The Lotus japonicus Genome

18

Proteomics

Svend Dam and Jens Stougaard

Abstract

Proteomics is an efficient tool to identify proteins present in specific

tissues, cell types, or organelles. The resulting proteome reference maps

and/or comparative analyses provide overviews of regulated proteins

between wild type and mutants or between different conditions together

with a comprehensive list of proteins. Post translation modifications

(PTMs), such as glycosylation and phosphorylation, are pivotal for protein

stability and function. Several strategies for enrichment of PTMs have

been developed where targeted proteomic approaches are used to identify

these PTMs. The sequenced and annotated Lotus japonicus (Lotus)

genome has been essential for obtaining high-quality protein identifica-

tions from proteomics studies. Furthermore, additional genomics and

transcriptomics studies from several Lotus species/ecotypes support

putative gene structures and these can be further supported using

proteomics data. Two characteristics of legumes are the high seed protein

level and the nitrogen fixing symbiosis. Thus, the majority of the

proteomics studies inLotushave been performed on seed/pod and nodule/

root tissues in order to create proteome reference maps and to enable

comparative analyses withinLotustissues or toward similar tissues from

other legume species. More recently,N-glycan structures and composi-

tions have been determined from matureLotusseeds using glycomics and

glycoproteomics, andfinally, phosphoproteomics has been employed.

18.1 Extraction and Separation of

Proteins/Peptides

The proteome defines the proteins expressed in

an organism, tissue, organ, cell, or subcellular

component (Wasinger et al. 1995 ). Proteomics is

a large scale study of the proteome and four

major steps, i.e., protein extraction, protein/pep-

tide separation, mass spectrometry, and data

S. Dam (&)
J. Stougaard
Centre for Carbohydrate Recognition and Signalling,
Department of Molecular Biology and Genetics,
Aarhus University, Gustav Wieds Vej 10,
8000 Aarhus C, Denmark
e-mail: [email protected]

S. Tabata and J. Stougaard (eds.),The Lotus japonicus Genome, Compendium of Plant Genomes,
DOI 10.1007/978-3-662-44270-8_18,©Springer-Verlag Berlin Heidelberg 2014

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