Patterns of codon usage in two ciliates that reassign the genetic code: Tetrahymena thermophila and Paramecium tetraurelia

We used the recently sequenced genomes of the ciliates Tetrahymena thermophila and Paramecium tetraurelia to analyze the codon usage patterns in both organisms; we have analyzed codon usage bias, Gln codon usage, GC content and the nucleotide contexts of initiation and termination codons in Tetrahymena and Paramecium. We also studied how these trends change along the length of the genes and in a subset of highly expressed genes. Our results corroborate some of the trends previously described in Tetrahymena, but also negate some specific observations. In both genomes we found a strong bias toward codons with low GC content; however, in highly expressed genes this bias is smaller and codons ending in GC tend to be more frequent. We also found that codon bias increases along gene segments and in highly expressed genes and that the context surrounding initiation and termination codons are always AT rich. Our results also suggest differences in the efficiency of translation of the reassigned stop codons between the two species and between the reassigned codons. Finally, we discuss some of the possible causes for such translational efficiency differences.     

Marked Amplification and Diversification of Products of ras Genes from Rat Brain,Rab GTPases,in the Ciliates Tetrahymena thermophila and Paramecium tetraurelia

ABSTRACT. Small GTPase Rab (products of ras genes from rat brain) is a widely conserved molecular switch among eukaryotes and regulates membrane trafficking pathways. It is generally considered that the number of Rab encoded in the genome correlates with multicellularity; however, we found that unicellular ciliates Tetrahymena thermophila (Tt) and Paramecium tetraurelia (Pt) possess many more Rab genes in their genome than the 64 HsRab genes in the human genome. We succeeded in isolating 86 cDNA clones of 88 TtRab genes in the Tetrahymena genome. By comparing the amino acid sequence of Rab in humans and the budding yeast Saccharomyces cerevisiae, 42 TtRab belonged to subfamilies functionally characterized and designated as conventional Rab, while the remaining 44 TtRab were considered to be species‐specific. To examine the diversity of Rab in ciliates, we searched for Rab genes in the genome database of P. tetraurelia. Overall, 229 PtRab genes were found and categorized as 157 conventional and 72 species‐specific PtRab, respectively. Among them, nine PtRab genes showed high homology to seven TtRab, suggesting the conservation of ciliate‐specific Rab. These data suggested that the range of Rab is markedly amplified and diversified in ciliates, which may support the elaborate cellular structures and vigorous phagocytosis of those organisms.     

Statistics in Human Genetics and Molecular Biology by REILLY,C.

Statistics in Human Genetics and Molecular Biology (C. Reilly) Xiang‐Yang Lou and David B. Allison Meta‐Analysis and Combining Information in Genetics and Genomics (R. Guerra and D. R. Goldstein) Peter H. Westfall Multivariate Nonparametric Methods with R. An Approach Based on Spatial Signs and Ranks (H. Oja) Mia Hubert Bayesian Analysis for Population Ecology (R. King, B. J. T. Morgan, O. Gimenez, and S. Brooks) Simon Bonner The Oxford Handbook of Functional Data Analysis (F. Ferraty and Y. Romain, Editors) Paul H. C. Eilers Design and Analysis of Experiments with SAS (J. Lawson) Francis Giesbrecht Spatial Statistics and Modeling (C. Gaetan and X. Guyon) Paulo J. Ribeiro Jr. Applied Statistical Genetics with R: For Population‐Based Association Studies (A. S. Foulkes) Kui Zhang