Evolution and assembly of an extremely scrambled gene

Abstract

The process of gene unscrambling in hypotrichous ciliates represents one of nature's ingenious solutions to the problem of gene assembly. With some essential genes scrambled in as many as 51 pieces, these ciliates rely on sequence and structural cues to rebuild their fragmented genes and genomes. Here we report the complex pattern of scrambling in the DNA polymerase ␣ gene of Stylonychia lemnae. The germline (micronuclear) copy of this gene is broken into 48 pieces with 47 dispersed over two loci, with no asymmetry in the placement of coding segments on either strand. Direct repeats present at the boundaries between coding and noncoding sequences provide pointers to help guide assembly of the functional (macronuclear) gene. We investigate the evolution of this complex gene in three hypotrichous species.A ll ciliates possess two types of nuclei: an active somatic macronucleus and a germline micronucleus that contributes to sexual reproduction. The macronucleus forms from the micronucleus after cell mating, during the course of development. Prescott and colleagues discovered that the genomic copies of some protein-coding genes in the micronucleus of hypotrichous ciliates are encrypted in three ways (reviewed in ref. 1): (i) intervening non-protein-coding DNA segments [internal eliminated segments (IESs)] interrupt protein-coding DNA segments [macronuclear destined segments (MDSs)] and must be removed from the DNA during macronuclear development (2), (ii) the MDS order in 3 of 10 micronuclear genes is permuted relative to the chronological order in the macronuclear copy (1, 3), and (iii) these scrambled MDSs may be encoded in either orientation on the micronuclear DNA (Fig. 1). Some IESs may be remnants of transposons that lost their transposase and are now excised by a ciliate-specific mechanism for DNA rearrangements (2, 4). The total amount of DNA eliminated from the micronucleus is as great as 98% in Stylonychia (1), a dramatic reduction of noncoding DNA. These acrobatic genome rearrangements therefore present a potentially complicated cellular computational paradigm (5).Homologous recombination between short repeats at MDS-IES boundaries has been implicated as the likely mechanism of gene unscrambling, as it could simultaneously remove the IESs and reorder the MDSs (1). Typically, a short DNA sequence present at the boundary between MDS n and the downstream IES is repeated between MDS n ϩ 1 and its upstream IES, such that this sequence provides a pointer between MDS n and MDS n ϩ 1 at a distance (refs. 1, 6, and 7; Table 1), with one copy of the repeat retained in the macronucleus. However, the presence of such short direct repeats [average length of 4 bp between nonscrambled MDSs and 9 bp between scrambled MDSs (ref. 8; Table 1)] suggested that, although these pointers are necessary, they cannot be sufficient to direct accurate splicing and may play more of a role in structure than recognition. Otherwise, incorrectly spliced sequences (the results of promiscuous recombination) would dominate. This incorrect h...

RNA-dependent control of gene amplification

“…The macronuclear precursor DNA sequences [macronucleus-destined sequences (MDS)] in the micronucleus are interrupted by short noncoding DNA sequences [internal eliminated sequences (IES)] and are not associated with telomeric repeats (11,12). In stichotrichous ciliates, such as Oxytricha and Stylonychia, these MDSs are not always arranged linearly but, in ∼30%, appear in scrambled disorder (14)(15)(16).…”

The scrambled Actin I gene in Uroleptus pisces

“…The black dots on the nodes represent clades that were supported by bootstrap values of 75% or higher in maximumlikelihood, neighbor-joining, and maximum-parsimony bootstrap analyses. Modified from Croft et al (2003) to include both Uroleptus pisces 1 and 2 loci (Hoffman and Prescott 1997;Landweber et al 2000;Kneeland and Prescott, unpublished).…”

Conserved linkage of two genes on the same macronuclear chromosome in spirotrichous ciliates

“…We PCRamplified the previously unsequenced central region of this molecule, using primers derived from UGC1O0006P23 against 1-2 ng S. histriomuscorum macronuclear DNA. To verify sequences from the pilot genome project, we used the newly obtained sequences and telomere-specific primers to PCR amplify the 5' and 3' ends of this macronuclear molecule, following published protocols (Chang et al 2004;Landweber et al 2000).…”

“…Thirty-five cycles of 30 s at 94°C, 1 min at 50°C, and 1 min at 72°C were followed by a 10-min extension at 72°C. The resulting sequences were used to design primers to amplify downstream sequences from the RPL29 gene following established protocols (Chang et al 2004;Landweber et al 2000). Sequences upstream from the RPL29 gene were amplified from the cyclophilin gene (in all species) or RPL29 gene (in Holosticha) using the same protocols.…”