Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus

Abstract

Background: To gain insight into the evolutionary features of the huntingtin (htt) gene in Chordata, we have sequenced and characterized the full-length htt mRNA in the ascidian Ciona intestinalis, a basal chordate emerging as new invertebrate model organism. Moreover, taking advantage of the availability of genomic and EST sequences, the htt gene structure of a number of chordate species, including the cogeneric ascidian Ciona savignyi, and the vertebrates Xenopus and Gallus was reconstructed.

Results: The C. intestinalis htt transcript exhibits some peculiar features, such as spliced leader trans-splicing in the 98 nt-long 5' untranslated region (UTR), an alternative splicing in the coding region, eight alternative polyadenylation sites, and no similarities of both 5' and 3'UTRs compared to homologs of the cogeneric C. savignyi. The predicted protein is 2946 amino acids long, shorter than its vertebrate homologs, and lacks the polyQ and the polyP stretches found in the the N-terminal regions of mammalian homologs. The exon-intron organization of the htt gene is almost identical among vertebrates, and significantly conserved between Ciona and vertebrates, allowing us to hypothesize an ancestral chordate gene consisting of at least 40 coding exons.

Conclusion: During chordate diversification, events of gain/loss, sliding, phase changes, and expansion of introns occurred in both vertebrate and ascidian lineages predominantly in the 5'-half of the htt gene, where there is also evidence of lineage-specific evolutionary dynamics in vertebrates. On the contrary, the 3'-half of the gene is highly conserved in all chordates at the level of both gene structure and protein sequence. Between the two Ciona species, a fast evolutionary rate and/or an early divergence time is suggested by the absence of significant similarity between UTRs, protein divergence comparable to that observed between mammals and fishes, and different distribution of repetitive elements.

Figure 1

Amino acid alignment of the huntingtin region corresponding to exon 50–51 of Ciona. The red box indicates the region absent in the alternatively spliced isoform. Identical, similar and conserved positions are reported with different backgrounds.

Figure 2

Bayesian phylogenetic tree of huntingtin, reconstructed from protein sequences. Branch lengths are proportional to the number of substitutions per site. Numbers close to the nodes represent Bayesian posterior probabilities.

Figure 3

Comparison of huntingtin gene structure between Ciona intestinalis (upper line) and Homo sapiens (lower line). Only protein-coding regions are indicated. Exons are represented by boxes, with upper numbers indicating exon numbering and inner number indicating exon length (in bp). Box size is unrelated to exon length. Square bracket: exon-block (see text). Yellow box: equivalent exon (see text). Gray box: exon belonging to an exon-block (see text). Introns positionally conserved in the two species are represented by dashed lines, in black for identical intron position, in red for slipped position (changes ≤ 18 bp). Intron phase is reported between dashed lines as a single number if common to the two species. Boxed phase number indicates that intron phase is not conserved in one vertebrate species (see text). Blue boxes below or above the gene structure indicate exons with length differences > 12 bp in vertebrates (below) or in the Ciona genus (above). Letters inside blue boxes indicates the species where the size difference is observed: M, difference between mammals and other-vertebrates; NM, difference within non-mammalian vertebrates; F, difference between fishes and other-vertebrates; G, difference only in Gallus. Arrows indicate the 5% longest introns in at least one vertebrate species (below), and in the Ciona genus (above). AS: alternative splicing experimentally identified in C. intestinalis. PuAS: putative alternative splicing identified "in silico" in Gallus, Xenopus and pufferfishes. Sp: presence of lineage-specific sequences only in non-mammalian species (SpNM) or only in Ciona (SpC).

Figure 4

Percentage amino acid identity calculated for each Equivalent exon (E, in yellow) and exon-Block (B, in gray). The percentage amino acid identity was calculated from the chordate protein alignment for each of the equivalent exons and exon-blocks described in Figure 1. Numbers refer to the Ciona exon numbering. Bold-dashed line represents the mean % identity (21.2%) calculated over the entire alignment length. Normal-dashed lines represent mean value +/- standard deviation (7.1).

Figure 5

Amino acid alignment of CSTs found in intron 12. The Conserved Sequence Tag (CST) corresponds to an internal cassette exon (12Bis) in non-mammalian tetrapods and to a longest splicing isoform of exon 12 (12L) in pufferfishes. Identical, similar and conserved positions are indicated with different background.