1
|
Cherrak Y, Salazar MA, Yilmaz K, Kreuzer M, Hardt WD. Commensal E. coli limits Salmonella gut invasion during inflammation by producing toxin-bound siderophores in a tonB-dependent manner. PLoS Biol 2024; 22:e3002616. [PMID: 38865418 PMCID: PMC11168627 DOI: 10.1371/journal.pbio.3002616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/05/2024] [Indexed: 06/14/2024] Open
Abstract
The gastrointestinal tract is densely colonized by a polymicrobial community known as the microbiota which serves as primary line of defence against pathogen invasion. The microbiota can limit gut-luminal pathogen growth at different stages of infection. This can be traced to specific commensal strains exhibiting direct or indirect protective functions. Although these mechanisms hold the potential to develop new approaches to combat enteric pathogens, they remain far from being completely described. In this study, we investigated how a mouse commensal Escherichia coli can outcompete Salmonella enterica serovar Typhimurium (S. Tm). Using a salmonellosis mouse model, we found that the commensal E. coli 8178 strain relies on a trojan horse trap strategy to limit S. Tm expansion in the inflamed gut. Combining mutants and reporter tools, we demonstrated that inflammation triggers the expression of the E. coli 8178 antimicrobial microcin H47 toxin which, when fused to salmochelin siderophores, can specifically alter S. Tm growth. This protective function was compromised upon disruption of the E. coli 8178 tonB-dependent catecholate siderophore uptake system, highlighting a previously unappreciated crosstalk between iron intake and microcin H47 activity. By identifying the genetic determinants mediating S. Tm competition, our work not only provides a better mechanistic understanding of the protective function displayed by members of the gut microbiota but also further expands the general contribution of microcins in bacterial antagonistic relationships. Ultimately, such insights can open new avenues for developing microbiota-based approaches to better control intestinal infections.
Collapse
Affiliation(s)
- Yassine Cherrak
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Miguel Angel Salazar
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Koray Yilmaz
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Markus Kreuzer
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
2
|
Sen O, Hinks J, Lin Q, Lin Q, Kjelleberg S, Rice SA, Seviour T. Escherichia coli displays a conserved membrane proteomic response to a range of alcohols. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:147. [PMID: 37789404 PMCID: PMC10546733 DOI: 10.1186/s13068-023-02401-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND Alcohol is a good and environment-friendly fuel that can be microbially produced, capable of eliminating many of the limitations of the present-day fossil fuels. However, the inherent toxic nature of alcohols to the microbial cells leads to end-product inhibition that limits large-scale alcohol production by fermentation. Fundamental knowledge about the stress responses of microorganisms to alcohols would greatly facilitate to improve the microbial alcohol tolerance. The current study elucidates and compares the changes in the membrane proteome of Escherichia coli in response to a range of alcohols. RESULTS Although alcohol toxicity increased exponentially with alcohol chain length (2-6 carbon), similar stress responses were observed in the inner and outer membrane proteome of E. coli in the presence of 2-, 4- and 6-carbon alcohols at the MIC50. This pertains to: (1) increased levels of inner membrane transporters for uptake of energy-producing metabolites, (2) reduced levels of non-essential proteins, associated with anaerobic, carbon starvation and osmotic stress, for energy conservation, (3) increased levels of murein degrading enzymes (MltA, EmtA, MliC and DigH) promoting cell elongation and 4) reduced levels of most outer membrane β-barrel proteins (LptD, FadL, LamB, TolC and BamA). Major outer membrane β-barrel protein OmpC, which is known to contribute to ethanol tolerance and membrane integrity, was notably reduced by alcohol stress. While LPS is important for OmpC trimerisation, LPS release by EDTA did not lower OmpC levels. This suggests that LPS release, which is reported under alcohol stress, does not contribute to the reduced levels of OmpC in the presence of alcohol. CONCLUSIONS Since alcohol primarily targets the integrity of the membrane, maintenance of outer membrane OmpC levels in the presence of alcohol might help in the survival of E. coli to higher alcohol concentrations. The study provides important information about the membrane protein responses of E. coli to a range of alcohols, which can be used to develop targeted strategies for increased microbial alcohol tolerance and hence bioalcohol production.
Collapse
Affiliation(s)
- Oishi Sen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jamie Hinks
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Qifeng Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- The Australian Institute for Microbiology and Immunology, University of Technology Sydney, Sydney, 2007, Australia
- CSIRO, Agriculture and Food, Westmead and Microbiomes for One Systems Health, Sydney, Australia
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
- WATEC Aarhus University Centre for Water Technology, Universitetsbyen 36, Bldg 1783, 8000, Aarhus, Denmark.
| |
Collapse
|
3
|
Nilaweera TD, Nyenhuis DA, Cafiso DS. Structural intermediates observed only in intact Escherichia coli indicate a mechanism for TonB-dependent transport. eLife 2021; 10:68548. [PMID: 34251336 PMCID: PMC8341980 DOI: 10.7554/elife.68548] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/11/2021] [Indexed: 12/17/2022] Open
Abstract
Outer membrane TonB-dependent transporters facilitate the uptake of trace nutrients and carbohydrates in Gram-negative bacteria and are essential for pathogenic bacteria and the health of the microbiome. Despite this, their mechanism of transport is still unknown. Here, pulse electron paramagnetic resonance (EPR) measurements were made in intact cells on the Escherichia coli vitamin B12 transporter, BtuB. Substrate binding was found to alter the C-terminal region of the core and shift an extracellular substrate binding loop 2 nm toward the periplasm; moreover, this structural transition is regulated by an ionic lock that is broken upon binding of the inner membrane protein TonB. Significantly, this structural transition is not observed when BtuB is reconstituted into phospholipid bilayers. These measurements suggest an alternative to existing models of transport, and they demonstrate the importance of studying outer membrane proteins in their native environment.
Collapse
Affiliation(s)
- Thushani D Nilaweera
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, United States
| | - David A Nyenhuis
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, United States
| | - David S Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, United States
| |
Collapse
|
4
|
James HE, Beare PA, Martin LW, Lamont IL. Mutational analysis of a bifunctional ferrisiderophore receptor and signal-transducing protein from Pseudomonas aeruginosa. J Bacteriol 2005; 187:4514-20. [PMID: 15968062 PMCID: PMC1151750 DOI: 10.1128/jb.187.13.4514-4520.2005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The FpvA protein of Pseudomonas aeruginosa strain PAO1 mediates uptake of a siderophore, ferripyoverdine. It is also a component of a signal transduction pathway that controls production of an exotoxin, a protease, pyoverdine, and FpvA itself. The purpose of the research described here was to dissect these different functions of FpvA. Signaling involves an N-terminal domain of FpvA, and it was shown that this domain is probably located in the periplasm, as expected. Short peptides were inserted at 36 sites within FpvA by linker insertion mutagenesis. The effects of these mutations on the presence of FpvA in the outer membrane, on FpvA-mediated uptake of ferripyoverdine, and on pyoverdine synthesis and gene expression were determined. Five of the mutations resulted in the absence of FpvA from the outer membrane of the bacteria. All of the remaining mutations eliminated either the transport or signaling function of FpvA and most affected both functions. Three mutations prevented transport of ferripyoverdine but had no effect on the signal transduction pathway showing that transport of ferripyoverdine is not required for the trans-membrane signaling process. Conversely, eight mutations affected pyoverdine-mediated signaling but had no effect on transport of ferripyoverdine. These data show that insertions throughout FpvA resulted in loss of function and that signaling and transport are separate and discrete functions of FpvA.
Collapse
Affiliation(s)
- H Ellen James
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand
| | | | | | | |
Collapse
|
5
|
Chimento DP, Kadner RJ, Wiener MC. Comparative structural analysis of TonB-dependent outer membrane transporters: Implications for the transport cycle. Proteins 2005; 59:240-51. [PMID: 15739205 DOI: 10.1002/prot.20416] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
TonB-dependent outer membrane transporters (TBDTs) transport organometallic substrates across the outer membranes of Gram-negative bacteria. Currently, structures of four different TBDTs have been determined by X-ray crystallography. TBDT structures consist of a 22-stranded beta-barrel enclosing a hatch domain. Structure-based sequence alignment of these four TBDTs indicates the presence of highly conserved motifs in both the hatch and barrel domains. The conserved motifs of the two domains are always in close proximity to each other and interact. We analyzed the very large interfaces between the barrel and hatch domains of TBDTs and compared their properties to those of other protein-protein interfaces. These interfaces are extensively hydrated. Most of the interfacial waters form hydrogen bonds to either the barrel or the hatch domain, with the remainder functioning as bridging waters in the interface. The hatch/barrel interfacial properties most resemble those of obligate transient protein complexes, suggesting that the interface is conducive to conformational change and/or movement of the hatch within the barrel. These results indicate that TBDTs can readily accommodate substantial conformational change and movement of their hatch domains during the active transport cycle. Also, these structural changes may require only modest forces exerted by the energy-coupling TonB protein upon the transporter.
Collapse
Affiliation(s)
- David P Chimento
- Department of Microbiology, University of Virginia, Charlottesville, Virginia, USA
| | | | | |
Collapse
|
6
|
Perkins-Balding D, Baer MT, Stojiljkovic I. Identification of functionally important regions of a haemoglobin receptor from Neisseria meningitidis. MICROBIOLOGY-SGM 2004; 149:3423-3435. [PMID: 14663076 DOI: 10.1099/mic.0.26448-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The HmbR outer-membrane receptor enables Neisseria meningitidis to use haemoglobin (Hb) as a source of iron. This protein functions by binding Hb, removing haem from it, and releasing the haem into the periplasm. Functionally important HmbR receptor domains were discerned using a series of HmbR deletions and site-directed mutations. Mutations exhibiting similar defective phenotypes in N. meningitidis fell into two groups. The first group of mutations affected Hb binding and were located in putative extracellular loops (L) L2 (amino acid residues (aa) 192-230) and L3 (aa 254-284). The second group of mutations resulted in a failure to utilize Hb but proficiency in Hb binding was retained. These mutations localized to the putative extracellular loops L6 (aa 420-462) and L7 (aa 486-516). A highly conserved protein motif found in all haem/Hb receptors, within putative extracellular loop L7 of HmbR, is essential for Hb utilization but not required for Hb binding. This finding suggests a mechanistic involvement of this motif in haem removal from Hb. In addition, an amino-terminal deletion in the putative cork-like domain of HmbR affected Hb usage but not Hb binding. This result supports a role of the cork domain in utilization steps that are subsequent to Hb binding.
Collapse
Affiliation(s)
- D Perkins-Balding
- Department of Microbiology and Immunology, Emory School of Medicine, 1510 Clifton Rd, Atlanta, GA 30322, USA
| | - M T Baer
- Department of Microbiology and Immunology, Emory School of Medicine, 1510 Clifton Rd, Atlanta, GA 30322, USA
| | - I Stojiljkovic
- Department of Microbiology and Immunology, Emory School of Medicine, 1510 Clifton Rd, Atlanta, GA 30322, USA
| |
Collapse
|
7
|
Etz H, Minh DB, Schellack C, Nagy E, Meinke A. Bacterial phage receptors, versatile tools for display of polypeptides on the cell surface. J Bacteriol 2001; 183:6924-35. [PMID: 11698382 PMCID: PMC95534 DOI: 10.1128/jb.183.23.6924-6935.2001] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Four outer membrane proteins of Escherichia coli were examined for their capabilities and limitations in displaying heterologous peptide inserts on the bacterial cell surface. The T7 tag or multiple copies of the myc epitope were inserted into loops 4 and 5 of the ferrichrome and phage T5 receptor FhuA. Fluorescence-activated cell sorting analysis showed that peptides of up to 250 amino acids were efficiently displayed on the surface of E. coli as inserts within FhuA. Strains expressing FhuA fusion proteins behaved similarly to those expressing wild-type FhuA, as judged by phage infection and colicin sensitivity. The vitamin B(12) and phage BF23 receptor BtuB could display peptide inserts of at least 86 amino acids containing the T7 tag. In contrast, the receptors of the phages K3 and lambda, OmpA and LamB, accepted only insertions in their respective loop 4 of up to 40 amino acids containing the T7 tag. The insertion of larger fragments resulted in inefficient transport and/or assembly of OmpA and LamB fusion proteins into the outer membrane. Cells displaying a foreign peptide fused to any one of these outer membrane proteins were almost completely recovered by magnetic cell sorting from a large pool of cells expressing the relevant wild-type platform protein only. Thus, this approach offers a fast and simple screening procedure for cells displaying heterologous polypeptides. The combination of FhuA, along with with BtuB and LamB, should provide a comprehensive tool for displaying complex peptide libraries of various insert sizes on the surface of E. coli for diverse applications.
Collapse
Affiliation(s)
- H Etz
- Antigen Discovery Group, InterCell Biomedizinische Forschungs- und Entwicklungs AG, Rennweg 95b, 1030 Vienna, Austria
| | | | | | | | | |
Collapse
|
8
|
German GJ, Misra R. The TolC protein of Escherichia coli serves as a cell-surface receptor for the newly characterized TLS bacteriophage 1 1Edited by B. Holland. J Mol Biol 2001; 308:579-85. [PMID: 11350161 DOI: 10.1006/jmbi.2001.4578] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The TolC protein of Escherichia coli is implicated in a variety of diverse cellular functions, including antibiotic efflux and alpha-hemolysin secretion. An incidental role of TolC is to facilitate the entry of the bacteriophage TLS and colicin E1 into the bacterial cell. Despite the resolution of TolC's atomic structure, the roles of specific residues in its diverse functions are unknown. Here, we describe a genetic strategy for isolating missense tolC mutations that abolish the bacteriophage receptor activity of the TolC protein without influencing its role in antibiotic efflux. These spontaneous mutations affected two regions of the TolC protein and included base-pair substitutions, insertions, and deletions. Comparison of the TolC sequence with those of its homologues revealed two hypervariable stretches that were predicted to represent loops. Interestingly, all but one of the TolC alterations preventing phage binding were located in these two hypervariable regions, which are likely to be exposed on the cell surface. This was substantiated by the recently solved three-dimensional structure of TolC. Curiously, all the phage-resistant TolC mutants showed varying degrees of resistance to colicin E1, suggesting the involvement of overlapping regions of TolC in colicin E1 import and phage binding. The phage used in this study, TLS, was earlier reported as a strain of U3. However, we show here that, unlike the previously reported lipopolysaccharide-specific U3 phage, this phage displays a distinctly different host range and discrete morphological features and, in addition to utilizing TolC as receptor, it requires the inner core of a lipopolysaccharide.
Collapse
Affiliation(s)
- G J German
- Department of Microbiology, Arizona State University, Tempe, AZ 85287, USA
| | | |
Collapse
|
9
|
Misra R, CastilloKeller M, Deng M. Overexpression of protease-deficient DegP(S210A) rescues the lethal phenotype of Escherichia coli OmpF assembly mutants in a degP background. J Bacteriol 2000; 182:4882-8. [PMID: 10940032 PMCID: PMC111368 DOI: 10.1128/jb.182.17.4882-4888.2000] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Replacement of OmpF's conserved carboxy-terminal phenylalanine with dissimilar amino acids severely impaired its assembly into stable trimers. In some instances, interactions of mutant proteins with the outer membrane were also affected, as judged by their hypersensitivity phenotype. Synthesis of all mutant OmpF proteins elevated the expression of periplasmic protease DegP, and synthesis of most of them made its presence obligatory for cell viability. These results showed a critical role for DegP in the event of aberrant outer membrane protein assembly. The lethal phenotype of mutant OmpF proteins in a degP null background was eliminated when a protease-deficient DegP(S210A) protein was overproduced. Our data showed that this rescue from lethality and a subsequent increase in mutant protein levels in the envelope did not lead to the proper assembly of the mutant proteins in the outer membrane. Rather, a detergent-soluble and thermolabile OmpF species resembling monomers accumulated in the mutants, and to a lesser extent in the parental strain, when DegP(S210A) was overproduced. Interestingly, this also led to the localization of a significant amount of mutant polypeptides to the inner membrane, where DegP(S210A) also fractionated. These results suggested that the DegP(S210A)-mediated rescue from toxicity involved preferential sequestration of misfolded OmpF monomers from the normal assembly pathway.
Collapse
Affiliation(s)
- R Misra
- Department of Microbiology, Arizona State University, Tempe, Arizona 85287, USA.
| | | | | |
Collapse
|
10
|
Bracken CS, Baer MT, Abdur-Rashid A, Helms W, Stojiljkovic I. Use of heme-protein complexes by the Yersinia enterocolitica HemR receptor: histidine residues are essential for receptor function. J Bacteriol 1999; 181:6063-72. [PMID: 10498719 PMCID: PMC103634 DOI: 10.1128/jb.181.19.6063-6072.1999] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The abilities of two bacterial active heme transporters, HmbR of Neisseria meningitidis and HemR of Yersinia enterocolitica, to use different heme sources were compared. While HmbR-expressing cells used only hemoglobin (Hb) and heme, HemR-expressing bacteria were able to grow on Hb, heme, myoglobin, hemopexin, catalase, human and bovine serum albumin-heme, and haptoglobin-hemoglobin complexes as sources of iron. Expression of functional HemR allowed Escherichia coli cells to respond to heme-containing peptides, microperoxidases MP-8, MP-9, and MP-11, suggesting the ability of HemR to transport heme covalently linked to other molecules. Comparison of HemR with other heme receptors identified several highly conserved histidine residues as well as two conserved amino acid motifs, the FRAP and NPNL boxes. A site-directed mutagenesis approach was used to investigate the roles of His128, His192, His352, and His461 residues in HemR function. The HemR receptor with histidine changed to lysine at position 128 (HemR(H128K)), HemR(H461L), HemR(H461A), and HemR(H128A,H461A) mutant receptors were unable to use Hb, human serum albumin-heme, and myoglobin as sources of porphyrin and iron. Utilization of free heme was also severely affected, with some residual heme uptake in cells expressing HemR(H128K), HemR(H461A), and HemR(H461L). Conversely, the HemR(H192T), HemR(H352A), HemR(H352K), and HemR(H192T,H352K) mutant receptors were fully functional. All mutant HemR proteins were expressed in the outer membrane at levels similar to that of the wild-type HemR receptor. Nonfunctional HemRs were able to bind heme- and Hb-agarose. A hypothetical model of the HemR function in which two conserved histidine residues, His128 and His461, participate in the transport of heme through the receptor pore is postulated.
Collapse
Affiliation(s)
- C S Bracken
- Department of Microbiology & Immunology, Emory University, Atlanta, Georgia 30322, USA
| | | | | | | | | |
Collapse
|
11
|
Lambert O, Moeck GS, Levy D, Plançon L, Letellier L, Rigaud JL. An 8-A projected structure of FhuA, A "ligand-gated" channel of the Escherichia coli outer membrane. J Struct Biol 1999; 126:145-55. [PMID: 10388625 DOI: 10.1006/jsbi.1999.4115] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure of FhuA, a siderophore and phage receptor in the outer membrane of Escherichia coli, has been investigated by electron crystallography. Bidimensional crystals of hexahistidine-tagged FhuA protein solubilized in N,N-dimethyldodecylamine-N-oxide were produced after detergent removal with polystyrene beads. Frozen-hydrated crystals (unit cell dimensions of a = 124 A, b = 98 A, gamma = 90 degrees ) exhibited a p22121 plane group symmetry. A projection map at 8 A resolution showed the presence of dimeric ring-like structures with an elliptical shape (48 x 40 A). Each monomer was composed of a ring of densities with a radial width of 8-10 A corresponding to a cylinder of beta sheets. Few densities are present inside the barrel, leaving a central channel approximately 25 A in diameter. A projection map of FhuA at 15 A resolution, which was calculated from negatively stained preparations, demonstrated that most of the central channel was masked by extramembrane domains. This map also revealed an asymmetric distribution of extramembrane domains in FhuA, with large domains located mainly on one side of the molecule. Comparison with density maps derived from recent atomic structure allowed further interpretation of the electron microscopy projection structures with regard to long hydrophilic loops governing the selectivity and opening of the channel.
Collapse
Affiliation(s)
- O Lambert
- Section de Recherche, Institut Curie, UMR 168 CNRS et, 11 rue Pierre et Marie Curie, Paris, F-75231, France
| | | | | | | | | | | |
Collapse
|
12
|
Newton SM, Igo JD, Scott DC, Klebba PE. Effect of loop deletions on the binding and transport of ferric enterobactin by FepA. Mol Microbiol 1999; 32:1153-65. [PMID: 10383757 DOI: 10.1046/j.1365-2958.1999.01424.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The siderophore ferric enterobactin enters Escherichia coli through the outer membrane (OM) porin FepA, which contains an aqueous transmembrane channel that is normally occluded by other parts of the protein. After binding the siderophore at a site within the surface loops, FepA undergoes conformational changes that promote ligand internalization. We assessed the participation of different loops in ligand recognition and uptake by creating and analysing a series of deletions. We genetically engineered 26 mutations that removed 9-75 amino acids from nine loops and two buried regions of the OM protein. The mutations had various effects on the uptake reaction, which we discerned by comparing the substrate concentrations of half-maximal binding (Kd) and uptake (Km): every loop deletion affected siderophore transport kinetics, decreasing or eliminating binding affinity and transport efficiency. We classified the mutations in three groups on the basis of their slight, strong or complete inhibition of the rate of ferric enterobactin transport across the OM. Finally, characterization of the FepA mutants revealed that prior experiments underestimated the affinity of FepA for ferric enterobactin: the interaction between the protein and the ferric siderophore is so avid (Kd < 0.2 nM) that FepA tolerated the large reductions in affinity that some loop deletions caused without loss of uptake functionality. That is, like other porins, many of the loops of FepA are superficially dispensable: ferric enterobactin transport occurred without them, at levels that allowed bacterial growth.
Collapse
Affiliation(s)
- S M Newton
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, OK 73019, USA
| | | | | | | |
Collapse
|
13
|
Larsen RA, Thomas MG, Postle K. Protonmotive force, ExbB and ligand-bound FepA drive conformational changes in TonB. Mol Microbiol 1999; 31:1809-24. [PMID: 10209752 DOI: 10.1046/j.1365-2958.1999.01317.x] [Citation(s) in RCA: 140] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
TonB couples the cytoplasmic membrane protonmotive force (pmf) to active transport across the outer membrane, potentially through a series of conformational changes. Previous studies of a TonB transmembrane domain mutant (TonB-delta V17) and its phenotypical suppressor (ExbB-A39E) suggested that TonB is conformationally sensitive. Here, two new mutations of the conserved TonB transmembrane domain SHLS motif were isolated, TonB-S16L and -H20Y, as were two new suppressors, ExbB-V35E and -V36D. Each suppressor ExbB restored at least partial function to the TonB mutants, although TonB-delta V17, for which both the conserved motif and the register of the predicted transmembrane domain alpha-helix are affected, was the most refractory. As demonstrated previously, TonB can undergo at least one conformational change, provided both ExbB and a functional TonB transmembrane domain are present. Here, we show that this conformational change reflects the ability of TonB to respond to the cytoplasmic membrane proton gradient, and occurs in proportion to the level of TonB activity attained by mutant-suppressor pairs. The phenotype of TonB-delta V17 was more complex than the -S16L and -H20Y mutations, in that, beyond the inability to be energized efficiently, it was also conditionally unstable. This second defect was evident only after suppression by the ExbB mutants, which allow transmembrane domain mutants to be energized, and presented as the rapid turnover of TonB-delta V17. Importantly, this degradation was dependent upon the presence of a TonB-dependent ligand, suggesting that TonB conformation also changes following the energy transduction event. Together, these observations support a dynamic model of energy transduction in which TonB cycles through a set of conformations that differ in potential energy, with a transition to a higher energy state driven by pmf and a transition to a lower energy state accompanying release of stored potential energy to an outer membrane receptor.
Collapse
Affiliation(s)
- R A Larsen
- Department of Microbiology, Washington State University, Pullman 99164-4233, USA
| | | | | |
Collapse
|
14
|
Abstract
This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.
Collapse
Affiliation(s)
- M K Berlyn
- Department of Biology and School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06520-8104, USA.
| |
Collapse
|
15
|
Moeck GS, Coulton JW. TonB-dependent iron acquisition: mechanisms of siderophore-mediated active transport. Mol Microbiol 1998; 28:675-81. [PMID: 9643536 DOI: 10.1046/j.1365-2958.1998.00817.x] [Citation(s) in RCA: 209] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cells growing in aerobic environments have developed intricate strategies to overcome the scarcity of iron, an essential nutrient. In gram-negative bacteria, high-affinity iron acquisition requires outer membrane-localized proteins that bind iron chelates at the cell surface and promote their uptake. Transport of bound chelates across the outer membrane depends upon TonB-ExbB-ExbD, a cytoplasmic membrane-localized complex that transduces energy from the proton motive force to high-affinity receptors in the outer membrane. Upon ligand binding to iron chelate receptors, conformational changes are induced, some of which are detected in the periplasm. These structural alterations signal the ligand-loaded status of the receptor and, therefore, the requirement for TonB-dependent energy transduction. Thus, TonB interacts preferentially and directly with ligand-loaded receptors. Such a mechanism ensures the productive use of cellular energy to drive active transport at the outer membrane.
Collapse
Affiliation(s)
- G S Moeck
- Department of Microbiology and Immunology, McGill University, Montreal, Canada.
| | | |
Collapse
|
16
|
Abstract
A computational strategy for determining the variability of long DNA sequences in microbial genomes is described. Composite portraits of bacterial genomes were obtained by computing tetranucleotide frequencies of sections of genomic DNA, converting the frequencies to color images and arranging the images according to their genetic position. The resulting images revealed that the tetranucleotide frequencies of genomic DNA sequences are highly conserved. Sections that were visibly different from those of the rest of the genome contained ribosomal RNA, bacteriophage, or undefined coding regions and had corresponding differences in the variances of tetranucleotide frequencies and GC content. Comparison of nine completely sequenced bacterial genomes showed that there was a nonlinear relationship between variances of the tetranucleotide frequencies and GC content, with the highest variances occurring in DNA sequences with low GC contents (less than 0.30 mol). High variances were also observed in DNA sequences having high GC contents (greater than 0.60 mol), but to a much lesser extent than DNA sequences having low GC contents. Differences in the tetranucleotide frequencies may be due to the mechanisms of intercellular genetic exchange and/or processes involved in maintaining intracellular genetic stability. Identification of sections that were different from those of the rest of the genome may provide information on the evolution and plasticity of bacterial genomes.
Collapse
Affiliation(s)
- P A Noble
- Belle W. Baruch Institute for Marine Biology and Coastal Research, University of South Carolina, Columbia 29208, USA.
| | | | | |
Collapse
|
17
|
Marenda M, Brito B, Callard D, Genin S, Barberis P, Boucher C, Arlat M. PrhA controls a novel regulatory pathway required for the specific induction of Ralstonia solanacearum hrp genes in the presence of plant cells. Mol Microbiol 1998; 27:437-53. [PMID: 9484898 DOI: 10.1046/j.1365-2958.1998.00692.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The Ralstonia solanacearum hrp gene cluster is organized in five transcriptional units. Expression of transcriptional units 2, 3 and 4 is induced in minimal medium and depends on the hrp regulatory gene hrpB, which belongs to unit 1. This regulatory gene also controls the expression of genes, such as popA, located to the left of the hrp cluster. Here, we show that, upon co-culture with Arabidopsis thaliana and tomato cell suspensions, the expression of the hrp transcriptional units 1, 2, 3 and 4 is induced 10- to 20-fold more than in minimal medium. This induction is not triggered by diffusible signals but requires the presence of plant cells. Moreover, we show that this specific plant cell induction of hrp genes is controlled by a gene, called prhA (plant regulator of hrp genes), located next to popA. This gene codes for a putative protein of 770 amino acids, which shows similarities with TonB-dependent outer membrane siderophore receptors. Expression of prhA and hrp genes is not regulated by iron status, and we postulate that iron is not the signal sensed by PrhA. In prhA mutants, the induction of hrpB and other hrp genes is abolished in co-culture with Arabidopsis cells, partially reduced in co-culture with tomato cells and not modified in minimal medium. prhA mutants are hypo-aggressive on Arabidopsis (accessions Col-0 and Col-5) but remain fully pathogenic on tomato plants, suggesting that the co-culture assays mimic the in planta conditions. A model suggesting that PrhA is a receptor for plant specific signals at the top of a novel hrp regulatory pathway is discussed.
Collapse
Affiliation(s)
- M Marenda
- Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, INRA-CNRS, Castanet-tolosan, France
| | | | | | | | | | | | | |
Collapse
|
18
|
Chapter 28 Communication between membranes in tonB-dependent transport across the bacterial outer membrane. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s1383-8121(96)80069-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|