The gram‐negative outer membrane modeler: Automated building of lipopolysaccharide‐rich bacterial outer membranes in four force fields

2019 ◽  
Vol 40 (18) ◽  
pp. 1727-1734 ◽  
Author(s):  
Fotis A. Baltoumas ◽  
Stavros J. Hamodrakas ◽  
Vassiliki A. Iconomidou
Keyword(s):  
Outer Membrane ◽  
Force Fields ◽  
Gram Negative ◽  
Outer Membranes

scholarly journals Requirements for the import of neisserial Omp85 into the outer membrane of human mitochondria

2013 ◽  
Vol 33 (2) ◽  
Author(s):  
Christine Ott ◽  
Mandy Utech ◽  
Monika Goetz ◽  
Thomas Rudel ◽  
Vera Kozjak-Pavlovic
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Outer Membrane ◽  
Gram Negative Bacteria ◽  
Mitochondrial Targeting ◽  
Gram Negative ◽  
Outer Membranes ◽  
Sorting Signal ◽  
Targeting Signal ◽  
And Function

β-Barrel proteins are present only in the outer membranes of Gram-negative bacteria, chloroplasts and mitochondria. Fungal mitochondria were shown to readily import and assemble bacterial β-barrel proteins, but human mitochondria exhibit certain selectivity. Whereas enterobacterial β-barrel proteins are not imported, neisserial ones are. Of those, solely neisserial Omp85 is integrated into the outer membrane of mitochondria. In this study, we wanted to identify the signal that targets neisserial β-barrel proteins to mitochondria. We exchanged parts of neisserial Omp85 and PorB with their Escherichia coli homologues BamA and OmpC. For PorB, we could show that its C-terminal quarter can direct OmpC to mitochondria. In the case of Omp85, we could identify several amino acids of the C-terminal β-sorting signal as crucial for mitochondrial targeting. Additionally, we found that at least two POTRA (polypeptide-transport associated) domains and not only the β-sorting signal of Omp85 are needed for its membrane integration and function in human mitochondria. We conclude that the signal that directs neisserial β-barrel proteins to mitochondria is not conserved between these proteins. Furthermore, a linear mitochondrial targeting signal probably does not exist. It is possible that the secondary structure of β-barrel proteins plays a role in directing these proteins to mitochondria.

scholarly journals Structure of LetB reveals a tunnel for lipid transport across the bacterial envelope

2019 ◽  
Author(s):  
Georgia L. Isom ◽  
Nicolas Coudray ◽  
Mark R. MacRae ◽  
Collin T. McManus ◽  
Damian C. Ekiert ◽  
...  
Keyword(s):  
Outer Membrane ◽  
Lipid Transport ◽  
Transport Systems ◽  
Permeability Barrier ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
E Coli ◽  
Outer Membranes ◽  
Hydrophobic Tunnel ◽  
Outer Membrane Permeability

Gram-negative bacteria are surrounded by an outer membrane composed of phospholipids and lipopolysaccharide (LPS), which acts as a barrier to the environment and contributes to antibiotic resistance. While mechanisms of LPS transport have been well characterised, systems that translocate phospholipids across the periplasm, such as MCE (Mammalian Cell Entry) transport systems, are less well understood. Here we show that E. coli MCE protein LetB (formerly YebT), forms a ∼0.6 megadalton complex in the periplasm. Our cryo-EM structure reveals that LetB consists of a stack of seven modular rings, creating a long hydrophobic tunnel through the centre of the complex. LetB is sufficiently large to span the gap between the inner and outer membranes, and mutations that shorten the tunnel abolish function. Lipids bind inside the tunnel, suggesting that it functions as a pathway for lipid transport. Cryo-EM structures in the open and closed states reveal a dynamic tunnel lining, with implications for gating or substrate translocation. Together, our results support a model in which LetB establishes a physical link between the bacterial inner and outer membranes, and creates a hydrophobic pathway for the translocation of lipids across the periplasm, to maintain the integrity of the outer membrane permeability barrier.

scholarly journals Correct Sorting of Lipoproteins into the Inner and Outer Membranes ofPseudomonas aeruginosaby theEscherichia coliLolCDE Transport System

mBio ◽  
2019 ◽  
Vol 10 (2) ◽  
Author(s):  
Christian Lorenz ◽  
Thomas J. Dougherty ◽  
Stephen Lory
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Outer Membrane ◽  
Transport Systems ◽  
Gram Negative Bacteria ◽  
Inner Membrane ◽  
Gram Negative ◽  
Content Type ◽  
E Coli ◽  
Outer Membranes

ABSTRACTBiogenesis of the outer membrane of Gram-negative bacteria depends on dedicated macromolecular transport systems. The LolABCDE proteins make up the machinery for lipoprotein trafficking from the inner membrane (IM) across the periplasm to the outer membrane (OM). The Lol apparatus is additionally responsible for differentiating OM lipoproteins from those for the IM. InEnterobacteriaceae, a default sorting mechanism has been proposed whereby an aspartic acid at position +2 of the mature lipoproteins prevents Lol recognition and leads to their IM retention. In other bacteria, the conservation of sequences immediately following the acylated cysteine is variable. Here we show that inPseudomonas aeruginosa, the three essential Lol proteins (LolCDE) can be replaced with those fromEscherichia coli. TheP. aeruginosalipoproteins MexA, OprM, PscJ, and FlgH, with different sequences at their N termini, were correctly sorted by either theE. coliorP. aeruginosaLolCDE. We further demonstrate that an inhibitor ofE. coliLolCDE is active againstP. aeruginosaonly when expressing theE. coliorthologues. Our work shows that Lol proteins recognize a wide range of signals, consisting of an acylated cysteine and a specific conformation of the adjacent domain, determining IM retention or transport to the OM.IMPORTANCEGram-negative bacteria build their outer membranes (OM) from components that are initially located in the inner membrane (IM). A fraction of lipoproteins is transferred to the OM by the transport machinery consisting of LolABCDE proteins. Our work demonstrates that the LolCDE complexes of the transport pathways ofEscherichia coliandPseudomonas aeruginosaare interchangeable, with theE. coliorthologues correctly sorting theP. aeruginosalipoproteins while retaining their sensitivity to a small-molecule inhibitor. These findings question the nature of IM retention signals, identified inE. colias aspartate at position +2 of mature lipoproteins. We propose an alternative model for the sorting of IM and OM lipoproteins based on their relative affinities for the IM and the ability of the promiscuous sorting machinery to deliver lipoproteins to their functional sites in the OM.

Omp85 in eukaryotic systems: one protein family with distinct functions

2011 ◽  
Vol 392 (1-2) ◽  
Author(s):  
Enrico Schleiff ◽  
Uwe G. Maier ◽  
Thomas Becker
Keyword(s):  
Outer Membrane ◽  
Structural Properties ◽  
Protein Transport ◽  
Protein Family ◽  
Gram Negative Bacteria ◽  
Membrane Systems ◽  
Gram Negative ◽  
Protein Insertion ◽  
Outer Membranes

AbstractOmp85-like proteins are evolutionary ancient components of bacterial outer membranes and their evolutionary offspring. As a consequence, proteins of this family can be found in the outer membrane systems of Gram-negative bacteria and endosymbiotically derived organelles. In the different membranes, they perform distinct functions such as catalyzing protein insertion into or protein transport across the bilayer. Here, the knowledge on the Omp85-like proteins in the eukaryotic system with regard to structural properties and physiological behavior is summarized.

scholarly journals Intermembrane transport: Glycerophospholipid homeostasis of the Gram-negative cell envelope

2019 ◽  
Vol 116 (35) ◽  
pp. 17147-17155 ◽  
Author(s):  
Matthew J. Powers ◽  
M. Stephen Trent
Keyword(s):  
Outer Membrane ◽  
Bacterial Cell ◽  
Cell Envelope ◽  
Lipid Transport ◽  
Lipid Asymmetry ◽  
Gram Negative ◽  
Outer Membranes ◽  
Negative Cell ◽  
Initial Discovery ◽  
Structural Methods

This perspective addresses recent advances in lipid transport across the Gram-negative inner and outer membranes. While we include a summary of previously existing literature regarding this topic, we focus on the maintenance of lipid asymmetry (Mla) pathway. Discovered in 2009 by the Silhavy group [J. C. Malinverni, T. J. Silhavy, Proc. Natl. Acad. Sci. U.S.A. 106, 8009–8014 (2009)], Mla has become increasingly appreciated for its role in bacterial cell envelope physiology. Through the work of many, we have gained an increasingly mechanistic understanding of the function of Mla via genetic, biochemical, and structural methods. Despite this, there is a degree of controversy surrounding the directionality in which Mla transports lipids. While the initial discovery and subsequent studies have posited that it mediated retrograde lipid transport (removing glycerophospholipids from the outer membrane and returning them to the inner membrane), others have asserted the opposite. This Perspective aims to lay out the evidence in an unbiased, yet critical, manner for Mla-mediated transport in addition to postulation of mechanisms for anterograde lipid transport from the inner to outer membranes.

scholarly journals Modeling the Kinetics of the Permeation of Antibacterial Agents into Growing Bacteria and Its Interplay with Efflux

2017 ◽  
Vol 61 (10) ◽  
Author(s):  
Wright W. Nichols
Keyword(s):  
Outer Membrane ◽  
Permeability Coefficient ◽  
Efflux Pump ◽  
Antibacterial Drug ◽  
Gram Negative Bacteria ◽  
Bacterial Cells ◽  
Gram Negative ◽  
Active Efflux ◽  
Outer Membranes ◽  
In Series

ABSTRACT A mathematical model of the passive permeation of a novel solute into bacteria that explicitly accounts for intracellular dilution through growth was developed. A bacterial cell envelope permeability coefficient of approximately >10−8 cm2 · s−1 is predicted to ensure passive permeation into rapidly replicating bacterial cells. The relative importance of the permeability coefficients of the cytoplasmic and outer membranes of Gram-negative bacteria in determining the overall envelope permeability coefficient was analyzed quantitatively. A mathematical description of the balance between passive influx and active efflux was also developed and shows that bacterial expansion through growth can usually be neglected for compounds likely to be prepared in antibacterial drug discovery programs and the balance between passive inward permeation and active outwardly directed efflux predominates. A new parameter, efflux efficiency (η, where η is equal to k/P, in which k is the rate coefficient for the efflux pump and P is the permeability coefficient for the membrane across which the pump acts), is introduced, and the consequences for the efficiency of efflux pumping by a single pump, two pumps in parallel across either the cytoplasmic or the outer membrane, and two pumps in series, one across the cytoplasmic membrane and one across the outer membrane of Gram-negative bacteria, are explored. The results, showing additive efficiency for two pumps acting across a single membrane and multiplicative efficiency for two pumps acting in series across the cytoplasmic and outer membranes, can be quantitatively related to the ratios between MICs measured against pump-sufficient and pump deletion strains and agree with those of previous experimental and theoretical studies.

scholarly journals Structural insight into outer membrane asymmetry maintenance of Gram-negative bacteria by the phospholipid transporter MlaFEDB

2020 ◽  
Author(s):  
Xiaodi Tang ◽  
Shenghai Chang ◽  
Wen Qiao ◽  
Qinghua Luo ◽  
Yuejia Chen ◽  
...  
Keyword(s):  
Outer Membrane ◽  
Bound State ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Membrane Asymmetry ◽  
Outer Membranes ◽  
Transport Direction ◽  
Insight Into

The asymmetric phospholipid outer membrane (OM) of Gram-negative bacteria serves as the first line of defense against cytotoxic substances such as antibiotics. The Mla pathway is known to maintain the lipid asymmetry of the OM by transporting phospholipids between the inner and outer membranes. Six Mla proteins MlaFEDBCA are involved, with the ABC transporter MlaFEDB acts through a mechanism yet to be elucidated. Here we determine cryo-EM structures of MlaFEDB in apo, phospholipid-, ADP- or AMP-PNP-bound state to 3.3-3.75 Å resolution and establish a proteoliposome-based transport system containing MlaFEDB, MlaC and MlaA/OmpF to reveal the transport direction of phospholipids. Mutagenetic in vitro transport assays and in vivo sensitivity assays reveal functional residues which recognize and transport phospholipids as well as regulate the activity and structural stability of the MlaFEDB complex. Our work provides molecular basis for understanding the mechanism of the Mla pathway which could be targeted for antimicrobial drug development.

The isolation and characterisation of cytoplasmic and outer membranes from Micrococcus cryophilus

1984 ◽  
Vol 30 (11) ◽  
pp. 1357-1366 ◽  
Author(s):  
Geoffrey M. Lloyd ◽  
Nicholas J. Russell
Keyword(s):  
Fatty Acid Composition ◽  
Fatty Acid ◽  
Outer Membrane ◽  
Cytoplasmic Membrane ◽  
Phospholipid Composition ◽  
Marker Enzymes ◽  
Negative Bacterium ◽  
Gram Negative ◽  
Outer Membranes ◽  
Phospholipid Classes

The cytoplasmic and outer membranes of the Gram-negative bacterium, Micrococcus cryophilus, have been separated and purified. Both membrane preparations consist of a mixture of closed and apparently open vesicles, which vary in size but those of the outer membrane are on average 1.5 times the diameter of those of the cytoplasmic membrane. The membranes were characterised by their 2-keto-3-deoxyoctonate content and the activity of marker enzymes. There are gross differences in the protein and phospholipid composition of the two membranes. The outer membrane contains three major polypeptides, whereas the cytoplasmic membrane has many more. In addition the outer membrane is enriched in cardiolipin, at the expense of phosphatidylglycerol and phosphatidylethanolamine, relative to the cytoplasmic membrane. There are no significant differences in the fatty acid composition of the phospholipid classes, but all phospholipids of the outer membrane were slightly more saturated than those of the cytoplasmic membrane. Wax esters are present in both cytoplasmic and outer membranes. The significance of these findings is discussed in relation to known differences in the fluidity of the cytoplasmic and outer membranes in M. cryophilus and the specialized roles these membranes play.

scholarly journals Weakening Effect of Cell Permeabilizers on Gram-Negative Bacteria Causing Biodeterioration

2006 ◽  
Vol 72 (7) ◽  
pp. 4695-4703 ◽  
Author(s):  
H.-L. Alakomi ◽  
A. Paananen ◽  
M.-L. Suihko ◽  
I. M. Helander ◽  
M. Saarela
Keyword(s):  
Outer Membrane ◽  
Benzalkonium Chloride ◽  
Phase Contrast ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Force Microscopy ◽  
Outer Membranes ◽  
Atomic Force ◽  
Stone Materials ◽  
Hydrophobic Probe

ABSTRACT Gram-negative bacteria play an important role in the formation and stabilization of biofilm structures on stone surfaces. Therefore, the control of growth of gram-negative bacteria offers a way to diminish biodeterioration of stone materials. The effect of potential permeabilizers on the outer membrane (OM) properties of gram-negative bacteria was investigated and further characterized. In addition, efficacy of the agents in enhancing the activity of a biocide (benzalkonium chloride) was assessed. EDTA, polyethylenimine (PEI), and succimer (meso-2,3-dimercaptosuccinic) were shown to be efficient permeabilizers of the members of Pseudomonas and Stenotrophomonas genera, as indicated by an increase in the uptake of a hydrophobic probe (1-N-phenylnaphthylamine) and sensitization to hydrophobic antibiotics. Visualization of Pseudomonas cells treated with EDTA or PEI by atomic force microscopy revealed damage in the outer membrane structure. PEI especially increased the surface area and bulges of the cells. Topographic images of EDTA-treated cells were compatible with events assigned for the effect of EDTA on outer membranes, i.e., release of lipopolysaccharide and disintegration of OM structure. In addition, the effect of EDTA treatment was visualized in phase-contrast images as large areas with varying hydrophilicity on cell surfaces. In liquid culture tests, EDTA and PEI supplementation enhanced the activity of benzalkonium chloride toward the target strains. Use of permeabilizers in biocide formulations would enable the use of decreased concentrations of the active biocide ingredient, thereby providing environmentally friendlier products.

scholarly journals “Asymmetry Is the Rhythmic Expression of Functional Design,” a Quotation from Jan Tschichold

2020 ◽  
Vol 202 (18) ◽  
Author(s):  
Joe Lutkenhaus
Keyword(s):  
Outer Membrane ◽  
Regulatory Role ◽  
Permeability Barrier ◽  
Gram Negative Bacteria ◽  
Functional Design ◽  
Lipid Asymmetry ◽  
Gram Negative ◽  
Outer Membranes ◽  
Rhythmic Expression

ABSTRACT The outer membranes of Gram-negative bacteria provide a permeability barrier to antibiotics and other harmful chemicals. The integrity of this barrier relies on the maintenance of the lipid asymmetry of the outer membrane, and studies of suppressors of a decades-old mutant reveal that YejM plays a key regulatory role and provide a model for the maintenance of this asymmetry.

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