Evolution and Sequence Diversity of FhuA inSalmonellaandEscherichia

ABSTRACTThefhuACDBoperon, present in a number ofEnterobacteriaceae, encodes components essential for the uptake of ferric hydroxamate type siderophores. FhuA acts not only as transporter for physiologically important chelated ferric iron, but also as receptor for various bacteriophages, toxins and antibiotics, which are pathogenic to bacterial cells. In this research, thefhuAgene distribution and sequence diversity were investigated inEnterobacteriaceae, especiallySalmonellaandEscherichia. Comparative sequence analysis resulted in afhuAphylogenetic tree that did not match the expected phylogeny based on housekeeping sequence analysis or trees offhuCDBgenes. ThefhuAsequences showed a unique mosaic-clustering pattern. On the other hand, the gene sequences showed high conservation for strains from the same serovar or serotype. In total, six clusters were identified from FhuA proteins inSalmonellaandEscherichia, among which typical peptide fragment variations could be defined. Six fragmental insertions / deletions and two substitution fragments were discovered, which could well classify the different clusters. Structure modeling demonstrated that all the six featured insertions/deletions and one substitution fragment are located at the apexes of the long loops of FhuA external pocket. These frequently mutated regions are likely under high selection pressure, and bacterial strains could have escaped from phage infection or toxin / antibiotics attack viafhuAgene mutations while maintaining the siderophore uptake activity essential for bacterial survival. The unusualfhuAclustering suggests that high frequency exchange offhuAgenes has occurred between enterobacterial strains after distinctive species were established.IMPORTANCEThe enterobacterialfhuACDBoperon encodes proteins which mediate the uptake of siderophores to supply the cells with iron essential for bacterial survival. Here we show different evolutionary patterns for thefhugenes within the same operon. ThefhuAhas a phylogenetic tree that does not match the species phylogeny, whereas the rest of thefhugenes do. ThefhuAgenes showed inter-species sequence convergence and conservation within specific serovars and serotypes. Nearly all of the significant sequence differences among FhuA clusters are located in potential ligand-binding sites on the extracellular surface of fhuA-encoding receptors. The unusualfhuAclustering suggests the frequent recombination and exchange offhuAgenes between enterobacterial strains in the evolutionary state after distinctive species were established.Our findings suggested either a new evolutionary mechanism or local gene recombination infhuAthat is in contrast to previous evolutionary hypotheses that have formed under the assumption of no recombination.

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EseE of Edwardsiella tarda Augments Secretion of Translocon Protein EseC and Expression of theescC-eseEOperon

Infection and Immunity ◽

10.1128/iai.00106-16 ◽

2016 ◽

Vol 84 (8) ◽

pp. 2336-2344 ◽

Cited By ~ 6

Author(s):

Jia Yi ◽

Shui Bing Xiao ◽

Zhi Xiong Zeng ◽

Jin Fang Lu ◽

Lu Yi Liu ◽

...

Keyword(s):

Gel Filtration ◽

Host Cells ◽

Edwardsiella Tarda ◽

Supernatant Fraction ◽

Bacterial Cells ◽

Bacterial Survival ◽

Content Type ◽

Chaperone Protein ◽

Pulldown Assay ◽

Novel Protein

Edwardsiella tardais an important Gram-negative pathogen that employs a type III secretion system (T3SS) to deliver effectors into host cells to facilitate bacterial survival and replication. These effectors are translocated into host cells through a translocon complex composed of three secreted proteins, namely, EseB, EseC, and EseD. The secretion of EseB and EseD requires a chaperone protein called EscC, whereas the secretion of EseC requires the chaperone EscA. In this study, we identified a novel protein (EseE) that also regulates the secretion of EseC. AneseEdeletion mutant secreted much less EseC into supernatants, accompanied by increased EseC levels within bacterial cells. We also demonstrated that EseE interacted directly with EseC in a pulldown assay. Interestingly, EseC, EseE, and EscA were able to form a ternary complex, as revealed by pulldown and gel filtration assays. Of particular importance, the deletion ofeseEresulted in decreased levels of EseB and EseD proteins in both the bacterial pellet and supernatant fraction. Furthermore, real-time PCR assays showed that EseE positively regulated the transcription of the translocon operonescC-eseE, comprisingescC,eseB,escA,eseC,eseD, andeseE. These effects of EseE on the translocon components/operon appeared to have a functional consequence, since the ΔeseEstrain was outcompeted by wild-typeE. tardain a mixed infection in blue gourami fish. Collectively, our results demonstrate that EseE not only functions as a chaperone for EseC but also acts as a positive regulator controlling the expression of the translocon operonescC-eseE, thus contributing to the pathogenesis ofE. tardain fish.

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A Matter of Timing: Contrasting Effects of Hydrogen Sulfide on Oxidative Stress Response in Shewanella oneidensis

Journal of Bacteriology ◽

10.1128/jb.00603-15 ◽

2015 ◽

Vol 197 (22) ◽

pp. 3563-3572 ◽

Cited By ~ 23

Author(s):

Genfu Wu ◽

Fen Wan ◽

Huihui Fu ◽

Ning Li ◽

Haichun Gao

Keyword(s):

Oxidative Stress ◽

Hydrogen Sulfide ◽

Shewanella Oneidensis ◽

Inhibitory Effect ◽

Time Dependent ◽

Bacterial Cells ◽

Bacterial Survival ◽

Intracellular Iron ◽

Content Type ◽

Stress Responding

ABSTRACTHydrogen sulfide (H2S), well known for its toxic properties, has recently become a research focus in bacteria, in part because it has been found to prevent oxidative stress caused by treatment with some antibiotics. H2S has the ability to scavenge reactive oxygen species (ROS), thus preventing oxidative stress, but it is also toxic, leading to conflicting reports of its effects in different organisms. Here, withShewanella oneidensisas a model, we report that the effects of H2S on the response to oxidative stress are time dependent. When added simultaneously with H2O2, H2S promoted H2O2toxicity by inactivating catalase, KatB, a heme-containing enzyme involved in H2O2degradation. Such an inhibitory effect may apply to other heme-containing proteins, such as cytochromecbb3oxidase. When H2O2was supplied 20 min or later after the addition of H2S, the oxidative-stress-responding regulator OxyR was activated, resulting in increased resistance to H2O2. The activation of OxyR was likely triggered by the influx of iron, a response to lowered intracellular iron due to the iron-sequestering property of H2S. Given thatShewanellabacteria thrive in redox-stratified environments that have abundant sulfur and iron species, our results imply that H2S is more important for bacterial survival in such environmental niches than previously believed.IMPORTANCEPrevious studies have demonstrated that H2S is either detrimental or beneficial to bacterial cells. While it can act as a growth-inhibiting molecule by damaging DNA and denaturing proteins, it helps cells to combat oxidative stress. Here we report that H2S indeed has these contrasting biological functions and that its effects are time dependent. Immediately after H2S treatment, there is growth inhibition due to damage of heme-containing proteins, at least to catalase and cytochromecoxidase. In contrast, when added a certain time later, H2S confers an enhanced ability to combat oxidative stress by activating the H2O2-responding regulator OxyR. Our data reconcile conflicting observations about the functions of H2S.

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Pse-T2, an Antimicrobial Peptide with High-Level, Broad-Spectrum Antimicrobial Potency and Skin Biocompatibility against Multidrug-ResistantPseudomonas aeruginosaInfection

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01493-18 ◽

2018 ◽

Vol 62 (12) ◽

Cited By ~ 7

Author(s):

Hee Kyoung Kang ◽

Chang Ho Seo ◽

Tudor Luchian ◽

Yoonkyung Park

Keyword(s):

Antimicrobial Peptide ◽

Membrane Integrity ◽

Helical Structure ◽

Multidrug Resistant ◽

Bacterial Cells ◽

Bacterial Strains ◽

Necrosis Factor Alpha ◽

Content Type ◽

Bacterial Membranes

ABSTRACTPseudin-2, isolated from the frogPseudis paradoxa, exhibits potent antibacterial activity but also cytotoxicity. In an effort to develop clinically applicable antimicrobial peptides (AMPs), we designed pseudin-2 analogs with Lys substitutions, resulting in elevated amphipathic α-helical structure and cationicity. In addition, truncated analogs of pseudin-2 and Lys-substituted peptides were synthesized to produce linear 18-residue amphipathic α-helices, which were further investigated for their mechanism and functions. These truncated analogs exhibited higher antimicrobial activity and lower cytotoxicity than pseudin-2. In particular, Pse-T2 showed marked pore formation, permeabilization of the outer/inner bacterial membranes, and DNA binding. Fluorescence spectroscopy and scanning electron microscopy showed that Pse-T2 kills bacterial cells by disrupting membrane integrity.In vivo, wounds infected with multidrug-resistant (MDR)Pseudomonas aeruginosahealed significantly faster when treated with Pse-T2 than did untreated wounds or wounds treated with ciprofloxacin. Moreover, Pse-T2 facilitated infected-wound closure by reducing inflammation through suppression of interleukin-1β (IL-1β), IL-6, and tumor necrosis factor alpha (TNF-α). These data suggest that the small antimicrobial peptide Pse-T2 could be useful for future development of therapeutic agents effective against MDR bacterial strains.

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Aging of a Bacterial Colony Enforces the Evolvement of Nondifferentiating Mutants

mBio ◽

10.1128/mbio.01414-19 ◽

2019 ◽

Vol 10 (5) ◽

Cited By ~ 1

Author(s):

Rachel Hashuel ◽

Sigal Ben-Yehuda

Keyword(s):

Cell Types ◽

Quiescent State ◽

Bacterial Cells ◽

Bacterial Survival ◽

Bacterial Colony ◽

Content Type ◽

Multiple Paths ◽

Novel Strategy ◽

Bacterial Aging ◽

Cancerous Cells

ABSTRACT Bacteria in nature are known to survive for long periods under restricting conditions, mainly by reducing their growth rate and metabolic activity. Here, we uncover a novel strategy utilized by bacterial cells to resist aging by propagating rather than halting division. Bacterial aging was monitored by inspecting colonies of the Gram-positive soil bacterium Bacillus subtilis, which is capable of differentiating into various cell types under nutrient exhaustion. We revealed that after days of incubation, rejuvenating subpopulations, arrayed over the mother colony, emerged. These subpopulations were found to harbor mutations in a variety of genes, restricting the ability of the cells to differentiate. Surprisingly, even mutations that are not classically designated to developmental pathways, concluded in differentiation deficiency, indicating that multiple paths can reach this same outcome. We provide evidence that the evolved mutants continue to divide under conditions that favor entry into quiescence, hence becoming abundant within the aging population. The occurrence of such nondifferentiating mutants could impact bacterial population dynamics in natural niches. IMPORTANCE Until now, bacterial cells facing nutrient deprivation were shown to enter dormancy as a strategy to survive prolonged stress, with the most established examples being sporulation, stationary phase, and persistence. Here, we uncovered an opposing strategy for long-term bacterial survival, in which mutant subpopulations cope with a challenging niche by proliferating rather than by stalling division. We show that this feature stems from mutations in genes disturbing the capability of the cells to differentiate into a quiescent state, enabling them to divide under restrictive conditions. Our study challenges the dogma of bacterial aging by highlighting an additional survival strategy resembling that of cancerous cells in animal organs.

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Antibacterial and Antioxidant Activity of Extracts from Rose Fruits (Rosa rugosa)

Molecules ◽

10.3390/molecules25061365 ◽

2020 ◽

Vol 25 (6) ◽

pp. 1365 ◽

Cited By ~ 2

Author(s):

Andrzej Cendrowski ◽

Karolina Kraśniewska ◽

Jarosław L. Przybył ◽

Agnieszka Zielińska ◽

Stanisław Kalisz

Keyword(s):

Antioxidant Activity ◽

Aqueous Extract ◽

Antioxidant Properties ◽

Bacterial Cells ◽

Bacterial Survival ◽

Bacterial Strains ◽

Rosa Rugosa ◽

Protein Food ◽

Freeze Dried ◽

The Rose

The aim of the present study was to determine the antioxidant and antimicrobial properties in freeze-dried extracts of rose fruits (Rosa rugosa) obtained using various extraction techniques and to determine the effect of a selected extract on bacterial survival in model fluids imitating protein food. Ethanolic extracts from rose fruits showed higher antioxidant activity compared to other tested extracts. The rose fruits aqueous extract showed the highest inhibitory activity against most of the 10 bacterial strains tested. From the group of Gram-positive bacteria, the Bacillus cereus strain proved to be the most sensitive to the action of the rose extract. From the Gram-negative bacteria: Escherichia coli and Klebsiella pneumoniae were the most sensitive. The reduction in the number of bacterial cells in matrices imitating protein food depended on the concentration of the aqueous extract used. However, at none of the concentrations used was a complete inhibition of bacterial growth observed. We have confirmed that the traditional extraction and freeze-drying of rose fruits is still suitable for the food industry due to obtaining extracts with good antibacterial and antioxidant properties and the use of bio-solvents, such as water or ethanol, which are easily available in high purity and completely biodegradable.

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Inhibition of Aminoglycoside Acetyltransferase Resistance Enzymes by Metal Salts

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00885-15 ◽

2015 ◽

Vol 59 (7) ◽

pp. 4148-4156 ◽

Cited By ~ 32

Author(s):

Yijia Li ◽

Keith D. Green ◽

Brooke R. Johnson ◽

Sylvie Garneau-Tsodikova

Keyword(s):

Inhibitory Effect ◽

Culture Collection ◽

Metal Salts ◽

Common Mechanism ◽

Bacterial Cells ◽

Bacterial Strains ◽

Content Type ◽

Gram Positive Bacteria ◽

Counter Ions ◽

Large Repertoire

ABSTRACTAminoglycosides (AGs) are clinically relevant antibiotics used to treat infections caused by both Gram-negative and Gram-positive bacteria, as well asMycobacteria. As with all current antibacterial agents, resistance to AGs is an increasing problem. The most common mechanism of resistance to AGs is the presence of AG-modifying enzymes (AMEs) in bacterial cells, with AG acetyltransferases (AACs) being the most prevalent. Recently, it was discovered that Zn2+metal ions displayed an inhibitory effect on the resistance enzyme AAC(6′)-Ib inAcinetobacter baumanniiandEscherichia coli. In this study, we explore a wide array of metal salts (Mg2+, Cr3+, Cr6+, Mn2+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Au3+with different counter ions) and their inhibitory effect on a large repertoire of AACs [AAC(2′)-Ic, AAC(3)-Ia, AAC(3)-Ib, AAC(3)-IV, AAC(6′)-Ib′, AAC(6′)-Ie, AAC(6′)-IId, and Eis]. In addition, we determine the MIC values for amikacin and tobramycin in combination with a zinc pyrithione complex in clinical isolates of various bacterial strains (two strains ofA. baumannii, three ofEnterobacter cloacae, and four ofKlebsiella pneumoniae) and one representative of each species purchased from the American Type Culture Collection.

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The Research of New Inhibitors of Bacterial Methionine Aminopeptidase by Structure Based Virtual Screening Approach of ZINC DATABASE and In Vitro Validation

Current Computer - Aided Drug Design ◽

10.2174/1573409915666190617165643 ◽

2020 ◽

Vol 16 (4) ◽

pp. 389-401 ◽

Cited By ~ 2

Author(s):

Hanane Boucherit ◽

Abdelouahab Chikhi ◽

Abderrahmane Bensegueni ◽

Amina Merzoug ◽

Jean-Michel Bolla

Keyword(s):

Virtual Screening ◽

Bacterial Survival ◽

Methionine Aminopeptidase ◽

Bacterial Strains ◽

Microdilution Method ◽

Zinc Database ◽

Promising Target ◽

New Antibiotics ◽

Potential Inhibitors

Background: The great emergence of multi-resistant bacterial strains and the low renewal of antibiotics molecules are leading human and veterinary medicine to certain therapeutic impasses. Therefore, there is an urgent need to find new therapeutic alternatives including new molecules in the current treatments of infectious diseases. Methionine aminopeptidase (MetAP) is a promising target for developing new antibiotics because it is essential for bacterial survival. Objective: To screen for potential MetAP inhibitors by in silico virtual screening of the ZINC database and evaluate the best potential lead molecules by in vitro studies. Methods: We have considered 200,000 compounds from the ZINC database for virtual screening with FlexX software to identify potential inhibitors against bacterial MetAP. Nine chemical compounds of the top hits predicted were purchased and evaluated in vitro. The antimicrobial activity of each inhibitor of MetAP was tested by the disc-diffusion assay against one Gram-positive (Staphylococcus aureus) and two Gram-negative (Escherichia coli & Pseudomonas aeruginosa) bacteria. Among the studied compounds, compounds ZINC04785369 and ZINC03307916 showed promising antibacterial activity. To further characterize their efficacy, the minimum inhibitory concentration was determined for each compound by the microdilution method which showed significant results. Results: These results suggest compounds ZINC04785369 and ZINC03307916 as promising molecules for developing MetAP inhibitors. Conclusion: Furthermore, they could therefore serve as lead molecules for further chemical modifications to obtain clinically useful antibacterial agents.

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Regulation of Cell Division in Bacteria by Monitoring Genome Integrity and DNA Replication Status

Journal of Bacteriology ◽

10.1128/jb.00408-19 ◽

2019 ◽

Vol 202 (2) ◽

Cited By ~ 5

Author(s):

Peter E. Burby ◽

Lyle A. Simmons

Keyword(s):

Cell Cycle ◽

Dna Damage ◽

Cell Division ◽

Dna Replication ◽

Cell Cycle Progression ◽

Genome Instability ◽

Sos Response ◽

Bacterial Cells ◽

Cycle Progression ◽

Content Type

ABSTRACT All organisms regulate cell cycle progression by coordinating cell division with DNA replication status. In eukaryotes, DNA damage or problems with replication fork progression induce the DNA damage response (DDR), causing cyclin-dependent kinases to remain active, preventing further cell cycle progression until replication and repair are complete. In bacteria, cell division is coordinated with chromosome segregation, preventing cell division ring formation over the nucleoid in a process termed nucleoid occlusion. In addition to nucleoid occlusion, bacteria induce the SOS response after replication forks encounter DNA damage or impediments that slow or block their progression. During SOS induction, Escherichia coli expresses a cytoplasmic protein, SulA, that inhibits cell division by directly binding FtsZ. After the SOS response is turned off, SulA is degraded by Lon protease, allowing for cell division to resume. Recently, it has become clear that SulA is restricted to bacteria closely related to E. coli and that most bacteria enforce the DNA damage checkpoint by expressing a small integral membrane protein. Resumption of cell division is then mediated by membrane-bound proteases that cleave the cell division inhibitor. Further, many bacterial cells have mechanisms to inhibit cell division that are regulated independently from the canonical LexA-mediated SOS response. In this review, we discuss several pathways used by bacteria to prevent cell division from occurring when genome instability is detected or before the chromosome has been fully replicated and segregated.

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Plasma-Activated Water (PAW) as a Disinfection Technology for Bacterial Inactivation with a Focus on Fruit and Vegetables

Foods ◽

10.3390/foods10010166 ◽

2021 ◽

Vol 10 (1) ◽

pp. 166

Author(s):

Aswathi Soni ◽

Jonghyun Choi ◽

Gale Brightwell

Keyword(s):

Fruit And Vegetables ◽

Atmospheric Plasma ◽

Model Systems ◽

Thermal Treatments ◽

Bacterial Cells ◽

Bacterial Inactivation ◽

Gas Temperature ◽

Bacterial Strains ◽

Sensory Qualities ◽

Plasma Activated Water

Plasma-activated water (PAW) is generated by treating water with cold atmospheric plasma (CAP) using controllable parameters, such as plasma-forming voltage, carrier gas, temperature, pulses, or frequency as required. PAW is reported to have lower pH, higher conductivity, and higher oxygen reduction potential when compared with untreated water due to the presence of reactive species. PAW has received significant attention from researchers over the last decade due to its non-thermal and non-toxic mode of action especially for bacterial inactivation. The objective of the current review is to develop a summary of the effect of PAW on bacterial strains in foods as well as model systems such as buffers, with a specific focus on fruit and vegetables. The review elaborated the properties of PAW, the effect of various treatment parameters on its efficiency in bacterial inactivation along with its usage as a standalone technology as well as a hurdle approach with mild thermal treatments. A section highlighting different models that can be employed to generate PAW alongside a direct comparison of the PAW characteristics on the inactivation potential and the existing research gaps are also included. The mechanism of action of PAW on the bacterial cells and any reported effects on the sensory qualities and shelf life of food has been evaluated. Based on the literature, it can be concluded that PAW offers a significant potential as a non-chemical and non-thermal intervention for bacterial inactivation, especially on food. However, the applicability and usage of PAW depend on the effect of environmental and bacterial strain-based conditions and cost-effectiveness.

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