Luxurious Nitrogen Fertilization of Two Sugar Cane Genotypes Contrasting for Lignin Composition Causes Changes in the Stem Proteome Related to Carbon, Nitrogen, and Oxidant Metabolism but Does Not Alter Lignin Content

Interactions between nitrogen and phosphorus modulate the food quality of the marine crop Pyropia haitanensis (T. J. Chang & B. F. Zheng) N. Kikuchi & M. Miyata (Porphyra haitanensis)

The quality of Pyropia haitanensis (T. J. Chang & B. F. Zheng) N. Kikuchi & M. Miyata (Porphyra haitanensis) is directly affected by nutrient availability. However, the molecular mechanism underlying the synergistic regulatory effects of nitrogen (N) and phosphorus (P) availability on P. haitanensis quality is unknown. Here, we performed physiological and multi-omics analyses to reveal the combined effects of N and P on P. haitanensis quality. The pigments accumulated under high N because of increases in N metabolism and porphyrin metabolism, ultimately resulting in intensely colored thalli. High N also promoted amino acid metabolism and inosine 5'-mononucleotide (IMP) synthesis, but inhibited carbohydrates accumulation. This resulted in increased amino acid, IMP and decreased agaro-carrageenan and cellulose contents, thereby improving the nutritional value and taste. Furthermore, high P promoted carbon metabolism and amino acid metabolism.This study provided the basis for elucidating the mechanism behind N and P regulating the seaweed quality.

1DE-MS Profiling for Proteoform-Correlated Proteomic Analysis, by Combining SDS-PAGE, Whole-Gel Slicing, Quantitative LC-MS/MS, and Reconstruction of Gel Distributions of Several Thousands of Proteins

SDS-PAGE has often been used in proteomic analysis, but generally for sample prefractionation although the technique separates proteins by molecular masses (M_ws) and the information would contribute to proteoform-level analysis. Here, we report a method that combines SDS-PAGE, whole-gel slicing, and quantitative LC-MS/MS for establishing gel distributions of several thousand proteins in a proteome. A previously obtained data set on rat cerebral cortex with cerebral ischemia-reperfusion injury¹ was analyzed, and the gel distributions of 5906 proteins were reconstructed. These distributions, referred to as 1DE-MS profiles, revealed that about 30% of the proteins had more than one proteoform detected in the gels. The profiles were categorized into six types by distribution (narrow, dispersed, or broad) and relative deviations between the abundance-peak apparent M_ws and calculated M_ws. Only 56% of the proteins showed narrow distributions and matched M_ws, while the others had rather complex profiles. Bioinformatic analysis on example profiles showed the resolved proteoforms involved alternative splicing, proteolytic processing, glycosylation and ubiquitination, fragmentation, and probably transmembrane structures. Profile-based differential analysis revealed that many of the disease-caused changes were proteoform dependent. This work provided a proteome-scale view of protein distributions in SDS-PAGE gels, and the method would be useful to obtain proteoform-correlated information for in-depth proteomics.

Multiomics Analysis Reveals New Insights into the Apple Fruit Quality Decline under High Nitrogen Conditions

Excessive application of nitrogen (N) fertilizer is common in Chinese apple production. High N reduced the contents of soluble sugar and total flavonoids by 16.05 and 19.01%, respectively, resulting in poor fruit quality. Moreover, high N increased the total N and decreased the total C and C/N ratio of apple fruits. On the basis of the transcriptomic, proteomic, and metabolomic analyses, the global network was revealed. High N inhibited the accumulation of carbohydrates (sucrose, glucose, and trehalose) and flavonoids (rhamnetin-3-O-rutinoside, rutin, and trihydroxyisoflavone-7-O-galactoside) in fruits, and more C skeletons were used to synthesize amino acids and their derivatives (especially low C/N ratio, e.g., arginine) to be transferred to N metabolism. This study revealed new insights into the decline in soluble sugar and flavonoids caused by high N, and hub genes (MD07G1172700, MD05G1222800, MD16G1227200, MD01G1174400, and MD02G1207200) and hub proteins (PFK, gapN, and HK) were obtained.

Applying Molecular Phenotyping Tools to Explore Sugarcane Carbon Potential

Sugarcane (Saccharum spp.), a C₄ grass, has a peculiar feature: it accumulates, gradient-wise, large amounts of carbon (C) as sucrose in its culms through a complex pathway. Apart from being a sustainable crop concerning C efficiency and bioenergetic yield per hectare, sugarcane is used as feedstock for producing ethanol, sugar, high-value compounds, and products (e.g., polymers and succinate), and bioelectricity, earning the title of the world's leading biomass crop. Commercial cultivars, hybrids bearing high levels of polyploidy, and aneuploidy, are selected from a large number of crosses among suitable parental genotypes followed by the cloning of superior individuals among the progeny. Traditionally, these classical breeding strategies have been favoring the selection of cultivars with high sucrose content and resistance to environmental stresses. A current paradigm change in sugarcane breeding programs aims to alter the balance of C partitioning as a means to provide more plasticity in the sustainable use of this biomass for metabolic engineering and green chemistry. The recently available sugarcane genetic assemblies powered by data science provide exciting perspectives to increase biomass, as the current sugarcane yield is roughly 20% of its predicted potential. Nowadays, several molecular phenotyping tools can be applied to meet the predicted sugarcane C potential, mainly targeting two competing pathways: sucrose production/storage and biomass accumulation. Here we discuss how molecular phenotyping can be a powerful tool to assist breeding programs and which strategies could be adopted depending on the desired final products. We also tackle the advances in genetic markers and mapping as well as how functional genomics and genetic transformation might be able to improve yield and saccharification rates. Finally, we review how "omics" advances are promising to speed up plant breeding and reach the unexplored potential of sugarcane in terms of sucrose and biomass production.

Initial Analysis on the Characteristics and Synthesis of Exopolysaccharides from Sclerotium rolfsii with Different Sugars as Carbon Sources

Scleroglucan is widely used in the food and chemical industries because of its good rheological property, stability, and emulsification activity. To investigate the influence of different carbon sources on the properties and synthesis of exopolysaccharides (EPS), the three EPSs (GEPS, glucose was used as the carbon source; LEPS, lactose was used as the carbon source; and SEPS, sucrose was used as the carbon source) were determined, respectively. It was found that the yield and viscosity of exopolysaccharides were different. When sucrose and glucose were used as the carbon sources, the viscosity and yield of EPS were both higher than lactose. The scanning electron microscopy (SEM) images showed that the three EPSs had different morphologies, but the monosaccharide analysis showed that they were all composed of glucose units. Fourier transform infrared spectroscopy (FT-IR) proved that there were no additional substituents for the three EPSs. Furthermore, the high performance liquid chromatography (HPLC) results showed that SEPS and LEPS had two fractions. Through the analysis of proteomics data, there were few differences in the metabolic pathways between GEPS and SEPS, but a significant difference between LEPS and SEPS. Our study provides a theoretical basis and reference for understanding the biosynthesis of exopolysaccharides and the development of different types of EPS products.

Sugarcane Omics: An Update on the Current Status of Research and Crop Improvement

Sugarcane is an important crop from Poaceae family, contributing about 80% of the total world's sucrose with an annual value of around US$150 billion. In addition, sugarcane is utilized as a raw material for the production of bioethanol, which is an alternate source of renewable energy. Moving towards sugarcane omics, a remarkable success has been achieved in gene transfer from a wide variety of plant and non-plant sources to sugarcane, with the accessibility of efficient transformation systems, selectable marker genes, and genetic engineering gears. Genetic engineering techniques make possible to clone and characterize useful genes and also to improve commercially important traits in elite sugarcane clones that subsequently lead to the development of an ideal cultivar. Sugarcane is a complex polyploidy crop, and hence no single technique has been found to be the best for the confirmation of polygenic and phenotypic characteristics. To better understand the application of basic omics in sugarcane regarding agronomic characters and industrial quality traits as well as responses to diverse biotic and abiotic stresses, it is important to explore the physiology, genome structure, functional integrity, and collinearity of sugarcane with other more or less similar crops/plants. Genetic improvements in this crop are hampered by its complex genome, low fertility ratio, longer production cycle, and susceptibility to several biotic and abiotic stresses. Biotechnology interventions are expected to pave the way for addressing these obstacles and improving sugarcane crop. Thus, this review article highlights up to date information with respect to how advanced data of omics (genomics, transcriptomic, proteomics and metabolomics) can be employed to improve sugarcane crops.