Proteomic Studies in Rice - Revision history

Zhennan at 02:13, 28 June 2016

2016-06-28T02:13:15Z

Zhennan at 08:50, 27 June 2016

2016-06-27T08:50:58Z

Xysj1987 at 01:38, 21 June 2016

2016-06-21T01:38:26Z

Xysj1987: /* Historical Perspectives */

2016-06-21T01:37:48Z

‎Historical Perspectives

Xysj1987: Created page with "==What is Proteomics?== '''Figure 1. Overview of the workflow for analysis of RNA-Seq data. ''' * Proteins are vital ..."

2016-06-21T01:37:25Z

Created page with "==What is Proteomics?== right|thumb|527px|'''Figure 1. Overview of the workflow for analysis of RNA-Seq data. ''' * Proteins are vital ..."

New page

==What is Proteomics?==
[[File:IC4R-Proteomics-overview-2.png|right|thumb|527px|'''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, www.masc-proteomics.org). <br><br>
[[File: IC4R-Proteomics-overview-1.png|center|thumb|970px|'''Figure 1. Timeline of plant proteomics development. Details are in the main text.''']] <br><br>
* 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, www.inppo.com). 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==
{|class="wikitable sortable" style="width:100%;text-align:center"
|-
!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]]
|}

@@ Line 74: / Line 74: @@
 |''Oryza sativa''
 |2007
-|J Proteome Res
+|Journal of Proteome Research
 |'''[[IC4R009-Proteomic-2007-17385905]]'''
 |-
@@ Line 92: / Line 92: @@
 |''Oryza sativa''
 |2009
-|Ann Bot
+|Annals of Botany
 |'''[[IC4R012-Proteomic-2009-19201764]]'''
 |}

@@ Line 64: / Line 64: @@
 |Journal of Plant Physiology
 |'''[[IC4R007-Proteomic-2010-19853963]]'''
 |}

@@ Line 27: / Line 27: @@
 |2003
 |Biological and Pharmaceutical Bulletin
-|[[IC4R001-Proteomic-2003-12576669]]
+|'''[[IC4R001-Proteomic-2003-12576669]]'''
 |-
 |'''Comparative Proteome Analyses Reveal that Nitric Oxide Is an Important Signal Molecule in the Response of Rice to Aluminum Toxicity'''
@@ Line 33: / Line 33: @@
 |2013
 |journal of proteome research
-|[[IC4R002-Proteomic-2013-23327584]]
+|'''[[IC4R002-Proteomic-2013-23327584]]'''
 |-
 |'''Proteomic analyses of Oryza sativa mature pollen reveal novel proteins associated with pollen germination and tube growth'''
@@ Line 39: / Line 39: @@
 |2016
 |Proteomics
-|[[IC4R003-Proteomic-2016-16548068]]
+|'''[[IC4R003-Proteomic-2016-16548068]]'''
 |-
 |'''Proteomic analysis of rice (Oryza sativa) seeds during germination'''
@@ Line 45: / Line 45: @@
 |2007
 |Proteomics
-|[[IC4R004-Proteomic-2007-17849412]]
+|'''[[IC4R004-Proteomic-2007-17849412]]'''
 |-
 |'''Physiological and proteomic approaches to address heat tolerance during anthesis in rice (Oryza sativa L.)'''
@@ Line 51: / Line 51: @@
 |2010
 |Journal of Experimental Botany
-|[[IC4R005-Proteomic-2010-19858118]]
+|'''[[IC4R005-Proteomic-2010-19858118]]'''
 |-
 |'''Proteomics Identification of Differentially Expressed Proteins Associated with Pollen Germination and Tube Growth Reveals Characteristics of Germinated Oryza sativa Pollen'''
@@ Line 57: / Line 57: @@
 |2007
 |Molecular & Cellular Proteomics
-|[[IC4R006-Proteomic-2007-17132620]]
+|'''[[IC4R006-Proteomic-2007-17132620]]'''
 |-
 |'''Comparative proteomic analysis of the short-term responses of rice roots and leaves to cadmium'''
@@ Line 63: / Line 63: @@
 |2010
 |Journal of Plant Physiology
-|[[IC4R007-Proteomic-2010-19853963]]
+|'''[[IC4R007-Proteomic-2010-19853963]]'''
 |}

@@ Line 11: / Line 11: @@
 ==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, www.masc-proteomics.org). <br><br>
-[[File: IC4R-Proteomics-overview-1.png|center|thumb|970px|'''Figure 1. Timeline of plant proteomics development. Details are in the main text.''']] <br><br>
+[[File: IC4R-Proteomics-overview-1.png|center|thumb|970px|'''Figure 1. Timeline of plant proteomics development. Details are in the main text.''']] <br>
 * 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, www.inppo.com). 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.