Towards an Ideal In Cell Hybridization-Based Strategy to Discover Protein Interactomes of Selected RNA Molecules

RNA-binding proteins are crucial to the function of coding and non-coding RNAs. The disruption of RNA–protein interactions is involved in many different pathological states. Several computational and experimental strategies have been developed to identify protein binders of selected RNA molecules. Amongst these, ‘in cell’ hybridization methods represent the gold standard in the field because they are designed to reveal the proteins bound to specific RNAs in a cellular context. Here, we compare the technical features of different ‘in cell’ hybridization approaches with a focus on their advantages, limitations, and current and potential future applications.     

Identification of miRNAs and Their Targets in Cotton Inoculated with Verticillium dahliae by High-Throughput Sequencing and Degradome Analysis

MicroRNAs (miRNAs) are a group of endogenous small non-coding RNAs that play important roles in plant growth, development, and stress response processes. Verticillium wilt is a vascular disease in plants mainly caused by Verticillium dahliae Kleb., the soil-borne fungal pathogen. However, the role of miRNAs in the regulation of Verticillium defense responses is mostly unknown. This study aimed to identify new miRNAs and their potential targets that are involved in the regulation of Verticillium defense responses. Four small RNA libraries and two degradome libraries from mock-infected and infected roots of cotton (both Gossypium hirsutum L. and Gossypium barbadense L.) were constructed for deep sequencing. A total of 140 known miRNAs and 58 novel miRNAs were identified. Among the identified miRNAs, many were differentially expressed between libraries. Degradome analysis showed that a total of 83 and 24 genes were the targets of 31 known and 14 novel miRNA families, respectively. Gene Ontology analysis indicated that many of the identified miRNA targets may function in controlling root development and the regulation of Verticillium defense responses in cotton. Our findings provide an overview of potential miRNAs involved in the regulation of Verticillium defense responses in cotton and the interactions between miRNAs and their corresponding targets. The profiling of these miRNAs lays the foundation for further understanding of the function of small RNAs in regulating plant response to fungal infection and Verticillium wilt in particular.     

Genome-Wide Identification and Expression Patterns of AcSWEET Family in Pineapple and AcSWEET11 Mediated Sugar Accumulation

Pineapple (Ananas comosus L.) is an important fruit crop in tropical regions, and it requires efficient sugar allocation during fruit development. Sugars Will Eventually be Exported Transporters (SWEETs) are a group of novel sugar transporters which play critical roles in seed and fruit development. However, the function of AcSWEETs remains unknown in the sugar accumulation. Herein, 17 AcSWEETs were isolated and unevenly located in 11 chromosomes. Analysis of a phylogenetic tree indicated that 17 genes were classified into four clades, and the majority of AcSWEETs in each clade shared similar conserved motifs and gene structures. Tissue-specific gene expression showed that expression profiles of AcSWEETs displayed differences in different tissues and five AcSWEETs were strongly expressed during fruit development. AcSWEET11 was highly expressed in the stage of mature fruits in ‘Tainong16’ and ‘Comte de paris’, which indicates that AcSWEET11 was important to fruit development. Subcellular localization analysis showed that AcSWEET11 was located in the cell membrane. Notably, overexpression of AcSWEET11 could improve sugar accumulation in pineapple callus and transgenic tomato, which suggests that AcSWEET11 might positively contribute to sugar accumulation in pineapple fruit development. These results may provide insights to enhance sugar accumulation in fruit, thus improving pineapple quality in the future.     

Changes in α-Farnesene and Phenolic Metabolism and the Expression of Associated Genes during the Development of Superficial Scald in Two Distinct Pear Cultivars

Superficial scald is a postharvest physiological disorder that occurs in pear during and after cold storage. In this study, the superficial scald index; α-farnesene and its oxidation products, conjugated trienols (CTols); phenolic content; and the expression of its related genes were investigated in two different pear cultivars, ‘Wujiuxiang’ (Pyrus communis L.) and ‘Yali’ (Pyrus bretschneideri R.), following 115 days of cold storage at 0 °C followed by 7 days of shelf life at 20 °C. The results indicated that the superficial scald occurred after 115 days of cold storage and became more severe during the shelf life of the ‘Wujiuxiang’ pear, whereas no scald was observed in ‘Yali’. The α-farnesene levels increased rapidly at first and then decreased, while the CTols contents increased significantly in ‘Wujiuxiang’ as compared to ‘Yali’, and the expression levels of the genes involved in α-farnesene and CTols metabolism (HMGR1, HMGR2, GSTU7, GPX5, and GPX6), as well as the phenolic synthesis (PAL1, PAL2, C4H1, 4CL2, C3H, and ANR) of the peel, were significantly up-regulated at the onset of the superficial scald. In addition, the relative conductivity and contents of catechin and epicatechin were higher, and the expression level of the laccase gene (LAC7) significantly increased with the development of superficial scald, while lower contents of chlorogenic acid, arbutin, and isorhamnetin-3-3-glucoside, as well as the lower expression levels of a phenolic-synthesis-related gene (C4H3) and polyphenol oxidase genes (PPO1 and PPO5), were noticed in ‘Wujiuxiang’ as compared to ‘Yali’. The results indicated that the onset and progression of superficial scald were associated with the accumulation of CTols, cell membrane breakdown, and higher catechin, epicatechin, and rutin contents, as well as the expression of associated genes of the peels of pear fruit.