TGA cysteine codons and intron sequences in conserved and nonconserved positions are found in macronuclear RNA polymerase genes of<i>Euplotes octocarinatus</i>

Kaufmann, Jörg; Florian, Volker; Klein, Albrecht

doi:10.1093/nar/20.22.5985

Cited by 11 publications

(4 citation statements)

References 31 publications

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“…We decided to investigate cysteine transport and metabolism because cysteine plays and important role in G. lamblia biology. We found that L-cysteine is an essential growth factor, as shown previously [ 1, [12][13][14]201, because this protozoan lacks the capacity to synthesize cysteine from sulfate or from methionine. Also, we show that uptake of L-cysteine by the parasite occurs principally by a non-saturable process.…”

supporting

confidence: 83%

“…Cystine, diffusion, methionine, sulfate, sulfur, transport. Previous studies demonstrated that various reducing agents are important for attachment and survival of Giardia trophozoites in a maintenance medium [12][13][14]. However, growth and long-term survival are totally dependent on the addition of exogenous L-cysteine to a complex medium [ 13, 201. Giardia has a unique requirement for cysteine.…”

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confidence: 99%

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The α‐ and β‐Tubulin Genes of Euplotes octocarinatus

Liang¹,

Schmidt²,

Heckmann³

1994

J Eukaryotic Microbiology

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The alpha- and the beta-tubulin genes of the hypotrichous ciliate Euplotes octocarinatus were isolated from a size-selected macronuclear DNA library. The alpha-tubulin gene is located on a 1,587 bp macronuclear DNA molecule and the beta-tubulin gene on a 1,524 bp macronuclear DNA molecule. Sequencing revealed that all the cysteine residues of the two genes are encoded by the common cysteine codons UGU and UGC and none by an UGA codon. This is in contrast to the genes of E. octocarinatus sequenced so far, where some of the cysteines are encoded by the opal codon UGA. The tubulin genes end like other Euplotes genes with a TAA. They do not contain introns. The last codon for an amino acid in the alpha-tubulin gene is a GAA which codes for glutamic acid. This is in contrast to what has been reported for most alpha-tubulin genes, but it supports for other hypotrichous ciliates. No evidence for the existence of more than one type of alpha- and one type of beta-tubulin genes could be obtained.

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confidence: 83%

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confidence: 99%

The α‐ and β‐Tubulin Genes of Euplotes octocarinatus

Liang¹,

Schmidt²,

Heckmann³

1994

J Eukaryotic Microbiology

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“….AG-3Ј) and are assumed to be recognized by a Paramecium spliceosome. Other organisms, including hypotrich ciliates (35,40,59), have some small introns, but they also have larger introns. The only exceptions are the nucleomorph genomes of chromophyte and chlorarachnean algae, organisms which originally gained photosynthetic functions by engulfing eukaryotic red and green algae in a process known as secondary endosymbiosis (18).…”

Section: Resultsmentioning

confidence: 99%

Random Sequencing of Paramecium Somatic DNA

et al. 2002

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We report a random survey of 1 to 2% of the somatic genome of the free-living ciliate Paramecium tetraurelia by single-run sequencing of the ends of plasmid inserts. As in all ciliates, the germ line genome of Paramecium (100 to 200 Mb) is reproducibly rearranged at each sexual cycle to produce a somatic genome of expressed or potentially expressed genes, stripped of repeated sequences, transposons, and AT-rich unique sequence elements limited to the germ line. We found the somatic genome to be compact (>68% coding, estimated from the sequence of several complete library inserts) and to feature uniformly small introns (18 to 35 nucleotides). This facilitated gene discovery: 722 open reading frames (ORFs) were identified by similarity with known proteins, and 119 novel ORFs were tentatively identified by internal comparison of the data set. We determined the phylogenetic position of Paramecium with respect to eukaryotes whose genomes have been sequenced by the distance matrix neighbor-joining method by using random combined protein data from the project. The unrooted tree obtained is very robust and in excellent agreement with accepted topology, providing strong support for the quality and consistency of the data set. Our study demonstrates that a random survey of the somatic genome of Paramecium is a good strategy for gene discovery in this organism.Alongside an ever-growing number of prokaryotic genomes, several fungal, invertebrate, plant, and vertebrate genomes have now been largely or completely sequenced and released to the public, providing a wealth of information for functional and comparative studies. Given the variety of unicellular eukaryotes and the great evolutionary distances even within protist phyla, it is striking that few protists have been subjected to systematic genomic investigation. Notable exceptions are the cellular slime mold Dictyostelium discoidium and a few parasites of great medical importance such as Plasmodium spp. Ciliates are one of the major eukaryotic groups for which no large-scale genome project has been undertaken.Ciliate models (Paramecium, Tetrahymena) have allowed major discoveries in biology such as variant nuclear genetic codes (13, 49), ribozymes (38), telomerase (33), and histone acetyltransferase as a transcription factor (10) and present fascinating epigenetic phenomena acting at DNA (14, 21, 42), RNA (51), and protein (6) levels. Unique among unicellular eukaryotes, ciliates separate germinal and somatic lines, in the form of nuclei (50). Somatic development involves programmed rearrangements of the entire germ line genome at each sexual generation, so that ciliates provide excellent experimental models for studying somatic DNA rearrangements similar to those that generate antibody diversity and malignant states in vertebrates.The germ line micronucleus is diploid, is transcriptionally silent during vegetative growth, and intervenes during sexual processes. The somatic macronucleus is highly polyploid and responsible for transcriptional activity but is not transmitt...

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“…Codon usage in some ciliates like Paramecium, Tetrahymena, Stylonychia, and Oxytricha, differs from the universal genetic code by translating either U A A or U A G as glutamine and by the use of U G A as the sole termination codon (Caron and Meyer, 1985;Helftenbein, 1985;Kuchino et al, 1985;Preer et al, 1985;Hanyu et al, 1986). In other ciliates, like Euplotes, U G A is translated as cysteine, and U A A functions as termination codon (Cohen et al, 1990;Kaufmann et al, 1992). Our analysis of the cDNA encoding P. dubius p60 shows no direct evidence that an unusual genetic code is used.…”

Section: Resultsmentioning

confidence: 99%

Major epiplasmic proteins of ciliates are articulins: cloning, recombinant expression, and structural characterization.

Huttenlauch

Geisler

Plessmann

et al. 1995

The Journal of Cell Biology

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Abstract. The cytoskeleton of certain protists comprises an extensive membrane skeleton, the epiplasm, which contributes to the cell shape and patterning of the species-specific cortical architecture. The isolated epiplasm of the ciliated protist Pseudomicrothorax dubius consists of two major groups of proteins with molecular masses of 78-80 kD and 11-13 kD, respectively. To characterize the structure of these proteins, peptide sequences of two major polypeptides (78-80 kD) as well as a cDNA representing the entire coding sequence of a minor and hitherto unidentified component (60 kD; p60) of the epiplasm have been determined. All three polypeptides share sequence similarities. They contain repeated valine-and proline-rich motifs of 12 residues with the consensus VPVP--V-V-V-. In p60 the central core domain consists of 24 tandemly repeated VPV motifs. Within the repeat motifs positively and negatively charged residues, when present, show an alternating pattern in register with the V and P positions. Recombinant p60 was purified in 8 M urea and dialyzed against buffer. Infrared spectroscopic measurements indicate 30% B-sheet. Electron microscopy reveals short filamentous polymers with a rather homogenous diameter (~15-20 nm), but variable lengths. The small polymers form thicker filaments, ribbons, and larger sheets or tubes. A core domain similar to that of P. dubius p60 is also found in the recently described epiplasmic proteins of the flagellate Euglena, the so-called articulins.Our results show that the members of this protein family are not restricted to flagellates, but are also present in the distantly related ciliates where they are major constituents of the epiplasm. Comparison of flagellate and ciliate articulins highlights common features of this novel family of cytoskeletal proteins.T HE membrane skeleton of eukaryotic cells is part of the cytoskeleton. It is involved in the organization and maintenance of cell shape and functions in the generation and stabilization of specialized membrane domains. This submembraneous organization is usually dictated by micro filamentous structures containing actin and a variety of actin-binding proteins. Particularly well-analyzed examples are, for instance, the membrane skeletons of vertebrate red blood cells (for review see Bennett, 1990) and the intestinal brush border cells of various vertebrates (for review see Louvard, 1989). An actin-based subplasma membrane organization occurs not only in metazoan cells, but is also typical for some protists such as Dictyostelium and Physarum (for reviews see Schleicher and Noegel, 1992;Stockem and Brix, 1994).In contrast, other protists possess a unique cortical cytoplasm: the epiplasm. The epiplasm is always in close conAddress all correspondence to Irm Huttenlauch,

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TGA cysteine codons and intron sequences in conserved and nonconserved positions are found in macronuclear RNA polymerase genes ofEuplotes octocarinatus

Cited by 11 publications

References 31 publications

The α‐ and β‐Tubulin Genes of Euplotes octocarinatus

The α‐ and β‐Tubulin Genes of Euplotes octocarinatus

Random Sequencing of Paramecium Somatic DNA

Major epiplasmic proteins of ciliates are articulins: cloning, recombinant expression, and structural characterization.

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