Alternative splicing and gene duplication differentially shaped the regulation of isochorismate synthase in Populus and Arabidopsis

Abstract

Isochorismate synthase (ICS) converts chorismate to isochorismate for the biosynthesis of phylloquinone, an essential cofactor for photosynthetic electron transport. ICS is also required for salicylic acid (SA) synthesis during Arabidopsis defense. In several other species, including Populus, SA is derived primarily from the phenylpropanoid pathway. We therefore sought to investigate ICS regulation in Populus to learn the extent of ICS involvement in SA synthesis and defense. Arabidopsis harbors duplicated AtICS genes that differ in their exon-intron structure, basal expression, and stress inducibility. In contrast, we found a single ICS gene in Populus and six other sequenced plant genomes, pointing to the AtICS duplication as a lineage-specific event. The Populus ICS encodes a functional plastidic enzyme, and was not responsive to stresses that stimulated phenylpropanoid accumulation. Populus ICS underwent extensive alternative splicing that was rare for the duplicated AtICSs. Sequencing of 184 RT-PCR Populus clones revealed 37 alternative splice variants, with normal transcripts representing Ϸ50% of the population. When expressed in Arabidopsis, Populus ICS again underwent alternative splicing, but did not produce normal transcripts to complement AtICS1 function. The splice-site sequences of Populus ICS are unusual, suggesting a causal link between junction sequence, alternative splicing, and ICS function. We propose that gene duplication and alternative splicing of ICS evolved independently in Arabidopsis and Populus in accordance with their distinct defense strategies. AtICS1 represents a divergent isoform for inducible SA synthesis during defense. Populus ICS primarily functions in phylloquinone biosynthesis, a process that can be sustained at low ICS transcript levels.defense ͉ phenylpropanoid ͉ splice site sequence ͉ phylloquinone ͉ salicylic acid

Salicylic Acid Biosynthesis and Metabolism

“…In addition to Arabidopsis, ICS homologs have been identified in a wide variety of plant species, including C. roseus, Capsicum annuum (pepper), N. tabacum (tobacco), N. benthamiana, Solanum lycopersicum (tomato), Oryza sativa (rice), Vitis vinifera (grapevine), Medicago truncatula (barrel medic), Sorghum bicolor (sorghum), Glycine max (soybean), Ricinus communis (castor bean), and Populus trichocarpa (poplar) (van Tegelen et al, 1999a;Ogawa et al, 2005;Uppalapati et al, 2007;Catinot et al, 2008;Yuan et al, 2009 and references therein). Given their role in phylloquinone synthesis, it is highly likely that ICS homologs will be identified in all plant species.…”

Induced Jasmonate Signaling Leads to Contrasting Effects on Root Damage and Herbivore Performance

“…We harvested plants 1, 4, 12, and 24 h after wounding or the beginning of cucumber beetle infestation and measured the concentrations of major stress hormones as well as the expression of corresponding biosynthetic marker genes in the roots. The following hormone biosynthetic genes were measured (Table I): a 13-lipoxygenase gene involved in JA biosynthesis (OsHI-LOX; Zhou et al, 2009), a JA-Ile synthase gene (OsJAR1; Riemann et al, 2008), a 9-cis-epoxycarotenoid dioxygenase gene involved in ABA biosynthesis (OsNCED3; Hwang et al, 2010), an isochorismate synthase gene involved in SA biosynthesis (OsICS; Yuan et al, 2009), and a 1-aminocyclopropane-1-carboxylic acid synthase gene involved in ET biosynthesis (OsACS2; Helliwell et al, 2013). In wounded plants, we observed a rapid and transient induction of JA, JA-Ile, ABA, and their corresponding biosynthetic genes (Fig.…”

Constitutively Elevated Salicylic Acid Levels Alter Photosynthesis and Oxidative State but Not Growth in Transgenic Populus

“…However, the utilization of SA as a direct precursor for PG biosynthesis has not been supported by feeding or tracer experiments (Zenk, 1967;Payyavula et al, 2009;Babst et al, 2010) or by transgenic expression of bacterial SA hydroxylase (NahG) in Populus (Morse et al, 2007). Regardless, both SA and PGs share the same phenylpropanoid origin in Populus (Yuan et al, 2009;Babst et al, 2010), suggesting a potential metabolic link that may be sensitive to various defense and adaptive functions.…”

“…Stress-induced SA synthesis in Arabidopsis occurs in the chloroplast and is mediated by ISOCHORISMATE SYNTHASE1 (Wildermuth et al, 2001;Garcion et al, 2008), a function that appears to have evolved following genome duplication in the Arabidopsis lineage (Yuan et al, 2009). By contrast, the single-copy ortholog of Populus retains the ancestral isochorismate synthase function in phylloquinone biosynthesis, while SA originates from cinnamic acid via the cytosolic phenylpropanoid pathway (Figure 1) (Yuan et al, 2009).…”

“…Stress-induced SA synthesis in Arabidopsis occurs in the chloroplast and is mediated by ISOCHORISMATE SYNTHASE1 (Wildermuth et al, 2001;Garcion et al, 2008), a function that appears to have evolved following genome duplication in the Arabidopsis lineage (Yuan et al, 2009). By contrast, the single-copy ortholog of Populus retains the ancestral isochorismate synthase function in phylloquinone biosynthesis, while SA originates from cinnamic acid via the cytosolic phenylpropanoid pathway (Figure 1) (Yuan et al, 2009). Ambient levels of SA in Populus are substantially higher than those reported in Arabidopsis (Nawrath and Métraux, 1999;Koch et al, 2000;Wildermuth et al, 2001), where constitutively elevated SA has been associated with dwarfism (reviewed in Rivas-San Vicente and Plasencia, 2011).…”