Abstract
BackgroundNyctotherus ovalis is a single-celled eukaryote that has hydrogen-producing mitochondria and lives in the hindgut of cockroaches. Like all members of the ciliate taxon, it has two types of nuclei, a micronucleus and a macronucleus. N. ovalis generates its macronuclear chromosomes by forming polytene chromosomes that subsequently develop into macronuclear chromosomes by DNA elimination and rearrangement.ResultsWe examined the structure of these gene-sized macronuclear chromosomes in N. ovalis. We determined the telomeres, subtelomeric regions, UTRs, coding regions and introns by sequencing a large set of macronuclear DNA sequences (4,242) and cDNAs (5,484) and comparing them with each other. The telomeres consist of repeats CCC(AAAACCCC)n, similar to those in spirotrichous ciliates such as Euplotes, Sterkiella (Oxytricha) and Stylonychia. Per sequenced chromosome we found evidence for either a single protein-coding gene, a single tRNA, or the complete ribosomal RNAs cluster. Hence the chromosomes appear to encode single transcripts. In the short subtelomeric regions we identified a few overrepresented motifs that could be involved in gene regulation, but there is no consensus polyadenylation site. The introns are short (21–29 nucleotides), and a significant fraction (1/3) of the tiny introns is conserved in the distantly related ciliate Paramecium tetraurelia. As has been observed in P. tetraurelia, the N. ovalis introns tend to contain in-frame stop codons or have a length that is not dividable by three. This pattern causes premature termination of mRNA translation in the event of intron retention, and potentially degradation of unspliced mRNAs by the nonsense-mediated mRNA decay pathway.ConclusionThe combination of short leaders, tiny introns and single genes leads to very minimal macronuclear chromosomes. The smallest we identified contained only 150 nucleotides.
Highlights
Nyctotherus ovalis is a single-celled eukaryote that has hydrogen-producing mitochondria and lives in the hindgut of cockroaches
We examined the structure of N. ovalis gene-sized chromosomes and the regulation of their transcription by combining information from large-scale cDNA (4,242 sequences) and cDNA libraries (5,484 sequences, including 327 complete macronuclear chromosomes)
Agarose gel electrophoresis revealed that the majority of the undigested DNA isolated from intact N. ovalis was present in the form of low molecular weight DNA
Summary
Nyctotherus ovalis is a single-celled eukaryote that has hydrogen-producing mitochondria and lives in the hindgut of cockroaches. Ciliates form an extremely diverse taxonomic group of protozoa They are the most complex single-celled eukaryotes, with some genomes containing more than 20,000 genes [1], Examples are the two completely sequenced ciliates Paramecium (39,642 genes) [2] and Tetrahymena (27,424 genes) [3]. They are abundant in almost every aqueous environment, from ocean waters to small ponds and even pockets of soil water; and they can grow as symbionts, commensals and parasites in pelagic, benthic, sapropelic or intestinal ecosystems. These molecules are capped with telomeres, and selectively amplified as individual "mini-chromosomes" [8,13,14]
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