Gene structure of the ciliate Sterkiella histriomuscorum based on a combined analysis of DNA and cDNA sequences from 21 macronuclear chromosomes

Abstract

Macronuclear deoxyribonucleic acid (DNA) in hypotrichous ciliates consists of a set of linear molecules ranging in size from 0.5 to several tens of kilobases and typically carrying a single gene. Each minichromosome is present at a ploidy of >or=1,000 per macronucleus. These molecules are known as gene-sized molecules. Multigene molecules are also present, but are still poorly described. In analyzing the encystment-excystment cycle of Sterkiella histriomuscorum, we have characterized a set of 21 macronuclear molecules both at the DNA and complementary DNA (cDNA) levels. On a total of 23 validated coding sequences, we mapped the 5' and 3' untranslated regions for a subset of 10 and 18 transcripts, respectively. A combination of DNA and cDNA data allows us to precisely determine several structural features of macronuclear chromosomes, such as the organization of multigene molecules, an intron content higher than expected, and a conserved sequence surrounding the initiation transcription site. It also reveals one coding sequence containing a transcribed 10-bp element that displays the characteristic features of internal eliminated sequences (IES). Its presence in a fraction of the minichromosomes carrying this gene raises the possibility of an incomplete IES excision process during the development of the S. histriomuscorum macronucleus.

α-Tubulin Minichromosome Promoters in the Stichotrichous Ciliate Stylonychia lemnae

“…In accordance with these findings, transcription of the analyzed S. lemnae and S. histriomuscorum minichromosomes initiates exclusively at an adenosine residue (Fig. 4) (19). Taken together, these data indicate that an initiator element is a common and conserved element in promoters of stichotrichous minichromosomes.…”

A new scrambled gene in the ciliate Uroleptus

“…Unexpectedly, we found three TSS at positions 49, 72 and 114, with 114 being the most represented (6 out of 9 clones). All three sites are on adenosine residues, similar to other published results (Ghosh et al, 1994;Chang et al, 2004;Kuo et al, in press;Lescasse et al, 2005;McFarland et al, in press), but share no common motif immediately preceding or following the TSS. We performed a side-by-side control using the actin I gene previously characterized in this species (Chang et al, 2005) and found only one TSS associated with actin I (Chang, unpublished data).…”

Coding genes and molecular structures of the diffusible signalling proteins (pheromones) of the polar ciliate, Euplotes nobilii

“…At odds with respect to the general organization of the gene-sized DNA molecules of the ciliate macronuclear genome (Jahn and Klobutcher, 2002;Prescott et al, 2002;Cavalcanti et al, 2004;Lescasse et al, 2005), this region exceeds the length of the coding region and shows high conservation, with a putative intron sequence and multiple potential TAA stop codons spaced in-frame with one another. All this strongly implies that, in addition to being functionally fundamental for the regulation of transcription, the 5′ region is itself a site of coding activity, possibly induced by mechanisms of alternative intron splicing and/or frame shifting.…”

“…The 5′ region appears to be significantly more strictly conserved than the 3′ region (88 to 97% vs. 43 to 92% identity), in which the only functional element common to all the seven sequences appears to be a substitution of the conventional AATAAA polyadenylation signal with a TTATTT motif. In addition to showing a functional replacement of the conventional TATA or CAAT boxes for the initiation of transcription with the less conventional GAAAA motif (Ghosh et al, 1994), the 5′ region includes several consensus donor GT and acceptor AG splice-site junctions (Lescasse et al, 2005). This suggests the presence of one or more intron sequences destined to be alternatively removed, with the consequence that more than one mRNA species and hence more than a single pheromone isoform are synthesized.…”