DOI: 10.5061/dryad.2bs69
title: Data from: Threshold effect of growth rate on population variability of Escherichia coli cell lengths

description: A long-standing question in biology is the effect of growth on cell size.
 Here, we estimate the effect of Escherichia coli growth rate (r) on
 population cell size distributions by estimating the coefficient of
 variation of cell lengths (CVL) from image analysis of fixed cells in DIC
 microscopy. We find that the CVL is constant at growth rates less than one
 division per hour, whereas above this threshold, CVL increases with an
 increase in the growth rate. We hypothesize that stochastic inhibition of
 cell division owing to replication stalling by a RecA-dependent mechanism,
 combined with the growth rate threshold of multi-fork replication
 (according to Cooper and Helmstetter), could form the basis of such a
 threshold effect. We proceed to test our hypothesis by increasing the
 frequency of stochastic stalling of replication forks with hydroxyurea
 (HU) treatment and find that cell length variability increases only when
 the growth rate exceeds this threshold. The population effect is also
 reproduced in single-cell studies using agar-pad cultures and ‘mother
 machine’-based experiments to achieve synchrony. To test the role of RecA,
 critical for the repair of stalled replication forks, we examine the CVL
 of E. coli ΔrecA cells. We find cell length variability in the mutant to
 be greater than wild-type, a phenotype that is rescued by plasmid-based
 RecA expression. Additionally, we find that RecA-GFP protein recruitment
 to nucleoids is more frequent at growth rates exceeding the growth rate
 threshold and is further enhanced on HU treatment. Thus, we find growth
 rates greater than a threshold result in increased E. coli cell lengths in
 the population, and this effect is, at least in part, mediated by RecA
 recruitment to the nucleoid and stochastic inhibition of division.
description: Program to analyze E.
 coli cell lengths from DIC imagesDIC cell length
 detection code developed in MATLAB and released into the Open Source
 community. This code is suited for all elongated cell types and has been
 optimized for the purposes of analyzing E. coli cells. All the data
 analyzed in the related manuscript for cell-lengths has been generated
 using this program.E. coli population cell
 lengths: mutants, drug-treatment and growth ratesThe file includes the
 raw-data used to calculate the coefficient of variation of E. coli cell
 lengths. The data encompasses (as marked in the tabs) the growth rate
 modulation, mother-mother machine analysis, microc-colony analysis,
 multiple Hydroxyurea concentrations, Trimethoprim treatment and
 mutants.20170119-cellLengths-athale-gangan.xlsxVideo legendDescription of the Supplementary Videos S1 through S4.videoLegend-gangan.pdfSupplementary video S1The growth and division of a population of E. coli MG1655 cells on an agar-pad is followed in DIC (green) simultaneously with the HupA-GFP (red). The time-stamp is in units hh:mm. The arrow indicates a cell elongation event corresponding to a delay in nucleoid segregation. The scale bar is 10 μm.videoS1-K12-DIC-hupAGfp.movSupplementary video S2Time-lapse images of continuous culture of E. coli MG1655 cells grown in LB were acquired in DIC microscopy. The channels restricting the movement of the cells correspond to the dead-end channels of the ‘mother machine’, while the central trench corresponds to the nutrient channel. The interval between each frame is 100 seconds. The time stamp is hh:mm:ss. Scale bar: 5 μm.VideoS2-LBmothermachine.movSupplementary video S3Time-lapse images of E. coli MG1655 cells in continuous culture grown in the ‘mother machine’ with M9 + succinate as the medium at 37°C were recorded in DIC. Images were acquired every 120 s. The time stamp is hh:mm:ss. Scale bar: 5 μm.VideoS3-M9mothermachine.movSupplementary video S4DIC time series of E. coli MG1655 micro-colony originated from single mother cell and growing on agar pad at 37°C was imaged at an interval of 2 minutes between every frame. The time stamp is hh:mm:ss (Scale bar: 5 μm).VideoS4-DICmicrocolony.mov