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Kahan R, Worm DJ, de Castro GV, Ng S, Barnard A. Modulators of protein-protein interactions as antimicrobial agents. RSC Chem Biol 2021; 2:387-409. [PMID: 34458791 PMCID: PMC8341153 DOI: 10.1039/d0cb00205d] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
Protein-Protein interactions (PPIs) are involved in a myriad of cellular processes in all living organisms and the modulation of PPIs is already under investigation for the development of new drugs targeting cancers, autoimmune diseases and viruses. PPIs are also involved in the regulation of vital functions in bacteria and, therefore, targeting bacterial PPIs offers an attractive strategy for the development of antibiotics with novel modes of action. The latter are urgently needed to tackle multidrug-resistant and multidrug-tolerant bacteria. In this review, we describe recent developments in the modulation of PPIs in pathogenic bacteria for antibiotic development, including advanced small molecule and peptide inhibitors acting on bacterial PPIs involved in division, replication and transcription, outer membrane protein biogenesis, with an additional focus on toxin-antitoxin systems as upcoming drug targets.
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Affiliation(s)
- Rashi Kahan
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Dennis J Worm
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Guilherme V de Castro
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Simon Ng
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Anna Barnard
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
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Lundstedt EA, Simpson BW, Ruiz N. Lipopolysaccharide transport involves long-range coupling between cytoplasmic and periplasmic domains of the LptB 2FGC extractor. J Bacteriol 2020; 203:JB.00618-20. [PMID: 33361195 PMCID: PMC8095461 DOI: 10.1128/jb.00618-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/18/2020] [Indexed: 01/04/2023] Open
Abstract
The cell surface of the Gram-negative cell envelope contains lipopolysaccharide (LPS) molecules, which form a permeability barrier against hydrophobic antibiotics. The LPS transport (Lpt) machine composed of LptB2FGCADE forms a proteinaceous trans-envelope bridge that allows for the rapid and specific transport of newly synthesized LPS from the inner membrane (IM) to the outer membrane (OM). This transport is powered from the IM by the ATP-binding cassette transporter LptB2FGC. The ATP-driven cycling between closed- and open-dimer states of the ATPase LptB2 is coupled to the extraction of LPS by the transmembrane domains LptFG. However, the mechanism by which LPS moves from a substrate-binding cavity formed by LptFG at the IM to the first component of the periplasmic bridge, the periplasmic β-jellyroll domain of LptF, is poorly understood. To better understand how LptB2FGC functions in Escherichia coli, we searched for suppressors of a defective LptB variant. We found that defects in LptB2 can be suppressed by both structural modifications to the core oligosaccharide of LPS and changes in various regions of LptFG, including a periplasmic loop in LptF that connects the substrate-binding cavity in LptFG to the periplasmic β-jellyroll domain of LptF. These novel suppressors suggest that interactions between the core oligosaccharide of LPS and periplasmic regions in the transporter influence the rate of LPS extraction by LptB2FGC. Together, our genetic data reveal a path for the bi-directional coupling between LptB2 and LptFG that extends from the cytoplasm to the entrance to the periplasmic bridge of the transporter.IMPORTANCEGram-negative bacteria are intrinsically resistant to many antibiotics due to the presence of lipopolysaccharide (LPS) at their cell surface. LPS is transported from its site of synthesis at the inner membrane to the outer membrane by the Lpt machine. Lpt proteins form a transporter that spans the entire envelope and is thought to function similarly to a PEZ candy dispenser. This trans-envelope machine is powered by the cytoplasmic LptB ATPase through a poorly understood mechanism. Using genetic analyses in Escherichia coli, we found that LPS transport involves long-ranging bi-directional coupling across cellular compartments between cytoplasmic LptB and periplasmic regions of the Lpt transporter. This knowledge could be exploited in developing antimicrobials that overcome the permeability barrier imposed by LPS.
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Affiliation(s)
- Emily A Lundstedt
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Brent W Simpson
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
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Abstract
In this study, we applied a CRISPR interference approach to knock down expression of essential genes involved in cell envelope biogenesis and determined if this can trigger Pseudomonas aeruginosa T6SS apparatus assembly. We found that disruption of envelope biogenesis can be sensed by the bacteria via a sensory pathway that involves phosphorylation leading to profound T6SS dynamic activation. Our data provide further evidence that membrane disruption is a key signal that drives T6SS organelle assembly. This process likely mimics natural activation pathways that allow P. aeruginosa to detect the attack by other aggressive bacteria species and thus sheds further light on the potential key signals that control T6SS organelle biogenesis. The type 6 secretion system (T6SS) is a dynamic organelle encoded by many gram-negative bacteria that can be used to kill competing bacterial prey species in densely occupied niches. Some predatory species, such as Vibrio cholerae, use their T6SS in an untargeted fashion while in contrast, Pseudomonas aeruginosa assembles and fires its T6SS apparatus only after detecting initial attacks by other bacterial prey cells; this targeted attack strategy has been termed the T6SS tit-for-tat response. Molecules that interact with the P. aeruginosa outer membrane such as polymyxin B can also trigger assembly of T6SS organelles via a signal transduction pathway that involves protein phosphorylation. Recent work suggests that a phospholipase T6SS effector (TseL) of V. cholerae can induce T6SS dynamic activity in P. aeruginosa when delivered to or expressed in the periplasmic space of this organism. Here, we report that inhibiting expression of essential genes involved in outer membrane biogenesis can also trigger T6SS activation in P. aeruginosa. Specifically, we developed a CRISPR interference (CRISPRi) system to knock down expression of bamA, tolB, and lptD and found that these knockdowns activated T6SS activity. This increase in T6SS activity was dependent on the same signal transduction pathway that was previously shown to be required for the tit-for-tat response. We conclude that outer membrane perturbation can be sensed by P. aeruginosa to activate the T6SS even when the disruption is generated by aberrant cell envelope biogenesis.
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Structure-Function Characterization of the Conserved Regulatory Mechanism of the Escherichia coli M48 Metalloprotease BepA. J Bacteriol 2020; 203:JB.00434-20. [PMID: 33106348 PMCID: PMC7950410 DOI: 10.1128/jb.00434-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/18/2020] [Indexed: 12/17/2022] Open
Abstract
M48 metalloproteases are widely distributed in all domains of life. E. coli possesses four members of this family located in multiple cellular compartments. The functions of these proteases are not well understood. Recent investigations revealed that one family member, BepA, has an important role in the maturation of a central component of the lipopolysaccharide (LPS) biogenesis machinery. Here, we present the structure of BepA and the results of a structure-guided mutagenesis strategy, which reveal the key residues required for activity that inform how all M48 metalloproteases function. The asymmetric Gram-negative outer membrane (OM) is the first line of defense for bacteria against environmental insults and attack by antimicrobials. The key component of the OM is lipopolysaccharide, which is transported to the surface by the essential lipopolysaccharide transport (Lpt) system. Correct folding of the Lpt system component LptD is regulated by a periplasmic metalloprotease, BepA. Here, we present the crystal structure of BepA from Escherichia coli, solved to a resolution of 2.18 Å, in which the M48 protease active site is occluded by an active-site plug. Informed by our structure, we demonstrate that free movement of the active-site plug is essential for BepA function, suggesting that the protein is autoregulated by the active-site plug, which is conserved throughout the M48 metalloprotease family. Targeted mutagenesis of conserved residues reveals that the negative pocket and the tetratricopeptide repeat (TPR) cavity are required for function and degradation of the BAM complex component BamA under conditions of stress. Last, we show that loss of BepA causes disruption of OM lipid asymmetry, leading to surface exposed phospholipid. IMPORTANCE M48 metalloproteases are widely distributed in all domains of life. E. coli possesses four members of this family located in multiple cellular compartments. The functions of these proteases are not well understood. Recent investigations revealed that one family member, BepA, has an important role in the maturation of a central component of the lipopolysaccharide (LPS) biogenesis machinery. Here, we present the structure of BepA and the results of a structure-guided mutagenesis strategy, which reveal the key residues required for activity that inform how all M48 metalloproteases function.
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Evolution of Colistin Resistance in the Klebsiella pneumoniae Complex Follows Multiple Evolutionary Trajectories with Variable Effects on Fitness and Virulence Characteristics. Antimicrob Agents Chemother 2020; 65:AAC.01958-20. [PMID: 33139278 DOI: 10.1128/aac.01958-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 10/25/2020] [Indexed: 12/14/2022] Open
Abstract
The increasing prevalence of multidrug-resistant Klebsiella pneumoniae has led to a resurgence in the use of colistin as a last-resort drug. Colistin is a cationic antibiotic that selectively acts on Gram-negative bacteria through electrostatic interactions with anionic phosphate groups of the lipid A moiety of lipopolysaccharides (LPSs). Colistin resistance in K. pneumoniae is mediated through loss of these phosphate groups, their modification by cationic groups, and by the hydroxylation of acyl groups of lipid A. Here, we study the in vitro evolutionary trajectories toward colistin resistance in four clinical K. pneumoniae complex strains and their impact on fitness and virulence characteristics. Through population sequencing during in vitro evolution, we found that colistin resistance develops through a combination of single nucleotide polymorphisms, insertions and deletions, and the integration of insertion sequence elements, affecting genes associated with LPS biosynthesis and modification and capsule structures. Colistin resistance decreased the maximum growth rate of one K. pneumoniae sensu stricto strain, but not those of the other three K. pneumoniae complex strains. Colistin-resistant strains had lipid A modified through hydroxylation, palmitoylation, and l-Ara4N addition. K. pneumoniae sensu stricto strains exhibited cross-resistance to LL-37, in contrast to the Klebsiella variicola subsp. variicola strain. Virulence, as determined in a Caenorhabditis elegans survival assay, was increased in two colistin-resistant strains. Our study suggests that nosocomial K. pneumoniae complex strains can rapidly develop colistin resistance through diverse evolutionary trajectories upon exposure to colistin. This effectively shortens the life span of this last-resort antibiotic for the treatment of infections with multidrug-resistant Klebsiella.
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Structural insights into outer membrane asymmetry maintenance in Gram-negative bacteria by MlaFEDB. Nat Struct Mol Biol 2020; 28:81-91. [PMID: 33199922 DOI: 10.1038/s41594-020-00532-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/14/2020] [Indexed: 02/05/2023]
Abstract
The highly asymmetric outer membrane of Gram-negative bacteria functions in the defense against cytotoxic substances, such as antibiotics. The Mla pathway maintains outer membrane lipid asymmetry by transporting phospholipids between the inner and outer membranes. It comprises six Mla proteins, MlaFEDBCA, including the ABC transporter MlaFEDB, which functions via an unknown mechanism. Here we determine cryo-EM structures of Escherichia coli MlaFEDB in an apo state and bound to phospholipid, ADP or AMP-PNP to a resolution of 3.3-4.1 Å and establish a proteoliposome-based transport system that includes MlaFEDB, MlaC and MlaA-OmpF to monitor the transport direction of phospholipids. In vitro transport assays and in vivo membrane permeability assays combined with mutagenesis identify functional residues that not only recognize and transport phospholipids but also regulate the activity and structural stability of the MlaFEDB complex. Our results provide mechanistic insights into the Mla pathway, which could aid antimicrobial drug development.
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Dynamics of an LPS translocon induced by substrate and an antimicrobial peptide. Nat Chem Biol 2020; 17:187-195. [PMID: 33199913 DOI: 10.1038/s41589-020-00694-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/12/2020] [Indexed: 01/11/2023]
Abstract
Lipopolysaccharide (LPS) transport to the outer membrane (OM) is a crucial step in the biogenesis of microbial surface defenses. Although many features of the translocation mechanism have been elucidated, molecular details of LPS insertion via the LPS transport (Lpt) OM protein LptDE remain elusive. Here, we integrate native MS with hydrogen-deuterium exchange MS and molecular dynamics simulations to investigate the influence of substrate and peptide binding on the conformational dynamics of LptDE. Our data reveal that LPS induces opening of the LptD β-taco domain, coupled with conformational changes on β-strands adjacent to the putative lateral exit gate. Conversely, an antimicrobial peptide, thanatin, stabilizes the β-taco, thereby preventing LPS transport. Our results illustrate that LPS insertion into the OM relies on concerted opening movements of both the β-barrel and β-taco domains of LptD, and suggest a means for developing antimicrobial therapeutics targeting this essential process in Gram-negative ESKAPE pathogens.
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Reversible autoinhibitory regulation of Escherichia coli metallopeptidase BepA for selective β-barrel protein degradation. Proc Natl Acad Sci U S A 2020; 117:27989-27996. [PMID: 33093205 DOI: 10.1073/pnas.2010301117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Escherichia coli periplasmic zinc-metallopeptidase BepA normally functions by promoting maturation of LptD, a β-barrel outer-membrane protein involved in biogenesis of lipopolysaccharides, but degrades it when its membrane assembly is hampered. These processes should be properly regulated to ensure normal biogenesis of LptD. The underlying mechanism of regulation, however, remains to be elucidated. A recently solved BepA structure has revealed unique features: In particular, the active site is buried in the protease domain and conceivably inaccessible for substrate degradation. Additionally, the His-246 residue in the loop region containing helix α9 (α9/H246 loop), which has potential flexibility and covers the active site, coordinates the zinc ion as the fourth ligand to exclude a catalytic water molecule, thereby suggesting that the crystal structure of BepA represents a latent form. To examine the roles of the α9/H246 loop in the regulation of BepA activity, we constructed BepA mutants with a His-246 mutation or a deletion of the α9/H246 loop and analyzed their activities in vivo and in vitro. These mutants exhibited an elevated protease activity and, unlike the wild-type BepA, degraded LptD that is in the normal assembly pathway. In contrast, tethering of the α9/H246 loop repressed the LptD degradation, which suggests that the flexibility of this loop is important to the exhibition of protease activity. Based on these results, we propose that the α9/H246 loop undergoes a reversible structural change that enables His-246-mediated switching (histidine switch) of its protease activity, which is important for regulated degradation of stalled/misassembled LptD.
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59
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Functions of the BamBCDE Lipoproteins Revealed by Bypass Mutations in BamA. J Bacteriol 2020; 202:JB.00401-20. [PMID: 32817097 DOI: 10.1128/jb.00401-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/13/2020] [Indexed: 12/27/2022] Open
Abstract
The heteropentomeric β-barrel assembly machine (BAM complex) is responsible for folding and inserting a diverse array of β-barrel outer membrane proteins (OMPs) into the outer membrane (OM) of Gram-negative bacteria. The BAM complex contains two essential proteins, the β-barrel OMP BamA and a lipoprotein BamD, whereas the auxiliary lipoproteins BamBCE are individually nonessential. Here, we identify and characterize three bamA mutations, the E-to-K change at position 470 (bamAE470K ), the A-to-P change at position 496 (bamAA496P ), and the A-to-S change at position 499 (bamAA499S ), that suppress the otherwise lethal ΔbamD, ΔbamB ΔbamC ΔbamE, and ΔbamC ΔbamD ΔbamE mutations. The viability of cells lacking different combinations of BAM complex lipoproteins provides the opportunity to examine the role of the individual proteins in OMP assembly. Results show that, in wild-type cells, BamBCE share a redundant function; at least one of these lipoproteins must be present to allow BamD to coordinate productively with BamA. Besides BamA regulation, BamD shares an additional essential function that is redundant with a second function of BamB. Remarkably, bamAE470K suppresses both, allowing the construction of a BAM complex composed solely of BamAE470K that is able to assemble OMPs in the absence of BamBCDE. This work demonstrates that the BAM complex lipoproteins do not participate in the catalytic folding of OMP substrates but rather function to increase the efficiency of the assembly process by coordinating and regulating the assembly of diverse OMP substrates.IMPORTANCE The folding and insertion of β-barrel outer membrane proteins (OMPs) are conserved processes in mitochondria, chloroplasts, and Gram-negative bacteria. In Gram-negative bacteria, OMPs are assembled into the outer membrane (OM) by the heteropentomeric β-barrel assembly machine (BAM complex). In this study, we probe the function of the individual BAM proteins and how they coordinate assembly of a diverse family of OMPs. Furthermore, we identify a gain-of-function bamA mutant capable of assembling OMPs independently of all four other BAM proteins. This work advances our understanding of OMP assembly and sheds light on how this process is distinct in Gram-negative bacteria.
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Dezanet C, Kempf J, Mingeot-Leclercq MP, Décout JL. Amphiphilic Aminoglycosides as Medicinal Agents. Int J Mol Sci 2020; 21:ijms21197411. [PMID: 33049963 PMCID: PMC7583001 DOI: 10.3390/ijms21197411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 09/27/2020] [Accepted: 10/02/2020] [Indexed: 12/25/2022] Open
Abstract
The conjugation of hydrophobic group(s) to the polycationic hydrophilic core of the antibiotic drugs aminoglycosides (AGs), targeting ribosomal RNA, has led to the development of amphiphilic aminoglycosides (AAGs). These drugs exhibit numerous biological effects, including good antibacterial effects against susceptible and multidrug-resistant bacteria due to the targeting of bacterial membranes. In the first part of this review, we summarize our work in identifying and developing broad-spectrum antibacterial AAGs that constitute a new class of antibiotic agents acting on bacterial membranes. The target-shift strongly improves antibiotic activity against bacterial strains that are resistant to the parent AG drugs and to antibiotic drugs of other classes, and renders the emergence of resistant Pseudomonas aeruginosa strains highly difficult. Structure–activity and structure–eukaryotic cytotoxicity relationships, specificity and barriers that need to be crossed in their development as antibacterial agents are delineated, with a focus on their targets in membranes, lipopolysaccharides (LPS) and cardiolipin (CL), and the corresponding mode of action against Gram-negative bacteria. At the end of the first part, we summarize the other recent advances in the field of antibacterial AAGs, mainly published since 2016, with an emphasis on the emerging AAGs which are made of an AG core conjugated to an adjuvant or an antibiotic drug of another class (antibiotic hybrids). In the second part, we briefly illustrate other biological and biochemical effects of AAGs, i.e., their antifungal activity, their use as delivery vehicles of nucleic acids, of short peptide (polyamide) nucleic acids (PNAs) and of drugs, as well as their ability to cleave DNA at abasic sites and to inhibit the functioning of connexin hemichannels. Finally, we discuss some aspects of structure–activity relationships in order to explain and improve the target selectivity of AAGs.
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Affiliation(s)
- Clément Dezanet
- Molecular Pharmacochemistry Department, University Grenoble Alpes, CNRS, 470 Rue de la Chimie, F-38000 Grenoble, France; (C.D.); (J.K.)
| | - Julie Kempf
- Molecular Pharmacochemistry Department, University Grenoble Alpes, CNRS, 470 Rue de la Chimie, F-38000 Grenoble, France; (C.D.); (J.K.)
| | - Marie-Paule Mingeot-Leclercq
- Cellular and Molecular Pharmacology Unit, Louvain Drug Research Institute, Catholic University of Louvain, Avenue E. Mounier 73, UCL B1.73.05, 1200 Brussels, Belgium
- Correspondence: (M.-P.M.-L.); (J.-L.D.)
| | - Jean-Luc Décout
- Molecular Pharmacochemistry Department, University Grenoble Alpes, CNRS, 470 Rue de la Chimie, F-38000 Grenoble, France; (C.D.); (J.K.)
- Correspondence: (M.-P.M.-L.); (J.-L.D.)
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61
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Lundstedt E, Kahne D, Ruiz N. Assembly and Maintenance of Lipids at the Bacterial Outer Membrane. Chem Rev 2020; 121:5098-5123. [PMID: 32955879 DOI: 10.1021/acs.chemrev.0c00587] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The outer membrane of Gram-negative bacteria is essential for their survival in harsh environments and provides intrinsic resistance to many antibiotics. This membrane is remarkable; it is a highly asymmetric lipid bilayer. The inner leaflet of the outer membrane contains phospholipids, whereas the fatty acyl chains attached to lipopolysaccharide (LPS) comprise the hydrophobic portion of the outer leaflet. This lipid asymmetry, and in particular the exclusion of phospholipids from the outer leaflet, is key to creating an almost impenetrable barrier to hydrophobic molecules that can otherwise pass through phospholipid bilayers. It has long been known that these lipids are not made in the outer membrane. It is now believed that conserved multisubunit protein machines extract these lipids after their synthesis is completed at the inner membrane and transport them to the outer membrane. A longstanding question is how the cell builds and maintains this asymmetric lipid bilayer in coordination with the assembly of the other components of the cell envelope. This Review describes the trans-envelope lipid transport systems that have been identified to participate in outer-membrane biogenesis: LPS transport via the Lpt machine, and phospholipid transport via the Mla pathway and several recently proposed transporters.
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Affiliation(s)
- Emily Lundstedt
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
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62
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Pandeya A, Ojo I, Alegun O, Wei Y. Periplasmic Targets for the Development of Effective Antimicrobials against Gram-Negative Bacteria. ACS Infect Dis 2020; 6:2337-2354. [PMID: 32786281 PMCID: PMC8187054 DOI: 10.1021/acsinfecdis.0c00384] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibiotic resistance has emerged as a serious threat to global public health in recent years. Lack of novel antimicrobials, especially new classes of compounds, further aggravates the situation. For Gram-negative bacteria, their double layered cell envelope and an array of efflux pumps act as formidable barriers for antimicrobials to penetrate. While cytoplasmic targets are hard to reach, proteins in the periplasm are clearly more accessible, as the drug only needs to breach the outer membrane. In this review, we summarized recent efforts on the validation and testing of periplasmic proteins as potential antimicrobial targets and the development of related inhibitors that either inhibit the growth of a bacterial pathogen or reduce its virulence during interaction with host cells. We conclude that the periplasm contains a promising pool of novel antimicrobial targets that should be scrutinized more closely for the development of effective treatment against multidrug-resistant Gram-negative bacteria.
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Affiliation(s)
- Ankit Pandeya
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Isoiza Ojo
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Olaniyi Alegun
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Yinan Wei
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
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63
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Chi X, Fan Q, Zhang Y, Liang K, Wan L, Zhou Q, Li Y. Structural mechanism of phospholipids translocation by MlaFEDB complex. Cell Res 2020; 30:1127-1135. [PMID: 32884137 PMCID: PMC7784689 DOI: 10.1038/s41422-020-00404-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 08/14/2020] [Indexed: 12/16/2022] Open
Abstract
In Gram-negative bacteria, phospholipids are major components of the inner membrane and the inner leaflet of the outer membrane, playing an essential role in forming the unique dual-membrane barrier to exclude the entry of most antibiotics. Understanding the mechanisms of phospholipid translocation between the inner and outer membrane represents one of the major challenges surrounding bacterial phospholipid homeostasis. The conserved MlaFEDB complex in the inner membrane functions as an ABC transporter to drive the translocation of phospholipids between the inner membrane and the periplasmic protein MlaC. However, the mechanism of phospholipid translocation remains elusive. Here we determined three cryo-EM structures of MlaFEDB from Escherichia coli in its nucleotide-free and ATP-bound conformations, and performed extensive functional studies to verify and extend our findings from structural analyses. Our work reveals unique structural features of the entire MlaFEDB complex, six well-resolved phospholipids in three distinct cavities, and large-scale conformational changes upon ATP binding. Together, these findings define the cycle of structural rearrangement of MlaFEDB in action, and suggest that MlaFEDB uses an extrusion mechanism to extract and release phospholipids through the central translocation cavity.
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Affiliation(s)
- Ximin Chi
- Center for Infectious Disease Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Qiongxuan Fan
- Center for Infectious Disease Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Yuanyuan Zhang
- Center for Infectious Disease Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Ke Liang
- Center for Infectious Disease Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Li Wan
- Center for Infectious Disease Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Qiang Zhou
- Center for Infectious Disease Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China. .,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China.
| | - Yanyan Li
- Center for Infectious Disease Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China. .,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China.
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64
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Collet JF, Cho SH, Iorga BI, Goemans CV. How the assembly and protection of the bacterial cell envelope depend on cysteine residues. J Biol Chem 2020; 295:11984-11994. [PMID: 32487747 PMCID: PMC7443483 DOI: 10.1074/jbc.rev120.011201] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/02/2020] [Indexed: 12/15/2022] Open
Abstract
The cell envelope of Gram-negative bacteria is a multilayered structure essential for bacterial viability; the peptidoglycan cell wall provides shape and osmotic protection to the cell, and the outer membrane serves as a permeability barrier against noxious compounds in the external environment. Assembling the envelope properly and maintaining its integrity are matters of life and death for bacteria. Our understanding of the mechanisms of envelope assembly and maintenance has increased tremendously over the past two decades. Here, we review the major achievements made during this time, giving central stage to the amino acid cysteine, one of the least abundant amino acid residues in proteins, whose unique chemical and physical properties often critically support biological processes. First, we review how cysteines contribute to envelope homeostasis by forming stabilizing disulfides in crucial bacterial assembly factors (LptD, BamA, and FtsN) and stress sensors (RcsF and NlpE). Second, we highlight the emerging role of enzymes that use cysteine residues to catalyze reactions that are necessary for proper envelope assembly, and we also explain how these enzymes are protected from oxidative inactivation. Finally, we suggest future areas of investigation, including a discussion of how cysteine residues could contribute to envelope homeostasis by functioning as redox switches. By highlighting the redox pathways that are active in the envelope of Escherichia coli, we provide a timely overview of the assembly of a cellular compartment that is the hallmark of Gram-negative bacteria.
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Affiliation(s)
| | - Seung-Hyun Cho
- de Duve Institute, UCLouvain, Brussels, Belgium; WELBIO, Brussels, Belgium
| | - Bogdan I Iorga
- de Duve Institute, UCLouvain, Brussels, Belgium; Université Paris-Saclay, CNRS UPR 2301, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
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65
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A β-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkL. Proc Natl Acad Sci U S A 2020; 117:21014-21021. [PMID: 32817429 PMCID: PMC7474606 DOI: 10.1073/pnas.2002598117] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Here we show how AlkL, a minimalistic outer-membrane protein from oil-consuming bacteria, exploits dynamics of extracellular loops to channel substrate across the polysaccharide barrier and into the hydrophobic interior of the outer membrane. This work represents a unique example of a side-by-side atomic-level structure determination by solution NMR in detergents and by solid-state NMR in lipid bilayers, which critically demonstrates the importance of a lipid environment to investigate function. Corroborating our experimental measurements, molecular-dynamics simulations capture substrate transit via lateral openings. The capacity to unravel membrane protein function under near-native conditions, fueled by the latest method developments, opens up a new frontier for their investigation, and provides thereby for improved fundamental insights into biological processes. The protein AlkL is known to increase permeability of the outer membrane of bacteria for hydrophobic molecules, yet the mechanism of transport has not been determined. Differing crystal and NMR structures of homologous proteins resulted in a controversy regarding the degree of structure and the role of long extracellular loops. Here we solve this controversy by determining the de novo NMR structure in near-native lipid bilayers, and by accessing structural dynamics relevant to hydrophobic substrate permeation through molecular-dynamics simulations and by characteristic NMR relaxation parameters. Dynamic lateral exit sites large enough to accommodate substrates such as carvone or octane occur through restructuring of a barrel extension formed by the extracellular loops.
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66
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Xu C, Soyfoo DM, Wu Y, Xu S. Virulence of Helicobacter pylori outer membrane proteins: an updated review. Eur J Clin Microbiol Infect Dis 2020; 39:1821-1830. [PMID: 32557327 PMCID: PMC7299134 DOI: 10.1007/s10096-020-03948-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/09/2020] [Indexed: 02/07/2023]
Abstract
Helicobacter pylori (H. pylori) infection is associated with some gastric diseases, such as gastritis, peptic ulcer, and gastric cancer. CagA and VacA are known virulence factors of H. pylori, which play a vital role in severe clinical outcomes. Additionally, the expression of outer membrane proteins (OMPs) helps H. pylori attach to gastric epithelial cells at the primary stage and increases the virulence of H. pylori. In this review, we have summarized the paralogs of H. pylori OMPs, their genomic loci, and the different receptors of OMPs identified so far. We focused on five OMPs, BabA (HopS), SabA (HopP), OipA (HopH), HopQ, and HopZ, and one family of OMPs: Hom. We highlight the coexpression of OMPs with other virulence factors and their relationship with clinical outcomes. In conclusion, OMPs are closely related to the pathogenic processes of adhesion, colonization, persistent infection, and severe clinical consequences. They are potential targets for the prevention and treatment of H. pylori–related diseases.
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Affiliation(s)
- Chenjing Xu
- Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | | | - Yao Wu
- Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shunfu Xu
- Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China. .,Jiangsu Province Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.
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67
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Whitfield C, Williams DM, Kelly SD. Lipopolysaccharide O-antigens-bacterial glycans made to measure. J Biol Chem 2020; 295:10593-10609. [PMID: 32424042 DOI: 10.1074/jbc.rev120.009402] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/17/2020] [Indexed: 01/05/2023] Open
Abstract
Lipopolysaccharides are critical components of bacterial outer membranes. The more conserved lipid A part of the lipopolysaccharide molecule is a major element in the permeability barrier imposed by the outer membrane and offers a pathogen-associated molecular pattern recognized by innate immune systems. In contrast, the long-chain O-antigen polysaccharide (O-PS) shows remarkable structural diversity and fulfills a range of functions, depending on bacterial lifestyles. O-PS production is vital for the success of clinically important Gram-negative pathogens. The biological properties and functions of O-PSs are mostly independent of specific structures, but the size distribution of O-PS chains is particularly important in many contexts. Despite the vast O-PS chemical diversity, most are produced in bacterial cells by two assembly strategies, and the different mechanisms employed in these pathways to regulate chain-length distribution are emerging. Here, we review our current understanding of the mechanisms involved in regulating O-PS chain-length distribution and discuss their impact on microbial cell biology.
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Affiliation(s)
- Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Danielle M Williams
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Steven D Kelly
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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68
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Moura ECCM, Baeta T, Romanelli A, Laguri C, Martorana AM, Erba E, Simorre JP, Sperandeo P, Polissi A. Thanatin Impairs Lipopolysaccharide Transport Complex Assembly by Targeting LptC-LptA Interaction and Decreasing LptA Stability. Front Microbiol 2020; 11:909. [PMID: 32477309 PMCID: PMC7237710 DOI: 10.3389/fmicb.2020.00909] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/17/2020] [Indexed: 11/13/2022] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is a highly selective permeability barrier due to its asymmetric structure with lipopolysaccharide (LPS) in the outer leaflet. In Escherichia coli, LPS is transported to the cell surface by the LPS transport (Lpt) system composed of seven essential proteins forming a transenvelope bridge. Transport is powered by the ABC transporter LptB2FGC, which extracts LPS from the inner membrane (IM) and transfers it, through LptC protein, to the periplasmic protein LptA. Then, LptA delivers LPS to the OM LptDE translocon for final assembly at the cell surface. The Lpt protein machinery operates as a single device, since depletion of any component leads to the accumulation of a modified LPS decorated with repeating units of colanic acid at the IM outer leaflet. Moreover, correct machine assembly is essential for LPS transit and disruption of the Lpt complex results in LptA degradation. Due to its vital role in cell physiology, the Lpt system represents a good target for antimicrobial drugs. Thanatin is a naturally occurring antimicrobial peptide reported to cause defects in membrane assembly and demonstrated in vitro to bind to the N-terminal β-strand of LptA. Since this region is involved in both LptA dimerization and interaction with LptC, we wanted to elucidate the mechanism of inhibition of thanatin and discriminate whether its antibacterial effect is exerted by the disruption of the interaction of LptA with itself or with LptC. For this purpose, we here implemented the Bacterial Adenylate Cyclase Two-Hybrid (BACTH) system to probe in vivo the Lpt interactome in the periplasm. With this system, we found that thanatin targets both LptC–LptA and LptA–LptA interactions, with a greater inhibitory effect on the former. We confirmed in vitro the disruption of LptC–LptA interaction using two different biophysical techniques. Finally, we observed that in cells treated with thanatin, LptA undergoes degradation and LPS decorated with colanic acid accumulates. These data further support inhibition or disruption of Lpt complex assembly as the main killing mechanism of thanatin against Gram-negative bacteria.
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Affiliation(s)
- Elisabete C C M Moura
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Tiago Baeta
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Alessandra Romanelli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milan, Italy
| | - Cedric Laguri
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Alessandra M Martorana
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Emanuela Erba
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milan, Italy
| | | | - Paola Sperandeo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Alessandra Polissi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
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69
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Kaito C, Yoshikai H, Wakamatsu A, Miyashita A, Matsumoto Y, Fujiyuki T, Kato M, Ogura Y, Hayashi T, Isogai T, Sekimizu K. Non-pathogenic Escherichia coli acquires virulence by mutating a growth-essential LPS transporter. PLoS Pathog 2020; 16:e1008469. [PMID: 32324807 PMCID: PMC7179839 DOI: 10.1371/journal.ppat.1008469] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 03/09/2020] [Indexed: 01/06/2023] Open
Abstract
The molecular mechanisms that allow pathogenic bacteria to infect animals have been intensively studied. On the other hand, the molecular mechanisms by which bacteria acquire virulence functions are not fully understood. In the present study, we experimentally evaluated the evolution of a non-pathogenic strain of Escherichia coli in a silkworm infection model and obtained pathogenic mutant strains. As one cause of the high virulence properties of E. coli mutants, we identified amino acid substitutions in LptD (G580S) and LptE (T95I) constituting the lipopolysaccharide (LPS) transporter, which translocates LPS from the inner to the outer membrane and is essential for E. coli growth. The growth of the LptD and LptE mutants obtained in this study was indistinguishable from that of the parent strain. The LptD and LptE mutants exhibited increased secretion of outer membrane vesicles containing LPS and resistance against various antibiotics, antimicrobial peptides, and host complement. In vivo cross-linking studies revealed that the conformation of the LptD-LptE complex was altered in the LptD and LptE mutants. Furthermore, several clinical isolates of E. coli carried amino acid substitutions of LptD and LptE that conferred resistance against antimicrobial substances. This study demonstrated an experimental evolution of bacterial virulence properties in an animal infection model and identified functional alterations of the growth-essential LPS transporter that led to high bacterial virulence by conferring resistance against antimicrobial substances. These findings suggest that non-pathogenic bacteria can gain virulence traits by changing the functions of essential genes, and provide new insight to bacterial evolution in a host environment. Pathogenic bacteria developed their virulence properties by changing the functions of various genes after the emergence of the host animals on earth. The types of gene function alterations that confer bacterial virulence properties, however, have remained unclear. We utilized a silkworm infection model to perform an experimental evolution of bacterial virulence activity. From a non-pathogenic strain of Escherichia coli, we obtained a mutant strain that exhibited 500-fold higher virulence than the original strain and identified mutations of the lipopolysaccharide (LPS) transporter, which translocates LPS onto the bacterial surface, as one cause of the high virulence. The mutations changed the structure of the LPS transporter, increased the secretion of outer membrane vesicles, and enabled bacterial survival in the presence of host antimicrobial substances. This mechanism to gain high virulence occurs naturally, as several E. coli clinical isolates carried mutations of the LPS transporter that confer resistance against antimicrobial substances. Our study unveiled a novel mechanism by which bacteria increase their virulence through modifying their gene function.
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Affiliation(s)
- Chikara Kaito
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Kita-ku, Okayama, Japan
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- * E-mail:
| | - Hirono Yoshikai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ai Wakamatsu
- Japan Biological Informatics Consortium (JBIC), Koto-ku, Tokyo, Japan
| | - Atsushi Miyashita
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yasuhiko Matsumoto
- Department of Microbiology, Meiji Pharmaceutical University, Kiyose, Tokyo, Japan
| | - Tomoko Fujiyuki
- The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Masaru Kato
- Devision of Bioanalytical Chemistry, School of Pharmacy, Showa University, Shinagawa-ku, Tokyo, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takao Isogai
- Translational Research Center, Fukushima Medical University, Fukushima, Japan
| | - Kazuhisa Sekimizu
- Institute of Medical Mycology, Teikyo University, Hachioji, Tokyo, Japan
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70
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Lundstedt EA, Simpson BW, Ruiz N. LptB-LptF coupling mediates the closure of the substrate-binding cavity in the LptB 2 FGC transporter through a rigid-body mechanism to extract LPS. Mol Microbiol 2020; 114:200-213. [PMID: 32236984 DOI: 10.1111/mmi.14506] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/20/2020] [Indexed: 02/06/2023]
Abstract
Lipopolysaccharides (LPS) are essential envelope components in many Gram-negative bacteria and provide intrinsic resistance to antibiotics. LPS molecules are synthesized in the inner membrane and then transported to the cell surface by the LPS transport (Lpt) machinery. In this system, the ATP-binding cassette (ABC) transporter LptB2 FGC extracts LPS from the inner membrane and places it onto a periplasmic protein bridge through a poorly understood mechanism. Here, we show that residue E86 of LptB is essential for coupling the function of this ATPase to that of its partners LptFG, specifically at the step where ATP binding drives the closure of the LptB dimer and the collapse of the LPS-binding cavity in LptFG that moves LPS to the Lpt periplasmic bridge. We also show that defects caused by changing residue E86 are suppressed by mutations altering either LPS structure or transmembrane helices in LptG. Furthermore, these suppressors also fix defects in the coupling helix of LptF, but not of LptG. Together, these results support a transport mechanism in which the ATP-driven movements of LptB and those of the substrate-binding cavity in LptFG are bi-directionally coordinated through the rigid-body coupling, with LptF's coupling helix being important in coordinating cavity collapse with LptB dimerization.
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Affiliation(s)
- Emily A Lundstedt
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Brent W Simpson
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
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71
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Lessen HJ, Majumdar A, Fleming KG. Backbone Hydrogen Bond Energies in Membrane Proteins Are Insensitive to Large Changes in Local Water Concentration. J Am Chem Soc 2020; 142:6227-6235. [PMID: 32134659 DOI: 10.1021/jacs.0c00290] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A hallmark feature of biological lipid bilayer structure is a depth-dependent polarity gradient largely resulting from the change in water concentration over the angstrom length scale. This gradient is particularly steep as it crosses the membrane interfacial regions where the water concentration drops at least a million-fold along the direction of the bilayer normal. Although local water content is often assumed to be a major determinant of membrane protein stability, the effect of the water-induced polarity gradient upon backbone hydrogen bond strength has not been systematically investigated. We addressed this question by measuring the free energy change for a number of backbone hydrogen bonds in the transmembrane protein OmpW. These values were obtained at 33 backbone amides from hydrogen/deuterium fractionation factors by nuclear magnetic resonance spectroscopy. We surprisingly found that OmpW backbone hydrogen bond energies do not vary over a wide range of water concentrations that are characteristic of the solvation environment in the bilayer interfacial region. We validated the interpretation of our results by determining the hydrodynamic and solvation properties of our OmpW-micelle complex using analytical ultracentrifugation and molecular dynamics simulations. The magnitudes of the backbone hydrogen bond free energy changes in our study are comparable to those observed in water-soluble proteins, the H-segment of the leader peptidase helix used in the von Heijne and White biological scale experiments, and several interfacial peptides. Our results agree with those reported for the transmembrane α-helical portion of the amyloid precursor protein after the latter values were adjusted for kinetic isotope effects. Overall, our work suggests that backbone hydrogen bonds provide modest thermodynamic stability to membrane protein structures and that many amides are unaffected by dehydration within the bilayer.
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Affiliation(s)
- Henry J Lessen
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ananya Majumdar
- The Johns Hopkins University Biomolecular NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Karen G Fleming
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
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72
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Investigation of the thermodynamic drivers of the interaction between the high mobility group box domain of Sox2 and bacterial lipopolysaccharide. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183106. [DOI: 10.1016/j.bbamem.2019.183106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/05/2019] [Accepted: 10/08/2019] [Indexed: 01/02/2023]
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73
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von Kügelgen A, Tang H, Hardy GG, Kureisaite-Ciziene D, Brun YV, Stansfeld PJ, Robinson CV, Bharat TAM. In Situ Structure of an Intact Lipopolysaccharide-Bound Bacterial Surface Layer. Cell 2020; 180:348-358.e15. [PMID: 31883796 PMCID: PMC6978808 DOI: 10.1016/j.cell.2019.12.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/22/2019] [Accepted: 12/04/2019] [Indexed: 12/15/2022]
Abstract
Most bacterial and all archaeal cells are encapsulated by a paracrystalline, protective, and cell-shape-determining proteinaceous surface layer (S-layer). On Gram-negative bacteria, S-layers are anchored to cells via lipopolysaccharide. Here, we report an electron cryomicroscopy structure of the Caulobacter crescentus S-layer bound to the O-antigen of lipopolysaccharide. Using native mass spectrometry and molecular dynamics simulations, we deduce the length of the O-antigen on cells and show how lipopolysaccharide binding and S-layer assembly is regulated by calcium. Finally, we present a near-atomic resolution in situ structure of the complete S-layer using cellular electron cryotomography, showing S-layer arrangement at the tip of the O-antigen. A complete atomic structure of the S-layer shows the power of cellular tomography for in situ structural biology and sheds light on a very abundant class of self-assembling molecules with important roles in prokaryotic physiology with marked potential for synthetic biology and surface-display applications.
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Affiliation(s)
- Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Haiping Tang
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3TA, United Kingdom
| | - Gail G Hardy
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | - Yves V Brun
- Department of Biology, Indiana University, Bloomington, IN 47405, USA; Département de microbiologie, infectiologie et immunologie, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3TA, United Kingdom
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, United Kingdom.
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74
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New insights into lipopolysaccharide assembly and export. Curr Opin Chem Biol 2019; 53:37-43. [DOI: 10.1016/j.cbpa.2019.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/14/2019] [Accepted: 07/18/2019] [Indexed: 01/22/2023]
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75
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Lee J, Tomasek D, Santos TM, May MD, Meuskens I, Kahne D. Formation of a β-barrel membrane protein is catalyzed by the interior surface of the assembly machine protein BamA. eLife 2019; 8:49787. [PMID: 31724945 PMCID: PMC6887485 DOI: 10.7554/elife.49787] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 11/13/2019] [Indexed: 01/02/2023] Open
Abstract
The β-barrel assembly machine (Bam) complex in Gram-negative bacteria and its counterparts in mitochondria and chloroplasts fold and insert outer membrane β-barrel proteins. BamA, an essential component of the complex, is itself a β-barrel and is proposed to play a central role in assembling other barrel substrates. Here, we map the path of substrate insertion by the Bam complex using site-specific crosslinking to understand the molecular mechanisms that control β-barrel folding and release. We find that the C-terminal strand of the substrate is stably held by BamA and that the N-terminal strands of the substrate are assembled inside the BamA β-barrel. Importantly, we identify contacts between the assembling β-sheet and the BamA interior surface that determine the rate of substrate folding. Our results support a model in which the interior wall of BamA acts as a chaperone to catalyze β-barrel assembly.
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Affiliation(s)
- James Lee
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - David Tomasek
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Thiago Ma Santos
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Mary D May
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Ina Meuskens
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Daniel Kahne
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
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76
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Patro LPP, Rathinavelan T. Targeting the Sugary Armor of Klebsiella Species. Front Cell Infect Microbiol 2019; 9:367. [PMID: 31781512 PMCID: PMC6856556 DOI: 10.3389/fcimb.2019.00367] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 10/09/2019] [Indexed: 12/25/2022] Open
Abstract
The emergence of multidrug-resistant strains of Gram-negative Klebsiella species is an urgent global threat. The World Health Organization has listed Klebsiella pneumoniae as one of the global priority pathogens in critical need of next-generation antibiotics. Compared to other Gram-negative pathogens, K. pneumoniae accumulates a greater diversity of antimicrobial-resistant genes at a higher frequency. The evolution of a hypervirulent phenotype of K. pneumoniae is yet another concern. It has a broad ecological distribution affecting humans, agricultural animals, plants, and aquatic animals. Extracellular polysaccharides of Klebsiella, such as lipopolysaccharides, capsular polysaccharides, and exopolysaccharides, play crucial roles in conferring resistance against the host immune response, as well as in colonization, surface adhesion, and for protection against antibiotics and bacteriophages. These extracellular polysaccharides are major virulent determinants and are highly divergent with respect to their antigenic properties. Wzx/Wzy-, ABC-, and synthase-dependent proteinaceous nano-machineries are involved in the biosynthesis, transport, and cell surface expression of these sugar molecules. Although the proteins involved in the biosynthesis and surface expression of these sugar molecules represent potential drug targets, variation in the amino acid sequences of some of these proteins, in combination with diversity in their sugar composition, poses a major challenge to the design of a universal drug for Klebsiella infections. This review discusses the challenges in universal Klebsiella vaccine and drug development from the perspective of antigen sugar compositions and the proteins involved in extracellular antigen transport.
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77
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Correa W, Brandenburg J, Behrends J, Heinbockel L, Reiling N, Paulowski L, Schwudke D, Stephan K, Martinez-de-Tejada G, Brandenburg K, Gutsmann T. Inactivation of Bacteria by γ-Irradiation to Investigate the Interaction with Antimicrobial Peptides. Biophys J 2019; 117:1805-1819. [PMID: 31676134 DOI: 10.1016/j.bpj.2019.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 11/27/2022] Open
Abstract
The activity of antimicrobial peptides (AMPs) has been investigated extensively using model membranes composed of phospholipids or lipopolysaccharides in aqueous environments. However, from a biophysical perspective, there is a large scientific interest regarding the direct interaction of membrane-active peptides with whole bacteria. Working with living bacteria limits the usability of experimental setups and the interpretation of the resulting data because of safety risks and the overlap of active and passive effects induced by AMPs. We killed or inactivated metabolic-active bacteria using γ-irradiation or sodium azide, respectively. Microscopy, flow cytometry, and SYTOX green assays showed that the cell envelope remained intact to a high degree at the minimal bactericidal dose. Furthermore, the tumor-necrosis-factor-α-inducing activity of the lipopolysaccharides and the chemical lipid composition was unchanged. Determining the binding capacity of AMPs to the bacterial cell envelope by calorimetry is difficult because of an overlapping of the binding heat and metabolic activities of the bacteria-induced by the AMPs. The inactivation of all active processes helps to decipher the complex thermodynamic information. From the isothermal titration calorimetry (ITC) results, we propose that the bacterial membrane potential (Δψ) is possibly an underestimated modulator of the AMP activity. The negative surface charge of the outer leaflet of the outer membrane of Gram-negative bacteria is already neutralized by peptide concentrations below the minimal inhibitory concentration. This proves that peptide aggregation on the bacterial membrane surface plays a decisive role in the degree of antimicrobial activity. This will not only enable many biophysical approaches for the investigation between bacteria and membrane-active peptides in the future but will also make it possible to compare biophysical parameters of active and inactive bacteria. This opens up new possibilities to better understand the active and passive interaction processes between AMPs and bacteria.
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Affiliation(s)
- Wilmar Correa
- Division of Biophysics, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany.
| | - Julius Brandenburg
- Microbial Interface Biology, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Jochen Behrends
- Fluorescence Cytometry Department, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | | | - Norbert Reiling
- Microbial Interface Biology, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Laura Paulowski
- Division of Biophysics, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Dominik Schwudke
- Bioanalytical Chemistry, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Kerstin Stephan
- Division of Biophysics, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | | | - Klaus Brandenburg
- Brandenburg Antiinfektiva GmbH, c/o Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Thomas Gutsmann
- Division of Biophysics, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
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Xue S, Shao Q, Zhu LB, Jiang YF, Wang C, Xue B, Lu HM, Sang WL, Ma JZ. LDC000067 suppresses RANKL-induced osteoclastogenesis in vitro and prevents LPS-induced osteolysis in vivo. Int Immunopharmacol 2019; 75:105826. [DOI: 10.1016/j.intimp.2019.105826] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/11/2019] [Accepted: 08/12/2019] [Indexed: 12/22/2022]
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80
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Lehman KM, Grabowicz M. Countering Gram-Negative Antibiotic Resistance: Recent Progress in Disrupting the Outer Membrane with Novel Therapeutics. Antibiotics (Basel) 2019; 8:antibiotics8040163. [PMID: 31554212 PMCID: PMC6963605 DOI: 10.3390/antibiotics8040163] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 10/27/2022] Open
Abstract
Gram-negative bacteria shield themselves from antibiotics by producing an outer membrane (OM) that forms a formidable permeability barrier. Multidrug resistance among these organisms is a particularly acute problem that is exacerbated by the OM. The poor penetrance of many available antibiotics prevents their clinical use, and efforts to discover novel classes of antibiotics against Gram-negative bacteria have been unsuccessful for almost 50 years. Recent insights into how the OM is built offer new hope. Several essential multiprotein molecular machines (Bam, Lpt, and Lol) work in concert to assemble the barrier and offer a swathe of new targets for novel therapeutic development. Murepavadin has been at the vanguard of these efforts, but its recently reported phase III clinical trial toxicity has tempered the anticipation of imminent new clinical options. Nonetheless, the many concerted efforts aimed at breaking down the OM barrier provide a source of ongoing optimism for what may soon come through the development pipeline. We will review the current state of drug development against the OM assembly targets, highlighting insightful new discovery approaches and strategies.
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Affiliation(s)
- Kelly M Lehman
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, GA 30322, USA.
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA 30322, USA.
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Marcin Grabowicz
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, GA 30322, USA.
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA 30322, USA.
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA.
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA.
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81
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Cabral L, Noronha MF, de Sousa STP, Lacerda-Júnior GV, Richter L, Fostier AH, Andreote FD, Hess M, Oliveira VMD. The metagenomic landscape of xenobiotics biodegradation in mangrove sediments. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 179:232-240. [PMID: 31051396 DOI: 10.1016/j.ecoenv.2019.04.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/08/2019] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
Metagenomics is a powerful approach to study microorganisms present in any given environment and their potential to maintain and improve ecosystem health without the need of cultivating these microorganisms in the laboratory. In this study, we combined a cultivation-independent metagenomics approach with functional assays to identify the detoxification potential of microbial genes evaluating their potential to contribute to xenobiotics resistance in oil-impacted mangrove sediments. A metagenomic fosmid library containing 12,960 clones from highly contaminated mangrove sediment was used in this study. For assessment of metal resistance, clones were grown in culture medium with increasing concentrations of mercury. The analyses metagenomic library sequences revealed the presence of genes related to heavy metals and antibiotics resistance in the oil-impacted mangrove microbiome. The taxonomic profiling of these sequences suggests that at the genus level, Geobacter was the most abundant genus in our dataset. A functional screening assessment of the metagenomic library successfully detected 24 potential heavy metal tolerant clones, six of which were capable of growing with increased concentrations of mercury. The genetic characterization of selected clones allowed the detection of genes related to detoxification processes, such as chromate transport protein ChrA, haloacid dehalogenase-like hydrolase, lipopolysaccharide transport system, and 3-oxoacyl-[acyl-carrier-protein] reductase. Clones were capable of growing in medium containing increased concentrations of metals and antibiotics, but none manifested strong mercury removal from culture medium characteristic of mercuric reductase activity. These results suggest that resistance to xenobiotic stress varies greatly and that additional studies to elucidate the potential of metal biotransformation need to be carried out with the goal of improving bioremediation application.
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Affiliation(s)
- Lucélia Cabral
- Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Institute of Biology (IB)- University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Melline Fontes Noronha
- Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Institute of Biology (IB)- University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Sanderson Tarciso Pereira de Sousa
- Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Institute of Biology (IB)- University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Gileno Vieira Lacerda-Júnior
- Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Institute of Biology (IB)- University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Larissa Richter
- Institute of Chemistry - University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Anne Hélène Fostier
- Institute of Chemistry - University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Fernando Dini Andreote
- Department of Soil Science, ''Luiz de Queiroz'' College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Matthias Hess
- University of California, Davis, Department of Animal Science, Davis, CA, USA
| | - Valéria Maia de Oliveira
- Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
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Cryo-EM structures of lipopolysaccharide transporter LptB 2FGC in lipopolysaccharide or AMP-PNP-bound states reveal its transport mechanism. Nat Commun 2019; 10:4175. [PMID: 31519889 PMCID: PMC6744409 DOI: 10.1038/s41467-019-11977-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 08/09/2019] [Indexed: 02/05/2023] Open
Abstract
Lipopolysaccharides (LPS) of Gram-negative bacteria are critical for the defence against cytotoxic substances and must be transported from the inner membrane (IM) to the outer membrane (OM) through a bridge formed by seven membrane proteins (LptBFGCADE). The IM component LptB2FG powers the process through a yet unclarified mechanism. Here we report three high-resolution cryo-EM structures of LptB2FG alone and complexed with LptC (LptB2FGC), trapped in either the LPS- or AMP-PNP-bound state. The structures reveal conformational changes between these states and substrate binding with or without LptC. We identify two functional transmembrane arginine-containing loops interacting with the bound AMP-PNP and elucidate allosteric communications between the domains. AMP-PNP binding induces an inward rotation and shift of the transmembrane helices of LptFG and LptC to tighten the cavity, with the closure of two lateral gates, to eventually expel LPS into the bridge. Functional assays reveal the functionality of the LptF and LptG periplasmic domains. Our findings shed light on the LPS transport mechanism. Seven lipopolysaccharide (LPS) transport proteins (LptBFGCADE) mediate the transport of LPS from the inner to the outer membrane of Gram-negative bacteria. Here the authors provide mechanistic insights into LPS recognition and transportation by determining the cryo-EM structures of the inner membrane complex LptB2FGC bound to either LPS or AMP-PNP.
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83
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Wang R, Wang W, Li A, Wang Y, Jin J, Huang Z, Huang G. Lipopolysaccharide enhances DNA-induced IFN-β expression and autophagy by upregulating cGAS expression in A549 cells. Exp Ther Med 2019; 18:4157-4164. [PMID: 31602251 DOI: 10.3892/etm.2019.8001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 07/05/2019] [Indexed: 12/12/2022] Open
Abstract
Cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS) is a newly identified cytosolic DNA sensor, but its function in lung epithelial cells is relatively unknown. In the present study, the effects of lipopolysaccharide (LPS) on the expression and function of cGAS in the A549 lung epithelial cell line was investigated. The cells were treated with LPS at different concentrations (e.g., 100, 200, 400 and 800 ng/ml), and the cGAS expression levels were examined via western blot analysis and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The cells were pretreated with LPS, followed by E. coli DNA transfection using Lipofectamine® 3000. After 24 h, interferon (IFN)-β production was measured using ELISA and the expression of the autophagic markers, microtubule-associated proteins 1A/1B light chain 3 and sequestosome-1, were determined using western blot analysis. The cells were also pretreated with either a toll-like receptor (TLR) 4 inhibitor, a serine/threonine-protein kinase TBK1 (TBK1) inhibitor or an nuclear factor (NF)-κB inhibitor, followed by LPS treatment, and the cGAS expression levels were examined via western blot analysis and RT-qPCR. The result showed that LPS treatment upregulated cGAS expression in a dose-dependent manner. E. coli DNA treatment could induce IFN-β production and autophagy via cGAS, which was enhanced by LPS pretreatment. The effect of LPS on cGAS expression was suppressed by treatment with a TLR4 inhibitor, a TBK1 inhibitor and an NF-κB inhibitor. In conclusion, LPS enhances DNA-induced IFN-β production and autophagy by upregulating cGAS expression through the myeloid differentiation primary response protein MyD88-independent TLR4 signaling pathway in A549 cells.
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Affiliation(s)
- Rong Wang
- Laboratory of Respiratory Disease, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, P.R. China
| | - Wei Wang
- Laboratory of Respiratory Disease, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, P.R. China
| | - Aili Li
- Laboratory of Respiratory Disease, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, P.R. China
| | - Yongqin Wang
- China-USA Lipids in Health and Disease Research Center, Guilin Medical University, Guilin, Guangxi 541001, P.R. China.,Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, Guilin Medical University, Guilin, Guangxi 541001, P.R. China.,Laboratory of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, P.R. China
| | - Junfei Jin
- China-USA Lipids in Health and Disease Research Center, Guilin Medical University, Guilin, Guangxi 541001, P.R. China.,Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, Guilin Medical University, Guilin, Guangxi 541001, P.R. China.,Laboratory of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, P.R. China
| | - Zhaoquan Huang
- Department of Pathology, Guilin Medical University, Guilin, Guangxi 541001, P.R. China
| | - Guojin Huang
- Laboratory of Respiratory Disease, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, P.R. China.,China-USA Lipids in Health and Disease Research Center, Guilin Medical University, Guilin, Guangxi 541001, P.R. China.,Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, Guilin Medical University, Guilin, Guangxi 541001, P.R. China
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84
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Abstract
The outer membrane (OM) of Gram-negative bacteria exhibits unique lipid asymmetry, with lipopolysaccharides (LPS) residing in the outer leaflet and phospholipids (PLs) in the inner leaflet. This asymmetric bilayer protects the bacterium against intrusion of many toxic substances, including antibiotics and detergents, yet allows acquisition of nutrients necessary for growth. To build the OM and ensure its proper function, the cell produces OM constituents in the cytoplasm or inner membrane and transports these components across the aqueous periplasmic space separating the two membranes. Of note, the processes by which the most basic membrane building blocks, i.e. PLs, are shuttled across the cell envelope remain elusive. This review highlights our current understanding (or lack thereof) of bacterial PL trafficking, with a focus on recent developments in the field. We adopt a mechanistic approach and draw parallels and comparisons with well-characterized systems, particularly OM lipoprotein and LPS transport, to illustrate key challenges in intermembrane lipid trafficking. Pathways that transport PLs across the bacterial cell envelope are fundamental to OM biogenesis and homeostasis and are potential molecular targets that could be exploited for antibiotic development.
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Affiliation(s)
- Rahul Shrivastava
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Shu-Sin Chng
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
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85
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Law ECY, Leung DTM, Tam FCH, Cheung KKT, Cheng NHY, Lim PL. IgM Antibodies Can Access Cryptic Antigens Denied to IgG: Hypothesis on Novel Binding Mechanism. Front Immunol 2019; 10:1820. [PMID: 31428101 PMCID: PMC6688401 DOI: 10.3389/fimmu.2019.01820] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/18/2019] [Indexed: 11/13/2022] Open
Abstract
Antibodies are well-known protein mediators of immunity. IgM is the primordial member and the neglected sibling of the later-evolved and more proficient IgG in regard to their therapeutic and diagnostic use. Serendipitously, however, we found a paradox: While murine IgM antibodies specific for guanosine triphosphate (GTP) were able to recognize native guanylyl antigens found in primate or rat muscle tissues by immunofluorescence assays (which mimicked the auto-antibodies from autoimmune patients to skeletal or smooth muscle), the murine and human IgG counterparts failed. The results were replicated in cell-free direct binding assays using small latex microspheres decorated densely with GTP. The IgG antibodies could bind, however, if GTP was presented more spaciously on larger particles or as a univalent hapten. Accordingly, oligomerization of GTP (30-mer) destroyed the binding of the IgG antibodies but enhanced that of the IgMs in inhibition ELISA. We reason that, contrary to current belief, IgM does not bind in a lock-and-key manner like IgG. We hypothesize that whereas the intact and rigid antigen-binding site of IgG hinders the antibody from docking with antigens that are obstructed, in IgM, the two component polypeptides of the antigen-binding site can dissociate from each other and navigate individually through obstacles like the ancestral single-polypeptide antibodies found in sharks and camelids, both components eventually re-grouping around the antigen. We further speculate that polyreactive IgMs, which enigmatically bind to more than one type of antigen, use the same modus operandi. These findings call for a re-look at the clinical potential of IgM antibodies particularly in specific areas of cancer therapy, tissue pathology and vaccine design, where IgG antibodies have failed due to target inaccessibility.
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Affiliation(s)
- Eric Chun Yiu Law
- Clinical Immunology Unit, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Frankie Chi Hang Tam
- Clinical Immunology Unit, The Chinese University of Hong Kong, Hong Kong, China.,IgGENE, FoTan, Hong Kong, China
| | | | - Naomi Hua Yin Cheng
- Clinical Immunology Unit, The Chinese University of Hong Kong, Hong Kong, China
| | - Pak Leong Lim
- Clinical Immunology Unit, The Chinese University of Hong Kong, Hong Kong, China.,IgGENE, FoTan, Hong Kong, China
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86
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The Lpt ABC transporter for lipopolysaccharide export to the cell surface. Res Microbiol 2019; 170:366-373. [PMID: 31376484 DOI: 10.1016/j.resmic.2019.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/11/2019] [Accepted: 07/13/2019] [Indexed: 10/26/2022]
Abstract
The surface of the outer membrane of Gram-negative bacteria is covered by a tightly packed layer of lipopolysaccharide molecules which provide a barrier against many toxic compounds and antibiotics. Lipopolysaccharide, synthesized in the cytoplasm, is assembled in the periplasmic leaflet of the inner membrane where the intermembrane Lpt system mediates its transport to the cell surface. The first step of lipopolysaccharide transport is its extraction from the outer leaflet of inner membrane powered by the atypical LptB2FGC ABC transporter. Here we review latest advances leading to understanding at molecular level how lipopolysaccharide is transported irreversibly to the outer membrane.
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87
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Lundquist KP, Gumbart JC. Presence of substrate aids lateral gate separation in LptD. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183025. [PMID: 31351059 DOI: 10.1016/j.bbamem.2019.07.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/25/2019] [Accepted: 07/14/2019] [Indexed: 10/26/2022]
Abstract
Lipopolysaccharides (LPS) provide the outer membrane (OM) of Gram-negative bacteria with a strong protective barrier. The periplasm-spanning Lpt machinery is responsible for the transport of LPS molecules across the periplasm, culminating in insertion by the outer-membrane proteins LptD and LptE. In order to elucidate the mechanisms of LPS insertion by LptDE, we performed over 14 microseconds of equilibrium molecular dynamics simulations. Bilayer-dependent differences in the fluctuations and secondary structure of LptD's extracellular loops are observed for a pure DMPE membrane vs. a model of the OM. Furthermore, LptD's periplasmic N-terminal domain is highly dynamic, which may help to maintain the integrity of the periplasm-spanning complex amidst relative motion of the inner-membrane and outer-membrane anchored domains. In addition, our simulations demonstrate that binding of LPS substrate activates a switching between the associated and dissociated states of two lumenal loops at the interface between the β-barrel and the N-terminal domain as well as LptD's lateral gate on the microsecond timescale, neither of which is observed for the apo state. Placement of a substrate LPS molecule also causes an increase in the average separation of the LptD lateral gate strands and a lowering of the energetic barrier to lateral gate opening.
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Affiliation(s)
- Karl P Lundquist
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30313, United States of America
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30313, United States of America.
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88
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Reta N, Michelmore A, Saint CP, Prieto-Simon B, Voelcker NH. Label-Free Bacterial Toxin Detection in Water Supplies Using Porous Silicon Nanochannel Sensors. ACS Sens 2019; 4:1515-1523. [PMID: 31140789 DOI: 10.1021/acssensors.8b01670] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lipopolysaccharides (LPS) are the major component of the outer membrane of all Gram-negative bacteria and some cyanobacteria and are released during growth and cell death. LPS pose a potential health risk in water, causing acute respiratory illnesses, inhalation fever, and gastrointestinal disorders. The need for rapid and accurate detection of LPS has become a major priority to facilitate more timely and efficacious intervention and, hence, avoid unsafe water distribution. In this context, a porous silicon membrane (pSiM)-based electrochemical biosensor was developed for direct and sensitive detection of LPS. pSiM, featuring arrays of nanochannels, was modified with polymyxin B (PmB), an antimicrobial peptide with strong affinity to LPS. Detection of LPS was based on measuring the changes in the diffusion through the nanochannels of an electroactive species added in solution, caused by the nanochannel blockage upon LPS binding to PmB. Results showed a limit of detection of 1.8 ng/mL, and a linear response up to 10,000 ng/mL spiked in buffer. Selectivity of the sensor toward potential interfering species in water supplies was also assessed. Sensor performance was then evaluated in water samples from a water treatment plant (WTP), and detection of LPS well below the levels encountered in episodes of water contamination and in humidifiers was demonstrated. The same platform was also tested for bacterial detection including Pseudomonas aeruginosa and Escherichia coli spiked in water samples from a WTP. Considering its performance characteristics, this platform represents a promising screening tool to identify the presence of LPS in water supplies and provide early warning of contamination events.
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Affiliation(s)
- Nekane Reta
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Andrew Michelmore
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
- School of Engineering, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Christopher P. Saint
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
- Natural & Built Environments Research Centre, School of Natural & Built Environments, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Beatriz Prieto-Simon
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Nicolas H. Voelcker
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, Victoria 3168, Australia
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89
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Storek KM, Chan J, Vij R, Chiang N, Lin Z, Bevers J, Koth CM, Vernes JM, Meng YG, Yin J, Wallweber H, Dalmas O, Shriver S, Tam C, Schneider K, Seshasayee D, Nakamura G, Smith PA, Payandeh J, Koerber JT, Comps-Agrar L, Rutherford ST. Massive antibody discovery used to probe structure-function relationships of the essential outer membrane protein LptD. eLife 2019; 8:46258. [PMID: 31237236 PMCID: PMC6592684 DOI: 10.7554/elife.46258] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/17/2019] [Indexed: 12/17/2022] Open
Abstract
Outer membrane proteins (OMPs) in Gram-negative bacteria dictate permeability of metabolites, antibiotics, and toxins. Elucidating the structure-function relationships governing OMPs within native membrane environments remains challenging. We constructed a diverse library of >3000 monoclonal antibodies to assess the roles of extracellular loops (ECLs) in LptD, an essential OMP that inserts lipopolysaccharide into the outer membrane of Escherichia coli. Epitope binning and mapping experiments with LptD-loop-deletion mutants demonstrated that 7 of the 13 ECLs are targeted by antibodies. Only ECLs inaccessible to antibodies were required for the structure or function of LptD. Our results suggest that antibody-accessible loops evolved to protect key extracellular regions of LptD, but are themselves dispensable. Supporting this hypothesis, no α-LptD antibody interfered with essential functions of LptD. Our experimental workflow enables structure-function studies of OMPs in native cellular environments, provides unexpected insight into LptD, and presents a method to assess the therapeutic potential of antibody targeting. The overuse and misuse of antibiotics has led to the rise of multi-drug resistant bacteria which threaten global public health. Antibiotics interfere with essential processes in bacteria so they are unable to divide or survive, but over time, the microbes have found ways to become immune to the drugs. New antibiotics are now desperately needed. Gram-negative bacteria are wrapped in an outer membrane made of large molecules called lipopolysaccharides. This structure is an extra barrier to molecules (such as drugs) that try to enter the cell, but it could also hold new targets for antibiotics to exploit. A protein called LptD is embedded in the outer membrane, where it inserts new lipopolysaccharides. It is critical for bacteria to grow and survive, and is a relatively new potential target for antibiotic development. The protein has a number of ‘extracellular loops’ that extend into the environment, but their roles in the structure and the activity of LptD are still largely unknown. This is partly due to a lack of tools to investigate these elements. In response, Storek et al. built a library of over 3,000 custom antibodies, which are small Y-shaped proteins that can each recognise a specific portion in one of the extracellular loops and potentially incapacitate LptD. The antibodies were used to target LptD in its native environment, when it is embedded in the bacteria. In parallel, mutant bacteria were created in which the loops were genetically removed one by one to assess their importance for LptD activity. The experiments revealed that although the antibodies could target most extracellular loops, they could not target the few loops that were essential for LptD to work properly. This suggests that antibody-accessible loops are expendable and that these structures could serve to shield other regions of LptD which are critical for survival. The findings will help to prioritise research that develops other approaches to inhibit LptD. Finally, the antibody workflow designed by Storek et al. can serve as a road map to study other membrane proteins in their native cellular environment.
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Affiliation(s)
- Kelly M Storek
- Department of Infectious Diseases, Genentech, Inc, South San Francisco, United States
| | - Joyce Chan
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
| | - Rajesh Vij
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Nancy Chiang
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Zhonghua Lin
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Jack Bevers
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Christopher M Koth
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - Jean-Michel Vernes
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
| | - Y Gloria Meng
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
| | - JianPing Yin
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - Heidi Wallweber
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - Olivier Dalmas
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - Stephanie Shriver
- Department of Biomolecular Resources, Genentech, Inc, South San Francisco, United States
| | - Christine Tam
- Department of Biomolecular Resources, Genentech, Inc, South San Francisco, United States
| | - Kellen Schneider
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Dhaya Seshasayee
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Gerald Nakamura
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Peter A Smith
- Department of Infectious Diseases, Genentech, Inc, South San Francisco, United States
| | - Jian Payandeh
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - James T Koerber
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Laetitia Comps-Agrar
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech, Inc, South San Francisco, United States
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90
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Tata M, Konovalova A. Improper Coordination of BamA and BamD Results in Bam Complex Jamming by a Lipoprotein Substrate. mBio 2019; 10:e00660-19. [PMID: 31113900 PMCID: PMC6529637 DOI: 10.1128/mbio.00660-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/16/2019] [Indexed: 12/13/2022] Open
Abstract
The β-barrel assembly machinery, the Bam complex, is central to the biogenesis of integral outer membrane proteins (OMPs) as well as OMP-dependent surface-exposed lipoproteins, such as regulator of capsule synthesis protein F (RcsF). Previous genetic analysis established the model that nonessential components BamE and BamB have overlapping, redundant functions to enhance the kinetics of the highly conserved BamA/BamD core. Here we report that BamE plays a specialized nonredundant role in the Bam complex required for surface exposure of RcsF. We show that the lack of bamE, but not bamB, completely abolishes assembly of RcsF/OMP complexes and establish that the inability to assemble RcsF/OMP complexes is a molecular reason underlying all synthetic lethal interactions of ΔbamE Our genetic analysis and biochemical cross-linking suggest that RcsF accumulates on BamA when BamA cannot engage with BamD because of its limited availability or the incompatible conformation. The role of BamE is to promote proper coordination of RcsF-bound BamA with BamD to complete OMP assembly around RcsF. We show that in the absence of BamE, RcsF is stalled on BamA, thus blocking its function, and we identify the lipoprotein RcsF as a bona fide jamming substrate of the Bam complex.IMPORTANCE The β-barrel assembly machinery, the Bam complex, consists of five components, BamA to -E, among which BamA and BamD are highly conserved and essential. The nonessential components are believed to play redundant roles simply by improving the rate of β-barrel folding. Here we show that BamE contributes a specific and nonoverlapping function to the Bam complex. BamE coordinates BamA and BamD to form a complex between the lipoprotein RcsF and its partner outer membrane β-barrel protein, allowing RcsF to reach the cell surface. In the absence of BamE, RcsF accumulates on BamA, thus blocking the activity of the Bam complex. As the Bam complex is a major antibiotic target in Gram-negative bacteria, the discovery that a lipoprotein can act as a jamming substrate may open the door for development of novel Bam complex inhibitors.
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Affiliation(s)
- Muralidhar Tata
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA
| | - Anna Konovalova
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA
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91
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Couch DG, Cook H, Ortori C, Barrett D, Lund JN, O'Sullivan SE. Palmitoylethanolamide and Cannabidiol Prevent Inflammation-induced Hyperpermeability of the Human Gut In Vitro and In Vivo-A Randomized, Placebo-controlled, Double-blind Controlled Trial. Inflamm Bowel Dis 2019; 25:1006-1018. [PMID: 31054246 DOI: 10.1093/ibd/izz017] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND AIMS We aimed to examine, for the first time, the effect of cannabidiol (CBD) and palmitoylethanolamide (PEA) on the permeability of the human gastrointestinal tract in vitro, ex vivo, and in vivo. METHODS Flux measurements of fluorescein-labeled dextrans 10 (FD10) and fluorescein-labeled dextrans 4 (FD4) dextran across Caco-2 cultures treated for 24 hours with interferon gamma (IFNγ) and tumour necrosis factor alpha (TNFα) (10 ng·mL-1) were measured, with or without the presence of CBD and PEA. Mechanisms were investigated using cannabinoid receptor 1 (CB1), cannabinoid receptor 2 (CB2), transient receptor potential vanilloid 1 (TRPV1), and proliferator activated receptors (PPAR) antagonists and protein kinase A (PKA), nitric oxide synthase, phosphoinositide 3-kinases, extracellular signal-regulated kinases (MEK/ERK), adenylyl cyclase, and protein kinase C (PKC) inhibitors. Human colonic mucosal samples collected from bowel resections were treated as previously stated. The receptors TRPV1, PPARα, PPARδ, PPARγ, CB1, CB2, G-coupled protein receptor 55 (GPR55), G-coupled protein receptor 119 (GPR119), and claudins-1, -2, -3, -4, -5, -7, and -8 mRNA were measured using multiplex. Aquaporin 3 and 4 were measured using enzyme-linked immunosorbent assay (ELISA). A randomized, double-blind, controlled-trial assessed the effect of PEA or CBD on the absorption of lactulose and mannitol in humans taking 600 mg of aspirin. Urinary concentrations of these sugars were measured using liquid chromatography mass spectrometry. RESULTS In vitro, PEA, and CBD decreased the inflammation-induced flux of dextrans (P < 0.0001), sensitive to PPARα and CB1 antagonism, respectively. Both PEA and CBD were prevented by PKA, MEK/ERK, and adenylyl cyclase inhibition (P < 0.001). In human mucosa, inflammation decreased claudin-5 mRNA, which was prevented by CBD (P < 0.05). Palmitoylethanolamide and cannabidiol prevented an inflammation-induced fall in TRPV1 and increase in PPARα transcription (P < 0.0001). In vivo, aspirin caused an increase in the absorption of lactulose and mannitol, which were reduced by PEA or CBD (P < 0.001). CONCLUSION Cannabidiol and palmitoylethanolamide reduce permeability in the human colon. These findings have implications in disorders associated with increased gut permeability, such as inflammatory bowel disease.
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Affiliation(s)
- Daniel G Couch
- Division of Medical Sciences and Graduate Entry Medicine, University of Nottingham, Derby, United Kingdom
| | - Hollie Cook
- Division of Medical Sciences and Graduate Entry Medicine, University of Nottingham, Derby, United Kingdom
| | - Catherine Ortori
- Faculty of Science, University of Nottingham, Nottingham, United Kingdom
| | - Dave Barrett
- Faculty of Science, University of Nottingham, Nottingham, United Kingdom
| | - Jonathan N Lund
- Division of Medical Sciences and Graduate Entry Medicine, University of Nottingham, Derby, United Kingdom
| | - Saoirse E O'Sullivan
- Division of Medical Sciences and Graduate Entry Medicine, University of Nottingham, Derby, United Kingdom
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92
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Lo Sciuto A, Martorana AM, Fernández-Piñar R, Mancone C, Polissi A, Imperi F. Pseudomonas aeruginosa LptE is crucial for LptD assembly, cell envelope integrity, antibiotic resistance and virulence. Virulence 2019; 9:1718-1733. [PMID: 30354941 PMCID: PMC7204523 DOI: 10.1080/21505594.2018.1537730] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Lipopolysaccharide (LPS) is an essential structural component of the outer membrane (OM) of most Gram-negative bacteria. In the model organism Escherichia coli, LPS transport to the OM requires seven essential proteins (LptABCDEFG) that form a continuous bridge across the cell envelope. In Pseudomonas aeruginosa the recently-demonstrated essentiality of LptD and LptH, the P. aeruginosa LptA homologue, confirmed the crucial role of the Lpt system and, thus, of LPS in OM biogenesis in this species. Surprisingly, independent high-throughput transposon mutagenesis studies identified viable P. aeruginosa insertion mutants in the lptE gene, suggesting that it might be dispensable for bacterial growth. To test this hypothesis, we generated an lptE conditional mutant in P. aeruginosa PAO1. LptE depletion only slightly impairs P. aeruginosa growth in vitro. Conversely, LptE is important for cell envelope stability, antibiotic resistance and virulence in an insect model. Interestingly, the maturation and OM localization of LPS is only marginally affected in LptE-depleted cells, while the levels of the OM component LptD are strongly reduced. This suggests that P. aeruginosa LptE might not be directly involved in LPS transport, although it is clearly essential for the maturation and/or stability of LptD. While poor functionality of LptD caused by LptE depletion is somehow tolerated by P. aeruginosa, this has a high cost in terms of cell integrity, drug resistance and virulence, highlighting LptE function(s) as an interesting target to weaken P. aeruginosa defenses and reduce its infectivity.
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Affiliation(s)
- Alessandra Lo Sciuto
- a Department of Biology and Biotechnology Charles Darwin , Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti , Rome , Italy
| | - Alessandra M Martorana
- b Department of Pharmacological and Biomolecular Sciences , University of Milan , Milan , Italy
| | - Regina Fernández-Piñar
- a Department of Biology and Biotechnology Charles Darwin , Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti , Rome , Italy
| | - Carmine Mancone
- c Department of Cellular Biotechnologies and Haematology , Sapienza University of Rome , Rome , Italy
| | - Alessandra Polissi
- b Department of Pharmacological and Biomolecular Sciences , University of Milan , Milan , Italy
| | - Francesco Imperi
- a Department of Biology and Biotechnology Charles Darwin , Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti , Rome , Italy
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93
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Correa W, Heinbockel L, Behrends J, Kaconis Y, Barcena-Varela S, Gutsmann T, Mauss K, Schürholz T, Schromm AB, Martinez de Tejada G, Brandenburg K. Antibacterial action of synthetic antilipopolysaccharide peptides (SALP) involves neutralization of both membrane-bound and free toxins. FEBS J 2019; 286:1576-1593. [PMID: 30843356 DOI: 10.1111/febs.14805] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 01/29/2019] [Accepted: 03/05/2019] [Indexed: 12/18/2022]
Abstract
Increasing failure of conventional antibiotics to combat bacterial infections requires the urgent development of new antibacterial drugs; a promising class of new drugs based on antimicrobial peptides. Here, we studied the molecular interaction of polycationic synthetic antilipopolysaccharide peptides (SALPs) with various gram-negative and gram-positive bacteria, including resistant strains. The analysis of antimicrobial activity by conventional techniques and atomic force microscopy showed a strict dependence on amino acid (aa) sequences, with the type of amino acid, its position within the primary structure, and the sequence length being critical parameters. By monitoring lipopolysaccharide (LPS)- or bacteria-induced cytokine production in human mononuclear cells and whole blood, we found a direct link between the binding of the lead compound Pep19-2.5 to Salmonella enterica and the anti-inflammatory activity of the peptide. Thermodynamic analysis of Pep19-2.5 binding to the bacterial cell envelope showed an exothermic reaction with saturation characteristics, whereas small-angle X-ray scattering data indicated a direct attachment of Pep19-2.5 to the bacterial cell envelope. This binding preferentially takes place to the LPS outer monolayer, as evidenced by the change in the LPS acyl chain and phosphate vibrational bands seen by Fourier-transform infrared spectroscopy. We report here that the anti-inflammatory activity of Pep19-2.5 is not only connected with neutralization of cell-free bacterial toxins but also with a direct binding of the peptide to the outer leaflet of the bacterial outer membrane.
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Affiliation(s)
- Wilmar Correa
- Division of Biophysics, Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel, Germany
| | | | - Jochen Behrends
- Core Facility Fluorescence Cytometrie, Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel, Germany
| | - Yani Kaconis
- Division of Biophysics, Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel, Germany
| | - Sergio Barcena-Varela
- Department of Microbiology and Parasitology, Universidad de Navarra, Pamplona, Spain
| | - Thomas Gutsmann
- Division of Biophysics, Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel, Germany
| | - Karl Mauss
- Plastic, Aesthetic and Reconstructive Surgery Section, Asklepios-Klinik Altona, Hamburg, Germany
| | - Tobias Schürholz
- Department of Anesthesia and Intensive Care, Universitätsmedizin Rostock, Germany
| | - Andra B Schromm
- Division of Immunobiophysics, Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel, Germany
| | | | - Klaus Brandenburg
- Brandenburg Antiinfektiva GmbH, c/o Forschungszentrum Borstel, Borstel, Germany
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94
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Li Y, Orlando BJ, Liao M. Structural basis of lipopolysaccharide extraction by the LptB 2FGC complex. Nature 2019; 567:486-490. [PMID: 30894744 PMCID: PMC6532066 DOI: 10.1038/s41586-019-1025-6] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/18/2019] [Indexed: 12/15/2022]
Abstract
In Gram-negative bacteria, lipopolysaccharide is essential for outer membrane formation and antibiotic resistance. The seven lipopolysaccharide transport (Lpt) proteins A-G move lipopolysaccharide from the inner to the outer membrane. The ATP-binding cassette transporter LptB2FG, which tightly associates with LptC, extracts lipopolysaccharide out of the inner membrane. The mechanism of the LptB2FG-LptC complex (LptB2FGC) and the role of LptC in lipopolysaccharide transport are poorly understood. Here we characterize the structures of LptB2FG and LptB2FGC in nucleotide-free and vanadate-trapped states, using single-particle cryo-electron microscopy. These structures resolve the bound lipopolysaccharide, reveal transporter-lipopolysaccharide interactions with side-chain details and uncover how the capture and extrusion of lipopolysaccharide are coupled to conformational rearrangements of LptB2FGC. LptC inserts its transmembrane helix between the two transmembrane domains of LptB2FG, which represents a previously unknown regulatory mechanism for ATP-binding cassette transporters. Our results suggest a role for LptC in achieving efficient lipopolysaccharide transport, by coordinating the action of LptB2FG in the inner membrane and Lpt protein interactions in the periplasm.
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Affiliation(s)
- Yanyan Li
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | | | - Maofu Liao
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
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95
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Robinson JA. Folded Synthetic Peptides and Other Molecules Targeting Outer Membrane Protein Complexes in Gram-Negative Bacteria. Front Chem 2019; 7:45. [PMID: 30788339 PMCID: PMC6372539 DOI: 10.3389/fchem.2019.00045] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 01/17/2019] [Indexed: 02/06/2023] Open
Abstract
Conformationally constrained peptidomimetics have been developed to mimic interfacial epitopes and target a wide selection of protein-protein interactions. ß-Hairpin mimetics based on constrained macrocyclic peptides have provided access to excellent structural mimics of ß-hairpin epitopes and found applications as interaction inhibitors in many areas of biology and medicinal chemistry. Recently, ß-hairpin peptidomimetics and naturally occurring ß-hairpin-shaped peptides have also been discovered with potent antimicrobial activity and novel mechanisms of action, targeting essential outer membrane protein (OMP) complexes in Gram-negative bacteria. This includes the Lpt complex, required for transporting LPS to the cell surface during OM biogenesis and the BAM complex that folds OMPs and inserts them into the OM bilayer. The Lpt complex is a macromolecular superstructure comprising seven different proteins (LptA-LptG) that spans the entire bacterial cell envelope, whereas the BAM complex is a folding machine comprising a ß-barrel OMP (BamA) and four different lipoproteins (BamB-BamE). Folded synthetic and natural ß-hairpin-shaped peptides appear well-suited for interacting with proteins within the Lpt and BAM complexes that are rich in ß-structure. Recent progress in identifying antibiotics targeting these complexes are reviewed here. Already a clinical candidate has been developed (murepavadin) that targets LptD, with potent antimicrobial activity specifically against pseudmonads. The ability of folded synthetic ß-hairpin epitope mimetics to interact with ß-barrel and ß-jellyroll domains in the Lpt and Bam complexes represent new avenues for antibiotic discovery, which may lead to the development of much needed new antimicrobials to combat the rise of drug-resistant pathogenic Gram-negative bacteria.
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Affiliation(s)
- John A Robinson
- Department of Chemistry, University of Zurich, Zurich, Switzerland
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96
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Klein G, Raina S. Regulated Assembly of LPS, Its Structural Alterations and Cellular Response to LPS Defects. Int J Mol Sci 2019; 20:ijms20020356. [PMID: 30654491 PMCID: PMC6358824 DOI: 10.3390/ijms20020356] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/11/2019] [Accepted: 01/13/2019] [Indexed: 12/21/2022] Open
Abstract
Distinguishing feature of the outer membrane (OM) of Gram-negative bacteria is its asymmetry due to the presence of lipopolysaccharide (LPS) in the outer leaflet of the OM and phospholipids in the inner leaflet. Recent studies have revealed the existence of regulatory controls that ensure a balanced biosynthesis of LPS and phospholipids, both of which are essential for bacterial viability. LPS provides the essential permeability barrier function and act as a major virulence determinant. In Escherichia coli, more than 100 genes are required for LPS synthesis, its assembly at inner leaflet of the inner membrane (IM), extraction from the IM, translocation to the OM, and in its structural alterations in response to various environmental and stress signals. Although LPS are highly heterogeneous, they share common structural elements defining their most conserved hydrophobic lipid A part to which a core polysaccharide is attached, which is further extended in smooth bacteria by O-antigen. Defects or any imbalance in LPS biosynthesis cause major cellular defects, which elicit envelope responsive signal transduction controlled by RpoE sigma factor and two-component systems (TCS). RpoE regulon members and specific TCSs, including their non-coding arm, regulate incorporation of non-stoichiometric modifications of LPS, contributing to LPS heterogeneity and impacting antibiotic resistance.
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Affiliation(s)
- Gracjana Klein
- Unit of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland.
| | - Satish Raina
- Unit of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland.
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97
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Abstract
Gram-negative bacteria have an outer membrane that is positioned at the frontline of the cell's interaction with the environment and that serves as a barrier against noxious molecules including many antibiotics. This protective function mainly relies on lipopolysaccharide, a complex glycolipid located in the outer leaflet of the outer membrane. In this chapter we will first summarize lipopolysaccharide structure, functions and biosynthetic pathway and then we will discuss how it is transported and assembled to the cell surface. This is a remarkably complex process, as amphipathic lipopolysaccharide molecules must traverse three different cellular compartments to reach their final destination.
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98
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Khownium K, Romsaiyud J, Borwornpinyo S, Wongkrasant P, Pongkorpsakol P, Muanprasat C, Boekfa B, Vilaivan T, Ruchirawat S, Limtrakul J. Turn-on fluorescent sensor for the detection of lipopolysaccharides based on a novel bispyrenyl terephtalaldehyde-bis-guanylhydrazone. NEW J CHEM 2019. [DOI: 10.1039/c9nj00323a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A “turn-on” bispyrenyl sensor for lipopolysaccharide detection with unique molecular conformations exhibits excimer emission with sensitivity down to nanomolar.
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Affiliation(s)
- Kriangsak Khownium
- Faculty of Medicine
- King Mongkut's Institute of Technology Ladkrabang
- Bangkok
- Thailand
| | - Jariya Romsaiyud
- Department of Chemistry and Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Ramkhamhaeng University
- Bangkok 10240
- Thailand
| | - Suparerk Borwornpinyo
- Department of Biotechnology
- Faculty of Science
- Mahidol University
- Bangkok 10400
- Thailand
| | | | - Pawin Pongkorpsakol
- Department of Physiology
- Faculty of Science
- Mahidol University
- Bangkok 10400
- Thailand
| | - Chatchai Muanprasat
- Excellent Center for Drug Discovery
- Faculty of Science
- Mahidol University
- Bangkok 10400
- Thailand
| | - Bundet Boekfa
- Chemistry Department
- Faculty of Liberal Arts and Science
- Kasetsart University Kamphaeng Saen Campus
- Nakhon Pathom 73140
- Thailand
| | - Tirayut Vilaivan
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
- Thailand
| | | | - Jumras Limtrakul
- Department of Materials Science and Engineering
- School of Molecular Science and Engineering
- Vidyasirimedhi Institute of Science and Technology
- Rayong 21210
- Thailand
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99
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Baarda BI, Martinez FG, Sikora AE. Proteomics, Bioinformatics and Structure-Function Antigen Mining For Gonorrhea Vaccines. Front Immunol 2018; 9:2793. [PMID: 30564232 PMCID: PMC6288298 DOI: 10.3389/fimmu.2018.02793] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/13/2018] [Indexed: 12/12/2022] Open
Abstract
Expanding efforts to develop preventive gonorrhea vaccines is critical because of the serious health consequences combined with the prevalence and the dire possibility of untreatable gonorrhea. Reverse vaccinology, which includes genome and proteome mining, has proven successful in the discovery of vaccine candidates against many pathogenic bacteria. Here, we describe proteomic applications including comprehensive, quantitative proteomic platforms and immunoproteomics coupled with broad-ranging bioinformatics that have been applied for antigen mining to develop gonorrhea vaccine(s). We further focus on outlining the vaccine candidate decision tree, describe the structure-function of novel proteome-derived antigens as well as ways to gain insights into their roles in the cell envelope, and underscore new lessons learned about the fascinating biology of Neisseria gonorrhoeae.
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Affiliation(s)
- Benjamin I. Baarda
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Fabian G. Martinez
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, United States
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100
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Villain E, Nikekhin AA, Kajava AV. Porins and Amyloids are Coded by Similar Sequence Motifs. Proteomics 2018; 19:e1800075. [DOI: 10.1002/pmic.201800075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/27/2018] [Indexed: 01/25/2023]
Affiliation(s)
- Etienne Villain
- Centre de Recherche en Biologie cellulaire de MontpellierUMR 5237 CNRSUniversité Montpellier 1919 Route de MendeCEDEX 5 34293 Montpellier France
- Institut de Biologie Computationnelle 34095 Montpellier France
| | | | - Andrey V. Kajava
- Centre de Recherche en Biologie cellulaire de MontpellierUMR 5237 CNRSUniversité Montpellier 1919 Route de MendeCEDEX 5 34293 Montpellier France
- Institut de Biologie Computationnelle 34095 Montpellier France
- Institute of BioengineeringITMO University St. Petersburg 197101 Russia
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