Alternative splicing drives the functional diversification for environmental adaptation
image: Working model of the trade-off between plant growth and drought tolerance mediated by OsbHLH59 in rice
Credit: ©Science China Press
This study is led by Professor Liyu Huang's research team from the School of Agriculture, Yunnan University. This study investigated the rice bHLH transcription factor OsbHLH59, which undergoes stress-induced AS to produce two splice variants, OsbHLH59.1 and OsbHLH59.2. The two transcripts exhibited different expression patterns in response to drought stress. Under normal conditions, OsbHLH59.1, encoding 236 amino acid residues, exhibited constitutive expression across different rice tissues. In contrast, OsbHLH59.2, encoding 167 amino acid residues, showed minimal expression in all tissues. Under drought stress, OsbHLH59.1 expression rapidly increased and then decreased, whereas the expression level of OsbHLH59.2 increased with prolonged stress.
The study revealed that OsbHLH59.1 is the predominant transcript isoform of OsbHLH59 and plays a key role in regulating plant growth and development. However, OsbHLH59.2 inhibited rice growth via the dominant-negative effect of the heterodimer of OsbHLH59.1 and OsbHLH59.2. Moreover, both OsbHLH59.1 and OsbHLH59.2 positively regulate drought tolerance in rice, with OsbHLH59.2 exhibiting a stronger effect.
The functional diversification of OsbHLH59.1 and OsbHLH59.2 in the control of rice development and drought response is attributed to distinct target genes and downstream pathways. Through a comprehensive analysis of the DEGs from the subcellular spatially resolved transcriptomes and OsbHLH59 transgenic plant transcriptomes, this study identified several development-related genes (TUD1, OsCYP51G3, CYP94C2b, cdc2Os-2 and OsNCED3) and drought tolerance genes (OsNCED3, ONAC022, ZFP252, OsNCED4, and OsMSR15) as targets of OsbHLH59.1. Moreover, OsbHLH59.2 binds to the promoters of drought tolerance genes (OsNCED4, OsMSR15, OsDREB1F, and SNAC1). In paddy fields, soil water deficits occur gradually. Similar expression patterns among OsbHLH59.1 or OsbHLH59.2 and their targets under drought stress suggest that the initial induced expression of OsbHLH59.1 stimulates root elongation via these development-related genes as a drought avoidance mechanism. Subsequently, under severe drought stress conditions, the upregulation of OsbHLH59.2 likely inhibits overall plant growth, including root expansion, and triggers drought tolerance pathways. Moreover, the subtle interplay between OsbHLH59.1 and OsbHLH59.2 orchestrates the balance between rice growth and drought adaptation. Furthermore, the evolutionary dynamics of OsbHLH59 have contributed to the divergence and domestication of rice subspecies.
The intricate process of gene family evolution in higher organisms is achieved through duplication, transfer, loss, neofunctionalization, etc. Recent insights into the diversity of gene regulation have challenged the traditional understanding of genome size and structural complexity. These findings highlight the crucial role of posttranscriptional regulation in generating novel gene functions and provide valuable genetic resources for future rice domestication research and breeding practices.
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Alternative splicing drives the functional diversification of a bHLH transcription factor in the control of growth and drought tolerance in rice.