- Meeting report
- Open Access
© GenomeBiology.com 2000
- Published: 6 December 2000
A report on the first annual Genomic Arabidopsis Resource Network (GARNet) meeting, York, UK, 2-3 October, 2000.
- Investigate Gene Function
- Nottingham Arabidopsis Stock Centre
- Heterochromatic Knob
- Thylakoid Membrane Lipid
Over 200 researchers from the UK plant research community met to find out more about the functional genomics resources that will become available through the GARNet program [http://garnet.arabidopsis.org.uk], which is funded by a £4 million grant from the UK BBRSC Investigating Gene Function (IGF) initiative. Such resources will include transcriptome analysis, bioinformatics, metabolite profiling, proteome analysis and tagged genes. Presentations from international speakers on the progress being made with functional genomics tools put the project in context and provided insights into how useful such shared resources can be.
Pam Green (Michigan State University, USA) described successes from initial rounds of the NSF-funded Arabidopsis Functional Genomics Consortium (AFGC; [http://afgc.stanford.edu]) microarray service, which has developed microarrays containing 11,000 expressed sequence tagged (EST) clones representing about 8,000 unique genes. Applications are submitted via the web, and data from completed experiments are made public either immediately or within three months, depending on customer preference. Green used the dst1 mutant, which results in defects in sequence-specific mRNA decay, as an example of the usefulness of microarrays for exploring previously recalcitrant regulatory pathways. Although dst1 plants have no visible phenotype, a comparison of their transcript profiles to that of wild-type parental plants revealed new molecular phenotypes that can provide insights into the role of the mutant genes and the pathway they affect. Green also described progress toward monitoring the stability of thousands of mRNAs simultaneously. These studies identified at least 50 genes that correspond to unstable mRNAs with a half-life of less than 60 minutes.
An important outcome of such profiling studies will be the use of 'spot histories' - the behavior of a particular gene through the range of experimental applications - for predictive modeling of gene networks. Such analyses will provide insights into signaling pathways involved in development and maintenance processes, with the ultimate goal of creating a virtual plant. The difficulties of comparative experimentation in plant biology, particularly having to deal with different accessions, variable growth conditions and the underlying diurnal and circadian rhythms, were highlighted in Green's talk and subsequent presentations.
In plants, proteomic analyses are less well developed than genomic analyses but are an essential step towards our understanding of coordinated gene function. Traditional two-dimensional (2D) electrophoresis continues to provide the basic technology for comparative proteomics. Paul Dupree (University of Cambridge, UK) described advances using dual Cy3/Cy5 labeling that enable the comparison of two proteomes on a single 2D gel. Justin Roberts (University of California, Riverside, USA), described the elegant use of affinity chromatography to selectively purify and concentrate classes of proteins that are not accessible using conventional subcellular fractionation techniques. The choice of resins with specific immobilized nucleotides or broad-spectrum metabolite analogs (dyes), coupled with sequential elution, enabled the resolution of classes of proteins with specific biochemical properties. In addition to achieving significant enrichment, affinity purification also facilitated the application of mass spectrometry (MS) and 2D electrophoresis to study associated multisubunit protein complexes. The selective use of ligands also has applications in the use of combinatorial chemistry in drug and herbicide discovery. Roberts tempered the discussion with a cautionary tale of technical bottlenecks, particularly the difficulty in achieving in vivo labeling reproducibly.
Bottlenecks in sample preparation were also addressed by Johan Gobom (Max-Planck-Institute for Molecular Genetics, Berlin, Germany). Gobom discussed improvements in high-throughput screening through the application of advanced materials technology. These included arraying multiple samples using 200 µm colloidal gold particles as hydrophilic 'anchors' on hydrophobic Teflon-coated matrix-assisted laser desorption ionization (MALDI) probes, and the rapid purification of 2D spots for MALDI-MS. The latter technique used pre-structured sample supports that efficiently bind peptides within 10 seconds of contact, enabling rapid and quantitative removal of salt, thus removing a major restriction to high-throughput MALDI screening. This clearly highlighted the value of on-site integration of plant functional genomics programs with related projects. Although only briefly touched on, systematic large-scale yeast two-hybrid screens, protein crystallization and associated structural genomics undertaken at 'The Protein Structure Factory' [http://userpage.chemie.fu-berlin.de/~psf/] clearly bear this out.
The meeting succeeded in bringing together the major players in Europe and the USA, and should stimulate greater collaboration, for example in the provision of gene-specific tags (GSTs) and informatics resources. The meeting also provided the platform to launch the IGF Brassica Functional Genomics initiative, which will interact closely with GARNet. Ottoline Leyser (Univeristy of York, UK; a GARNet principal investigator) hopes results arising directly from this initiative will be discussed in future meetings, which will be crucial to assess the progress of the different technologies and to shape research policy for future initiatives.