A unique serine-specific elongation factor Tu found in nematode mitochondria

Ohtsuki, Takashi; Sato, Aya; Watanabe, Yoh Ichi; Watanabe, Kimitsuna

doi:10.1038/nsb826

Cited by 49 publications

(53 citation statements)

References 27 publications

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“…In Caenorhabditis elegans mitochondrial EF-Tu2, a Val (Val 258 ) is found at the position of this threonine. This valine possibly contributes to the strong affinity of EF-Tu2 toward Ser-tRNAs (48). Variations in the amino acid composition of the ␤7, ␤8, and ␤14 strands may therefore explain the relative specificity of each factor toward the various aminoacyl moieties attached to tRNAs.…”

Section: Discussionmentioning

confidence: 99%

Functional Molecular Mapping of Archaeal Translation Initiation Factor 2

Yatime¹,

Schmitt

Blanquet

et al. 2004

Journal of Biological Chemistry

125

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Eukaryotic and archaeal initiation factors 2 (e/aIF2) are heterotrimeric proteins (␣␤␥) carrying methionylated initiator tRNA to the small subunit of the ribosome. The three-dimensional structure of aIF2␥ from the Archaea Pyrococcus abyssi was previously solved. This subunit forms the core of the heterotrimer. The ␣ and ␤ subunits bind the ␥, but do not interact together. aIF2␥ shows a high resemblance with elongation factor EF1-A. In this study, we characterize the role of each subunit in the binding of the methionylated initiator tRNA. Studying various aminoacyl-tRNA ligands shows that the methionyl group is a major determinant for recognition by aIF2. aIF2␥ alone is able to specifically bind Met-tRNA i Met , although with a reduced affinity as compared with the intact trimer. Site-directed mutagenesis confirms a binding mode of the tRNA molecule similar to that observed with the elongation factor. Under our assay conditions, aIF2␤ is not involved in the docking of the tRNA molecule. In contrast, aIF2␣ provides the heterotrimer its full tRNA binding affinity. Furthermore, the isolated C-domain of aIF2␣ is responsible for binding of the ␣ subunit to ␥. This binding involves an idiosyncratic loop of domain 2 of aIF2␥. Association of the C-domain of aIF2␣ to aIF2␥ is enough to retrieve the binding affinity of tRNA for aIF2. The N-terminal and central domains of aIF2␣ do not interfere with tRNA binding. However, the N-domain of aIF2␣ interacts with RNA unspecifically. Based on this property, a possible contribution of aIF2␣ to formation of a productive complex between aIF2 and the small ribosomal subunit is envisaged.In the initiation of translation, the recognition of a start codon on a mRNA involves a specialized initiator tRNA. This tRNA is always esterified with methionine. Several proteins, called initiation factors, contribute along with the ribosome to the success of the initiator tRNA-mRNA interaction. Such initiation factors differ in the three domains of life.

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Section: Discussionmentioning

confidence: 99%

Functional Molecular Mapping of Archaeal Translation Initiation Factor 2

Yatime¹,

Schmitt

Blanquet

et al. 2004

Journal of Biological Chemistry

125

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“…For instance, gene content is certainly affected by the ability of exchange of genetic material between the mitochondrial and nuclear compartments, the permeability and/or the presence of specific carriers on the mitochondrial membranes, gene dispensability and the difference in multimeric structure of the respiratory chain complexes between organisms. The secondary structure and size of transfer RNAs (tRNAs) and rRNAs are related to peculiarities of the mitochondrial translational apparatus, as demonstrated in nematodes by the concomitant unusual structure of mt tRNA, ribosomal RNAs (rRNA) and elongation factors (Okimoto and Wolstenholme, 1990;Okimoto et al, 1994;Sakurai et al, 2001Sakurai et al, , 2006Ohtsuki et al, 2002). The number, size and location of non-coding regions is mostly related to the presence of replication and transcription regulatory signals, although the overlap between regulatory signals and coding sequences cannot be excluded in the compact metazoan mtDNA (Valverde et al, 1994;Peleg et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species

2008

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The mitochondrial genome (mtDNA) of Metazoa is a good model system for evolutionary genomic studies and the availability of more than 1000 sequences provides an almost unique opportunity to decode the mechanisms of genome evolution over a large phylogenetic range. In this paper, we review several structural features of the metazoan mtDNA, such as gene content, genome size, genome architecture and the new parameter of gene strand asymmetry in a phylogenetic framework. The data reviewed here show that: (1) the plasticity of Metazoa mtDNA is higher than previously thought and mainly due to variation in number and location of tRNA genes; (2) an exceptional trend towards stabilization of genomic features occurred in deuterostomes and was exacerbated in vertebrates, where gene content, genome architecture and gene strand asymmetry are almost invariant. Only tunicates exhibit a very high degree of genome variability comparable to that found outside deuterostomes. In order to analyse the genomic evolutionary process at short evolutionary distances, we have also compared mtDNAs of species belonging to the same genus: the variability observed in congeneric species significantly recapitulates the evolutionary dynamics observed at higher taxonomic ranks, especially for taxa showing high levels of genome plasticity and/or fast nucleotide substitution rates. Thus, the analysis of congeneric species promises to be a valuable approach for the assessment of the mtDNA evolutionary trend in poorly or not yet sampled metazoan groups.

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“…However, unusual truncations detected in some animal mitochondrial tRNAs appear to prevent recognition via a canonical EF-Tu [33]. Also, it was previously demonstrated that the chromadorean nematode harbors two distinct EF-Tus, one of which (EF-Tu1) binds only to T-armless aminoacyl-tRNAs, whereas the other (EF-Tu2) binds to D-armless Ser-tRNAs [33,34]. Neither of the EF-Tus can bind to canonical cloverleaf tRNAs.…”

Section: Discussionmentioning

confidence: 99%

Expressed Sequence Tags of Trichinella spiralis Muscle Stage Larvae

et al. 2008

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Abstract:In order to obtain greater insight into the relevant genomic expression patterns of Trichinella spiralis, 992 expressed sequence tags (ESTs) were collected from a cDNA library of T. spiralis muscle stage larvae and assembled into 60 clusters and 385 singletons. Of them, 445 (44.7%) ESTs were annotated to their homologous genes, and small fractions were matched to known genes of nematodes. The annotated ESTs were classified into 25 eukaryotic orthologous groups (KOG). Cytochrome C oxidase (34 clones) was found to be most frequent species.

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A unique serine-specific elongation factor Tu found in nematode mitochondria

Cited by 49 publications

References 27 publications

Functional Molecular Mapping of Archaeal Translation Initiation Factor 2

Functional Molecular Mapping of Archaeal Translation Initiation Factor 2

Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species

Expressed Sequence Tags of Trichinella spiralis Muscle Stage Larvae

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