Genetic and physiological characterization of a spontaneous mutant of Escherichia coli B/r with aberrant control of deoxyribonucleic acid replication

Fundamental principles in bacterial physiology-history, recent progress, and the future with focus on cell size control: a review

Bacterial physiology is a branch of biology that aims to understand overarching principles of cellular reproduction. Many important issues in bacterial physiology are inherently quantitative, and major contributors to the field have often brought together tools and ways of thinking from multiple disciplines. This article presents a comprehensive overview of major ideas and approaches developed since the early 20th century for anyone who is interested in the fundamental problems in bacterial physiology. This article is divided into two parts. In the first part (sections 1-3), we review the first 'golden era' of bacterial physiology from the 1940s to early 1970s and provide a complete list of major references from that period. In the second part (sections 4-7), we explain how the pioneering work from the first golden era has influenced various rediscoveries of general quantitative principles and significant further development in modern bacterial physiology. Specifically, section 4 presents the history and current progress of the 'adder' principle of cell size homeostasis. Section 5 discusses the implications of coarse-graining the cellular protein composition, and how the coarse-grained proteome 'sectors' re-balance under different growth conditions. Section 6 focuses on physiological invariants, and explains how they are the key to understanding the coordination between growth and the cell cycle underlying cell size control in steady-state growth. Section 7 overviews how the temporal organization of all the internal processes enables balanced growth. In the final section 8, we conclude by discussing the remaining challenges for the future in the field.

Chromosome replication in Escherichia coli induced by oversupply of DnaA

Overexpression of DnaA protein from a multicopy plasmid accompanied by a shift to 42 degrees C causes initiation of one extra round of replication in a dnaA+ strain grown in glycerol minimal medium. This extra round of replication does not lead to an extra cell division, such that cells contain twice the normal number of chromosomes.

Analysis of the physiological control of replication of ColE1-type plasmids

The physiology of ColE1-type plasmid replication in a growing host has been examined both theoretically, using computer simulation, and experimentally, by observing replication of the plasmid pBR322 after a nutritional shift-up from glycerol minimal medium (doubling time 71 min) to LB medium (doubling time 24 min). The theory was based on a negative control model and uses three rate equations: for the accumulation of cell mass, for the accumulation of the replication inhibitor, and for the rate of plasmid synthesis. The implications of the theory were explored by simulating the effects of changes in the expression of replication control genes. The nutritional shift-up experiment showed that plasmid replication was blocked immediately after the shift for about half a mass doubling time; after that time, replication rapidly increased until plasmid numbers per unit volume of culture parallelled the increase in culture mass. After the establishment of steady-state growth in the post-shift medium, the plasmid concentration (plasmids per cell mass) was reduced in comparison to pre-shift growth in the same proportion as the culture doubling time. The results showed that plasmid replication factors are under metabolic control and that the changes in the control of these factors compensate one another during steady-state growth, but not immediately after the medium shift.

A stochastic process determines the time at which cell division begins in Escherichia coli

The theoretical distributions of cell masses in exponential cultures of bacteria were derived for both total cells and cells having formed a constriction in preparation for division. The parameters used for this derivation include the mass doubling time, tau, the T-period, and 3 statistical parameters (h, sigma 1, sigma 2) which describe the variability of the cell cycle. The theoretical distributions were compared with observed distributions from E. coli B/rA growing in glucose minimal medium (45 min doubling time) to determine whether a stochastic process in the division pathway affects the time of initiation of constriction or the duration of the constriction process. The results indicate that the stochastic process determines the onset rather than the completion of constriction and that the timing of this process is coupled (6% variability, = sigma 1) to a given cell mass. The values obtained for the duration of the T-period, T = 9.3 min, and for a half-life parameter associated with the stochastic process, h = 4.3 min, agree with previously reported data.

Cell division in Escherichia coli after changes in the velocity of DNA replication

A method of computer analysis was developed to evaluate the kinetic changes in the rate of cell division in non-synchronous cultures of E. coli resulting from changes in the velocity or initiation of chromosome replication. This method takes into account that the cell division pathway in E. coli includes a reaction of indeterminate length described by a probability function that applies to the cell population. The analysis yields a hypothetical cell number kinetics as it would be observed if the stochastic element in the division pathway were absent. Since this derived cell number curve responds to experimentally induced perturbations of replication at defined times whereas the actual cell number curve reflects these perturbations only in a blurred fashion, replication and division events can be precisely correlated with this method. The method was applied to the evaluation of thymine starvation experiments with two Thy- derivatives of E. coli B/r; one of the strains has a mutationally altered (60% increased) cell mass at initiation of chromosome replication. In both strains, the stochastic phase of the cell cycle had the same half-life value of 10 min and began 18 min after each termination of replication. This suggests that the time of cell division is linked to replication, not to cell mass or length. This interpretation is supported by results of experiments in which the rate of cell growth was altered at the time of thymine starvation.

Transcription in bacteria at different DNA concentrations

The effect of changing the DNA concentration on RNA synthesis, protein synthesis, and cell growth rate was studied in Escherichia coli B/r. The DNA concentration was varied by changing the replication velocity or by changing replication initiation in a thymine-requiring strain with a mutation in replication control. The results demonstrate that changes in DNA concentration (per mass) have no effect on the cell growth rate and the rates of synthesis (per mass) of stable RNA (rRNA, tRNA), bulk mRNA, or protein or on the concentration of RNA polymerase (total RNA polymerase per mass). Thus, transcription in E. coli is not limited by the concentration of DNA, but rather by the concentration of functional RNA polymerase in the cytoplasm. Changing the DNA concentration does, however, affect fully induced lac gene activity, here used as a model for constitutive gene expression. The magnitude of the effect of DNA concentration on lac gene activity depends on the distribution of replication forks over the chromosome, which is a function of the replication velocity. Analysis of these date reinforces the conclusion that transcription is limited by the concentration of functional RNA polymerase in the cytoplasm.

Growth rate-dependent control of chromosome replication initiation in Escherichia coli

The initiation mass, defined as cell mass per origin of deoxyribonucleic acid replication (optical density units at 460 nm of culture/origins per milliliter of culture), reflects the intracellular concentration or activity of a hypothetical factor that controls initiation of chromosome replication in bacteria. In Escherichia coli B/r, the initiation mass was found to increase about twofold with increasing growth rate between 0.6 and 1.6 doublings per h; at higher growth rates it remained essentially constant (measured up to 2.4 doublings per h). A low-thymine-requiring (thyA deoB) derivative of E. coli B/r, strain TJK16, was found to have a 60 to 80% greater initiation mass than B/r which was independent of the replication velocity and not related to the thyA and deoB mutations. It is suggested that TJK16 had acquired, during its isolation, a mutation in a gene affecting the initiation of deoxyribonucleic acid replication. The initiation age was not altered by this mutation, but other parameters, including deoxyribonucleic acid concentration and cell size, were changed in comparison with the B/r parent, as expected from theoretical considerations.