Abstract
BackgroundThe ubiquitin 26S/proteasome system (UPS), a serial cascade process of protein ubiquitination and degradation, is the last step for most cellular proteins. There are many genes involved in this system, but are not identified in many species. The accumulating availability of genomic sequence data is generating more demands in data management and analysis. Genomics data of plants such as Populus trichocarpa, Medicago truncatula, Glycine max and others are now publicly accessible. It is time to integrate information on classes of genes for complex protein systems such as UPS.ResultsWe developed a database of higher plants' UPS, named 'plantsUPS'. Both automated search and manual curation were performed in identifying candidate genes. Extensive annotations referring to each gene were generated, including basic gene characterization, protein features, GO (gene ontology) assignment, microarray probe set annotation and expression data, as well as cross-links among different organisms. A chromosome distribution map, multi-sequence alignment, and phylogenetic trees for each species or gene family were also created. A user-friendly web interface and regular updates make plantsUPS valuable to researchers in related fields.ConclusionThe plantsUPS enables the exploration and comparative analysis of UPS in higher plants. It now archives > 8000 genes from seven plant species distributed in 11 UPS-involved gene families. The plantsUPS is freely available now to all users at .
Highlights
The ubiquitin 26S/proteasome system (UPS), a serial cascade process of protein ubiquitination and degradation, is the last step for most cellular proteins
UPS can affect all aspects of cellular function, and plays an important role in physiological processes like hormonal responses, biotic stress and photomorphogenesis
In UPS, substrate proteins destined for degradation are tagged with 76-residue ubiquitin proteins through a serial cascade process of so-called ubiquitination, and hydrolysed by 26S proteasome
Summary
The ubiquitin 26S/proteasome system (UPS), a serial cascade process of protein ubiquitination and degradation, is the last step for most cellular proteins. The accumulating availability of genomic sequence data is generating more demands in data management and analysis. It is time to integrate information on classes of genes for complex protein systems such as UPS. In UPS, substrate proteins destined for degradation are tagged with 76-residue ubiquitin proteins through a serial cascade process of so-called ubiquitination, and hydrolysed by 26S proteasome. There are approximately 1300 E3s in the Arabidopsis genome, and large numbers in other plants. In most plant species, the genome-wide classification and annotation of UPS genes, especially E3 families, are not yet available. The rapidly accumulating genome sequences has (page number not for citation purposes)
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