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Phenotypic divergence of thermotolerance: Molecular basis and cold adaptive evolution related to intrinsic DNA flexibility of glacier‐inhabiting Cryobacterium strains

Liu, Qing, Song, Wei‐Zhi, Zhou, Yu‐Guang, Dong, Xiu‐Zhu, Xin, Yu‐Hua
Environmental microbiology 2020 v.22 no.4 pp. 1409-1420
Cryobacterium, DNA, codon usage, cohesion, cold, evolutionary adaptation, genomics, heat tolerance, molecular dynamics, natural selection, phenotypic variation, phylogeny, temperature
The link between guanine–cytosine (GC) content and thermal adaptation is controversial. Here, we compared maximum growth temperature (TMGT) and genomics of 78 Cryobacterium strains to avoid unreliable conclusions resulting from distantly phylogenetic groups. Phylogenomic analysis revealed this taxon had much higher diversification than we knew. Interestingly, these strains showed thermotolerance divergence with phylogenetic cohesion. A significant difference was found between TMGT ≤ 20°C strains and TMGT > 20°C strains in genomic GC content which mainly caused by variation of GC3. TMGT ≤ 20°C strains tended to use synonymous codons ended with A/U, but TMGT > 20°C strains tended to use G/C. Lower GC content at synonymous sites (≈GC3) of TMGT ≤ 20°C strains could provide lower intrinsic DNA flexibility which strongly associated with optimal molecular dynamics, and then guarantee DNA function at lower growth temperatures. This analysis of codon bias revealed close relationships for thermal adaptation, GC content at synonymous sites (≈GC3), intrinsic DNA flexibility and optimal DNA dynamics. Natural selection was main force driving this codon bias; strains with lower TMGT endured stronger natural selection. Therefore, this study provided molecular basis for bacterial adaptive evolution from moderate temperature to low temperature.