The miniaturized nuclear genome of eukaryotic endosymbiont contains genes that overlap, genes that are cotranscribed, and the smallest known spliceosomal introns.

Abstract

Chlorarachniophyte algae contain a complex, multi-membraned chloroplast derived from the endosymbiosis of a eukaryotic alga. The vestigial nucleus of the endosymbiont, called the nucleomorph, contains only three small linear chromosomes with a haploid genome size of 380 kb and is the smallest known eukaryotic genome. Nucleotide sequence data from a subtelomeric fragment of chromosome III were analyzed as a preliminary investigation of the coding capacity of this vestigial genome. Several housekeeping genes including U6 small nuclear RNA (snRNA), ribosomal proteins S4 and S13, a core protein of the spliceosome [small nuclear ribonucleoprotein (snRNP) E], and a clp-like protease (clpP) were identified. Expression of these genes was confirmed by combinations of Northern blot analysis, in situ hybridization, immunocytochemistry, and cDNA analysis. The proteinencoding genes are typically eukaryotic in overall structure and their messenger RNAs are polyadenylylated. A novel feature is the abundance of 18-, 19-, or 20-nucleotide introns; the smallest spliceosomal introns known. Two of the genes, U6 and S13, overlap while another two genes, snRNP E and clpP, are cotranscribed in a single mRNA. The overall gene organization is extraordinarily compact, making the nucleomorph a unique model for eukaryotic genomics.

Epizootiologic Survey for <i>Babesia microti</i> among Small Wild Mammals in Northeastern Eurasia and a Geographic Deversity in the &beta;-Tubulin Gene Sequences

“…While the position of the first intron is precisely conserved for most parasites in phylum Apicomplexa [4][5][6]24], the presence and position of the second intron are probably unique to B. microti group (B. microti and closely related parasites, including B. rodhaini), because the other parasites belonging to genera Babesia and Theileria apparently lack it (M. Tsuji, unpublished data). The two introns were very small in size, 20 and 22 bp for the first and second ones, respectively, which are comparable to the smallest introns found in chloroplast nucleomorph of Chlorarachniophyte algae [10]. Since such introns may be too small to be recognized by the splicing mechanism known for general spliceisomal introns [12], B. microti may have a unique splicing mechanism.…”

Recent de novo origin of human protein-coding genes

“…Likely orthologous ORFs at the expected location were defined as BLAT (Kent 2002) or SSearch (Pearson and Lipman 1988) sequence matches, where the translated sequence had $90% identity with the human protein in each of the exons and no inframe stop codons in the first half of the alignment, and where any inferred introns were at least 18 nucleotides (nt) long (very short introns of 1-5 bp are frequently inferred by automated pipelines to avoid frameshifts and to force a match, but there is no evidence for splicing of introns of less than 18 nt [Gilson and McFadden 1996]). …”

Origin and Evolution of the Mitochondrial Proteome

“…Neutralized genes are subject to mutational degradation (101). When genes required for the free-living mode are forfeited, the facultative symbiont has evolved into an obligate symbiont or an obligate parasite, with a coding capacity that can be extremely limited (70,71,72,94,147,170,172). For example, the obligate parasites of the genus Rickettsia, like mitochondria, have virtually no genes for amino acid or nucleoside biosynthesis, but their facultative parasitic relatives, the Bartonella spp., are fully able to produce these intermediates in their free-living mode (20; Andersson et al, unpublished data).…”