The present study aimed to analyze the metaproteome of the microbial community comprising harmful algal bloom (HAB) in the Daechung reservoir, Korea. HAB samples located at GPS coordinates of 36°29’N latitude and 127°28’E longitude were harvested in October 2013. Microscopic observation of the HAB samples revealed red signals that were presumably caused by the autofluorescence of chlorophyll and phycocyanin in viable cyanobacteria. Metaproteomic analysis was performed by a gelbased shotgun proteomic method. Protein identification was conducted through a two-step analysis including a forward search strategy (FSS) (random search with the National Center for Biotechnology Information (NCBI), Cyanobase, and Phytozome), and a subsequent reverse search strategy (RSS) (additional Cyanobase search with a decoy database). The total number of proteins identified by the two-step analysis (FSS and RSS) was 1.8-fold higher than that by one-step analysis (FSS only). A total of 194 proteins were assigned to 12 cyanobacterial species (99 mol%) and one green algae species (1 mol%). Among the species identified, the toxic microcystin-producing Microcystis aeruginosa NIES-843 (62.3%) species was the most dominant. The largest functional category was proteins belonging to the energy category (39%), followed by metabolism (15%), and translation (12%). This study will be a good reference for monitoring ecological variations at the meta-protein level of aquatic microalgae for understanding HAB.

식중독 유발 바이러스인 HAV는 제 1군 감염병원으로 규정되면서 감염 시 원인식품을 빠르게 분석하게 되었으며 그로 인해 정확하면서 빠른 검출기술을 요구하게 되었다. 본 연구에서는 HAV에 오염된 상추에서 신속하게 바이러스를 검사하기 위해서 IMS를 통하여 신속하게 HAV를 순수 분리 및 농축하였고, 형광물질인 quantum dot을 활용하여 형광검출을 실시하였다. 또한 일반적으로 바이러스 농축에 사용되는 PEG 농축방법과 비교하였을 때 검출능은 유사한 결과를 얻었으나, 농축시간 면에서는 IMS를 통한 방법이 효과적이었다. 또한 IMS 방법으로 확보된 항원을 Quantum dot을 활용하여 10분 이내에 바이러스를 검출할 수 있었다. 본 연구에서 제시된 검출기반은 식품 유통 과정 중 다양한 식중독 바이러스로부터 소비자를 보호 할 수 있는 검사방법으로 활용될 수 있다고 기대된다.

Sub-cellular proteomics provide insight into the molecular mechanisms of plant cell modulation of protein accumulation in intracellular compartments regarding various perturbations, and thus provides rectified knowledge about signal transduction in organelles. Mitochondria are important organelles for cellular respiration within the eukaryotic cell and serve many important functions including vitamin synthesis, amino acid metabolism and photorespiration for the cell as well. To define the mitochondrial proteome of the roots of wheat seedling, a systematical and targeting analysis were carried out on the mitochondrial proteome from 15 days-old wheat seedling roots material. Mitochondria were isolated by Percoll gradient centrifugation; and extracted proteins were separated and analyzed using Tricine SDS-PAGE along with LTQ-FTICR mass spectrometry. From the isolated mitochondrial proteins, a total of 140 proteins were identified. The identified proteins were functionally classified into 12 classes using ProtFun 2.2 server based on cellular roles, Proteins were shown to be involved in including amino acid biosynthesis (17.1%), biosynthesis of cofactors (6.4%), cell envelope (11.4%), central intermediary metabolism (10%), energy metabolism (20%), fatty acid metabolism (0.7%), purines and pyrimidines (5.7%), regulatory functions (0.7%), replication and transcription (1.4%), translation (22.1%), transport and binding (1.4%), and unknown (2.8%). These results indicated that many of the protein components present and functions of identified proteins are common to other profiles of mitochondrial proteomes performed to date. The data presented here will begin to reveal a better understanding the characteristics of proteins and metabolic activity in mitochondria in wheat roots.

High temperature impediment in developing stages of crops has been occurred due to the impact of global warming. Rice production is notable to be sensitive to increasing environmental temperature and grain filling temperatures are already approaching threatening levels in many countries with rice cultivation. Recent proteomic analyses exposed impulsive changes of metabolisms during rice grain development. Interestingly, proteins involved in glycolysis, citric acid cycle, lipid metabolism, and proteolysis were accumulated at higher levels in mature grain than those of developing stages. High temperature (HT) stress in rice ripening period enhances damaged (chalky) grains which have loosely compacted shape starch granules. We carried out two-dimensional gel electrophoresis to analyze protein profiles during grain filling and different developmental stages of rice seed maturation. Proteins were separated from the fertilized seeds (seeds from 7 days and 21 days after fertilization) and seed maturation stage using IEF in the first-dimension and SDS-PAGE in the second dimension along with MALDI-TOF mass spectrometry. More than 1,000 protein spots were detected on a two-dimensional gel electrophoresis. A total of 120 different protein spots out of 140 protein spots were identified by MALDI-TOF and nano LCQ-TOF mass spectrometer. The identified proteins were categorized into six (6) different groups according to their expression patterns during grain filling and seed maturation. Some proteins were confirmed during seed development stages such as cytoplasmic malate dehydrogenase, whereas others were appeared at a specific stage like putative subtilisin-like protease, germin-like, seed allergenic proteins. Furthermore, the chalking mechanism of rice grain under the HT stress could be discussed in terms of grain starch glycome, transcriptome, and proteome.

Recently, proteome analysis is becoming a powerful tool for the functional characterization of plants. Due to the availability of vast nucleotide sequence information and based on the progress achieved in sensitive and rapid protein identification by mass spectrometry, proteome approaches open up now perspectives to analyze the complex functions of model crop species at different level. In this study, we have N-terminal sequencing data for the 100 embryo and 53 seed proteins of rice separated by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) were collected and systematically organized for a protein sequence data-file. An attempt was made to link the embryo proteins of rice to DNA sequences for understanding their functions. One hundred proteins of the 700 spots were detected in the embryo using 2-DE gels whereas we used micro sequenced. Of these, 28% of the embryo proteins were matched to DNA sequences with known functions, but 72% of the proteins were identified to be unknown functions as previously reported by Woo et al.,. In addition, twenty-four spots of protein with 100% of homology and nine with over 80% were matched to ESTs (expressed sequence tags) after expanding the amino acid sequences of the protein spots by Database searches using the available EST databases of rice at the NCBI (http://www/ncbi.nlm.nih.gov/) and DDBJ (http://www.ddbj.nig.ac.jp/). Also, a total of 53 proteins out of 700 protein spots separated on the 2-DE gels were analyzed by the peptide mass fingerprinting method (MALDI-TOF/MS). High-quality mass spectra suitable for peptide mass fingerprinting were obtained from 41 spots. Using the ESI-Q-TOF/MS, however, we were able to identify 53 seed proteins of rice, including 12 proteins not registered in database. The rapid expansion of DNA sequence databases to the utilization of EST now provides the whole or partial gene sequences of model organisms, and the recent advances in protein micro-characterization by mass spectrometry allow the possibility of linking these DNA sequences to the proteins in functional complexes. Proteome Database of rice is updated, and is available on the World Wide Web at http://gene64.rda.affrc.go. This work shows that the proteome analysis could be a useful strategy to link the sequence information to the functional genomics.

Wheat-rye translocation lines were developed to produce a main crop resistant to biological and physical stress. 'Chaupon' rye contains 2RL chromatin to harbor resistance genes for powdery mildew and leaf rust. In order to identify chromosome 2RL-derived rye proteins and 2RL-perturbed proteins in wheat-rye translocation lines, the gel-based proteomics was employed with 'Coker797' (non-2RL), 'Hamlet' (2RL) and 'near-isogenic line' (stabilized 2RL). The leaf proteome was resolved on 2D-gel, resulting in 216 spots in a final selection. A total of 90 proteins were identified with the identification success rate of 42%. The identified proteins were classified by functional annotation: metabolism (64%), cellular process (5%), translation (2%), regulatory function (1%) and hypothetical (28%). The proteins belonged to metabolism were subdivided into carbohydrate metabolism (36%), energy metabolism (35%), metabolism of lipid, amino acid, other amino acid and biosynthesis of secondary metabolites (each 6%) and others (5%). A total of 53 proteins were differentially expressed, in which β-glucosidase, in particular, originated from the chromosome 2RL of rye, was exclusively appeared in NIL. In addition, small Ras-related GTP binding-protein assigned to wheat was predominantly found in 2RL rye chromatin-possessing NIL. These results suggest that the acquired genetic traits obtained from rye 2RL enhance the resistance to biotic and abiotic stress in wheat-rye translocation lines by altered the proteome expression. In leaf metabolome analysis, 11 predominant metabolites containing trans-aconitate, glutamate, and betaine were identified by 1H-NMR-based metabolite fingerprinting. The overall metabolites pattern of NIH appears to be closer to Coker797 rather than Hamlet. Thus, the metabolic phenotype of NIL was not so much lineated from Hamlet contrast to proteomic phenotyping.

Comparison of the distribution and utilization of free amino acids in buckwheat is required of understanding the amino acid metabolism. The buckwheat sprouts contained the most abundant amino acid Val (40%) followed by Tyr (28%) in common buckwheat (CB), whereas Val was the most predominant amino acid in tatary buckwheat (TB), accounting for 62%. The buckwheat stem and root contained commonly Gln (40~42% in stem; 30~37% in root). Thus, soluble amino nitrogen source is used for Gln in buckwheat. The main difference of amino acid distribution in three tissues between CB and TB was Tyr in sprouts. Low level of Tyr in TB is presumably resulted from the conversion to other phenolic metabolites. The content of essential free amino acids in TB sprout was 53% higher than that in CB. Thus, the TB sprouts are benefit to the human nutrition. The basic study of amino acids gives a clear evidence for different interconversion and metabolism of amino acids in two buckwheat species.