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Narukawa H, Yokoyama R, Kuroha T, Nishitani K. Host-produced ethylene is required for marked cell expansion and endoreduplication in dodder search hyphae. PLANT PHYSIOLOGY 2021; 185:491-502. [PMID: 33721891 PMCID: PMC8133569 DOI: 10.1093/plphys/kiaa010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/28/2020] [Indexed: 05/13/2023]
Abstract
The genus Cuscuta comprises stem holoparasitic plant species with wide geographic distribution. Cuscuta spp. obtain water, nutrients, proteins, and mRNA from their host plants via a parasitic organ called the haustorium. As the haustorium penetrates into the host tissue, search hyphae elongate within the host tissue and finally connect with the host's vascular system. Invasion by Cuscuta spp. evokes various reactions within the host plant's tissues. Here, we show that, when Arabidopsis (Arabidopsis thaliana) is invaded by Cuscuta campestris, ethylene biosynthesis by the host plant promotes elongation of the parasite's search hyphae. The expression of genes encoding 1-aminocylclopropane-1-carboxylic acid (ACC) synthases, ACC SYNTHASE2 (AtACS2) and ACC SYNTHASE6 (AtACS6), was activated in the stem of Arabidopsis plants upon invasion by C. campestris. When the ethylene-deficient Arabidopsis acs octuple mutant was invaded by C. campestris, cell elongation and endoreduplication of the search hyphae were significantly reduced, and the inhibition of search hyphae growth was complemented by exogenous application of ACC. In contrast, in the C. campestris-infected Arabidopsis ethylene-insensitive mutant etr1-3, no growth inhibition of search hyphae was observed, indicating that ETHYLENE RESPONSE1-mediated ethylene signaling in the host plant is not essential for parasitism by C. campestris. Overall, our results suggest that C. campestris recognizes host-produced ethylene as a stimulatory signal for successful invasion.
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Affiliation(s)
- Hideki Narukawa
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Ryusuke Yokoyama
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Takeshi Kuroha
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Kazuhiko Nishitani
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan
- Author for communication: (K.N.)
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Xie J, Li J, Jie Y, Xie D, Yang D, Shi H, Zhong Y. Comparative transcriptomics of stem bark reveals genes associated with bast fiber development in Boehmeria nivea L. gaud (ramie). BMC Genomics 2020; 21:40. [PMID: 31931705 PMCID: PMC6958601 DOI: 10.1186/s12864-020-6457-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 01/07/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Boehmeria nivea L. Gaud (Ramie) produces one of the longest natural fibers in nature. The bark of ramie mainly comprises of the phloem tissue of stem and is the raw material for fiber. Therefore, identifying the molecular regulation of phloem development is important for understanding of bast fiber biosynthesis and improvement of fiber quality in ramie. RESULTS In this study, we collected top bud (TB), bark from internode elongating region (ER) and bark from internode fully elongated region (FER) from the ramie variety Zhongzhu No. 1. Histological study indicated that these samples contain phloem tissues at different developmental and maturation stages, with a higher degree of maturation of phloem tissue in FER. RNA sequencing (RNA-seq) was performed and de novo transcriptome was assembled. Unigenes and differentially expressed genes (DEGs) in these three samples were identified. The analysis of DEGs by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed clear differences in gene expression between ER and FER. Some unigenes involved in secondary cell wall biosynthesis were up-regulated in both ER and FER, while unigenes for some cell wall components or cell wall modifications showed differential expression between ER and FER. In addition, the ethylene respond factors (ERFs) in the ethylene signaling pathway were up-regulated in FER, and ent-kaurenoic acid oxidase (KAO) and GA 20-oxidase (GA20ox) for gibberellins biosynthesis were up-regulated while GA 2-oxidase (GA2ox) for gibberellin inactivation was down-regulated in FER. CONCLUSIONS Both morphological study and gene expression analysis supported a burst of phloem and vascular developmental processes during the fiber maturation in the ramie stem, and ethylene and gibberellin are likely to be involved in this process. Our findings provide novel insights into the phloem development and fiber maturation in ramie, which could be useful for fiber improvement in ramie and other fiber crops.
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Affiliation(s)
- Jiyong Xie
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Jiaqi Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Yucheng Jie
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Deyu Xie
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.,Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Di Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Yingli Zhong
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
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Arora K, Panda KK, Mittal S, Mallikarjuna MG, Thirunavukkarasu N. In Silico Characterization and Functional Validation of Cell Wall Modification Genes Imparting Waterlogging Tolerance in Maize. Bioinform Biol Insights 2017; 11:1177932217747277. [PMID: 29317803 PMCID: PMC5753887 DOI: 10.1177/1177932217747277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 11/11/2017] [Indexed: 01/10/2023] Open
Abstract
Cell wall modification (CWM) promotes the formation of aerenchyma in roots under waterlogging conditions as an adaptive mechanism. Lysigenous aerenchyma formation in roots improves oxygen transfer in plants, which highlights the importance of CWM as a focal point in waterlogging stress tolerance. We investigated the structural and functional compositions of CWM genes and their expression patterns under waterlogging conditions in maize. Cell wall modification genes were identified for 3 known waterlogging-responsive cis-acting regulatory elements, namely, GC motif, anaerobic response elements, and G-box, and 2 unnamed elements. Structural motifs mapped in CWM genes were represented in genes regulating waterlogging stress-tolerant pathways, including fermentation, glycolysis, programmed cell death, and reactive oxygen species signaling. The highly aligned regions of characterized and uncharacterized CWM proteins revealed common structural domains amongst them. Membrane spanning regions present in the protein structures revealed transmembrane activity of CWM proteins in the plant cell wall. Cell wall modification proteins had interacted with ethylene-responsive pathway regulating genes (E3 ubiquitin ligases RNG finger and F-box) in a maize protein-protein interaction network. Cell wall modification genes had also coexpressed with energy metabolism, programmed cell death, and reactive oxygen species signaling, regulating genes in a single coexpression cluster. These configurations of CWM genes can be used to modify the protein expression in maize under waterlogging stress condition. Our study established the importance of CWM genes in waterlogging tolerance, and these genes can be used as candidates in introgression breeding and genome editing experiments to impart tolerance in maize hybrids.
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Affiliation(s)
- Kanika Arora
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India.,Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Kusuma Kumari Panda
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Shikha Mittal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Nepolean Thirunavukkarasu
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India.,Maize Research Lab, Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Nawaz MA, Rehman HM, Imtiaz M, Baloch FS, Lee JD, Yang SH, Lee SI, Chung G. Systems Identification and Characterization of Cell Wall Reassembly and Degradation Related Genes in Glycine max (L.) Merill, a Bioenergy Legume. Sci Rep 2017; 7:10862. [PMID: 28883533 PMCID: PMC5589831 DOI: 10.1038/s41598-017-11495-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/24/2017] [Indexed: 12/22/2022] Open
Abstract
Soybean is a promising biomass resource for generation of second-generation biofuels. Despite the utility of soybean cellulosic biomass and post-processing residues in biofuel generation, there is no comprehensive information available on cell wall loosening and degradation related gene families. In order to achieve enhanced lignocellulosic biomass with softened cell walls and reduced recalcitrance, it is important to identify genes involved in cell wall polymer loosening and degrading. Comprehensive genome-wide analysis of gene families involved in cell wall modifications is an efficient stratagem to find new candidate genes for soybean breeding for expanding biofuel industry. We report the identification of 505 genes distributed among 12 gene families related to cell wall loosening and degradation. 1262 tandem duplication events contributed towards expansion and diversification of studied gene families. We identified 687 Simple Sequence Repeat markers and 5 miRNA families distributed on 316 and 10 genes, respectively. Publically available microarray datasets were used to explore expression potential of identified genes in soybean plant developmental stages, 68 anatomical parts, abiotic and biotic stresses. Co-expression networks revealed transcriptional coordination of different gene families involved in cell wall loosening and degradation process.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Muhammad Imtiaz
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510275, China
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, 14280, Bolu, Turkey
| | - Jeong Dong Lee
- Division of Plant Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Soo In Lee
- Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences (NAS), Jeonju, 54874, Republic of Korea.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea.
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Pei M, Niu J, Li C, Cao F, Quan S. Identification and expression analysis of genes related to calyx persistence in Korla fragrant pear. BMC Genomics 2016; 17:132. [PMID: 26911295 PMCID: PMC4765163 DOI: 10.1186/s12864-016-2470-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 02/12/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The objective of this study was to increase understanding about genetic mechanisms affecting calyx persistence in Korla fragrant pear (Pyrus brestschneideri Rehd). Flowers were collected at early bloom, full bloom, and late bloom. The RNA was extracted from the flowers and then combined according to calyx type. Transcriptome and digital gene expression (DGE) profiles of flowers, ovaries, and sepals with persistent calyx (SC_hua, SC_ep, and SC_zf, respectively) were compared with those of flowers, ovaries, and sepals with deciduous calyx (TL_hua, TL_ep, and TL_zf, respectively). Temporal changes in the expression of selected genes in floral organs with either persistent or deciduous calyx were compared using real-time quantitative PCR (qRT-PCR). RESULTS Comparison of the transcriptome sequences for SC_hua and TL_hua indicated 26 differentially expressed genes (DEGs) with known relationship to abscission and 10 DEGs with unknown function. We identified 98 MYB and 21 SPL genes from the assembled unigenes. From SC_zf vs TL_zf, we identified 21 DEGs with known relationship to abscission and 18 DEGs with unknown function. From SC_ep vs TL_ep, 12 DEGs with known relationship to abscission were identified along with 11 DEGs with unknown function. Ten DEGs were identified by both transcriptome sequencing and DGE sequencing. CONCLUSIONS More than 50 DEGs were observed that were related to calyx persistence in Korla fragrant pear. Some of the genes were related to cell wall degradation, plant hormone signal transduction, and stress response. Other DEGs were identified as zinc finger protein genes and lipid transfer protein genes. Further analysis showed that calyx persistence in Korla fragment pear was a metabolic process regulated by many genes related to cell wall degradation and plant hormones.
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Affiliation(s)
- Maosong Pei
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, Xinjiang, China. .,Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003, Xinjiang, China.
| | - Jianxin Niu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, Xinjiang, China. .,Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003, Xinjiang, China.
| | - Chenjing Li
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, Xinjiang, China. .,Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003, Xinjiang, China.
| | - Fujun Cao
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, Xinjiang, China. .,Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003, Xinjiang, China.
| | - Shaowen Quan
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, Xinjiang, China. .,Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003, Xinjiang, China.
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Hall H, Ellis B. Transcriptional programming during cell wall maturation in the expanding Arabidopsis stem. BMC PLANT BIOLOGY 2013; 13:14. [PMID: 23350960 PMCID: PMC3635874 DOI: 10.1186/1471-2229-13-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/21/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Plant cell walls are complex dynamic structures that play a vital role in coordinating the directional growth of plant tissues. The rapid elongation of the inflorescence stem in the model plant Arabidopsis thaliana is accompanied by radical changes in cell wall structure and chemistry, but analysis of the underlying mechanisms and identification of the genes that are involved has been hampered by difficulties in accurately sampling discrete developmental states along the developing stem. RESULTS By creating stem growth kinematic profiles for individual expanding Arabidopsis stems we have been able to harvest and pool developmentally-matched tissue samples, and to use these for comparative analysis of global transcript profiles at four distinct phases of stem growth: the period of elongation rate increase, the point of maximum growth rate, the point of stem growth cessation and the fully matured stem. The resulting profiles identify numerous genes whose expression is affected as the stem tissues pass through these defined growth transitions, including both novel loci and genes identified in earlier studies. Of particular note is the preponderance of highly active genes associated with secondary cell wall deposition in the region of stem growth cessation, and of genes associated with defence and stress responses in the fully mature stem. CONCLUSIONS The use of growth kinematic profiling to create tissue samples that are accurately positioned along the expansion growth continuum of Arabidopsis inflorescence stems establishes a new standard for transcript profiling analyses of such tissues. The resulting expression profiles identify a substantial number of genes whose expression is correlated for the first time with rapid cell wall extension and subsequent fortification, and thus provide an important new resource for plant biologists interested in gene discovery related to plant biomass accumulation.
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Affiliation(s)
- Hardy Hall
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Currently: Swedish University of Agricultural Sciences (SLU), Umeå, 901 83, Sweden
| | - Brian Ellis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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7
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Etchells JP, Moore L, Jiang WZ, Prescott H, Capper R, Saunders NJ, Bhatt AM, Dickinson HG. A role for BELLRINGER in cell wall development is supported by loss-of-function phenotypes. BMC PLANT BIOLOGY 2012; 12:212. [PMID: 23148846 PMCID: PMC3538058 DOI: 10.1186/1471-2229-12-212] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 09/17/2012] [Indexed: 05/05/2023]
Abstract
BACKGROUND Homeodomain transcription factors play critical roles in metazoan development. BELLRINGER (BLR), one such transcription factor, is involved in diverse developmental processes in Arabidopsis, acting in vascular differentiation, phyllotaxy, flower and fruit development. BLR also has a redundant role in meristem maintenance. Cell wall remodelling underpins many of these processes, and BLR has recently been shown to regulate expression of PECTIN METHYL-ESTERASE 5 (PME5), a cell wall modifying enzyme in control of phyllotaxy. We have further explored the role of BLR in plant development by analysing phenotypes and gene expression in a series of plants over-expressing BLR, and generating combinatorial mutants with blr, brevipedicellus (bp), a member of the KNOX1 family of transcription factors that has previously been shown to interact with blr, and the homeodomain transcription factor revoluta (rev), required for radial patterning of the stem. RESULTS Plants over-expressing BLR exhibited a wide range of phenotypes. Some were defective in cell size and demonstrated misregulation of genes predominantly affecting cell wall development. Other lines with more extreme phenotypes failed to generate lateral organs, consistent with BLR repressing transcription in the shoot apex. Cell wall dynamics are also affected in blr mutant plants, and BLR has previously been shown to regulate vascular development in conjunction with BP. We found that when bp and blr were combined with rev, a set of defects was observed that were distinct from those of bp blr lines. In these triple mutants xylem development was most strikingly affected, resulting in an almost complete lack of vessels and xylem parenchyma with secondary thickening. CONCLUSIONS Our data support a role for BLR in ordering the shoot apex and, in conjunction with BP and REV, playing a part in determining the composition and organisation of the vascular system. Microarray analysis strongly indicates that the striking vascular phenotypes of blr bp rev triple mutants and plants over-expressing BLR result from the misregulation of a suite of genes, targets of BLR in wild type plants, that determine cell size and structure in the developing vasculature.
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Affiliation(s)
- J Peter Etchells
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, UK
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Lucy Moore
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, UK
| | - Wen Zhi Jiang
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, UK
- Present address: Department of Biochemistry, University of Nebraska, Lincoln, NE, USA
| | - Helen Prescott
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, UK
| | - Richard Capper
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, UK
- Present address: Agilent Technologies, Wokingham, UK
| | - Nigel J Saunders
- Department of Pathology, University of Oxford, South Parks Road, Oxford, UK
- Present address: Centre for Systems and Synthetic Biology, Brunel University, London, UK
| | - Anuj M Bhatt
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, UK
| | - Hugh G Dickinson
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, UK
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Shi T, Gao Z, Wang L, Zhang Z, Zhuang W, Sun H, Zhong W. Identification of differentially-expressed genes associated with pistil abortion in Japanese apricot by genome-wide transcriptional analysis. PLoS One 2012; 7:e47810. [PMID: 23091648 PMCID: PMC3472986 DOI: 10.1371/journal.pone.0047810] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 09/17/2012] [Indexed: 12/05/2022] Open
Abstract
The phenomenon of pistil abortion widely occurs in Japanese apricot, and imperfect flowers with pistil abortion seriously decrease the yield in production. Although transcriptome analyses have been extensively studied in the past, a systematic study of differential gene expression has not been performed in Japanese apricot. To investigate genes related to the pistil development of Japanese apricot, high-throughput sequencing technology (Illumina) was employed to survey gene expression profiles from perfect and imperfect Japanese apricot flower buds. 3,476,249 and 3,580,677 tags were sequenced from two libraries constructed from perfect and imperfect flower buds of Japanese apricot, respectively. There were 689 significant differentially-expressed genes between the two libraries. GO annotation revealed that highly ranked genes were those implicated in small molecule metabolism, cellular component organisation or biogenesis at the cellular level and fatty acid metabolism. According to the results, we assumed that late embryogenesis abundant protein (LEA), Dicer-like 3 (DCL3) Xyloglucan endotransglucosylase/hydrolase 2 (XTH2), Pectin lyase-like superfamily protein (PPME1), Lipid transfer protein 3 (LTP3), Fatty acid biosynthesis 1 (FAB1) and Fatty acid desaturase 5 (FAD5) might have relationships with the pistil abortion in Japanese apricot. The expression patterns of 36 differentially expressed genes were confirmed by real-time (RT)-PCR. This is the first report of the Illumina RNA-seq technique being used for the analysis of differentially-expressed gene profiles related to pistil abortion that both computationally and experimentally provides valuable information for the further functional characterisation of genes associated with pistil development in woody plants.
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Affiliation(s)
- Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
- * E-mail:
| | - Liangju Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
| | - Zhen Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
| | - Weibing Zhuang
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
| | - Hailong Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
| | - Wenjun Zhong
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
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Shi T, Zhuang W, Zhang Z, Sun H, Wang L, Gao Z. Comparative proteomic analysis of pistil abortion in Japanese apricot (Prunus mume Sieb. et Zucc). JOURNAL OF PLANT PHYSIOLOGY 2012; 169:1301-1310. [PMID: 22717137 DOI: 10.1016/j.jplph.2012.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Revised: 04/28/2012] [Accepted: 05/08/2012] [Indexed: 06/01/2023]
Abstract
The phenomenon of pistil abortion widely occurs in Japanese apricot and has seriously affected the yield in production. We used a combination of two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time of flight/time of flight (MALDI-TOF/TOF) approaches to identify the differentially expressed proteome between perfect and imperfect flower buds in Japanese apricot. More than 400 highly reproducible protein spots (P<0.05) were detected and 27 protein spots showed a greater than two-fold difference in their expression values. The proteins identified were classified into eight functional classifications and ten process categories, according to the Gene Ontology (GO). Acetyl-CoA produced by ATP citrate lyase (ACL) as a structural substance during formation of the cell wall could regulate pistil abortion in Japanese apricot. S-adenosylmethionine (SAM), xyloglucan endotransglucosylase/hydrolases (XTHs) and caffeoyl-CoA-O-methyl transferase (CCoAOMT) could promote cell wall formation in perfect flower buds of Japanese apricot, greatly contributing to pistil development. Spermidine hydroxycinnamoyl transferase (SHT) may be involved in the O-methylation of spermidine conjugates and could contribute to abnormal floral development. The identification of such differentially expressed proteins provides new targets for future studies that will assess their physiological roles and significance in pistil abortion.
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Affiliation(s)
- Ting Shi
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, PR China
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10
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Hall H, Ellis B. Developmentally equivalent tissue sampling based on growth kinematic profiling of Arabidopsis inflorescence stems. THE NEW PHYTOLOGIST 2012; 194:287-296. [PMID: 22313381 DOI: 10.1111/j.1469-8137.2012.04060.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
• Directional growth in Arabidopsis thaliana during bolting of the inflorescence stem makes this an attractive system for study of the underlying processes of tissue elongation and cell wall extension. Analysis of local molecular events accompanying Arabidopsis inflorescence stem elongation is hampered by difficulties in isolating developmentally matched tissue samples from different plants. • Here, we present a novel sampling approach in which specific developmental stages along the developing stem are defined nonintrusively in terms of their relative elemental growth rate by use of time-lapse imagery and subsequent derivation of growth kinematic profiles for individual plants. • Growth kinematic profiling reveals that key developmental transitions such as the point of maximum elongation rate and the point of cessation of elongation occur over broad and overlapping ranges across individuals within a population of the Columbia (Col-0) ecotype. The position of these transitions is only weakly correlated with overall plant height, which undermines the common assumption that physically similar plants have closely matched growth profiles. • This kinematic profiling approach provides high-resolution growth phenotyping of the developing stem and thereby enables the harvest, pooling and analysis of developmentally matched tissue samples from multiple Arabidopsis plants.
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Affiliation(s)
- Hardy Hall
- Department of Botany and the Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Brian Ellis
- Department of Botany and the Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, Canada, V6T 1Z4
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11
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Sharma R, Tan F, Jung KH, Sharma MK, Peng Z, Ronald PC. Transcriptional dynamics during cell wall removal and regeneration reveals key genes involved in cell wall development in rice. PLANT MOLECULAR BIOLOGY 2011; 77:391-406. [PMID: 21887580 DOI: 10.1007/s11103-011-9819-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 08/13/2011] [Indexed: 05/23/2023]
Abstract
Efficient and cost-effective conversion of plant biomass to usable forms of energy requires a thorough understanding of cell wall biosynthesis, modification and degradation. To elucidate these processes, we assessed the expression dynamics during enzymatic removal and regeneration of rice cell walls in suspension cells over time. In total, 928 genes exhibited significant up-regulation during cell wall removal, whereas, 79 genes were up-regulated during cell wall regeneration. Both gene sets are enriched for kinases, transcription factors and genes predicted to be involved in cell wall-related functions. Integration of the gene expression datasets with a catalog of known and/or predicted biochemical pathways from rice, revealed metabolic and hormonal pathways involved in cell wall degradation and regeneration. Rice lines carrying Tos17 mutations in genes up-regulated during cell wall removal exhibit dwarf phenotypes. Many of the genes up-regulated during cell wall development are also up-regulated in response to infection and environmental perturbations indicating a coordinated response to diverse types of stress.
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Affiliation(s)
- Rita Sharma
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
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12
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Pedreira J, Herrera MT, Zarra I, Revilla G. The overexpression of AtPrx37, an apoplastic peroxidase, reduces growth in Arabidopsis. PHYSIOLOGIA PLANTARUM 2011; 141:177-87. [PMID: 21044085 DOI: 10.1111/j.1399-3054.2010.01427.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Understanding peroxidase function in plants is difficult because of the lack of substrate specificity, the high number of genes and their diversity in structure. In the present study, the relative expression of 22 genes coding putative peroxidases (E.C 1.11.1.x) in Arabidopsis was studied. The relative expression of AtPrx37 showed a correlation with the cessation of growth in rosette leaves as well as with the growth capacity along the flower stem. Using AtPrx37::GUS construction, its expression was associated with the vascular bundles. Furthermore, the overexpression of AtPrx37 under the control of CaMV 35S promoter rendered a dwarf phenotype with smaller plants and delayed development. The plants overexpressing AtPrx37 also showed an increase in the amount of esterified phenolic material associated with their walls. A role in the growth cessation and phenolic cross-linking during lignin deposition is postulated.
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Affiliation(s)
- Jorge Pedreira
- Departamento de Fisiología Vegetal, Facultad de Biología, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
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13
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Opazo MC, Figueroa CR, Henríquez J, Herrera R, Bruno C, Valenzuela PDT, Moya-León MA. Characterization of two divergent cDNAs encoding xyloglucan endotransglycosylase/hydrolase (XTH) expressed in Fragaria chiloensis fruit. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2010; 179:479-88. [PMID: 21802606 DOI: 10.1016/j.plantsci.2010.07.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 07/21/2010] [Accepted: 07/22/2010] [Indexed: 05/18/2023]
Abstract
Chilean strawberry (Fragaria chiloensis), the maternal progenitor of Fragaria×ananassa, has emerged as a new berry fruit with excellent organoleptic characteristics. The fast softening of strawberries is a limiting step for their commercialization. Fruit softening has been shown to be related to cell wall degradation. Several enzymatic activities related to this process have been isolated in strawberry fruit, however xyloglucan endotransglycosylase/hydrolase (XTH) enzymes have not been identified or characterized so far. Two XTH genes were identified in an EST database of F. chiloensis fruit with high homology to other plant XTHs. We isolated the full-length cDNAs associated to these ESTs in F. chiloensis (Fc-XTH1, Fc-XTH2). Phylogenetic analysis suggests that both F. chiloensis XTH genes belong to distant phylogenetic groups of XTHs. Moreover, DNA gel-blot analysis indicates different genomic organization between the two genes. By means of Real Time qPCR analysis, gene expression profiles show a transcriptional profile of Fc-XTH1 transcripts congruent with a probable role during strawberry ripening, while that exhibited by Fc-XTH2 could be related with vegetative processes like leaf growth. On the other hand, immunodetection and enzyme activity assays allow the detection of XTH-related proteins and high xyloglucan transglycosylating (XETA) and degrading (XDA) activities at the turning stage. The data presented confirms the existence of two divergent XTH genes, and XET and XEH activities, in F. chiloensis fruit.
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Affiliation(s)
- María C Opazo
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Biología Vegetal y Biotecnología, Universidad de Talca, Casilla 747, Talca, Chile
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14
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Sasidharan R, Chinnappa C, Staal M, Elzenga JTM, Yokoyama R, Nishitani K, Voesenek LA, Pierik R. Light quality-mediated petiole elongation in Arabidopsis during shade avoidance involves cell wall modification by xyloglucan endotransglucosylase/hydrolases. PLANT PHYSIOLOGY 2010; 154:978-90. [PMID: 20688978 PMCID: PMC2949003 DOI: 10.1104/pp.110.162057] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 08/02/2010] [Indexed: 05/18/2023]
Abstract
Some plants can avoid shaded conditions via rapid shoot elongation, thus growing into better lit areas in a canopy. Cell wall-modifying mechanisms promoting this elongation response, therefore, are important regulatory points during shade avoidance. Two major cell wall-modifying protein families are expansins and xyloglucan endotransglucosylase/hydrolases (XTHs). The role of these proteins during shade avoidance was studied in Arabidopsis (Arabidopsis thaliana). In response to two shade cues, low red to far-red light (implying neighbor proximity) and green shade (mimicking dense canopy conditions), Arabidopsis showed classic shade avoidance features: petiole elongation and leaf hyponasty. Measurement of the apoplastic proton flux in green shade-treated petioles revealed a rapid efflux of protons into the apoplast within minutes, unlike white light controls. This apoplastic acidification probably provides the acidic pH required for the optimal activity of cell wall-modifying proteins like expansins and XTHs. Acid-induced extension, expansin susceptibility, and extractable expansin activity were similar in petioles from white light- and shade-treated plants. XTH activity, however, was high in petioles exposed to shade treatments. Five XTH genes (XTH9, -15, -16, -17, and -19) were positively regulated by low red to far-red light conditions, while the latter four and XTH22 showed a significant up-regulation also in response to green shade. Consistently, knockout mutants for two of these XTH genes also had reduced or absent shade avoidance responses to these light signals. These results point toward the cell wall as a vital regulatory point during shade avoidance.
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Affiliation(s)
| | | | | | | | | | | | | | - Ronald Pierik
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CA Utrecht, The Netherlands (R.S., L.A.C.J.V., R.P.); Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4 (C.C.C.); Ecophysiology of Plants, University of Groningen, 9750AA Haren, The Netherlands (M.S., J.T.M.E.); Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai 980–8578, Japan (R.Y., K.N.)
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15
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Koizumi K, Yokoyama R, Nishitani K. Mechanical load induces upregulation of transcripts for a set of genes implicated in secondary wall formation in the supporting tissue of Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2009; 122:651-659. [PMID: 19582540 DOI: 10.1007/s10265-009-0251-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2009] [Accepted: 06/05/2009] [Indexed: 05/28/2023]
Abstract
We examined the effects of mechanical load on transcripts of a set of cell wall related genes that are implicated in the formation of supporting tissues, by applying a 50 mg strip of aluminum foil to the inflorescence stem of Arabidopsis thaliana, a weight roughly half the fresh weight of the stem. Transcript levels of 12 of the 15 genes examined were increased by load application, as were the levels of some transcription factors that regulate secondary wall formation. These findings support the involvement of a load-sensing system in regulation of supporting tissue formation via transcriptional regulation of cell wall related genes.
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Affiliation(s)
- Kento Koizumi
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578, Japan
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16
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Ndamukong I, Chetram A, Saleh A, Avramova Z. Wall-modifying genes regulated by the Arabidopsis homolog of trithorax, ATX1: repression of the XTH33 gene as a test case. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 58:541-53. [PMID: 19154201 DOI: 10.1111/j.1365-313x.2009.03798.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The plant cell wall is a dynamic structure playing important roles in the control of plant cell growth and differentiation. These processes involve global reprogramming of the genome driven by dynamic changes in chromatin structure. The chromatin modifier ARABIDOPSIS HOMOLOG OF TRITHORAX (ATX1) methylates lysine residue 4 on histone H3 (H3K4me), acting as an epigenetic mark on associated genes. The remarkable overrepresentation in the ATX1-regulated gene fraction of genes encoding plasma membrane and cell wall-remodeling activities suggested a link between two separate factors affecting growth, development and adaptation in Arabidopsis: the wall-modifying activities regulating cell extension, growth and fate, and the epigenetic mechanisms regulating chromatin structure and gene expression. A co-regulated fraction of specific wall-modifying proteins suggests that they may function together. Here, we study the ATX1-dependent expression of the gene encoding the wall-loosening factor XTH33 as a test case for development- and tissue-specific effects displayed by the chromatin modifier. In addition, we show that XTH33 is, most likely, an integral plasma membrane protein. A putative transmembrane domain is conserved in some, but not all, XTH family members, suggesting that they may be differently positioned when functioning as wall modifiers.
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17
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Kurasawa K, Matsui A, Yokoyama R, Kuriyama T, Yoshizumi T, Matsui M, Suwabe K, Watanabe M, Nishitani K. The AtXTH28 gene, a xyloglucan endotransglucosylase/hydrolase, is involved in automatic self-pollination in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2009; 50:413-22. [PMID: 19139039 PMCID: PMC2642609 DOI: 10.1093/pcp/pcp003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Accepted: 01/04/2009] [Indexed: 05/22/2023]
Abstract
Successful automatic self-pollination in flowering plants is dependent on the correct development of reproductive organs. In the stamen, the appropriate growth of the filament, which largely depends on the mechanical properties of the cell wall, is required to position the anther correctly close to the stigma at the pollination stage. Xyloglucan endotransglucosylase/hydrolases (XTHs) are a family of enzymes that mediate the construction and restructuring of xyloglucan cross-links, thereby controlling the extensibility or mechanical properties of the cell wall in a wide variety of plant tissues. Our reverse genetic analysis has revealed that a loss-of-function mutation of an Arabidopsis XTH family gene, AtXTH28, led to a decrease in capability for self-pollination, probably due to inhibition of stamen filament growth. Our results also suggest that the role of AtXTH28 in the development of the stamen is not functionally redundant with its closest paralog, AtXTH27. Thus, our finding indicates that AtXTH28 is specifically involved in the growth of stamen filaments, and is required for successful automatic self-pollination in certain flowers in Arabidopsis thaliana.
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Affiliation(s)
- Kasumi Kurasawa
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Akihiro Matsui
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Ryusuke Yokoyama
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Tomoko Kuriyama
- Plant Functional Genomics Research Team, Plant Functional Genomics Research Group, Plant Science Center, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Takeshi Yoshizumi
- Plant Functional Genomics Research Team, Plant Functional Genomics Research Group, Plant Science Center, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Minami Matsui
- Plant Functional Genomics Research Team, Plant Functional Genomics Research Group, Plant Science Center, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Keita Suwabe
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
| | - Masao Watanabe
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
- The 21st Century Center of Excellence Program, Iwate University, Morioka, 020-8550 Japan
| | - Kazuhiko Nishitani
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
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18
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Minic Z, Jamet E, San-Clemente H, Pelletier S, Renou JP, Rihouey C, Okinyo DPO, Proux C, Lerouge P, Jouanin L. Transcriptomic analysis of Arabidopsis developing stems: a close-up on cell wall genes. BMC PLANT BIOLOGY 2009; 9:6. [PMID: 19149885 PMCID: PMC2649120 DOI: 10.1186/1471-2229-9-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2008] [Accepted: 01/16/2009] [Indexed: 05/17/2023]
Abstract
BACKGROUND Different strategies (genetics, biochemistry, and proteomics) can be used to study proteins involved in cell biogenesis. The availability of the complete sequences of several plant genomes allowed the development of transcriptomic studies. Although the expression patterns of some Arabidopsis thaliana genes involved in cell wall biogenesis were identified at different physiological stages, detailed microarray analysis of plant cell wall genes has not been performed on any plant tissues. Using transcriptomic and bioinformatic tools, we studied the regulation of cell wall genes in Arabidopsis stems, i.e. genes encoding proteins involved in cell wall biogenesis and genes encoding secreted proteins. RESULTS Transcriptomic analyses of stems were performed at three different developmental stages, i.e., young stems, intermediate stage, and mature stems. Many genes involved in the synthesis of cell wall components such as polysaccharides and monolignols were identified. A total of 345 genes encoding predicted secreted proteins with moderate or high level of transcripts were analyzed in details. The encoded proteins were distributed into 8 classes, based on the presence of predicted functional domains. Proteins acting on carbohydrates and proteins of unknown function constituted the two most abundant classes. Other proteins were proteases, oxido-reductases, proteins with interacting domains, proteins involved in signalling, and structural proteins. Particularly high levels of expression were established for genes encoding pectin methylesterases, germin-like proteins, arabinogalactan proteins, fasciclin-like arabinogalactan proteins, and structural proteins. Finally, the results of this transcriptomic analyses were compared with those obtained through a cell wall proteomic analysis from the same material. Only a small proportion of genes identified by previous proteomic analyses were identified by transcriptomics. Conversely, only a few proteins encoded by genes having moderate or high level of transcripts were identified by proteomics. CONCLUSION Analysis of the genes predicted to encode cell wall proteins revealed that about 345 genes had moderate or high levels of transcripts. Among them, we identified many new genes possibly involved in cell wall biogenesis. The discrepancies observed between results of this transcriptomic study and a previous proteomic study on the same material revealed post-transcriptional mechanisms of regulation of expression of genes encoding cell wall proteins.
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Affiliation(s)
- Zoran Minic
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- Laboratoire de Biologie Cellulaire, Institut National de la Recherche Agronomique (INRA), Route de St-Cyr, 78026 Versailles Cedex, France
| | - Elisabeth Jamet
- Surfaces Cellulaires et Signalisation chez les Végétaux, UMR 5546 CNRS-UPS, Université de Toulouse, 24 Chemin de Borde Rouge, BP42617, 31326-Castanet-Tolosan, France
| | - Hélène San-Clemente
- Surfaces Cellulaires et Signalisation chez les Végétaux, UMR 5546 CNRS-UPS, Université de Toulouse, 24 Chemin de Borde Rouge, BP42617, 31326-Castanet-Tolosan, France
| | - Sandra Pelletier
- Unité de Recherche en Génomique Végétale, UMR INRA 1165-CNRS 8114, UEVE, 91057 Evry cedex, France
| | - Jean-Pierre Renou
- Unité de Recherche en Génomique Végétale, UMR INRA 1165-CNRS 8114, UEVE, 91057 Evry cedex, France
| | - Christophe Rihouey
- Faculté des Sciences, FRE CNRS 3090, IFRMP23, Université de Rouen, F-76821 Mont Saint Aignan Cedex, France
| | - Denis PO Okinyo
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
| | - Caroline Proux
- Unité de Recherche en Génomique Végétale, UMR INRA 1165-CNRS 8114, UEVE, 91057 Evry cedex, France
| | - Patrice Lerouge
- Faculté des Sciences, FRE CNRS 3090, IFRMP23, Université de Rouen, F-76821 Mont Saint Aignan Cedex, France
| | - Lise Jouanin
- Laboratoire de Biologie Cellulaire, Institut National de la Recherche Agronomique (INRA), Route de St-Cyr, 78026 Versailles Cedex, France
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19
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Gantulga D, Turan Y, Bevan DR, Esen A. The Arabidopsis At1g45130 and At3g52840 genes encode beta-galactosidases with activity toward cell wall polysaccharides. PHYTOCHEMISTRY 2008; 69:1661-70. [PMID: 18359051 DOI: 10.1016/j.phytochem.2008.01.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Revised: 01/15/2008] [Accepted: 01/21/2008] [Indexed: 05/21/2023]
Abstract
The Arabidopsis genes At1g45130 and At3g52840 encode the beta-galactosidase isozymes Gal-5 and Gal-2 that belong to Glycosyl Hydrolase Family 35 (GH 35). The two enzymes share 60% sequence identity with each other and 38-81% with other plant beta-galactosidases that are reported to be involved in cell wall modification. We studied organ-specific expression of the two isozymes. According to our western blot analysis using peptide-specific antibodies, Gal-5 and Gal-2 are most highly expressed in stem and rosette leaves. We show by dot-immunoblotting that Gal-5 and Gal-2 are associated with the cell wall in Arabidopsis. We also report expression of the recombinant enzymes in P. pastoris and describe their substrate specificities. Both enzymes hydrolyze the synthetic substrate para-nitrophenyl-beta-d-galactopyranoside and display optimal enzyme activity between pH 4.0 and 4.5, similar to the pH optimum reported for other well-characterized plant beta-galactosidases. Both Gal-5 and Gal-2 show a broad specificity for the aglycone moiety and a strict specificity for the glycone moiety in that they prefer galactose and its 6-deoxy analogue, fucose. Both enzymes cleave beta-(1,4) and beta-(1,3) linkages in galacto-oligosaccharides and hydrolyze the pectic fraction of Arabidopsis cell wall. These findings suggest that Gal-5 and Gal-2 could be involved in the modification of cell wall polysaccharides.
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Affiliation(s)
- Dashzeveg Gantulga
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
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Yang X, Tu L, Zhu L, Fu L, Min L, Zhang X. Expression profile analysis of genes involved in cell wall regeneration during protoplast culture in cotton by suppression subtractive hybridization and macroarray. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:3661-74. [PMID: 18775953 PMCID: PMC2561149 DOI: 10.1093/jxb/ern214] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2008] [Revised: 07/27/2008] [Accepted: 07/30/2008] [Indexed: 05/18/2023]
Abstract
The molecular mechanisms underlying cell wall biosynthesis are poorly understood. In this study, microscopic analysis showed that protoplasts generated a new cell wall within 48 h after transfer to a wall-regeneration medium. To identify genes related to cell wall biosynthesis in cotton, suppression subtractive hybridization was used to visualize differential gene expression at seven time points within the first 48 h. In total, 412 differentially expressed sequence tags (ESTs; >3-fold) were identified, and 210 unigenes were sequenced successfully. As confirmed by reverse-transcription PCR (RT-PCR) and real-time quantitative reverse-transcription PCR (QRT-PCR) analysis, the selected genes displayed complex expression patterns during cell wall regeneration from protoplasts and included most previously published cell-wall-associated genes. ESTs similar to cell-wall-protein genes, such as proline-rich protein (PRPL), glycine-rich protein (GRP), extension (EPR1), fasciclin-like arabinogalactan protein (FLA2), and expensing-like protein (EXLA and EXLB), which might participate in primary cell wall or secondary cell wall construction and modification, were up-regulated during cell wall regeneration from protoplasts. Sucrose synthase, an important enzyme in the sugar signalling pathway, played important roles in cellulose biosynthesis. Our findings also highlighted the function of some transcription factors during cell wall regeneration from protoplasts, including the squamosa promoter binding protein-like 14 (SPL14), NAC, Gbiaa-re, MYB, WRKY, swellmap 1 (SMP1), RAD5, and zinc finger family protein, as well as the enrichment of Ca(2+)-calmodulin signal molecules. On the basis of the gene expression profiles, a model of cell wall regeneration from protoplasts derived from cotton suspension cultures is proposed.
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21
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Tucker ML, Burke A, Murphy CA, Thai VK, Ehrenfried ML. Gene expression profiles for cell wall-modifying proteins associated with soybean cyst nematode infection, petiole abscission, root tips, flowers, apical buds, and leaves. JOURNAL OF EXPERIMENTAL BOTANY 2007; 58:3395-406. [PMID: 17916637 DOI: 10.1093/jxb/erm188] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Changes in transcript accumulation for cell wall-modifying proteins were examined in excised soybean root pieces colonized by soybean cyst nematodes (SCN), Heterodera glycines, using RT-PCR and soybean Affymetrix GeneChips. Sequence-specific PCR primer pairs were prepared from sequence data for core sequences in the GenBank soybean database and consensus sequences derived from the assembly of soybean ESTs. In addition, to identify previously uncharacterized soybean transcripts, degenerate primers were prepared for conserved motifs in cellulases (endo-1,4-beta-glucanases, EGases) and polygalacturonases (PGs) and these were used to amplify segments of transcripts that were then extended with 3' and 5' RACE. Several novel EGase and PG transcripts were identified. Gene expression patterns were determined by real-time RT-PCR for 11 EGases, three expansins (EXPs), 14 PGs, two pectate lyases (PLs), and two xyloglucan endotransglucosylase/hydrolases (XTHs) in soybean roots inoculated with SCN, non-inoculated roots, serial dissections of root tips, leaf abscission zones, flowers, apical buds, and expanding leaves. A large number of genes associated with cell wall modifications are strongly up-regulated in root pieces colonized by SCN. However, in contrast to most of the transcripts for cell wall proteins, two XTH transcripts were specifically down-regulated in the colonized root pieces. Gene expression in serial dissections of root tips (0-2 mm, and 2-7 mm) and whole roots indicate that the SCN up-regulated genes are associated with a wide range of developmental processes in roots. Also of interest, many of the cDNAs examined were up-regulated in petiole abscission zones induced to abscise with ethylene.
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Affiliation(s)
- Mark L Tucker
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Bldg 006, 10300 Baltimore Ave, Beltsville, MD 20705-2350, USA.
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22
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Koizumi K, Yokoyama R, Kamada M, Omori K, Ishioka N, Takeoka H, Shimazu T, Nishitani K. Reverse Genetic Approach to Exploring Genes Responsible for Cell-Wall Dynamics in Supporting Tissues of Arabidopsis thaliana under Microgravity Conditions. ACTA ACUST UNITED AC 2007. [DOI: 10.2187/bss.21.48] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Nakano T, Suzuki K, Ohtsuki N, Tsujimoto Y, Fujimura T, Shinshi H. Identification of genes of the plant-specific transcription-factor families cooperatively regulated by ethylene and jasmonate in Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2006; 119:407-13. [PMID: 16820983 DOI: 10.1007/s10265-006-0287-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2005] [Accepted: 03/31/2006] [Indexed: 05/08/2023]
Abstract
The analysis of expression patterns of transcription-factor genes will be the basis for a better understanding of their biological functions in plants. In this study, we designed and developed an oligo-DNA macroarray consisting of gene-specific probes of 60-65 nucleotides for 288 transcription-factor genes, which cover COL, DOF, ERF, and NAC family genes. To investigate transcription-factor genes that are cooperatively regulated by jasmonate and ethylene in arabidopsis (Arabidopsis thaliana (L.) Heynh.) plants, we analyzed the expression profile of transcription-factor genes using the oligo-DNA macroarray technique in arabidopsis plants treated with methyl jasmonate and 1-aminocyclopropane-1-carboxylic acid. Then, transcript levels of candidate genes-which were selected based on the result of macroarray analysis-were evaluated by the quantitative real-time RT-PCR method. Finally, we identified an ERF family gene that is cooperatively regulated by both hormones, and designated as cooperatively regulated by ethylene and jasmonate 1 (CEJ1).
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Affiliation(s)
- Toshitsugu Nakano
- Molecular and Cellular Breeding Research Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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24
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Saladié M, Rose JKC, Cosgrove DJ, Catalá C. Characterization of a new xyloglucan endotransglucosylase/hydrolase (XTH) from ripening tomato fruit and implications for the diverse modes of enzymic action. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 47:282-95. [PMID: 16774648 DOI: 10.1111/j.1365-313x.2006.02784.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Xyloglucan endotransglucosylase/hydrolases (XTHs) are cell wall-modifying enzymes that align within three or four distinct phylogenetic subgroups. One explanation for this grouping is association with different enzymic modes of action, as XTHs can have xyloglucan endotransglucosylase (XET) or endohydrolase (XEH) activities. While Group 1 and 2 XTHs predominantly exhibit XET activity, to date the activity of only one member of Group 3 has been reported: nasturtium TmXH1, which has a highly specialized function and hydrolyses seed-storage xyloglucan rather than modifying cell wall structure. Tomato fruit ripening was selected as a model to test the hypothesis that preferential XEH activity might be a defining characteristic of Group 3 XTHs, which would be expressed during processes where net xyloglucan depolymerization occurs. Database searches identified 25 tomato XTHs, and one gene (SlXTH5) was of particular interest as it aligned within Group 3 and was expressed abundantly during ripening. Recombinant SlXTH5 protein acted primarily as a transglucosylase in vitro and depolymerized xyloglucan more rapidly in the presence than in the absence of xyloglucan oligosaccharides (XGOs), indicative of XET activity. Thus, there is no correlation between the XTH phylogenetic grouping and the preferential enzymic activities (XET or XEH) of the proteins in those groups. Similar analyses of SlXTH2, a Group 2 tomato XTH, and nasturtium seed TmXTH1 revealed a spectrum of modes of action, suggesting that all XTHs have the capacity to function in both modes. The biomechanical properties of plant walls were unaffected by incubation with SlXTH5, with or without XGOs, suggesting that XTHs do not represent primary cell wall-loosening agents. The possible roles of SlXTH5 in vivo are discussed.
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Affiliation(s)
- Montserrat Saladié
- Department of Plant Biology, 228 Plant Science Building, Cornell University, Ithaca, NY 14853, USA
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25
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Yokoyama R, Nishitani K. Identification and characterization of Arabidopsis thaliana genes involved in xylem secondary cell walls. JOURNAL OF PLANT RESEARCH 2006; 119:189-94. [PMID: 16552477 DOI: 10.1007/s10265-006-0261-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2005] [Accepted: 12/15/2005] [Indexed: 05/07/2023]
Abstract
The xylem of higher plants offers support to aerial portions of the plant body and serves as conduit for the translocation of water and nutrients. Terminal differentiation of xylem cells typically involves deposition of thick secondary cell walls. This is a dynamic cellular process accompanied by enhanced rates of cellulose deposition and the induction of synthesis of specific secondary-wall matrix polysaccharides and lignin. The secondary cell wall is essential for the function of conductive and supportive xylem tissues. Recently, significant progress has been made in identifying the genes responsible for xylem secondary cell wall formation. However, our present knowledge is still insufficient to account for the molecular processes by which this complex system operates. To acquire further information about xylem secondary cell walls, we initially focused our research effort on a set of genes specifically implicated in secondary cell wall formation, as well as on loss-of-function mutants. Results from two microarray screens identified several key candidate genes responsible for secondary cell wall formation. Reverse genetic analyses led to the identification of a glycine-rich protein involved in maintaining the stable structure of protoxylem, which is essential for the transport of water and nutrients. A combination of expression analyses and reverse genetics allows us to systematically identify new genes required for the development of physical properties of the xylem secondary wall.
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Affiliation(s)
- Ryusuke Yokoyama
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan
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Osato Y, Yokoyama R, Nishitani K. A principal role for AtXTH18 in Arabidopsis thaliana root growth: a functional analysis using RNAi plants. JOURNAL OF PLANT RESEARCH 2006; 119:153-62. [PMID: 16477366 DOI: 10.1007/s10265-006-0262-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Accepted: 12/16/2005] [Indexed: 05/06/2023]
Abstract
Rearrangement of cellulose microfibrils within cell-wall matrices is considered one of the most critical steps in the regulation of both the orientation and extent of cell expansion in plants. Xyloglucan endotransglucosylase/hydrolases (XTHs) are a family of enzymes that mediate the construction and restructuring of load-bearing cross links among cellulose microfibrils. The Arabidopsis thaliana XTH genes AtXTH17, 18, 19, and 20 are phylogenetically closely related to one another and are preferentially expressed in the roots. However, they exhibit different expression profiles within the root and respond to hormonal signals differently. To investigate their functions in root growth, we examined phenotypes of loss-of-function mutants for these genes using T-DNA insertion lines and RNAi plants. These functional analyses disclosed a principal role for the AtXTH18 gene in primary root elongation. Of the four XTH genes, AtXTH18 exhibits the highest level of mRNA expression. We also determined auxin-signaling pathways for these genes using a mutant with a defect in the AXR2/IAA7 gene and found that the expression of AtXTH19 in the elongation/maturation region of the root is under the control of the AXR2/IAA7 signaling pathway.
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Affiliation(s)
- Yasue Osato
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8576, Japan
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Iglesias N, Abelenda JA, Rodiño M, Sampedro J, Revilla G, Zarra I. Apoplastic Glycosidases Active Against Xyloglucan Oligosaccharides of Arabidopsis thaliana. ACTA ACUST UNITED AC 2006; 47:55-63. [PMID: 16267099 DOI: 10.1093/pcp/pci223] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
All four glycanases necessary for the degradation of xyloglucan oligosaccharides (alpha-fucosidase, alpha-xylosidase, beta-galactosidase and beta-glucosidase) were found in the apoplastic fluid of Arabidopsis thaliana. These activities acted cooperatively on xyloglucan oligosaccharides (XLFG), leading to the sequential formation of XXFG, XXLG, XXXG, GXXG and XXG, as identified by matrix-assisted laser desorption ionization time of flight (MALDI-TOF). AtFXG1 (At1g67830) and AtXYL1 (At1g68560) had been previously identified as the Arabidopsis genes coding for alpha-fucosidase and alpha-xylosidase, respectively. As for the genes coding for beta-galactosidase activity, we identified in phylogenetic trees 12 candidates from family 35 of glycoside hydrolases. Similarly, four genes from family 3 were selected as possible beta-glucosidases active on xyloglucan. The expression level of all the selected genes was studied in different plant regions (young and mature rosette leaves, apical and basal region of the inflorescence stem, roots, flower and siliques) using quantitative real-time reverse transcription-PCR. The expression patterns were very diverse as well as their relationship with growth rates, showing a very complex situation. This could lead to highly varying proportions of the different xyloglucan oligosaccharides in different plant regions and developmental stages.
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Affiliation(s)
- Natalia Iglesias
- Departamento de Fisiología Vegetal, Facultad de Biología, Universidad de Santiago de Compostela, Spain
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Tsukaya H, Beemster GTS. Genetics, cell cycle and cell expansion in organogenesis in plants. JOURNAL OF PLANT RESEARCH 2006; 119:1-4. [PMID: 16365786 DOI: 10.1007/s10265-005-0254-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Hirokazu Tsukaya
- Graduate School of Science, University of Tokyo, Science Building #2, 7-3-1 Hongo, Tokyo 113-0033, Japan.
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Galbraith DW, Birnbaum K. Global studies of cell type-specific gene expression in plants. ANNUAL REVIEW OF PLANT BIOLOGY 2006; 57:451-75. [PMID: 16669770 DOI: 10.1146/annurev.arplant.57.032905.105302] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Technological advances in expression profiling and in the ability to collect minute quantities of tissues have come together to allow a growing number of global transcriptional studies at the cell level in plants. Microarray technology, with a choice of cDNA or oligo-based slides, is now well established, with commercial full-genome platforms for rice and Arabidopsis and extensive expressed sequence tag (EST)-based designs for many other species. Microdissection and cell sorting are two established methodologies that have been used in conjunction with microarrays to provide an early glimpse of the transcriptional landscape at the level of individual cell types. The results indicate that much of the transcriptome is compartmentalized. A minor but consistent percentage of transcripts appear to be unique to specific cell types. Functional analyses of cell-specific patterns of gene expression are providing important clues to cell-specific functions. The spatial dissection of the transcriptome has also yielded insights into the localized mediators of hormone inputs and promises to provide detail on cell-specific effects of microRNAs.
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Affiliation(s)
- David W Galbraith
- Department of Plant Sciences and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, USA.
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