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09/01/17 Céline Brochier (UCBL)

Molecular mechanisms of adaptation to temperature: Methanococcales as a case study (a la Doua, salle Fontannes Batiment Darwin)
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Molecular mechanisms of adaptation to temperature: Methanococcales as a case study

 

 

Understanding the mechanisms involved in protein thermostability is a major challenge in molecular biology and ecology with many applications in biotechnology and evolutionary biology. The sequencing of complete genomes has revealed a strong correlation between proteome amino acid composition and optimal growth temperature (OGT) of prokaryotes [1].

However, temperature is not the only factor influencing the amino acid composition of proteomes. In fact, other biological and environmental factors, such as the G+C content of genomes, salinity and metabolisms are also involved. Accordingly, it is difficult to determine the exact contribution of each of these factors on proteome amino acid evolution.

In this context, Methanococcales represent a very interesting model to tackle this issue, because representatives of this order of methanogens harbour very diverse OGTs (ranging from 35°C to 90°C) but similar genomic G+C content and similar metabolisms.

We have analysed the 18 complete (or nearly complete) genomes of Methanococcales available in public databases. We showed that (i) OGT is the primary factor affecting the amino acid composition of Methanococcales proteomes, (ii) all proteins are significantly impacted regardless of their function, and (iii) horizontal gene transfer did not play a major role in this adaptation. Using COaLA [2], a probabilistic model developed in the lab, we reconstructed the ancestral proteomes of Methanococcales. Based on the correlation between OGT and proteome amino acid composition [3], and Bayesian approaches [4], we determined ancestral OGTs at each node of the Methanococcales phylogeny.

The accurate analysis of the substitution patterns all along the tree allowed us to disentangle the dynamics of this process and to decipher the major evolutionary steps that drive temperature adaptation during the diversification of Methanococcales.

[1] Zeldovich KB, Berezovsky IN, Shakhnovich EI: Protein and DNA sequence determinants of thermophilic adaptation. PLoS computational biology 2007, 3(1):e5.

[2] Groussin M, Boussau B, Gouy M: A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences. Syst Biol 2013.

[3] Groussin M, Gouy M: Adaptation to environmental temperature is a major determinant of molecular evolutionary rates in archaea. Molecular biology and evolution 2011, 28(9):2661-2674.

[4] Lartillot N: A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data. Bioinformatics 2014, 30(4):488-496.

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