Xie, L.-J. | Search bioRxiv

bioRxiv2020

In silico characteration of GmSOS1 provides a comprehensive understaning for its role in soybean salt tolerance

Plant SOS1 encodes plasma membrane Na+/H+ antiporter, which helps in the exclusion of Na+ and improves plant salt tolerance. However, detailed studies of SOS1 in the important oil crop, soybean (Glycine max), are still lacking. In the present study, we carried out a comprehensive in silico analysis of SOS1 in soybean. Referring to the analysis of physicochemical properties and structural characteristics, the GmSOS1 is an acidic protein with instability and hydrophobicity. Subcellular localization of GmSOS1 supports the presumption that GmSOS1 is a plasma membrane Na+/H+ antiporter. Post-translational modification site prediction indicates 4 amino acids that may be phosphorylated. Further, the protein-protein interaction network and co-functional network signify the potential role of GmSOS1 in salt stress tolerance. Although the interaction between GmSOS1 and GmHKT1 remains elusive, some of the intermediary signaling components of SOS pathway in soybean have been predicted. In addition, in silico expression analysis based on transcriptome datasets using publicly available database revealed that GmSOS1 was differentially expressed in tissues and different times. Due to the analysis of its regulation mechanism, we found transcription factors such as WRKY and ERF as well as three miRNAs can regulate the expression of GmSOS1. Phylogenetic analysis using the homologous amino acid sequence of SOS1s from 26 species was performed to study the conserved motifs among these SOS1 members. Overall, we provide an extensive analysis of the GmSOS1 and it promises the primary basis for the study in development and response to salt tolerance.

plant biology↗

bioRxiv2018

Alternative splicing and translation play important roles in parallel with transcriptional regulation during rice hypoxic germination

Post-transcriptional mechanisms, including alternative splicing (AS) and alternative translation initiation (ATI), have been used to explain the protein diversity involved in plant developmental processes and stress responses. Rice germination under hypoxia conditions is a classical model system for the study of low oxygen stress. It is known that there is transcriptional regulation during rice hypoxic germination, but the potential roles of AS and ATI in this process are not well understood. In this study, a proteogenomic approach was used to integrate the data from RNA sequencing, qualitative and quantitative proteomics to discover new players or pathways in the response to hypoxia stress. The improved analytical pipeline of proteogenomics led to the identification of 10,253 intron-containing genes, 1,729 of which were not present in the current annotation. Approximately 1,741 differentially expressed AS (DAS) events from 811 genes were identified in hypoxia-treated seeds in comparison to controls. Over 95% of these were not present in the list of differentially expressed genes (DEG). In particular, regulatory pathways such as spliceosome, ribosome, ER protein processing and export, proteasome, phagosome, oxidative phosphorylation and mRNA surveillance showed substantial AS changes under hypoxia, suggesting that AS responses are largely independent of traditional transcriptional regulation. Massive AS changes were identified, including the preference usage of certain non-conventional splice sites and enrichment of splicing factors in the DAS datasets. In addition, using self-constructed protein libraries by 6-frame translation, thousands of novel proteins/peptides contributed by ATI were identified. In summary, these results provide deeper insights towards understanding the underlying mechanisms of AS and ATI during rice hypoxic germination.

plant biology↗