Genome concentration limits cell growth and modulates proteome composition in Escherichia coli

• Published in: eLife 2024-12, Vol.13
• Main Authors: Mäkelä, Jarno, Papagiannakis, Alexandros, Lin, Wei-Hsiang, Lanz, Michael Charles, Glenn, Skye, Swaffer, Matthew, Marinov, Georgi K, Skotheim, Jan M, Jacobs-Wagner, Christine
• Format: Article
• Language: English
• Subjects: Caulobacter crescentus; Caulobacter crescentus - genetics; Caulobacter crescentus - growth & development; Caulobacter crescentus - metabolism; Cell Biology; cell growth; DNA Replication; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Gene Expression Regulation, Bacterial; Genome, Bacterial; limitation; Proteome - metabolism; proteome allocation; ribosomes; Ribosomes - metabolism; transcription
• ISSN: 2050-084X; 2050-084X
• 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.