Matsumoto Yuki, Murakami Yoshie, Tsuru Saburo, Ying Bei-Wen, Yomo Tetsuya
Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
BMC Genomics. 2013 Nov 20;14:808. doi: 10.1186/1471-2164-14-808.
Cell growth rate reflects an organism's physiological state and largely relies on the ability of gene expression to respond to the environment. The relationship between cellular growth rate and gene expression remains unknown.
Growth rate-coordinated changes in gene expression were discovered by analyzing exponentially growing Escherichia coli cells cultured under multiple defined environments, in which osmotic pressure, temperature and starvation status were varied. Gene expression analyses showed that all 3,740 genes in the genome could be simply divided into three clusters (C1, C2 and C3), which were accompanied by a generic trend in the growth rate that was coordinated with transcriptional changes. The direction of transcriptional change in C1 indicated environmental specificity, whereas those in C2 and C3 were correlated negatively and positively with growth rates, respectively. The three clusters exhibited differentiated gene functions and gene regulation task division.
We identified three gene clusters, exhibiting differential gene functions and distinct directions in their correlations with growth rates. Reverses in the direction of the growth rate correlated transcriptional changes and the distinguished duties of the three clusters indicated how transcriptome homeostasis is maintained to balance the total expression cost for sustaining life in new habitats.
细胞生长速率反映了生物体的生理状态，并且在很大程度上依赖于基因表达对环境作出反应的能力。细胞生长速率与基因表达之间的关系仍然未知。
通过分析在多种限定环境下培养的指数生长的大肠杆菌细胞发现了生长速率协调的基因表达变化，在这些环境中渗透压、温度和饥饿状态是变化的。基因表达分析表明基因组中的所有3740个基因可以简单地分为三个簇（C1、C2和C3），这伴随着与转录变化协调的生长速率的一般趋势。C1中转录变化的方向表明环境特异性，而C2和C3中的转录变化分别与生长速率呈负相关和正相关。这三个簇表现出不同的基因功能和基因调控任务分工。
我们鉴定出三个基因簇，它们在与生长速率的相关性方面表现出不同的基因功能和不同的方向。生长速率相关转录变化方向的逆转以及这三个簇的不同职责表明了转录组稳态是如何维持的，以平衡在新栖息地维持生命的总表达成本。
