Role of auxin-responsive genes in biotic stress responses

Abstract

Although the phytohormone auxin has been implicated primarily in developmental processes, some recent studies suggest its involvement in stress/defense responses as well. Recently, we identified auxin-responsive genes and reported their comprehensive transcript profiling during various stages of development and abiotic stress responses in crop plant rice. The analysis revealed tissue-specific and overlapping expression profiles of auxin-responsive genes during various stages of reproductive development. In addition, a large number of auxin-responsive genes were also found to be differentially expressed under various abiotic stress conditions. Here, we further analyze the expression profiles of auxin-responsive genes during various biotic stress conditions. Several auxin-responsive genes showed response to biotic stress as well. Our analysis provides evidence for role of auxin in plant defense responses and suggests cross-talk between auxin, abiotic stress and biotic stress signaling pathways.

The phytohormone auxin has been implicated in diverse developmental processes throughout the life cycle of plants, including apical dominance, tropic responses, vascular development, organ patterning, flower development and fruit development. Auxin regulates these developmental processes by altering the expression of a large number of genes, including primary auxin-responsive genes of Aux/IAA, GH3 and SAUR gene families.¹ Several studies have contributed to our present understanding of the molecular mechanisms underlying auxin-regulated processes.^2–4 In a recent study, we identified at least 315 auxin-responsive genes and provided evidence for their diverse roles during various stages of reproductive development, including floral transition, floral organ development and endosperm development in rice as revealed by comprehensive transcript profiling.⁵

Plants respond to different environmental stress conditions at molecular level by altering expression of several genes involved in various pathways. Plant hormones, abscisic acid, ethylene, salicylic acid and jasmonic acid, have been implicated in abiotic and biotic stress responses. Some recent studies suggest that auxin is also involved in abiotic and biotic stress signaling pathways.^6–10 Recently, we also reported that a significantly large number of auxin-responsive genes are differentially expressed during various abiotic stress conditions in rice, which suggested a crosstalk between auxin and abiotic stress signaling.⁵ In this study, we have analyzed the expression profiles of auxin-responsive genes (239 auxin-induced and 76 auxin-repressed) and members of auxin-related gene families (GH3, Aux/IAA, SAUR and ARF) during various biotic stress conditions and their overlap with abiotic stress responses.

To understand the possible role of auxin in plant defense responses at molecular level, the expression of auxin-responsive genes was analyzed under various biotic stress conditions in rice. The microarray data for rice seedlings infected with Magnaporthe grisea, an ascomycete fungus, and Striga hermonthica, an obligate root hemiparasite, available at Gene Expression Omnibus database under series accession numbers GSE7256 and GSE10373, respectively, was used for this analysis. The series GSE7256 include microarray data for two-week old seedlings of rice cultivar Nipponbare treated with spore suspension of M. grisea virulent strain FR13 in gelatine or gelatine alone and consists of 8 hybridizations representing two biological replicates of mock and infected samples for two time periods (3 and 4 dpi).¹¹ The series GSE10373 include microarray data of root tissues from three-week old seedlings of two rice cultivars IAC165 (susceptible) and Nipponbare (resistant) treated with S. hermonthica and consists of 24 hybridizations representing two biological replicates of mock and infected samples for three time points (2, 4 and 11 dpi).¹²

Differential gene expression analysis of pathogen treated samples as compared to mock treated samples was performed for the auxin-responsive genes after normalization of the whole genome data with GeneChip Robust Multi Array method and log transformation. We performed a stringent statistical analysis consisting of one-way ANOVA over all the samples in a series and the Benjamini-Hoschberg multiple testing correction was applied to the data. The auxin-responsive genes that are up or downregulated under at least one condition ≥two-fold with a p-value of ≤0.05 were considered to be differentially expressed significantly. The data analysis revealed that at least 154 auxin-induced and 61 auxin-repressed genes were differentially expressed under one or more of the biotic stress conditions analyzed (Fig. 1A and B; Fig. S1; Table S1). Among the 154 auxin-induced genes, 62 genes showed response to both M. grisea and S. hermonthica infection. However, other 55 and 37 genes showed specific response to M. grisea and S. hermonthica infection, respectively. Similarly, among the 61 auxin-repressed genes, 16 genes showed response to both M. grisea and S. hermonthica infection. However, other 10 and 35 genes showed specific response to M. grisea and S. hermonthica infection, respectively. Further, among the 50 members of auxin-related gene families (GH3, Aux/IAA, SAUR and ARF), which were differentially expressed under various biotic stress conditions, 14 (one GH3, six Aux/IAA, five SAUR and two ARF) showed response to both M. grisea and S. hermonthica infection and other 20 (two GH3, three Aux/IAA, seven SAUR and eight ARF) and 16 (three GH3, seven Aux/IAA, five SAUR and one ARF) genes showed specific response to M. grisea and S. hermonthica infection, respectively (Figs. 1C and S1; Table S1). Furthermore, we studied the overlapping response of auxin-responsive genes under both biotic (present study) and abiotic stress conditions.⁵ The analysis revealed that several auxin-responsive genes (112 auxin-induced and 44 auxin-repressed) and members of auxin-related gene families (26) responded to both biotic and abiotic stresses (Fig. S2). However, comparatively lesser number of auxin-responsive genes exhibited specific response to biotic and abiotic stress. These results indicate role of auxin in mediating crosstalk between biotic and abiotic stress signaling pathways.

Figure 1.

Differential expression of auxin-induced (A), auxin-repressed (B) and members of auxin-related gene families (C) in response to various biotic stress conditions. Venn diagrams represent number of genes commonly and uniquely differentially expressed by M. grisea and S. hermonthica infection. Hierarchical clustering of the genes showing significant differential expression in at least one condition is shown. The fold change values in treated sample as compared to its corresponding mock-treated control sample were used for clustering. The color scale for fold change values is shown at the bottom. Dpi, days post-inoculation. An enlarged version of heatmaps from this figure and fold change values are available as Supplemental Figure S1 and Table S1, respectively.

Some earlier studies have provided evidence for involvement of auxin signal transduction pathway in defense responses.¹³ It has been shown that pathogen infection results in auxin imbalance and alteration of gene expression. A global downregulation of auxin-responsive genes was reported during Bortrytis cinerea infection in Arabidopsis.¹⁴ Another gene expression profiling study in cotton in response to infection with Fusarium oxysporum f. sp vasinfectum also revealed differential expression of auxin-responsive genes.⁷ It has been reported that a microRNA-mediated repression of auxin signaling confers resistance in Arabidopsis against Pseudomonas syringae infection.⁹ The interaction of auxin with other hormones to mediate plant defense responses has also been reported. Salicylic acid (SA), a phytohormone involved in defense responses in plants, has been reported to repress auxin signaling pathway as a part of disease resistance mechanism.¹⁰ An elevated accumulation of Aux/IAA proteins was reported after treatment with SA analog, which suggested that the accumulation/stabilization of these short-lived negative regulators may account for the repression of auxin-regulated expression. 10 Similarly, jasmonic acid (JA) biosynthesis genes are downregulated in auxin-treated Arabidopsis seedlings suggesting the inhibitory effect of auxin on JA biosynthesis pathway.¹⁵ The members of auxin-responsive GH3 gene family have been shown to play role in plant defense responses. The Arabidopsis GH3.5 acts as a bifunctional modulator in auxin and SA signaling.¹⁶ The overexpression of GH3.5 resulted in elevated accumulation of SA and expression of Pathogenesis-related-1 (PR-1) genes and in gh3.5 mutant systemic acquired resistance is partially compromised.¹⁶ Similarly, the overexpression of GH3–8 enhances disease resistance in rice against Xanthomonas oryzae pv oryzae.¹⁷ Our study also revealed that the expression of several members of auxin-related gene families (including GH3 and Aux/IAA) is altered in response to pathogen infection. It has been suggested that the altered auxin homeostasis (distribution and metabolism) and generation of reactive oxygen species influence the auxin response in response to various environmental stress conditions.^5,18

Taken together, these results suggest that auxin acts as an important component involved in defense responses via regulating the expression of a large number of genes and mediates crosstalk between abiotic and biotic stress responses. Although these observations provide some clues, the exact mechanism of auxin-mediated stress/defense responses still remains to be elucidated.

Addendum to: Jain M, Khurana JP. Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. FEBS J. 2009;276:3148–3162. doi: 10.1111/j.17424658.2009.07033.x.