Scenedesmus obliquus

Mitochondrial genome organization, gene content, genetic code

Draft - for internal use only.

The mitochondrial genome of S. obliquus is 42,917 bp in size and codes for a total of 42 genes and two ORFs. Gene density is low. As much as 46.1 % of the mtDNA is without detectable coding content. Intergenic regions have a higher A+T content (68.1%) than coding regions (56.3%). Intergenic spacers (on average 424-bp long, 2/3 being 2-600 bp in length), are larger than those found in other chlorophyte mtDNAs. Three intergenic regions are >1000 bp. Numerous repeats make up about 25% of the 19.505 kb intergenic spacers. At least 7 different repeat motifs (between 50 -170 bp long) are found dispersed over the genome, as well as one ~735-bp long tandem repeat array.
Transcribed genes are found on one DNA strand only, with the exception of atp6 which is located on the opposite strand, relative to all other genes.

We observed that conceptual translation of most conserved protein-coding genes by using a genetic code that includes TAA and TGA as sole stop codons, predicts reading frames that are significant longer in the C-terminal region than counterparts in other species. Possible explanations are:

• (a) The genetic code comprises an additional stop codon, besides TAA and TGA;
• (b) RNA-editing generates a standard stop codon;
• (c) Polyadenylation generates a standard stop codon.

• there are only TCA codons in those protein-coding regions in which we expected the gene ends, nowhere else; no TAA and TGA codons occur upstream of these TCA codons in the corresponding reading frames;
• none of the conserved proteins, nor the single, free-standing orf end in TAA or TGA. Only the intron orf (in rnl) ends in TAA; there might be a TCA codon further downstream, but it would fall into the exon region of rnl; and
• the absence of TCG-Ser codons protein-coding genes and the presence of a mitochondrial-encoded trnS(gga) gene. The tRNA-Ser(gga) gene in is thought to decode TCC and TCT, but not TCG and TCA codons, which is consistent with the notion that TCA might act as a stop codon.

The mitochondrial genome of S. obliquus specifies the genes commonly found in other mtDNAs, i.e., the protein-coding genes nad1, 2, 3, 4, 4L, 5, 6, cob, cox1, 2, 3 and atp6, 9, as well as the large and small subunit rRNA genes (rnl, rns) and 27 tRNA genes. The encoded set of tRNAs is sufficient to recognize all but ACN-threonine codons in protein-coding sequences. We infer from and the presence of a mt-encoded trnL(cua), as well as from muliple protein alignments, that TAG codes for Leu, a codon assignment that has been observed in a few other chlorophyte as well as in some fungal mtDNAs.
In agreement with the above mentioned, inferred assignment of TCA=stop is the absence of TCG-Ser codons from protein-coding genes and the presence of a tRNA-Ser(gga) gene in S. obliquus mtDNA, the latter tRNA thought to decode TCC and TCT, but not TCG and TCA codons.
Both rRNA genes are fragmented and most fragments are dispersed over the genome. The rnl gene is split into four pieces (referred as to _a, _b, etc), rns into two.
Four introns are found in S. obliquus mtDNA: one in nad5 (group I), two in rnl_d (intron 1 belongs to group II, intron 2 to group I) and one in rns_a (group II). Only the second intron in rnl_d contains an orf, and this orf displays characteristics that are shared by the majority of group I intron orfs.
Genes typical of protist but not animal or fungal mtDNAs are not present.

List of all mitochondrial encoded tRNA genes:

trnA(ugc)
trnC(gca)
trnD(guc)
trnE(uuc)
trnF(gaa)
trnG(ucc)
trnH(gug)
trnI(gau)
trnI(uau)
trnK(uuu)
trnL(aag)
trnL(caa)
trnL(cag)
trnL(cua)
trnM(cau)
trnM(cau)
trnN(guu)
trnP(ugg)
trnQ(uug)
trnR(acg)
trnR(ccu)
trnR(ucu)
trnS(gcu)
trnS(gga)
trnV(uac)
trnW(cca)
trnY(gua)