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Galibina NA, Moshchenskaya YL, Tarelkina TV, Nikerova KM, Korzhenevskii MA, Serkova AA, Afoshin NV, Semenova LI, Ivanova DS, Guljaeva EN, Chirva OV. Identification and Expression Profile of CLE41/44-PXY-WOX Genes in Adult Trees Pinus sylvestris L. Trunk Tissues during Cambial Activity. PLANTS (BASEL, SWITZERLAND) 2023; 12:835. [PMID: 36840180 PMCID: PMC9961183 DOI: 10.3390/plants12040835] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
WUSCHEL (WUS)-related homeobox (WOX) protein family members play important roles in the maintenance and proliferation of the stem cells in the cambium, the lateral meristem that forms all the wood structural elements. Most studies have examined the function of these genes in angiosperms, and very little was known about coniferous trees. Pine is one of the most critical forest-forming conifers globally, and in this research, we studied the distribution of WOX4, WOX13, and WOXG genes expression in Pinus sylvestris L. trunk tissues. Further, we considered the role of TDIF(CLE41/44)/TDR(PXY) signaling in regulating Scots pine cambial activity. The distribution of CLE41/44-PXY-WOXs gene expression in Scots pine trunk tissues was studied: (1) depending on the stage of ontogenesis (the first group of objects); and (2) depending on the stage of cambial growth (the second group of objects). The first group of objects is lingonberry pine forests of different ages (30-, 80-, and 180-year-old stands) in the middle taiga subzone. At the time of selection, all the trees of the studied groups were at the same seasonal stage of development: the formation of late phloem and early xylem was occurring in the trunk. The second group of objects is 40-year-old pine trees that were selected growing in the forest seed orchard. We took the trunk tissue samples on 27 May 2022, 21 June 2022, and 21 July 2022. We have indicated the spatial separation expressed of PsCLE41/44 and PsPXY in pine trunk tissues. PsCLE41/44 was differentially expressed in Fraction 1, including phloem cells and cambial zone. Maximum expression of the PsPXY gene occurred in Fraction 2, including differentiating xylem cells. The maximum expression of the PsCLE41/44 gene occurred on 27 May, when the number of cells in the cambial zone was the highest, and then it decreased to almost zero. The PsPXY gene transcript level increased from May to the end of July. We found that the highest transcript level of the PsWOX4 gene was during the period of active cell proliferation in the cambial zone, and also in the trees with the cambial age 63 years, which were characterized by the largest number of cell layers in the cambial zone. In this study, we have examined the expression profiles of genes belonging to the ancient clade (PsWOXG and PsWOX13) in stem tissues in Scots pine for the first time. We found that, in contrast to PsWOX4 (high expression that was observed during the period of active formation of early tracheids), the expression of genes of the ancient clade of the WOX genes was observed during the period of decreased cambial activity in the second half of the growing season. We found that PsWOX13 expression was shifted to Fraction 1 in most cases and increased from the phloem side, while PsWOXG expression was not clearly bound to a certain fraction. Based on the data, the role of the CLE41/44-PXY-WOX signaling module in regulating P. sylvestris cambial growth is discussed.
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Fischer U, Kucukoglu M, Helariutta Y, Bhalerao RP. The Dynamics of Cambial Stem Cell Activity. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:293-319. [PMID: 30822110 DOI: 10.1146/annurev-arplant-050718-100402] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Stem cell populations in meristematic tissues at distinct locations in the plant body provide the potency of continuous plant growth. Primary meristems, at the apices of the plant body, contribute mainly to the elongation of the main plant axes, whereas secondary meristems in lateral positions are responsible for the thickening of these axes. The stem cells of the vascular cambium-a secondary lateral meristem-produce the secondary phloem (bast) and secondary xylem (wood). The sites of primary and secondary growth are spatially separated, and mobile signals are expected to coordinate growth rates between apical and lateral stem cell populations. Although the underlying mechanisms have not yet been uncovered, it seems likely that hormones, peptides, and mechanical cues orchestrate primary and secondary growth. In this review, we highlight the current knowledge and recent discoveries of how cambial stem cell activity is regulated, with a focus on mobile signals and the response of cambial activity to environmental and stress factors.
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Affiliation(s)
- Urs Fischer
- KWS SAAT SE, 37555 Einbeck, Germany
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden;
| | - Melis Kucukoglu
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Ykä Helariutta
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Rishikesh P Bhalerao
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden;
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
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Nascimento LC, Salazar MM, Lepikson-Neto J, Camargo ELO, Parreiras LS, Pereira GAG, Carazzolle MF. EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2017:4564812. [PMID: 29220468 PMCID: PMC5737058 DOI: 10.1093/database/bax079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/29/2017] [Indexed: 12/05/2022]
Abstract
Tree species of the genus Eucalyptus are the most valuable and widely planted hardwoods in the world. Given the economic importance of Eucalyptus trees, much effort has been made towards the generation of specimens with superior forestry properties that can deliver high-quality feedstocks, customized to the industrýs needs for both cellulosic (paper) and lignocellulosic biomass production. In line with these efforts, large sets of molecular data have been generated by several scientific groups, providing invaluable information that can be applied in the development of improved specimens. In order to fully explore the potential of available datasets, the development of a public database that provides integrated access to genomic and transcriptomic data from Eucalyptus is needed. EUCANEXT is a database that analyses and integrates publicly available Eucalyptus molecular data, such as the E. grandis genome assembly and predicted genes, ESTs from several species and digital gene expression from 26 RNA-Seq libraries. The database has been implemented in a Fedora Linux machine running MySQL and Apache, while Perl CGI was used for the web interfaces. EUCANEXT provides a user-friendly web interface for easy access and analysis of publicly available molecular data from Eucalyptus species. This integrated database allows for complex searches by gene name, keyword or sequence similarity and is publicly accessible at http://www.lge.ibi.unicamp.br/eucalyptusdb. Through EUCANEXT, users can perform complex analysis to identify genes related traits of interest using RNA-Seq libraries and tools for differential expression analysis. Moreover, all the bioinformatics pipeline here described, including the database schema and PERL scripts, are readily available and can be applied to any genomic and transcriptomic project, regardless of the organism. Database URL:http://www.lge.ibi.unicamp.br/eucalyptusdb
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Affiliation(s)
- Leandro Costa Nascimento
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil.,Laboratório Central de Tecnologias de Alto Desempenho (LaCTAD), Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - Marcela Mendes Salazar
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - Jorge Lepikson-Neto
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - Eduardo Leal Oliveira Camargo
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - Lucas Salera Parreiras
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil.,Centro Nacional de Processamento de Alto Desempenho em São Paulo (CENAPAD), Universidade Estadual de Campinas, Campinas, SP, Brasil
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Nguyen HP, Jeong HY, Jeon SH, Kim D, Lee C. Rice pectin methylesterase inhibitor28 (OsPMEI28) encodes a functional PMEI and its overexpression results in a dwarf phenotype through increased pectin methylesterification levels. JOURNAL OF PLANT PHYSIOLOGY 2017; 208:17-25. [PMID: 27889517 DOI: 10.1016/j.jplph.2016.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 10/30/2016] [Accepted: 11/14/2016] [Indexed: 05/02/2023]
Abstract
Pectin methylesterases (PMEs, EC 3.1.1.11) belonging to carbohydrate esterase family 8 cleave the ester bond between a galacturonic acid and an methyl group and the resulting change in methylesterification level plays an important role during the growth and development of plants. Optimal pectin methylesterification status in each cell type is determined by the balance between PME activity and post-translational PME inhibition by PME inhibitors (PMEIs). Rice contains 49 PMEIs and none of them are functionally characterized. Genomic sequence analysis led to the identification of rice PMEI28 (OsPMEI28). Recombinant OsPMEI28 exhibited inhibitory activity against commercial PME protein with the highest activities detected at pH 8.5. Overexpression of OsPMEI28 in rice resulted in an increased level of cell wall bound methylester groups and differential changes in the composition of cell wall neutral monosaccharides and lignin content in culm tissues. Consequently, transgenic plants overexpressing OsPMEI28 exhibited dwarf phenotypes and reduced culm diameter. Our data indicate that OsPMEI28 functions as a critical structural modulator by regulating the degree of pectin methylesterification and that an impaired status of pectin methylesterification affects physiochemical properties of the cell wall components and causes abnormal cell extensibility in rice culm tissues.
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Affiliation(s)
- Hong Phuong Nguyen
- Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Ho Young Jeong
- Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Seung Ho Jeon
- Seed Research Center, Gyeongnam National University of Science and Technology, Jinju-Si 52725, Republic of Korea
| | - Donghyuk Kim
- Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Chanhui Lee
- Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Republic of Korea; Department of Plant and Environmental New Resources, Kyung Hee University, Yongin 446-701, Republic of Korea.
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Budzinski IGF, Moon DH, Morosini JS, Lindén P, Bragatto J, Moritz T, Labate CA. Integrated analysis of gene expression from carbon metabolism, proteome and metabolome, reveals altered primary metabolism in Eucalyptus grandis bark, in response to seasonal variation. BMC PLANT BIOLOGY 2016; 16:149. [PMID: 27364638 PMCID: PMC4929727 DOI: 10.1186/s12870-016-0839-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 06/22/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND Seasonal variation is presumed to play an important role in the regulation of tree growth, especially for Eucalyptus grandis, a fast-growing tree. This variation may induce changes in the whole tree at transcriptional, protein and metabolite levels. Bark represents an important group of tissues that protect trees from desiccation and pathogen attack, and it has been identified as potential feedstock for lignocellulosic derived biofuels. Despite the growing interest, little is known about the molecular mechanisms that regulates bark metabolism, particularly in tropical countries. RESULTS In this study we report the changes observed in the primary metabolism of E. grandis bark during two contrasting seasons in Brazil, summer (wet) and winter (dry), through the combination of transcripts (RT-qPCR), proteome (2-DE gels) and metabolome (GC-MS) analysis, in an integrated manner. Twenty-four genes, involved in carbon metabolism, were analyzed in the two seasons. Eleven were up-regulated in summer, three were up-regulated in winter and ten did not show statistical differences in the expression pattern. The proteomic analysis using 2-DE gels showed 77 proteins expressing differences in abundance, with 38 spots up-regulated in summer and 37 in winter. Different metabolites significantly accumulated during winter. CONCLUSIONS This study revealed a metabolic reconfiguration in the primary metabolism of E. grandis bark, triggered by seasonal variation. Transcripts and protein data suggests that during winter carbohydrate formation seems to be favored by tree metabolism. Glucose, fructose and sucrose accumulated at significant levels during the winter.
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Affiliation(s)
- Ilara Gabriela Frasson Budzinski
- />Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP 13418-900 Brasil
| | - David H. Moon
- />Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP 13418-900 Brasil
| | - Júlia Silva Morosini
- />Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP 13418-900 Brasil
| | - Pernilla Lindén
- />Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE-901 83 Sweden
| | - Juliano Bragatto
- />Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP 13418-900 Brasil
| | - Thomaz Moritz
- />Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE-901 83 Sweden
| | - Carlos Alberto Labate
- />Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP 13418-900 Brasil
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Budzinski IGF, Moon DH, Lindén P, Moritz T, Labate CA. Seasonal Variation of Carbon Metabolism in the Cambial Zone of Eucalyptus grandis. FRONTIERS IN PLANT SCIENCE 2016; 7:932. [PMID: 27446160 PMCID: PMC4923158 DOI: 10.3389/fpls.2016.00932] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/11/2016] [Indexed: 05/09/2023]
Abstract
Eucalyptus species are the most widely hardwood planted in the world. It is one of the successful examples of commercial forestry plantation in Brazil and other tropical and subtropical countries. The tree is valued for its rapid growth, adaptability and wood quality. Wood formation is the result of cumulative annual activity of the vascular cambium. This cambial activity is generally related to the alternation of cold and warm, and/or dry and rainy seasons. Efforts have focused on analysis of cambial zone in response to seasonal variations in trees from temperate zones. However, little is known about the molecular changes triggered by seasonal variations in trees from tropical countries. In this work we attempted to establish a global view of seasonal alterations in the cambial zone of Eucalyptus grandis Hill ex Maiden, emphasizing changes occurring in the carbon metabolism. Using transcripts, proteomics and metabolomics we analyzed the tissues harvested in summer-wet and winter-dry seasons. Based on proteomics analysis, 70 proteins that changed in abundance were successfully identified. Transcripts for some of these proteins were analyzed and similar expression patterns were observed. We identified 19 metabolites differentially abundant. Our results suggest a differential reconfiguration of carbon partioning in E. grandis cambial zone. During summer, pyruvate is primarily metabolized via ethanolic fermentation, possibly to regenerate NAD(+) for glycolytic ATP production and cellular maintenance. However, in winter there seems to be a metabolic change and we found that some sugars were highly abundant. Our results revealed a dynamic change in E. grandis cambial zone due to seasonality and highlight the importance of glycolysis and ethanolic fermentation for energy generation and maintenance in Eucalyptus, a fast growing tree.
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Affiliation(s)
- Ilara G. F. Budzinski
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São PauloPiracicaba, Brazil
| | - David H. Moon
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São PauloPiracicaba, Brazil
| | - Pernilla Lindén
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural SciencesUmeå, Sweden
| | - Thomas Moritz
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural SciencesUmeå, Sweden
| | - Carlos A. Labate
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São PauloPiracicaba, Brazil
- *Correspondence: Carlos A. Labate
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Ruedell CM, de Almeida MR, Fett-Neto AG. Concerted transcription of auxin and carbohydrate homeostasis-related genes underlies improved adventitious rooting of microcuttings derived from far-red treated Eucalyptus globulus Labill mother plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 97:11-9. [PMID: 26397200 DOI: 10.1016/j.plaphy.2015.09.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 08/29/2015] [Accepted: 09/02/2015] [Indexed: 05/13/2023]
Abstract
Economically important plant species, such as Eucalyptus globulus, are often rooting recalcitrant. We have previously shown that far-red light enrichment applied to E. globulus donor-plants improved microcutting rooting competence and increased rooting zone/shoot carbohydrate ratio. To better understand this developmental response, the relative expression profiles of genes involved in auxin signaling (ARF6, ARF8, AGO1), biosynthesis (YUC3) and transport (AUX1, PIN1, PIN2); sucrose cleavage (SUS1, CWINV1), transport (SUC5), hexose phosphorylation (HXK1, FLN1) and starch biosynthesis (SS3) were quantified during adventitious rooting of E. globulus microcuttings derived from donor plants exposed to far-red or white light. Expression of auxin transport-related genes increased in the first days of root induction. Far-red enrichment of donor plants induced ARF6, ARF8 and AGO1 in microcuttings. The first two gene products could activate GH3 and other rooting related genes, whereas AGO1 deregulation of the repressor ARF17 may relief rooting inhibition. Increased sink strength at the basal stem with sucrose unloading in root tissue mediated by SUC and subsequent hydrolysis by SUS1 were also supported by gene expression profile. Fructose phosphorylation and starch biosynthesis could also contribute to proper carbon allocation at the site of rooting, as evidenced by increased expression of related genes. These data are in good agreement with increased contents of hexoses and starch at the cutting base severed from far-red exposed donor plants. To sum up, pathways integrating auxin and carbohydrate metabolism were activated in microcuttings derived from donor plants exposed to far red light enrichment, thereby improving rooting response in E. globulus.
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Affiliation(s)
- Carolina Michels Ruedell
- Department of Botany, Federal University of Rio Grande do Sul, P.O. Box 15005, 91501-970 Porto Alegre, RS, Brazil
| | - Márcia Rodrigues de Almeida
- Center for Biotechnology, Federal University of Rio Grande do Sul, P.O. Box 15005, 91501-970 Porto Alegre, RS, Brazil
| | - Arthur Germano Fett-Neto
- Department of Botany, Federal University of Rio Grande do Sul, P.O. Box 15005, 91501-970 Porto Alegre, RS, Brazil; Center for Biotechnology, Federal University of Rio Grande do Sul, P.O. Box 15005, 91501-970 Porto Alegre, RS, Brazil.
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8
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Versatility of germin-like proteins in their sequences, expressions, and functions. Funct Integr Genomics 2015; 15:533-48. [DOI: 10.1007/s10142-015-0454-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/28/2015] [Accepted: 07/02/2015] [Indexed: 12/19/2022]
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Leonardi GDA, Carlos NA, Mazzafera P, Balbuena TS. Eucalyptus urograndis stem proteome is responsive to short-term cold stress. Genet Mol Biol 2015; 38:191-8. [PMID: 26273222 PMCID: PMC4530643 DOI: 10.1590/s1415-475738220140235] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 11/07/2014] [Indexed: 01/03/2023] Open
Abstract
Eucalyptus urograndis is a hybrid eucalyptus of major economic importance to the Brazilian pulp and paper industry. Although widely used in forest nurseries around the country, little is known about the biochemical changes imposed by environmental stress in this species. In this study, we evaluated the changes in the stem proteome after short-term stimulation by exposure to low temperature. Using two-dimensional gel electrophoresis coupled to high-resolution mass spectrometry-based protein identification, 12 proteins were found to be differentially regulated and successfully identified after stringent database searches against a protein database from a closely related species (Eucalyptus grandis). The identification of these proteins indicated that the E. urograndis stem proteome responded quickly to low temperature, mostly by down-regulating specific proteins involved in energy metabolism, protein synthesis and signaling. The results of this study represent the first step in understanding the molecular and biochemical responses of E. urograndis to thermal stress.
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Affiliation(s)
- Gabriela de Almeida Leonardi
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - Natália Aparecida Carlos
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - Paulo Mazzafera
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Tiago Santana Balbuena
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
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Sénéchal F, Wattier C, Rustérucci C, Pelloux J. Homogalacturonan-modifying enzymes: structure, expression, and roles in plants. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5125-60. [PMID: 25056773 PMCID: PMC4400535 DOI: 10.1093/jxb/eru272] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/20/2014] [Accepted: 05/22/2014] [Indexed: 05/18/2023]
Abstract
Understanding the changes affecting the plant cell wall is a key element in addressing its functional role in plant growth and in the response to stress. Pectins, which are the main constituents of the primary cell wall in dicot species, play a central role in the control of cellular adhesion and thereby of the rheological properties of the wall. This is likely to be a major determinant of plant growth. How the discrete changes in pectin structure are mediated is thus a key issue in our understanding of plant development and plant responses to changes in the environment. In particular, understanding the remodelling of homogalacturonan (HG), the most abundant pectic polymer, by specific enzymes is a current challenge in addressing its fundamental role. HG, a polymer that can be methylesterified or acetylated, can be modified by HGMEs (HG-modifying enzymes) which all belong to large multigenic families in all species sequenced to date. In particular, both the degrees of substitution (methylesterification and/or acetylation) and polymerization can be controlled by specific enzymes such as pectin methylesterases (PMEs), pectin acetylesterases (PAEs), polygalacturonases (PGs), or pectate lyases-like (PLLs). Major advances in the biochemical and functional characterization of these enzymes have been made over the last 10 years. This review aims to provide a comprehensive, up to date summary of the recent data concerning the structure, regulation, and function of these fascinating enzymes in plant development and in response to biotic stresses.
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Affiliation(s)
- Fabien Sénéchal
- EA3900 BIOPI Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 33 Rue St Leu, F-80039 Amiens, France
| | - Christopher Wattier
- EA3900 BIOPI Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 33 Rue St Leu, F-80039 Amiens, France
| | - Christine Rustérucci
- EA3900 BIOPI Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 33 Rue St Leu, F-80039 Amiens, France
| | - Jérôme Pelloux
- EA3900 BIOPI Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 33 Rue St Leu, F-80039 Amiens, France
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Wang Z, Chen J, Liu W, Luo Z, Wang P, Zhang Y, Zheng R, Shi J. Transcriptome characteristics and six alternative expressed genes positively correlated with the phase transition of annual cambial activities in Chinese Fir (Cunninghamia lanceolata (Lamb.) Hook). PLoS One 2013; 8:e71562. [PMID: 23951189 PMCID: PMC3741379 DOI: 10.1371/journal.pone.0071562] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 07/01/2013] [Indexed: 11/24/2022] Open
Abstract
Background The molecular mechanisms that govern cambial activity in angiosperms are well established, but little is known about these molecular mechanisms in gymnosperms. Chinese fir (Cunninghamia lanceolata (Lamb.) Hook), a diploid (2n = 2x = 22) gymnosperm, is one of the most important industrial and commercial timber species in China. Here, we performed transcriptome sequencing to identify the repertoire of genes expressed in cambium tissue of Chinese fir. Methodology/Principal Findings Based on previous studies, the four stage-specific cambial tissues of Chinese fir were defined using transmission electron microscopy (TEM). In total, 20 million sequencing reads (3.6 Gb) were obtained using Illumina sequencing from Chinese fir cambium tissue collected at active growth stage, with a mean length of 131 bp and a N50 of 90 bp. SOAPdenovo software was used to assemble 62,895 unigenes. These unigenes were further functionally annotated by comparing their sequences to public protein databases. Expression analysis revealed that the altered expression of six homologous genes (ClWOX1, ClWOX4, ClCLV1-like, ClCLV-like, ClCLE12, and ClPIN1-like) correlated positively with changes in cambial activities; moreover, these six genes might be directly involved in cambial function in Chinese fir. Further, the full-length cDNAs and DNAs for ClWOX1 and ClWOX4 were cloned and analyzed. Conclusions In this study, a large number of tissue/stage-specific unigene sequences were generated from the active growth stage of Chinese fir cambium. Transcriptome sequencing of Chinese fir not only provides extensive genetic resources for understanding the molecular mechanisms underlying cambial activities in Chinese fir, but also is expected to be an important foundation for future genetic studies of Chinese fir. This study indicates that ClWOX1 and ClWOX4 could be possible reverse genetic target genes for revealing the molecular mechanisms of cambial activities in Chinese fir.
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Affiliation(s)
- Zhanjun Wang
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Nanjing Forestry University, Nanjing, China
| | - Weidong Liu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Nanjing Forestry University, Nanjing, China
| | - Zhanshou Luo
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Nanjing Forestry University, Nanjing, China
| | - Pengkai Wang
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Nanjing Forestry University, Nanjing, China
| | - Yanjuan Zhang
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Nanjing Forestry University, Nanjing, China
| | - Renhua Zheng
- Fujian Academies of Forestry, Southern Mountain Timber Forest Cultivation Lab, the Ministry of Forestry, Fuzhou, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Nanjing Forestry University, Nanjing, China
- * E-mail:
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12
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Salazar MM, Nascimento LC, Camargo ELO, Gonçalves DC, Lepikson Neto J, Marques WL, Teixeira PJPL, Mieczkowski P, Mondego JMC, Carazzolle MF, Deckmann AC, Pereira GAG. Xylem transcription profiles indicate potential metabolic responses for economically relevant characteristics of Eucalyptus species. BMC Genomics 2013; 14:201. [PMID: 23521840 PMCID: PMC3618336 DOI: 10.1186/1471-2164-14-201] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 03/08/2013] [Indexed: 12/02/2022] Open
Abstract
Background Eucalyptus is one of the most important sources of industrial cellulose. Three species of this botanical group are intensively used in breeding programs: E. globulus, E. grandis and E. urophylla. E. globulus is adapted to subtropical/temperate areas and is considered a source of high-quality cellulose; E. grandis grows rapidly and is adapted to tropical/subtropical climates; and E. urophylla, though less productive, is considered a source of genes related to robustness. Wood, or secondary xylem, results from cambium vascular differentiation and is mostly composed of cellulose, lignin and hemicelluloses. In this study, the xylem transcriptomes of the three Eucalyptus species were investigated in order to provide insights on the particularities presented by each of these species. Results Data analysis showed that (1) most Eucalyptus genes are expressed in xylem; (2) most genes expressed in species-specific way constitutes genes with unknown functions and are interesting targets for future studies; (3) relevant differences were observed in the phenylpropanoid pathway: E. grandis xylem presents higher expression of genes involved in lignin formation whereas E. urophylla seems to deviates the pathway towards flavonoid formation; (4) stress-related genes are considerably more expressed in E. urophylla, suggesting that these genes may contribute to its robustness. Conclusions The comparison of these three transcriptomes indicates the molecular signatures underlying some of their distinct wood characteristics. This information may contribute to the understanding of xylogenesis, thus increasing the potential of genetic engineering approaches aiming at the improvement of Eucalyptus forest plantations productivity.
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Affiliation(s)
- Marcela Mendes Salazar
- Laboratório de Genômica e Expressão, Departamento de Genética Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo CEP: 13083-970, Campinas, Brasil
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13
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Cassan-Wang H, Soler M, Yu H, Camargo ELO, Carocha V, Ladouce N, Savelli B, Paiva JAP, Leplé JC, Grima-Pettenati J. Reference genes for high-throughput quantitative reverse transcription-PCR analysis of gene expression in organs and tissues of Eucalyptus grown in various environmental conditions. PLANT & CELL PHYSIOLOGY 2012; 53:2101-16. [PMID: 23161857 DOI: 10.1093/pcp/pcs152] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Interest in the genomics of Eucalyptus has skyrocketed thanks to the recent sequencing of the genome of Eucalyptus grandis and to a growing number of large-scale transcriptomic studies. Quantitative reverse transcription-PCR (RT-PCR) is the method of choice for gene expression analysis and can now also be used as a high-throughput method. The selection of appropriate internal controls is becoming of utmost importance to ensure accurate expression results in Eucalyptus. To this end, we selected 21 candidate reference genes and used high-throughput microfluidic dynamic arrays to assess their expression among a large panel of developmental and environmental conditions with a special focus on wood-forming tissues. We analyzed the expression stability of these genes by using three distinct statistical algorithms (geNorm, NormFinder and ΔCt), and used principal component analysis to compare methods and rankings. We showed that the most stable genes identified depended not only on the panel of biological samples considered but also on the statistical method used. We then developed a comprehensive integration of the rankings generated by the three methods and identified the optimal reference genes for 17 distinct experimental sets covering 13 organs and tissues, as well as various developmental and environmental conditions. The expression patterns of Eucalyptus master genes EgMYB1 and EgMYB2 experimentally validated our selection. Our findings provide an important resource for the selection of appropriate reference genes for accurate and reliable normalization of gene expression data in the organs and tissues of Eucalyptus trees grown in a range of conditions including abiotic stresses.
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Affiliation(s)
- Hua Cassan-Wang
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse III, UPS, CNRS, BP 42617, Auzeville, 31326 Castanet Tolosan, France.
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14
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Beaulieu J, Doerksen T, Boyle B, Clément S, Deslauriers M, Beauseigle S, Blais S, Poulin PL, Lenz P, Caron S, Rigault P, Bicho P, Bousquet J, Mackay J. Association genetics of wood physical traits in the conifer white spruce and relationships with gene expression. Genetics 2011; 188:197-214. [PMID: 21385726 PMCID: PMC3120141 DOI: 10.1534/genetics.110.125781] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 02/22/2011] [Indexed: 01/01/2023] Open
Abstract
Marker-assisted selection holds promise for highly influencing tree breeding, especially for wood traits, by considerably reducing breeding cycles and increasing selection accuracy. In this study, we used a candidate gene approach to test for associations between 944 single-nucleotide polymorphism markers from 549 candidate genes and 25 wood quality traits in white spruce. A mixed-linear model approach, including a weak but nonsignificant population structure, was implemented for each marker-trait combination. Relatedness among individuals was controlled using a kinship matrix estimated either from the known half-sib structure or from the markers. Both additive and dominance effect models were tested. Between 8 and 21 single-nucleotide polymorphisms (SNPs) were found to be significantly associated (P ≤ 0.01) with each of earlywood, latewood, or total wood traits. After controlling for multiple testing (Q ≤ 0.10), 13 SNPs were still significant across as many genes belonging to different families, each accounting for between 3 and 5% of the phenotypic variance in 10 wood characters. Transcript accumulation was determined for genes containing SNPs associated with these traits. Significantly different transcript levels (P ≤ 0.05) were found among the SNP genotypes of a 1-aminocyclopropane-1-carboxylate oxidase, a β-tonoplast intrinsic protein, and a long-chain acyl-CoA synthetase 9. These results should contribute toward the development of efficient marker-assisted selection in an economically important tree species.
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Affiliation(s)
- Jean Beaulieu
- Natural Resources Canada, Canadian Wood Fibre Centre, Québec City, Québec, Canada.
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15
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Labate MTV, Bertolo ALF, do Nascimento DD, Gutmanis G, de Andrade A, Rodrigues MJC, Camargo ELO, Boaretto LF, Moon DH, Bragatto J, Labate CA. Cloning and endogenous expression of a Eucalyptus grandis UDP-glucose dehydrogenase cDNA. Genet Mol Biol 2010; 33:686-95. [PMID: 21637578 PMCID: PMC3036151 DOI: 10.1590/s1415-47572010005000078] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 03/17/2010] [Indexed: 11/21/2022] Open
Abstract
UDP-glucose dehydrogenase (UGDH) catalyzes the oxidation of UDP-glucose (UDP-Glc) to UDP-glucuronate (UDP-GlcA), a key sugar nucleotide involved in the biosynthesis of plant cell wall polysaccharides. A full-length cDNA fragment coding for UGDH was cloned from the cambial region of 6-month-old E. grandis saplings by RT-PCR. The 1443-bp-ORF encodes a protein of 480 amino acids with a predicted molecular weight of 53 kDa. The recombinant protein expressed in Escherichia coli catalyzed the conversion of UDP-Glc to UDP-GlcA, confirming that the cloned cDNA encodes UGDH. The deduced amino acid sequence of the cDNA showed a high degree of identity with UGDH from several plant species. The Southern blot assay indicated that more than one copy of UGDH is present in Eucalyptus. These results were also confirmed by the proteomic analysis of the cambial region of 3- and 22-year-old E. grandis trees by 2-DE and LC-MS/MS, showing that at least two isoforms are present. The cloned gene is mainly expressed in roots, stem and bark of 6-month-old saplings, with a lower expression in leaves. High expression levels were also observed in the cambial region of 3- and 22-year-old trees. The results described in this paper provide a further view of the hemicellulose biosynthesis during wood formation in E. grandis.
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Affiliation(s)
- Mônica T Veneziano Labate
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP Brazil
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16
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de Almeida MR, Ruedell CM, Ricachenevsky FK, Sperotto RA, Pasquali G, Fett-Neto AG. Reference gene selection for quantitative reverse transcription-polymerase chain reaction normalization during in vitro adventitious rooting in Eucalyptus globulus Labill. BMC Mol Biol 2010; 11:73. [PMID: 20854682 PMCID: PMC2955024 DOI: 10.1186/1471-2199-11-73] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Accepted: 09/20/2010] [Indexed: 01/10/2023] Open
Abstract
Background Eucalyptus globulus and its hybrids are very important for the cellulose and paper industry mainly due to their low lignin content and frost resistance. However, rooting of cuttings of this species is recalcitrant and exogenous auxin application is often necessary for good root development. To date one of the most accurate methods available for gene expression analysis is quantitative reverse transcription-polymerase chain reaction (qPCR); however, reliable use of this technique requires reference genes for normalization. There is no single reference gene that can be regarded as universal for all experiments and biological materials. Thus, the identification of reliable reference genes must be done for every species and experimental approach. The present study aimed at identifying suitable control genes for normalization of gene expression associated with adventitious rooting in E. globulus microcuttings. Results By the use of two distinct algorithms, geNorm and NormFinder, we have assessed gene expression stability of eleven candidate reference genes in E. globulus: 18S, ACT2, EF2, EUC12, H2B, IDH, SAND, TIP41, TUA, UBI and 33380. The candidate reference genes were evaluated in microccuttings rooted in vitro, in presence or absence of auxin, along six time-points spanning the process of adventitious rooting. Overall, the stability profiles of these genes determined with each one of the algorithms were very similar. Slight differences were observed in the most stable pair of genes indicated by each program: IDH and SAND for geNorm, and H2B and TUA for NormFinder. Both programs indentified UBI and 18S as the most variable genes. To validate these results and select the most suitable reference genes, the expression profile of the ARGONAUTE1 gene was evaluated in relation to the most stable candidate genes indicated by each algorithm. Conclusion Our study showed that expression stability varied between putative reference genes tested in E. globulus. Based on the AGO1 relative expression profile obtained using the genes suggested by the algorithms, H2B and TUA were considered as the most suitable reference genes for expression studies in E. globulus adventitious rooting. UBI and 18S were unsuitable for use as controls in qPCR related to this process. These findings will enable more accurate and reliable normalization of qPCR results for gene expression studies in this economically important woody plant, particularly related to rooting and clonal propagation.
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Affiliation(s)
- Márcia R de Almeida
- Center for Biotechnology, Federal University of Rio Grande do Sul, P,O, Box 15005, 91501-970 Porto Alegre, RS, Brazil
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17
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Jaspers P, Overmyer K, Wrzaczek M, Vainonen JP, Blomster T, Salojärvi J, Reddy RA, Kangasjärvi J. The RST and PARP-like domain containing SRO protein family: analysis of protein structure, function and conservation in land plants. BMC Genomics 2010; 11:170. [PMID: 20226034 PMCID: PMC2848248 DOI: 10.1186/1471-2164-11-170] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 03/12/2010] [Indexed: 02/05/2023] Open
Abstract
Background The SROs (SIMILAR TO RCD-ONE) are a group of plant-specific proteins which have important functions in stress adaptation and development. They contain the catalytic core of the poly(ADP-ribose) polymerase (PARP) domain and a C-terminal RST (RCD-SRO-TAF4) domain. In addition to these domains, several, but not all, SROs contain an N-terminal WWE domain. Results SROs are present in all analyzed land plants and sequence analysis differentiates between two structurally distinct groups; cryptogams and monocots possess only group I SROs whereas eudicots also contain group II. Group I SROs possess an N-terminal WWE domain (PS50918) but the WWE domain is lacking in group II SROs. Group I domain structure is widely represented in organisms as distant as humans (for example, HsPARP11). We propose a unified nomenclature for the SRO family. The SROs are able to interact with transcription factors through the C-terminal RST domain but themselves are generally not regulated at the transcriptional level. The most conserved feature of the SROs is the catalytic core of the poly(ADP-ribose) polymerase (PS51059) domain. However, bioinformatic analysis of the SRO PARP domain fold-structure and biochemical assays of AtRCD1 suggested that SROs do not possess ADP-ribosyl transferase activity. Conclusions The SROs are a highly conserved family of plant specific proteins. Sequence analysis of the RST domain implicates a highly preserved protein structure in that region. This might have implications for functional conservation. We suggest that, despite the presence of the catalytic core of the PARP domain, the SROs do not possess ADP-ribosyl transferase activity. Nevertheless, the function of SROs is critical for plants and might be related to transcription factor regulation and complex formation.
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Affiliation(s)
- Pinja Jaspers
- Plant Biology Division, Department of Biosciences, University of Helsinki, Viikinkaari 1, FI-00014 Helsinki, Finland
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18
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Berta M, Giovannelli A, Sebastiani F, Camussi A, Racchi ML. Transcriptome changes in the cambial region of poplar (Populus alba L.) in response to water deficit. PLANT BIOLOGY (STUTTGART, GERMANY) 2010; 12:341-54. [PMID: 20398240 DOI: 10.1111/j.1438-8677.2009.00320.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A transcriptome analysis of the Populus alba cambial region was performed with the aim of elucidating the gene network underlying the response to water deficit within the cambium and differentiating derivative cambial cells. Water stress was induced in 1-year-old P. alba plants by withholding water for 9 days. At that time, leaf predawn water potential fell to -0.8 MPa, resulting in a significant reduction in stomatal conductance, CO(2) assimilation and a consistent increment of stem shrinkage. These effects were almost fully reversed by re-hydration. The water deficit resulted in changes in gene expression that affected several functional categories, such as protein metabolism, cell wall metabolism, stress response, transporters and transcriptional regulation. The function of up- and down-regulated genes is discussed considering the physiological response of the plants to water deficit.
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Affiliation(s)
- M Berta
- Department of Agricultural Biotechnology, Genetics section, Florence, Italy
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19
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Grattapaglia D, Plomion C, Kirst M, Sederoff RR. Genomics of growth traits in forest trees. CURRENT OPINION IN PLANT BIOLOGY 2009; 12:148-56. [PMID: 19186096 DOI: 10.1016/j.pbi.2008.12.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2008] [Revised: 12/08/2008] [Accepted: 12/10/2008] [Indexed: 05/21/2023]
Abstract
Growth traits in trees are fundamental components of adaptation in a forest ecosystem and of productivity in planted forests. A number of processes determine tree growth, which are controlled by genetic and epigenetic factors that respond dynamically to environmental signals throughout centuries. Advances in genomics have allowed an increased comprehension of the complex mechanisms of tree growth and adaptation. Yet, the application of genomics to improving forest productivity and sustainability still entails capturing a large proportion of the total genetic variation controlling the component traits. Nonetheless, genetics and genomics are unifying disciplines that will serve well to dissect the variables and mechanisms of tree growth and development.
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Affiliation(s)
- Dario Grattapaglia
- EMBRAPA Genetic Resources and Biotechnology, CP 2372, Brasília 70770-970 DF, and Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília - SGAN 916 módulo B, Brasília 70790-160 DF, Brazil.
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20
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Rengel D, Clemente HS, Servant F, Ladouce N, Paux E, Wincker P, Couloux A, Sivadon P, Grima-Pettenati J. A new genomic resource dedicated to wood formation in Eucalyptus. BMC PLANT BIOLOGY 2009; 9:36. [PMID: 19327132 PMCID: PMC2670833 DOI: 10.1186/1471-2229-9-36] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 03/27/2009] [Indexed: 05/17/2023]
Abstract
BACKGROUND Renowned for their fast growth, valuable wood properties and wide adaptability, Eucalyptus species are amongst the most planted hardwoods in the world, yet they are still at the early stages of domestication because conventional breeding is slow and costly. Thus, there is huge potential for marker-assisted breeding programs to improve traits such as wood properties. To this end, the sequencing, analysis and annotation of a large collection of expressed sequences tags (ESTs) from genes involved in wood formation in Eucalyptus would provide a valuable resource. RESULTS We report here the normalization and sequencing of a cDNA library from developing Eucalyptus secondary xylem, as well as the construction and sequencing of two subtractive libraries (juvenile versus mature wood and vice versa). A total of 9,222 high quality sequences were collected from about 10,000 cDNA clones. The EST assembly generated a set of 3,857 wood-related unigenes including 2,461 contigs (Cg) and 1,396 singletons (Sg) that we named 'EUCAWOOD'. About 65% of the EUCAWOOD sequences produced matches with poplar, grapevine, Arabidopsis and rice protein sequence databases. BlastX searches of the Uniref100 protein database allowed us to allocate gene ontology (GO) and protein family terms to the EUCAWOOD unigenes. This annotation of the EUCAWOOD set revealed key functional categories involved in xylogenesis. For instance, 422 sequences matched various gene families involved in biosynthesis and assembly of primary and secondary cell walls. Interestingly, 141 sequences were annotated as transcription factors, some of them being orthologs of regulators known to be involved in xylogenesis. The EUCAWOOD dataset was also mined for genomic simple sequence repeat markers, yielding a total of 639 putative microsatellites. Finally, a publicly accessible database was created, supporting multiple queries on the EUCAWOOD dataset. CONCLUSION In this work, we have identified a large set of wood-related Eucalyptus unigenes called EUCAWOOD, thus creating a valuable resource for functional genomics studies of wood formation and molecular breeding in this economically important genus. This set of publicly available annotated sequences will be instrumental for candidate gene approaches, custom array development and marker-assisted selection programs aimed at improving and modulating wood properties.
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Affiliation(s)
- David Rengel
- UMR CNRS/Université Toulouse III 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP42617 Auzeville, 31326 Castanet Tolosan, France
| | - Hélène San Clemente
- UMR CNRS/Université Toulouse III 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP42617 Auzeville, 31326 Castanet Tolosan, France
| | - Florence Servant
- UMR CNRS/Université Toulouse III 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP42617 Auzeville, 31326 Castanet Tolosan, France
- Current address : Syngenta Seeds SAS, BP27, 31790 Saint Sauveur, France
| | - Nathalie Ladouce
- UMR CNRS/Université Toulouse III 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP42617 Auzeville, 31326 Castanet Tolosan, France
| | - Etienne Paux
- UMR CNRS/Université Toulouse III 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP42617 Auzeville, 31326 Castanet Tolosan, France
- Current address : INRA-UBP, UMR 1095, INRA Site de Crouël, 234 avenue du Brézet, 63100 Clermont-Ferrand, France
| | - Patrick Wincker
- Génoscope, CNRS, UMR 8030 and Université d'Evry, 91057 Evry, France
| | - Arnaud Couloux
- Génoscope, CNRS, UMR 8030 and Université d'Evry, 91057 Evry, France
| | - Pierre Sivadon
- UMR CNRS/Université Toulouse III 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP42617 Auzeville, 31326 Castanet Tolosan, France
- Current address : Université de Pau et des Pays de l'Adour, UMR CNRS 5254 IPREM, IBEAS – BP1155, 64013 Pau Cedex, France
| | - Jacqueline Grima-Pettenati
- UMR CNRS/Université Toulouse III 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP42617 Auzeville, 31326 Castanet Tolosan, France
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Foucart C, Jauneau A, Gion JM, Amelot N, Martinez Y, Panegos P, Grima-Pettenati J, Sivadon P. Overexpression of EgROP1, a Eucalyptus vascular-expressed Rac-like small GTPase, affects secondary xylem formation in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2009; 183:1014-1029. [PMID: 19549133 DOI: 10.1111/j.1469-8137.2009.02910.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
To better understand the genetic control of secondary xylem formation in trees we analysed genes expressed during Eucalyptus xylem development. Using eucalyptus xylem cDNA libraries, we identified EgROP1, a member of the plant ROP family of Rho-like GTPases. These signalling proteins are central regulators of many important processes in plants, but information on their role in xylogenesis is scarce. Quantitative real-time reverse-transcriptase polymerase chain reaction (qRT-PCR) confirmed that EgROP1 was preferentially expressed in the cambial zone and differentiating xylem in eucalyptus. Genetic mapping performed in a eucalyptus breeding population established a link between EgROP1 sequence polymorphisms and quantitative trait loci (QTLs) related to lignin profiles and fibre morphology. Overexpression of various forms of EgROP1 in Arabidopsis thaliana altered anisotropic cell growth in transgenic leaves, but most importantly affected vessel element and fibre growth in secondary xylem. Patches of fibre-like cells in the secondary xylem of transgenic plants showed changes in secondary cell wall thickness, lignin and xylan composition. These results suggest a role for EgROP1 in fibre cell morphology and secondary cell wall formation making it a good candidate gene for marker-based selection of eucalyptus trees.
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Affiliation(s)
- Camille Foucart
- UMR 5546 CNRS/Université Toulouse III, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP 42617 Auzeville, F-31326 Castanet Tolosan, France
| | - Alain Jauneau
- IFR 40, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP 42617 Auzeville, F-31326 Castanet Tolosan, France
| | - Jean-Marc Gion
- UPR39 Génétique Forestière, Cirad-BIOS, Campus de Baillarguet TA 10C, F-34398 Montpellier Cedex 5, France
| | - Nicolas Amelot
- UMR 5546 CNRS/Université Toulouse III, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP 42617 Auzeville, F-31326 Castanet Tolosan, France
| | - Yves Martinez
- IFR 40, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP 42617 Auzeville, F-31326 Castanet Tolosan, France
| | - Patricia Panegos
- UMR 5546 CNRS/Université Toulouse III, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP 42617 Auzeville, F-31326 Castanet Tolosan, France
| | - Jacqueline Grima-Pettenati
- UMR 5546 CNRS/Université Toulouse III, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP 42617 Auzeville, F-31326 Castanet Tolosan, France
| | - Pierre Sivadon
- UMR 5546 CNRS/Université Toulouse III, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP 42617 Auzeville, F-31326 Castanet Tolosan, France
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