On the evolution and expression of Chlamydomonas reinhardtii nucleus-encoded transfer RNA genes - PubMed (original) (raw)

Phylogenetic analyses of (A) cysteine, (B) tyrosine, and (C) isoleucine tRNA genes show their evolutionary link either to plant or to animal counterparts. The trees are representative of three different situations: Chamydomonas tRNACys branches with Arabidopsis tRNACys sequences, tRNATyr branches with fungi and human tRNATyr sequences, and tRNAIle with either Arabidopsis or human tRNAIle, depending on the tRNA isoacceptor considered. The phylogenetic trees constructed for the other amino acids are presented in supplemental Figure 6. Construction of the trees is described in detail in

materials and methods

. Phyla are differentiated by colors: bacteria (red), archaebacteria (pink), eukaryotes (blue), algae (green), and protozoans (black). Species used for the phylogenetic analysis are as follows: Aeropyrum pernix (Ape), Archaeoglobus fulgidus (Afu), Methanococcus jannaschii (Mja), Methanopyrus kandleri (Mka), Methanosarcina mazei (Mma), Methanobacterium thermoautotrophicum (Mth), Pyrococcus abyssi (Pab), Pyrobaculum aerophilum (Paer), Sulfolobus solfataricus (Sso), and Thermoplasma acidophilum (Tac) for Archae; Agrobacterium tumefaciens C58 Cereon (Atu), Bacillus subtilis (Bsu), Bordetella parapertussis (Bpa), Brucella melitensis (Bme), Campylobacter jejuni (Cje), Caulobacter crescentus (Ccr), Chlamydophyla pneumoniae AR39 (Cpn), Clostridium perfringens (Cpe), Escherichia coliK12 (Eco), Haemophilus influenzae (Hin), Helicobacter pylori 26695 (Hpy), Listeria monocytogenes (Lmo), Mycoplasma pneumoniae (Mpn), Mycobacterium tuberculosis CDC1551 (Mtu), Pseudomonas aeruginosa (Paea), Rickettsia prowazekii (Rpr), Salmonella enterica typhi (Sen), and Synechocystis PCC6 (Syn) for bacteria; and Arabidopsis thaliana (Ath), Caenorhabditis elegans (Cel), Chlamydomonas reinhardtii (Cre), Cyanidioschyzon merolae (Cme), Dictyostelium discoideum (Ddi), Drosophila melanogaster (Dme), Homo sapiens (Hsa), Saccharomyces cerevisiae (Sce), and Schizosaccharomyces pombe (Spo). The nomenclature used is illustrated with one example as follows: CreYcGTA is chloroplastic tRNATyr with a GTA anticodon from Chlamydomonas reinhardtii. When a mitochondrial tRNA is on the tree, the letter m follows the one-letter code amino acid. When a number is after the anticodon, it corresponds to one of the tRNA isoacceptors of the same family differing by point mutations. Branch lengths are the maximum-likelihood values for the consensus tree topology. The values along each branch are the node Bayesian posterior probability (only values > 50 are indicated).