1
|
Tran BM, Punter CM, Linnik D, Iyer A, Poolman B. Single-protein Diffusion in the Periplasm of Escherichia coli. J Mol Biol 2024; 436:168420. [PMID: 38143021 DOI: 10.1016/j.jmb.2023.168420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
The width of the periplasmic space of Gram-negative bacteria is only about 25-30 nm along the long axis of the cell, which affects free diffusion of (macro)molecules. We have performed single-particle displacement measurements and diffusion simulation studies to determine the impact of confinement on the apparent mobility of proteins in the periplasm of Escherichia coli. The diffusion of a reporter protein and of OsmY, an osmotically regulated periplasmic protein, is characterized by a fast and slow component regardless of the osmotic conditions. The diffusion coefficient of the fast fraction increases upon osmotic upshift, in agreement with a decrease in macromolecular crowding of the periplasm, but the mobility of the slow (immobile) fraction is not affected by the osmotic stress. We observe that the confinement created by the inner and outer membranes results in a lower apparent diffusion coefficient, but this can only partially explain the slow component of diffusion in the particle displacement measurements, suggesting that a fraction of the proteins is hindered in its mobility by large periplasmic structures. Using particle-based simulations, we have determined the confinement effect on the apparent diffusion coefficient of the particles for geometries akin the periplasmic space of Gram-negative bacteria.
Collapse
Affiliation(s)
- Buu Minh Tran
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Christiaan Michiel Punter
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Dmitrii Linnik
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Aditya Iyer
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.
| |
Collapse
|
2
|
Serratia marcescens DUF1471-Containing Protein SrfN Is Needed for Adaptation to Acid and Oxidative Stresses. mSphere 2022; 7:e0021222. [PMID: 36218346 PMCID: PMC9769812 DOI: 10.1128/msphere.00212-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Bacteria can quickly adapt to constantly changing environments through a number of mechanisms, including secretion of secondary metabolites, peptides, and proteins. Serratia marcescens, an emerging pathogen with growing clinical importance due to its intrinsic resistance to several classes of antibiotics, can cause an array of infections in immunocompromised individuals. To better control the spread of S. marcescens infections, it is critical to identify additional targets for bacterial growth inhibition. We found that extracellular metabolites produced by the wild-type organism in response to peroxide exposure had a protective effect on an otherwise-H2O2-sensitive ΔmacAB indicator strain. Detailed analysis of the conditioned medium demonstrated that the protective effect was associated with a low-molecular-weight heat-sensitive and proteinase K-sensitive metabolite. Furthermore, liquid chromatography-tandem mass spectrometry analysis of the low-molecular-weight proteins present in the conditioned medium led to identification of the previously uncharacterized DUF1471-containing protein TBU67220 (SrfN). We found that loss of the srfN gene did not have an impact on the production of extracellular enzymes. However, the S. marcescens mutant lacking SrfN was significantly more sensitive to growth in medium with a low pH and to exposure to oxidative stress. Both defects were fully rescued by complementation. Thus, our results indicate that SrfN, a low-molecular-weight DUF1471-containing protein, is involved in S. marcescens SM6 adaptation to adverse environmental conditions. IMPORTANCE Serratia marcescens is ubiquitous in the environment and can survive in water, soil, plants, insects, and animals, and it can also cause infections in humans. In the face of disturbances such as oxidative or low-pH stress, bacteria adapt, survive, and recover through several mechanisms, including changes in their secretome. We show that a hydrogen peroxide-exposed S. marcescens milieu contains a small previously uncharacterized DUF1471-containing protein similar to the SrfN protein in Salmonella enterica serovar Typhimurium, and we illustrate the role of this protein in bacterial survival during acid and oxidative stresses.
Collapse
|
3
|
Peng H, Zhou G, Yang XM, Chen GJ, Chen HB, Liao ZL, Zhong QP, Wang L, Fang X, Wang J. Transcriptomic Analysis Revealed Antimicrobial Mechanisms of Lactobacillus rhamnosus SCB0119 against Escherichia coli and Staphylococcus aureus. Int J Mol Sci 2022; 23:ijms232315159. [PMID: 36499483 PMCID: PMC9739798 DOI: 10.3390/ijms232315159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/26/2022] [Accepted: 11/27/2022] [Indexed: 12/03/2022] Open
Abstract
Lactic acid bacteria were reported as a promising alternative to antibiotics against pathogens. Among them, Lactobacillus rhamnosus could be used as probiotics and inhibit several pathogens, but its antibacterial mechanisms are still less known. Here, L. rhamnosus SCB0119 isolated from fermented pickles could inhibit bacterial growth or even cause cell death in Escherichia coli ATCC25922 and Staphylococcus aureus ATCC6538, which was mainly attributed to the cell-free culture supernatant (CFS). Moreover, CFS induced the accumulation of reactive oxygen species and destroyed the structure of the cell wall and membrane, including the deformation in cell shape and cell wall, the impairment of the integrity of the cell wall and inner membrane, and the increases in outer membrane permeability, the membrane potential, and pH gradient in E. coli and S. aureus. Furthermore, the transcriptomic analysis demonstrated that CFS altered the transcripts of several genes involved in fatty acid degradation, ion transport, and the biosynthesis of amino acids in E. coli, and fatty acid degradation, protein synthesis, DNA replication, and ATP hydrolysis in S. aureus, which are important for bacterial survival and growth. In conclusion, L. rhamnosus SCB0119 and its CFS could be used as a biocontrol agent against E. coli and S. aureus.
Collapse
Affiliation(s)
- Huan Peng
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Gang Zhou
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xi-Miao Yang
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Guo-Jun Chen
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Hai-Bin Chen
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhen-Lin Liao
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Qing-Ping Zhong
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Li Wang
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Xiang Fang
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (X.F.); (J.W.)
| | - Jie Wang
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (X.F.); (J.W.)
| |
Collapse
|
4
|
Huynh MS, Hooda Y, Li YR, Jagielnicki M, Lai CCL, Moraes TF. Reconstitution of surface lipoprotein translocation through the slam translocon. eLife 2022; 11:72822. [PMID: 35475756 PMCID: PMC9090332 DOI: 10.7554/elife.72822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Surface lipoproteins (SLPs) are peripherally attached to the outer leaflet of the outer membrane in many Gram-negative bacteria, playing significant roles in nutrient acquisition and immune evasion in the host. While the factors that are involved in the synthesis and delivery of SLPs in the inner membrane are well characterized, the molecular machinery required for the movement of SLPs to the surface are still not fully elucidated. In this study, we investigated the translocation of a SLP TbpB through a Slam1-dependent pathway. Using purified components, we developed an in vitro translocation assay where unfolded TbpB is transported through Slam1-containing proteoliposomes, confirming Slam1 as an outer membrane translocon. While looking to identify factors to increase translocation efficiency, we discovered the periplasmic chaperone Skp interacted with TbpB in the periplasm of Escherichia coli. The presence of Skp was found to increase the translocation efficiency of TbpB in the reconstituted translocation assays. A knockout of Skp in Neisseria meningitidis revealed that Skp is essential for functional translocation of TbpB to the bacterial surface. Taken together, we propose a pathway for surface destined lipoproteins, where Skp acts as a holdase for Slam-mediated TbpB translocation across the outer membrane.
Collapse
Affiliation(s)
- Minh Sang Huynh
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Yogesh Hooda
- MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
| | - Yuzi Raina Li
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | | | | | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, Canada
| |
Collapse
|
5
|
Wang X, Bernstein HD. The Escherichia coli outer membrane protein OmpA acquires secondary structure prior to its integration into the membrane. J Biol Chem 2022; 298:101802. [PMID: 35257747 PMCID: PMC8987393 DOI: 10.1016/j.jbc.2022.101802] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 11/25/2022] Open
Abstract
Almost all proteins that reside in the outer membrane (OM) of Gram-negative bacteria contain a membrane-spanning segment that folds into a unique β barrel structure and inserts into the membrane by an unknown mechanism. To obtain further insight into outer membrane protein (OMP) biogenesis, we revisited the surprising observation reported over 20 years ago that the Escherichia coli OmpA β barrel can be assembled into a native structure in vivo when it is expressed as two noncovalently linked fragments. Here, we show that disulfide bonds between β strand 4 in the N-terminal fragment and β strand 5 in the C-terminal fragment can form in the periplasmic space and greatly increase the efficiency of assembly of "split" OmpA, but only if the cysteine residues are engineered in perfect register (i.e., they are aligned in the fully folded β barrel). In contrast, we observed only weak disulfide bonding between β strand 1 in the N-terminal fragment and β strand 8 in the C-terminal fragment that would form a closed or circularly permutated β barrel. Our results not only demonstrate that β barrels begin to fold into a β-sheet-like structure before they are integrated into the OM but also help to discriminate among the different models of OMP biogenesis that have been proposed.
Collapse
Affiliation(s)
- Xu Wang
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Harris D Bernstein
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA.
| |
Collapse
|
6
|
Xue Z, Pang Y, Quan S. Revisiting the functions of periplasmic chaperones in the quality control of the autotransporter Ag43 using a phenotypically homogeneous Escherichia coli strain. Biochem Biophys Res Commun 2021; 591:37-43. [PMID: 34995984 DOI: 10.1016/j.bbrc.2021.12.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/28/2021] [Indexed: 11/02/2022]
Abstract
Antigen 43 is a surface-displayed autotransporter protein that mediates bacterial self-association and pathogenicity. The quality control factors that facilitate Ag43 crossing the periplasm and inserting into the outer membrane remain enigmatic, mostly because Ag43 is phase variable and associated with heterologous phenotypes, which obscures the mutational effects of potential quality control factors. Here, we describe a screening method that allowed us to isolate a subpopulation of Escherichia coli that consistently displays an Ag43-mediated autoaggregation phenotype. Based on this subpopulation, we analyzed how disruptions of known periplasmic chaperones affect Ag43 biogenesis. We found that only the disruption of surA reduced Ag43 levels and abolished the autoaggregation phenotype of cells, but surA disruption did not affect the phase-variable expression of agn43. Using purified proteins, we showed that SurA effectively protected the β-barrel domain of Ag43 from aggregation. In contrast, the previously reported Ag43 biogenesis factor OsmY showed weak chaperoning effects on Ag43 only in the absence of SurA. Our results shed light on the roles of different periplasmic chaperones in Ag43 biogenesis and provide a methodology applicable to the study of other phase-variable proteins.
Collapse
Affiliation(s)
- Zixiao Xue
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Yonghao Pang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai, 200237, China.
| |
Collapse
|
7
|
BonA from Acinetobacter baumannii Forms a Divisome-Localized Decamer That Supports Outer Envelope Function. mBio 2021; 12:e0148021. [PMID: 34311571 PMCID: PMC8406262 DOI: 10.1128/mbio.01480-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Acinetobacter baumannii is a high-risk pathogen due to the rapid global spread of multidrug-resistant lineages. Its phylogenetic divergence from other ESKAPE pathogens means that determinants of its antimicrobial resistance can be difficult to extrapolate from other widely studied bacteria. A recent study showed that A. baumannii upregulates production of an outer membrane lipoprotein, which we designate BonA, in response to challenge with polymyxins. Here, we show that BonA has limited sequence similarity and distinct structural features compared to lipoproteins from other bacterial species. Analyses through X-ray crystallography, small-angle X-ray scattering, electron microscopy, and multiangle light scattering demonstrate that BonA has a dual BON (Bacterial OsmY and Nodulation) domain architecture and forms a decamer via an unusual oligomerization mechanism. This analysis also indicates this decamer is transient, suggesting dynamic oligomerization plays a role in BonA function. Antisera recognizing BonA shows it is an outer membrane protein localized to the divisome. Loss of BonA modulates the density of the outer membrane, consistent with a change in its structure or link to the peptidoglycan, and prevents motility in a clinical strain (ATCC 17978). Consistent with these findings, the dimensions of the BonA decamer are sufficient to permeate the peptidoglycan layer, with the potential to form a membrane-spanning complex during cell division. IMPORTANCE The pathogen Acinetobacter baumannii is considered an urgent threat to human health. A. baumannii is highly resistant to treatment with antibiotics, in part due to its protective cell envelope. This bacterium is only distantly related to other bacterial pathogens, so its cell envelope has distinct properties and contains components distinct from those of other bacteria that support its function. Here, we report the discovery of BonA, a protein that supports A. baumannii outer envelope function and is required for cell motility. We determine the atomic structure of BonA and show that it forms part of the cell division machinery and functions by forming a complex, features that mirror those of distantly related homologs from other bacteria. By improving our understanding of the A. baumannii cell envelope this work will assist in treating this pathogen.
Collapse
|
8
|
Dautin N. Folding Control in the Path of Type 5 Secretion. Toxins (Basel) 2021; 13:341. [PMID: 34064645 PMCID: PMC8151025 DOI: 10.3390/toxins13050341] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 12/17/2022] Open
Abstract
The type 5 secretion system (T5SS) is one of the more widespread secretion systems in Gram-negative bacteria. Proteins secreted by the T5SS are functionally diverse (toxins, adhesins, enzymes) and include numerous virulence factors. Mechanistically, the T5SS has long been considered the simplest of secretion systems, due to the paucity of proteins required for its functioning. Still, despite more than two decades of study, the exact process by which T5SS substrates attain their final destination and correct conformation is not totally deciphered. Moreover, the recent addition of new sub-families to the T5SS raises additional questions about this secretion mechanism. Central to the understanding of type 5 secretion is the question of protein folding, which needs to be carefully controlled in each of the bacterial cell compartments these proteins cross. Here, the biogenesis of proteins secreted by the Type 5 secretion system is discussed, with a focus on the various factors preventing or promoting protein folding during biogenesis.
Collapse
Affiliation(s)
- Nathalie Dautin
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005 Paris, France
| |
Collapse
|
9
|
Ranava D, Yang Y, Orenday-Tapia L, Rousset F, Turlan C, Morales V, Cui L, Moulin C, Froment C, Munoz G, Rech J, Marcoux J, Caumont-Sarcos A, Albenne C, Bikard D, Ieva R. Lipoprotein DolP supports proper folding of BamA in the bacterial outer membrane promoting fitness upon envelope stress. eLife 2021; 10:67817. [PMID: 33847565 PMCID: PMC8081527 DOI: 10.7554/elife.67817] [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: 02/24/2021] [Accepted: 04/04/2021] [Indexed: 01/03/2023] Open
Abstract
In Proteobacteria, integral outer membrane proteins (OMPs) are crucial for the maintenance of the envelope permeability barrier to some antibiotics and detergents. In Enterobacteria, envelope stress caused by unfolded OMPs activates the sigmaE (σE) transcriptional response. σE upregulates OMP biogenesis factors, including the β-barrel assembly machinery (BAM) that catalyses OMP folding. Here we report that DolP (formerly YraP), a σE-upregulated and poorly understood outer membrane lipoprotein, is crucial for fitness in cells that undergo envelope stress. We demonstrate that DolP interacts with the BAM complex by associating with outer membrane-assembled BamA. We provide evidence that DolP is important for proper folding of BamA that overaccumulates in the outer membrane, thus supporting OMP biogenesis and envelope integrity. Notably, mid-cell recruitment of DolP had been linked to regulation of septal peptidoglycan remodelling by an unknown mechanism. We now reveal that, during envelope stress, DolP loses its association with the mid-cell, thereby suggesting a mechanistic link between envelope stress caused by impaired OMP biogenesis and the regulation of a late step of cell division.
Collapse
Affiliation(s)
- David Ranava
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yiying Yang
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Luis Orenday-Tapia
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - François Rousset
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
| | - Catherine Turlan
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Violette Morales
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Lun Cui
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
| | - Cyril Moulin
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Carine Froment
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Gladys Munoz
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jérôme Rech
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Anne Caumont-Sarcos
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Cécile Albenne
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - David Bikard
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
| | - Raffaele Ieva
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| |
Collapse
|
10
|
Bryant JA, Morris FC, Knowles TJ, Maderbocus R, Heinz E, Boelter G, Alodaini D, Colyer A, Wotherspoon PJ, Staunton KA, Jeeves M, Browning DF, Sevastsyanovich YR, Wells TJ, Rossiter AE, Bavro VN, Sridhar P, Ward DG, Chong ZS, Goodall EC, Icke C, Teo AC, Chng SS, Roper DI, Lithgow T, Cunningham AF, Banzhaf M, Overduin M, Henderson IR. Structure of dual BON-domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation. eLife 2020; 9:62614. [PMID: 33315009 PMCID: PMC7806268 DOI: 10.7554/elife.62614] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/11/2020] [Indexed: 12/16/2022] Open
Abstract
The Gram-negative outer-membrane envelops the bacterium and functions as a permeability barrier against antibiotics, detergents, and environmental stresses. Some virulence factors serve to maintain the integrity of the outer membrane, including DolP (formerly YraP) a protein of unresolved structure and function. Here, we reveal DolP is a lipoprotein functionally conserved amongst Gram-negative bacteria and that loss of DolP increases membrane fluidity. We present the NMR solution structure for Escherichia coli DolP, which is composed of two BON domains that form an interconnected opposing pair. The C-terminal BON domain binds anionic phospholipids through an extensive membrane:protein interface. This interaction is essential for DolP function and is required for sub-cellular localisation of the protein to the cell division site, providing evidence of subcellular localisation of these phospholipids within the outer membrane. The structure of DolP provides a new target for developing therapies that disrupt the integrity of the bacterial cell envelope.
Collapse
Affiliation(s)
- Jack Alfred Bryant
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Faye C Morris
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Timothy J Knowles
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Riyaz Maderbocus
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Eva Heinz
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Gabriela Boelter
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Dema Alodaini
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Adam Colyer
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Peter J Wotherspoon
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Kara A Staunton
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Mark Jeeves
- Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Douglas F Browning
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | | | - Timothy J Wells
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Amanda E Rossiter
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Vassiliy N Bavro
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Pooja Sridhar
- School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Douglas G Ward
- School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Zhi-Soon Chong
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Emily Ca Goodall
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,Institute for Molecular Bioscience, University of Queensland, St. Lucia, Australia
| | - Christopher Icke
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,Institute for Molecular Bioscience, University of Queensland, St. Lucia, Australia
| | - Alvin Ck Teo
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Shu-Sin Chng
- Department of Chemistry, National University of Singapore, Singapore, Singapore.,School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - David I Roper
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Trevor Lithgow
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Adam F Cunningham
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,Institute of Inflammation and Immunotherapy, University of Birmingham, Edgbaston, United Kingdom
| | - Manuel Banzhaf
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Michael Overduin
- School of Biosciences, University of Birmingham, Edgbaston, United Kingdom.,Department of Biochemistry, University of Alberta, Edmonton, Canada
| | - Ian R Henderson
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,Department of Chemistry, National University of Singapore, Singapore, Singapore
| |
Collapse
|
11
|
Lee C, Betschinger P, Wu K, Żyła DS, Glockshuber R, Bardwell JC. A metabolite binding protein moonlights as a bile-responsive chaperone. EMBO J 2020; 39:e104231. [PMID: 32882062 DOI: 10.15252/embj.2019104231] [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: 12/09/2019] [Revised: 07/12/2020] [Accepted: 07/17/2020] [Indexed: 12/27/2022] Open
Abstract
Bile salts are secreted into the gastrointestinal tract to aid in the absorption of lipids. In addition, bile salts show potent antimicrobial activity in part by mediating bacterial protein unfolding and aggregation. Here, using a protein folding sensor, we made the surprising discovery that the Escherichia coli periplasmic glycerol-3-phosphate (G3P)-binding protein UgpB can serve, in the absence of its substrate, as a potent molecular chaperone that exhibits anti-aggregation activity against bile salt-induced protein aggregation. The substrate G3P, which is known to accumulate in the later compartments of the digestive system, triggers a functional switch between UgpB's activity as a molecular chaperone and its activity as a G3P transporter. A UgpB mutant unable to bind G3P is constitutively active as a chaperone, and its crystal structure shows that it contains a deep surface groove absent in the G3P-bound wild-type UgpB. Our work illustrates how evolution may be able to convert threats into signals that first activate and then inactivate a chaperone at the protein level in a manner that bypasses the need for ATP.
Collapse
Affiliation(s)
- Changhan Lee
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Patrick Betschinger
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Kevin Wu
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.,Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Dawid S Żyła
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - James Ca Bardwell
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
12
|
Tsaplina O, Demidyuk I, Artamonova T, Khodorkovsky M, Khaitlina S. Cleavage of the outer membrane protein OmpX by protealysin regulates
Serratia proteamaculans
invasion. FEBS Lett 2020; 594:3095-3107. [DOI: 10.1002/1873-3468.13897] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/18/2020] [Accepted: 06/21/2020] [Indexed: 12/12/2022]
Affiliation(s)
| | | | - Tatiana Artamonova
- Peter the Great St. Petersburg Polytechnic University Saint‐Petersburg Russia
| | | | | |
Collapse
|
13
|
Bam complex-mediated assembly of bacterial outer membrane proteins synthesized in an in vitro translation system. Sci Rep 2020; 10:4557. [PMID: 32165713 PMCID: PMC7067875 DOI: 10.1038/s41598-020-61431-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 02/21/2020] [Indexed: 02/01/2023] Open
Abstract
Bacterial outer membrane proteins (OMPs) contain a unique "β barrel" segment that is inserted into the membrane by the barrel assembly machinery (Bam) complex by an unknown mechanism. OMP assembly has been reconstituted in vitro, but assembly reactions have involved the use of urea-denatured protein purified from inclusion bodies. Here we show that the E. coli Bam complex catalyzes the efficient assembly of OMPs synthesized de novo in a coupled in vitro transcription/translation system. Interestingly, the in vitro translated forms of the OMPs we analyzed were assembled more rapidly and were effectively engaged by fewer periplasmic chaperones than their urea-denatured counterparts. Taken together, our results strongly suggest that the mode of production influences the conformational states sampled by OMPs and thereby affects their recognition by both chaperones and the Bam complex. Besides providing insights into OMP biogenesis, our work describes a novel, streamlined method to reconstitute OMP assembly in vitro.
Collapse
|