SYM-4 : Proteomics in multi-disciplinary approaches
Organizer : J. Eugene Lee (Korea Research Institute of Standards and Science, Korea)
In “Proteomics in multi-disciplinary approaches” session, we will learn about five exciting research programs. These research programs address how rapidly evolving proteomic technologies can be applied to various areas of science including plant genetics, oncology, protein biochemistry, and even material analysis of violin.
Proteomic technique to identify the abiotic stress tolerant mechanism in crop
Abstract
Climate change is considered a major threat to world agriculture and food security. To improve the agricultural productivity and sustainability, the development of high-yielding stress-tolerant and climate-resilient crops is essential. Of the abiotic stresses, flooding stress is a very serious hazard because it markedly reduces plant growth and yield. Proteomic analyses indicate that the effects of flooding stress are not limited to oxygen deprivation, but include many other factors. Although many flooding response mechanisms have been reported, flooding tolerance mechanisms have not been fully clarified for soybean because there was limitationin soybean materials such as mutants and varieties while they were abundant in rice and Arabidopsis. Here, plant proteomic technologies are introduced to identify the mechanismof flooding tolerance in soybeans using the flooding-tolerant mutant isolated by our group and other materialsof soybean.Furthermore, the upstream event controlling the regulation of many kinds of flooding-responsive proteinswas elucidatedbased onproteomic analyses of nuclear proteins and phosphoproteins. This work will expedite transgenic or marker-assisted genetic enhancement studies in crop for developing stress-tolerant lines or varieties under abiotic stress.
References:
1) Komatsu S, Tougou M, Nanjo Y (2015) Review-Proteomic techniques and management of flooding tolerance in soybean. J Proteome Res 14:3768-3778
2) Komatsu S, Sakata K, Nanjo Y (2015) Review-Omics’ techniques and their use to identify how soybean responds to flooding. J Anal Sci Technol 6:9
Developments in Glycoproteomics Facilitate the Discovery of a New Class of Functionally Important Cancer and Inflammation-Centric Human Glycoproteins
Abstract
The human glycoproteome remains severely understudied due to the analytical challenges associated with the system-wide site-specific analysis of intact glycopeptides defined as glycoproteomics. We here demonstrate how our recent advances in LC-MS/MS-based glycoproteomics have paved the way for the discovery of a new class of previously overlooked truncated human asparagine (N)-linked glycoproteins, called paucimannosidic proteins, with the relative simple monosaccharide composition N-acetylglucosamine2mannose1-3fucose0-1. Protein paucimannosylation was shown to be highly enriched in inflamed and tumour-microenvironments in several isolated human cells, tissues and bodily fluids. Importantly, orthogonal evidence supported and mechanistically explained the immune-centric expression and biosynthesis of paucimannosidic proteins in human immune cells and demonstrated their immune functions including complement activation and pathogen defence. With equal emphasis on recent technological advances and biological applications, this talk will showcase the enormous potential of the rapidly maturing discipline of glycoproteomics.
Proteomics analysis of antique glue on a Stradivari violin
Abstract
Antique violins made in Cremona, Italy by Antonio Stradivari (1644-1737) have unsurpassed qualities strongly preferred by musicians and collectors. The tonal quality and visual beauty of Stradivari violins have survived for over three centuries and still cannot be reproduced. There are strong historical and practical interests in understanding what materials were used to construct these highly valuable violins. Protein-based glues are used for two purposes on the violin. The first is to join different pieces of wood together, and the second is to seal the wood surface before varnishing. Some have proposed that Stradivari used casein (cheese) glue to join wood together, but there lacks analytical evidence. During our research into wood treatment of Stradivari violins, we accidentally encountered a piece of 18th-century glue used for neck extension. Although it may not be the original glue applied by Stradivari, it represents the first and the only old glue analyzed from an antique violin to date. Proteomics analysis by shotgun mass spectrometry reveals that the glue is highly purified collagen, with the closest sequence match to modern goat collagen, instead of bovine, horse, rabbit, or fish collagen as commonly expected. No casein was found. The use of goat collagen is surprisingly consistent with Cennino Ceninni’s 15th-century instructions about using goat glue to make lutes, the precursor of all modern string instruments. We will also discuss protein sealers and wood treatment on Stradivari violins revealed by modern chemical analysis, and how this may ultimately lead us to decode “Stradivari’ssecrets.”
Gwangju Institute of Science and Technology, Korea
Title
Analytical Platform for High-Throughput Measurement of in vivo Turnover Rates of Biomolecules
Abstract
The quantity and quality of major biological components like protein, nucleic acid, carbohydrate, and lipid in the human body is maintained by recurrent degradation and replenishment events, called biological turnover. Biological dysfunctions accompanied by neurodegenerative diseases, cancers, or aging are implicated with the failure of precise regulation of biological turnover. Current quantitative omics techniques are primarily devoted to comparing steady-state abundances of biomolecules between normal and disease states and they are missing the dynamic nature of cellular processes. Here we present an ananlytical tool to study in vivo biomolecular turnover in a high-throughput fashion based on metabolic heavy water (D2O) labeling. Compared with general quantitative omics studies, measurement of the turnover rates of biomolecules imposes much heavier analytical challenges on the data handling mainly because of data acquisition on multiple time points. The key factors in performing the experiments, which includes sample preparation, sample separation, mass spectrometry, data processing, and statistical analysis, to determine biological turnover rates are discussed. Some preliminary results on the in vivo turnover rates of lipids and proteins in HeLa cells are also presented.
Extractive Ambient Ionization Mass Spectrometry for Protein Analysis
Abstract
After the invention of desorption electrospray ionization (DESI) in 2005, numerous atmospheric pressure ionization (API) methods have been developed for ambient mass spectrometry. A majority of recent API methods including DESI, nano-electrospray desorption ionization (nano-DESI), and paper spray ionization (PSI) utilizes an in situ liquid-solid microextraction process for sampling target analytes from raw materials. In this presentation, we will discuss applications of extractive ambient ionization MS in the analysis of peptides or proteins. First, reactive DESI MS for probing citrullinated peptides will be demonstrated. In reactive DESI MS, chemical reagents that can react with the target analyte molecules are carried via spraying solvent delivery. When chemical reagent-containing droplets hit on sample surface, in situ chemical reaction or derivatization of analytes on a sample surface can occur. By using this method, we tried selective in situ modification of citrulline residues in a given peptide with phenylglyoxal (PG) under acidic condition. Second, fundamental aspects and possible applications of PSI MS in the analysis of proteins will be presented.
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