Building a tRNA thermometer to estimate microbial adaptation to temperature.
Nucleic Acids Res
; 48(21): 12004-12015, 2020 12 02.
Article
en En
| MEDLINE
| ID: mdl-33196821
ABSTRACT
Because ambient temperature affects biochemical reactions, organisms living in extreme temperature conditions adapt protein composition and structure to maintain biochemical functions. While it is not feasible to experimentally determine optimal growth temperature (OGT) for every known microbial species, organisms adapted to different temperatures have measurable differences in DNA, RNA and protein composition that allow OGT prediction from genome sequence alone. In this study, we built a 'tRNA thermometer' model using tRNA sequence to predict OGT. We used sequences from 100 archaea and 683 bacteria species as input to train two Convolutional Neural Network models. The first pairs individual tRNA sequences from different species to predict which comes from a more thermophilic organism, with accuracy ranging from 0.538 to 0.992. The second uses the complete set of tRNAs in a species to predict optimal growth temperature, achieving a maximum ${r^2}$ of 0.86; comparable with other prediction accuracies in the literature despite a significant reduction in the quantity of input data. This model improves on previous OGT prediction models by providing a model with minimum input data requirements, removing laborious feature extraction and data preprocessing steps and widening the scope of valid downstream analyses.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Bacterias
/
ARN de Transferencia
/
Adaptación Fisiológica
/
Genoma Bacteriano
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Archaea
/
Genoma Arqueal
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
Nucleic Acids Res
Año:
2020
Tipo del documento:
Article
País de afiliación:
Estados Unidos