Abstract
BackgroundMost biological functions controlled by the brain and their related disorders are closely associated with activation in specific regions of the brain. Neuroproteomics has been applied to the analysis of whole brain, and the general pattern of protein expression in all regions has been elucidated. However, the comprehensive proteome of each brain region remains unclear.ResultsIn this study, we carried out comparative proteomics of six regions of the adult rat brain: thalamus, hippocampus, frontal cortex, parietal cortex, occipital cortex, and amygdala using semi-quantitative analysis by Mascot Score of the identified proteins. In order to identify efficiently the proteins that are present in the brain, the proteins were separated by a combination of SDS-PAGE on a C18 column-equipped nano-liquid chromatograph, and analyzed by quadrupole-time of flight-tandem-mass spectrometry. The proteomic data show 2,909 peptides in the rat brain, with more than 200 identified as region-abundant proteins by semi-quantitative analysis. The regions containing the identified proteins are membrane (20.0%), cytoplasm (19.5%), mitochondrion (17.1%), cytoskeleton (8.2%), nucleus (4.7%), extracellular region (3.3%), and other (18.0%). Of the identified proteins, the expressions of glial fibrillary acidic protein, GABA transporter 3, Septin 5, heat shock protein 90, synaptotagmin, heat shock protein 70, and pyruvate kinase were confirmed by immunoblotting. We examined the distributions in rat brain of GABA transporter 3, glial fibrillary acidic protein, and heat shock protein 70 by immunohistochemistry, and found that the proteins are localized around the regions observed by proteomic analysis and immunoblotting. IPA analysis indicates that pathways closely related to the biological functions of each region may be activated in rat brain.ConclusionsThese observations indicate that proteomics in each region of adult rat brain may provide a novel way to elucidate biological actions associated with the activation of regions of the brain.
Highlights
Most biological functions controlled by the brain and their related disorders are closely associated with activation in specific regions of the brain
Identification of proteins in each region of rat brain To identify proteins expressing in each region of rat brain, the removed brains were divided into six regions, thalamus, hippocampus, frontal cortex, parietal cortex, occipital cortex, and amygdala, according to the atlas of Paxinos and Watson
Each gel lane was sliced into 24 pieces, and the proteins extracted from the gel pieces were applied to nano-LCQ-TOF-tandem mass spectrometry (MS/MS) and analyzed by the Mascot search engine to identify amino acid sequences (Fig. 1)
Summary
Most biological functions controlled by the brain and their related disorders are closely associated with activation in specific regions of the brain. Neuroproteomics has been applied to the analysis of whole brain, and the general pattern of protein expression in all regions has been elucidated [14,15,16] In specific regions, such as the hippocampus, thalamus, and striatum, the relationships between protein stimulations or diseases have been examined by proteomic analysis [17,18,19,20]. We have identified a total of 2,909 peptides in all regions of the rat brain, and found proteins expressed in each region of brain: 63 proteins in the thalamus, 38 in the hippocampus, 14 in the frontal cortex, 66 in the parietal cortex, 24 in the occipital cortex, and 36 in the amygdala by semi-quantitative analysis
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