The DNA of ciliated protozoa.

Prescott, David M.

doi:10.1128/mmbr.58.2.233-267.1994

Cited by 455 publications

(358 citation statements)

References 212 publications

(301 reference statements)

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“…This has led Ninio (1986) to speculate that a deviant code was favored in ciliates because it constitutes a mechanism preventing the expression of foreign DNA. Similarly, Prescott (1994) has noted that all ciliates studied to date are devoid of virus although bacterial symbionts are very common. These ideas may, however, be over simplifications since many ciliates contain transposable elements, at least some of which appear to be ancient.…”

Section: Discussionmentioning

confidence: 91%

“…In this case, we expect to find a correlation between an increase in AT pressure and an increase in the use of UAA termination codons as sense codons. In hypotrichs, in which deviant codons are not frequently used, it seems that macronuclear non-coding DNA is not as A + T rich as in Paramecium and Tetrahymena (Prescott, 1994). The following arguments do not support a strong AT driving force.…”

Section: Discussionmentioning

confidence: 91%

“…The apparently non-deviated code of Blepharisma would thus correspond to the ancestral state of the genetic code in the phylum as suggested by Liang and Heckmann (1993). However, an early origin of the deviant code followed by reversion in the Blepharisma and Euplotes lineages has also been proposed (Prescott, 1994). This alternative may be resolved by extending the codon usage data base to species belonging to all the major groups of the ciliates, including representatives from the most ancient ones.…”

Section: Introductionmentioning

confidence: 98%

“…A remarkable feature of the ciliates is their genetic code which is one of the few deviating from the universal code. In several species (Paramecium, Tetrahymena, Stylonychia and Oxytricha), the universal termination codons UAA and UAG are translated into glutamine and UGA is the only termination codon (see Caron, 1990;Prescott, 1994 and references therein). Evidence was obtained that this deviant code is derived and not the relic of a primordial genetic code.…”

Section: Introductionmentioning

confidence: 99%

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Genetic code deviations in the ciliates: evidence for multiple and independent events.

et al. 1995

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In several species of ciliates, the universal stop codons UAA and UAG are translated into glutamine, while in the euplotids, the glutamine codon usage is normal, but UGA appears to be translated as cysteine. Because the emerging position of this monophyletic group in the eukaryotic lineage is relatively late, this deviant genetic code represents a derived state of the universal code. The question is therefore raised as to how these changes arose within the evolutionary pathways of the phylum. Here, we have investigated the presence of stop codons in alpha tubulin and/or phosphoglycerate kinase gene coding sequences from diverse species of ciliates scattered over the phylogenetic tree constructed from 28S rRNA sequences. In our data set, when deviations occur they correspond to in frame UAA and UAG coding for glutamine. By combining these new data with those previously reported, we show that (i) utilization of UAA and UAG codons occurs to different extents between, but also within, the different classes of ciliates and (ii) the resulting phylogenetic pattern of deviations from the universal code cannot be accounted for by a scenario involving a single transition to the unusual code. Thus, contrary to expectations, deviations from the universal genetic code have arisen independently several times within the phylum.

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Section: Discussionmentioning

confidence: 91%

Section: Discussionmentioning

confidence: 91%

Section: Introductionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

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Genetic code deviations in the ciliates: evidence for multiple and independent events.

et al. 1995

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“…The glutamine-encoding TAA and TAG in Hexamita genes presumably arose from CAA and CAG codons. Other organisms (ciliates and Acetabularia) where TAR codes for glutamine are very AT rich (as high as 76%; Schneider et al, 1989;Prescott, 1994), and this has led to the suggestion (Osawa and Jukes, 1989;Osawa et al, 1992) that the AT mutation pressure which biased the overall composition of these genomes has also driven the conversion of many CAR codons to TAR once the original chain-terminating TARs had been fortuitously reduced in number to the point where release factors recognizing them could be lost. However, the genome of Hexamita appears to be GC rich: the overall and third position GC content of these genes from Hexamita 50330 are 53 and 63%, respectively, and from H.inflata are 52 and 64%, respectively.…”

Section: Discussionmentioning

confidence: 99%

A non-canonical genetic code in an early diverging eukaryotic lineage.

Keeling

Doolittle

1996

The EMBO Journal

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The nearly invariant nature of the ‘Universal Genetic Code’ attests to its early establishment in evolution and to the difficulty of altering it now, since so many molecules are required for, and depend upon, faithful translation. Nevertheless, variations on the universal code are known in a handful of genomes. We have found one such variant in diplomonads, an early‐diverging eukaryotic lineage. Genes for alpha‐tubulin, beta‐tubulin and elongation factor 1 alpha (EF‐1alpha) from two unclassified strains of Hexamitidae were found to contain TAA and TAG (TAR) triplets at positions suggesting a variant code in which TAR codes for glutamine. We found confirmation of this hypothesis by identifying genes encoding glutamine‐tRNAs with CUA and UUA anticodons. The alpha‐tubulin and EF‐1alpha genes from two other diplomonads, Spironucleus muris and Hexamita inflata, were also sequenced and shown to contain no such non‐canonical codons. However, tRNA genes with the anticodons UUA and CUA were found in H.inflata, suggesting that this diplomonad also uses these codons, albeit infrequently. The high GC content of these genomes and the presence of two isoaccepting tRNAs compound the difficulty of understanding how this variant code arose by strictly neutral means.

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Two two-gene macronuclear chromosomes of the hypotrichous ciliatesOxytricha fallax andO. trifallax generated by alternative processing of the 81 locus

1997

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We describe the first known macronuclear chromosomes that carry more than one gene in hypotrichous ciliated protozoa. These 4.9‐ and 2.8‐kbp chromosomes each consist almost exclusively of two protein‐coding genes, which are conserved and transcribed. The two chromosomes share a common region that consists of a gene that is a member of the family of mitochondrial solute carrier genes (CR‐MSC; [Williams and Herrick (1991): Nucleic Acids Res 19:4717–4724]. Each chromosome also carries another gene appended to its common region: The 4.9‐kbp chromosome also carries a gene that encodes a protein that is rich in glutamine and charged amino acids and bears regions of heptad repeats characteristic of coiled‐coils. Its function is unknown. The second gene of the 2.8 kbp chromosome is a mitochondrial solute carrier gene (LA‐MSC); thus, the 2.8‐kbp chromosome consists of two mitochondrial solute carrier paralogs. Phylogenetic analysis indicates that the two genes were duplicated before ciliates diverged from the main eukaryotic lineage and were subsequently juxtaposed. The CR‐ and LA‐MSC genes are each interrupted by three introns. The introns are not in homologous positions, suggesting that they may have originated from multiple group II intron transpositions. These chromosomes and their genes are encoded in the Oxytricha germline by the 81 locus. This locus is alternatively processed to generate a nested set of three macronuclear chromosomes, the 4.9‐ and 2.8‐kbp chromosomes and a third (1.6 kbp) which consists almost exclusively of the shared common gene, CR‐MSC. Such alternative processing is common in macronuclear development of O. fallax [Cartinhour and Herrick (1984): Mol Cell Biol 4:931–938]. Possible functions for alternative processing are considered; e.g., it may serve to physically link genes to allow co‐regulation or co‐replication by a common cis‐acting sequence. Dev. Genet. 20:348–357, 1997. © 1997 Wiley‐Liss, Inc.

show abstract

The DNA of ciliated protozoa.

Cited by 455 publications

References 212 publications

Genetic code deviations in the ciliates: evidence for multiple and independent events.

Genetic code deviations in the ciliates: evidence for multiple and independent events.

A non-canonical genetic code in an early diverging eukaryotic lineage.

Two two-gene macronuclear chromosomes of the hypotrichous ciliatesOxytricha fallax andO. trifallax generated by alternative processing of the 81 locus

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