Current initiatives in proteomics research: the plant perspective

Abstract

The recent upsurge in structural genomics is leading to the accumulation of a huge wealth of literature on nucleotide sequences. After the nucleotide sequence of a given stretch of DNA is obtained (by manual or robotic methods), the next step is to use some software program to distinguish the possible open reading frames in the thick of sequences. However, the acid test, whether the new sequence corresponds to any functionality in terms of transcription and translation is to identify the protein which it encodes. Functional genomics and proteomics are the buzzwords in modern-day genomics. The science of proteomics is a possible approach to relate the skeletal nucleotide sequence information to functional attributes of the cell. The identification and isolation of novel genes with potential biotechnological applications warrant that genomics and proteomics must go hand in hand. Three major steps in proteome analysis are the separation of complex protein mixtures by two-dimensional protein gel electrophoresis (2D), characterization of the separated proteins by mass spectrometer (MS) and database searching. The power of 2D is such that it allows even minor changes in gene expression caused by internal or external cues to be effectively scored. Most proteins resolved by 2D have high purity, which can facilitate their identification by MS. In recent years, methods for automated proteomics based on incorporation of new ideas in both hardware and software development have been optimized to a great deal. We discuss the progress and applications of the proteomics science, with special reference to plants.