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

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
_50% 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.