[Paper Review] Fluctuations in growth rates determine the generation time and size distributions of E. coli cells

Mats Walldén, David Fange+2 more|arXiv (Cornell University)|Apr 13, 2015

DNA and Nucleic Acid Chemistry4 citations

TL;DR

This study demonstrates that cell-to-cell fluctuations in growth rates in isogenic E. coli populations are sufficient to explain the observed distributions of division size and generation time. Using single-molecule microscopy and a mechanistic model, the authors show that chromosome replication initiation occurs at a fixed volume per origin, followed by division after a growth rate-dependent delay, implying minimal additional regulation beyond volume-based initiation.

ABSTRACT

Isogenic Escherichia coli growing exponentially in a constant environment display large variation in growth-rates, division-sizes and generation-times. It is unclear how these seemingly random cell cycles can be reconciled with the precise regulation required under conditions where the generation time is shorter than the time to replicate the genome. Here we use single molecule microscopy to map the location of the replication machinery to the division cycle of individual cells. We find that the cell-to-cell variation in growth rate is sufficient to explain the corresponding variation in cell size and division timing assuming a simple mechanistic model. In the model, initiation of chromosome replication is triggered at a fixed volume per origin region, and associated with each initiation event is a division event at a growth rate dependent time later. The result implies that cell division in E. coli has no other regulation beyond what is needed to initiate DNA replication at the right volume.

Motivation & Objective

• To understand the origin of cell-to-cell variation in E. coli generation time and size under constant conditions.
• To determine whether growth rate fluctuations alone can account for observed distributions of division size and timing.
• To test whether a minimal mechanistic model based on volume-dependent replication initiation and fixed delay to division can reproduce experimental data.
• To assess whether additional regulatory mechanisms beyond volume sensing are required for cell cycle control in E. coli.

Proposed method

• Employed single-molecule fluorescence microscopy to visualize the location of the replication machinery (e.g., DnaX-GFP) in individual E. coli cells.
• Tracked the cell cycle stages—initiation of chromosome replication and cell division—over time in live, isogenic cells.
• Measured individual cell growth rates, division sizes, and generation times from time-lapse imaging data.
• Proposed a mechanistic model in which replication initiation occurs at a fixed cell volume per origin region.
• Assumed that each initiation event leads to cell division after a time delay that depends on the cell's growth rate.
• Used the model to simulate size and generation time distributions and compared them to experimental data.

Experimental results

Research questions

• RQ1 To what extent do fluctuations in individual growth rates explain the observed variation in E. coli cell size and division timing?
• RQ2 Is a volume-based initiation of DNA replication sufficient to account for the observed size and timing distributions?
• RQ3 Does the delay between replication initiation and cell division depend on growth rate, and if so, how?
• RQ4 Can a minimal model based on volume-dependent initiation and growth rate-dependent delay reproduce experimental data without additional regulation?
• RQ5 What is the role of additional regulatory mechanisms in E. coli cell cycle control, given the observed variability?

Key findings

• Cell-to-cell variation in growth rate alone is sufficient to explain the observed distributions of division size and generation time in isogenic E. coli populations.
• Replication initiation occurs at a fixed cell volume per origin region, independent of growth rate.
• The time delay between replication initiation and cell division is inversely proportional to the growth rate, meaning faster-growing cells divide sooner after initiation.
• Simulations based on the proposed model quantitatively reproduce the experimentally observed size and generation time distributions.
• The model implies that no additional regulatory mechanisms beyond volume-based initiation are required to explain the data.
• The study resolves the paradox of precise genome replication timing despite high cell-to-cell variability in growth and division.