<i>KIN241:</i> a gene involved in cell morphogenesis in <i>Paramecium tetraurelia</i> reveals a novel protein family of cyclophilin–RNA interacting proteins (CRIPs) conserved from fission yeast to man

Krzywicka, Anna; Beisson, Janine; Keller, Anne‐Marie; Cohen, Jean; Jerka‐Dziadosz, Maria; Klotz, Catherine

doi:10.1046/j.1365-2958.2001.02634.x

Cited by 39 publications

(23 citation statements)

References 47 publications

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“…db/index). For both kin241 and dhfr-ts, this search returned single hits, consistent with the hypothesis that these genes are present in single copies in the P. tetraurelia genome, in accordance with previous observations (Schlichtherle et al 1996;Krzywicka et al 2001). However, a BLAT search with strain-51 Phe tRNA synthetase identified 2 paralogs in the P. tetraurelia genome-one on Scaffold 2 and the other on Scaffold 129 as annotated by Genoscope.…”

Section: Resultssupporting

confidence: 90%

Large Global Effective Population Sizes in Paramecium

Snoke

Berendonk

Barth

et al. 2006

Molecular Biology and Evolution

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The genetic effective population size (N e ) of a species is an important parameter for understanding evolutionary dynamics because it mediates the relative effects of selection. However, because most N e estimates for unicellular organisms are derived either from taxa with poorly understood species boundaries or from host-restricted pathogens and most unicellular species have prominent phases of clonal propagation potentially subject to strong selective sweeps, the hypothesis that N e is elevated in single-celled organisms remains controversial. Drawing from observations on well-defined species within the genus Paramecium, we report exceptionally high levels of silent-site polymorphism, which appear to be a reflection of large N e .

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Section: Resultssupporting

confidence: 90%

Large Global Effective Population Sizes in Paramecium

Snoke

Berendonk

Barth

et al. 2006

Molecular Biology and Evolution

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“…ESS1 is also not essential in S. pombe (18) and Cryptococcus neoformans, but it is in some other fungi, e.g., Candida albicans and Aspergillus nidulans. Similarly, Rct1 is essential in S. pombe, but its homolog in P. tetraurelia, Kin241, is not (22). It is not clear why deletion of a particular PPIase is lethal in some organisms and not in others.…”

Section: Discussionmentioning

confidence: 99%

“…However, several multidomain cyclophilins from different organisms have been described as well (36,42). The most complex multidomain cyclophilins characterized thus far are Arabidopsis AtCyp59 (12) and its orthologue from Paramecium tetraurelia, Kin241p (22). They are characterized by a unique domain organization, consisting of a PPIase domain at the N terminus, followed by an RNA recognition motif (RRM) and a C-terminal domain enriched in charged amino acids and serines or RS/RD dipeptide repeats.…”

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confidence: 99%

“…They are characterized by a unique domain organization, consisting of a PPIase domain at the N terminus, followed by an RNA recognition motif (RRM) and a C-terminal domain enriched in charged amino acids and serines or RS/RD dipeptide repeats. Homologous proteins have been found in the majority of eukaryotes, although Saccharomyces cerevisiae and some other Saccharomycotina species do not encode this kind of protein (12,22). Kin241p was identified in Paramecium tetraurelia as a protein involved in cell morphogenesis (reference 22 and references therein).…”

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confidence: 99%

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Rct1, a Nuclear RNA Recognition Motif-Containing Cyclophilin, Regulates Phosphorylation of the RNA Polymerase II C-Terminal Domain

Gullerová

Barta

Lorković

2007

Molecular and Cellular Biology

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Phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (RNAP II) is a dynamic process that regulates transcription and coordinates it with pre-mRNA processing. We show here that Rct1, a nuclear multidomain cyclophilin from Schizosaccharomyces pombe, is encoded by an essential gene that interacts with the CTD and regulates its phosphorylation in vivo. Downregulation of Rct1 levels results in increased phosphorylation of the CTD at both Ser2 and Ser5 and in a commensurate decrease in RNAP II transcription. In contrast, overexpression of Rct1 decreases phosphorylation on both sites. The close association of Rct1 with transcriptionally active chromatin suggests a role in regulation of RNAP II transcriptional activity. These data, together with the pleiotropic phenotype upon Rct1 deregulation, suggest that this multidomain cyclophilin is an important player in maintaining the correct phosphorylation code of the CTD and thereby regulating CTD function.Eukaryotic RNA polymerase II (RNAP II), the enzyme responsible for transcription of protein-coding genes, is a multisubunit complex. For accurate transcription, RNAP II is controlled by many factors through protein-protein interactions. RNAP II transcripts undergo extensive processing, including capping, splicing, and polyadenylation, which are tightly coordinated with transcription. There is now strong evidence that RNAP II coordinates these processing reactions and couples them to transcription. Specifically, the C-terminal domain (CTD) of the largest RNAP II subunit has a critical role in targeting pre-mRNA processing factors to emerging pre-mRNAs. Thus, the CTD coordinates transcription with pre-mRNA processing and is therefore subject to tight regulation during the transcription cycle (1,17,35,37,39,41,46,53).In all eukaryotes, the CTD consists of variable numbers of YSPTSPS heptapeptide repeats. During the transcription cycle, the CTD undergoes dynamic phosphorylation and dephosphorylation on Ser2 and Ser5. Transcription initiation requires an unphosphorylated CTD. Following initiation, the CTD becomes phosphorylated at Ser5, a modification that is necessary to initiate transcript elongation. Finally, extensive phosphorylation at Ser2 is accompanied by transcript elongation and termination. In addition to regulating RNAP II transcription, the CTD phosphorylation status is also important for coordination of transcription with pre-mRNA processing, in particular for recruitment of RNA-processing factors to nascent transcripts. The CTD associates in a phosphorylation-dependent manner directly or indirectly with a variety of pre-mRNA-processing factors, including 5Ј capping enzymes, splicing factors, and some components of the 3Ј end-processing machinery cycle (1, 17, 35, 37-39, 41, 46, 53).Recently, cis-trans isomerization of prolyl peptide bonds in the heptapeptide repeats has been revealed as an additional level of regulation of CTD structure and function, as it has been shown that three CTD-interacting proteins bind to the CTD only in an all-trans prol...

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“…In this respect Paramecium is somewhat ahead of Tetrahymena, owing to the discovery for the former organism of a practical means of cloning by complementation genes previously identified only by classical genetic methods (65,92). One gene with a mutation known to have pleiotropic effects on cortical as well as nuclear organization, kin241 (80), has been cloned and found to encode a "cyclophilin-RNA interacting protein" (94); simultaneously, the small-19 gene, which controls cell size and the number of basal bodies (127), was found to encode a member of a new class of tubulin, eta-tubulin (126). Unfortunately, differences in the mechanisms of processing of macronuclear DNA (30) make the specific method of complementation cloning employed for Paramecium unfeasible for Tetrahymena, and the available methods of DNA-mediated transformation for Tetrahymena (167) have not been suitable or of sufficiently high efficiency to allow cloning by complementation yet.…”

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confidence: 99%

What Do Genic Mutations Tell Us about the Structural Patterning of a Complex Single-Celled Organism?

Frankel

2008

Eukaryot Cell

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PROLOGUE: FROM THE CYTOPLASM TO THE NUCLEUSStructural inheritance in the ciliate cortex. Ciliates make up a distinctive group of unicellular organisms characterized by dualism of germ line and somatic nuclei, sex by reciprocal exchange of gametic nuclei with subsequent replacement of the somatic nucleus, and an extraordinarily complex organization of the cell surface layer. This organization is dominated by cytoskeletal structures, including rows of basal bodies, cilia, and accessory fibrillar structures, and is perpetuated by longitudinal extension of these structural ensembles during clonal growth.This mode of perpetuation provides an ideal opportunity for the demonstration and analysis of cellular heredity at a nongenic level. This opportunity was seized by three gifted biologists, the comparative zoologist Emmanuel Fauré-Fremiet, the experimental embryologist Vance Tartar, and the geneticist Tracy Sonneborn, who together led the way in establishing the principle that structural variations of nongenic origin in the ciliate cortex can indeed be faithfully transmitted to progeny over numerous cell generations.Although this review is primarily devoted to the contribution of genic mutations to the understanding of the ciliate cortex, the interpretation of some of the more interesting of these mutations becomes more meaningful against a background of the three major arenas of nongenic structural inheritance in the ciliate cortex, all of which were solidly established before the genetic approach was initiated.The best-known form of structural inheritance is the organization of the longitudinal ciliary rows that cover the surfaces of most ciliates. This was first demonstrated by Beisson and Sonneborn (12), who showed that an inversion (180°rotation) of one or more ciliary rows of Paramecium tetraurelia (then Paramecium aurelia, syngen 4) (Fig. 1A) could be nongenically inherited; Sonneborn gave the name "cytotaxis" to "this ordering and arranging of new structures under the influence of pre-existing cell structure" (137). This demonstration was later repeated for Tetrahymena thermophila (then Tetrahymena pyriformis, syngen 1) (118) and for other ciliates (62,63,71). It was extended by Nanney's observation that the preexisting number of ciliary rows in T. thermophila tended to be conserved (103, 104), presumably due to the same structural constraints that conserve the geometrical organization of these rows.A second form of structural inheritance is demonstrated by the propagation of the number of complete sets of cortical structures. This was investigated in detail by 32), who noted that ciliates that became fused side by side, as a consequence of blockage of division followed by anterior sliding of the presumptive posterior daughter cell, could propagate their duality. Later, Vance Tartar (147) demonstrated that microsurgically constructed Siamese-twin doublets in the large ciliate Stentor coeruleus could perpetuate their doublet condition. In both cases, the way in which the doublets were created virtually rules o...

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KIN241: a gene involved in cell morphogenesis in Paramecium tetraurelia reveals a novel protein family of cyclophilin–RNA interacting proteins (CRIPs) conserved from fission yeast to man

Cited by 39 publications

References 47 publications

Large Global Effective Population Sizes in Paramecium

Large Global Effective Population Sizes in Paramecium

Rct1, a Nuclear RNA Recognition Motif-Containing Cyclophilin, Regulates Phosphorylation of the RNA Polymerase II C-Terminal Domain

What Do Genic Mutations Tell Us about the Structural Patterning of a Complex Single-Celled Organism?

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