Parallel Loss of Plastid Introns and Their Maturase in the Genus Cuscuta

Joel R Mcneal,Claude W Depamphilis,Jennifer V Kuehl,Jim Leebens-Mack,Jeffrey L Boore

doi:10.1371/journal.pone.0005982

Abstract

Plastid genome content and arrangement are highly conserved across most land plants and their closest relatives, streptophyte algae, with nearly all plastid introns having invaded the genome in their common ancestor at least 450 million years ago. One such intron, within the transfer RNA trnK-UUU, contains a large open reading frame that encodes a presumed intron maturase, matK. This gene is missing from the plastid genomes of two species in the parasitic plant genus Cuscuta but is found in all other published land plant and streptophyte algal plastid genomes, including that of the nonphotosynthetic angiosperm Epifagus virginiana and two other species of Cuscuta. By examining matK and plastid intron distribution in Cuscuta, we add support to the hypothesis that its normal role is in splicing seven of the eight group IIA introns in the genome. We also analyze matK nucleotide sequences from Cuscuta species and relatives that retain matK to test whether changes in selective pressure in the maturase are associated with intron deletion. Stepwise loss of most group IIA introns from the plastid genome results in substantial change in selective pressure within the hypothetical RNA-binding domain of matK in both Cuscuta and Epifagus, either through evolution from a generalist to a specialist intron splicer or due to loss of a particular intron responsible for most of the constraint on the binding region. The possibility of intron-specific specialization in the X-domain is implicated by evidence of positive selection on the lineage leading to C. nitida in association with the loss of six of seven introns putatively spliced by matK. Moreover, transfer RNA gene deletion facilitated by parasitism combined with an unusually high rate of intron loss from remaining functional plastid genes created a unique circumstance on the lineage leading to Cuscuta subgenus Grammica that allowed elimination of matK in the most species-rich lineage of Cuscuta.

Highlights

Introns within organellar genes have unique features
Using PCR assays that gave clear positive or negative results based on band size, we surveyed for the presence of matK at the trnK-UUU locus along with all known group IIA introns and three group IIB introns from a variety of Cuscuta species representing all three currently recognized subgenera (Table 1)
The trnK gene itself is absent across all Cuscuta species, all sampled members of subgenus Monogyna and subgenus Cuscuta retain an open reading frame for matK, paralleling the condition in Epifagus and Zygnema

Summary

Introduction

Introns within organellar genes have unique features. Unlike those in eukaryotic nuclear genes, they do not rely on spliceosomes for excision from RNA transcripts, and unlike the structured self-splicing introns of prokaryotes, they typically require other trans-acting factors for efficient splicing in vivo[1,2]. Land plant plastid genomes usually contain between 17 and 20 of these introns, all of which are classified as group II based on putative folding structure except for a single group I intron within the transfer RNA gene trnL-UAA[3]. The plastid genome of the nonphotosynthetic, parasitic angiosperm Epifagus encodes only four proteins not involved in transcription or translation and lacks a functional trnK gene[7]. Various studies have shown that without translation of plastid-encoded proteins, seven group IIA introns in the plastid genome remain in an unspliced transcript form, whereas group IIB introns are largely unaffected and have been shown in maize to primarily rely upon a nuclear-encoded factor, crs, for splicing[3,9,10]. 6. Epifagus virginiana Positive Selection bXs (nonX-domain regions)

Methods

Results

Conclusion