The structure of OmpF porin in a tetragonal crystal form

Cowan, SW; Garavito, R. Michael; Jansonius, Johan N.; Jenkins, J.A.; Karlsson, Rolf; Konig, Nicola; Pai, E.F.; Pauptit, RA; Rizkallah, P.J.; Rosenbusch, J P; Rummel, Gabriele; Schirmer, Tilman

doi:10.1016/s0969-2126(01)00240-4

Cited by 184 publications

(168 citation statements)

References 35 publications

(55 reference statements)

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“…Mutations in the ompF sequence were detected by alignment between sequences using Bioedit software (downloaded from: (http://www.mbio.ncsu.edu/bioedit/). The OmpF structure (Cowan et al, 1995) was obtained from the Protein Data Bank and the position of mutations were visualized using PyMOL (downloaded from: http://www.pymol.org/…”

Section: Outer Membrane Protein Analysismentioning

confidence: 99%

A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli

Phan

Ferenci

2013

The ISME Journal

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Bacterial species are internally diverse in genomic and multi-locus gene comparisons. The ecological causes of phenotypic and genotypic diversity within species are far less well understood. Here, we focus on the competitive fitness for growth on nutrients within Escherichia coli, an internally rich species. Competition experiments in nutrient-limited chemostats revealed that members of the ECOR collection exhibited a wide continuum of competitive abilities, with some fitter and some less fit than the lab strain MG1655. We observed an inverse relationship between competitiveness and the resistance of strains to detergent and antibiotic, consistent with the notion that membrane permeability and competitive fitness are linked by a trade-off between selfpreservation and nutritional competence (SPANC); high permeability has a postulated cost in antibacterial sensitivity whereas a low permeability has a cost in nutrient affinity. Isolates moved along the markedly nonlinear trade-off curve by mutational adaptation; an ECOR strain sensitive to antibacterials and a good competitor was easily converted by mutation into a mutant with higher resistance but poorer competition in the presence of low antibiotic concentrations. Conversely, a resistant ECOR strain changed into a better competitor after a short period of selection under nutrient limitation. In both directions, mutations can affect porin proteins and outer membrane permeability, as indicated by protein analysis, gene sequencing and an independent assay of outer membrane permeability. The extensive, species-wide diversity of E. coli in ecologically important traits can thus be explained as an evolutionary consequence of a SPANC trade-off driven by antagonistic pleiotropy.

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Section: Outer Membrane Protein Analysismentioning

confidence: 99%

A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli

Phan

Ferenci

2013

The ISME Journal

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“…Molecular Visualization and Electrostatic Analysis-Crystal structure of OmpF trimer (Protein Data Bank code 1OPF) (23) and OmpC trimer (2J1N) were visualized by PyMOL (Version 1.6.x.). The structures of mutated porins were predicted by SWISS-MODEL.…”

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confidence: 99%

High Salt Concentrations Increase Permeability through OmpC Channels of Escherichia coli

Kojima

Nikaido

2014

Journal of Biological Chemistry

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Background: OmpC porin is less permeable than OmpF, but there is little difference in channel size. Results: There are more charged residues in the OmpC channel, and mutating them or increasing ionic strength made it more permeable and OmpF-like. Conclusion: Charged residues produce the low permeability of OmpC. Significance: OmpC, produced in a high ionic strength environment, has properties optimized for this environment.

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“…When folding is inefficient, unassembled porins accumulate and their C termini activate DegS to initiate cleavage of RseA (Walsh et al 2003). Exposed C termini are an excellent indicator of impaired folding as they are normally sequestered in the porin trimer interface (Cowan et al 1995). Free DegS is inactive in cleaving RseA because its catalytic triad is inappropriately positioned.…”

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confidence: 99%

Design principles of the proteolytic cascade governing the σ^E-mediated envelope stress response in Escherichia coli: keys to graded, buffered, and rapid signal transduction

Chaba¹,

Grigorova²,

Flynn³

et al. 2007

Genes Dev.

104

119

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Proteolytic cascades often transduce signals between cellular compartments, but the features of these cascades that permit efficient conversion of a biological signal into a transcriptional output are not well elucidated. E mediates an envelope stress response in Escherichia coli, and its activity is controlled by regulated degradation of RseA, a membrane-spanning anti-factor. Examination of the individual steps in this protease cascade reveals that the initial, signal-sensing cleavage step is rate-limiting; that multiple ATP-dependent proteases degrade the cytoplasmic fragment of RseA and that dissociation of E from RseA is so slow that most free E must be generated by the active degradation of RseA. As a consequence, the degradation rate of RseA is set by the amount of inducing signal, and insulated from the "load" on and activity of the cytoplasmic proteases. Additionally, changes in RseA degradation rate are rapidly reflected in altered E activity. These design features are attractive as general components of signal transduction pathways governed by unstable negative regulators. Proteolytic cascades are widely used to transduce signals across membranes to enable cells to respond to environmental stress and coordinate processes in different cellular compartments. However, the molecular properties of these cascades that facilitate the desired outputs have rarely been examined. In this work, we examine the individual steps in the protease cascade governing the activity of the E -mediated envelope stress response in Escherichia coli to determine the construction features of this cascade that facilitate faithful transmission of signal and a rapid output.E directs RNA polymerase to transcribe genes encoding proteins that ensure the synthesis, assembly, and homeostasis of outer membrane porins and lipopolysaccharide, the two major components of the unique outer membrane of Gram-negative bacteria (Dartigalongue et al. 2001;Rezuchova et al. 2003;Rhodius et al. 2006). Envelope integrity is required under all growth conditions, and E is an essential transcription factor (De Las Penas et al. 1997a). Perturbations in the integrity and protein-folding state of the envelope caused by temperature upshift, chaperone depletion, or accumulation of unassembled porins increase E activity; conversely, temperature downshift and/or depletion of porins decrease E activity (Mecsas et al. 1993;Hiratsu et al. 1995;Raina et al. 1995;Rouviere et al. 1995;Missiakas et al. 1996;Rouviere and Gross 1996;Ades et al. 2003).The components of the signal transduction system that control E activity are shown in Figure 1. RseA, a membrane-spanning anti-factor, inhibits E activity. The cytoplasmic domain of RseA (RseA 1-108 ) binds to E and its periplasmic domain binds to RseB (De Las Penas et al. 1997b;Missiakas et al. 1997

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The structure of OmpF porin in a tetragonal crystal form

Cited by 184 publications

References 35 publications

A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli

A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli

High Salt Concentrations Increase Permeability through OmpC Channels of Escherichia coli

Design principles of the proteolytic cascade governing the σ^E-mediated envelope stress response in Escherichia coli: keys to graded, buffered, and rapid signal transduction

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The structure of OmpF porin in a tetragonal crystal form

Cited by 184 publications

References 35 publications

A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli

A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli

High Salt Concentrations Increase Permeability through OmpC Channels of Escherichia coli

Design principles of the proteolytic cascade governing the σE-mediated envelope stress response in Escherichia coli: keys to graded, buffered, and rapid signal transduction

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Design principles of the proteolytic cascade governing the σ^E-mediated envelope stress response in Escherichia coli: keys to graded, buffered, and rapid signal transduction