The group I intron of apocytochrome b gene from Chlamydomonas smithii encodes a site-specific endonuclease

Ma, Ding; King, Yueh-Tsu; Young, Kim Nam; Luckett, William

doi:10.1007/bf00019218

Cited by 17 publications

(9 citation statements)

References 24 publications

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“…Nucleotide substitution rates (6 standard errors) between C. reinhardtii and C. incerta mitochondrial protein-coding genes The presence of the group I intron encoding the LAGLIDADG motif in the cob gene of both C. incerta (this study) and an interfertile relative of C. reinhardtii, namely, Chlamydomonas smithii (Colleaux et al 1990;Ma et al 1992), suggests that the last ancestor of the three taxa harbored such an intron and that C. reinhardtii cob lost the intron. The presence in C. incerta mtDNA of a truncated rrnL3a sequence may not be surprising as no rrnL3a homolog has been identified in the mtDNA of other more distantly related chlorophyceans (DenovanWright and Lee 1994;Fan et al 2003).…”

Section: Tablementioning

confidence: 70%

Mitochondrial Genome Sequence Evolution in Chlamydomonas

Popescu

Lee

2007

Genetics

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The mitochondrial genomes of the Chlorophyta exhibit significant diversity with respect to gene content and genome compactness; however, quantitative data on the rates of nucleotide substitution in mitochondrial DNA, which might help explain the origin of this diversity, are lacking. To gain insight into the evolutionary forces responsible for mitochondrial genome diversification, we sequenced to near completion the mitochondrial genome of the chlorophyte Chlamydomonas incerta, estimated the evolutionary divergence between Chlamydomonas reinhardtii and C. incerta mitochondrial protein-coding genes and rRNA-coding regions, and compared the relative evolutionary rates in mitochondrial and nuclear genes. Synonymous and nonsynonymous substitution rates do not differ significantly between the mitochondrial and nuclear protein-coding genes. The mitochondrial rRNA-coding regions, however, are evolving much faster than their nuclear counterparts, and this difference might be explained by relaxed functional constraints on the mitochondrial translational apparatus due to the small number of proteins synthesized in Chlamydomonas mitochondria. Substitution rates at synonymous sites in a nonstandard mitochondrial gene (rtl) and at intronic and synonymous sites in nuclear genes expressed at low levels suggest that the mutation rate is similar in these two genetic compartments. Potential evolutionary forces shaping mitochondrial genome evolution in Chlamydomonas are discussed.

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Section: Tablementioning

confidence: 70%

Mitochondrial Genome Sequence Evolution in Chlamydomonas

Popescu

Lee

2007

Genetics

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“…Some group I introns behave as mobile elements, as first described for the optional omega intron (Sc LSU 1) of Saccharomyces cerevisiae (9). Additional mobile group I introns have been found in yeast mitochondria (32,45,53), bacteriophage (42), Chlamydomonas chloroplasts (11,23), Chlamydomonas mitochondria (8,26), and nuclear rDNA of slime molds (16,36). In each of these cases, the mobile intron is copied into an intron-allele of the gene in which it resides, converting it to intron+ by gene conversion initiated at a double-strand break near the site of insertion.…”

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confidence: 82%

“…This process, known as intron homing (10), is mediated by an endonuclease encoded within the intron, which recognizes and cleaves the intron-DNA within a few nucleotides of the insertion site (for reviews, see references 22 and 33). In three cases, the procaryotic enzymes I-TevI, I-TevII, and I-TevIII, the DNA cut is somewhat more removed, 13 to 26 bp from the point of intron insertion (for a review, see reference 33). In any case, the homology between the intron-allele and the DNA sequences flanking the intron in the intron+ allele allows the break to be repaired via a gene conversion event which uses the intron+ allele as a template.…”

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confidence: 99%

Interaction of the intron-encoded mobility endonuclease I-PpoI with its target site.

Ellison¹,

Vogt²

1993

Mol. Cell. Biol.

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Endonucleases encoded by mobile group I introns are highly specific DNases that induce a double-strand break near the site to which the intron moves. I-PpoI from the acellular slime mold Physarum polycephalum mediates the mobility of intron 3 (Pp LSU 3) in the extrachromosomal nuclear ribosomal DNA of this organism. We showed previously that cleavage by I-PpoI creates a four-base staggered cut near the point of intron insertion. We have now characterized several further properties of the endonuclease. As determined by deletion analysis, the minimal target site recognized by I-PpoI was a sequence of 13 to 15 bp spanning the cleavage site. The purified protein behaved as a globular dimer in sedimentation and gel filtration. In gel mobility shift assays in the presence of EDTA, I-PpoI formed a stable and specific complex with DNA, dissociating with a half-life of 45 min. By footprinting and interference assays with methidiumpropyl-EDTAiron(II), I-PpoI contacted a 22-to 24-bp stretch of DNA. The endonuclease protected most of the purines found in both the major and minor grooves of the DNA helix from modification by dimethyl sulfate (DMS). However, the reactivity to DMS was enhanced at some purines, suggesting that binding leads to a conformational change in the DNA. The pattern of DMS protection differed fundamentally in the two partially symmetrical halves of the recognition sequence.More than 100 group I introns, which are defined by a common RNA secondary structure and mechanism of splicing, have been identified in the organellar genomes of lower eucaryotes (for reviews, see references 4 and 29). Several of these introns also have been found in bacteria, bacteriophage, and extrachromosomal nuclear ribosomal DNA (rDNA). The RNAs of many group I introns are capable of self-splicing in vitro. Some group I introns behave as mobile elements, as first described for the optional omega intron (Sc LSU 1) of Saccharomyces cerevisiae (9). Additional mobile group I introns have been found in yeast mitochondria (32,45,53), bacteriophage (42), Chlamydomonas chloroplasts (11,23), Chlamydomonas mitochondria (8, 26), and nuclear rDNA of slime molds (16,36). In each of these cases, the mobile intron is copied into an intron-allele of the gene in which it resides, converting it to intron+ by gene conversion initiated at a double-strand break near the site of insertion. This process, known as intron homing (10), is mediated by an endonuclease encoded within the intron, which recognizes and cleaves the intron-DNA within a few nucleotides of the insertion site (for reviews, see references 22 and 33). In three cases, the procaryotic enzymes I-TevI, I-TevII, and I-TevIII, the DNA cut is somewhat more removed, 13 to 26 bp from the point of intron insertion (for a review, see reference 33). In any case, the homology between the intron-allele and the DNA sequences flanking the intron in the intron+ allele allows the break to be repaired via a gene conversion event which uses the intron+ allele as a template. Since intron insertion render...

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“…This Chlamydomonas sp intron shares with its Nephroselmis homolog a similar secondary structure (Colleaux et al, 1990) as well as an ORF encoding a specific DNA endonuclease (Ma et al, 1992).…”

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confidence: 99%

The Complete Mitochondrial DNA Sequences of Nephroselmis olivacea and Pedinomonas minor: Two Radically Different Evolutionary Patterns within Green Algae

et al. 1999

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Green plants appear to comprise two sister lineages, Chlorophyta (classes Chlorophyceae, Ulvophyceae, Trebouxiophyceae, and Prasinophyceae) and Streptophyta (Charophyceae and Embryophyta, or land plants). To gain insight into the nature of the ancestral green plant mitochondrial genome, we have sequenced the mitochondrial DNAs (mtDNAs) of Nephroselmis olivacea and Pedinomonas minor . These two green algae are presumptive members of the Prasinophyceae. This class is thought to include descendants of the earliest diverging green algae. We find that Nephroselmis and Pedinomonas mtDNAs differ markedly in size, gene content, and gene organization. Of the green algal mtDNAs sequenced so far, that of Nephroselmis (45,223 bp) is the most ancestral (minimally diverged) and occupies the phylogenetically most basal position within the Chlorophyta. Its repertoire of 69 genes closely resembles that in the mtDNA of Prototheca wickerhamii , a later diverging trebouxiophycean green alga. Three of the Nephroselmis genes ( nad10 , rpl14 , and rnpB ) have not been identified in previously sequenced mtDNAs of green algae and land plants. In contrast, the 25,137-bp Pedinomonas mtDNA contains only 22 genes and retains few recognizably ancestral features. In several respects, including gene content and rate of sequence divergence, Pedinomonas mtDNA resembles the reduced mtDNAs of chlamydomonad algae, with which it is robustly affiliated in phylogenetic analyses. Our results confirm the existence of two radically different patterns of mitochondrial genome evolution within the green algae. INTRODUCTIONOf the three main kingdoms of evolutionarily advanced eukaryotes (animals, fungi, and land plants), plants have the most clearly defined antecedents. Combined molecular, biochemical, and ultrastructural data demonstrate that the unicellular progenitors of land plants lie within the green algae, which together with land plants form a monophyletic lineage that is characterized by the presence of chloroplasts surrounded by two membranes and containing stacked thylakoids and chlorophylls a and b (Bhattacharya and Medlin, 1998;Chapman et al., 1998). The evolutionary coherence of land plants and green algae is apparent at the levels of both the nuclear and chloroplast genomes; however, at the level of the mitochondrial genome, this affiliation breaks down (see below; Gray et al., 1989).Phycologists generally recognize five classes of green algae: the Charophyceae, which include the closest relatives of land plants; the Chlorophyceae; the Trebouxiophyceae; the Ulvophyceae; and a nonmonophyletic group known as the Prasinophyceae (reviewed in Friedl, 1997;Bhattacharya and Medlin, 1998;Chapman et al., 1998). The latter class is extremely diverse and is thought to include descendants of the earliest diverging green algae (Melkonian, 1990a). Comparison of nuclear small subunit (SSU) rRNA gene sequences suggests that extant green eukaryotes ("green plants") divide into two major evolutionary lineages: the Streptophyta, containing the charophytes, land ...

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The group I intron of apocytochrome b gene from Chlamydomonas smithii encodes a site-specific endonuclease

Cited by 17 publications

References 24 publications

Mitochondrial Genome Sequence Evolution in Chlamydomonas

Mitochondrial Genome Sequence Evolution in Chlamydomonas

Interaction of the intron-encoded mobility endonuclease I-PpoI with its target site.

The Complete Mitochondrial DNA Sequences of Nephroselmis olivacea and Pedinomonas minor: Two Radically Different Evolutionary Patterns within Green Algae

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