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Birth of Archaeal Cells: Molecular Phylogenetic Analyses of G1P Dehydrogenase, G3P Dehydrogenases, and Glycerol Kinase Suggest Derived Features of Archaeal Membranes Having G1P Polar Lipids

2016 Academic Editor: Hans-Peter Klenk Copyright © 2016 Shin-ichi Yokobori et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted ... Yokobori,1 Yoshiki Nakajima,1 Satoshi Akanuma,2 and Akihiko Yamagishi1 1Laboratory of Extremophiles, Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life

tRNA Modification and Genetic Code Variations in Animal Mitochondria

, Tokyo 113-8657, Japan Received 31 May 2011; Accepted 4 July 2011 Academic Editor: Daisuke Miyoshi Copyright © 2011 Kimitsuna Watanabe and Shin-ichi Yokobori. This is an open access article

Life without tRNAArg–adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes

In most bacteria, two tRNAs decode the four arginine CGN codons. One tRNA harboring a wobble inosine (tRNAArgICG) reads the CGU, CGC and CGA codons, whereas a second tRNA harboring a wobble cytidine (tRNAArgCCG) reads the remaining CGG codon. The reduced genomes of Mycoplasmas and other Mollicutes lack the gene encoding tRNAArgCCG. This raises the question of how these organisms...

Improvement of Bacillus circulans β-amylase activity attained using the ancestral mutation method

Thermostabilization of enzymes is one of the greatest challenges of protein engineering. The ancestral mutation method, which introduces ancestral residues into a target enzyme, has previously been developed and used to improve the thermostabilities of thermophilic enzymes. Herein, we report a study that used the ancestral mutation method to improve the thermostability of...

Gain and loss of an intron in a protein-coding gene in Archaea: the case of an archaeal RNA pseudouridine synthase gene

Background We previously found the first examples of splicing of archaeal pre-mRNAs for homologs of the eukaryotic CBF5 protein (also known as dyskerin in humans) in Aeropyrum pernix, Sulfolobus solfataricus, S. tokodaii, and S. acidocaldarirus, and also showed that crenarchaeal species in orders Desulfurococcales and Sulfolobales, except for Hyperthermus butylicus, Pyrodictium...

Functional reconstitution of an archaeal splicing endonuclease in vitro

Sulfolobus tokodaii strain 7 is one of archaea whose entire genome has been sequenced. The genome sequence revealed that it possesses two open reading frames (ORFs) that are homologous to endA, a protein responsible for splicing endonuclease activity in archaea. Interestingly, one of these two ORFs lacks a putative catalytic amino acid residue for the nuclease activity. To...

Long-Term Conservation of Six Duplicated Structural Genes in Cephalopod Mitochondrial Genomes

The complete nucleotide sequences of the mitochondrial (mt) genomes of three cephalopods, Octopus vulgaris (Octopodiformes, Octopoda, Incirrata), Todarodes pacificus (Decapodiformes, Oegopsida, Ommastrephidae), and Watasenia scintillans (Decapodiformes, Oegopsida, Enoploteuthidae), were determined. These three mt genomes encode the standard set of metazoan mt genes. However, W...

An extra tRNAGly(U*CU) found in ascidian mitochondria responsible for decoding non-universal codons AGA/AGG as glycine

Amino acid assignments of metazoan mitochondrial codons AGA/AGG are known to vary among animal species; arginine in Cnidaria, serine in invertebrates and stop in vertebrates. We recently found that in the mitochondria of the ascidian Halocynthia roretzi these codons are exceptionally used for glycine, and postulated that they are probably decoded by a tRNA(UCU). In order to...