Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.
DNA Res. 2020 Jun 1;27(3). doi: 10.1093/dnares/dsaa018.
The growth rate, representing the fitness of a bacterial population, is determined by the transcriptome. Chromosomal periodicity, which is known as the periodic spatial pattern of a preferred chromosomal distance in microbial genomes, is a representative overall feature of the transcriptome; however, whether and how it is associated with the bacterial growth rate are unknown. To address these questions, we analysed a total of 213 transcriptomes of multiple Escherichia coli strains growing in an assortment of culture conditions varying in terms of temperature, nutrition level and osmotic pressure. Intriguingly, Fourier transform analyses of the transcriptome identified a common chromosomal periodicity of transcriptomes, which was independent of the variation in genomes and environments. In addition, fitting of the data to a theoretical model, we found that the amplitudes of the periodic transcriptomes were significantly correlated with the growth rates. These results indicated that the amplitude of periodic transcriptomes is a parameter representing the global pattern of gene expression in correlation with the bacterial growth rate. Thus, our study provides a novel parameter for evaluating the adaptiveness of a growing bacterial population and quantitatively predicting the growth dynamics according to the global expression pattern.
增长率代表了细菌群体的适应性，由转录组决定。染色体周期性是微生物基因组中优选染色体距离的周期性空间模式的代表整体特征，但它是否以及如何与细菌的生长速度相关尚不清楚。为了解决这些问题，我们分析了在不同温度、营养水平和渗透压的培养条件下生长的 213 株大肠杆菌的总转录组。有趣的是，对转录组的傅里叶变换分析确定了转录组的常见染色体周期性，该周期性独立于基因组和环境的变化。此外，通过将数据拟合到理论模型，我们发现周期性转录组的幅度与生长速率显著相关。这些结果表明，周期性转录组的幅度是一个与细菌生长速率相关的基因表达整体模式的参数。因此，我们的研究为评估生长中细菌群体的适应性提供了一个新的参数，并根据全局表达模式定量预测生长动态。
