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Germination is a plant developmental process by which radicle of mature seeds start to penetrate surrounding barriers for seedling establishment and multiple environmental factors have been shown to affect it. Little is known how high salinity affects seed germination of C4 plant, Zea mays. Preliminary germination assay suggested that isolated embryo alone was able to germinate under 200 mM NaCl treatment, whereas the intact seeds were highly repressed. We hypothesized that maize endosperm may function in perception and transduction of salt signal to surrounding tissues such as embryo, showing a completely different response to that in Arabidopsis. Since salt response involves ABA, we analysed in vivo ABA distribution and quantity and the result demonstrated that ABA level in isolated embryo under NaCl treatment failed to increase in comparison with the water control, suggesting that the elevation of ABA level is an endosperm dependent process. Subsequently, by using advanced profiling techniques such as RNA sequencing and SWATH‐MS‐based quantitative proteomics, we found substantial differences in post‐transcriptional and translational changes between salt‐treated embryo and endosperm. In summary, our results indicate that these regulatory mechanisms, such as alternative splicing, are likely to mediate early responses to salt stress during maize seed germination. This study demonstrated that maize endosperm may function in sensation and transduction of salt signal to surrounding tissues during salt stress, which is a completely different responsive model from that of Arabidopsis. [ABSTRACT FROM AUTHOR]

Serine/arginine-rich (SR) proteins are widely found in higher eukaryotes, including metazoans and plants. They form a major family of essential splicing factors that function in both constitutive splicing (CS) and alternative splicing (AS). Some SR proteins can also shuttle between the nucleus and cytoplasm and have roles beyond splicing. The activities of SR proteins are required for many living organisms to maintain normal growth and development. Although SR genes have been identified in numerous plants, they are less studied than those found in animals. The results of existing research suggest that plant SR proteins share many similar properties with their animal counterparts. However, plants generally have a higher number of SR proteins that display largely redundant functions under normal conditions but participate in specific stress responses. Moreover, many animal and plant SR genes are alternatively spliced and can be regulated by themselves or other SR proteins. These AS events, often coupled to nonsense-mediated decay (NMD), enable a mechanism for protein amount control under different conditions but sometimes also lead to translated protein isoforms with different functions. Here, we summarize the key findings of SR proteins in animals and plants and compare the essential characteristics of SR studies in these two research areas. [ABSTRACT FROM AUTHOR]

Post-transcriptional mechanisms (PTMs), including alternative splicing (AS) and alternative translation initiation (ATI), may explain the diversity of proteins involved in plant development and stress responses. Transcriptional regulation is important during the hypoxic germination of rice seeds, but the potential roles of PTMs in this process have not been characterized. We used a combination of proteomics and RNA sequencing to discover how AS and ATI contribute to plant responses to hypoxia. In total, 10 253 intron-containing genes were identified. Of these, ~1741 differentially expressed AS (DAS) events from 811 genes were identified in hypoxia-treated seeds compared with controls. Over 95% of these were not present in the list of differentially expressed genes. In particular, regulatory pathways such as the spliceosome, ribosome, endoplasmic reticulum 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 transcriptional regulation. Considerable AS changes were identified, including the preferential usage of some non-conventional splice sites and enrichment of splicing factors in the DAS data sets. Taken together, these results not only demonstrate that AS and ATI function during hypoxic germination but they have also allowed the identification of numerous novel proteins/peptides produced via ATI. [ABSTRACT FROM AUTHOR]

In eukaryotes, mechanisms such as alternative splicing ( AS) and alternative translation initiation ( ATI) contribute to organismal protein diversity. Specifically, splicing factors play crucial roles in responses to environment and development cues; however, the underlying mechanisms are not well investigated in plants. Here, we report the parallel employment of short-read RNA sequencing, single molecule long-read sequencing and proteomic identification to unravel AS isoforms and previously unannotated proteins in response to abscisic acid ( ABA) treatment. Combining the data from the two sequencing methods, approximately 83.4% of intron-containing genes were alternatively spliced. Two AS types, which are referred to as alternative first exon ( AFE) and alternative last exon ( ALE), were more abundant than intron retention ( IR); however, by contrast to AS events detected under normal conditions, differentially expressed AS isoforms were more likely to be translated. ABA extensively affects the AS pattern, indicated by the increasing number of non-conventional splicing sites. This work also identified thousands of unannotated peptides and proteins by ATI based on mass spectrometry and a virtual peptide library deduced from both strands of coding regions within the Arabidopsis genome. The results enhance our understanding of AS and alternative translation mechanisms under normal conditions, and in response to ABA treatment. [ABSTRACT FROM AUTHOR]