Karcagi Ildikó, Draskovits Gábor, Umenhoffer Kinga, Fekete Gergely, Kovács Károly, Méhi Orsolya, Balikó Gabriella, Szappanos Balázs, Györfy Zsuzsanna, Fehér Tamás, Bogos Balázs, Blattner Frederick R, Pál Csaba, Pósfai György, Papp Balázs
Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.
Scarab Genomics LLC, Madison, WI.
Mol Biol Evol. 2016 May;33(5):1257-69. doi: 10.1093/molbev/msw009. Epub 2016 Jan 14.
Why are certain bacterial genomes so small and compact? The adaptive genome streamlining hypothesis posits that selection acts to reduce genome size because of the metabolic burden of replicating DNA. To reveal the impact of genome streamlining on cellular traits, we reduced the Escherichia coli genome by up to 20% by deleting regions which have been repeatedly subjects of horizontal transfer in nature. Unexpectedly, horizontally transferred genes not only confer utilization of specific nutrients and elevate tolerance to stresses, but also allow efficient usage of resources to build new cells, and hence influence fitness in routine and stressful environments alike. Genome reduction affected fitness not only by gene loss, but also by induction of a general stress response. Finally, we failed to find evidence that the advantage of smaller genomes would be due to a reduced metabolic burden of replicating DNA or a link with smaller cell size. We conclude that as the potential energetic benefit gained by deletion of short genomic segments is vanishingly small compared with the deleterious side effects of these deletions, selection for reduced DNA synthesis costs is unlikely to shape the evolution of small genomes.
为什么某些细菌基因组如此小而紧凑？适应性基因组精简假说认为，由于复制DNA的代谢负担，选择作用会减小基因组大小。为了揭示基因组精简对细胞特性的影响，我们通过删除自然界中多次发生水平转移的区域，将大肠杆菌基因组减少了多达20%。出乎意料的是，水平转移基因不仅赋予了对特定营养物质的利用能力并提高了对压力的耐受性，还能使资源有效地用于构建新细胞，从而在常规和压力环境中均影响适应性。基因组减少不仅通过基因丢失影响适应性，还通过诱导一般应激反应来实现。最后，我们没有找到证据表明较小基因组的优势是由于复制DNA的代谢负担减轻或与较小细胞大小有关。我们得出结论，由于与这些缺失的有害副作用相比，删除短基因组片段所获得的潜在能量益处微乎其微，因此选择降低DNA合成成本不太可能塑造小基因组的进化。
