Since the completion of the genomic sequencing of various plant species, including Arabidopsis (1) and rice (2,3), postgenomic approaches such as microarrays and mass spectrometry-based proteomics have been used extensively in the field of plant science, and results acquired by these high-throughput techniques are publicly accessible through various genome-wide databases. Integrative biological and genome information databases established for Arabidopsis and rice provide significant insights into genetic composition, gene expression and the prediction of protein localization (4–8). Recently, databases for individual organelles, including chloroplasts (9,10), mitochondria (11), vacuoles (12), nuclei (13), peroxisomes (14,15) and cell walls (16), have been made available to provide information on organellar proteins identified in proteomic and/or sequence-based analyses. However, these databases are limited to individual organelles and provide only still images of each organelle. It is now widely known that plant organelles dramatically change their shape, number, size and localization in cells depending on tissue type, developmental stage and environmental stimuli, and that such flexible organelle dynamics support the integrated functions of higher plants. The availability of a database that surveyed such flexible organelle dynamics would assist in the progress of plant science.
In this article, we present the plant organelles database (PODB), a database of visualized plant organelles and protocols for plant organelle research. The joint research project of ‘Organelle Differentiation as the Strategy for Environmental Adaptation in Plants’ started with a Grant-in-Aid for Scientific Research of Priority Areas to clarify the molecular mechanisms underlying the induction, differentiation and interaction of organelles and to understand the integrated function of individual plants through organelle dynamics (http://www.nibb.ac.jp/organelles/). The PODB (http://podb.nibb.ac.jp/Organellome) is a publicly available database that was built to accelerate plant organelle research as one part of this joint research project. Since its public release at the end of September 2006, this database has provided information on plant organelles that are labeled with fluorescent and/or nonfluorescent probes, as well as useful protocols for plant organelle research.
Unlike the protein localization databases available for Arabidopsis (17–20), mouse (21), Saccharomyces cerevisiae (22) and several other eukaryotic organisms (23,24), which collect annotations of the subcellular localization of proteins, the aim of the PODB is to provide information on the dynamics of plant organelles in addition to the localizations of specific proteins.
We expect that this database will be a useful tool to help researchers gain greater knowledge about plant organelles, as well as an easily accessible platform for both biologists and members of the general public who might want to explore the basics of plant cell biology.
Answers to all your Biology Questions
