Complete Sequence of the Mitochondrial DNA of the Chlorophyte Alga Prototheca wickerhamii: Gene Content and Genome Organization

• Published in: Journal of molecular biology Vol. 237; no. 1; pp. 75 - 86
• Main Authors: Wolff, Gabriele, Plante, Isabelle, Lang, B.Franz, Kück, Ulrich, Burger, Gertraud
• Format: Journal Article
• Language: English
• Published: Oxford Elsevier Ltd 18.03.1994; Elsevier
• Subjects: algae and seaweeds; Amino Acid Sequence; Base Sequence; Biological and medical sciences; chromosome mapping; complete mtDNA sequence; DNA, Mitochondrial - chemistry; Freshwater; Fundamental and applied biological sciences. Psychology; genbank/u02970; gene expression; Genes. Genome; Genetic Code; genetic map; Genome; green alga; Introns; mitochondrial DNA; Molecular and cellular biology; Molecular genetics; Molecular Sequence Data; Nucleic Acid Conformation; nucleotide sequences; Open Reading Frames; protist; Prototheca - genetics; Prototheca wickerhamii; repeated elements; repetitive sequences; RNA, Ribosomal - genetics; RNA, Transfer - genetics; structural genes; transcription (genetics); Transcription, Genetic; complete mtDNA sequence; repeated elements; genetic map; green alga; protist; Genetic mapping; Genome organization; Nucleotide sequence; Ribosomal RNA; Algae; Mitochondrial DNA; Secondary structure; Thallophyta; Structural analysis; Prototheca wickerhamii
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1006/jmbi.1994.1210

The complete nucleotide sequence of the circular mitochondrial (mt) DNA of the chlorophyte alga Prototheca wickerhamii has been determined (55,328 base-pairs, A+T content 74·2%). The genes identified encode three subunits of the cytochome oxidase, apocytochrome b, nine subunits of the NADH dehydrogenase complex ( nad1 to 7, nad4L and nad9), three ATPase subunits ( atp6, atp9, atp1 (also referred to as atpA )), three ribosomal RNAs (5 S ( rrn5), small subunit ( srn) and large subunit ( lrn) RNA), 26 tRNAs, and 13 ribosome proteins. A total of five group I introns reside in lrn and cox1, two of which include intronic open reading frames (ORFs). Five free-standing ORFs longer than 60 codons are present. Three of these ORFs are counterparts to genes encoding proteins of unknown function in plant mitochondria ( orf25 and orfB of angiosperms and orf244 of liverwort), whereas two of them are unique. Mitochondrial genes are encoded on both DNA strands in a way that suggest the existence of two transcription units, each including approximately one half of the mitochondrial genome. The two intergenic regions in which transcription is believed to initiate and terminate are about ten times longer than other intergenic regions (1118 and 1993 nt versus 100 to 150 nt). A total of 29 recurring sequence motifs (30 to 200 nt long) have been found in intergenic regions. Nine different types of motifs are present, most of them arranged as tandem repeats. These motifs may be implicated in transcription, e.g. as signals for initiation and/or processing. Phylogenetic analysis on the basis of the cox1 gene strongly suggested that P. wickerhamii and plant mitochondrial genomes are monophyletic. The finding of plant-specific mitochondrial genes such as orf25, orf244, orfB and rrn5 in P. wickerhamii mitochondria corroborates this idea.