scholarly journals Optimization of lag phase shapes the evolution of a bacterial enzyme

2016 ◽  
Author(s):  
Bharat V. Adkar ◽  
Michael Manhart ◽  
Sanchari Bhattacharyya ◽  
Jian Tian ◽  
Michael Musharbash ◽  
...  
Keyword(s):  
Growth Rates ◽  
Adenylate Kinase ◽  
Fitness Landscape ◽  
Lag Phase ◽  
E Coli ◽  
Fitness Effects ◽  
Bacterial Enzyme ◽  
Lag Times ◽  
Essential Enzyme ◽  
Catalytic Capacity

AbstractMutations provide the variation that drives evolution, yet their effects on fitness remain poorly understood. Here we explore how mutations in the essential enzyme Adenylate Kinase (Adk) ofE. coliaffect multiple phases of population growth. We introduce a biophysical fitness landscape for these phases, showing how they depend on molecular and cellular properties of Adk. We find that Adk catalytic capacity in the cell (product of activity and abundance) is the major determinant of mutational fitness effects. We show that bacterial lag times are at a well-defined optimum with respect to Adk’s catalytic capacity, while exponential growth rates are only weakly affected by variation in Adk. Direct pairwise competitions between strains show how environmental conditions modulate the outcome of a competition where growth rates and lag times have a tradeoff, altogether shedding light on the multidimensional nature of fitness and its importance in the evolutionary optimization of enzymes.

scholarly journals Genome-Based Analyses of Fitness Effects and Compensatory Changes Associated with Acquisition of blaCMY-, blaCTX-M-, and blaOXA-48/VIM-1-Containing Plasmids in Escherichia coli

Antibiotics ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 90
Author(s):  
Michael Pietsch ◽  
Yvonne Pfeifer ◽  
Stephan Fuchs ◽  
Guido Werner
Keyword(s):  
Escherichia Coli ◽  
Growth Rates ◽  
Beta Lactamase ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genomic Changes ◽  
E Coli ◽  
Fitness Effects ◽  
Growth Differences

(1) Background: Resistance plasmids are under selective conditions beneficial for the bacterial host, but in the absence of selective pressure, this carriage may cause fitness costs. Compensation of this fitness burden is important to obtain competitive ability under antibiotic-free conditions. In this study, we investigated fitness effects after a conjugative transfer of plasmids containing various beta-lactamase genes transferred into Escherichia coli. (2) Methods: Fourteen beta-lactamase-encoding plasmids were transferred from clinical donor strains to E. coli J53. Growth rates were compared for all transconjugants and the recipient. Selected transconjugants were challenged in long-term growth experiments. Growth rates were assessed at different time points during growth for 500 generations. Whole-genome sequencing (WGS) of initial and evolved transconjugants was determined. Results: Most plasmid acquisitions resulted in growth differences, ranging from −4.5% to 7.2%. Transfer of a single blaCMY-16-carrying plasmid resulted in a growth burden and a growth benefit in independent mating. Long-term growth led to a compensation of fitness burdens and benefits. Analyzing WGS revealed genomic changes caused by Single Nucleotide Polymorphisms (SNPs) and insertion sequences over time. Conclusions: Fitness effects associated with plasmid acquisitions were variable. Potential compensatory mutations identified in transconjugants’ genomes after 500 generations give interesting insights into aspects of plasmid–host adaptations.

scholarly journals Substrate inhibition imposes fitness penalty at high protein stability

2018 ◽  
Author(s):  
Bharat V. Adkar ◽  
Sanchari Bhattacharyya ◽  
Amy I. Gilson ◽  
Wenli Zhang ◽  
Eugene I. Shakhnovich
Keyword(s):  
Adenylate Kinase ◽  
Narrow Range ◽  
Substrate Inhibition ◽  
Purifying Selection ◽  
Neutral Drift ◽  
E Coli ◽  
Physiological Conditions ◽  
Fitness Effects ◽  
Excess Substrate ◽  
Excess Stability

AbstractProteins are only moderately stable. It has long been debated whether this narrow range of stabilities is solely a result of neutral drift towards lower stability or purifying selection against excess stability is also at work — for which no experimental evidence was found so far. Here we show that mutations outside the active site in the essential E. coli enzyme adenylate kinase result in stability-dependent increase in substrate inhibition by AMP, thereby impairing overall enzyme activity at high stability. Such inhibition caused substantial fitness defects not only in the presence of excess substrate but also under physiological conditions. In the latter case, substrate inhibition caused differential accumulation of AMP in the stationary phase for the inhibition prone mutants. Further, we show that changes in flux through Adk could accurately describe the variation in fitness effects. Taken together, these data suggest that selection against substrate inhibition and hence excess stability may have resulted in a narrow range of optimal stability observed for modern proteins.

scholarly journals Growth of Listeria monocytogenes in Thawed Frozen Foods

2017 ◽  
Vol 80 (3) ◽  
pp. 447-453 ◽  
Author(s):  
Ai Kataoka ◽  
Hua Wang ◽  
Philip H. Elliott ◽  
Richard C. Whiting ◽  
Melinda M. Hayman
Keyword(s):  
Growth Rate ◽  
Listeria Monocytogenes ◽  
Growth Rates ◽  
Storage Temperature ◽  
Growth Parameters ◽  
Quadratic Model ◽  
Lag Phase ◽  
Frozen Foods ◽  
Phase Duration ◽  
Primary Model

ABSTRACT The growth characteristics of Listeria monocytogenes inoculated onto frozen foods (corn, green peas, crabmeat, and shrimp) and thawed by being stored at 4, 8, 12, and 20°C were investigated. The growth parameters, lag-phase duration (LPD) and exponential growth rate (EGR), were determined by using a two-phase linear growth model as a primary model and a square root model for EGR and a quadratic model for LPD as secondary models, based on the growth data. The EGR model predictions were compared with growth rates obtained from the USDA Pathogen Modeling Program, calculated with similar pH, salt percentage, and NaNO2 parameters, at all storage temperatures. The results showed that L. monocytogenes grew well in all food types, with the growth rate increasing with storage temperature. Predicted EGRs for all food types demonstrated the significance of storage temperature and similar growth rates among four food types. The predicted EGRs showed slightly slower rate compared with the values from the U.S. Department of Agriculture Pathogen Modeling Program. LPD could not be accurately predicted, possibly because there were not enough sampling points. These data established by using real food samples demonstrated that L. monocytogenes can initiate growth without a prolonged lag phase even at refrigeration temperature (4°C), and the predictive models derived from this study can be useful for developing proper handling guidelines for thawed frozen foods during production and storage.

Antibacterial Effects of Long-Chain Polyphosphates on Selected Spoilage and Pathogenic Bacteria

2008 ◽  
Vol 71 (7) ◽  
pp. 1401-1405 ◽  
Author(s):  
JEREMY A. OBRITSCH ◽  
DOJIN RYU ◽  
LUCINA E. LAMPILA ◽  
LLOYD B. BULLERMAN
Keyword(s):  
Food Industry ◽  
Pathogenic Bacteria ◽  
Antimicrobial Activities ◽  
Lag Phase ◽  
E Coli ◽  
Inhibition Of Growth ◽  
K 12 ◽  
Chain Lengths ◽  
And Staphylococcus Aureus ◽  
Long Chain

The antimicrobial activities of four long-chain food-grade polyphosphates were studied at concentrations allowed in the food industry (<5,000 ppm) in defined basal media by determining the inhibition of growth of three gram-negative and four gram-positive spoilage and pathogenic bacteria. Both generation time and lag phase of Escherichia coli K-12, E. coli O157: H7, and Salmonella Typhimurium were increased with all of the polyphosphates tested. Bacillus subtilis and Staphylococcus aureus were more sensitive to polyphosphates, but not in all cases, with multiphased growth. The growth of Lactobacillus plantarum was inhibited by polyphosphates at concentrations above 750 ppm, but the lag time of Listeria monocytogenes was shortened by the presence of polyphosphates. No single polyphosphate was maximally inhibitory against all bacteria. Polyphosphates with chain lengths of 12 to 15 were significantly different from those with chain lengths of 18 to 21 depending on the organism and concentrations of polyphosphate used. Overall, higher polyphosphate concentrations resulted in greater inhibition of bacterial growth.

scholarly journals Biophysical principles predict fitness landscapes of drug resistance

2016 ◽  
Vol 113 (11) ◽  
pp. E1470-E1478 ◽  
Author(s):  
João V. Rodrigues ◽  
Shimon Bershtein ◽  
Anna Li ◽  
Elena R. Lozovsky ◽  
Daniel L. Hartl ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Protein Quality ◽  
Fitness Landscape ◽  
Catalytic Efficiency ◽  
Fitness Landscapes ◽  
Resistance Mutations ◽  
Chlamydia Muridarum ◽  
Complete Set ◽  
Essential Enzyme

Fitness landscapes of drug resistance constitute powerful tools to elucidate mutational pathways of antibiotic escape. Here, we developed a predictive biophysics-based fitness landscape of trimethoprim (TMP) resistance for Escherichia coli dihydrofolate reductase (DHFR). We investigated the activity, binding, folding stability, and intracellular abundance for a complete set of combinatorial DHFR mutants made out of three key resistance mutations and extended this analysis to DHFR originated from Chlamydia muridarum and Listeria grayi. We found that the acquisition of TMP resistance via decreased drug affinity is limited by a trade-off in catalytic efficiency. Protein stability is concurrently affected by the resistant mutants, which precludes a precise description of fitness from a single molecular trait. Application of the kinetic flux theory provided an accurate model to predict resistance phenotypes (IC50) quantitatively from a unique combination of the in vitro protein molecular properties. Further, we found that a controlled modulation of the GroEL/ES chaperonins and Lon protease levels affects the intracellular steady-state concentration of DHFR in a mutation-specific manner, whereas IC50 is changed proportionally, as indeed predicted by the model. This unveils a molecular rationale for the pleiotropic role of the protein quality control machinery on the evolution of antibiotic resistance, which, as we illustrate here, may drastically confound the evolutionary outcome. These results provide a comprehensive quantitative genotype–phenotype map for the essential enzyme that serves as an important target of antibiotic and anticancer therapies.

Combined Effect of Hop Resins and Sodium Hexametaphosphate against Certain Strains of Escherichia coli

2000 ◽  
Vol 63 (6) ◽  
pp. 735-740 ◽  
Author(s):  
TADASHI FUKAO ◽  
HARUMICHI SAWADA ◽  
YOSHIYUKI OHTA
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Activity ◽  
Food Systems ◽  
Combined Effect ◽  
Sodium Hexametaphosphate ◽  
Lag Phase ◽  
Phase Growth ◽  
E Coli ◽  
Cell Components ◽  
Strong Antimicrobial Activity

The combined antimicrobial effects of hop resins with sodium hexametaphosphate, glycerol monocaprate, and lysozyme were investigated aiming to make an effective agent against Escherichia coli. When they are used separately, the antimicrobial activity against E. coli was minimal. However, the combination of hop resins with sodium hexametaphosphate exhibited strong antimicrobial activity against E. coli, but no effect was found in combinations of hop resins with the other agents. The activity was strongest when the combination was added at the beginning of growth of the bacteria, resulting in a prolonged lag phase. However, when the antimicrobials were added during the log phase, growth was depressed considerably. By addition of these materials, cell components with absorbance near 260 nm were leaked out. This possibly may have resulted from damage to the cell membranes of the bacteria. The combined effect was also detected in model food systems such as mashed potatos. The use of hop resins and sodium hexametaphosphate in combination may thus be useful for controlling E. coli.

scholarly journals Increased Survival of Antibiotic-Resistant Escherichia coli inside Macrophages

2012 ◽  
Vol 57 (1) ◽  
pp. 189-195 ◽  
Author(s):  
Migla Miskinyte ◽  
Isabel Gordo
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Bacterial Infections ◽  
Resistance Mutation ◽  
Fitness Cost ◽  
Resistance Mutations ◽  
Content Type ◽  
E Coli ◽  
Fitness Effects ◽  
K 12

ABSTRACTMutations causing antibiotic resistance usually incur a fitness cost in the absence of antibiotics. The magnitude of such costs is known to vary with the environment. Little is known about the fitness effects of antibiotic resistance mutations when bacteria confront the host's immune system. Here, we study the fitness effects of mutations in therpoB,rpsL, andgyrAgenes, which confer resistance to rifampin, streptomycin, and nalidixic acid, respectively. These antibiotics are frequently used in the treatment of bacterial infections. We measured two important fitness traits—growth rate and survival ability—of 12Escherichia coliK-12 strains, each carrying a single resistance mutation, in the presence of macrophages. Strikingly, we found that 67% of the mutants survived better than the susceptible bacteria in the intracellular niche of the phagocytic cells. In particular, allE. colistreptomycin-resistant mutants exhibited an intracellular advantage. On the other hand, 42% of the mutants incurred a high fitness cost when the bacteria were allowed to divide outside of macrophages. This study shows that single nonsynonymous changes affecting fundamental processes in the cell can contribute to prolonged survival ofE. coliin the context of an infection.

scholarly journals Combined Effect of Modified Atmosphere Packaging and UV-C Radiation on Pathogens Reduction, Biogenic Amines, and Shelf Life of Refrigerated Tilapia (Oreochromis niloticus) Fillets

Molecules ◽  
2020 ◽  
Vol 25 (14) ◽  
pp. 3222
Author(s):  
César A. Lázaro ◽  
Maria Lúcia G. Monteiro ◽  
Carlos A. Conte-Junior
Keyword(s):  
Ultraviolet Radiation ◽  
Shelf Life ◽  
Biogenic Amines ◽  
Modified Atmosphere Packaging ◽  
Storage Period ◽  
Lag Phase ◽  
Modified Atmosphere ◽  
E Coli ◽  
Tilapia Fillets ◽  
Uv C

This study investigated the isolated effect of modified atmosphere packaging (MAP; 50% CO2 and 50% N2) and ultraviolet radiation (UV; 0.30 J/cm2) as well as their combined (MAP/UV) effect on reduction of Salmonella typhimurium and Escherichia coli O157:H7, biogenic amines (BA), and on shelf life of tilapia fillets stored at 4 ± 1 °C for 10 days. UV samples had the highest reduction of S. typhimurium (1.13 log colony forming units/g; CFU/g) and E. coli O157:H7 (0.70 log CFU/g). MAP and MAP/UV reduced the growth of S. typhimurium in 0.50 log CFU/g and did not affect the growth of E. coli O157:H7. UV, MAP, and MAP/UV increased lag phase and/or generation time of all evaluated bacterial groups, decreased pH values, ammonia formation, texture changes, and, in general, the BA formation throughout storage period, and, therefore, UV, MAP, and MAP/UV extended the shelf life for two, three, and at least five days, respectively. MAP/UV, MAP, and UV decreased redness, MAP/UV and MAP increased yellowness and lipid oxidation, while UV did not affect it. MAP/UV demonstrated promising results for shelf life extension; however, different gas ratios in combination with other ultraviolet radiation type C (UV-C) doses should be investigated to reach the highest microbiological safety and maintenance of the overall quality of tilapia fillets.

scholarly journals Inhibitory Activities of Gatifloxacin (AM-1155), a Newly Developed Fluoroquinolone, against Bacterial and Mammalian Type II Topoisomerases

1998 ◽  
Vol 42 (10) ◽  
pp. 2678-2681 ◽  
Author(s):  
Masaya Takei ◽  
Hideyuki Fukuda ◽  
Tokutaro Yasue ◽  
Masaki Hosaka ◽  
Yasuo Oomori
Keyword(s):  
Hela Cell ◽  
Topoisomerase Ii ◽  
Dna Gyrase ◽  
Antibacterial Activities ◽  
Type Ii ◽  
Topoisomerase Iv ◽  
E Coli ◽  
Bacterial Enzyme ◽  
Inhibitory Activities ◽  
Bacterial Type

ABSTRACT We determined the inhibitory activities of gatifloxacin againstStaphylococcus aureus topoisomerase IV,Escherichia coli DNA gyrase, and HeLa cell topoisomerase II and compared them with those of several quinolones. The inhibitory activities of quinolones against these type II topoisomerases significantly correlated with their antibacterial activities or cytotoxicities (correlation coefficient [r] = 0.926 forS. aureus, r = 0.972 for E. coli, and r = 0.648 for HeLa cells). Gatifloxacin possessed potent inhibitory activities against bacterial type II topoisomerases (50% inhibitory concentration [IC50] = 13.8 μg/ml for S. aureustopoisomerase IV; IC50 = 0.109 μg/ml for E. coli DNA gyrase) but the lowest activity against HeLa cell topoisomerase II (IC50 = 265 μg/ml) among the quinolones tested. There was also a significant correlation between the inhibitory activities of quinolones against S. aureustopoisomerase IV and those against E. coli DNA gyrase (r = 0.969). However, the inhibitory activity against HeLa cell topoisomerase II did not correlate with that against either bacterial enzyme. The IC50 of gatifloxacin for HeLa cell topoisomerase II was 19 and was more than 2,400 times higher than that for S. aureus topoisomerase IV and that for E. coli DNA gyrase. These ratios were higher than those for other quinolones, indicating that gatifloxacin possesses a higher selectivity for bacterial type II topoisomerases.

scholarly journals The Transcriptional Factors MurR and Catabolite Activator Protein Regulate N-Acetylmuramic Acid Catabolism in Escherichia coli

2008 ◽  
Vol 190 (20) ◽  
pp. 6598-6608 ◽  
Author(s):  
Tina Jaeger ◽  
Christoph Mayer
Keyword(s):  
Escherichia Coli ◽  
Cell Wall ◽  
Sole Source ◽  
Lag Phase ◽  
Face To Face ◽  
E Coli ◽  
Catabolite Activator Protein ◽  
Activator Protein ◽  
High Level ◽  
First Time

ABSTRACT The MurNAc etherase MurQ of Escherichia coli is essential for the catabolism of the bacterial cell wall sugar N-acetylmuramic acid (MurNAc) obtained either from the environment or from the endogenous cell wall (i.e., recycling). High-level expression of murQ is required for growth on MurNAc as the sole source of carbon and energy, whereas constitutive low-level expression of murQ is sufficient for the recycling of peptidoglycan fragments continuously released from the cell wall during growth of the bacteria. Here we characterize for the first time the expression of murQ and its regulation by MurR, a member of the poorly characterized RpiR/AlsR family of transcriptional regulators. Deleting murR abolished the extensive lag phase observed for E. coli grown on MurNAc and enhanced murQ transcription some 20-fold. MurR forms a stable multimer (most likely a tetramer) and binds to two adjacent inverted repeats within an operator region. In this way MurR represses transcription from the murQ promoter and also interferes with its own transcription. MurNAc-6-phosphate, the substrate of MurQ, was identified as a specific inducer that weakens binding of MurR to the operator. Moreover, murQ transcription depends on the activation by cyclic AMP (cAMP)-catabolite activator protein (CAP) bound to a class I site upstream of the murQ promoter. murR and murQ are divergently orientated and expressed from nonoverlapping face-to-face (convergent) promoters, yielding transcripts that are complementary at their 5′ ends. As a consequence of this unusual promoter arrangement, cAMP-CAP also affects murR transcription, presumably by acting as a roadblock for RNA polymerase.

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