Microarray Analyses of Gene Expression during the Tetrahymena thermophila Life Cycle

Background: The model eukaryote, Tetrahymena thermophila, is the first ciliated protozoan whose genome has been sequenced, enabling genome-wide analysis of gene expression. Methodology/Principal Findings: A genome-wide microarray platform containing the predicted coding sequences (putative genes) for T. thermophila is described, validated and used to study gene expression during the three major stages of the organism's life cycle: growth, starvation and conjugation. Conclusions/Significance: Of the,27,000 predicted open reading frames, transcripts homologous to only,5900 are not detectable in any of these life cycle stages, indicating that this single-celled organism does indeed contain a large number of functional genes. Transcripts from over 5000 predicted genes are expressed at levels >5x corrected background and 95 genes are expressed at >250x corrected background in all stages. Transcripts homologous to 91 predicted genes are specifically expressed and 155 more are highly up-regulated in growing cells, while 90 are specifically expressed and 616 are up-regulated during starvation. Strikingly, transcripts homologous to 1068 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation. The patterns of gene expression during conjugation correlate well with the developmental stages of meiosis, nuclear differentiation and DNA elimination. The relationship between gene expression and chromosome fragmentation is analyzed. Genes encoding proteins known to interact or to function in complexes show similar expression patterns, indicating that co-ordinate expression with putative genes of known function can identify genes with related functions. New candidate genes associated with the RNAi-like process of DNA elimination and with meiosis are identified and the late stages of conjugation are shown to be characterized by specific expression of an unexpectedly large and diverse number of genes not involved in nuclear functions.

Metal-Ion Catalysis In the Tetrahymena Ribozyme Reaction

LL catalytic RNAs (ribozymes) require or are stimulated by divalent metal ions, but it has been difficult to separate the contribution of these metal ions to formation of the RNA tertiary structure1 from a more direct role in catalysis. The Tetrahymena ribozyme catalyses cleavage of exogenous RNA2,3 or DNA4,5 substrates with an absolute requirement for Mg2+ or Mn2+ (ref. 6). A DNA substrate, in which the bridging 3' oxygen atom at the cleavage site is replaced by sulphur, is cleaved by the ribozyme about 1,000 times more slowly than the corresponding unmodified DNA substrate when Mg2+ is present as the only divalent metal ion. But addition of Mn2+ or Zn2+ to the reaction relieves this negative effect, with the 3' S–P bond being cleaved nearly as fast as the 3' O–P bond. Considering that Mn2+ and Zn2+ coordinate sulphur more strongly than Mg2+ does7,8, these results indicate that the metal ion contributes directly to catalysis by coordination to the 3' oxygen atom in the transition state, presumably stabilizing the developing negative charge on the leaving group. We conclude that the Tetrahymena ribozyme is a metalloenzyme, with mechanistic similarities to several protein enzymes9–12.

Potencial de inibição da regeneração de raízes e plântulas em sementes germinantes de Eugenia pyriformis

O objetivo deste trabalho foi avaliar o potencial de inibição da formação de raízes e plântulas, em sementes germinantes de uvaieira (Eugenia pyriformis), fragmentadas e fissuradas. As sementes foram separadas por tamanho em dois grupos. Cada grupo foi separado em dois subgrupos, um dos quais foi submetido a teste de germinação. As sementes de cada subgrupo foram submetidas a dois tipos de incisão (total ou parcial) e, em seguida, foram avaliadas quanto à produção de raízes e plântulas. em sementes com incisão parcial, que apresentavam apenas uma plântula desenvolvida, completou-se a incisão até que as metades fossem separadas. A metade com a raiz foi descartada, e sua complementar foi colocada para germinar, para avaliação da produção de raízes e plântulas nessas frações sem raízes. em todos os experimentos, utilizou-se o delineamento inteiramente casualizado, em arranjo fatorial 2x2 (tamanho das sementes x germinação visível) e 2x4 (tamanho das sementes x tipo de incisão). As sementes fracionadas de uvaieira apresentam potencial para regeneração de raízes e plântulas, e podem produzir mais de uma muda por semente. A germinação inicia processos de inibição da regeneração de novas raízes e plântulas na semente, e a incisão dos cotilédones pode bloquear essa inibição.

Maturation of Eugenia pyriformis seeds under different hydric and thermal conditions

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Extraction and quantification of phenolic acids and flavonols from Eugenia pyriformis using different solvents

The recovery of phenolic compounds of Eugenia pyriformis using different solvents was investigated in this study. The compounds were identified and quantified by reverse-phase high-performance liquid chromatography coupled with ultraviolet-visible diode-array detector (RP-HPLC-DAD/UV-vis). Absolute methanol was the most effective extraction agent of phenolic acids and flavonols (588.31 mg/Kg) from Eugenia pyriformis, although similar results (p ≤ 0.05) were observed using methanol/water (1:1 ratio). Our results clearly showed that higher contents of phenolic compounds were not obtained either with the most or the least polar solvents used. Several phenolic compounds were identified in the samples whereas gallic acid and quercetin were the major compounds recovered. © 2012 Association of Food Scientists & Technologists (India).

Compostos voláteis da uvaia (Eugenia pyriformis cambess)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Processos de indução e de inibição da regeneração de plântulas de sementes de Eugenia pyriformis cambess

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Variabilidade espacial de atributos do solo e sua relação com características agronômicas de genótipos de uvaieira (Eugenia pyriformis, Cambess)

Pós-graduação em Agronomia (Ciência do Solo) - FCAV

Relação entre o perfil metabólico da semente de Eugenia pyriformis e sua capacidade de regenerar novas plântulas

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Phosphorylation of histone H3 at serine 10 is correlated with chromosome condensation during mitosis and meiosis in Tetrahymena

H3 phosphorylation has been correlated with mitosis temporally in mammalian cells and spatially in ciliated protozoa. In logarithmically growing Tetrahymena thermophila cells, for example, H3 phosphorylation can be detected in germline micronuclei that divide mitotically but not in somatic macronuclei that divide amitotically. Here, we demonstrate that micronuclear H3 phosphorylation occurs at a single site (Ser-10) in the amino-terminal domain of histone H3, the same site phosphorylated during mitosis in mammalian cells. Using an antibody specific for Ser-10 phosphorylated H3, we show that, in Tetrahymena, this modification is correlated with mitotic and meiotic divisions of micronuclei in a fashion that closely coincides with chromosome condensation. Our data suggest that H3 phosphorylation at Ser-10 is a highly conserved event among eukaryotes and is likely involved in both mitotic and meiotic chromosome condensation.

Three metal ions at the active site of the Tetrahymena group I ribozyme

Metal ions are critical for catalysis by many RNA and protein enzymes. To understand how these enzymes use metal ions for catalysis, it is crucial to determine how many metal ions are positioned at the active site. We report here an approach, combining atomic mutagenesis with quantitative determination of metal ion affinities, that allows individual metal ions to be distinguished. Using this approach, we show that at the active site of the Tetrahymena group I ribozyme the previously identified metal ion interactions with three substrate atoms, the 3′-oxygen of the oligonucleotide substrate and the 3′- and 2′-moieties of the guanosine nucleophile, are mediated by three distinct metal ions. This approach provides a general tool for distinguishing active site metal ions and allows the properties and roles of individual metal ions to be probed, even within the sea of metal ions bound to RNA.

An optimal Mg2+ concentration for kinetic folding of the Tetrahymena ribozyme

Divalent metal ions, such as Mg2+, are generally required for tertiary structure formation in RNA. Although the role of Mg2+ binding in RNA-folding equilibria has been studied extensively, little is known about the role of Mg2+ in RNA-folding kinetics. In this paper, we explore the effect of Mg2+ on the rate-limiting step in the kinetic folding pathway of the Tetrahymena ribozyme. Analysis of these data reveals the presence of a Mg2+-stabilized kinetic trap that slows folding at higher Mg2+ concentrations. Thus, the Tetrahymena ribozyme folds with an optimal rate at 2 mM Mg2+, just above the concentration required for stable structure formation. These results suggest that thermodynamic and kinetic folding of RNA are cooptimized at a Mg2+ concentration that is sufficient to stabilize the folded form but low enough to avoid kinetic traps and misfolding.

DNA double-strand break formation and repair in Tetrahymena meiosis

Acknowledgements We wish to thank Anura Shodhan for sharing unpublished results and Peter Schlögelhofer and Anura Shodhan for critically reading the manuscript. Part of this work was supported by grant P 27313-B20 from the Austrian Science Fund to JL.

Analysis of exocytosis mutants indicates close coupling between regulated secretion and transcription activation in Tetrahymena

Stimulation of regulated secretory cells promotes protein release via the fusion of cytoplasmic storage vesicles with the plasma membrane. In Tetrahymena thermophila, brief exposure to secretagogue results in synchronous fusion of the entire set of docked dense-core granules with the plasma membrane. We show that stimulation is followed by rapid new dense-core granule synthesis involving gene induction. Two genes encoding granule matrix proteins, GRL1 and GRL4, are shown to undergo induction following stimulation, resulting in ≈10-fold message accumulation within 1 h. The mechanism of induction involves transcriptional regulation, and the upstream region of GRL1 functions in vivo as an inducible promoter in a heterologous reporter construct using the gene encoding green fluorescent protein. Taking advantage of the characterized exocytosis (exo−) mutants available in this system, we asked whether the signals for regranulation were generated directly by the initial stimulation, or whether downstream events were required for transcription activation. Three mutants, with defects at three distinct stages in the regulated secretory pathway, failed to show induction of GRL1 and GRL4 after exposure to secretagogue. These results argue that regranulation depends upon signals generated by the final steps in exocytosis.