China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
Centre for Marine Bio-Innovation, University of New South Wales, Sydney, New South Wales, Australia.
Environ Microbiol. 2020 Apr;22(4):1409-1420. doi: 10.1111/1462-2920.14957. Epub 2020 Feb 28.
The link between guanine-cytosine (GC) content and thermal adaptation is controversial. Here, we compared maximum growth temperature (T ) 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 T ≤ 20°C strains and T > 20°C strains in genomic GC content which mainly caused by variation of GC3. T ≤ 20°C strains tended to use synonymous codons ended with A/U, but T > 20°C strains tended to use G/C. Lower GC content at synonymous sites (≈GC3) of T ≤ 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 T endured stronger natural selection. Therefore, this study provided molecular basis for bacterial adaptive evolution from moderate temperature to low temperature.
鸟嘌呤-胞嘧啶（GC）含量与热适应性之间的联系存在争议。在这里，我们比较了 78 株 Cryobacterium 菌株的最大生长温度（T）和基因组，以避免由于远缘系统发育群而导致不可靠的结论。系统基因组分析表明，该分类群的多样性比我们所知的要高得多。有趣的是，这些菌株表现出与系统发育凝聚力相关的耐热性分化。在基因组 GC 含量方面，T≤20°C 菌株和 T>20°C 菌株之间存在显著差异，这主要是由于 GC3 的变化引起的。T≤20°C 菌株倾向于使用以 A/U 结尾的同义密码子，而 T>20°C 菌株则倾向于使用 G/C。T≤20°C 菌株同义位点（≈GC3）的 GC 含量较低，可能提供较低的固有 DNA 柔韧性，这与最佳分子动力学密切相关，从而保证了在较低生长温度下的 DNA 功能。对密码子偏好性的分析揭示了热适应性、同义位点（≈GC3）的 GC 含量、固有 DNA 柔韧性和最佳 DNA 动力学之间的密切关系。自然选择是驱动这种密码子偏好性的主要力量；T 值较低的菌株承受着更强的自然选择。因此，本研究从分子水平上为细菌从中等温度到低温的适应性进化提供了依据。
