/j.jplph.2018.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 06/08/2023]
Abstract
Auxin is involved in hypocotyl elongation in response to different environmental factors. BIIDXI is a cell wall DUF642 protein that participates in the regulation of the degree of pectin-methylesterification of the cell wall in different tissues, including hypocotyls. Under continuous light, bdx-1 seedlings presented longer hypocotyls than those of WT, while BIIDXI-overexpressed hypocotyls were auxin resistant. Auxin accumulation was observed in epidermal cells from bdx-1 hypocotyls, and the distribution pattern of PIN1 proteins differed. Moreover, the gravitropic response of bdx-1, a process that is highly dependent on auxin flux, was increased. In this study, we determined that BIIDXI is involved in hypocotyl elongation through the regulation of auxin flux.
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Affiliation(s)
- Alexis Salazar-Iribe
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria CP. 04510, Ciudad de México, México
| | - José Erik Cruz-Valderrama
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria CP. 04510, Ciudad de México, México
| | - Karina Jímenez-Durán
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria CP. 04510, Ciudad de México, México
| | - Ximena Gómez-Maqueo
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria CP. 04510, Ciudad de México, México
| | - Alicia Gamboa-deBuen
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria CP. 04510, Ciudad de México, México.
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15
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Salazar-Iribe A, Zúñiga-Sánchez E, Mejía EZ, Gamboa-deBuen A. Cell Wall Localization of Two DUF642 Proteins, BIIDXI and TEEBE, during Meloidogyne incognita Early Inoculation. THE PLANT PATHOLOGY JOURNAL 2017; 33:614-618. [PMID: 29238286 PMCID: PMC5720610 DOI: 10.5423/ppj.nt.05.2017.0101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/02/2017] [Accepted: 07/20/2017] [Indexed: 06/07/2023]
Abstract
The root-knot nematode Meloidogyne incognita infects a variety of plants, including Arabidopsis thaliana. During migration, root-knot nematodes secrete different proteins to modify cell walls, which include pectolytic enzymes. However, the contribution of host cell wall proteins has not been described during this process. The function of two DUF642 cell wall proteins, BIIDXI (BDX, At4g32460) and TEEBE (TEB, At2g41800), in plant development could be related to the regulation of pectin methyl esterification status in the cell walls of different tissues. Accordingly, the expression of these two genes is up-regulated by auxin. BDX and TEB were highly induced during early M. incognita inoculation. Moreover, cell wall localization of the proteins was also induced. The cell wall localization of BDX and TEB DUF642 proteins during M. incognita early inoculation suggested that these two proteins could be involved in the regulation of the degree of pectin methylation during cell separation.
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Affiliation(s)
- Alexis Salazar-Iribe
- Instituto de Ecología, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, C.P. 04510
| | - Esther Zúñiga-Sánchez
- Facultad de Química, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, C.P. 04510. Edificio E Laboratorio L-102
| | - Emma Zavaleta Mejía
- Colegio de Postgraduados (CP), Instituto de Fitosanidad, km 35.5 Carr. México-Texcoco, Montecillo, Edo. de México CP 56230
| | - Alicia Gamboa-deBuen
- Instituto de Ecología, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, C.P. 04510
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16
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Arbelaez JD, Maron LG, Jobe TO, Piñeros MA, Famoso AN, Rebelo AR, Singh N, Ma Q, Fei Z, Kochian LV, McCouch SR. ALUMINUM RESISTANCE TRANSCRIPTION FACTOR 1 ( ART1) contributes to natural variation in aluminum resistance in diverse genetic backgrounds of rice ( O. sativa). PLANT DIRECT 2017; 1:e00014. [PMID: 31245663 PMCID: PMC6508803 DOI: 10.1002/pld3.14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/22/2017] [Accepted: 09/01/2017] [Indexed: 05/13/2023]
Abstract
Transcription factors (TFs) regulate the expression of other genes to indirectly mediate stress resistance mechanisms. Therefore, when studying TF-mediated stress resistance, it is important to understand how TFs interact with genes in the genetic background. Here, we fine-mapped the aluminum (Al) resistance QTL Alt12.1 to a 44-kb region containing six genes. Among them is ART1, which encodes a C2H2-type zinc finger TF required for Al resistance in rice. The mapping parents, Al-resistant cv Azucena (tropical japonica) and Al-sensitive cv IR64 (indica), have extensive sequence polymorphism within the ART1 coding region, but similar ART1 expression levels. Using reciprocal near-isogenic lines (NILs) we examined how allele-swapping the Alt12.1 locus would affect plant responses to Al. Analysis of global transcriptional responses to Al stress in roots of the NILs alongside their recurrent parents demonstrated that the presence of the Alt12.1 from Al-resistant Azucena led to greater changes in gene expression in response to Al when compared to the Alt12.1 from IR64 in both genetic backgrounds. The presence of the ART1 allele from the opposite parent affected the expression of several genes not previously implicated in rice Al tolerance. We highlight examples where putatively functional variation in cis-regulatory regions of ART1-regulated genes interacts with ART1 to determine gene expression in response to Al. This ART1-promoter interaction may be associated with transgressive variation for Al resistance in the Azucena × IR64 population. These results illustrate how ART1 interacts with the genetic background to contribute to quantitative phenotypic variation in rice Al resistance.
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Affiliation(s)
- Juan D. Arbelaez
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
- Present address:
Plant BreedingInternational Rice Research InstituteLos BañosPhilippines
| | - Lyza G. Maron
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Timothy O. Jobe
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
- Present address:
Botanical InstituteUniversity of CologneCologneGermany
| | - Miguel A. Piñeros
- Robert W. Holley Center for Agriculture and HealthUSDA‐ARSCornell UniversityIthacaNYUSA
| | - Adam N. Famoso
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
- Present address:
LSU AgCenterH. Rouse Caffey Rice Research StationRayneLAUSA
| | - Ana Rita Rebelo
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
- Present address:
Boyce Thompson InstituteCornell UniversityIthacaNYUSA
| | - Namrata Singh
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Qiyue Ma
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
| | - Zhangjun Fei
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
| | - Leon V. Kochian
- Robert W. Holley Center for Agriculture and HealthUSDA‐ARSCornell UniversityIthacaNYUSA
- Present address:
Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Susan R. McCouch
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
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17
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Palmeros-Suárez PA, Massange-Sánchez JA, Sánchez-Segura L, Martínez-Gallardo NA, Espitia Rangel E, Gómez-Leyva JF, Délano-Frier JP. AhDGR2, an amaranth abiotic stress-induced DUF642 protein gene, modifies cell wall structure and composition and causes salt and ABA hyper-sensibility in transgenic Arabidopsis. PLANTA 2017; 245:623-640. [PMID: 27988887 DOI: 10.1007/s00425-016-2635-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/02/2016] [Indexed: 05/26/2023]
Abstract
An amaranth DGR gene, induced under abiotic stress, modifies cell wall structure and causes hypersensitivity to ABA and salt when overexpressed in Arabidopsis. DUF642 is a highly conserved plant-specific family of unknown cell wall-associated proteins. The AhDGR2 gene, coding for a DUF642 protein, was significantly induced in grain amaranth (Amaranthus hypochondriacus) plants subjected to water-deficit and salinity stress, thereby suggesting its participation in abiotic stress tolerance in this plant. A role in development was also inferred from the higher AhDGR2 expression rates detected in young tissues. Subsequent overexpression of AhDGR2 in transgenic Arabidopsis plants (OE-AhDGR2) supported its possible role in development processes. Thus, OE-AhDGR2 plants generated significantly longer roots when grown in normal MS medium. However, they showed a hypersensitivity to increasing concentrations of abscisic acid or NaCl in the medium, as manifested by shorter root length, smaller and slightly chlorotic rosettes, as well as highly reduced germination rates. Contrary to expectations, OE-AhDGR2 plants were intolerant to abiotic stress. Moreover, cell walls in transgenic plants were thinner, in leaves, and more disorganized, in roots, and had significantly modified pectin levels. Lower pectin methylesterase activity detected in leaves of OE-AhDGR2 plants, but not in roots, was contrary to previous reports associating DUF642 proteins and decreased pectin esterification levels in cell walls. Nonetheless, microarray data identified candidate genes whose expression levels explained the phenotypes observed in leaves of OE-AhDGR2 plants, including several involved in cell wall integrity and extension, growth and development, and resistance to abiotic stress. These results support the role of DUF642 proteins in cell wall-related processes and offer novel insights into their possible role(s) in plants.
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Affiliation(s)
- Paola A Palmeros-Suárez
- Laboratorio de Biología Molecular, Instituto Tecnológico de Tlajomulco, Jalisco, km 10 Carretera a San Miguel Cuyutlán, CP 45640, Tlajomulco de Zúñiga, Jalisco, Mexico
| | - Julio A Massange-Sánchez
- Biotechnology and Biochemistry Department, Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad Irapuato, Km 9.6 del Libramiento Norte Carretera Irapuato-León, CP 36821, Irapuato, GTO., Mexico
| | - Lino Sánchez-Segura
- Biotechnology and Biochemistry Department, Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad Irapuato, Km 9.6 del Libramiento Norte Carretera Irapuato-León, CP 36821, Irapuato, GTO., Mexico
| | - Norma A Martínez-Gallardo
- Biotechnology and Biochemistry Department, Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad Irapuato, Km 9.6 del Libramiento Norte Carretera Irapuato-León, CP 36821, Irapuato, GTO., Mexico
| | - Eduardo Espitia Rangel
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Km 13.5 Carrretera Los Reyes-Texcoco, CP 56250, Coatlinchán Texcoco, Estado de México, Mexico
| | - Juan F Gómez-Leyva
- Laboratorio de Biología Molecular, Instituto Tecnológico de Tlajomulco, Jalisco, km 10 Carretera a San Miguel Cuyutlán, CP 45640, Tlajomulco de Zúñiga, Jalisco, Mexico
| | - John P Délano-Frier
- Biotechnology and Biochemistry Department, Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad Irapuato, Km 9.6 del Libramiento Norte Carretera Irapuato-León, CP 36821, Irapuato, GTO., Mexico.
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18
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Duruflé H, Hervé V, Balliau T, Zivy M, Dunand C, Jamet E. Proline Hydroxylation in Cell Wall Proteins: Is It Yet Possible to Define Rules? FRONTIERS IN PLANT SCIENCE 2017; 8:1802. [PMID: 29089960 PMCID: PMC5651053 DOI: 10.3389/fpls.2017.01802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/04/2017] [Indexed: 05/08/2023]
Abstract
Cell wall proteins (CWPs) play critical and dynamic roles in plant cell walls by contributing to developmental processes and response to environmental cues. Since the CWPs go through the secretion pathway, most of them undergo post-translational modifications (PTMs) which can modify their biological activity. Glycosylation is one of the major PTMs of CWPs and refers to N-glycosylation, O-glycosylation and glypiation. Each of these PTMs occurs in different amino acid contexts which are not all well defined. This article deals with the hydroxylation of Pro residues which is a prerequisite for O-glycosylation of CWPs on hydroxyproline (Hyp) residues. The location of Hyp residues is well described in several structural CWPs, but yet rarely described in other CWPs. In this article, it is studied in detail in five Arabidopsis thaliana proteins using mass spectrometry data: one of them (At4g38770, AtPRP4) is a structural CWP containing 32.5% of Pro residues arranged in typical motifs, the others are either rich (27-28%, At1g31580 and At2g10940) or poor (6-8%, At1g09750 and At3g08030) in Pro residues. The known rules of Pro hydroxylation allowed a good prediction of Hyp location in AtPRP4. However, they could not be applied to the other proteins whatever their Pro content. In addition, variability of the Pro hydroxylation patterns was observed within some amino acid motifs in all the proteins and new patterns of Pro hydroxylation are described. Altogether, this work shows that Hyp residues are present in more protein families than initially described, and that Pro hydroxylation patterns could be different in each of them. This work paves the way for completing the existing Pro hydroxylation code.
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Affiliation(s)
- Harold Duruflé
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Vincent Hervé
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse, France
- INRS – Institut Armand Frappier, Laval, Canada
| | - Thierry Balliau
- PAPPSO, GQE Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Michel Zivy
- PAPPSO, GQE Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse, France
- *Correspondence: Elisabeth Jamet,
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Salazar-Iribe A, Agredano-Moreno LT, Zúñiga-Sánchez E, Jiménez-Garcia LF, Gamboa-deBuen A. The cell wall DUF642 At2g41800 (TEB) protein is involved in hypocotyl cell elongation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 253:206-214. [PMID: 27968989 DOI: 10.1016/j.plantsci.2016.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 10/10/2016] [Accepted: 10/12/2016] [Indexed: 05/11/2023]
Abstract
In plants, the cell wall is a complex and dynamic structure comprising high molecular weight carbohydrates and proteins. The cell wall plays an important role in several stages of the plant life cycle, including cell division, elongation and differentiation. The DUF642 family of cell wall proteins is highly conserved in spermatophytes and might be involved in pectin structural modifications. Particularly, At2g41800 is one of the most highly induced genes during the M/G1 phases of the cell cycle, and the protein encodes by this gene has been detected in cell wall proteomes of cell suspension cultures. In the present study, the expression of At2g41800 (TEB) was confirmed in primary and lateral roots, stigmatic papillae and hypocotyls. Subcellular localization studies showed that TEB is located in the cell wall. The root length and lateral root density were not affected in either of the two teb mutants studied, but the length of the hypocotyls from seedlings grown under light and dark conditions was increased. Immunogold labelling studies using JIM5 antibodies on sections of hypocotyl epidermal cells showed an important reduction of gold particles in teb mutants. The results suggested that TEB is involved in hypocotyl elongation.
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Affiliation(s)
- Alexis Salazar-Iribe
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP. 04510, México DF, Mexico
| | | | - Esther Zúñiga-Sánchez
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP. 04510, México DF, Mexico
| | - Luis Felipe Jiménez-Garcia
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP. 04510, México DF, Mexico
| | - Alicia Gamboa-deBuen
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP. 04510, México DF, Mexico.
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Xie X, Wang Y. VqDUF642, a gene isolated from the Chinese grape Vitis quinquangularis, is involved in berry development and pathogen resistance. PLANTA 2016; 244:1075-1094. [PMID: 27424038 DOI: 10.1007/s00425-016-2569-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/08/2016] [Indexed: 06/06/2023]
Abstract
The DUF642 gene VqDUF642 , isolated from the Chinese grape species V. quinquangularis accession Danfeng-2, participates in berry development and defense responses against Erysiphe necator and Botrytis cinerea. The proteins with domains of unknown function 642 (DUF642) comprise a large protein family according to cell wall proteomic analyses in plants. However, the works about functional characterization of DUF642s in plant development and resistance to pathogens are scarce. In this study, a gene encoding a DUF642 protein was isolated from Chinese grape V. quinquangularis accession Danfeng-2, and designated as VqDUF642. Its full-length cDNA contains a 1107-bp open reading frame corresponding to a deduced 368-amino acid protein. Multiple sequence alignments and phylogenetic analysis showed that VqDUF642 is highly homologous to one of the DUF642 proteins (VvDUF642) in V. vinifera. The VqDUF642 was localized to the cell wall of tobacco epidermal cells. Accumulation of VqDUF642 protein and VqDUF642 transcript abundance increased at the later stage of grape berry development in Danfeng-2. Overexpression of VqDUF642 in transgenic tomato plants accelerated plant growth and reduced susceptibility to Botrytis cinerea. Transgenic Thompson Seedless grapevine plants overexpressing VqDUF642 exhibited enhanced resistance to Erysiphe necator and B. cinerea. Moreover, VqDUF642 overexpression affected the expression of a couple of pathogenesis-related (PR) genes in transgenic tomato and grapevine upon pathogen inoculation. Taken together, these results suggest that VqDUF642 is involved in plant development and defense against pathogenic infections.
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Affiliation(s)
- Xiaoqing Xie
- College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China
| | - Yuejin Wang
- College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China.
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China.
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21
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Calderan-Rodrigues MJ, Jamet E, Douché T, Bonassi MBR, Cataldi TR, Fonseca JG, San Clemente H, Pont-Lezica R, Labate CA. Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases. BMC PLANT BIOLOGY 2016; 16:14. [PMID: 26754199 PMCID: PMC4709929 DOI: 10.1186/s12870-015-0677-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/05/2015] [Indexed: 05/25/2023]
Abstract
BACKGROUND Sugarcane has been used as the main crop for ethanol production for more than 40 years in Brazil. Recently, the production of bioethanol from bagasse and straw, also called second generation (2G) ethanol, became a reality with the first commercial plants started in the USA and Brazil. However, the industrial processes still need to be improved to generate a low cost fuel. One possibility is the remodeling of cell walls, by means of genetic improvement or transgenesis, in order to make the bagasse more accessible to hydrolytic enzymes. We aimed at characterizing the cell wall proteome of young sugarcane culms, to identify proteins involved in cell wall biogenesis. Proteins were extracted from the cell walls of 2-month-old culms using two protocols, non-destructive by vacuum infiltration vs destructive. The proteins were identified by mass spectrometry and bioinformatics. RESULTS A predicted signal peptide was found in 84 different proteins, called cell wall proteins (CWPs). As expected, the non-destructive method showed a lower percentage of proteins predicted to be intracellular than the destructive one (33% vs 44%). About 19% of CWPs were identified with both methods, whilst the infiltration protocol could lead to the identification of 75% more CWPs. In both cases, the most populated protein functional classes were those of proteins related to lipid metabolism and oxido-reductases. Curiously, a single glycoside hydrolase (GH) was identified using the non-destructive method whereas 10 GHs were found with the destructive one. Quantitative data analysis allowed the identification of the most abundant proteins. CONCLUSIONS The results highlighted the importance of using different protocols to extract proteins from cell walls to expand the coverage of the cell wall proteome. Ten GHs were indicated as possible targets for further studies in order to obtain cell walls less recalcitrant to deconstruction. Therefore, this work contributed to two goals: enlarge the coverage of the sugarcane cell wall proteome, and provide target proteins that could be used in future research to facilitate 2G ethanol production.
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Affiliation(s)
- Maria Juliana Calderan-Rodrigues
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil.
| | - Elisabeth Jamet
- Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France.
- CNRS; UMR 5546, BP 42617, F-31326, Castanet-Tolosan, France.
| | - Thibaut Douché
- Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France.
- CNRS; UMR 5546, BP 42617, F-31326, Castanet-Tolosan, France.
| | - Maria Beatriz Rodrigues Bonassi
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil.
| | - Thaís Regiani Cataldi
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil.
| | - Juliana Guimarães Fonseca
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil.
| | - Hélène San Clemente
- Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France.
- CNRS; UMR 5546, BP 42617, F-31326, Castanet-Tolosan, France.
| | - Rafael Pont-Lezica
- Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France
- CNRS; UMR 5546, BP 42617, F-31326, Castanet-Tolosan, France
| | - Carlos Alberto Labate
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil.
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Ferl RJ, Koh J, Denison F, Paul AL. Spaceflight induces specific alterations in the proteomes of Arabidopsis. ASTROBIOLOGY 2015; 15:32-56. [PMID: 25517942 PMCID: PMC4290804 DOI: 10.1089/ast.2014.1210] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Life in spaceflight demonstrates remarkable acclimation processes within the specialized habitats of vehicles subjected to the myriad of unique environmental issues associated with orbital trajectories. To examine the response processes that occur in plants in space, leaves and roots from Arabidopsis (Arabidopsis thaliana) seedlings from three GFP reporter lines that were grown from seed for 12 days on the International Space Station and preserved on orbit in RNAlater were returned to Earth and analyzed by using iTRAQ broad-scale proteomics procedures. Using stringent criteria, we identified over 1500 proteins, which included 1167 leaf proteins and 1150 root proteins we were able to accurately quantify. Quantification revealed 256 leaf proteins and 358 root proteins that showed statistically significant differential abundance in the spaceflight samples compared to ground controls, with few proteins differentially regulated in common between leaves and roots. This indicates that there are measurable proteomics responses to spaceflight and that the responses are organ-specific. These proteomics data were compared with transcriptome data from similar spaceflight samples, showing that there is a positive but limited relationship between transcriptome and proteome regulation of the overall spaceflight responses of plants. These results are discussed in terms of emergence understanding of plant responses to spaceflight particularly with regard to cell wall remodeling, as well as in the context of deriving multiple omics data sets from a single on-orbit preservation and operations approach.
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Affiliation(s)
- Robert J. Ferl
- Department of Horticultural Sciences, Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, Florida
- Interdisciplinary Center for Biotechnology, University of Florida, Gainesville, Florida
| | - Jin Koh
- Interdisciplinary Center for Biotechnology, University of Florida, Gainesville, Florida
| | - Fiona Denison
- Department of Horticultural Sciences, Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, Florida
| | - Anna-Lisa Paul
- Department of Horticultural Sciences, Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, Florida
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23
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Zúñiga-Sánchez E, Soriano D, Martínez-Barajas E, Orozco-Segovia A, Gamboa-deBuen A. BIIDXI, the At4g32460 DUF642 gene, is involved in pectin methyl esterase regulation during Arabidopsis thaliana seed germination and plant development. BMC PLANT BIOLOGY 2014; 14:338. [PMID: 25442819 PMCID: PMC4264326 DOI: 10.1186/s12870-014-0338-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 11/17/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND DUF642 proteins constitute a highly conserved family of proteins that are associated with the cell wall and are specific to spermatophytes. Transcriptome studies have suggested that members of this family are involved in seed development and germination processes. Previous in vitro studies have revealed that At4g32460- and At5g11420-encoded proteins interact with the catalytic domain of pectin methyl esterase 3 (AtPME3, which is encoded by At3g14310). PMEs play an important role in plant development, including seed germination. The aim of this study was to evaluate the function of the DUF642 gene At4g32460 during seed germination and plant development and to determine its relation to PME activity regulation. RESULTS Our results indicated that the DUF642 proteins encoded by At4g32460 and At5g11420 could be positive regulators of PME activity during several developmental processes. Transgenic lines overexpressing these proteins showed increased PME activity during seed germination, and improved seed germination performance. In plants expressing At4g32460 antisense RNA, PME activity was decreased in the leaves, and the siliques were very short and contained no seeds. This phenotype was also present in the SALK_142260 and SALK_054867 lines for At4g32460. CONCLUSIONS Our results suggested that the DUF642 family contributes to the complexity of the methylesterification process by participating in the fine regulation of pectin status during plant development.
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Affiliation(s)
- Esther Zúñiga-Sánchez
- />Instituto de Ecología, Universidad Nacional Autónoma de México, Apartado Postal 70-275, Ciudad Universitaria, México, 04510 Distrito Federal Mexico
| | - Diana Soriano
- />Instituto de Ecología, Universidad Nacional Autónoma de México, Apartado Postal 70-275, Ciudad Universitaria, México, 04510 Distrito Federal Mexico
| | - Eleazar Martínez-Barajas
- />Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, 04510 Distrito Federal Mexico
| | - Alma Orozco-Segovia
- />Instituto de Ecología, Universidad Nacional Autónoma de México, Apartado Postal 70-275, Ciudad Universitaria, México, 04510 Distrito Federal Mexico
| | - Alicia Gamboa-deBuen
- />Instituto de Ecología, Universidad Nacional Autónoma de México, Apartado Postal 70-275, Ciudad Universitaria, México, 04510 Distrito Federal Mexico
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24
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Calderan-Rodrigues MJ, Jamet E, Bonassi MBCR, Guidetti-Gonzalez S, Begossi AC, Setem LV, Franceschini LM, Fonseca JG, Labate CA. Cell wall proteomics of sugarcane cell suspension cultures. Proteomics 2014; 14:738-49. [PMID: 24436144 DOI: 10.1002/pmic.201300132] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Revised: 11/10/2013] [Accepted: 12/01/2013] [Indexed: 12/21/2022]
Abstract
The use of cell walls to produce cellulosic ethanol from sugarcane bagasse is a new challenge. A better knowledge of proteins involved in cell wall remodelling is essential to improve the saccharification processes. Cell suspension cultures were used for this first cell wall proteomics study of sugarcane. Proteins extracted from cell walls were identified using an adapted protocol. They were extracted using 0.2 M CaCl2 and 2 M LiCl after purification of cell walls. The proteins were then identified by the innovative nanoACQUITY UPLC MS/MS technology and bioinformatics using the translated SUCEST EST cluster database of sugarcane. The experiments were reproduced three times. Since Sorghum bicolor is the closest plant with a fully sequenced genome, homologous proteins were searched for to complete the annotation of proteins, that is, prediction of subcellular localization and functional domains. Altogether, 69 different proteins predicted to be secreted were identified among 377 proteins. The reproducibility of the experiments is discussed. These proteins were distributed into eight functional classes. Oxidoreductases such as peroxidases were well represented, whereas glycoside hydrolases were scarce. This work provides information about the proteins that could be manipulated through genetic transformation, to increase second-generation ethanol production.
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Affiliation(s)
- Maria Juliana Calderan-Rodrigues
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba-SP, Brazil
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25
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Mewalal R, Mizrachi E, Mansfield SD, Myburg AA. Cell wall-related proteins of unknown function: missing links in plant cell wall development. PLANT & CELL PHYSIOLOGY 2014; 55:1031-43. [PMID: 24683037 DOI: 10.1093/pcp/pcu050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Lignocellulosic biomass is an important feedstock for the pulp and paper industry as well as emerging biofuel and biomaterial industries. However, the recalcitrance of the secondary cell wall to chemical or enzymatic degradation remains a major hurdle for efficient extraction of economically important biopolymers such as cellulose. It has been estimated that approximately 10-15% of about 27,000 protein-coding genes in the Arabidopsis genome are dedicated to cell wall development; however, only about 130 Arabidopsis genes thus far have experimental evidence validating cell wall function. While many genes have been implicated through co-expression analysis with known genes, a large number are broadly classified as proteins of unknown function (PUFs). Recently the functionality of some of these unknown proteins in cell wall development has been revealed using reverse genetic approaches. Given the large number of cell wall-related PUFs, how do we approach and subsequently prioritize the investigation of such unknown genes that may be essential to or influence plant cell wall development and structure? Here, we address the aforementioned question in two parts; we first identify the different kinds of PUFs based on known and predicted features such as protein domains. Knowledge of inherent features of PUFs may allow for functional inference and a concomitant link to biological context. Secondly, we discuss omics-based technologies and approaches that are helping identify and prioritize cell wall-related PUFs by functional association. In this way, hypothesis-driven experiments can be designed for functional elucidation of many proteins that remain missing links in our understanding of plant cell wall biosynthesis.
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Affiliation(s)
- Ritesh Mewalal
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Hatfield, Pretoria, 0028, South Africa
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26
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Albenne C, Canut H, Hoffmann L, Jamet E. Plant Cell Wall Proteins: A Large Body of Data, but What about Runaways? Proteomes 2014; 2:224-242. [PMID: 28250379 PMCID: PMC5302738 DOI: 10.3390/proteomes2020224] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/08/2014] [Accepted: 04/08/2014] [Indexed: 11/16/2022] Open
Abstract
Plant cell wall proteomics has been a very dynamic field of research for about fifteen years. A full range of strategies has been proposed to increase the number of identified proteins and to characterize their post-translational modifications. The protocols are still improving to enlarge the coverage of cell wall proteomes. Comparisons between these proteomes have been done based on various working strategies or different physiological stages. In this review, two points are highlighted. The first point is related to data analysis with an overview of the cell wall proteomes already described. A large body of data is now available with the description of cell wall proteomes of seventeen plant species. CWP contents exhibit particularities in relation to the major differences in cell wall composition and structure between these plants and between plant organs. The second point is related to methodology and concerns the present limitations of the coverage of cell wall proteomes. Because of the variety of cell wall structures and of the diversity of protein/polysaccharide and protein/protein interactions in cell walls, some CWPs can be missing either because they are washed out during the purification of cell walls or because they are covalently linked to cell wall components.
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Affiliation(s)
- Cécile Albenne
- Université de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617 Auzeville, F-31326 Castanet-Tolosan, France.
- CNRS, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France.
| | - Hervé Canut
- Université de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617 Auzeville, F-31326 Castanet-Tolosan, France.
- CNRS, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France.
| | - Laurent Hoffmann
- Université de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617 Auzeville, F-31326 Castanet-Tolosan, France.
- CNRS, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France.
| | - Elisabeth Jamet
- Université de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617 Auzeville, F-31326 Castanet-Tolosan, France.
- CNRS, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France.
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27
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Rejón JD, Delalande F, Schaeffer-Reiss C, Carapito C, Zienkiewicz K, de Dios Alché J, Rodríguez-García MI, Van Dorsselaer A, Castro AJ. Proteomics profiling reveals novel proteins and functions of the plant stigma exudate. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:5695-705. [PMID: 24151302 PMCID: PMC3871823 DOI: 10.1093/jxb/ert345] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Proteomic analysis of the stigmatic exudate of Lilium longiflorum and Olea europaea led to the identification of 51 and 57 proteins, respectively, most of which are described for the first time in this secreted fluid. These results indicate that the stigmatic exudate is an extracellular environment metabolically active, participating in at least 80 different biological processes and 97 molecular functions. The stigma exudate showed a markedly catabolic profile and appeared to possess the enzyme machinery necessary to degrade large polysaccharides and lipids secreted by papillae to smaller units, allowing their incorporation into the pollen tube during pollination. It may also regulate pollen-tube growth in the pistil through the selective degradation of tube-wall components. Furthermore, some secreted proteins were involved in pollen-tube adhesion and orientation, as well as in programmed cell death of the papillae cells in response to either compatible pollination or incompatible pollen rejection. Finally, the results also revealed a putative cross-talk between genetic programmes regulating stress/defence and pollination responses in the stigma.
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Affiliation(s)
- Juan David Rejón
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín (C.S.I.C.), C/ Profesor Albareda 1,18008 Granada, Spain
- These authors contributed equally to this work
| | - François Delalande
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC-DSA, UdS, CNRS, UMR 7178, 25 rue Becquerel, 67087 Strasbourg, France
- These authors contributed equally to this work
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC-DSA, UdS, CNRS, UMR 7178, 25 rue Becquerel, 67087 Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC-DSA, UdS, CNRS, UMR 7178, 25 rue Becquerel, 67087 Strasbourg, France
| | - Krzysztof Zienkiewicz
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín (C.S.I.C.), C/ Profesor Albareda 1,18008 Granada, Spain
- Department of Cell Biology, Institute of General and Molecular Biology, Nicolaus Copernicus University, Gargarina 9, 87–100 Toruń, Poland
| | - Juan de Dios Alché
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín (C.S.I.C.), C/ Profesor Albareda 1,18008 Granada, Spain
| | - María Isabel Rodríguez-García
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín (C.S.I.C.), C/ Profesor Albareda 1,18008 Granada, Spain
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC-DSA, UdS, CNRS, UMR 7178, 25 rue Becquerel, 67087 Strasbourg, France
| | - Antonio Jesús Castro
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín (C.S.I.C.), C/ Profesor Albareda 1,18008 Granada, Spain
- * To whom correspondence should be addressed. E-mail:
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28
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Douché T, Clemente HS, Burlat V, Roujol D, Valot B, Zivy M, Pont-Lezica R, Jamet E. Brachypodium distachyon
as a model plant toward improved biofuel crops: Search for secreted proteins involved in biogenesis and disassembly of cell wall polymers. Proteomics 2013; 13:2438-54. [DOI: 10.1002/pmic.201200507] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 04/19/2013] [Accepted: 05/27/2013] [Indexed: 01/06/2023]
Affiliation(s)
- Thibaut Douché
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse; UPS, UMR 5546; Castanet-Tolosan France
- CNRS, UMR 5546; Castanet-Tolosan France
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse; UPS, UMR 5546; Castanet-Tolosan France
- CNRS, UMR 5546; Castanet-Tolosan France
| | - Vincent Burlat
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse; UPS, UMR 5546; Castanet-Tolosan France
- CNRS, UMR 5546; Castanet-Tolosan France
| | - David Roujol
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse; UPS, UMR 5546; Castanet-Tolosan France
- CNRS, UMR 5546; Castanet-Tolosan France
| | - Benoît Valot
- CNRS, PAPPSO, UMR 0320/UMR 8120 Génétique Végétale; Gif sur Yvette France
- INRA, PAPPSO, UMR 0320/UMR 8120 Génétique Végétale; Gif sur Yvette France
| | - Michel Zivy
- CNRS, PAPPSO, UMR 0320/UMR 8120 Génétique Végétale; Gif sur Yvette France
- INRA, PAPPSO, UMR 0320/UMR 8120 Génétique Végétale; Gif sur Yvette France
| | - Rafael Pont-Lezica
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse; UPS, UMR 5546; Castanet-Tolosan France
- CNRS, UMR 5546; Castanet-Tolosan France
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse; UPS, UMR 5546; Castanet-Tolosan France
- CNRS, UMR 5546; Castanet-Tolosan France
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Garza-Caligaris LE, Avendaño-Vázquez AO, Alvarado-López S, Zúñiga-Sánchez E, Orozco-Segovia A, Pérez-Ruíz RV, Gamboa-Debuen A. At3g08030 transcript: a molecular marker of seed ageing. ANNALS OF BOTANY 2012; 110:1253-60. [PMID: 22975286 PMCID: PMC3478058 DOI: 10.1093/aob/mcs200] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 07/23/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Prolonged storage generally reduces seed viability and vigour, although the rate of deterioration varies among species and environmental conditions. Here, we suggest a possible ageing molecular marker: At3g08030 mRNA. At3g08030 is a member of the DUF642 highly conserved family of cell-wall-associated proteins that is specific for spermatophytes. METHODS At3g08030 expression was performed by RT-PCR and qRT-PCR analysis in seed samples differing in their rate of germination and final germination following a matrix priming and/or controlled deterioration (rapid ageing) treatment. KEY RESULTS The At3g08030 gene transcript was present during the entire Arabidopsis thaliana plant life cycle and in seeds, during maturation, the ripening period and after germination. Matrix priming treatment increased the rate of germination of control seeds and seeds aged by controlled deterioration. Priming treatments also increased At3g08030 expression. To determine whether the orthologues of this gene are also age markers in other plant species, At3g08030 was cloned in two wild species, Ceiba aesculifolia and Wigandia urens. As in A. thaliana, the At3g08030 transcript was not present in aged seeds of the tested species but was present in recently shed seeds. A reduction in germination performance of the aged seeds under salt stress was determined by germination assays. CONCLUSIONS At3g08030 mRNA detection in a dry seed lot has potential for use as a molecular marker for germination performance in a variety of plant species.
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Affiliation(s)
- Luz Elena Garza-Caligaris
- Instituto de Ecología, Universidad Nacional Autónoma de México, Apartado Postal 70-275, Ciudad Universitaria 04510, México, DF México.
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