Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 79

Chloroplasts, Mitochondia and Organelles
Proteomic analyses of chloroplasts, mitochondria and othercell fractions have been
carried out to determine detailed localisation of proteins in sub-cellular compart-
ments. Methods for organelle isolation and purification are already available, and
are essential in the initial steps before protein is isolated and identified from them
(Sakai et al. 2004 ; Holy and Perkins 2009 ).Techniques for quantitative proteomics,
such as ICAT and iTRAQ described above, are then applied to resolve quantita-
tive data on the proteome in each organelle or cell compartment. In Arabidopsis ,
rice and algae, differential proteome profiles of the plant plasma membranes were
obtained, and used to identify different proteins expressed in response to environ-
mental stresses such as cold, salt stress and bacterial elicitors (Benschop et al. 2007 ;
Katz et al. 2007 ; Cheng et al. 2009 ; Minami et al. 2009 ). Listed below are the most
important web-based sites for sub-cellular proteomics, their purpose and the URL
are detailed in Table 2.7 . Several databases below provide subcellular proteome
information.
Rice Proteome Database
The rice proteome database is a 2-DE image information base for rice that con-
tains data from various tissues, as well as subcellular compartments and organelles
(Komatsu 2005 ).
Plant Organelle Database and GOBASE
These two web sites detail numerous external links to plant organelles (O'Brien
et al. 2009 ).
NASC Proteomics Database
The Nottingham Arabidopsis Stock Centre (NASC) Proteomics database is also
useful for both cellular and organelle data mining of proteins.
SUBA
The Sub-cellular location database for Arabidopsis proteins (SUBA) provides sub-
cellular proteome analytical and energy data on proteins in subcellular compart-
ments (Dunkley et al. 2006 ).