Hua Qiang, Joyce Andrew R, Palsson Bernhard Ø, Fong Stephen S
Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093-0412, USA.
Appl Environ Microbiol. 2007 Jul;73(14):4639-47. doi: 10.1128/AEM.00527-07. Epub 2007 May 18.
In comparison with intensive studies of genetic mechanisms related to biological evolutionary systems, much less analysis has been conducted on metabolic network responses to adaptive evolution that are directly associated with evolved metabolic phenotypes. Metabolic mechanisms involved in laboratory evolution of Escherichia coli on gluconeogenic carbon sources, such as lactate, were studied based on intracellular flux states determined from 13C tracer experiments and 13C-constrained flux analysis. At the end point of laboratory evolution, strains exhibited a more than doubling of the average growth rate and a 50% increase in the average biomass yield. Despite different evolutionary trajectories among parallel evolved populations, most improvements were obtained within the first 250 generations of evolution and were generally characterized by a significant increase in pathway capacity. Partitioning between gluconeogenic and pyruvate catabolic flux at the pyruvate node remained almost unchanged, while flux distributions around the key metabolites phosphoenolpyruvate, oxaloacetate, and acetyl-coenzyme A were relatively flexible over the course of evolution on lactate to meet energetic and anabolic demands during rapid growth on this gluconeogenic carbon substrate. There were no clear qualitative correlations between most transcriptional expression and metabolic flux changes, suggesting complex regulatory mechanisms at multiple levels of genetics and molecular biology. Moreover, higher fitness gains for cell growth on both evolutionary and alternative carbon sources were found for strains that adaptively evolved on gluconeogenic carbon sources compared to those that evolved on glucose. These results provide a novel systematic view of the mechanisms underlying microbial adaptation to growth on a gluconeogenic substrate.
与对生物进化系统相关遗传机制的深入研究相比，对于与进化后的代谢表型直接相关的代谢网络对适应性进化的反应所进行的分析要少得多。基于从13C示踪实验和13C约束通量分析确定的细胞内通量状态，研究了大肠杆菌在糖异生碳源（如乳酸）上的实验室进化中涉及的代谢机制。在实验室进化的终点，菌株的平均生长速率增加了一倍多，平均生物量产量增加了50%。尽管平行进化群体之间的进化轨迹不同，但大多数改进是在进化的前250代内实现的，并且通常以途径能力的显著增加为特征。丙酮酸节点处糖异生和丙酮酸分解代谢通量之间的分配几乎保持不变，而在乳酸进化过程中，关键代谢物磷酸烯醇丙酮酸、草酰乙酸和乙酰辅酶A周围的通量分布相对灵活，以满足在这种糖异生碳底物上快速生长期间的能量和合成代谢需求。大多数转录表达和代谢通量变化之间没有明显的定性相关性，这表明在遗传学和分子生物学的多个水平上存在复杂的调控机制。此外，与在葡萄糖上进化的菌株相比，在糖异生碳源上适应性进化的菌株在进化碳源和替代碳源上细胞生长的适应性增益更高。这些结果为微生物适应在糖异生底物上生长的潜在机制提供了一个新的系统观点。
