The Escherichia coli cell cycle

Transcription-replication interactions reveal bacterial genome regulation

Organisms determine the transcription rates of thousands of genes through a few modes of regulation that recur across the genome1. In bacteria, the relationship between the regulatory architecture of a gene and its expression is well understood for individual model gene circuits2,3. However, a broader perspective of these dynamics at the genome scale is lacking, in part because bacterial transcriptomics has hitherto captured only a static snapshot of expression averaged across millions of cells4. As a result, the full diversity of gene expression dynamics and their relation to regulatory architecture remains unknown. Here we present a novel genome-wide classification of regulatory modes based on the transcriptional response of each gene to its own replication, which we term the transcription-replication interaction profile (TRIP). Analysing single-bacterium RNA-sequencing data, we found that the response to the universal perturbation of chromosomal replication integrates biological regulatory factors with biophysical molecular events on the chromosome to reveal the local regulatory context of a gene. Whereas the TRIPs of many genes conform to a gene dosage-dependent pattern, others diverge in distinct ways, and this is shaped by factors such as intra-operon position and repression state. By revealing the underlying mechanistic drivers of gene expression heterogeneity, this work provides a quantitative, biophysical framework for modelling replication-dependent expression dynamics.

Modes of cytometric bacterial DNA pattern: a tool for pursuing growth

Analyses of DNA pattern provide an excellent tool to determine activity states of bacteria. Bacterial cell cycle behaviour is generally different from the eukaryotic one and is pre-determined by the bacteria's diversity within the phylogenetic tree, and their metabolic traits. As a result, every species creates its specific proliferation pattern that differs from every other one. Up to now, just few bacterial species have been investigated and little information is available concerning DNA cycling even in already known species. This prevents understanding of the complexity and diversity of ongoing bacterial interactions in many ecosystems or in biotechnology. Flow cytometry is the only possible technique to shed light on the dynamics of bacterial communities and DNA patterns will help to unlock the hidden principles of their life. This review provides basic knowledge about the molecular background of bacterial cell cycling, discusses modes of cell cycle phases and presents techniques to both obtain DNA patterns and to combine the contained information with physiological cell states.

Regulation of DNA synthesis in bacteria: Analysis of the Bates/Kleckner licensing/initiation-mass model for cell cycle control

Bates and Kleckner have recently proposed that bacterial cell division is a licensing agent for a subsequent initiation of DNA replication. They also propose that initiation mass for DNA replication is not constant. These two proposals do not take into account older data showing that initiation of DNA replication can occur prior to the division event. This critical analysis is derived from measurements of DNA replication during the division cycle in cells growing at different, and more rapid, growth rates. Furthermore, mutants impaired in division can initiate DNA synthesis. The data presented by Bates and Kleckner do not support the proposal that initiation mass is variable, and the proposed pattern of DNA replication during the division cycle of the K12 cells analysed is not consistent with prior data on the pattern of DNA replication during the division cycle.

Distinguishing between linear and exponential cell growth during the division cycle: single-cell studies, cell-culture studies, and the object of cell-cycle research

BACKGROUND

Two approaches to understanding growth during the cell cycle are single-cell studies, where growth during the cell cycle of a single cell is measured, and cell-culture studies, where growth during the cell cycle of a large number of cells as an aggregate is analyzed. Mitchison has proposed that single-cell studies, because they show variations in cell growth patterns, are more suitable for understanding cell growth during the cell cycle, and should be preferred over culture studies. Specifically, Mitchison argues that one can glean the cellular growth pattern by microscopically observing single cells during the division cycle. In contrast to Mitchison's viewpoint, it is argued here that the biological laws underlying cell growth are not to be found in single-cell studies. The cellular growth law can and should be understood by studying cells as an aggregate.

RESULTS

The purpose or objective of cell cycle analysis is presented and discussed. These ideas are applied to the controversy between proponents of linear growth as a possible growth pattern during the cell cycle and the proponents of exponential growth during the cell cycle. Differential (pulse) and integral (single cell) experiments are compared with regard to cell cycle analysis and it is concluded that pulse-labeling approaches are preferred over microscopic examination of cell growth for distinguishing between linear and exponential growth patterns. Even more to the point, aggregate experiments are to be preferred to single-cell studies.

CONCLUSION

The logical consistency of exponential growth--integrating and accounting for biochemistry, cell biology, and rigorous experimental analysis--leads to the conclusion that proposals of linear growth are the result of experimental perturbations and measurement limitations. It is proposed that the universal pattern of cell growth during the cell cycle is exponential.

Synthesis of the cell surface during the division cycle of rod-shaped, gram-negative bacteria

When the growth of the gram-negative bacterial cell wall is considered in relation to the synthesis of the other components of the cell, a new understanding of the pattern of wall synthesis emerges. Rather than a switch in synthesis between the side wall and pole, there is a partitioning of synthesis such that the volume of the cell increases exponentially and thus perfectly encloses the exponentially increasing cytoplasm. This allows the density of the cell to remain constant during the division cycle. This model is explored at both the cellular and molecular levels to give a unified description of wall synthesis which has the following components: (i) there is no demonstrable turnover of peptidoglycan during cell growth, (ii) the side wall grows by diffuse intercalation, (iii) pole synthesis starts by some mechanism and is preferentially synthesized compared with side wall, and (iv) the combined side wall and pole syntheses enclose the newly synthesized cytoplasm at a constant cell density. The central role of the surface stress model in wall growth is distinguished from, and preferred to, models that propose cell-cycle-specific signals as triggers of changes in the rate of wall synthesis. The actual rate of wall synthesis during the division cycle is neither exponential nor linear, but is close to exponential when compared with protein synthesis during the division cycle.

Growth rate of Escherichia coli

It should be possible to predict the rate of growth of Escherichia coli of a given genotype in a specified environment. The idea that the rate of synthesis of ATP determines the rate of growth and that the yield of ATP determines the yield of growth is entrenched in bacterial physiology, yet this idea is inconsistent with experimental results. In minimal media the growth rate and yield vary with the carbon source in a manner independent of the rate of formation and yield of ATP. With acetate as the carbon source, anapleurotic reactions, not ATP synthesis, limit the growth rate. For acetate and other gluconeogenic substrates the limiting step appears to be the formation of triose phosphate. I conclude that the rate of growth is controlled by the rate of formation of a precursor metabolite and, thus, of monomers such as amino acids derived from it. The protein-synthesizing system is regulated according to demand for protein synthesis. I examine the conjecture that the signal for this regulation is the ratio of uncharged tRNA to aminoacyl-tRNA, that this signal controls the concentration of guanosine tetraphosphate, and that the concentration of guanosine tetraphosphate controls transcription of rrn genes. Differential equations describing this system were solved numerically for steady states of growth; the computed values of ribosomes and guanosine tetraphosphate and the maximal growth rate agree with experimental values obtained from the literature of the past 35 years. These equations were also solved for dynamical states corresponding to nutritional shifts up and down.