Adaptive thermal control of stem gravitropism through alternative RNA splicing in Arabidopsis

Abstract

Gravitropism is an important growth movement in response to gravity in virtually all higher plants: the roots showing positive gravitropism and the shoots showing negative gravitropism. The gravitropic orientation of plant organs is also influenced by environmental factors, such as light and temperature. It is known that a zinc finger (ZF)-containing transcription factor SHOOT GRAVITROPISM 5/INDETERMINATE DOMAIN 15 (SGR5/IDD15) mediates the early events of gravitropic responses occurring in inflorescence stems. We have recently found that SGR5 gene undergoes alternative splicing to produce 2 protein variants, the full-size SGR5α transcription factor and the truncated SGR5β form lacking functional ZF motifs. The SGR5β form inhibits SGR5α function possibly by forming nonfunctional heterodimers that are excluded from DNA binding. Notably, SGR5 alternative splicing is accelerated at high temperatures, resulting in a high-level accumulation of SGR5β proteins. Accordingly, transgenic plants overexpressing SGR5β exhibit a reduction in the negative gravitropism of inflorescence stems, as observed in the SGR5-defective mutant. It is proposed that the thermos-responsive alternative splicing of SGR5 gene provides an adaptation strategy by which plants protect the shoots from aerial heat frequently occurring in natural habitats.

Gravitropism is a gravity-directed growth behavior that triggers asymmetric cell extension in plant organs. In response to gravitropic stimuli, it proceeds through 3 successive, distinct phases in the responding organs: gravity perception, signal transduction, and asymmetric cell elongation.¹ While the roots exhibit downward growth in the direction of gravitational pull, the stems exhibit upward growth in the opposite direction.

The gravitropic responses of plant organs are also affected by diverse environmental cues, among which the effects of light are most extensively studied. The phytochrome photoreceptors inhibit the function of phytochrome-interacting factors (PIFs) under red and far-red light conditions, reducing the negative gravitropism of the stems.^2,3 Under blue light conditions, ENHANCED BENDING 1, a component of the phototropin-mediated blue light signaling pathways, suppresses the gravitropic response of hypocotyls through interactions with NONPHOTOTROPIC HYPOCOTYL3, which mediates the root and hypocotyl bending.⁴

Temperature also influences the gravitropic response of plant organs, although underlying molecular schemes are not well established. At low temperatures, the gravitropism of inflorescence stems is declined in Arabidopsis, although gravity perception occurs normally.⁵ When Arabidopsis plants are exposed to horizontal gravitropic stimulation under cold conditions and then returned to vertical orientation at 23°C, inflorescence stems bend in response to the previous horizontal gravistimulation, and statolith sedimentation occurs normally,^5,6 indicating that cold temperatures exert its effects after gravity perception.

Recent studies on Arabidopsis mutants displaying distured gravitropic responses have identified several genes, termed SHOOT GRAVITROPISM genes (SGRs), that are involved in the gravitropism of the roots, hypocotyls, and inflorescence stems.^7,8 Individual SGR genes are involved in the gravitropic responses of different plant organs.^5,9 Among the SGR proteins examined, SGR5 is functionally distinct from other SGR members in that it functions primarily in the early steps of gravity perception in inflorescence stems.¹⁰

We recently observed that SGR5 gene undergoes alternative splicing, producing 2 protein variants (SGR5α and SGR5β). The SGR5α form is equivalent to the previously characterized SGR5 transcription factor.¹⁰ In contrast, the SGR5β form is a truncated form lacking the functional ZF motifs at the N-terminus.¹¹ It is interesting that SGR5 alternative splicing is enhanced at high temperatures, resulting in the high-level accumulation of the SGR5β form.¹¹ Transgenic studies revealed that SGR5β-overproducing plants (35S: SGR5β) exhibit a reduction in the negative gravitropism of inflorescence stems like the SGR5-defective sgr5–5 mutant.¹¹ As a result, whereas wild-type plants exhibit a reduced gravitropic growth of inflorescence stems under high temperature conditions, the negative gravitropism of both 35S: SGR5β and sgr5–5 inflorescence stems are less influenced by high temperature stress. These observations indicate that the thermos-responsive alternative splicing of SGR5 gene contributes to the protection of inflorescence stems from aerial heat.

It is currently unclear how SGR5β attenuates SGR5α function. SGR5β interacts with SGR5α in the nucleus. Both the SGR5α and SGR5β forms are transcriptionally active. Therefore, a plausible scenario would be that the SGR5β and SGR5α forms a non-DNA-binding heterodimer that are excluded from the promoters of target genes (Fig. 1). Identification of the targets of SGR5 transcription factor and DNA binding analysis will clarify the uncertainty. There have been precedents supporting the working hypothesis of the SGR5 variants. The CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) gene, a central component of the plant circadian clock,¹² the INDETERMINATE DOMAIN 14 (IDD14) gene, which mediates starch degradation during cold adaptation,¹³ are also regulated at the posttranscriptional level by alternative splicing. Similar to the SGR5β form, the truncated forms of CCA1 and IDD15 transcription factors lack DNA-binding motifs but are transcriptionally active. It has been found that the truncated forms act as a negative regulator of the cognate transcription factor by forming non-DNA-binding heterodimers, which are excluded from DNA binding.^12,13 This working scheme has been designated as ‘peptide interference’, in which a small interfering protein or peptide inactivate its target transcription factor by forming nonfunctional heterodimers.¹⁴

Figure 1.

SGR5 alternative splicing modulates the negative gravitropism of inflorescence stems under high temperature conditions. SGR5β, which accumulates under high temperature conditions, inhibits SGR5α function by forming nonfunctional SGR5α-SGR5β heterodimers, causing a reduction in the negative gravitropism of inflorescence stems. This signaling scheme provides an adaptation strategy by which aerial plant parts are protected from hot air.

A related question is whether the effects of high temperature on SGR5 alternative splicing are specific events or simply caused by non-specific inactivation of splicing machinery. Accumulating evidence support that gene transcription and alternative splicing are concurrently mediated by epigenetic control.^15,16 Histone modifications influence alternative splicing by affecting the recruitment of splicing regulators.^17,18 In addition, gene expression is regulated at the chromatin level in many cases under high temperature conditions,^19,20 entailing that thermos-responsive factors play a role in both the transcriptional regulation and alternative splicing events. It is therefore likely that the effects of high temperatures on SGR5 alternative splicing reflect specific regulatory schemes for fine-tuned control of gene expression.

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.

Funding

This work was supported by the Leaping Research (NRF-20151A2A1A05001636) and Global Research Lab (NRF-2012K1A1A2055546) Programs provided by the National Research Foundation of Korea and the Next-Generation BioGreen 21 Program (PJO111532015) provided by the Rural Development Administration of Korea.