Genome‐scale metabolic modelling of extremophiles and its applications in astrobiological environments

Abstract

Metabolic modelling approaches have become the powerful tools in modern biology. These mathematical models are widely used to predict metabolic phenotypes of the organisms or communities of interest, and to identify metabolic targets in metabolic engineering. Apart from a broad range of industrial applications, the possibility of using metabolic modelling in the contexts of astrobiology are poorly explored. In this mini‐review, we consolidated the concepts and related applications of applying metabolic modelling in studying organisms in space‐related environments, specifically the extremophilic microbes. We recapitulated the current state of the art in metabolic modelling approaches and their advantages in the astrobiological context. Our review encompassed the applications of metabolic modelling in the theoretical investigation of the origin of life within prebiotic environments, as well as the compilation of existing uses of genome‐scale metabolic models of extremophiles. Furthermore, we emphasize the current challenges associated with applying this technique in extreme environments, and conclude this review by discussing the potential implementation of metabolic models to explore theoretically optimal metabolic networks under various space conditions. Through this mini‐review, our aim is to highlight the potential of metabolic modelling in advancing the study of astrobiology.

Polyextremophile engineering: a review of organisms that push the limits of life

“…Rational design requires adding exogenous DNA with a known function, such as the tardigrade Dsup DNA repair gene which enhances survival by 2 orders of magnitude when transferred to E. coli grown in harsh conditions ( Puig et al, 2021 ). Knowledge of specific extremophilic genes like tardigrade Dsup , as well as genome-scale models such as flux balance analysis ( Noirungsee et al, 2024 ; Saldivar et al, 2024 ), can both be invaluable for engineering ( Swayambhu et al, 2020 ). If there are no known genes with the needed function, metagenomic libraries sourced from extreme environments can search for genes that confer protection without foreknowledge of the sequence-function relationships ( Biver et al, 2014 ; Culligan et al, 2014 ; Forsberg et al, 2016 ; Ausec et al, 2017 ).…”