Biology Reference
In-Depth Information
Chapter 3
Plant Proteomics: From Genome Sequencing
to Proteome Databases and Repositories
Katsumi Sakata and Setsuko Komatsu
Abstract
Proteomic approaches are useful for the identifi cation of functional proteins. These have been enhanced
not only by the development of proteomic techniques but also in concert with genome sequencing. In this
chapter, 30 databases and Web sites relating to plant proteomics are reviewed and recent technologies
relating to data collection and annotation are surveyed.
Key words
Plant genome, Proteome, Database, 2-DE, MS, Shotgun proteomics, Annotation
Abbreviations
EST Expressed sequence tag
MS Mass spectrometry
n
-DE
n
-Dimensional electrophoresis
SDS-PAGE Sodium dodecyl sulfate-polyacrylamide gel electrophoresis
1
Introduction
Comprehensive approaches for biomarker searching and functional
analysis include proteomics, transcriptomics, and metabolomics.
Proteomic approaches allow us to directly analyze the proteins that
exist in a living body just at the emergence of biological functions [
1
].
The identifi cation of proteins has been dramatically enhanced by mass
spectrometers and homology searches against large-scale genome
sequence data [
2
]. Furthermore, many proteins have been discovered
in relation to the differentiation and growth of plants, as well as pro-
teins differentially expressed depending on the environmental condi-
tions, based on proteomic techniques that can comprehensively
analyze protein interactions [
3
,
4
]. As with genomic data, large vol-
umes of proteomic data have been accumulated in recent years cou-
pled with the development of high- throughput analysis methodologies.
