Mäkelä Jarno, Papagiannakis Alexandros, Lin Wei-Hsiang, Lanz Michael Charles, Glenn Skye, Swaffer Matthew, Marinov Georgi K, Skotheim Jan M, Jacobs-Wagner Christine
Howard Hughes Medical Institute, Stanford University, Stanford, United States.
Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, United States.
Elife. 2024 Dec 23;13:RP97465. doi: 10.7554/eLife.97465.
Defining the cellular factors that drive growth rate and proteome composition is essential for understanding and manipulating cellular systems. In bacteria, ribosome concentration is known to be a constraining factor of cell growth rate, while gene concentration is usually assumed not to be limiting. Here, using single-molecule tracking, quantitative single-cell microscopy, and modeling, we show that genome dilution in cells arrested for DNA replication limits total RNA polymerase activity within physiological cell sizes across tested nutrient conditions. This rapid-onset limitation on bulk transcription results in sub-linear scaling of total active ribosomes with cell size and sub-exponential growth. Such downstream effects on bulk translation and cell growth are near-immediately detectable in a nutrient-rich medium, but delayed in nutrient-poor conditions, presumably due to cellular buffering activities. RNA sequencing and tandem-mass-tag mass spectrometry experiments further reveal that genome dilution remodels the relative abundance of mRNAs and proteins with cell size at a global level. Altogether, our findings indicate that chromosome concentration is a limiting factor of transcription and a global modulator of the transcriptome and proteome composition in . Experiments in and comparison with eukaryotic cell studies identify broadly conserved DNA concentration-dependent scaling principles of gene expression.
确定驱动生长速率和蛋白质组组成的细胞因子对于理解和操纵细胞系统至关重要。在细菌中，核糖体浓度是细胞生长速率的限制因素，而基因浓度通常被认为不是限制因素。在这里，我们使用单分子追踪、定量单细胞显微镜和建模方法，发现在因DNA复制而停滞的细胞中，基因组稀释在测试的营养条件下限制了生理细胞大小内的总RNA聚合酶活性。这种对整体转录的快速限制导致总活性核糖体与细胞大小呈亚线性缩放以及亚指数生长。这种对整体翻译和细胞生长的下游影响在富含营养的培养基中几乎可以立即检测到，但在营养贫乏条件下会延迟，这可能是由于细胞缓冲活动所致。RNA测序和串联质量标签质谱实验进一步揭示，基因组稀释在全球范围内重塑了mRNA和蛋白质相对于细胞大小的相对丰度。总之，我们的研究结果表明，染色体浓度是转录的限制因素，也是转录组和蛋白质组组成的全局调节剂。在大肠杆菌中的实验以及与真核细胞研究的比较确定了基因表达中广泛保守的DNA浓度依赖性缩放原则。
