scholarly journals The protein translation machinery is expressed for maximal efficiency in Escherichia coli

2019 ◽  
Author(s):  
Xiao-Pan Hu ◽  
Hugo Dourado ◽  
Martin J. Lercher
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Protein Synthesis ◽  
Growth Rates ◽  
Mechanistic Model ◽  
Limited Resource ◽  
Protein Translation ◽  
Free Ribosome ◽  
Elongation Factors ◽  
E Coli

AbstractProtein synthesis is the most expensive process in fast-growing bacteria1,2. The economic aspects of protein synthesis at the cellular level have been investigated by estimating ribosome activity3–5 and the expression of ribosomes3,6, tRNA7–9, mRNA2, and elongation factors10,11. The observed growth-rate dependencies form the basis of powerful phenomenological bacterial growth laws5,12–16; however, a quantitative theory allowing us to understand these phenomena on the basis of fundamental biophysical and biochemical principles is currently lacking. Here, we show that the observed growth-rate dependence of the concentrations of ribosomes, tRNAs, mRNA, and elongation factors in Escherichia coli can be predicted accurately by minimizing cellular costs in a detailed mathematical model of protein translation; the mechanistic model is only constrained by the physicochemical properties of the molecules and requires no parameter fitting. We approximate the costs of molecule species through their masses, justified by the observation that cellular dry mass per volume is roughly constant across growth rates17 and hence represents a limited resource. Our results also account quantitatively for observed RNA/protein ratios and ribosome activities in E. coli across diverse growth conditions, including antibiotic stresses. Our prediction of active and free ribosome abundance facilitates an estimate of the deactivated ribosome reserve14,18,19, which reaches almost 50% at the lowest growth rates. We conclude that the growth rate dependent composition of E coli’s protein synthesis machinery is a consequence of natural selection for minimal total cost under physicochemical constraints, a paradigm that might generally be applied to the analysis of resource allocation in complex biological systems.

scholarly journals The protein translation machinery is expressed for maximal efficiency in Escherichia coli

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Xiao-Pan Hu ◽  
Hugo Dourado ◽  
Peter Schubert ◽  
Martin J. Lercher
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Protein Synthesis ◽  
Cost Minimization ◽  
Mechanistic Model ◽  
Protein Translation ◽  
Translation Machinery ◽  
Growth Laws ◽  
Molecular Masses ◽  
Expensive Process

Abstract Protein synthesis is the most expensive process in fast-growing bacteria. Experimentally observed growth rate dependencies of the translation machinery form the basis of powerful phenomenological growth laws; however, a quantitative theory on the basis of biochemical and biophysical constraints is lacking. Here, we show that the growth rate-dependence of the concentrations of ribosomes, tRNAs, mRNA, and elongation factors observed in Escherichia coli can be predicted accurately from a minimization of cellular costs in a mechanistic model of protein translation. The model is constrained only by the physicochemical properties of the molecules and has no adjustable parameters. The costs of individual components (made of protein and RNA parts) can be approximated through molecular masses, which correlate strongly with alternative cost measures such as the molecules’ carbon content or the requirement of energy or enzymes for their biosynthesis. Analogous cost minimization approaches may facilitate similar quantitative insights also for other cellular subsystems.

scholarly journals Rapid Growth of UropathogenicEscherichia coliduring Human Urinary Tract Infection

mBio ◽  
2018 ◽  
Vol 9 (2) ◽  
Author(s):  
Valerie S. Forsyth ◽  
Chelsie E. Armbruster ◽  
Sara N. Smith ◽  
Ali Pirani ◽  
A. Cody Springman ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Urinary Tract ◽  
Growth Rates ◽  
High Growth ◽  
Replication Forks ◽  
Chromosomal Replication ◽  
E Coli ◽  
Tract Infections

ABSTRACTUropathogenicEscherichia coli(UPEC) strains cause most uncomplicated urinary tract infections (UTIs). These strains are a subgroup of extraintestinal pathogenicE. coli(ExPEC) strains that infect extraintestinal sites, including urinary tract, meninges, bloodstream, lungs, and surgical sites. Here, we hypothesize that UPEC isolates adapt to and grow more rapidly within the urinary tract than otherE. coliisolates and survive in that niche. To date, there has not been a reliable method available to measure their growth ratein vivo. Here we used two methods: segregation of nonreplicating plasmid pGTR902, and peak-to-trough ratio (PTR), a sequencing-based method that enumerates bacterial chromosomal replication forks present during cell division. In the murine model of UTI, UPEC strain growth was robustin vivo, matching or exceedingin vitrogrowth rates and only slowing after reaching high CFU counts at 24 and 30 h postinoculation (hpi). In contrast, asymptomatic bacteriuria (ABU) strains tended to maintain high growth ratesin vivoat 6, 24, and 30 hpi, and population densities did not increase, suggesting that host responses or elimination limited population growth. Fecal strains displayed moderate growth rates at 6 hpi but did not survive to later times. By PTR,E. coliin urine of human patients with UTIs displayed extraordinarily rapid growth during active infection, with a mean doubling time of 22.4 min. Thus, in addition to traditional virulence determinants, including adhesins, toxins, iron acquisition, and motility, very high growth ratesin vivoand resistance to the innate immune response appear to be critical phenotypes of UPEC strains.IMPORTANCEUropathogenicEscherichia coli(UPEC) strains cause most urinary tract infections in otherwise healthy women. While we understand numerous virulence factors are utilized byE. colito colonize and persist within the urinary tract, these properties are inconsequential unless bacteria can divide rapidly and survive the host immune response. To determine the contribution of growth rate to successful colonization and persistence, we employed two methods: one involving the segregation of a nonreplicating plasmid in bacteria as they divide and the peak-to-trough ratio, a sequencing-based method that enumerates chromosomal replication forks present during cell division. We found that UPEC strains divide extraordinarily rapidly during human UTIs. These techniques will be broadly applicable to measurein vivogrowth rates of other bacterial pathogens during host colonization.

Quantitative relationships for specific growth rates and macromolecular compositions of Mycobacterium tuberculosis, Streptomyces coelicolor A3(2) and Escherichia coli B/r: an integrative theoretical approach

Microbiology ◽  
2004 ◽  
Vol 150 (5) ◽  
pp. 1413-1426 ◽  
Author(s):  
Robert A. Cox
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Mycobacterium Tuberculosis ◽  
Growth Rates ◽  
Specific Growth ◽  
Streptomyces Coelicolor ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
E Coli ◽  
Specific Growth Rates

Further understanding of the physiological states of Mycobacterium tuberculosis and other mycobacteria was sought through comparisons with the genomic properties and macromolecular compositions of Streptomyces coelicolor A3(2), grown at 30 °C, and Escherichia coli B/r, grown at 37 °C. A frame of reference was established based on quantitative relationships observed between specific growth rates (μ) of cells and their macromolecular compositions. The concept of a schematic cell based on transcription/translation coupling, average genes and average proteins was developed to provide an instantaneous view of macromolecular synthesis carried out by cells growing at their maximum rate. It was inferred that the ultra-fast growth of E. coli results from its ability to increase the average number of rRNA (rrn) operons per cell through polyploidy, thereby increasing its capacity for ribosome synthesis. The maximum growth rate of E. coli was deduced to be limited by the rate of uptake and consumption of nutrients providing energy. Three characteristic properties of S. coelicolor A3(2) growing optimally (μ=0·30 h−1) were identified. First, the rate of DNA replication was found to approach the rate reported for E. coli (μ=1·73 h−1); secondly, all rrn operons were calculated to be fully engaged in precursor-rRNA synthesis; thirdly, compared with E. coli, protein synthesis was found to depend on higher concentrations of ribosomes and lower concentrations of aminoacyl-tRNA and EF-Tu. An equation was derived for E. coli B/r relating μ to the number of rrn operons per genome. Values of μ=0·69 h−1 and μ=1·00 h−1 were obtained respectively for cells with one or two rrn operons per genome. Using the author's equation relating the number of rrn operons per genome to maximum growth rate, it is expected that M. tuberculosis with one rrn operon should be capable of growing much faster than it actually does. Therefore, it is suggested that the high number of insertion sequences in this species attenuates growth rate to still lower values.

scholarly journals Threshold effect of growth rate on population variability of Escherichia coli cell lengths

2017 ◽  
Vol 4 (2) ◽  
pp. 160417 ◽  
Author(s):  
Manasi S. Gangan ◽  
Chaitanya A. Athale
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Cell Size ◽  
Growth Rates ◽  
Threshold Effect ◽  
Cell Length ◽  
Replication Forks ◽  
E Coli ◽  
Cell Size Distributions ◽  
Rate Threshold

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 (CV L ) from image analysis of fixed cells in DIC microscopy. We find that the CV L is constant at growth rates less than one division per hour, whereas above this threshold, CV L 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 CV L 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.

scholarly journals Slowdown of Translational Elongation in Escherichia coli under Hyperosmotic Stress

mBio ◽  
2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Xiongfeng Dai ◽  
Manlu Zhu ◽  
Mya Warren ◽  
Rohan Balakrishnan ◽  
Hiroyuki Okano ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Protein Synthesis ◽  
Cell Growth ◽  
Bacterial Growth ◽  
Protein Translation ◽  
Hyperosmotic Stress ◽  
Bacterial Growth Rate ◽  
Translation Elongation ◽  
Bacterial Protein Synthesis

ABSTRACTIn nature, bacteria frequently experience many adverse conditions, including heat, oxidation, acidity, and hyperosmolarity, which all tend to slow down if not outright stop cell growth. Previous work on bacterial stress mainly focused on understanding gene regulatory responses. Much less is known about how stresses compromise protein synthesis, which is the major driver of cell growth. Here, we quantitatively characterize the translational capacity ofEscherichia colicells growing exponentially under hyperosmotic stress. We found that hyperosmotic stress affects bacterial protein synthesis through reduction of the translational elongation rate, which is largely compensated for by an increase in the cellular ribosome content compared with nutrient limitation at a similar growth rate. The slowdown of translational elongation is attributed to a reduction in the rate of binding of tRNA ternary complexes to the ribosomes.IMPORTANCEHyperosmotic stress is a common stress condition confronted byE. coliduring infection of the urinary tract. It can significantly compromise the bacterial growth rate. Protein translation capacity is a critical component of bacterial growth. In this study, we find for the first time that hyperosmotic stress causes substantial slowdown in bacterial ribosome translation elongation. The slowdown of translation elongation originates from a reduced binding rate of tRNA ternary complex to the ribosomes.

scholarly journals Specific Growth Rate Determines the Sensitivity of Escherichia coli to Thermal, UVA, and Solar Disinfection

2006 ◽  
Vol 72 (4) ◽  
pp. 2586-2593 ◽  
Author(s):  
Michael Berney ◽  
Hans-Ulrich Weilenmann ◽  
Julian Ihssen ◽  
Claudio Bassin ◽  
Thomas Egli
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Specific Growth Rate ◽  
Growth Rates ◽  
Specific Growth ◽  
E Coli ◽  
Mild Heat ◽  
Uva Light ◽  
Specific Growth Rates ◽  
Slow Growing

ABSTRACT Knowledge about the sensitivity of the test organism is essential for the evaluation of any disinfection method. In this work we show that sensitivity of Escherichia coli MG1655 to three physical stresses (mild heat, UVA light, and sunlight) that are relevant in the disinfection of drinking water with solar radiation is determined by the specific growth rate of the culture. Batch- and chemostat-cultivated cells from cultures with similar specific growth rates showed similar stress sensitivities. Generally, fast-growing cells were more sensitive to the stresses than slow-growing cells. For example, slow-growing chemostat-cultivated cells (D = 0.08 h−1) and stationary-phase bacteria from batch culture that were exposed to mild heat had very similar T 90 (time until 90% of the population is inactivated) values (T 90, chemostat = 2.66 h; T 90, batch = 2.62 h), whereas T 90 for cells growing at a μ of 0.9 h−1 was 0.2 h. We present evidence that the stress sensitivity of E. coli is correlated with the intracellular level of the alternative sigma factor RpoS. This is also supported by the fact that E. coli rpoS mutant cells were more stress sensitive than the parent strain by factors of 4.9 (mild heat), 5.3 (UVA light), and 4.1 (sunlight). Furthermore, modeling of inactivation curves with GInaFiT revealed that the shape of inactivation curves changed depending on the specific growth rate. Inactivation curves of cells from fast-growing cultures (μ = 1.0 h−1) that were irradiated with UVA light showed a tailing effect, while for slow-growing cultures (μ = 0.3 h−1), inactivation curves with shoulders were obtained. Our findings emphasize the need for accurate reporting of specific growth rates and detailed culture conditions in disinfection studies to allow comparison of data from different studies and laboratories and sound interpretation of the data obtained.

Alterations in lipopolysaccharide produced by chemostat-grown Escherichia coli O157:H7 as a function of growth rate and growth-limiting nutrient

1987 ◽  
Vol 33 (5) ◽  
pp. 452-458 ◽  
Author(s):  
Karen L. Dodds ◽  
Malcolm B. Perry ◽  
Ian J. McDonald
Keyword(s):  
Escherichia Coli ◽  
Molecular Weight ◽  
Growth Rate ◽  
High Molecular Weight ◽  
Growth Rates ◽  
Sodium Dodecyl ◽  
High Growth ◽  
Escherichia Coli O157 ◽  
E Coli ◽  
Sds Page

Escherichia coli O157:H7 was grown in chemostats as continuous cultures at different controlled growth rates and under different nutrient limitations to determine the effects on lipopolysaccharide (LPS) structure. LPS from whole cells and extracted using the hot aqueous phenol method was examined by sodium dodecyl sulfate – polyacrylamide gel electrophoresis (SDS–PAGE) and by gel filtration after hydrolysis with acetic acid. At low growth rates under glucose limitation (D = 0.1 h−1, doubling time (td), approx. 416 min; or D = 0.4 h−1, td, approx. 104 min), E. coli O157 produced high molecular weight LPS identical to that previously characterized from cells grown in batch culture. At a high growth rate (D = 0.8 h−1, td, approx. 52 min), the ratio of high molecular weight LPS to low molecular weight LPS produced greatly decreased. A small amount of high molecular weight LPS, containing O-polysaccharide which lacked amino sugars, and which thus was chemically different from that previously characterized, was produced by the cells at high growth rates. The predominant form of LPS from these cells was of slightly higher molecular weight than rough LPS, probably S–R LPS, and it consistently formed aggregates on SDS–PAGE. This form of LPS was also predominant when E. coli O157 was grown under Mg2+ limitation at an intermediate growth rate (D = 0.4 h−1, td, approx. 104 min).

scholarly journals In vitro reconstitution of the GTPase-associated centre of the archaebacterial ribosome: the functional features observed in a hybrid form with Escherichia coli 50S subunits

2006 ◽  
Vol 396 (3) ◽  
pp. 565-571 ◽  
Author(s):  
Takaomi Nomura ◽  
Kohji Nakano ◽  
Yasushi Maki ◽  
Takao Naganuma ◽  
Takashi Nakashima ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Ribosomal Proteins ◽  
Synthetic Activity ◽  
23S Rrna ◽  
Elongation Factors ◽  
Hybrid Form ◽  
Pyrococcus Horikoshii ◽  
E Coli ◽  
Functional Features

We cloned the genes encoding the ribosomal proteins Ph (Pyrococcus horikoshii)-P0, Ph-L12 and Ph-L11, which constitute the GTPase-associated centre of the archaebacterium Pyrococcus horikoshii. These proteins are homologues of the eukaryotic P0, P1/P2 and eL12 proteins, and correspond to Escherichia coli L10, L7/L12 and L11 proteins respectively. The proteins and the truncation mutants of Ph-P0 were overexpressed in E. coli cells and used for in vitro assembly on to the conserved domain around position 1070 of 23S rRNA (E. coli numbering). Ph-L12 tightly associated as a homodimer and bound to the C-terminal half of Ph-P0. The Ph-P0·Ph-L12 complex and Ph-L11 bound to the 1070 rRNA fragments from the three biological kingdoms in the same manner as the equivalent proteins of eukaryotic and eubacterial ribosomes. The Ph-P0·Ph-L12 complex and Ph-L11 could replace L10·L7/L12 and L11 respectively, on the E. coli 50S subunit in vitro. The resultant hybrid ribosome was accessible for eukaryotic, as well as archaebacterial elongation factors, but not for prokaryotic elongation factors. The GTPase and polyphenylalanine-synthetic activity that is dependent on eukaryotic elongation factors was comparable with that of the hybrid ribosomes carrying the eukaryotic ribosomal proteins. The results suggest that the archaebacterial proteins, including the Ph-L12 homodimer, are functionally accessible to eukaryotic translation factors.

scholarly journals Escherichia colipopulations adapt to complex, unpredictable fluctuations without any trade-offs across environments

2016 ◽  
Author(s):  
Shraddha Karve ◽  
Devika Bhave ◽  
Dhanashri Nevgi ◽  
Sutirth Dey
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Growth Rates ◽  
Complex Environments ◽  
Multiple Stresses ◽  
Trade Off ◽  
Trade Offs ◽  
Fluctuating Environments ◽  
Laboratory Populations ◽  
Lower Variation

AbstractIn nature, organisms are simultaneously exposed to multiple stresses (i.e. complex environments) that often fluctuate unpredictably. While both these factors have been studied in isolation, the interaction of the two remains poorly explored. To address this issue, we selected laboratory populations ofEscherichia coliunder complex (i.e. stressful combinations of pH, H2O2and NaCl) unpredictably fluctuating environments for ~900 generations. We compared the growth rates and the corresponding trade-off patterns of these populations to those that were selected under constant values of the component stresses (i.e. pH, H2O2and NaCl) for the same duration. The fluctuation-selected populations had greater mean growth rate and lower variation for growth rate over all the selection environments experienced. However, while the populations selected under constant stresses experienced severe tradeoffs in many of the environments other than those in which they were selected, the fluctuation-selected populations could by-pass the across-environment trade-offs completely. Interestingly, trade-offs were found between growth rates and carrying capacities. The results suggest that complexity and fluctuations can strongly affect the underlying trade-off structure in evolving populations.

scholarly journals Molecular Control of Sucrose Utilization in Escherichia coli W, an Efficient Sucrose-Utilizing Strain

2012 ◽  
Vol 79 (2) ◽  
pp. 478-487 ◽  
Author(s):  
Suriana Sabri ◽  
Lars K. Nielsen ◽  
Claudia E. Vickers
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Good Growth ◽  
Knockout Mutant ◽  
Sucrose Transport ◽  
Molecular Control ◽  
Content Type ◽  
E Coli ◽  
K 12 ◽  
Sucrose Utilization

ABSTRACTSucrose is an industrially important carbon source for microbial fermentation. Sucrose utilization inEscherichia coli, however, is poorly understood, and most industrial strains cannot utilize sucrose. The roles of the chromosomally encoded sucrose catabolism (csc) genes inE. coliW were examined by knockout and overexpression experiments. At low sucrose concentrations, thecscgenes are repressed and cells cannot grow. Removal of either the repressor protein (cscR) or the fructokinase (cscK) gene facilitated derepression. Furthermore, combinatorial knockout ofcscRandcscKconferred an improved growth rate on low sucrose. The invertase (cscA) and sucrose transporter (cscB) genes are essential for sucrose catabolism inE. coliW, demonstrating that no other genes can provide sucrose transport or inversion activities. However,cscKis not essential for sucrose utilization. Fructose is excreted into the medium by thecscK-knockout strain in the presence of high sucrose, whereas at low sucrose (when carbon availability is limiting), fructose is utilized by the cell. Overexpression ofcscA,cscAK, orcscABcould complement the WΔcscRKABknockout mutant or confer growth on a K-12 strain which could not naturally utilize sucrose. However, phenotypic stability and relatively good growth rates were observed in the K-12 strain only when overexpressingcscAB, and full growth rate complementation in WΔcscRKABalso requiredcscAB. Our understanding of sucrose utilization can be used to improveE. coliW and engineer sucrose utilization in strains which do not naturally utilize sucrose, allowing substitution of sucrose for other, less desirable carbon sources in industrial fermentations.

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