Tissue-specific zein synthesis in maize kernel

easyMF: A Web Platform for Matrix Factorization-Based Gene Discovery from Large-scale Transcriptome Data

With the development of high-throughput experimental technologies, large-scale RNA sequencing (RNA-Seq) data have been and continue to be produced, but have led to challenges in extracting relevant biological knowledge hidden in the produced high-dimensional gene expression matrices. Here, we develop easyMF ( https://github.com/cma2015/easyMF ), a web platform that can facilitate functional gene discovery from large-scale transcriptome data using matrix factorization (MF) algorithms. Compared with existing MF-based software packages, easyMF exhibits several promising features, such as greater functionality, flexibility and ease of use. The easyMF platform is equipped using the Big-Data-supported Galaxy system with user-friendly graphic user interfaces, allowing users with little programming experience to streamline transcriptome analysis from raw reads to gene expression, carry out multiple-scenario MF analysis, and perform multiple-way MF-based gene discovery. easyMF is also powered with the advanced packing technology to enhance ease of use under different operating systems and computational environments. We illustrated the application of easyMF for seed gene discovery from temporal, spatial, and integrated RNA-Seq datasets of maize (Zea mays L.), resulting in the identification of 3,167 seed stage-specific, 1,849 seed compartment-specific, and 774 seed-specific genes, respectively. The present results also indicated that easyMF can prioritize seed-related genes with superior prediction performance over the state-of-art network-based gene prioritization system MaizeNet. As a modular, containerized and open-source platform, easyMF can be further customized to satisfy users' specific demands of functional gene discovery and deployed as a web service for broad applications.

Sweet potato cysteine proteases SPAE and SPCP2 participate in sporamin degradation during storage root sprouting

Sweet potato sporamins are trypsin inhibitors and exhibit strong resistance to digestion by pepsin, trypsin and chymotrypsin. In addition, they constitute the major storage proteins in the sweet potato and, after degradation, provide nitrogen as a nutrient for seedling regrowth in sprouting storage roots. In this report, four cysteine proteases-one asparaginyl endopeptidase (SPAE), two papain-like cysteine proteases (SPCP1 and SPCP2), and one granulin-containing cysteine protease (SPCP3)-were studied to determine their association with sporamin degradation in sprouting storage roots. Sporamin degradation became significant in the flesh of storage roots starting from week 4 after sprouting and this correlated with expression levels of SPAE and SPCP2, but not of SPCP1 and SPCP3. In the outer flesh near the skin, sporamin degradation was more evident and occurred earlier than in the inner flesh of storage roots. Degradation of sporamins in the outer flesh was inversely correlated with the distance of the storage root from the sprout. Exogenous application of SPAE and SPCP2, but not SPCP3, fusion proteins to crude extracts of the outer flesh (i.e., extracted from a depth of 0.3cm and within 2cm of one-week-old sprouts) promoted in vitro sporamin degradation in a dose-dependent manner. Pre-treatment of SPAE and SPCP2 fusion proteins at 95°C for 5min prior to their application to the crude extracts reduced sporamin degradation. These data show that sweet potato asparaginyl endopeptidase SPAE and papain-like cysteine protease SPCP2 participate in sporamin degradation during storage root sprouting.

High-performance liquid chromatography and capillary electrophoresis for the analysis of maize proteins

Methods for the analysis of maize proteins using HPLC and CE are reviewed. Most of the references cited in this review concern HPLC methods. Size-exclusion HPLC and especially RP-HPLC methods have been developed for characterization of normal and genetically modified maize, cultivar differentiation, and prediction of quality. Few CE methods for the analysis of maize proteins were found in the existing literature. Most of these methods focus on optimization of the separation of maize proteins using CZE and SDS-capillary gel electrophoresis.

Albumins and globulins in developing maize grains

Quantitative and qualitative (amino acid composition) changes of albumins and globulins in developing grain of normal and opaque-2 (o2) maizes were examined in proteins extracted sequentially with water and 0.5 M NaCl, and isolated by salting out with trichloroacetic acid. The amount of albumins per grain reached a maximum at mid-development the declined. Globulins, virtually absent in very young grain, increased in level until maturity. The variations were more marked for o2 than normal maize. Amino acid compositions changed little with development. The selectivity and exhaustiveness of sequential extraction, and the physiological role of albumins and globulins in grain are discussed.

Zein synthesis in the embryo and endosperm of maize mutants

Zein synthesis in the developing (22 and 50 days postpollination) endosperm and embryo of maize (Zea mays L.) double mutants, brittle-1; opaque-2 and brittle-2;opaque-2, were compared and correlated with sucrose concentration and RNase activity in order to test the hypothesis that high sucrose concentrations may prevent the interaction between zein polyribosomes and endoplasmic reticulum and make the zein mRNAs more susceptible to hydrolysis by high RNase activity, resulting in a severe reduction in zein synthesis. The double-mutant combinations of opaque-2 with each of the starch-deficient mutants, brittle-1 and brittle-2, maintained not only a high sucrose concentration in the endosperm but also a higher RNase activity than either one of the single mutants alone. Consequently, these double mutants severely suppressed the synthesis of two major zein components in their endosperms. In contrast to the endosperm system, embryos of the double mutants produced amounts of zein (and electrophoretic patterns) similar to that of the opaque-2 embryo, and their embryos contained levels of sucrose and RNase activity comparable to that of the o2 and normal control. These results are consistent with the notion that a posttranscriptional degradation of zein mRNAs by RNase, rather than a specific transcriptional block, is involved in the endosperm to suppress zein synthesis in these double mutants.

Subcellular localization of glutelin-2 in maize (Zea mays L.) endosperm

Accumulation of the 28 KD protein of the glutelin-(G2) fraction was followed in developing maize endosperm, using sodium dodecylsulphate polyacrylamide gel electrophoresis (SDS-PAGE) and peak integration of scanned gels. 28 KD glutelin-2 could already be observed from 15 days after pollination and its accumulates reached a plateau during the second half of the development period. The process of biosynthesis of 28 KD glutelin-2 and zeins occurs in a parallel way. Subcellular fractions obtained from linear sucrose gradient centrifugation of developing maize endosperms were analyzed by SDS-PAGE and immunoblotting using a serum reacting against glutelin-2 and 14 KD Z2. Glutelin-2 was found to be present in the protein bodies when subcellular fractionation was carried out without dithiothreitol (DTT). The presence of a reducing agent causes the elution of glutelin-2 from protein bodies. Immunocytochemical labelling using the protein A-colloidal gold technique in protein bodies incubated with anti-G2 IgG revealed that G2 is located mainly in the periphery of protein bodies. These results are interpreted as indicating a structural role for glutelins in protein bodies.