scholarly journals Investigation of gating in outer membrane porins provides new perspectives on antibiotic resistance mechanisms

2021 ◽  
Author(s):  
Archit Kumar Vasan ◽  
Nandan Haloi ◽  
Rebecca Joy Ulrich ◽  
Mary Elizabeth Metcalf ◽  
Po-Chao Wen ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Outer Membrane ◽  
Large Scale ◽  
Dynamic Equilibrium ◽  
Resistance Mechanisms ◽  
Health Concern ◽  
Gram Negative Bacteria ◽  
Bacterial Strains ◽  
Gram Negative ◽  
Scale Motion

AbstractGram-negative bacteria pose a serious public health concern, primarily due to a higher frequency of antibiotic resistance conferred to them as a result of low permeability of their outer membrane (OM). Antibiotics capable of traversing the OM typically permeate through OM porins; thus, understanding the permeation properties of these porins is instrumental to the development of new antibiotics. A common macroscopic feature of many OM porins is their ability to transition between functionally distinct open and closed states that regulate transport properties and rate. To obtain a molecular basis for these processes, we performed tens of microseconds of molecular dynamics simulations of E. coli OM porin, OmpF. We observed that large-scale motion of the internal loop, L3, leads to widening and narrowing of the pore, suggesting its potential role in gating. Furthermore, Markov state analysis revealed multiple energetically stable conformations of L3 corresponding to open and closed states of the porin. Dynamics between these functional states occurs on the time scale of tens of microseconds and are mediated by the movement of highly conserved acidic residues of L3 to form H-bonds with opposing sides of the barrel wall of the pore. To validate our mechanism, we mutated key residues involved in the gating process that alter the H-bond pattern in the open/closed states and performed additional simulations. These mutations shifted the dynamic equilibrium of the pore towards open or closed states. Complementarily, the mutations favoring the open/closed states lead to increased/decreased accumulation of multiple antibiotics in our whole-cell accumulation assays. Notably, porins containing one of the mutations favoring the closed state has previously been found in antibiotic resistant bacterial strains. Overall, our 180 µs of simulation data (wild type and mutants) with concerted experiments suggests that regulation of the dynamic equilibrium between open and closed states of OM porins could be a mechanism by which Gram-negative bacteria acquire antibiotic resistance.

Success and Challenges Associated with Large Scale Collaborative Surveillance for Carbapenemase Genes in Gram Negative Bacteria

2021 ◽  
Author(s):  
Sanchita Das ◽  
Karen Bush
Keyword(s):  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Large Scale ◽  
Resistance Mechanisms ◽  
Gram Negative Bacteria ◽  
Routine Laboratory ◽  
Significant Morbidity ◽  
Gram Negative ◽  
Surveillance Studies ◽  
The One

The emergence and spread of antimicrobial resistance, especially in Gram negative bacteria has led to significant morbidity and increased cost of healthcare. Large surveillance studies such as the one performed by the Antibiotic Resistance Laboratory Network are immensely valuable in understanding the scope of resistance mechanisms especially among carbapenemase producing Gram negative bacteria. However, the routine laboratory detection of carbapenemases in these bacteria remain challenging and require further optimization.

scholarly journals Rationalizing generation of broad spectrum antibiotics with the addition of a positive charge

2021 ◽  
Author(s):  
nandan haloi ◽  
Archit Kumar Vasan ◽  
Emily Jane Geddes ◽  
Arjun Prasanna ◽  
Po-Chao Wen ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Outer Membrane ◽  
Broad Spectrum ◽  
Positive Charge ◽  
Low Permeability ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Broad Spectrum Antibiotics

Antibiotic resistance of Gram-negative bacteria is largely attributed to the low permeability of their outer membrane (OM). Recently, we disclosed the eNTRy rules, a key lesson of which is that...

scholarly journals Investigating colistin drug resistance: The role of high-throughput sequencing and bioinformatics

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 150 ◽  
Author(s):  
Dickson Aruhomukama ◽  
Ivan Sserwadda ◽  
Gerald Mboowa
Keyword(s):  
Antibiotic Resistance ◽  
High Throughput ◽  
Bacterial Infections ◽  
High Throughput Sequencing ◽  
Health Concern ◽  
Gram Negative Bacteria ◽  
Drug Resistant ◽  
Colistin Resistance ◽  
Gram Negative

Bacterial infections involving antibiotic resistant gram-negative bacteria continue to increase and represent a major global public health concern. Resistance to antibiotics in these bacteria is mediated by chromosomal and/or acquired resistance mechanisms, these give rise to multi-drug resistant (MDR) or extensive drug resistant (XDR) bacterial strains. Most recently, a novel acquired plasmid mediated resistance mechanism to colistin, an antibiotic that had been set apart as the last resort antibiotic in the treatment of infections involving MDR and XDR gram-negative bacteria, has been reported. Plasmid mediated colistin resistant gram-negative bacteria have been described to be pan-drug resistant, implying a state devoid of alternative antibiotic therapeutic options. This review describes the evolution of antibiotic resistance to plasmid mediated colistin resistance, and discusses the potential role of high-throughput sequencing technologies, genomics and bioinformatics towards improving antibiotic resistance surveillance, the search for novel drug targets and precision antibiotic therapy focused at combating colistin resistance, and antimicrobial resistance as a whole.

scholarly journals The essential inner membrane protein YejM is a metalloenzyme

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Uma Gabale ◽  
Perla Arianna Peña Palomino ◽  
HyunAh Kim ◽  
Wenya Chen ◽  
Susanne Ressl
Keyword(s):  
Antibiotic Resistance ◽  
Membrane Protein ◽  
Outer Membrane ◽  
Critical Role ◽  
Membrane Properties ◽  
Gram Negative Bacteria ◽  
Inner Membrane ◽  
Gram Negative ◽  
Periplasmic Domain ◽  
Inner Membrane Protein

Abstract Recent recurrent outbreaks of Gram-negative bacteria show the critical need to target essential bacterial mechanisms to fight the increase of antibiotic resistance. Pathogenic Gram-negative bacteria have developed several strategies to protect themselves against the host immune response and antibiotics. One such strategy is to remodel the outer membrane where several genes are involved. yejM was discovered as an essential gene in E. coli and S. typhimurium that plays a critical role in their virulence by changing the outer membrane permeability. How the inner membrane protein YejM with its periplasmic domain changes membrane properties remains unknown. Despite overwhelming structural similarity between the periplasmic domains of two YejM homologues with hydrolases like arylsulfatases, no enzymatic activity has been previously reported for YejM. Our studies reveal an intact active site with bound metal ions in the structure of YejM periplasmic domain. Furthermore, we show that YejM has a phosphatase activity that is dependent on the presence of magnesium ions and is linked to its function of regulating outer membrane properties. Understanding the molecular mechanism by which YejM is involved in outer membrane remodeling will help to identify a new drug target in the fight against the increased antibiotic resistance.

scholarly journals An Essential Membrane Protein Modulates the Proteolysis of LpxC to Control Lipopolysaccharide Synthesis in Escherichia coli

mBio ◽  
2020 ◽  
Vol 11 (3) ◽  
Author(s):  
Elayne M. Fivenson ◽  
Thomas G. Bernhardt
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Outer Membrane ◽  
Unknown Function ◽  
Barrier Function ◽  
Major Determinant ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Content Type ◽  
Essential Protein

ABSTRACT Gram-negative bacteria are surrounded by a complex cell envelope that includes two membranes. The outer membrane prevents many drugs from entering these cells and is thus a major determinant of their intrinsic antibiotic resistance. This barrier function is imparted by the asymmetric architecture of the membrane with lipopolysaccharide (LPS) in the outer leaflet and phospholipids in the inner leaflet. The LPS and phospholipid synthesis pathways share an intermediate. Proper membrane biogenesis therefore requires that the flux through each pathway be balanced. In Escherichia coli, a major control point in establishing this balance is the committed step of LPS synthesis mediated by LpxC. Levels of this enzyme are controlled through its degradation by the inner membrane protease FtsH and its presumed adapter protein LapB (YciM). How turnover of LpxC is controlled has remained unclear for many years. Here, we demonstrate that the essential protein of unknown function YejM (PbgA) participates in this regulatory pathway. Suppressors of YejM essentiality were identified in lpxC and lapB, and LpxC overproduction was shown to be sufficient to allow survival of ΔyejM mutants. Furthermore, the stability of LpxC was shown to be reduced in cells lacking YejM, and genetic and physical interactions between LapB and YejM were detected. Taken together, our results are consistent with a model in which YejM directly modulates LpxC turnover by FtsH-LapB to regulate LPS synthesis and maintain membrane homeostasis. IMPORTANCE The outer membrane is a major determinant of the intrinsic antibiotic resistance of Gram-negative bacteria. It is composed of both lipopolysaccharide (LPS) and phospholipid, and the synthesis of these lipid species must be balanced for the membrane to maintain its barrier function in blocking drug entry. In this study, we identified an essential protein of unknown function as a key new factor in modulating LPS synthesis in the model bacterium Escherichia coli. Our results provide novel insight into how this organism and most likely other Gram-negative bacteria maintain membrane homeostasis and their intrinsic resistance to antibiotics.

scholarly journals Screening for multi-drug-resistant Gram-negative bacteria: what is effective and justifiable?

2020 ◽  
Vol 38 (S1) ◽  
pp. 72-90 ◽  
Author(s):  
Niels Nijsingh ◽  
Christian Munthe ◽  
Anna Lindblom ◽  
Christina Åhrén
Keyword(s):  
Staphylococcus Aureus ◽  
Antibiotic Resistance ◽  
Large Scale ◽  
Population Level ◽  
Gram Negative Bacteria ◽  
Drug Resistant ◽  
Gram Negative ◽  
Screening Programs ◽  
Scale Population ◽  
Current Screening

AbstractEffectiveness is a key criterion in assessing the justification of antibiotic resistance interventions. Depending on an intervention’s effectiveness, burdens and costs will be more or less justified, which is especially important for large scale population-level interventions with high running costs and pronounced risks to individuals in terms of wellbeing, integrity and autonomy. In this paper, we assess the case of routine hospital screening for multi-drug-resistant Gram-negative bacteria (MDRGN) from this perspective. Utilizing a comparison to screening programs for Methicillin-Resistant Staphylococcus aureus (MRSA) we argue that current screening programmes for MDRGN in low endemic settings should be reconsidered, as its effectiveness is in doubt, while general downsides to screening programs remain. To accomplish justifiable antibiotic stewardship, MDRGN screening should not be viewed as a separate measure, but rather as part of a comprehensive approach. The program should be redesigned to focus on those at risk of developing symptomatic infections with MDRGN rather than merely detecting those colonised.

scholarly journals Thrombin-Derived Peptides Potentiate the Activity of Gram-Positive-Specific Antibiotics against Gram-Negative Bacteria

Molecules ◽  
2021 ◽  
Vol 26 (7) ◽  
pp. 1954
Author(s):  
Charlotte M. J. Wesseling ◽  
Thomas M. Wood ◽  
Kristine Bertheussen ◽  
Samantha Lok ◽  
Nathaniel I. Martin
Keyword(s):  
Antibiotic Resistance ◽  
Outer Membrane ◽  
Therapeutic Range ◽  
Structural Features ◽  
Gram Negative Bacteria ◽  
Binding Properties ◽  
Gram Positive ◽  
Gram Negative ◽  
Recent Attention ◽  
Lps Binding

The continued rise of antibiotic resistance threatens to undermine the utility of the world’s current antibiotic arsenal. This problem is particularly troubling when it comes to Gram-negative pathogens for which there are inherently fewer antibiotics available. To address this challenge, recent attention has been focused on finding compounds capable of disrupting the Gram-negative outer membrane as a means of potentiating otherwise Gram-positive-specific antibiotics. In this regard, agents capable of binding to the lipopolysaccharide (LPS) present in the Gram-negative outer membrane are of particular interest as synergists. Recently, thrombin-derived C-terminal peptides (TCPs) were reported to exhibit unique LPS-binding properties. We here describe investigations establishing the capacity of TCPs to act as synergists with the antibiotics erythromycin, rifampicin, novobiocin, and vancomycin against multiple Gram-negative strains including polymyxin-resistant clinical isolates. We further assessed the structural features most important for the observed synergy and characterized the outer membrane permeabilizing activity of the most potent synergists. Our investigations highlight the potential for such peptides in expanding the therapeutic range of antibiotics typically only used to treat Gram-positive infections.

scholarly journals The Antibacterial Activities of NiO Nanoparticles Against Some Gram-Positive and Gram-Negative Bacterial Strains

2019 ◽  
Vol 4 (2) ◽  
pp. 69-74
Author(s):  
Ghazaleh Ilbeigi ◽  
Ashraf Kariminik ◽  
Mohammad Hasan Moshafi
Keyword(s):  
Antibiotic Resistance ◽  
Antibacterial Properties ◽  
Diffusion Method ◽  
Resistance Pattern ◽  
Resistant Bacteria ◽  
Gram Negative Bacteria ◽  
Nio Nanoparticles ◽  
Bacterial Strains ◽  
Gram Positive ◽  
Gram Negative

Introduction: Given the increasing rate of antibiotic resistance among bacterial strains, many researchers have been working to produce new and efficient and inexpensive antibacterial agents. It has been reported that some nanoparticles may be used as novel antimicrobial agents.Here, we evaluated antibacterial properties of nickel oxide (NiO) nanoparticles. Methods: NiO nanoparticles were synthesized using microwave method. In order to control the quality and morphology of nanoparticles, XRD (X-ray diffraction) and SEM (scanning electronmicroscope) were utilized. The antibacterial properties of the nanoparticles were assessed against eight common bacterial strains using agar well diffusion assay. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were measured. Antibiotic resistance pattern of the bacteria to nine antibiotics was obtained by Kirby-Bauer disk diffusion method. Results: The crystalline size and diameter (Dc) of NiO nanoparticles were obtained 40-60 nm. The nanoparticles were found to inhibit the growth of both gram-positive and gram-negative bacteria with higher activity against gram-positive organisms. Among bacterial strains, maximum sensitivity was observed in Staphylococcus epidermidis with MIC and MBC of 0.39 and 0.78 mg/mL, respectively. The bacteria had high resistance to cefazolin, erythromycin, rifampicin,ampicillin, penicillin and streptomycin.Conclusion: NiO nanoparticles exhibited remarkable antibacterial properties against gram positive and gram-negative bacteria and can be a new treatment for human pathogenic and antibiotic-resistant bacteria.

scholarly journals An essential membrane protein modulates the proteolysis of LpxC to control lipopolysaccharide synthesis in Escherichia coli

2020 ◽  
Author(s):  
Elayne M. Fivenson ◽  
Thomas G. Bernhardt
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Outer Membrane ◽  
Unknown Function ◽  
Barrier Function ◽  
Adaptor Protein ◽  
Major Determinant ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Essential Protein

ABSTRACTGram-negative bacteria are surrounded by a complex cell envelope that includes two membranes. The outer membrane prevents many drugs from entering these cells and is thus a major determinant of their intrinsic antibiotic resistance. This barrier function is imparted by the asymmetric architecture of the membrane with lipopolysaccharide (LPS) in the outer leaflet and phospholipids in the inner leaflet. The LPS and phospholipid synthesis pathways share a common intermediate. Proper membrane biogenesis therefore requires that the flux through each pathway be balanced. In Escherichia coli, a major control point in establishing this balance is the committed step of LPS synthesis mediated by LpxC. Levels of this enzyme are controlled through its degradation by the inner membrane protease FtsH and its presumed adaptor protein LapB(YciM). How turnover of LpxC is controlled has remained unclear for many years. Here, we demonstrate that the essential protein of unknown function YejM(PbgA), which we have renamed ClxD (control of LpxC degradation), participates in this regulatory pathway. Suppressors of ClxD essentiality were identified in lpxC and lapB, and LpxC overproduction was shown to be sufficient to allow survival of ΔclxD mutants. Furthermore, the half-life of LpxC was shown to be reduced in cells lacking ClxD, and genetic and physical interactions between LapB and ClxD were detected. Taken together, our results are consistent with a model in which ClxD directly modulates LpxC turnover by FtsH-LapB to regulate LPS synthesis and maintain membrane homeostasis.SIGNIFICANCEThe outer membrane is a major determinant of the intrinsic antibiotic resistance of Gram-negative bacteria. It is composed of both lipopolysaccharide (LPS) and phospholipid, and the synthesis of these lipid species must be balanced for the membrane to maintain its barrier function in blocking drug entry. In this report, we identify an essential protein of unknown function as a key new factor in maintaining LPS/phospholipid balance in the model bacterium Escherichia coli. Our results provide novel insight into how this organism and most likely other Gram-negative bacteria maintain membrane homeostasis and their intrinsic resistance to antibiotics.

Exploring Nature’s Treasure to Inhibit β-Barrel Assembly Machinery of Antibiotic Resistant Bacteria: An In-Silico Approach

2020 ◽  
Vol 18 ◽  
Author(s):  
Shalja Verma ◽  
Anand Kumar Pandey
Keyword(s):  
Antibiotic Resistance ◽  
Outer Membrane ◽  
In Silico ◽  
Membrane Integrity ◽  
Natural Compounds ◽  
Resistant Bacteria ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Bam Complex ◽  
In Silico Admet

Background: Development of antibiotic resistance in bacteria is a matter of global concern due to the exceptionally high morbidity and mortality rates. Outer membrane of most Gram-negative bacteria act as a highly efficient barrier and blocks the entry of the majority of antibiotics, making them ineffective. Bam complex, β-barrel assembly machinery complex, contains five subunits (BamA,B,C,D,E) which plays a vital role in folding and insertion of essential outer membrane proteins into membrane thus maintains outer membrane integrity. Bam A and Bam D are essential subunits to fulfil this purpose. Thus, targeting this complex to treat antibiotic resistance can be an incredibly effective approach. Natural bacterial pigment like violacein, phytochemicals like withanone, semasin and several polyphenols have often been reported for their effective antibiotic, antioxidant, anti-inflammatory, antiviral and anti-carcinogenic properties. Objective: Structural inhibition of Bam complex by natural compounds can provide safe and effective treatment to antibiotic resistance by targeting outer membrane integrity. Methods: In-silico ADMET and Molecular docking analysis was performed with 10 natural compounds namely violacein, withanone, sesamin, resveratrol, naringenin, quercetin, epicatechin, gallic acid, ellagic acid and galangin to analyse their inhibitory potential against Bam complex. Results: Docking complexes of Violacein gave high binding energies of -10.385 and -9.46 Kcal/mol at C and D subunits interface, and at A subunits of the Bam complex respectively. Conclusion: Henceforth, violacein can be an effective antibiotic against till date reported resistant Gram-negative bacteria by inhibiting the Bam complex of their outer membrane, therefore urgent need for exhaustive research in this concern is highly demanded.

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