Variation and Evolution in Plants and Microorganisms Toward a New Synthesis 50 Years After Stebbins (2000) / Chapter Skim
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8 Evolution of RNA Editing in Trypanosome Mitochondria
8 Evolution of RNA Editing in Trypanosome Mitochondria
Pages 117-142
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From page 117... ...
The first involves the precise insertion and deletion of U residues mostly within the coding regions of maxicircle-encoded mRNAs to produce open reading frames. This editing is mediated by short overlapping complementary guide RNAs encoded in both the maxicircle and the minicircle molecules and involves a series of enzymatic cleavage-ligation steps.
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From page 118... ...
The driving force for the evolutionary fixation of these retroposition events was postulated to be the stochastic loss of entire minicircle sequence classes and their encoded guide RNAs upon segregation of the single kinetoplast DNA network into daughter cells at cell division. A large plasticity in the relative abundance of minicircle sequence classes has been observed during cell culture in the laboratory.
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From page 119... ...
Phylogenetic tree of Kinetoplastida based on SSU rRNA sequences. Only representative species for each trypanosomatid lineage are shown.
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From page 120... ...
It is of some interest that the UGA stop codon is used to encode tryptophan in the mitochondrial genome of all kinetoplastid species including Diplonema, but not in the Euglenoids (Yasuhira and Simpson, 1997~. KINETOPLASTIDS CONTAIN A SINGLE EXTENDED TUBULAR MITOCHONDRION WITH AN UNUSUAL MITOCHONDRIAL DNA The trypanosomatids contain a single tubular mitochondrion (Paulin, 1975; Simpson and Kretzer, 1997)
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From page 121... ...
This division of the mitochondrial genome into two physically separate genomes, with the RNA transcripts of one interacting with the incomplete mRNA transcripts of the other to produce translatable mRNAs is unprecedented and is suggestive of an unique evolutionary origin. The mechanism of U-insertion/deletion editing involves a series of enzymatic cleavage-ligation steps, with the precise cleavages determined by base pairing with the cognate gRNAs (Alfonzo et al., 1997~.
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From page 123... ...
and gB4 (=gND3-IX) , represent nonessential gRNAs for these nonfunctional editing cascades.
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From page 124... ...
serpens (D.A.M., unpublished results) implies that the corresponding minicircle-encoded gRNAs also exist in these species, and this provides phylogenetic evidence for our hypothesis that the ancestral cell had a complete complement of minicircle classes.
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From page 125... ...
We proposed that partially edited mRNAs were being frequently converted to cDNAs by a postulated mitochondrial reverse transcriptase activity, and those cells that had replaced the original pan-edited cryptogene with a partially edited gene would survive a loss of an entire minicircle sequence class encoding a specific gRNA involved in that editing cascade. The retention of editing at the 5' end of a domain may allow regulation of translation by creation of a methionine initiation codon and a possible ribosome-binding site.
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From page 126... ...
. Quantitation of the copy numbers of 17 specific minicircle sequence classes in the UC strain was previously performed by Southern blot analysis using specific oligonucleotide probes for specific gRNAs.
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From page 127... ...
As was found previously (Maslov and Simpson, 1992) , there was no correlation of minicircle copy number and gRNA relative abundance (data not shown)
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From page 128... ...
The actual number of copies is randomly chosen according to a binomial distribution that models a purely random segregation process. All daughter cells that receive the full complement of minicircle classes and have fewer than 12,000 minicircles in total are randomly chosen to populate the next generation up to a maximum population size.
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From page 129... ...
The average frequencies of 17 minicircle classes undergoing random segregation over 2,000 generations. Random segregation causes fluctuations in the frequencies, giving rise to the experimentally observed distribution of many classes having low frequency and few classes having high frequency.
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From page 130... ...
However, as unnecessary classes are lost because of random segregation over time, there are fewer classes that can make up this difference. Finally, there will be only one unnecessary class left to make up at least 70% of the minicircles in the kinetoplast.
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From page 131... ...
Hence some fraction of the total population of daughter cells is viable; we term this the daughter cell viability. We find that cell viability increases with increasing kinetoplast size and decreasing number of minicircle sequence classes (Fig.
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From page 132... ...
In the case of T brucei, random segregation of the 250+ sequence classes would lead to a predicted cell viability in this model of less than 0.5, and hence population extinction.
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From page 133... ...
However, the appearance of a new gene for a tRNA decoding UGA for tryptophan did not occur in these species, perhaps because of the early loss of all mitochondrial-encoded tRNA genes. C to U Editing of tRNATrP Alfonzo et al.
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From page 134... ...
and Cavalier-Smith (1997) , which involved the pre-existence of editing enzymatic activities that were used for other biochemical functions, genetic drift in a mitochondrial gene, appearance of complementary gRNAs by partial gene duplication and antisense transcription, and finally utilization of editing for gene regulation.
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From page 135... ...
If one accepts this proposal, then the observed guiding of U-insertions to produce UGA tryptophan codons suggests that this codon reassignment also occurred before the appearance of U-insertion editing. It should be noted that the presence of guiding G residues in the gRNAs that base pair with inserted Us presents a potential problem for the gene duplication scenario for the origin of gRNAs.
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From page 136... ...
borreli or a catenation of the plasmids into a network such as in the trypanosomatids. The fact that daughter cells must receive a complete complement of all of the minicircle sequence classes encoding the gRNAs required for editing has led to the evolution of mechanisms for the random distribution of minicircles within the single network.
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From page 137... ...
evansi, which have lost the sexual cycle in the fly and are transmitted by sexual intercourse and by mechanism transmission by tabanid flies, respectively, have networks consisting of one of several single minicircle sequence classes and mutated or deleted maxicircle DNA (Frasch et al., 1980; Barrois et al., 1982; Borst et al., 1987; Songa et al., 1990; Lun et al., 1992; Shu and Stuart, 1994~. Another derived feature of the kinetoplastid mitochondrial genome is the complete lack of tRNA genes and the importation of all mitochondrial tRNAs from the cytosol (Simpson et al., 1989~.
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From page 138... ...
(1993~. Trypanosoma brucei minicircles encode multiple guide RNAs which can direct editing of extensively overlapping sequences.
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From page 139... ...
(1992~. Kinetoplast DNA and molecular karyotypes of Trypanosoma evansi and Trypanosoma equiperdum from China.
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From page 140... ...
(1974~. Replication of the kinetoplast DNA of Leishmania tarentolae and Crithidia fasciculata.
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From page 141... ...
. Kinetoplast DNA minicircles encode guide RNAs for editing of cytochrome oxidase subunit III mRNA.
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