Brief guide on rice proteome
Authors: Ashish G Vala1, Bhupendra Singh Punwar2, Ravi J Shah3 and Jalpa P Panchal4
1Anand Agriculture University, Anand.
2National Research Centre on Plant Biotechnology, New Delhi.
3,4Department of Agriculture and cooperation, Gandhinagar


Proteomics is the large-scale study of proteins, particularly their structures and functions:

1. The initial objective of proteomics was the large-scale identification of all protein species in a cell or tissue.

2. Analyze various functional aspects of proteins such as posttranslational modifications, protein-protein interactions, activities and structures.

Types of proteome

Protein Expression
Quantitative study of protein expression between samples that differ by some variable
Structural Proteomics
Goal is to map out the 3-D structure of proteins and protein complexes
Functional Proteomics
To study protein-protein interaction, 3-D structures, cellular localization and in order to understand the physiological function of the whole set of proteome.

Technology of Proteomics

Proteome profiling/separation

1. 2D SDS PAGE (two-dimensional sodium dodecylsulphate polyacrylamide gel electrophoresis)
2. 2-D LC/LC (LC = Liquid Chromatography)
3. 2-D LC/MS (MS= Mass spectrometry)

Protein identification

1. Peptide mass fingerprint
2. Tandem Mass Spectrometry (MS/MS)

Quantative proteomics
1. ICAT (isotope-coded affinity tag)
2. SILAC (stable isotopic labeling of amino acids)

Rice proteomic :

1. In rice improved analytical methods for protein characterization, or the study of the entire protein content of a cell or tissue, has become a major field of functional genomics.

2. Identification of function, regulation, protein -protein interaction and type of post translational modification of each encoded protein of rice.

3. Large scale identification of all protein species in a cell or tissue.

4. A system for direct differential display using two dimensional polyacralamide gel (2D-PAGE) electrophoresis for identification of rice proteins that vary in expression under different physiological conditions and among different tissues.

5. Analyze their structure by comparison with the rice proteome database, or by mass spectrometry.

An important of rice proteome research :

(1) To determine whether the cDNA encoding particular proteins from the cDNA library constructed from rice can be identified by a computer search of an amino acid sequence homology.

(2) To predict the function of the proteins and study the physiological significance of functional proteins in rice.

Strategy to determine the amino acid sequence in rice proteome analysis :

1. Gel electrophoresis
2. N-terminal amino acid sequence analysis
3. Internal amino acid sequence analysis
4. Analysis using mass spectrometry
5. Homology search of amino acid sequences

Functional analysis using differential proteomics

Stress : To identifying proteins that are differentially regulated in response to abiotic and biotic stress under environmental conditions.

1. Cold
2. Drought
3. Salinity
4. Ozone
5. Fungus
6. Virus
7. Insect

Hormones : To identifying hormone which play an important role in may aspects of signal transduction in cells as well as in several growth and development pathways.

1. Gibberellin
2. Brassinosteroid
3. Jasmonic acid
4. Auxin

Rice proteome database..

Database based on Two-Dimensional Polyacrylamide Gel Electrohoresis

2D-PAGE of plant protein (WORLD -2D PAGE (http://expasy.org/ch2d/2d-index.html ) )
Public domain : Rice Membrane Protein Library (http://www.cbs.edu.rice )
Rice protein database (http://gene64.dna.affrc.go.jp/RPD )

The rice proteome database has link to the NAIS rice genome tools, which are :

Rice expression database(RED), The rice full length cDNA database (KOME),
The rice genome integrated mape database(INE),
The rice mutant panel database (Tos 17) ,
The rice genome annotation database (Rice GAAS)

General flow of rice proteome database

1. RAP-DB Rice Annotation Project Database
2. INE Integrated Rice Genome Explorer
3. RAD Rice Annotation Database
4. Rice Proteome Database
5. KOME Knowledge oriented molecular biological encyclopedia
6. Rice Tos17insertion mutant database
7. RED Rice Expression Database
8. RGP Rice cDNA sequence Database
9. RMOS Rice Microarray Opening Site
10. Rice PIPELINE
11. PLACE PLAnt Cis-acting regulatory DNA Elements Database
12. Rice Mitochondrial genome information RMG
13. RPSD Rice Protein structure Database



Proteomics Database

1. WORLD-2DPAGE
2. SWISS-2DPAGE
3. YPM
4. YEAST 2D-PAGE
5. ECO2DBASE
6. Sub2D
7. Cyano2Dbase
8. Abeerden 2-D db
9. Maize 2-D db
10. Fly 2-D db
11. ECO2DBASE (VanBogelen et al, 1997)
12. HSC-2DPAGE (Dunn et al., 1997)
13. SIENA-2DPAGE (Bini et al., 1997a; Bini et al., 1997b)
14. PHCI-2DPAGE (Shaw et al., 1999a; Shaw et al., 1999b)

Conclusion

2D-PAGE provides a convenient way to study and identify the various rice proteins under different stress.
Using advance techniques large scale identification of rice protein in a cell or tissue of rice under different environmental, abiotic and biotic stress conditions.
Knowing where and when individual proteins are synthesized in rice, with respect to developmental stage, can also provide clues to their function.
Proteins related to energy metabolism were up-regulated, and defense-related proteins were down-regulated in leaf blades, by cold stress.
Heat shock protein(HSPs) , Energy and metabolism related protein ,Redox homeostatis and Regulatory proteins were identified during heat stress.
Identify Granule-Bound Starch Synthase (GBSS, Wx protein) and globulin which is important in starch biosynthesis and rice grain quality under drought stress.
In leaf sheath, root and cultured suspension, protein which regulated by GA may play a significant role in tissue growth.
Easy to identify those protein of rice that regulated in response to different stress condition with knowing where and when individual protein may synthesized, with respect to specific stages, and also provide clues to their function using rice proteome database. New technology, promises a great deal for developing the high yield and sustainable agriculture tomorrow.

Future thrust

1. To analyze various functional aspects of proteins such as post translation modification, protein - protein interaction, activities and structures.

2. Large scale identification of rice protein in a cell or tissue under different environmental abiotic and biotic stress condition.

3. Nee to be carryout identification of protein modification for functional analysis and predication in rice.


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About Author / Additional Info:
I did doctorate in plant biotechnology and area of interest is Rice Genomics