Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
Mol Biol Evol. 2022 Apr 10;39(4). doi: 10.1093/molbev/msac069.
Analysis of bacterial genomes shows that, whereas diverse species share many genes in common, their linear order on the chromosome is often not conserved. Whereas rearrangements in gene order could occur by genetic drift, an alternative hypothesis is rearrangement driven by positive selection during niche adaptation (SNAP). Here, we provide the first experimental support for the SNAP hypothesis. We evolved Salmonella to adapt to growth on malate as the sole carbon source and followed the evolutionary trajectories. The initial adaptation to growth in the new environment involved the duplication of 1.66 Mb, corresponding to one-third of the Salmonella chromosome. This duplication is selected to increase the copy number of a single gene, dctA, involved in the uptake of malate. Continuing selection led to the rapid loss or mutation of duplicate genes from either copy of the duplicated region. After 2000 generations, only 31% of the originally duplicated genes remained intact and the gene order within the Salmonella chromosome has been significantly and irreversibly altered. These results experientially validate predictions made by the SNAP hypothesis and show that SNAP can be a strong driving force for rearrangements in chromosomal gene order.
对细菌基因组的分析表明，尽管不同的物种有许多共同的基因，但它们在染色体上的线性排列顺序往往并不保守。基因顺序的重排可能是由于遗传漂变引起的，另一种假设是在生态位适应（SNAP）过程中由正选择驱动的重排。在这里，我们首次为 SNAP 假说提供了实验证据。我们使沙门氏菌进化以适应以苹果酸作为唯一碳源的生长，并跟踪了进化轨迹。最初适应新环境的生长涉及 1.66 Mb 的重复，相当于沙门氏菌染色体的三分之一。这种重复是为了增加参与苹果酸摄取的单个基因 dctA 的拷贝数而选择的。持续的选择导致重复区域的两个拷贝中重复基因的快速丢失或突变。经过 2000 代后，只有 31%的原始重复基因保持完整，沙门氏菌染色体上的基因顺序发生了显著且不可逆转的改变。这些结果从实验上验证了 SNAP 假说的预测，并表明 SNAP 可以成为染色体基因顺序重排的强大驱动力。
