Computational and experimental analysis identifies Arabidopsis genes specifically expressed during early seed development

BACKGROUND: Plant seeds are complex organs in which maternal tissues, embryo and endosperm, follow distinct but coordinated developmental programs. Some morphogenetic and metabolic processes are exclusively associated with seed development. The goal of this study was to explore the feasibility of incorporating the available online bioinformatics databases to discover Arabidopsis genes specifically expressed in certain organs, in our case immature seeds. RESULTS: A total of 11,032 EST sequences obtained from isolated immature seeds were used as the initial dataset (178 of them newly described here). A pilot study was performed using EST virtual subtraction followed by microarray data analysis, using the Genevestigator tool. These techniques led to the identification of 49 immature seed-specific genes. The findings were validated by RT-PCR analysis and in situ hybridization. CONCLUSION: We conclude that the combined in silico data analysis is an effective data mining strategy for the identification of tissue-specific gene expression

ZmXTH1, a new xyloglucan endotransglucosylase/hydrolase in maize, affects cell wall structure and composition in Arabidopsis thaliana

15 pages, 9 figures.-- PMID: 18316315[PubMed].-- Supporting information available at: http://jxb.oxfordjournals.org/content/59/4/875/suppl/DC1Xyloglucan endotransglucosylase/hydrolases (XTHs; EC 2.4.1.207 and/or EC 3.2.1.151) are enzymes involved in the modification of cell wall structure by cleaving and, often, also re-joining xyloglucan molecules in primary plant cell walls. Using a pool of antibodies raised against an enriched cell wall protein fraction, a new XTH cDNA in maize, ZmXTH1, has been isolated from a cDNA expression library obtained from the elongation zone of the maize root. The predicted protein has a putative N-terminal signal peptide and possesses the typical domains of this enzyme family, such as a catalytic domain that is homologous to that of Bacillus macerans beta-glucanase, a putative N-glycosylation motif, and four cysteine residues in the central and C terminal regions of the ZmXTH1 protein. Phylogenetic analysis of ZmXTH1 reveals that it belongs to subgroup 4, so far only reported from Poaceae monocot species. ZmXTH1 has been expressed in Pichia pastoris (a methylotrophic yeast) and the recombinant enzyme showed xyloglucan endotransglucosylase but not xyloglucan endohydrolase activity, representing the first enzyme belonging to subgroup 4 characterized in maize so far. Expression data indicate that ZmXTH1 is expressed in elongating tissues, modulated by culture conditions, and induced by gibberellins. Transient expression assays in onion cells reveal that ZmXTH1 is directed to the cell wall, although weakly bound. Finally, Arabidopsis thaliana plants expressing ZmXTH1 show slightly increased xyloglucan endohydrolase activity and alterations in the cell wall structure and composition.This work was funded by the Spanish ‘Ministerio de Ciencia y Tecnología’ (BIO2001-1140). VG was financed by a pre-doctoral grant from the ‘Generalitat de Catalunya’ (2003-FI00090). In addition, VG was funded by two grants from the Generalitat de Catalunya (2005-BE00104 and 2006-BE00668) for her work performed at Professor Fry's and Dr Ruel's laboratories. SF was financed by a post-doctoral grant from the ‘Generalitat de Catalunya’ (2003PIV-A-00033) and by an I3P contract from the ‘Consejo Superior de Investigaciones Científicas’. DC-R was financed by the Spanish ‘Ministerio de Educacion y Ciencia’ (‘Ramon y Cajal’ Program). This work was carried out within the framework of the ‘Xarxa de Referència en Biotecnologia’ from the ‘Generalitat de Catalunya’. SCF was funded by the UK Biotechnology and Biological Sciences Research Council. We are indebted to Dr Castresana (IBMB-CSIC) for his advice on the phylogenetic analyses, Dr Capellades for her technical support and the sequencing, and the greenhouse teams of IBMB-CSIC.Peer reviewe

European Union needs agro-bioeconomy

Bioeconomy, biotechnology and genetically-modified organisms in particular have been the subject of discussion for a long time. Biotechnology is applied in a variety of economic areas which include biopharmaceuticals, biobased products and agriculture. During the last 20 years, innovative biotechnological techniques for plant genome improvement have been developed. Many factors worldwide have led to the status quo : different legislations around the world, the lack of public acceptance in the EU and high expectations for new strategies for sustainability and food security. Therefore, a clear regulatory status for new techniques is crucial for research and development, as well as for their practical implementation. This should be based on solid science which plays a critical role in developing the bioeconomy

The Ionic Environment Controls the Contribution of the Barley HvHAK1 Transporter to Potassium Acquisition1[W][OA]

The control of potassium (K+) acquisition is a critical requirement for plant growth. Although HAK1 (high affinity K+ 1) transporters provide a pathway for K+ acquisition, the effect exerted by the ionic environment on their contribution to K+ capture remains essentially unknown. Here, the influence of the ionic environment on the accumulation of transcripts coding for the barley (Hordeum vulgare) HvHAK1 transporter as well as on HvHAK1-mediated K+ capture has been examined. In situ mRNA hybridization studies show that HvHAK1 expression occurs in most root cells, being augmented at the outermost cell layers. Accumulation of HvHAK1 transcripts is enhanced by K+ deprivation and transiently by exposure to high salt concentrations. In addition, studies on the accumulation of transcripts coding for HvHAK1 and its close homolog HvHAK1b revealed the presence of two K+-responsive pathways, one repressed and the other insensitive to ammonium. Experiments with Arabidopsis (Arabidopsis thaliana) HvHAK1-expressing transgenic plants showed that K+ deprivation enhances the capture of K+ mediated by HvHAK1. A detailed study with HvHAK1-expressing Saccharomyces cerevisiae cells also revealed an increase of K+ uptake after K+ starvation. This increase did not occur in cells grown at high Na+ concentrations but took place for cells grown in the presence of NH4+. 3,3′-Dihexyloxacarbocyanine iodide accumulation measurements indicate that the increased capture of K+ in HvHAK1-expressing yeast cells cannot be explained only by changes in the membrane potential. It is shown that the yeast protein phosphatase PPZ1 as well as the halotolerance HAL4/HAL5 kinases negatively regulate the HvHAK1-mediated K+ transport