Proteomic Studies in Rice

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What is Proteomics?

Figure 1. Overview of the workflow for analysis of RNA-Seq data.
  • Proteins are vital parts of living organisms as they are the main components of the physiological metabolic pathways of cells, and Proteomics is the large-scale study of proteins, particularly their structures and functions. The word proteome is a portmanteau of protein and genome, it was initially coined by Marc Wilkins (Ph. D. student at Australia's Macquarie University) during the first Siena meeting (2D Electrophoresis-From Protein Maps to Genomes, Siena, Italy, September 5-7, 1994). Three years later, by 1997, the first book on proteomics was published. As the genomes of an increasing number of species were sequenced and released, and mass spectrometry equipment and bioinformatics tools more and more developed, proteomics took leadership in the biological research arena, and was alternately considered to be the El Dorado or andora’s Box that would allow us to decipher the biological meaning of the sequenced genes. Nowadays, within the omics techniques, proteomics constitutes a priority research for any organism and configures a fundamental discipline in the post-genomic era.

Plant proteomics as reflected in Proteomics

  • By January 2001 the first Proteomics issue appeared, with no plant papers on it. Up to May 2014, 5179 reports in the journal appeared according to the ISI Web of Knowledge, with 365 corresponding to plants, representing 7% of the total. Obviously, unlike model biological systems, the full potential of proteomics is far from being fully exploited in plant biology research. Thus, only a low number of plant species have been investigated at the proteomics level and, mainly, by using strategies based on 2-DE coupled to MS, this resulting in low proteome coverage.

Classification of Proteomics

  • In proteomics, several areas can be defined: (i) Descriptive Proteomics, including Intracellular and Subcellular Proteomics; (ii) Differential Expression Proteomics; (iii) Post-translational Modifications; (iv) Interactomics; and (v) Proteinomics (targeted or hypothesis-driven Proteomics). With few exceptions, most of the forest tree proteomics papers so far published (Table 4) deal with the first two areas (Liu et al., 2010). Objectives ranged from the study of biological processes such as growth and development, responses to stresses, organogenesis, embryogenesis, heredity, to practical aspects, including proteotyping and the identification of proteins characterizing natural variability and phylogeny or to be used as markers in breeding programs (Figure 1).

Historical Perspectives

  • Figure 2 tells about the progress in plant proteomics. The prestage can be considered the beginning of proteomics where 1(one)-DGE and 2-DGE techniques were applied to separate proteins and their identification using N-terminal Edman sequencing. The initial stage started with the genome revolution in the year 2000 onwards. Since the publication of the draft genome sequences of two plants, Arabidopsis thaliana (weed and dicot model) (The Arabidopsis Genome Initiative, 2000) and rice (Oryza sativa L., cereal crop and monocot model: Goff et al., 2002; Yu et al., 2002) in 2000 and 2002, respectively, plant proteomics research has seen a rapid growth. In this initial phase we also could see an effort by the Arabidopsis scientific community to start working toward the proteome of this mod- el plant via the establishment of a Multinational Arabidopsis Steering Committee Proteomics subcommittee (MASCP,

Figure 1. Timeline of plant proteomics development. Details are in the main text.

  • Since then, plant proteomics has moved into the progression stage, where researchers have been involved in enriching the scientific community by con- certed efforts to publish reviews in series on rice, plants, and protein phosphorylation and publication of five books in plant proteomics. The initial years of this decade also saw the devel- opment of an idea on a global initiative on plant proteomics that led to the establishment of the International Plant Proteo- mics Organization (INPPO, With more plant genomes being sequenced, from model to non-models (Feuillet et al., 2010; Agrawal et al., 2011), there is no turning back to the utilization of proteomics approaches in various aspects of plant biology research.

Projects List

Project Title Species Published years Academic Journal RiceWiki Project ID
Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL Mapping Oryza sativa L. ssp. Japnoica 2003 Biological and Pharmaceutical Bulletin IC4R001-Proteomic-2003-12576669
Comparative Proteome Analyses Reveal that Nitric Oxide Is an Important Signal Molecule in the Response of Rice to Aluminum Toxicity Oryza sativa 2013 journal of proteome research IC4R002-Proteomic-2013-23327584
Proteomic analyses of Oryza sativa mature pollen reveal novel proteins associated with pollen germination and tube growth Oryza sativa L. ssp. Japnoica 2016 Proteomics IC4R003-Proteomic-2016-16548068
Proteomic analysis of rice (Oryza sativa) seeds during germination Oryza sativa L. ssp. indica 2007 Proteomics IC4R004-Proteomic-2007-17849412
Physiological and proteomic approaches to address heat tolerance during anthesis in rice (Oryza sativa L.) Oryza sativa L. ssp. Japnoica 2010 Journal of Experimental Botany IC4R005-Proteomic-2010-19858118
Proteomics Identification of Differentially Expressed Proteins Associated with Pollen Germination and Tube Growth Reveals Characteristics of Germinated Oryza sativa Pollen Oryza sativa L. ssp. Japnoica 2007 Molecular & Cellular Proteomics IC4R006-Proteomic-2007-17132620
Comparative proteomic analysis of the short-term responses of rice roots and leaves to cadmium Oryza sativa L. cv. Dongjin 2010 Journal of Plant Physiology IC4R007-Proteomic-2010-19853963
Proteome analysis of differentially displayed proteins as a tool for investigating ozone stress in rice (Oryza sativa L.) seedlings Oryza sativa L 2002 Proteomics IC4R008-Proteomic-2002-12203890
Proteome and phosphoproteome differential expression under salinity stress in rice (Oryza sativa) roots Oryza sativa 2007 Journal of Proteome Research IC4R009-Proteomic-2007-17385905
Proteome analysis of cultivar‐specific deregulations of Oryza sativa indica and O. sativa japonica cellular suspensions undergoing Rice yellow mottle virus infection Oryza sativa 2004 Proteomics IC4R010-Proteomic-2004-14730683
Separation and characterization of proteins from green and etiolated shoots of rice (Oryza sativa L.): towards a rice proteom Oryza sativa L 1999 Electrophoresis IC4R011-Proteomic-1999-10217180
Proteomic identification of small, copper-responsive proteins in germinating embryos of Oryza sativa Oryza sativa 2009 Annals of Botany IC4R012-Proteomic-2009-19201764