Gel-based and gel-free search for plasma membrane proteins in chickpea (Cicer arietinum L.) augments the comprehensive data sets of membrane protein repertoire.
Plasma membrane (PM) encompasses total cellular contents, serving as semi-porous barrier to cell exterior. This living barrier regulates all cellular exchanges in a spatio-temporal fashion. Most of the essential tasks of PMs including molecular transport, cell-cell interaction and signal transduction are carried out by their proteinaceous components, which make the PM protein repertoire to be diverse and dynamic. Here, we report the systematic analysis of PM proteome of a food legume, chickpea and develop a PM proteome reference map. Proteins were extracted from highly enriched PM fraction of four-week-old seedlings using aqueous two-phase partitioning. To address a population of PM proteins that is as comprehensive as possible, both gel-based and gel-free approaches were employed, which led to the identification of a set of 2732 non-redundant proteins. These included both integral proteins having bilayer spanning domains as well as peripheral proteins associated with PMs through posttranslational modifications or protein-protein interactions. Further, the proteins were subjected to various in-silico analyses and functionally classified based on their gene ontology. Finally an inventory of the complete set of PM proteins, identified in several monocot and dicot species, was created for comparative study with the generated PM protein dataset of chickpea.



Chickpea, a rich source of dietary proteins, is the second most cultivated legume, which is grown over 10 million hectares of land worldwide. The annual global production of chickpea hovers around 8.5 million metric tons. Recent chickpea genome sequencing effort has provided a broad genetic basis for highlighting the important traits that may fortify other crop legumes. Improvement in chickpea varieties can further strengthen the world food security, which includes food availability, access and utilization. It is known that the phenotypic trait of a cultivar is the manifestation of the orchestrated functions of its proteins. Study of the PM proteome offers insights into the mechanism of communication between the cell and its environment by identification of receptors, signalling proteins and membrane transporters. Knowledge of the PM protein repertoire of a relatively dehydration tolerant chickpea variety, JG-62, can contribute in development of strategies for metabolic reprograming of crop species and breeding applications.
National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India.
Pragya
P
Barua
YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575 018, India.
Pratigya
P
Subba
National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India.
Nilesh Vikram
NV
Lande
Institute of Bioinformatics, International Technology Park, Bengaluru 560066, India.
Kiran K
KK
Mangalaparthi
YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575 018, India; Institute of Bioinformatics, International Technology Park, Bengaluru 560066, India.
T S Keshava
TSK
Prasad
National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India.
Subhra
S
Chakraborty
National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India. Electronic address: nchakraborty@nipgr.ac.in.
Niranjan
N
Chakraborty
D000222:Adaptation, Physiological; D029863:Cicer / Q000737:chemistry*; D030562:Databases, Protein; D055864:Droughts; D008565:Membrane Proteins / Q000032:analysis*; D010940:Plant Proteins / Q000032:analysis; D020543:Proteome / Q000032:analysis; D036226:Seedlings / Q000737:chemistry
D008565:Membrane Proteins; D010940:Plant Proteins; D020543:Proteome
Food legume; Hydropathy indices; LC-MS/MS analysis; Plasma membrane proteome; Posttranslational modifications; Trans-membrane domain