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1.
Nature ; 626(7999): 617-625, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38081298

RESUMO

The outer membrane in Gram-negative bacteria consists of an asymmetric phospholipid-lipopolysaccharide bilayer that is densely packed with outer-membrane ß-barrel proteins (OMPs) and lipoproteins1. The architecture and composition of this bilayer is closely monitored and is essential to cell integrity and survival2-4. Here we find that SlyB, a lipoprotein in the PhoPQ stress regulon, forms stable stress-induced complexes with the outer-membrane proteome. SlyB comprises a 10 kDa periplasmic ß-sandwich domain and a glycine zipper domain that forms a transmembrane α-helical hairpin with discrete phospholipid- and lipopolysaccharide-binding sites. After loss in lipid asymmetry, SlyB oligomerizes into ring-shaped transmembrane complexes that encapsulate ß-barrel proteins into lipid nanodomains of variable size. We find that the formation of SlyB nanodomains is essential during lipopolysaccharide destabilization by antimicrobial peptides or acute cation shortage, conditions that result in a loss of OMPs and compromised outer-membrane barrier function in the absence of a functional SlyB. Our data reveal that SlyB is a compartmentalizing transmembrane guard protein that is involved in cell-envelope proteostasis and integrity, and suggest that SlyB represents a larger family of broadly conserved lipoproteins with 2TM glycine zipper domains with the ability to form lipid nanodomains.


Assuntos
Proteínas da Membrana Bacteriana Externa , Membrana Celular , Bactérias Gram-Negativas , Bicamadas Lipídicas , Proteínas da Membrana Bacteriana Externa/química , Proteínas da Membrana Bacteriana Externa/metabolismo , Membrana Celular/química , Membrana Celular/metabolismo , Glicina/metabolismo , Lipopolissacarídeos/metabolismo , Lipoproteínas/química , Lipoproteínas/metabolismo , Fosfolipídeos/metabolismo , Sítios de Ligação , Proteostase , Bicamadas Lipídicas/química , Bicamadas Lipídicas/metabolismo , Proteoma/química , Proteoma/metabolismo , Regulon , Domínios Proteicos , Peptídeos Antimicrobianos/metabolismo , Bactérias Gram-Negativas/química , Bactérias Gram-Negativas/citologia , Bactérias Gram-Negativas/metabolismo
2.
Nature ; 623(7988): 814-819, 2023 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-37938784

RESUMO

Gram-negative bacteria are surrounded by two membranes. A special feature of the outer membrane is its asymmetry. It contains lipopolysaccharide (LPS) in the outer leaflet and phospholipids in the inner leaflet1-3. The proper assembly of LPS in the outer membrane is required for cell viability and provides Gram-negative bacteria intrinsic resistance to many classes of antibiotics. LPS biosynthesis is completed in the inner membrane, so the LPS must be extracted, moved across the aqueous periplasm that separates the two membranes and translocated through the outer membrane where it assembles on the cell surface4. LPS transport and assembly requires seven conserved and essential LPS transport components5 (LptA-G). This system has been proposed to form a continuous protein bridge that provides a path for LPS to reach the cell surface6,7, but this model has not been validated in living cells. Here, using single-molecule tracking, we show that Lpt protein dynamics are consistent with the bridge model. Half of the inner membrane Lpt proteins exist in a bridge state, and bridges persist for 5-10 s, showing that their organization is highly dynamic. LPS facilitates Lpt bridge formation, suggesting a mechanism by which the production of LPS can be directly coupled to its transport. Finally, the bridge decay kinetics suggest that there may be two different types of bridges, whose stability differs according to the presence (long-lived) or absence (short-lived) of LPS. Together, our data support a model in which LPS is both a substrate and a structural component of dynamic Lpt bridges that promote outer membrane assembly.


Assuntos
Membrana Externa Bacteriana , Proteínas de Transporte , Bactérias Gram-Negativas , Lipopolissacarídeos , Proteínas de Membrana , Membrana Externa Bacteriana/química , Membrana Externa Bacteriana/metabolismo , Proteínas da Membrana Bacteriana Externa/química , Proteínas da Membrana Bacteriana Externa/metabolismo , Transporte Biológico , Proteínas de Transporte/química , Proteínas de Transporte/metabolismo , Escherichia coli/química , Escherichia coli/citologia , Escherichia coli/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Bactérias Gram-Negativas/química , Bactérias Gram-Negativas/citologia , Bactérias Gram-Negativas/metabolismo , Lipopolissacarídeos/química , Lipopolissacarídeos/metabolismo , Proteínas de Membrana/química , Proteínas de Membrana/metabolismo
3.
J Biol Chem ; 299(9): 105146, 2023 09.
Artigo em Inglês | MEDLINE | ID: mdl-37562569

RESUMO

The Maintenance of outer membrane (OM) Lipid Asymmetry system mediates retrograde phospholipid transport from the OM to the inner membrane (IM) in Gram-negative bacteria. However, the interactions between the various subunits of the IM and OM complexes are not well understood. In a recent study in 2023 by MacRae et al. in the Journal of Biological Chemistry, the authors examine components in the Maintenance of OM Lipid Asymmetry complex, define the interaction interfaces between members of the pathway, and propose a molecular model of the lipid transfer process from the OM to the IM that will help elucidate intricacies of lipid transport.


Assuntos
Proteínas da Membrana Bacteriana Externa , Membrana Externa Bacteriana , Bactérias Gram-Negativas , Metabolismo dos Lipídeos , Lipídeos de Membrana , Membrana Externa Bacteriana/química , Membrana Externa Bacteriana/metabolismo , Proteínas da Membrana Bacteriana Externa/química , Proteínas da Membrana Bacteriana Externa/metabolismo , Transporte Biológico , Bactérias Gram-Negativas/citologia , Bactérias Gram-Negativas/metabolismo , Lipídeos de Membrana/metabolismo , Fosfolipídeos/metabolismo
4.
Nature ; 613(7945): 729-734, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-36450357

RESUMO

Peptidoglycan and almost all surface glycopolymers in bacteria are built in the cytoplasm on the lipid carrier undecaprenyl phosphate (UndP)1-4. These UndP-linked precursors are transported across the membrane and polymerized or directly transferred to surface polymers, lipids or proteins. UndP is then flipped to regenerate the pool of cytoplasmic-facing UndP. The identity of the flippase that catalyses transport has remained unknown. Here, using the antibiotic amphomycin that targets UndP5-7, we identified two broadly conserved protein families that affect UndP recycling. One (UptA) is a member of the DedA superfamily8; the other (PopT) contains the domain DUF368. Genetic, cytological and syntenic analyses indicate that these proteins are UndP transporters. Notably, homologues from Gram-positive and Gram-negative bacteria promote UndP transport in Bacillus subtilis, indicating that recycling activity is broadly conserved among family members. Inhibitors of these flippases could potentiate the activity of antibiotics targeting the cell envelope.


Assuntos
Proteínas de Bactérias , Proteínas de Transporte , Sequência Conservada , Evolução Molecular , Bactérias Gram-Negativas , Bactérias Gram-Positivas , Fosfatos de Poli-Isoprenil , Antibacterianos/farmacologia , Bacillus subtilis/citologia , Bacillus subtilis/efeitos dos fármacos , Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/classificação , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Proteínas de Transporte/química , Proteínas de Transporte/classificação , Proteínas de Transporte/genética , Proteínas de Transporte/metabolismo , Membrana Celular/efeitos dos fármacos , Membrana Celular/metabolismo , Bactérias Gram-Negativas/citologia , Bactérias Gram-Negativas/efeitos dos fármacos , Bactérias Gram-Negativas/genética , Bactérias Gram-Negativas/metabolismo , Bactérias Gram-Positivas/citologia , Bactérias Gram-Positivas/efeitos dos fármacos , Bactérias Gram-Positivas/genética , Bactérias Gram-Positivas/metabolismo , Fosfatos de Poli-Isoprenil/metabolismo , Sintenia , Peptidoglicano/metabolismo , Parede Celular/química , Parede Celular/metabolismo
5.
Nature ; 613(7945): 721-728, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-36450355

RESUMO

The microbial cell wall is essential for maintenance of cell shape and resistance to external stressors1. The primary structural component of the cell wall is peptidoglycan, a glycopolymer with peptide crosslinks located outside of the cell membrane1. Peptidoglycan biosynthesis and structure are responsive to shifting environmental conditions such as pH and salinity2-6, but the mechanisms underlying such adaptations are incompletely understood. Precursors of peptidoglycan and other cell surface glycopolymers are synthesized in the cytoplasm and then delivered across the cell membrane bound to the recyclable lipid carrier undecaprenyl phosphate7 (C55-P, also known as UndP). Here we identify the DUF368-containing and DedA transmembrane protein families as candidate C55-P translocases, filling a critical gap in knowledge of the proteins required for the biogenesis of microbial cell surface polymers. Gram-negative and Gram-positive bacteria lacking their cognate DUF368-containing protein exhibited alkaline-dependent cell wall and viability defects, along with increased cell surface C55-P levels. pH-dependent synthetic genetic interactions between DUF368-containing proteins and DedA family members suggest that C55-P transporter usage is dynamic and modulated by environmental inputs. C55-P transporter activity was required by the cholera pathogen for growth and cell shape maintenance in the intestine. We propose that conditional transporter reliance provides resilience in lipid carrier recycling, bolstering microbial fitness both inside and outside the host.


Assuntos
Proteínas de Bactérias , Proteínas de Transporte , Aptidão Genética , Bactérias Gram-Negativas , Bactérias Gram-Positivas , Fosfatos de Poli-Isoprenil , Proteínas de Bactérias/metabolismo , Proteínas de Transporte/metabolismo , Membrana Celular/metabolismo , Parede Celular/química , Parede Celular/metabolismo , Lipídeos/análise , Peptidoglicano/metabolismo , Fosfatos de Poli-Isoprenil/metabolismo , Bactérias Gram-Negativas/química , Bactérias Gram-Negativas/citologia , Bactérias Gram-Negativas/metabolismo , Bactérias Gram-Positivas/química , Bactérias Gram-Positivas/citologia , Bactérias Gram-Positivas/metabolismo , Viabilidade Microbiana
6.
Nature ; 606(7912): 160-164, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35585231

RESUMO

Cellular iron homeostasis is vital and maintained through tight regulation of iron import, efflux, storage and detoxification1-3. The most common modes of iron storage use proteinaceous compartments, such as ferritins and related proteins4,5. Although lipid-bounded iron compartments have also been described, the basis for their formation and function remains unknown6,7. Here we focus on one such compartment, herein named the 'ferrosome', that was previously observed in the anaerobic bacterium Desulfovibrio magneticus6. Using a proteomic approach, we identify three ferrosome-associated (Fez) proteins that are responsible for forming ferrosomes in D. magneticus. Fez proteins are encoded in a putative operon and include FezB, a P1B-6-ATPase found in phylogenetically and metabolically diverse species of bacteria and archaea. We show that two other bacterial species, Rhodopseudomonas palustris and Shewanella putrefaciens, make ferrosomes through the action of their six-gene fez operon. Additionally, we find that fez operons are sufficient for ferrosome formation in foreign hosts. Using S. putrefaciens as a model, we show that ferrosomes probably have a role in the anaerobic adaptation to iron starvation. Overall, this work establishes ferrosomes as a new class of iron storage organelles and sets the stage for studying their formation and structure in diverse microorganisms.


Assuntos
Compostos Férricos , Bactérias Gram-Negativas , Família Multigênica , Organelas , Proteínas de Bactérias/genética , Desulfovibrio , Bactérias Gram-Negativas/citologia , Bactérias Gram-Negativas/genética , Organelas/genética , Organelas/metabolismo , Filogenia , Proteômica , Rodopseudomonas , Shewanella putrefaciens
7.
Biotechnol Bioeng ; 119(1): 34-47, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34698385

RESUMO

Outer membrane vesicles (OMVs) are nanoscale spherical vesicles released from Gram-negative bacteria. The lipid bilayer membrane structure of OMVs consists of similar components as bacterial membrane and thus has attracted more and more attention in exploiting OMVs' bio-applications. Although the endotoxic lipopolysaccharide on natural OMVs may impose potential limits on their clinical applications, genetic modification can reduce their endotoxicity and decorate OMVs with multiple functional proteins. These genetically engineered OMVs have been employed in various fields including vaccination, drug delivery, cancer therapy, bioimaging, biosensing, and enzyme carrier. This review will first briefly introduce the background of OMVs followed by recent advances in functionalization and various applications of engineered OMVs with an emphasis on the working principles and their performance, and then discuss about the future trends of OMVs in biomedical applications.


Assuntos
Membrana Externa Bacteriana , Sistemas de Liberação de Medicamentos , Vesículas Extracelulares , Bactérias Gram-Negativas/citologia , Vacinas , Animais , Engenharia Genética , Humanos , Imunoensaio , Camundongos
8.
Nat Microbiol ; 6(7): 910-920, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34183815

RESUMO

Bacterial species have diverse cell shapes that enable motility, colonization and virulence. The cell wall defines bacterial shape and is primarily built by two cytoskeleton-guided synthesis machines, the elongasome and the divisome. However, the mechanisms producing complex shapes, like the curved-rod shape of Vibrio cholerae, are incompletely defined. Previous studies have reported that species-specific regulation of cytoskeleton-guided machines enables formation of complex bacterial shapes such as cell curvature and cellular appendages. In contrast, we report that CrvA and CrvB are sufficient to induce complex cell shape autonomously of the cytoskeleton in V. cholerae. The autonomy of the CrvAB module also enables it to induce curvature in the Gram-negative species Escherichia coli, Pseudomonas aeruginosa, Caulobacter crescentus and Agrobacterium tumefaciens. Using inducible gene expression, quantitative microscopy and biochemistry, we show that CrvA and CrvB circumvent the need for patterning via cytoskeletal elements by regulating each other to form an asymmetrically localized, periplasmic structure that binds directly to the cell wall. The assembly and disassembly of this periplasmic structure enables dynamic changes in cell shape. Bioinformatics indicate that CrvA and CrvB may have diverged from a single ancestral hybrid protein. Using fusion experiments in V. cholerae, we find that a synthetic CrvA/B hybrid protein is sufficient to induce curvature on its own, but that expression of two distinct proteins, CrvA and CrvB, promotes more rapid curvature induction. We conclude that morphological complexity can arise independently of cell-shape specification by the core cytoskeleton-guided synthesis machines.


Assuntos
Proteínas de Bactérias/metabolismo , Bactérias Gram-Negativas/citologia , Proteínas de Bactérias/genética , Parede Celular/metabolismo , Citoesqueleto/metabolismo , Evolução Molecular , Bactérias Gram-Negativas/crescimento & desenvolvimento , Bactérias Gram-Negativas/metabolismo , Peptidoglicano/metabolismo , Periplasma/metabolismo , Vibrio cholerae/citologia , Vibrio cholerae/crescimento & desenvolvimento , Vibrio cholerae/metabolismo
9.
Proc Natl Acad Sci U S A ; 118(11)2021 03 16.
Artigo em Inglês | MEDLINE | ID: mdl-33836615

RESUMO

Gram-positive bacteria assemble a multilayered cell wall that provides tensile strength to the cell. The cell wall is composed of glycan strands cross-linked by nonribosomally synthesized peptide stems. Herein, we modify the peptide stems of the Gram-positive bacterium Bacillus subtilis with noncanonical electrophilic d-amino acids, which when in proximity to adjacent stem peptides form novel covalent 5,3-cross-links. Approximately 20% of canonical cell-wall cross-links can be replaced with synthetic cross-links. While a low level of synthetic cross-link formation does not affect B. subtilis growth and phenotype, at higher levels cell growth is perturbed and bacteria elongate. A comparison of the accumulation of synthetic cross-links over time in Gram-negative and Gram-positive bacteria highlights key differences between them. The ability to perturb cell-wall architecture with synthetic building blocks provides a novel approach to studying the adaptability, elasticity, and porosity of bacterial cell walls.


Assuntos
Parede Celular/química , Bacilos Gram-Positivos/química , Peptidoglicano/química , Aminoácidos/química , Aminoácidos/metabolismo , Bacillus subtilis/química , Bacillus subtilis/citologia , Bacillus subtilis/crescimento & desenvolvimento , Bacillus subtilis/metabolismo , Parede Celular/metabolismo , Bactérias Gram-Negativas/química , Bactérias Gram-Negativas/citologia , Bactérias Gram-Negativas/metabolismo , Bacilos Gram-Positivos/citologia , Bacilos Gram-Positivos/crescimento & desenvolvimento , Bacilos Gram-Positivos/metabolismo , Peptidoglicano/metabolismo , Peptidil Transferases/genética , Peptidil Transferases/metabolismo , Fenótipo
10.
J Oleo Sci ; 70(4): 571-580, 2021 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-33692238

RESUMO

Polyglycerol monolaurates are generally recognized as safe food additives and are commonly used as food emulsifiers. In this study, the antimicrobial effect of four polyglycerol monolaurates on two Gram-positive bacteria (Staphylococcus aureus and Bacillus subtilis) and two Gram-negative bacteria (Escherichia. coli and Pseudomonas aeruginosa) were investigated. The minimum inhibitory concentration (MIC) of diglycerol monolaurate (PG2ML), triglycerol monolaurate (PG3ML), hexaglycerol monolaurate (PG6ML), and decaglycerol monolaurate (PG10ML) against S. aureus was 0.16, 0.32, 0.63, and 1.25 mg/mL, respectively. The MIC of PG2ML, PG3ML, PG6ML, and PG10ML against B. subtilis was 0.32, 0.63, 1.25, and 3.75 mg/mL, respectively. No apparent antimicrobial effect of these four polyglycerol monolaurates on E. coli and P. aeruginosa was observed even up to 10.00 mg/mL. The underlying mechanism was investigated by assessing cell membrane permeability, the integrity of cell membrane, and morphology. We concluded that polyglycerol monolaurates might eliminate Gram-positive bacteria by disrupting the cell membrane, thereby increasing cell membrane permeability, releasing the cellular contents, and altering the cell morphology.


Assuntos
Antibacterianos , Emulsificantes , Aditivos Alimentares , Glicerol/farmacologia , Bactérias Gram-Negativas/efeitos dos fármacos , Bactérias Gram-Positivas/efeitos dos fármacos , Lauratos/farmacologia , Polímeros/farmacologia , Membrana Celular/efeitos dos fármacos , Permeabilidade da Membrana Celular/efeitos dos fármacos , Relação Dose-Resposta a Droga , Farmacorresistência Bacteriana , Microbiologia de Alimentos , Glicerol/química , Bactérias Gram-Negativas/citologia , Bactérias Gram-Positivas/citologia , Lauratos/química , Testes de Sensibilidade Microbiana , Polímeros/química , Relação Estrutura-Atividade
11.
Anal Chem ; 93(2): 843-850, 2021 01 19.
Artigo em Inglês | MEDLINE | ID: mdl-33301291

RESUMO

Droplet microfluidics disrupted analytical biology with the introduction of digital polymerase chain reaction and single-cell sequencing. The same technology may also bring important innovation in the analysis of bacteria, including antibiotic susceptibility testing at the single-cell level. Still, despite promising demonstrations, the lack of a high-throughput label-free method of detecting bacteria in nanoliter droplets prohibits analysis of the most interesting strains and widespread use of droplet technologies in analytical microbiology. We use a sensitive and fast measurement of scattered light from nanoliter droplets to demonstrate reliable detection of the proliferation of encapsulated bacteria. We verify the sensitivity of the method by simultaneous readout of fluorescent signals from bacteria expressing fluorescent proteins and demonstrate label-free readout on unlabeled Gram-negative and Gram-positive species. Our approach requires neither genetic modification of the cells nor the addition of chemical markers of metabolism. It is compatible with a wide range of bacterial species of clinical, research, and industrial interest, opening the microfluidic droplet technologies for adaptation in these fields.


Assuntos
Bactérias Gram-Negativas/isolamento & purificação , Bactérias Gram-Positivas/isolamento & purificação , Ensaios de Triagem em Larga Escala , Técnicas Analíticas Microfluídicas , Nanopartículas/química , Análise de Célula Única , Bactérias Gram-Negativas/citologia , Bactérias Gram-Positivas/citologia , Tamanho da Partícula , Propriedades de Superfície
12.
PLoS Comput Biol ; 16(10): e1008355, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-33112853

RESUMO

In Gram-negative bacteria, the folding and insertion of ß-barrel outer membrane proteins (OMPs) to the outer membrane are mediated by the ß-barrel assembly machinery (BAM) complex. Two leading models of this process have been put forth: the hybrid barrel model, which claims that a lateral gate in BamA's ß-barrel can serve as a template for incoming OMPs, and the passive model, which claims that a thinned membrane near the lateral gate of BamA accelerates spontaneous OMP insertion. To examine the key elements of these two models, we have carried out 45.5 µs of equilibrium molecular dynamics simulations of BamA with and without POTRA domains from Escherichia coli, Salmonella enterica, Haemophilus ducreyi and Neisseria gonorrhoeae, together with BamA's homolog, TamA from E. coli, in their native, species-specific outer membranes. In these equilibrium simulations, we consistently observe membrane thinning near the lateral gate for all proteins. We also see occasional spontaneous lateral gate opening and sliding of the ß-strands at the gate interface for N. gonorrhoeae, indicating that the gate is dynamic. An additional 14 µs of free-energy calculations shows that the energy necessary to open the lateral gate in BamA/TamA varies by species, but is always lower than the Omp85 homolog, FhaC. Our combined results suggest OMP insertion utilizes aspects of both the hybrid barrel and passive models.


Assuntos
Proteínas da Membrana Bacteriana Externa , Membrana Celular , Proteínas da Membrana Bacteriana Externa/química , Proteínas da Membrana Bacteriana Externa/metabolismo , Membrana Celular/química , Membrana Celular/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Bactérias Gram-Negativas/química , Bactérias Gram-Negativas/citologia , Bactérias Gram-Negativas/metabolismo , Simulação de Dinâmica Molecular , Conformação Proteica em Folha beta , Dobramento de Proteína
13.
Mikrochim Acta ; 187(10): 558, 2020 09 10.
Artigo em Inglês | MEDLINE | ID: mdl-32914337

RESUMO

A single-tube method based on a dual-electrostatic interaction (EI) strategy for bacteria capture and DNA extraction was designed to enable the highly sensitive detection of nucleic acids. Specially designed magnetic nanoparticles were developed to meet the opposing requirements of a single-tube method, which exist between the strong EI required for efficient bacteria capture and the weak EI required for DNA extraction with minimal DNA adsorption. A dual-EI strategy for the single-tube (DESIGN) method was thus developed to integrate bacteria enrichment, bacteria cell lysis, and DNA recovery in a single tube, thereby minimizing precious sample loss and reducing handling time. Subsequently, we evaluated the performance with a variety of concentrations from 5 to 100 colony-forming units (CFU)/10 mL human urine and milk samples. The DESIGN method achieved the simple and sensitive detection of Salmonella enterica serovar Typhimurium in 10 mL of human urine and milk samples up to 5 CFU by quantitative PCR. Furthermore, the DESIGN method detected Brucella ovis and Escherichia coli from 10 mL of human urine with a detection limit up to 5 CFU/10 mL. Graphical abstract.


Assuntos
Bactérias Gram-Negativas/metabolismo , Nanopartículas/química , Bactérias Gram-Negativas/citologia , Humanos , Eletricidade Estática
14.
Adv Biosyst ; 4(9): e2000074, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32803868

RESUMO

Nontoxic carbon nanoparticle samples prepared by both bottom-up and top-down approaches do not inhibit Gram-negative bacterial growth, indicating excellent biocompatibilities. However, cell growth inhibitory efficacies increase considerably when the carbon nanoparticles are conjugated with the antibiotic tetracycline. In tetracycline-resistant bacteria, these efficacies can approach tenfold higher activities when compared to tetracycline alone. No structural abnormality such as membrane disruptions is evident in the tested bacterial strains; this is in contrast with other nanocarbon systems such as graphene oxides, carbon nanotubes, and amine-functionalized carbon nanoparticles which do exhibit membrane disruptions. In comparison, the tetracycline-conjugated carbon nanoparticles induce membrane perturbations (but not membrane disruptions), inhibiting bacterial efflux mechanisms. It is proposed that when tetracycline is conjugated to the surface of carbon nanoparticles, it functions to direct the nanoparticles to membrane-associated tetracycline efflux pumps, thereby blocking and subsequently inhibiting their function. The conjugation between biocompatible carbon nanoparticles and subtherapeutic but well-established antibiotic molecules may provide hybrid antibiotic assembly strategies resulting in effective multidrug efflux inhibition for combating antibiotic resistance.


Assuntos
Antibacterianos , Farmacorresistência Bacteriana/efeitos dos fármacos , Bactérias Gram-Negativas/efeitos dos fármacos , Nanotubos de Carbono/química , Tetraciclina , Antibacterianos/química , Antibacterianos/farmacologia , Proteínas de Bactérias/metabolismo , Bactérias Gram-Negativas/citologia , Bactérias Gram-Negativas/metabolismo , Proteínas de Membrana Transportadoras/metabolismo , Tetraciclina/química , Tetraciclina/farmacologia
15.
J Chem Theory Comput ; 16(8): 5369-5384, 2020 Aug 11.
Artigo em Inglês | MEDLINE | ID: mdl-32628849

RESUMO

The bacterial cell envelope of Gram-negative bacteria is a complex biological barrier with multiple layers consisting of the inner membrane, periplasm of peptidoglycan, and the outer membrane with lipopolysaccharides (LPS). With rising antimicrobial resistance there is increasing interest in understanding interactions of small molecules with the cell membrane to aid in the development of novel drug molecules. Hence suitable representations of the bacterial membrane are required to carry out meaningful molecular dynamics simulations. Given the complexity of the cell envelope, fully atomistic descriptions of the cell membrane with explicit solvent are computationally prohibitive, allowing limited sampling with small system sizes. However, coarse-grained (CG) models such as MARTINI allow one to study phenomena at physiologically relevant length and time scales. Although MARTINI models for lipids and the LPS are available in literature, a suitable CG model of peptidoglycan is lacking. Using an all-atom model described by Gumbart et al. [PLoS Comput. Biol. 2014, 10, e1003475], we develop a CG model of the peptidoglycan network within the MARTINI framework. The model is parametrized to reproduce the end-to-end distance of glycan strands. The structural properties such as the equilibrium angle between adjacent peptides along the strands, area per disaccharide, and cavity size distributions agree well with the atomistic simulation results. Mechanical properties such as the area compressibility and the bending modulus are accurately reproduced. While developing novel antibiotics it is important to assess barrier properties of the peptidogylcan network. We evaluate and compare the free energy of insertion for a thymol molecule using umbrella sampling on both the MARTINI and all-atom peptidoglycan models. The insertion free energy was found to be less than kBT for both the MARTINI and all-atom models. Additional restraint free simulations reveal rapid translocation of thymol across peptidogylcan. We expect that the proposed MARTINI model for peptidoglycan will be useful in understanding phenomena associated with bacterial cell walls at larger length and time scales, thereby overcoming the current limitations of all-atom models.


Assuntos
Parede Celular/química , Bactérias Gram-Negativas/química , Lipopolissacarídeos/metabolismo , Modelos Biológicos , Peptidoglicano/metabolismo , Termodinâmica , Parede Celular/metabolismo , Bactérias Gram-Negativas/citologia , Bactérias Gram-Negativas/metabolismo , Lipopolissacarídeos/química , Conformação Molecular , Simulação de Dinâmica Molecular , Peptidoglicano/química
16.
Biointerphases ; 15(3): 031007, 2020 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-32456440

RESUMO

Antimicrobial peptides (AMPs) are attractive as biomaterial coatings because they have broad spectrum activity against different microbes, with a low likelihood of incurring antimicrobial resistance. Direct action against the bacterial membrane is the most common mechanism of action (MOA) of AMPs, with specific MOAs dependent on membrane composition, peptide concentration, and environmental factors that include temperature. Chrysophsin-1 (CHY1) is a broad spectrum salt-tolerant AMP that is derived from a marine fish. A cysteine modification was made to the peptide to facilitate attachment to a surface, such as a biomedical device. The authors used quartz crystal microbalance with dissipation monitoring to study how temperature (23 and 37 °C) and lipid composition influence the MOA of cysteine-modified peptide (C-CHY1) with model membranes comprised of supported lipid bilayers (SLBs). These two temperatures were used so that the authors could better understand the differences in behavior between typical lab temperatures and physiologic conditions. The authors created model membranes that mimicked properties of Gram-negative and Gram-positive bacteria in order to understand how the mechanisms might differ for different types of bacterial systems. SLB models of Gram-positive bacterial membranes were formed using combinations of phosphatidylcholine, phosphatidylglycerol (PG), and S. aureus-derived lipoteichoic acid (LTA). SLB models of Gram-negative bacterial membranes were formed using combinations of phosphatidylethanolamine (PE), PG, and E. coli-derived lipopolysaccharides (LPS). The molecules that distinguish Gram-positive and Gram-negative membranes (LTA and LPS) have the potential to alter the MOA of C-CHY1 with the SLBs. The authors' results showed that the MOA for the Gram-positive SLBs was not sensitive to temperature, but the LTA addition did have an effect. Specifically, similar trends in frequency and dissipation changes across all overtones were observed, and the same mechanistic trends were observed in the polar plots at 23 and 37 °C. However, when LTA was added, polar plots showed an association between C-CHY1 and LTA, leading to SLB saturation. This was demonstrated by significant changes in dissipation, while the frequency (mass) was not increasing after the saturation point. For the Gram-negative SLBs, the composition did not have a significant effect on MOA, but the authors saw more differences between the two temperatures studied. The authors believe this is due to the fact that the gel-liquid crystal transition temperature of PE is 25 °C, which means that the bilayer is more rigid at 23 °C, compared to temperatures above the transition point. At 23 °C, a significant energetic shift would be required to allow for additional AMP insertion. This could be seen in the polar plots, where there was a steep slope but there was very little mass addition. At 37 °C, the membrane is more fluid and there is less of an energetic requirement for insertion. Therefore, the authors observed greater mass addition and fewer changes in dissipation. A better understanding of C-CHY1 MOA using different SLB models will allow for the more rational design of future therapeutic solutions that make use of antimicrobial peptides, including those involving biomaterial coatings.


Assuntos
Peptídeos Catiônicos Antimicrobianos/metabolismo , Membrana Celular/metabolismo , Bactérias Gram-Negativas/citologia , Bactérias Gram-Positivas/citologia , Lipopolissacarídeos/farmacologia , Ácidos Teicoicos/farmacologia , Membrana Celular/efeitos dos fármacos , Bactérias Gram-Negativas/efeitos dos fármacos , Bactérias Gram-Positivas/efeitos dos fármacos , Bicamadas Lipídicas/química , Peptídeos/química , Temperatura
17.
Anal Chem ; 92(11): 7523-7531, 2020 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-32330016

RESUMO

In diagnostics of infectious diseases, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) can be applied for the identification of pathogenic microorganisms. However, to achieve a trustworthy identification from MALDI-TOF MS data, a significant amount of biomass should be considered. The bacterial load that potentially occurs in a sample is therefore routinely amplified by culturing, which is a time-consuming procedure. In this paper, we show that culturing can be avoided by conducting MALDI-TOF MS on individual bacterial cells. This results in a more rapid identification of species with an acceptable accuracy. We propose a deep learning architecture to analyze the data and compare its performance with traditional supervised machine learning algorithms. We illustrate our workflow on a large data set that contains bacterial species related to urinary tract infections. Overall we obtain accuracies up to 85% in discriminating five different species.


Assuntos
Aprendizado Profundo , Bactérias Gram-Negativas/citologia , Bactérias Gram-Negativas/patogenicidade , Bactérias Gram-Positivas/citologia , Bactérias Gram-Positivas/patogenicidade , Análise de Célula Única , Aerossóis/química , Bactérias Gram-Negativas/isolamento & purificação , Bactérias Gram-Positivas/isolamento & purificação , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
18.
Angew Chem Int Ed Engl ; 59(22): 8517-8521, 2020 05 25.
Artigo em Inglês | MEDLINE | ID: mdl-32023354

RESUMO

Multi-drug resistance in Gram-negative bacteria is often associated with low permeability of the outer membrane. To investigate the role of membrane channels in the uptake of antibiotics, we present an approach using fusion of native outer membrane vesicles (OMVs) into a planar lipid bilayer, allowing characterization of membrane protein channels in their native environment. Two major membrane channels from E. coli, OmpF and OmpC, were overexpressed from the host and the corresponding OMVs were collected. Each OMV fusion surprisingly revealed only single or few channel activities. The asymmetry of the OMVs translates after fusion into the lipid membrane with the lipopolysaccharides (LPS) dominantly present at the side of OMV addition. Compared to the conventional reconstitution method, the channels fused from OMVs containing LPS have similar conductance but a much broader distribution and significantly lower permeation. We suggest using outer membrane vesicles for functional and structural studies of membrane channels in the native membrane.


Assuntos
Membrana Celular/efeitos dos fármacos , Membrana Celular/metabolismo , Fenômenos Eletrofisiológicos/efeitos dos fármacos , Bactérias Gram-Negativas/citologia , Bactérias Gram-Negativas/fisiologia , Lipopolissacarídeos/farmacologia , Transporte Biológico/efeitos dos fármacos , Bactérias Gram-Negativas/efeitos dos fármacos , Bactérias Gram-Negativas/metabolismo , Porinas/genética , Porinas/metabolismo
19.
Chembiochem ; 21(6): 759-768, 2020 03 16.
Artigo em Inglês | MEDLINE | ID: mdl-31709676

RESUMO

Quorum sensing (QS) is widely accepted as a procedure that bacteria use to converse. However, prevailing thinking places acyl homoserine lactones (AHLs) at the forefront of this communication pathway in Gram-negative bacteria. With the advent of high-throughput genomics and the subsequent influx of bacterial genomes, bioinformatics analysis has determined that the genes encoding AHL biosynthesis, originally discovered to be indispensable for QS (LuxI-like proteins and homologues), are often absent in QS-capable bacteria. Instead, the sensing protein (LuxR-like proteins) is present with an apparent inability to produce any outgoing AHL signal. Recently, several signals for these LuxR solos have been identified. Herein, advances in the field of QS are discussed, with a particular focus on recent research in the field of bacterial cell-cell communication.


Assuntos
Acil-Butirolactonas/metabolismo , Bactérias Gram-Negativas/metabolismo , Comunicação Celular , Bactérias Gram-Negativas/citologia , Bactérias Gram-Negativas/genética , Percepção de Quorum
20.
Protein Sci ; 29(3): 629-646, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-31747090

RESUMO

The history of modern medicine cannot be written apart from the history of the antibiotics. Antibiotics are cytotoxic secondary metabolites that are isolated from Nature. The antibacterial antibiotics disproportionately target bacterial protein structure that is distinct from eukaryotic protein structure, notably within the ribosome and within the pathways for bacterial cell-wall biosynthesis (for which there is not a eukaryotic counterpart). This review focuses on a pre-eminent class of antibiotics-the ß-lactams, exemplified by the penicillins and cephalosporins-from the perspective of the evolving mechanisms for bacterial resistance. The mechanism of action of the ß-lactams is bacterial cell-wall destruction. In the monoderm (single membrane, Gram-positive staining) pathogen Staphylococcus aureus the dominant resistance mechanism is expression of a ß-lactam-unreactive transpeptidase enzyme that functions in cell-wall construction. In the diderm (dual membrane, Gram-negative staining) pathogen Pseudomonas aeruginosa a dominant resistance mechanism (among several) is expression of a hydrolytic enzyme that destroys the critical ß-lactam ring of the antibiotic. The key sensing mechanism used by P. aeruginosa is monitoring the molecular difference between cell-wall construction and cell-wall deconstruction. In both bacteria, the resistance pathways are manifested only when the bacteria detect the presence of ß-lactams. This review summarizes how the ß-lactams are sensed and how the resistance mechanisms are manifested, with the expectation that preventing these processes will be critical to future chemotherapeutic control of multidrug resistant bacteria.


Assuntos
Antibacterianos/farmacologia , Parede Celular/efeitos dos fármacos , Bactérias Gram-Negativas/efeitos dos fármacos , Bactérias Gram-Positivas/efeitos dos fármacos , beta-Lactamas/farmacologia , Antibacterianos/química , Farmacorresistência Bacteriana/efeitos dos fármacos , Bactérias Gram-Negativas/citologia , Bactérias Gram-Positivas/citologia , Testes de Sensibilidade Microbiana , beta-Lactamas/química
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