Civil and Environmental Engineering Department, Northeastern University, Boston, MA, 02115, USA.
Simon F. S. Li Marine Science Laboratory of School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
ISME J. 2018 May;12(5):1180-1187. doi: 10.1038/s41396-017-0023-7. Epub 2018 Jan 12.
An important unanswered question in evolutionary genomics is the source of considerable variation of genomic base composition (GC content) even among organisms that share one habitat. Evolution toward GC-poor genomes has been considered a major adaptive pathway in the oligotrophic ocean, but GC-rich bacteria are also prevalent and highly successful in this environment. We quantify the contribution of multiple factors to the change of genomic GC content of Ruegeria pomeroyi DSS-3, a representative and GC-rich member in the globally abundant Roseobacter clade, using an agent-based model. The model simulates 2 × 10 cells, which allows random genetic drift to act in a realistic manner. Each cell has a whole genome subject to base-substitution mutation and recombination, which affect the carbon and nitrogen requirements of DNA and protein pools. Nonsynonymous changes can be functionally deleterious. Together, these factors affect the growth and fitness. Simulations show that experimentally determined mutation bias toward GC is not sufficient to build the GC-rich genome of DSS-3. While nitrogen availability has been repeatedly hypothesized to drive the evolution of GC content in marine bacterioplankton, our model instead predicts that DSS-3 and its ancestors have been evolving in environments primarily limited by carbon.
进化基因组学中一个重要的未解决问题是，即使在共享同一栖息地的生物中，基因组碱基组成（GC 含量）也存在相当大的变异。在贫营养海洋中，向 GC 贫乏基因组的进化被认为是一种主要的适应性途径，但 GC 丰富的细菌在这种环境中也很普遍且非常成功。我们使用基于主体的模型来量化多种因素对全球丰富的玫瑰杆菌目中代表性且 GC 含量丰富的鲁氏菌（Ruegeria pomeroyi DSS-3）基因组 GC 含量变化的贡献。该模型模拟了 2×10 个细胞，允许随机遗传漂变以真实的方式发挥作用。每个细胞都有一个完整的基因组，易受碱基替换突变和重组的影响，这会影响 DNA 和蛋白质库的碳氮需求。非同义突变可能具有功能破坏性。这些因素共同影响着细胞的生长和适应性。模拟表明，实验确定的 GC 偏向突变不足以构建 DSS-3 的 GC 丰富基因组。尽管氮可用性一再被假设为驱动海洋细菌浮游生物中 GC 含量进化的因素，但我们的模型预测，DSS-3 及其祖先一直在主要受碳限制的环境中进化。
