A genomic approach to investigate developmental cell death in woody tissues of Populus trees

Genome Biology, Mar 2005

Background Poplar (Populus sp.) has emerged as the main model system for molecular and genetic studies of forest trees. A Populus expressed sequence tag (EST) database (POPULUSDB) was previously created from 19 cDNA libraries each originating from different Populus tree tissues, and opened to the public in September 2004. We used this dataset for in silico transcript profiling of a particular process in the woody tissues of the Populus stem: the programmed death of xylem fibers. Results One EST library in POPULUSDB originates from woody tissues of the Populus stem where xylem fibers undergo cell death. Analysis of EST abundances and library distribution within the POPULUSDB revealed a large number of previously uncharacterized transcripts that were unique in this library and possibly related to the death of xylem fibers. The in silico analysis was complemented by a microarray analysis utilizing a novel Populus cDNA array with a unigene set of 25,000 sequences. Conclusions In silico analysis, combined with the microarray analysis, revealed the usefulness of non-normalized EST libraries in elucidating transcriptional regulation of previously uncharacterized physiological processes. The data suggested the involvement of two novel extracellular serine proteases, nodulin-like proteins and an Arabidopsis thaliana OPEN STOMATA 1 (AtOST1) homolog in signaling fiber-cell death, as well as mechanisms responsible for hormonal control, nutrient remobilization, regulation of vacuolar integrity and autolysis of the dying fibers.

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A genomic approach to investigate developmental cell death in woody tissues of Populus trees

Genome Biology Re e2VMt0ooa0lruls5.emaeuea6r,cIshsue 4, Article R34 A genomic approach to investigate developmental cell death in woody tissues of Populus trees Charleen Moreau*, Nikolay Aksenov*, Maribel Garca Lorenzo, Bo Segerman*, Christiane Funk, Peter Nilsson, Stefan Jansson* and Hannele Tuominen* Correspondence: Hannele Tuominen. E-mail: 0 Department of Biochemistry, Umea University , SE-901 87 Umea , Sweden 1 Department of Biotechnology, KTH - Royal Institute of Technology, AlbaNova University Center , SE-10691, Stockholm , Sweden 2 Department of Plant Physiology, Umea Plant Science Centre, Umea University , SE-901 87 Umea , Sweden Background: Poplar (Populus sp.) has emerged as the main model system for molecular and genetic studies of forest trees. A Populus expressed sequence tag (EST) database (POPULUSDB) was previously created from 19 cDNA libraries each originating from different Populus tree tissues, and opened to the public in September 2004. We used this dataset for in silico transcript profiling of a particular process in the woody tissues of the Populus stem: the programmed death of xylem fibers. Results: One EST library in POPULUSDB originates from woody tissues of the Populus stem where xylem fibers undergo cell death. Analysis of EST abundances and library distribution within the POPULUSDB revealed a large number of previously uncharacterized transcripts that were unique in this library and possibly related to the death of xylem fibers. The in silico analysis was complemented by a microarray analysis utilizing a novel Populus cDNA array with a unigene set of 25,000 sequences. Conclusions: In silico analysis, combined with the microarray analysis, revealed the usefulness of non-normalized EST libraries in elucidating transcriptional regulation of previously uncharacterized physiological processes. The data suggested the involvement of two novel extracellular serine proteases, nodulin-like proteins and an Arabidopsis thaliana OPEN STOMATA 1 (AtOST1) homolog in signaling fiber-cell death, as well as mechanisms responsible for hormonal control, nutrient remobilization, regulation of vacuolar integrity and autolysis of the dying fibers. Background cell walls. The final phase in maturation of both vessel elements and fibers is cell death and autolysis of the cell contents. http://genomebiology.com/2005/6/4/R34 Genome Biology 2005, Volume 6, Issue 4, Article R34 Moreau et al. R34.3 Fs V Fs V 100 m Secondary cell wall deposition Cell expansion Fiber cell death Early fiber development Fiber cell death Tension wood Leaf senescence Unassigned Biological process unknown Development Response to stimulus Cell communication Photosynthesis Cell growth and/or maintenance Biosynthesis Catabolism Electron transport Transcription Other metabolism POPLAR.161 glycine hydroxymethyltransferase POPLAR.862 arabinogalactan-protein AGP13 POPLAR.58 polyubiquitin 4 POPLAR.155 S-adenosylmethionine synthetase POPLAR.5071 expressed protein POPLAR.5157 nodulin MtN21family protein POPLAR.843 DREPP plasma membrane polypeptide family protein POPLAR.9335 protease inhibitor/seed storage/lipid transfer protein POPLAR.649 5-methyltetrahydropteroyltriglutamate homocysteine S-MT POPLAR.999 Arabinogalactan protein Pop14A9. POPLAR.912 caffeoyl-CoA 3-O-methyltransferase POPLAR.1250 cysteine proteinase RD19a (RD19A) POPLAR.756 dormancy-associated protein POPLAR.1776 glycine-richprotein POPLAR.613 auxin/aluminum-responsive protein POPLAR.153 calmodulin-binding family protein POPLAR.700 alkaline alpha galactosidase POPLAR.2996 glutamate decarboxylase POPLAR.1754 senescence-associated protein-related POPLAR.3203 fasciclin-like arabinogalactan protein FLA12 POPLAR.3328 transaldolase POPLAR.9554 extensin-like protein POPLAR.9968 expressed protein POPLAR.39 vacuolar calcium-binding protein-related POPLAR.102 Glutamine synthetase POPLAR.147 Adenosylhomocysteinase POPLAR.166 trans-cinnamate 4-monooxygenase POPLAR.3587 glycosyl hydrolase family 17 protein X024D04 peptide/amino acid transporter P031B09 Cytochrome b (Fragment). Euphlyctis hexadactylus X010D05 expressed protein POPLAR.10080 Glycine-rich protein LeGRP1. Lycopersicon esculentum POPLAR.11632 prolylcarboxypeptidase-like protein POPLAR.6175 lipase POPLAR.11628 glycosyl hydrolase family 1 protein P062H06 glycine-rich protein X002G05 nodulin-like protein POPLAR.10013 Suspensor-specific protein. Phaseoluscoccineus X027A08 2310043L02Rik protein. Mus musculus. POSSIBLY proline-rich protein POPLAR.11144 vacuolar protein sorting protein. Oryza sativa X053F08 protein kinase like protein POPLAR.11659 peroxidase POPLAR.872 aminotransferase X024F05 expressed protein POPLAR.4667 nodulin-like protein POPLAR.10536 expressed protein V031H02 bHLH transcription factor POPLAR.44 expressed protein R040B06 P-glycoprotein, putative POPLAR.7952 pescadillo-like protein POPLAR.6205 expressed protein POPLAR.10503 transporter POPLAR.10724 prolylcarboxypeptidase-like protein P055F10 glycine-rich (...truncated)


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Charleen Moreau, Nikolay Aksenov, Maribel Lorenzo, Bo Segerman, Christiane Funk, Peter Nilsson, Stefan Jansson, Hannele Tuominen. A genomic approach to investigate developmental cell death in woody tissues of Populus trees, Genome Biology, 2005, pp. R34, 6, DOI: 10.1186/gb-2005-6-4-r34