Getting into shape: How do rod-like bacteria control their geometry?

Amir, Ariel; Teeffelen, Sven van

doi:10.1007/s11693-014-9143-9

Cited by 19 publications

(25 citation statements)

References 65 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Numerical simulations validate our predictions as shown in Figure 6, where increasing the transcription factor size leads to higher (lower) repression when the target DNA is localized at the cell poles (mid-cell) with respect to a well-mixed model. The simulation results also show agreement between the predictions of the full PDE ((66) in SI Section 2.8) and reduced ODE model (21). Figure 16 in SI Section 2.8, further shows the temporal trajectories corresponding to Figure 6, also showing agreement between the full PDE model and the reduced ODE model.…”

Section: Gene Expression Regulation By Transcription Factorssupporting

confidence: 66%

“…This general set of reactions captures many core biological processes such as genes transcribed by RNA polymerase, mRNA translated by ribosomes, or proteins degraded by a common protease [1]. E. coli actively regulates its geometry to achieve a near-perfect cylindrical shape [21]. Thus, we model the cell as a cylinder of length 2L and radius R c .…”

Section: 11mentioning

confidence: 99%

“…Specifically, we are interested in how the steady state levels of P is affected by the spatial quantities r/r * and x * . From setting (21) to steady state, we obtain…”

Section: Gene Expression Regulation By Transcription Factorsmentioning

confidence: 99%

See 2 more Smart Citations

Effects of spatial heterogeneity on bacterial genetic circuits

Barajas

Vecchio

2019

Preprint

View full text Add to dashboard Cite

Highlights:• Intracellular spatial heterogeneity modulates the effective association rate constant of binding reactions through a binding correction factor (BCF) that fully captures spatial effects Abstract Intracellular spatial heterogeneity is frequently observed in bacteria, where the chromosome occupies part of the cell's volume and a circuit's DNA often localizes within the cell. How this heterogeneity affects core processes and genetic circuits is still poorly understood. In fact, commonly used ordinary differential equation (ODE) models of genetic circuits assume a well-mixed ensemble of molecules and, as such, do not capture spatial aspects. Reaction-diffusion partial differential equation (PDE) models have been only occasionally used since they are difficult to integrate and do not provide mechanistic understanding of the effects of spatial heterogeneity. In this paper, we derive a reduced ODE model that captures spatial effects, yet has the same dimension as commonly used well-mixed models. In particular, the only difference with respect to a well-mixed ODE model is that the association rate constant of binding reactions is multiplied by a coefficient, which we refer to as the binding correction factor (BCF). The BCF depends on the size of interacting molecules and on their location when fixed in space and it is equal to unity in a well-mixed ODE model. The BCF can be used to investigate how spatial heterogeneity affects the behavior of core processes and genetic circuits. Specifically, our reduced model indicates that transcription and its regulation are more effective for genes located at the cell poles than for genes located on the chromosome. The extent of these effects depends on the value of the BCF, which we found to be close to unity. For translation, the value of the BCF is always greater than unity, it increases with mRNA size, and, with biologically relevant parameters, is substantially larger than unity. Our model has broad validity, has the same dimension as a well-mixed model, yet it incorporates spatial heterogeneity. This simple-to-use model can be used to both analyze and design genetic circuits while accounting for spatial intracellular effects.

show abstract

Section: Gene Expression Regulation By Transcription Factorssupporting

confidence: 66%

Section: 11mentioning

confidence: 99%

See 1 more Smart Citation

Effects of spatial heterogeneity on bacterial genetic circuits

Barajas

Vecchio

2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Ref. [5] measures the newborn size distribution of E. coli using the membrane elution technique, and shows that it has non-negligible positive skewness and it agrees very well with a log-normal distribution.…”

Section: Cell Size Regulation In Microorganisms - Supplementary Informentioning

confidence: 99%

“…In spite of decades of research, we still do not have a good understanding of how cells regulate their shape, both mechanically (i.e., what is the biophysical feedback necessary to achieve a rod-shape cell? [5]) and dimensionally: the coefficient of variation (standard deviation:mean, CV) can be as low as 0.1 for bacteria [2]. Bacteria are also remarkable in their ability to have a generation time that is shorter than the time it takes them to replicate DNA: doubling time τ d for E. coli in rich media at 37°C is about 20 mins, while T r ≈ 60 mins are needed from initiation of DNA replication to cell division.…”

mentioning

confidence: 99%

Cell size regulation in bacteria

Amir

2014

Preprint

Self Cite

157

358

View full text Add to dashboard Cite

Various rod-shaped bacteria such as the canonical gram negative Escherichia coli or the wellstudied gram positive Bacillus subtilis divide symmetrically after they approximately double their volume. Their size at division is not constant, but is typically distributed over a narrow range. Here, we propose an analytically tractable model for cell size control, and calculate the cell size and interdivision time distributions. We suggest ways of extracting the model parameters from experimental data. Existing data for E. coli supports partial size control, and a particular explanation: a cell attempts to add a constant volume from the time of initiation of DNA replication to the next initiation event. This hypothesis explains how bacteria control their tight size distributions and accounts for the experimentally observed correlations between parents and daughters as well as the exponential dependence of size on growth rate.

show abstract

Spatial Organization of Cell Wall-Anchored Proteins at the Surface of Gram-Positive Bacteria

Dramsi¹,

Bierne²

2016

Current Topics in Microbiology and Immunology

View full text Add to dashboard Cite

Bacterial surface proteins constitute an amazing repertoire of molecules with important functions such as adherence, invasion, signalling and interaction with the host immune system or environment. In Gram-positive bacteria, many surface proteins of the "LPxTG" family are anchored to the peptidoglycan (PG) by an enzyme named sortase. While this anchoring mechanism has been clearly deciphered, less is known about the spatial organization of cell wall-anchored proteins in the bacterial envelope. Here, we review the question of the precise spatial and temporal positioning of LPxTG proteins in subcellular domains in spherical and ellipsoid bacteria (Staphylococcus aureus, Streptococcus pyogenes, Streptococcus agalactiae and Enterococcus faecalis) and in the rod-shaped bacterium Listeria monocytogenes. Deposition at specific sites of the cell wall is a dynamic process tightly connected to cell division, secretion, cell morphogenesis and levels of gene expression. Studying spatial occupancy of these cell wall-anchored proteins not only provides information on PG dynamics in responses to environmental changes, but also suggests that pathogenic bacteria control the distribution of virulence factors at specific sites of the surface, including pole, septa or lateral sites, during the infectious process.

show abstract

Getting into shape: How do rod-like bacteria control their geometry?

Cited by 19 publications

References 65 publications

Effects of spatial heterogeneity on bacterial genetic circuits

Effects of spatial heterogeneity on bacterial genetic circuits

Cell size regulation in bacteria

Spatial Organization of Cell Wall-Anchored Proteins at the Surface of Gram-Positive Bacteria

Contact Info

Product

Resources

About