Since life started on the Earth, the organisms undergone several modifications and are diversified to populate most environments. All observed phenotypic adaptations are ultimately, encoded in the genome but identifying which changes in the DNA underlie the evolution of novel phenotypes has proven to be a difficult task. Alternative splicing (AS), a process that is involved in creation of variability which has been proved to be an important tool in the evolution of such novel phenotypic changes1.

Alternative splicing is a process where by multiple functionally distinct transcripts are encoded from a single gene by the selective removal or retention of exons and/or introns from the maturing RNA. The process is highly regulated, involving trans-acting splicing factors and cis-acting regulatory motifs. It has been proposed that, alternative splicing can contribute to the evolution of novel phenotypes as small number of mutations (those in the 5’ or 3’ splice sites, for instance) can give rise to alternative splicing isoforms consisting of novel combinations of exons from existing genes, providing an opportunity for the evolution of new functions. Thus, alternative splicing has a role in almost every aspect of protein function, including binding between proteins and ligands, nucleic acids or membranes, localization and enzymatic properties. Taken together, alternative splicing is a central element in gene expression2.

Polar auxin transport in the Arabidopsis thaliana root requires the action of a Major Facilitator Superfamily (MFS) transporter, Zinc-Induced Facilitator-Like 1 (ZIFL1). Sequencing, promoter-reporter, and fluorescent protein fusion experiments indicate that the full-length ZIFL1.1 protein and a truncated splice isoform, ZIFL1.3, localize to the tonoplast of root cells and the plasma membrane of leaf stomatal guard cells, respectively. Using reverse genetics, it was shown that the ZIFL1.1 transporter regulates various root auxin-related processes, while the ZIFL1.3 isoform produced from ZIFL1 gene mediates drought tolerance by regulating stomatal closure3. Genome wide alternative splicing divergence in the maize hybrid ZD808 compared to its parents NG5 and CL11 showed large number of significant differential alternative splicing (DAS) events in the hybrids relative to its parents, which are further categorised into parental dominant and novel DAS patterns. Parental-dominant, especially NG5-dominant, events were prevalent in the hybrid, accounting for 42% of all analysed DAS events, functional enrichment analysis revealed that the NG5-dominant AS events and novel AS patterns were involved mainly in regulating the expression of genes associated with carbon/nitrogen metabolism and cell division processes and contributed greatly to maize ear heterosis4.

Understanding how developmental and environmental signals are transduced into AS regulation and elucidating the role of AS in reprogramming gene expression to give novel phenotypes in response to biotic and abiotic stresses will have implications in crop improvement under changing climate. This will open new avenues to enhance and/or fine-tune gene regulation for biotechnological applications.

References:

1. BUSH, S. J., CHEN, L., TOVAR-CORONA, J. M. AND URRUTIA, A. O., 2017, Alternative splicing and the evolution of phenotypic novelty. Phil. Trans. R. Soc., 372: 20150474.

2. VERTA, J. AND JACOBS, A., 2022, The role of alternative splicing in adaptation and evolution. Trends Ecol. Evol., 37(4): 299-307.

3. REMY, E., CABRITO, T. R., BASTER, P., BATISTA, R. A., TEIXEIRA, M. C., FRIML, J., SÁ-CORREIA, I. AND DUQUEA, P., 2013, A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell, 25: 901–926.

4. HU, X., WANG, H., LI, K., LIU, X., LIU, Z., WU, Y., LI, S. AND HUANG, C., 2020, Genome-wide alternative splicing variation and its potential contribution to maize immature-ear heterosis. Crop J., 2214: 1-11.