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PubMed1999

Life with no sugars?

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Archaeoglobus fulgidus↗
PubMed2002

Representation and processing of complex DNA spatial architecture and its annotated genomic content.

This paper presents a new general approach for the spatial representation and visualization of DNA molecule and its annotated information. This approach is based on a biological 3D model that predicts the complex spatial trajectory of huge naked DNA. With such modeling, a global vision of the sequence is possible, which is different and complementary to other representations as textual, linguistics or syntactic ones. The DNA is well known as a three-dimensional structure. Whereas, the spatial information plays a great part during its evolution and its interaction with the other biological elements This work will motivate investigations in order to launch new bioinformatics studies for the analysis of the spatial architecture of the genome. Besides, in order to obtain a friendly interactive visualization, a powerful graphic modeling is proposed including DNA complex trajectory management and its annotated-based content structuring. The paper describes spatial architecture modeling, with consideration of both biological and computational constraints. This work is implemented through a powerful graphic software tool, named ADN-Viewer. Several examples of visualization are shown for various organisms and biological elements.

DNA↗
PubMed2004

Synthesis of cysteinyl-tRNACys by a prolyl-tRNA synthetase.

The question of how cysteinyl-tRNA(Cys) is synthesized in organisms that lack a canonical cysteinyl-tRNA synthetase (CysRS) is an important open question in understanding protein synthesis. The prolyl-tRNA synthetase (ProRS) of wide ranging organisms has the ability to mis-activate cysteine without editing. This raises the question of whether the mis-activated cysteine can be charged to tRNA(Cys) to synthesize the correctly matched cys-tRNA(Cys), which may serve as an option in organisms that lack the conventional CysRS. Despite intense searches, such an activity has not been found. Here we show that the ProRS of the radiation-resistant bacterium Deinococcus radiodurans has the ability to charge cysteine to tRNA(Cys) and to retain the cognate pair cys-tRNA(Cys) stably without editing. The cysteinylation by D. radiodurans ProRS is not the major route for synthesis of cys-tRNA(Cys), however, because the organism encodes the conventional CysRS. Nonetheless, the synthesis of cys-tRNA(Cys) in vitro is important and it is unlike previously documented mis-charging of Methanocaldococcus jannaschii ProRS, which synthesizes cys-tRNA(Pro) but not cys-tRNA(Cys). We suggest that the cysteinylation activity of D. radiodruans ProRS may, in the presence of additional factors, offer one option to organisms that lack the conventional CysRS to synthesize cysteinyl-tRNA(Cys) in vivo.

Amino Acids↗
PubMed1997

Three-dimensional comparative modeling of RNA.

Comparative sequence analysis and ERNA-3D software were used to model the three-dimensional structure of the small domain of signal recognition particle RNA. RNA secondary structures were established by allowing only phylogenetically-supported base pairs. The folding of the RNA molecules was constrained further to include a well-supported pseudoknot. Helical sections were oriented coaxially where a continuous helical stack was formed in the RNA of another species. Finally, RNA helices were placed at distances that preserved the connectivity of the molecule with the smallest number of single-stranded nucleotide residues as identified from the aligned sequences. We show that the comparative three-dimensional structure modeling approach is an extremely powerful tool as it requires only a critical number of carefully aligned sequences.

Bacillus subtilis↗