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)