1
|
Ostan NKH, Cole GB, Wang FZ, Reichheld SE, Moore G, Pan C, Yu R, Lai CCL, Sharpe S, Lee HO, Schryvers AB, Moraes TF. A secreted bacterial protein protects bacteria from cationic antimicrobial peptides by entrapment in phase-separated droplets. PNAS Nexus 2024; 3:pgae139. [PMID: 38633880 PMCID: PMC11022072 DOI: 10.1093/pnasnexus/pgae139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/26/2024] [Indexed: 04/19/2024]
Abstract
Mammalian hosts combat bacterial infections through the production of defensive cationic antimicrobial peptides (CAPs). These immune factors are capable of directly killing bacterial invaders; however, many pathogens have evolved resistance evasion mechanisms such as cell surface modification, CAP sequestration, degradation, or efflux. We have discovered that several pathogenic and commensal proteobacteria, including the urgent human threat Neisseria gonorrhoeae, secrete a protein (lactoferrin-binding protein B, LbpB) that contains a low-complexity anionic domain capable of inhibiting the antimicrobial activity of host CAPs. This study focuses on a cattle pathogen, Moraxella bovis, that expresses the largest anionic domain of the LbpB homologs. We used an exhaustive biophysical approach employing circular dichroism, biolayer interferometry, cross-linking mass spectrometry, microscopy, size-exclusion chromatography with multi-angle light scattering coupled to small-angle X-ray scattering (SEC-MALS-SAXS), and NMR to understand the mechanisms of LbpB-mediated protection against CAPs. We found that the anionic domain of this LbpB displays an α-helical secondary structure but lacks a rigid tertiary fold. The addition of antimicrobial peptides derived from lactoferrin (i.e. lactoferricin) to the anionic domain of LbpB or full-length LbpB results in the formation of phase-separated droplets of LbpB together with the antimicrobial peptides. The droplets displayed a low rate of diffusion, suggesting that CAPs become trapped inside and are no longer able to kill bacteria. Our data suggest that pathogens, like M. bovis, leverage anionic intrinsically disordered domains for the broad recognition and neutralization of antimicrobials via the formation of biomolecular condensates.
Collapse
Affiliation(s)
- Nicholas K H Ostan
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gregory B Cole
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Flora Zhiqi Wang
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sean E Reichheld
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Gaelen Moore
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Chuxi Pan
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ronghua Yu
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada
| | | | - Simon Sharpe
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Hyun O Lee
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anthony B Schryvers
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| |
Collapse
|
2
|
Maunders EA, Giles MW, Ganio K, Cunningham BA, Bennett-Wood V, Cole GB, Ng D, Lai CC, Neville SL, Moraes TF, McDevitt CA, Tan A. Zinc acquisition and its contribution to Klebsiella pneumoniae virulence. Front Cell Infect Microbiol 2024; 13:1322973. [PMID: 38249299 PMCID: PMC10797113 DOI: 10.3389/fcimb.2023.1322973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/08/2023] [Indexed: 01/23/2024] Open
Abstract
Klebsiella pneumoniae is a World Health Organization priority pathogen and a significant clinical concern for infections of the respiratory and urinary tracts due to widespread and increasing resistance to antimicrobials. In the absence of a vaccine, there is an urgent need to identify novel targets for therapeutic development. Bacterial pathogens, including K. pneumoniae, require the d-block metal ion zinc as an essential micronutrient, which serves as a cofactor for ~6% of the proteome. During infection, zinc acquisition necessitates the use of high affinity uptake systems to overcome niche-specific zinc limitation and host-mediated nutritional immunity. Here, we report the identification of ZnuCBA and ZniCBA, two ATP-binding cassette permeases that are highly conserved in Klebsiella species and contribute to K. pneumoniae AJ218 zinc homeostasis, and the high-resolution structure of the zinc-recruiting solute-binding protein ZniA. The Znu and Zni permeases appear functionally redundant with abrogation of both systems required to reduce K. pneumoniae zinc accumulation. Disruption of both systems also exerted pleiotropic effects on the homeostasis of other d-block elements. Zinc limitation perturbed K. pneumoniae cell morphology and compromised resistance to stressors, such as salt and oxidative stress. The mutant strain lacking both systems showed significantly impaired virulence in acute lung infection models, highlighting the necessity of zinc acquisition in the virulence and pathogenicity of K. pneumoniae.
Collapse
Affiliation(s)
- Eve A. Maunders
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Matthew W. Giles
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Katherine Ganio
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Bliss A. Cunningham
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Vicki Bennett-Wood
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Gregory B. Cole
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Dixon Ng
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Christine C. Lai
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Stephanie L. Neville
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Trevor F. Moraes
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Aimee Tan
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|
3
|
Awate OA, Ng D, Stoudenmire JL, Moraes TF, Cornelissen CN. Investigating the importance of surface exposed loops in the gonococcal HpuB transporter for hemoglobin binding and utilization. bioRxiv 2023:2023.10.30.564842. [PMID: 37961140 PMCID: PMC10634946 DOI: 10.1101/2023.10.30.564842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Neisseria gonorrhoeae is the etiological agent of the sexually-transmitted infection gonorrhea and a global health challenge since no protective immunity results from infection and far fewer treatment options are available with increasing antimicrobial resistance. With no efficacious vaccines, researchers are exploring new targets for vaccine development and innovative therapeutics. The outer membrane TonB-dependent transporters (TdTs) produced by N. gonorrhoeae are considered promising antigen targets as they are highly conserved and play crucial roles in overcoming nutritional immunity. One of these TdTs, the hemoglobin transport system comprised of HpuA and HpuB, allows N. gonorrhoeae to acquire iron from hemoglobin (hHb). In the current study, mutations in the hpuB gene were generated to better understand the structure-function relationships in HpuB. This study is one of the first to demonstrate that N. gonorrhoeae can bind to and utilize hemoglobin produced by animals other than humans. This study also determined that when HpuA is absent, mutations targeting extracellular loop 7 of HpuB led to defective hHb binding and utilization. However, when the lipoprotein HpuA is present, these loop 7 mutants recovered their ability to bind hHB, although their growth phenotype remained significantly impaired. Interestingly, loop 7 contains putative heme binding motifs and a hypothetical α-helical region. Taken together, these results highlight the importance of loop 7 in the functionality of HpuB in binding hHb, and extracting and internalizing iron.
Collapse
|
4
|
Ng D, Moraes TF. Dynamic players and intricate interactions: An integrated investigation of the Mla lipid transport system. J Biol Chem 2023; 299:105146. [PMID: 37562569 PMCID: PMC10474453 DOI: 10.1016/j.jbc.2023.105146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2023] [Indexed: 08/12/2023] Open
Abstract
The Maintenance of outer membrane (OM) Lipid Asymmetry system mediates retrograde phospholipid transport from the OM to the inner membrane (IM) in Gram-negative bacteria. However, the interactions between the various subunits of the IM and OM complexes are not well understood. In a recent study in 2023 by MacRae et al. in the Journal of Biological Chemistry, the authors examine components in the Maintenance of OM Lipid Asymmetry complex, define the interaction interfaces between members of the pathway, and propose a molecular model of the lipid transfer process from the OM to the IM that will help elucidate intricacies of lipid transport.
Collapse
Affiliation(s)
- Dixon Ng
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
5
|
Ferguson MR, Delgado KN, McBride S, Orbe IC, La Vake CJ, Caimano MJ, Mendez Q, Moraes TF, Schryvers AB, Moody MA, Radolf JD, Weiner MP, Hawley KL. Use of Epivolve phage display to generate a monoclonal antibody with opsonic activity directed against a subdominant epitope on extracellular loop 4 of Treponema pallidum BamA (TP0326). Front Immunol 2023; 14:1222267. [PMID: 37675118 PMCID: PMC10478084 DOI: 10.3389/fimmu.2023.1222267] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/19/2023] [Indexed: 09/08/2023] Open
Abstract
Introduction Syphilis, a sexually transmitted infection caused by the spirochete Treponema pallidum (Tp), is resurging globally. Tp's repertoire of outer membrane proteins (OMPs) includes BamA (β-barrel assembly machinery subunit A/TP0326), a bipartite protein consisting of a 16-stranded β-barrel with nine extracellular loops (ECLs) and five periplasmic POTRA (polypeptide transport-associated) domains. BamA ECL4 antisera promotes internalization of Tp by rabbit peritoneal macrophages. Methods Three overlapping BamA ECL4 peptides and a two-stage, phage display strategy, termed "Epivolve" (for epitope evolution) were employed to generate single-chain variable fragments (scFvs). Additionally, antisera generated by immunizing mice and rabbits with BamA ECL4 displayed by a Pyrococcus furiosus thioredoxin scaffold (PfTrxBamA/ECL4). MAbs and antisera reactivities were evaluated by immunoblotting and ELISA. A comparison of murine and rabbit opsonophagocytosis assays was conducted to evaluate the functional ability of the Abs (e.g., opsonization) and validate the mouse assay. Sera from Tp-infected mice (MSS) and rabbits (IRS) were evaluated for ECL4-specific Abs using PfTrxBamA/ECL4 and overlapping ECL4 peptides in immunoblotting and ELISA assays. Results Each of the five mAbs demonstrated reactivity by immunoblotting and ELISA to nanogram amounts of PfTrxBamA/ECL4. One mAb, containing a unique amino acid sequence in both the light and heavy chains, showed activity in the murine opsonophagocytosis assay. Mice and rabbits hyperimmunized with PfTrxBamA/ECL4 produced opsonic antisera that strongly recognized the ECL presented in a heterologous scaffold and overlapping ECL4 peptides, including S2. In contrast, Abs generated during Tp infection of mice and rabbits poorly recognized the peptides, indicating that S2 contains a subdominant epitope. Discussion Epivolve produced mAbs target subdominant opsonic epitopes in BamA ECL4, a top syphilis vaccine candidate. The murine opsonophagocytosis assay can serve as an alternative model to investigate the opsonic potential of vaccinogens. Detailed characterization of BamA ECL4-specific Abs provided a means to dissect Ab responses elicited by Tp infection.
Collapse
Affiliation(s)
- Mary R. Ferguson
- Department of Molecular Sciences, Abbratech, Branford, CT, United States
| | | | | | - Isabel C. Orbe
- Department of Pediatrics, UConn Health, Farmington, CT, United States
| | - Carson J. La Vake
- Department of Pediatrics, UConn Health, Farmington, CT, United States
| | - Melissa J. Caimano
- Department of Medicine, UConn Health, Farmington, CT, United States
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Qiana Mendez
- Department of Molecular Sciences, Abbratech, Branford, CT, United States
| | - Trevor F. Moraes
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Anthony B. Schryvers
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - M. Anthony Moody
- Duke Human Vaccine Institute, Durham, NC, United States
- Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
- Department of Integrative Immunobiology, Duke University Medical Center, Durham, NC, United States
| | - Justin D. Radolf
- Department of Medicine, UConn Health, Farmington, CT, United States
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
- Department of Immunology, UConn Health, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, United States
| | - Michael P. Weiner
- Department of Molecular Sciences, Abbratech, Branford, CT, United States
| | - Kelly L. Hawley
- Department of Medicine, UConn Health, Farmington, CT, United States
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Immunology, UConn Health, Farmington, CT, United States
- Division of Infectious Diseases and Immunology, Connecticut Children’s, Hartford, CT, United States
| |
Collapse
|
6
|
Islam EA, Fegan JE, Tefera TA, Curran DM, Waeckerlin RC, Ng D, Ahn SK, Lai CHR, Nguyen QH, Shah M, Tesfaw L, Adamu K, Medhin WW, Legesse A, Deresse G, Getachew B, Rawlyk N, Evans B, Potter A, Schryvers AB, Gray-Owen SD, Moraes TF. Reverse vaccinology-based identification of a novel surface lipoprotein that is an effective vaccine antigen against bovine infections caused by Pasteurella multocida. PLoS Pathog 2023; 19:e1011249. [PMID: 36961851 PMCID: PMC10075479 DOI: 10.1371/journal.ppat.1011249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 04/05/2023] [Accepted: 02/27/2023] [Indexed: 03/25/2023] Open
Abstract
Pasteurella multocida can infect a multitude of wild and domesticated animals, with infections in cattle resulting in hemorrhagic septicemia (HS) or contributing to bovine respiratory disease (BRD) complex. Current cattle vaccines against P. multocida consist of inactivated bacteria, which only offer limited and serogroup specific protection. Here, we describe a newly identified surface lipoprotein, PmSLP, that is present in nearly all annotated P. multocida strains isolated from cattle. Bovine associated variants span three of the four identified phylogenetic clusters, with PmSLP-1 and PmSLP-2 being restricted to BRD associated isolates and PmSLP-3 being restricted to isolates associated with HS. Recombinantly expressed, soluble PmSLP-1 (BRD-PmSLP) and PmSLP-3 (HS-PmSLP) vaccines were both able to provide full protection in a mouse sepsis model against the matched P. multocida strain, however no cross-protection and minimal serum IgG cross-reactivity was identified. Full protection against both challenge strains was achieved with a bivalent vaccine containing both BRD-PmSLP and HS-PmSLP, with serum IgG from immunized mice being highly reactive to both variants. Year-long stability studies with lyophilized antigen stored under various temperatures show no appreciable difference in biophysical properties or loss of efficacy in the mouse challenge model. PmSLP-1 and PmSLP-3 vaccines were each evaluated for immunogenicity in two independent cattle trials involving animals of different age ranges and breeds. In all four trials, vaccination with PmSLP resulted in an increase in antigen specific serum IgG over baseline. In a blinded cattle challenge study with a recently isolated HS strain, the matched HS-PmSLP vaccine showed strong efficacy (75-87.5% survival compared to 0% in the control group). Together, these data suggest that cattle vaccines composed of PmSLP antigens can be a practical and effective solution for preventing HS and BRD related P. multocida infections.
Collapse
Affiliation(s)
- Epshita A Islam
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jamie E Fegan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Takele A Tefera
- Department of Veterinary Bacteriology, National Veterinary Institute, Bishoftu, Ethiopia
| | - David M Curran
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Regula C Waeckerlin
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Dixon Ng
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Sang Kyun Ahn
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Chun Heng Royce Lai
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Quynh Huong Nguyen
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Megha Shah
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Liyuwork Tesfaw
- Department of Veterinary Bacteriology, National Veterinary Institute, Bishoftu, Ethiopia
| | - Kassaye Adamu
- Department of Veterinary Bacteriology, National Veterinary Institute, Bishoftu, Ethiopia
| | - Wubet W Medhin
- Department of Veterinary Bacteriology, National Veterinary Institute, Bishoftu, Ethiopia
| | - Abinet Legesse
- Department of Veterinary Bacteriology, National Veterinary Institute, Bishoftu, Ethiopia
| | - Getaw Deresse
- Department of Veterinary Bacteriology, National Veterinary Institute, Bishoftu, Ethiopia
| | - Belayneh Getachew
- Department of Veterinary Bacteriology, National Veterinary Institute, Bishoftu, Ethiopia
| | - Neil Rawlyk
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Brock Evans
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Andrew Potter
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Anthony B Schryvers
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Scott D Gray-Owen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
7
|
Hwang S, Shah M, Garcia B, Hashem N, Davidson AR, Moraes TF, Maxwell KL. Anti-CRISPR Protein AcrIIC5 Inhibits CRISPR-Cas9 by Occupying the Target DNA Binding Pocket. J Mol Biol 2023; 435:167991. [PMID: 36736884 DOI: 10.1016/j.jmb.2023.167991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/10/2023] [Accepted: 01/24/2023] [Indexed: 02/04/2023]
Abstract
Anti-CRISPR proteins inhibit CRISPR-Cas immune systems through diverse mechanisms. Previously, the anti-CRISPR protein AcrIIC5Smu was shown to potently inhibit a type II-C Cas9 from Neisseria meningitidis (Nme1Cas9). In this work, we explore the mechanism of activity of the AcrIIC5 homologue from Neisseria chenwenguii (AcrIIC5Nch) and show that it prevents Cas9 binding to target DNA. We show that AcrIIC5Nch targets the PAM-interacting domain (PID) of Nme1Cas9 for inhibition, agreeing with previous findings for AcrIIC5Smu, and newly establish that strong binding of the anti-CRISPR requires guide RNA be pre-loaded on Cas9. We determined the crystal structure of AcrIIC5Nch using X-ray crystallography and identified amino acid residues that are critical for its function. Using a protein docking algorithm we show that AcrIIC5Nch likely occupies the Cas9 DNA binding pocket, thereby inhibiting target DNA binding through a mechanism similar to that previously described for AcrIIA2 and AcrIIA4.
Collapse
Affiliation(s)
- Sungwon Hwang
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario M5G 1M1, Canada. https://twitter.com/s1hwang_21
| | - Megha Shah
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario M5G 1M1, Canada
| | - Bianca Garcia
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario M5G 1M1, Canada
| | - Noor Hashem
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario M5G 1M1, Canada
| | - Alan R Davidson
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario M5G 1M1, Canada; Department of Molecular Genetics, University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario M5G 1M1, Canada. https://twitter.com/ARDavidson_UofT
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario M5G 1M1, Canada. https://twitter.com/MoraesTrevor
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario M5G 1M1, Canada.
| |
Collapse
|
8
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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
|
9
|
Hwang S, Pan C, Garcia B, Davidson AR, Moraes TF, Maxwell KL. Structural and mechanistic insight into CRISPR-Cas9 inhibition by anti-CRISPR protein AcrIIC4 Hpa. J Mol Biol 2021; 434:167420. [PMID: 34954237 DOI: 10.1016/j.jmb.2021.167420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/16/2021] [Accepted: 12/18/2021] [Indexed: 11/25/2022]
Abstract
Phages, plasmids, and other mobile genetic elements express inhibitors of CRISPR-Cas immune systems, known as anti-CRISPR proteins, to protect themselves from targeted destruction. These anti-CRISPR proteins have been shown to function through very diverse mechanisms. In this work we investigate the activity of an anti-CRISPR isolated from a prophage in Haemophilus parainfluenzae that blocks CRISPR-Cas9 DNA cleavage activity. We determine the three-dimensional crystal structure of AcrIIC4Hpa and show that it binds to the Cas9 Recognition Domain. This binding does not prevent the Cas9-anti-CRISPR complex from interacting with target DNA but does inhibit DNA cleavage. AcrIIC4Hpa likely acts by blocking the conformational changes that allow the HNH and RuvC endonuclease domains to contact the DNA sites to be nicked.
Collapse
Affiliation(s)
| | | | - Bianca Garcia
- Department of Molecular Genetics. University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario, M5G 1M1, Canada
| | - Alan R Davidson
- Department of Biochemistry; Department of Molecular Genetics. University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario, M5G 1M1, Canada
| | | | | |
Collapse
|
10
|
Bateman TJ, Shah M, Ho TP, Shin HE, Pan C, Harris G, Fegan JE, Islam EA, Ahn SK, Hooda Y, Gray-Owen SD, Chen W, Moraes TF. A Slam-dependent hemophore contributes to heme acquisition in the bacterial pathogen Acinetobacter baumannii. Nat Commun 2021; 12:6270. [PMID: 34725337 PMCID: PMC8560813 DOI: 10.1038/s41467-021-26545-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 10/06/2021] [Indexed: 12/02/2022] Open
Abstract
Nutrient acquisition systems are often crucial for pathogen growth and survival during infection, and represent attractive therapeutic targets. Here, we study the protein machinery required for heme uptake in the opportunistic pathogen Acinetobacter baumannii. We show that the hemO locus, which includes a gene encoding the heme-degrading enzyme, is required for high-affinity heme acquisition from hemoglobin and serum albumin. The hemO locus includes a gene coding for a heme scavenger (HphA), which is secreted by a Slam protein. Furthermore, heme uptake is dependent on a TonB-dependent receptor (HphR), which is important for survival and/or dissemination into the vasculature in a mouse model of pulmonary infection. Our results indicate that A. baumannii uses a two-component receptor system for the acquisition of heme from host heme reservoirs.
Collapse
Affiliation(s)
- Thomas J Bateman
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Megha Shah
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Timothy Pham Ho
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | | | - Chuxi Pan
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Greg Harris
- National Research Council Canada, Human Health Therapeutics (HHT) Research Center, Ottawa, ON, Canada
| | - Jamie E Fegan
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Epshita A Islam
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Sang Kyun Ahn
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Yogesh Hooda
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Scott D Gray-Owen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Wangxue Chen
- National Research Council Canada, Human Health Therapeutics (HHT) Research Center, Ottawa, ON, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
11
|
Pan C, Zimmer A, Shah M, Huynh MS, Lai CCL, Sit B, Hooda Y, Curran DM, Moraes TF. Actinobacillus utilizes a binding protein-dependent ABC transporter to acquire the active form of vitamin B 6. J Biol Chem 2021; 297:101046. [PMID: 34358566 PMCID: PMC8427247 DOI: 10.1016/j.jbc.2021.101046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 07/28/2021] [Accepted: 08/02/2021] [Indexed: 12/02/2022] Open
Abstract
Bacteria require high-efficiency uptake systems to survive and proliferate in nutrient-limiting environments, such as those found in host organisms. ABC transporters in the bacterial plasma membrane provide a mechanism for transport of many substrates. In this study, we examine an operon containing a periplasmic binding protein in Actinobacillus for its potential role in nutrient acquisition. The electron density map of 1.76 Å resolution obtained from the crystal structure of the periplasmic binding protein was best fit with a molecular model containing a pyridoxal-5'-phosphate (P5P/pyridoxal phosphate/the active form of vitamin B6) ligand within the protein's binding site. The identity of the P5P bound to this periplasmic binding protein was verified by isothermal titration calorimetry, microscale thermophoresis, and mass spectrometry, leading us to name the protein P5PA and the operon P5PAB. To illustrate the functional utility of this uptake system, we introduced the P5PAB operon from Actinobacillus pleuropneumoniae into an Escherichia coli K-12 strain that was devoid of a key enzyme required for P5P synthesis. The growth of this strain at low levels of P5P supports the functional role of this operon in P5P uptake. This is the first report of a dedicated P5P bacterial uptake system, but through bioinformatics, we discovered homologs mainly within pathogenic representatives of the Pasteurellaceae family, suggesting that this operon exists more widely outside the Actinobacillus genus.
Collapse
Affiliation(s)
- Chuxi Pan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Alexandra Zimmer
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Megha Shah
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Minh Sang Huynh
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Brandon Sit
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yogesh Hooda
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - David M Curran
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
12
|
Abstract
In this short review, we outline the major events that led to the development of iron acquisition systems in Gram-negative bacteria and mammals since the beginning of life on earth. Naturally, the interaction between these organisms led to the development of a wonderfully complex set of protein systems used for competition over a once prevalent (but no longer) biocatalytic cofactor. These events led to the appearance of the lactoferrin gene, which has since been exploited into adopting countless new functions, including the provision of highly bactericidal degradation products. In parallel to lactoferrin's evolution, evolving bacterial receptors have countered the bactericidal properties of this innate immunity protein.
Collapse
Affiliation(s)
- Nicholas K H Ostan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Anthony B Schryvers
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
13
|
Shah M, Taylor VL, Bona D, Tsao Y, Stanley SY, Pimentel-Elardo SM, McCallum M, Bondy-Denomy J, Howell PL, Nodwell JR, Davidson AR, Moraes TF, Maxwell KL. A phage-encoded anti-activator inhibits quorum sensing in Pseudomonas aeruginosa. Mol Cell 2021; 81:571-583.e6. [PMID: 33412111 DOI: 10.1016/j.molcel.2020.12.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/19/2020] [Accepted: 12/03/2020] [Indexed: 11/28/2022]
Abstract
The arms race between bacteria and phages has led to the evolution of diverse anti-phage defenses, several of which are controlled by quorum-sensing pathways. In this work, we characterize a quorum-sensing anti-activator protein, Aqs1, found in Pseudomonas phage DMS3. We show that Aqs1 inhibits LasR, the master regulator of quorum sensing, and present the crystal structure of the Aqs1-LasR complex. The 69-residue Aqs1 protein also inhibits PilB, the type IV pilus assembly ATPase protein, which blocks superinfection by phages that require the pilus for infection. This study highlights the remarkable ability of small phage proteins to bind multiple host proteins and disrupt key biological pathways. As quorum sensing influences various anti-phage defenses, Aqs1 provides a mechanism by which infecting phages might simultaneously dampen multiple defenses. Because quorum-sensing systems are broadly distributed across bacteria, this mechanism of phage counter-defense may play an important role in phage-host evolutionary dynamics.
Collapse
Affiliation(s)
- Megha Shah
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Véronique L Taylor
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Diane Bona
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Yvonne Tsao
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Sabrina Y Stanley
- Department of Molecular Genetics, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Sheila M Pimentel-Elardo
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Matthew McCallum
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - P Lynne Howell
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Justin R Nodwell
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Alan R Davidson
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Department of Molecular Genetics, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, MaRS West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
| |
Collapse
|
14
|
Cole GB, Bateman TJ, Moraes TF. The surface lipoproteins of gram-negative bacteria: Protectors and foragers in harsh environments. J Biol Chem 2021; 296:100147. [PMID: 33277359 PMCID: PMC7857515 DOI: 10.1074/jbc.rev120.008745] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 11/06/2022] Open
Abstract
Gram-negative pathogens are enveloped by an outer membrane that serves as a double-edged sword: On the one hand, it provides a layer of protection for the bacterium from environmental insults, including other bacteria and the host immune system. On the other hand, it restricts movement of vital nutrients into the cell and provides a plethora of antigens that can be detected by host immune systems. One strategy used to overcome these limitations is the decoration of the outer surface of gram-negative bacteria with proteins tethered to the outer membrane through a lipid anchor. These surface lipoproteins (SLPs) fulfill critical roles in immune evasion and nutrient acquisition, but as more bacterial genomes are sequenced, we are beginning to discover their prevalence and their different roles and mechanisms and importantly how we can exploit them as antimicrobial targets. This review will focus on representative SLPs that gram-negative bacteria use to overcome host innate immunity, specifically the areas of nutritional immunity and complement system evasion. We elaborate on the structures of some notable SLPs required for binding target molecules in hosts and how this information can be used alongside bioinformatics to understand mechanisms of binding and in the discovery of new SLPs. This information provides a foundation for the development of therapeutics and the design of vaccine antigens.
Collapse
Affiliation(s)
- Gregory B Cole
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Thomas J Bateman
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
15
|
Chen A, Arora PD, Lai CC, Copeland JW, Moraes TF, McCulloch CA, Lavoie BD, Wilde A. The scaffold-protein IQGAP1 enhances and spatially restricts the actin-nucleating activity of Diaphanous-related formin 1 (DIAPH1). J Biol Chem 2020; 295:3134-3147. [PMID: 32005666 DOI: 10.1074/jbc.ra119.010476] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 01/24/2020] [Indexed: 11/06/2022] Open
Abstract
The actin cytoskeleton is a dynamic array of filaments that undergoes rapid remodeling to drive many cellular processes. An essential feature of filament remodeling is the spatio-temporal regulation of actin filament nucleation. One family of actin filament nucleators, the Diaphanous-related formins, is activated by the binding of small G-proteins such as RhoA. However, RhoA only partially activates formins, suggesting that additional factors are required to fully activate the formin. Here we identify one such factor, IQ motif containing GTPase activating protein-1 (IQGAP1), which enhances RhoA-mediated activation of the Diaphanous-related formin (DIAPH1) and targets DIAPH1 to the plasma membrane. We find that the inhibitory intramolecular interaction within DIAPH1 is disrupted by the sequential binding of RhoA and IQGAP1. Binding of RhoA and IQGAP1 robustly stimulates DIAPH1-mediated actin filament nucleation in vitro In contrast, the actin capping protein Flightless-I, in conjunction with RhoA, only weakly stimulates DIAPH1 activity. IQGAP1, but not Flightless-I, is required to recruit DIAPH1 to the plasma membrane where actin filaments are generated. These results indicate that IQGAP1 enhances RhoA-mediated activation of DIAPH1 in vivo Collectively these data support a model where the combined action of RhoA and an enhancer ensures the spatio-temporal regulation of actin nucleation to stimulate robust and localized actin filament production in vivo.
Collapse
Affiliation(s)
- Anan Chen
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Pam D Arora
- Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Christine C Lai
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - John W Copeland
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | | | - Brigitte D Lavoie
- Department Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Andrew Wilde
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada; Department Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada.
| |
Collapse
|
16
|
Thavalingam A, Cheng Z, Garcia B, Huang X, Shah M, Sun W, Wang M, Harrington L, Hwang S, Hidalgo-Reyes Y, Sontheimer EJ, Doudna J, Davidson AR, Moraes TF, Wang Y, Maxwell KL. Inhibition of CRISPR-Cas9 ribonucleoprotein complex assembly by anti-CRISPR AcrIIC2. Nat Commun 2019; 10:2806. [PMID: 31243272 PMCID: PMC6594998 DOI: 10.1038/s41467-019-10577-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 05/15/2019] [Indexed: 01/25/2023] Open
Abstract
CRISPR-Cas adaptive immune systems function to protect bacteria from invasion by foreign genetic elements. The CRISPR-Cas9 system has been widely adopted as a powerful genome-editing tool, and phage-encoded inhibitors, known as anti-CRISPRs, offer a means of regulating its activity. Here, we report the crystal structures of anti-CRISPR protein AcrIIC2Nme alone and in complex with Nme1Cas9. We demonstrate that AcrIIC2Nme inhibits Cas9 through interactions with the positively charged bridge helix, thereby preventing sgRNA loading. In vivo phage plaque assays and in vitro DNA cleavage assays show that AcrIIC2Nme mediates its activity through a large electronegative surface. This work shows that anti-CRISPR activity can be mediated through the inhibition of Cas9 complex assembly.
Collapse
Affiliation(s)
- Annoj Thavalingam
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Zhi Cheng
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bianca Garcia
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Xue Huang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,Hefei National Research Center for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Megha Shah
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Wei Sun
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Min Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lucas Harrington
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Sungwon Hwang
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Yurima Hidalgo-Reyes
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Jennifer Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, CA, 94704, USA.,Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA.,Department of Chemistry, University of California, Berkeley, CA, 94720, USA.,Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Alan R Davidson
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada.,Department of Molecular Genetics, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Yanli Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada.
| |
Collapse
|
17
|
Fegan JE, Calmettes C, Islam EA, Ahn SK, Chaudhuri S, Yu RH, Gray-Owen SD, Moraes TF, Schryvers AB. Utility of Hybrid Transferrin Binding Protein Antigens for Protection Against Pathogenic Neisseria Species. Front Immunol 2019; 10:247. [PMID: 30837995 PMCID: PMC6389628 DOI: 10.3389/fimmu.2019.00247] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/29/2019] [Indexed: 01/03/2023] Open
Abstract
The surface transferrin receptor proteins from Neisseria gonorrhoeae have been recognized as ideal vaccine targets due to their critical role in survival in the human male genitourinary tract. Recombinant forms of the surface lipoprotein component of the receptor, transferrin binding protein B (TbpB), can be readily produced at high levels in the Escherichia coli cytoplasm and is suitable for commercial vaccine production. In contrast, the integral outer membrane protein, transferrin binding protein A (TbpA), is produced at relatively low levels in the outer membrane and requires detergents for solubilization and stabilization, processes not favorable for commercial applications. Capitalizing on the core β-barrel structural feature common to the lipoprotein and integral outer membrane protein we engineered the lipoprotein as a scaffold for displaying conserved surface epitopes from TbpA. A stable version of the C-terminal domain of TbpB was prepared by replacing four larger exposed variable loops with short linking peptide regions. Four surface regions from the plug and barrel domains of Neisseria TbpA were transplanted onto this TbpB C-lobe scaffold, generating stable hybrid antigens. Antisera generated in mice and rabbits against the hybrid antigens recognized TbpA at the surface of Neisseria meningitidis and inhibited transferrin-dependent growth at levels comparable or better than antisera directed against the native TbpA protein. Two of the engineered hybrid antigens each elicited a TbpA-specific bactericidal antibody response comparable to that induced by TbpA. A hybrid antigen generated using a foreign scaffold (TbpB from the pig pathogen Haemophilus parasuis) displaying neisserial TbpA loop 10 was evaluated in a model of lower genital tract colonization by N. gonorrhoeae and a model of invasive infection by N. meningitidis. The loop 10 hybrid antigen was as effective as full length TbpA in eliminating N. gonorrhoeae from the lower genital tract of female mice and was protective against the low dose invasive infection by N. meningitidis. These results demonstrate that TbpB or its derivatives can serve as an effective scaffold for displaying surface epitopes of integral outer membrane antigens and these antigens can elicit protection against bacterial challenge.
Collapse
Affiliation(s)
- Jamie E Fegan
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Charles Calmettes
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Epshita A Islam
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Sang Kyun Ahn
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Somshukla Chaudhuri
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Rong-Hua Yu
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Scott D Gray-Owen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Anthony B Schryvers
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
18
|
Bateman TJ, Shah M, Hooda Y, Moraes TF. Investigation of a novel Slam-dependent heme acquisition system in the bacterial pathogen Acinetobacter baumannii. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318097507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
19
|
Abstract
The human solute carriers (SLCs) comprise over 400 different transporters, organized into 65 families ( http://slc.bioparadigms.org/ ) based on their sequence homology and transport function. SLCs are responsible for transporting extraordinarily diverse solutes across biological membranes, including inorganic ions, amino acids, lipids, sugars, neurotransmitters and drugs. Most of these membrane proteins function as coupled symporters (co-transporters) utilizing downhill ion (H+ or Na+) gradients as the driving force for the transport of substrate against its concentration gradient into cells. Other members work as antiporters (exchangers) that typically contain a single substrate-binding site with an alternating access mode of transport, while a few members exhibit channel-like properties. Dysfunction of SLCs is correlated with numerous human diseases and therefore they are potential therapeutic drug targets. In this review, we identified all of the SLC crystal structures that have been determined, most of which are from prokaryotic species. We further sorted all the SLC structures into four main groups with different protein folds and further discuss the well-characterized MFS (major facilitator superfamily) and LeuT (leucine transporter) folds. This review provides a systematic analysis of the structure, molecular basis of substrate recognition and mechanism of action in different SLC family members.
Collapse
Affiliation(s)
- Xiaoyun Bai
- a Department of Biochemistry , University of Toronto , Toronto , Canada
| | - Trevor F Moraes
- a Department of Biochemistry , University of Toronto , Toronto , Canada
| | | |
Collapse
|
20
|
Hooda Y, Lai CCL, Moraes TF. Identification of a Large Family of Slam-Dependent Surface Lipoproteins in Gram-Negative Bacteria. Front Cell Infect Microbiol 2017; 7:207. [PMID: 28620585 PMCID: PMC5449769 DOI: 10.3389/fcimb.2017.00207] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/09/2017] [Indexed: 02/01/2023] Open
Abstract
The surfaces of many Gram-negative bacteria are decorated with soluble proteins anchored to the outer membrane via an acylated N-terminus; these proteins are referred to as surface lipoproteins or SLPs. In Neisseria meningitidis, SLPs such as transferrin-binding protein B (TbpB) and factor-H binding protein (fHbp) are essential for host colonization and infection because of their essential roles in iron acquisition and immune evasion, respectively. Recently, we identified a family of outer membrane proteins called Slam (Surface lipoprotein assembly modulator) that are essential for surface display of neisserial SLPs. In the present study, we performed a bioinformatics analysis to identify 832 Slam related sequences in 638 Gram-negative bacterial species. The list included several known human pathogens, many of which were not previously reported to possess SLPs. Hypothesizing that genes encoding SLP substrates of Slams may be present in the same gene cluster as the Slam genes, we manually curated neighboring genes for 353 putative Slam homologs. From our analysis, we found that 185 (~52%) of the 353 putative Slam homologs are located adjacent to genes that encode a protein with an N-terminal lipobox motif. This list included genes encoding previously reported SLPs in Haemophilus influenzae and Moraxella catarrhalis, for which we were able to show that the neighboring Slams are necessary and sufficient to display these lipoproteins on the surface of Escherichia coli. To further verify the authenticity of the list of predicted SLPs, we tested the surface display of one such Slam-adjacent protein from Pasteurella multocida, a zoonotic pathogen. A robust Slam-dependent display of the P. multocida protein was observed in the E. coli translocation assay indicating that the protein is a Slam-dependent SLP. Based on multiple sequence alignments and domain annotations, we found that an eight-stranded beta-barrel domain is common to all the predicted Slam-dependent SLPs. These findings suggest that SLPs with a TbpB-like fold are found widely in Proteobacteria where they exist with their interaction partner Slam. In the future, SLPs found in pathogenic bacteria can be investigated for their role in virulence and may also serve as candidates for vaccine development.
Collapse
Affiliation(s)
- Yogesh Hooda
- Department of Biochemistry, University of TorontoToronto, ON, Canada
| | - Christine C L Lai
- Department of Biochemistry, University of TorontoToronto, ON, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of TorontoToronto, ON, Canada
| |
Collapse
|
21
|
Hooda Y, Shin HE, Bateman TJ, Moraes TF. Neisserial surface lipoproteins: structure, function and biogenesis. Pathog Dis 2017; 75:2966469. [PMID: 28158534 DOI: 10.1093/femspd/ftx010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/29/2017] [Indexed: 11/14/2022] Open
Abstract
The surface of many Gram-negative bacteria contains lipidated protein molecules referred to as surface lipoproteins or SLPs. SLPs play critical roles in host immune evasion, nutrient acquisition and regulation of the bacterial stress response. The focus of this review is on the SLPs present in Neisseria, a genus of bacteria that colonise the mucosal surfaces of animals. Neisseria contains two pathogens of medical interest, namely Neisseria meningitidis and N. gonorrhoeae. Several SLPs have been identified in Neisseria and their study has elucidated key strategies used by these pathogens to survive inside the human body. Herein, we focus on the identification, structure and function of SLPs that have been identified in Neisseria. We also survey the translocation pathways used by these SLPs to reach the cell surface. Specifically, we elaborate on the strategies used by neisserial SLPs to translocate across the outer membrane with an emphasis on Slam, a novel outer membrane protein that has been implicated in SLP biogenesis. Taken together, the study of SLPs in Neisseria illustrates the widespread roles played by this family of proteins in Gram-negative bacteria.
Collapse
|
22
|
Ostan NKH, Yu RH, Ng D, Lai CCL, Pogoutse AK, Sarpe V, Hepburn M, Sheff J, Raval S, Schriemer DC, Moraes TF, Schryvers AB. Lactoferrin binding protein B - a bi-functional bacterial receptor protein. PLoS Pathog 2017; 13:e1006244. [PMID: 28257520 PMCID: PMC5352143 DOI: 10.1371/journal.ppat.1006244] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 03/15/2017] [Accepted: 02/15/2017] [Indexed: 11/18/2022] Open
Abstract
Lactoferrin binding protein B (LbpB) is a bi-lobed outer membrane-bound lipoprotein that comprises part of the lactoferrin (Lf) receptor complex in Neisseria meningitidis and other Gram-negative pathogens. Recent studies have demonstrated that LbpB plays a role in protecting the bacteria from cationic antimicrobial peptides due to large regions rich in anionic residues in the C-terminal lobe. Relative to its homolog, transferrin-binding protein B (TbpB), there currently is little evidence for its role in iron acquisition and relatively little structural and biophysical information on its interaction with Lf. In this study, a combination of crosslinking and deuterium exchange coupled to mass spectrometry, information-driven computational docking, bio-layer interferometry, and site-directed mutagenesis was used to probe LbpB:hLf complexes. The formation of a 1:1 complex of iron-loaded Lf and LbpB involves an interaction between the Lf C-lobe and LbpB N-lobe, comparable to TbpB, consistent with a potential role in iron acquisition. The Lf N-lobe is also capable of binding to negatively charged regions of the LbpB C-lobe and possibly other sites such that a variety of higher order complexes are formed. Our results are consistent with LbpB serving dual roles focused primarily on iron acquisition when exposed to limited levels of iron-loaded Lf on the mucosal surface and effectively binding apo Lf when exposed to high levels at sites of inflammation.
Collapse
Affiliation(s)
- Nicholas K. H. Ostan
- Department of Microbiology & Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Rong-Hua Yu
- Department of Microbiology & Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Dixon Ng
- Department of Microbiology & Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | | | | | - Vladimir Sarpe
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Morgan Hepburn
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Joey Sheff
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada
| | - Shaunak Raval
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada
| | - David C. Schriemer
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Trevor F. Moraes
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Anthony B. Schryvers
- Department of Microbiology & Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
| |
Collapse
|
23
|
Abstract
Transferrin is one of the sources of iron that is most readily available to colonizing and invading pathogens. In this review, we look at iron uptake by the bacterial transferrin receptor that is found in the families Neisseriaceae, Pasteurellaceae and Moraxellaceae. This bipartite receptor consists of the TonB-dependent transporter, TbpA, and the surface lipoprotein, TbpB. In the past three decades, major advancements have been made in our understanding of the mechanism through which the Tbps take up iron. We summarize these findings and discuss how they relate to the diversity and specificity of the transferrin receptor. We also outline several of the remaining unanswered questions about iron uptake via the bacterial transferrin receptor and suggest directions for future research.
Collapse
Affiliation(s)
| | - Trevor F Moraes
- a Department of Biochemistry , University of Toronto , Toronto , Canada
| |
Collapse
|
24
|
Thurlow B, Davis JH, Leong V, Moraes TF, Williamson JR, Ortega J. Binding properties of YjeQ (RsgA), RbfA, RimM and Era to assembly intermediates of the 30S subunit. Nucleic Acids Res 2016; 44:9918-9932. [PMID: 27382067 PMCID: PMC5175332 DOI: 10.1093/nar/gkw613] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 06/26/2016] [Accepted: 06/27/2016] [Indexed: 11/13/2022] Open
Abstract
Our understanding regarding the function of YjeQ (also called RsgA), RbfA, RimM and Era in ribosome biogenesis has been derived in part from the study of immature 30S particles that accumulate in null strains lacking one of these factors. However, their mechanistic details are still unknown. Here, we demonstrate that these immature particles are not dead-end products of assembly, but progress into mature 30S subunits. Mass spectrometry analysis revealed that in vivo the occupancy level of these factors in these immature 30S particles is below 10% and that the concentration of factors does not increase when immature particles accumulate in cells. We measured by microscale thermophoresis that YjeQ and Era binds to the mature 30S subunit with high affinity. However, the binding affinity of these factors to the immature particles and of RimM and RbfA to mature or immature particles was weak, suggesting that binding is not occurring at physiological concentrations. These results suggest that in the absence of these factors, the immature particles evolve into a thermodynamically stable intermediate that exhibits low affinity for the assembly factors. These results imply that the true substrates of YjeQ, RbfA, RimM and Era are immature particles that precede the ribosomal particles accumulating in the knockouts strains.
Collapse
Affiliation(s)
- Brett Thurlow
- Department of Biochemistry and Biomedical Sciences and M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada
| | - Joseph H Davis
- Department of Integrative Computational and Structural Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Vivian Leong
- Department of Biochemistry and Biomedical Sciences and M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S1A8, Canada
| | - James R Williamson
- Department of Integrative Computational and Structural Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences and M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada
| |
Collapse
|
25
|
Abstract
The outer membrane of Gram-negative bacteria is predominantly populated by β-Barrel proteins and lipid anchored proteins that serve a variety of biological functions. The proper folding and assembly of these proteins is essential for bacterial viability and often plays a critical role in virulence and pathogenesis. The β-barrel assembly machinery (Bam) complex is responsible for the proper assembly of β-barrels into the outer membrane of Gram-negative bacteria, whereas the localization of lipoproteins (Lol) system is required for proper targeting of lipoproteins to the outer membrane.
Collapse
Affiliation(s)
- Charles Calmettes
- Department of Biochemistry, University of Toronto, Medical Science Building, Rm. 5366, 1 King's College Circle, Toronto, ON, Canada, M5S 1A8.
| | - Andrew Judd
- Department of Biochemistry, University of Toronto, Medical Science Building, Rm. 5366, 1 King's College Circle, Toronto, ON, Canada, M5S 1A8.
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Medical Science Building, Rm. 5366, 1 King's College Circle, Toronto, ON, Canada, M5S 1A8.
| |
Collapse
|
26
|
McCallum M, Tammam S, Little DJ, Robinson H, Koo J, Shah M, Calmettes C, Moraes TF, Burrows LL, Howell PL. PilN Binding Modulates the Structure and Binding Partners of the Pseudomonas aeruginosa Type IVa Pilus Protein PilM. J Biol Chem 2016; 291:11003-15. [PMID: 27022027 DOI: 10.1074/jbc.m116.718353] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Indexed: 01/05/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic bacterial pathogen that expresses type IVa pili. The pilus assembly system, which promotes surface-associated twitching motility and virulence, is composed of inner and outer membrane subcomplexes, connected by an alignment subcomplex composed of PilMNOP. PilM binds to the N terminus of PilN, and we hypothesize that this interaction causes functionally significant structural changes in PilM. To characterize this interaction, we determined the crystal structures of PilM and a PilM chimera where PilM was fused to the first 12 residues of PilN (PilM·PilN(1-12)). Structural analysis, multiangle light scattering coupled with size exclusion chromatography, and bacterial two-hybrid data revealed that PilM forms dimers mediated by the binding of a novel conserved motif in the N terminus of PilM, and binding PilN abrogates this binding interface, resulting in PilM monomerization. Structural comparison of PilM with PilM·PilN(1-12) revealed that upon PilN binding, there is a large domain closure in PilM that alters its ATP binding site. Using biolayer interferometry, we found that the association rate of PilN with PilM is higher in the presence of ATP compared with ADP. Bacterial two-hybrid data suggested the connectivity of the cytoplasmic and inner membrane components of the type IVa pilus machinery in P. aeruginosa, with PilM binding to PilB, PilT, and PilC in addition to PilN. Pull-down experiments demonstrated direct interactions of PilM with PilB and PilT. We propose a working model in which dynamic binding of PilN facilitates functionally relevant structural changes in PilM.
Collapse
Affiliation(s)
- Matthew McCallum
- From the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, the Program in Molecular Structure and Function, Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Stephanie Tammam
- the Program in Molecular Structure and Function, Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Dustin J Little
- From the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, the Program in Molecular Structure and Function, Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Howard Robinson
- the Photon Sciences Division, Brookhaven National Laboratory, Upton, New York 11973-5000, and
| | - Jason Koo
- the Program in Molecular Structure and Function, Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Megha Shah
- From the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Charles Calmettes
- From the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Trevor F Moraes
- From the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Lori L Burrows
- the Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - P Lynne Howell
- From the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, the Program in Molecular Structure and Function, Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada,
| |
Collapse
|
27
|
Hooda Y, Lai CCL, Judd A, Buckwalter CM, Shin HE, Gray-Owen SD, Moraes TF. Slam is an outer membrane protein that is required for the surface display of lipidated virulence factors in Neisseria. Nat Microbiol 2016; 1:16009. [DOI: 10.1038/nmicrobiol.2016.9] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/19/2016] [Indexed: 11/09/2022]
|
28
|
Pogoutse AK, Lai CCL, Ostan N, Yu RH, Schryvers AB, Moraes TF. A method for measuring binding constants using unpurified in vivo biotinylated ligands. Anal Biochem 2016; 501:35-43. [PMID: 26898305 DOI: 10.1016/j.ab.2016.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/29/2016] [Accepted: 02/02/2016] [Indexed: 11/26/2022]
Abstract
Obtaining accurate kinetics and steady-state binding constants for biomolecular interactions normally requires pure and homogeneous protein preparations. Furthermore, in many cases, one of the ligands must be labeled. Over the past decade, several technologies have been introduced that allow for the measurement of kinetics constants for multiple different interactions in parallel. One such technology is bio-layer interferometry (BLI), which has been used to develop systems that can measure up to 96 biomolecular interactions simultaneously. However, despite the ever-increasing throughput of the tools available for measuring protein-protein interactions, the preparation of pure protein still remains a bottleneck in the process of producing high-quality kinetics data. Here, we show that high-quality binding data can be obtained using soluble lysate fractions containing protein that has been biotinylated in vivo using BirA and then applied to BLI sensors without further purification. Furthermore, we show that BirA ligase does not necessarily need to be co-overexpressed with the protein of interest for biotinylation of the biotin acceptor peptide to occur, suggesting that the activity of endogenous BirA in Escherichia coli is sufficient for producing enough biotinylated protein for a binding experiment.
Collapse
Affiliation(s)
| | | | - Nicholas Ostan
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Rong-hua Yu
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Anthony B Schryvers
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
| |
Collapse
|
29
|
Sit B, Crowley SM, Bhullar K, Lai CCL, Tang C, Hooda Y, Calmettes C, Khambati H, Ma C, Brumell JH, Schryvers AB, Vallance BA, Moraes TF. Active Transport of Phosphorylated Carbohydrates Promotes Intestinal Colonization and Transmission of a Bacterial Pathogen. PLoS Pathog 2015; 11:e1005107. [PMID: 26295949 PMCID: PMC4546632 DOI: 10.1371/journal.ppat.1005107] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 07/22/2015] [Indexed: 12/22/2022] Open
Abstract
Efficient acquisition of extracellular nutrients is essential for bacterial pathogenesis, however the identities and mechanisms for transport of many of these substrates remain unclear. Here, we investigate the predicted iron-binding transporter AfuABC and its role in bacterial pathogenesis in vivo. By crystallographic, biophysical and in vivo approaches, we show that AfuABC is in fact a cyclic hexose/heptose-phosphate transporter with high selectivity and specificity for a set of ubiquitous metabolites (glucose-6-phosphate, fructose-6-phosphate and sedoheptulose-7-phosphate). AfuABC is conserved across a wide range of bacterial genera, including the enteric pathogens EHEC O157:H7 and its murine-specific relative Citrobacter rodentium, where it lies adjacent to genes implicated in sugar sensing and acquisition. C. rodentium ΔafuA was significantly impaired in an in vivo murine competitive assay as well as its ability to transmit infection from an afflicted to a naïve murine host. Sugar-phosphates were present in normal and infected intestinal mucus and stool samples, indicating that these metabolites are available within the intestinal lumen for enteric bacteria to import during infection. Our study shows that AfuABC-dependent uptake of sugar-phosphates plays a critical role during enteric bacterial infection and uncovers previously unrecognized roles for these metabolites as important contributors to successful pathogenesis. Essentially all Gram-negative pathogens are reliant on specific transport machineries termed binding protein-dependent transporters (BPDTs) to transport solutes such as amino acids, sugars and metal ions across their membranes. In this study we investigated AfuABC, a predicted iron-transporting BPDT found in many bacterial pathogens. We show by structural and functional approaches that AfuABC is not an iron transporter. Instead, AfuABC is a trio of proteins that bind and transport sugar-phosphates such as glucose-6-phosphate (G6P). In doing so, we present the first structural solution of a G6P-specific transport protein and add to the few known unique machineries for sugar-phosphate uptake by bacteria. Furthermore, we show that AfuABC is required by the intestinal pathogen C. rodentium to effectively transmit between mice and re-establish infection, leading us to propose that the transport of sugar-phosphates is an important part of general bacterial pathogenesis.
Collapse
Affiliation(s)
- Brandon Sit
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Shauna M. Crowley
- Department of Pediatrics and the Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kirandeep Bhullar
- Department of Pediatrics and the Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Calvin Tang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yogesh Hooda
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Charles Calmettes
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Husain Khambati
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Caixia Ma
- Department of Pediatrics and the Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - John H. Brumell
- Department of Molecular Genetics and Institute of Medical Science, University of Toronto, Ontario, Canada
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- SickKids Inflammatory Bowel Disease Centre, Toronto, Ontario, Canada
| | - Anthony B. Schryvers
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Bruce A. Vallance
- Department of Pediatrics and the Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail: (BAV); (TFM)
| | - Trevor F. Moraes
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (BAV); (TFM)
| |
Collapse
|
30
|
Calmettes C, Ing C, Buckwalter CM, El Bakkouri M, Chieh-Lin Lai C, Pogoutse A, Gray-Owen SD, Pomès R, Moraes TF. The molecular mechanism of Zinc acquisition by the neisserial outer-membrane transporter ZnuD. Nat Commun 2015; 6:7996. [PMID: 26282243 PMCID: PMC4557270 DOI: 10.1038/ncomms8996] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 07/03/2015] [Indexed: 11/09/2022] Open
Abstract
Invading bacteria from the Neisseriaceae, Acinetobacteriaceae, Bordetellaceae and Moraxellaceae families express the conserved outer-membrane zinc transporter zinc-uptake component D (ZnuD) to overcome nutritional restriction imposed by the host organism during infection. Here we demonstrate that ZnuD is required for efficient systemic infections by the causative agent of bacterial meningitis, Neisseria meningitidis, in a mouse model. We also combine X-ray crystallography and molecular dynamics simulations to gain insight into the mechanism of zinc recognition and transport across the bacterial outer-membrane by ZnuD. Because ZnuD is also considered a promising vaccine candidate against N. meningitidis, we use several ZnuD structural intermediates to map potential antigenic epitopes, and propose a mechanism by which ZnuD can maintain high sequence conservation yet avoid immune recognition by altering the conformation of surface-exposed loops. ZnuD is a conserved zinc transporter expressed in several bacterial pathogens with potential as a target against infection. Here the authors demonstrate a requirement for ZnuD in systemic infection by N. meningitidis and define the molecular mechanism of ZnuD-mediated Zinc transport across the bacterial outer membrane.
Collapse
Affiliation(s)
- Charles Calmettes
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Christopher Ing
- 1] Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada [2] Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Carolyn M Buckwalter
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Majida El Bakkouri
- Structural Genomic Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Christine Chieh-Lin Lai
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Anastassia Pogoutse
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Scott D Gray-Owen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Régis Pomès
- 1] Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada [2] Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
31
|
Adamiak P, Calmettes C, Moraes TF, Schryvers AB. Patterns of structural and sequence variation within isotype lineages of the Neisseria meningitidis transferrin receptor system. Microbiologyopen 2015; 4:491-504. [PMID: 25800619 PMCID: PMC4475390 DOI: 10.1002/mbo3.254] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 02/18/2015] [Accepted: 02/24/2015] [Indexed: 11/26/2022] Open
Abstract
Neisseria meningitidis inhabits the human upper respiratory tract and is an important cause of sepsis and meningitis. A surface receptor comprised of transferrin-binding proteins A and B (TbpA and TbpB), is responsible for acquiring iron from host transferrin. Sequence and immunological diversity divides TbpBs into two distinct lineages; isotype I and isotype II. Two representative isotype I and II strains, B16B6 and M982, differ in their dependence on TbpB for in vitro growth on exogenous transferrin. The crystal structure of TbpB and a structural model for TbpA from the representative isotype I N. meningitidis strain B16B6 were obtained. The structures were integrated with a comprehensive analysis of the sequence diversity of these proteins to probe for potential functional differences. A distinct isotype I TbpA was identified that co-varied with TbpB and lacked sequence in the region for the loop 3 α-helix that is proposed to be involved in iron removal from transferrin. The tightly associated isotype I TbpBs had a distinct anchor peptide region, a distinct, smaller linker region between the lobes and lacked the large loops in the isotype II C-lobe. Sequences of the intact TbpB, the TbpB N-lobe, the TbpB C-lobe, and TbpA were subjected to phylogenetic analyses. The phylogenetic clustering of TbpA and the TbpB C-lobe were similar with two main branches comprising the isotype 1 and isotype 2 TbpBs, possibly suggesting an association between TbpA and the TbpB C-lobe. The intact TbpB and TbpB N-lobe had 4 main branches, one consisting of the isotype 1 TbpBs. One isotype 2 TbpB cluster appeared to consist of isotype 1 N-lobe sequences and isotype 2 C-lobe sequences, indicating the swapping of N-lobes and C-lobes. Our findings should inform future studies on the interaction between TbpB and TbpA and the process of iron acquisition.
Collapse
Affiliation(s)
- Paul Adamiak
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Charles Calmettes
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Anthony B Schryvers
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| |
Collapse
|
32
|
Morgenthau A, Pogoutse A, Adamiak P, Moraes TF, Schryvers AB. Bacterial receptors for host transferrin and lactoferrin: molecular mechanisms and role in host–microbe interactions. Future Microbiol 2013; 8:1575-85. [DOI: 10.2217/fmb.13.125] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Iron homeostasis in the mammalian host limits the availability of iron to invading pathogens and is thought to restrict iron availability for microbes inhabiting mucosal surfaces. The presence of surface receptors for the host iron-binding glycoproteins transferrin (Tf) and lactoferrin (Lf) in globally important Gram-negative bacterial pathogens of humans and food production animals suggests that Tf and Lf are important sources of iron in the upper respiratory or genitourinary tracts, where they exclusively reside. Lf receptors have the additional function of protecting against host cationic antimicrobial peptides, suggesting that the bacteria expressing these receptors reside in a niche where exposure is likely. In this review we compare Tf and Lf receptors with respect to their structural and functional features, their role in colonization and infection, and their distribution among pathogenic and commensal bacteria.
Collapse
Affiliation(s)
- Ari Morgenthau
- Department of Microbiology, Immunology & Infectious Diseases, Health Sciences Centre, 3330 Hospital Drive Northwest Calgary, Alberta, T2N 4N1, Canada
| | - Anastassia Pogoutse
- Department of Biochemistry, Medical Sciences Building, King’s College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Paul Adamiak
- Department of Microbiology, Immunology & Infectious Diseases, Health Sciences Centre, 3330 Hospital Drive Northwest Calgary, Alberta, T2N 4N1, Canada
| | - Trevor F Moraes
- Department of Biochemistry, Medical Sciences Building, King’s College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Anthony B Schryvers
- Department of Biochemistry & Molecular Biology, Health Sciences Centre, 3330 Hospital Drive Northwest Calgary, Alberta, T2N 4N1, Canada
| |
Collapse
|
33
|
Shnitsar V, Li J, Li X, Calmettes C, Basu A, Casey JR, Moraes TF, Reithmeier RAF. A substrate access tunnel in the cytosolic domain is not an essential feature of the solute carrier 4 (SLC4) family of bicarbonate transporters. J Biol Chem 2013; 288:33848-33860. [PMID: 24121512 DOI: 10.1074/jbc.m113.511865] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Anion exchanger 1 (AE1; Band 3; SLC4A1) is the founding member of the solute carrier 4 (SLC4) family of bicarbonate transporters that includes chloride/bicarbonate AEs and Na(+)-bicarbonate co-transporters (NBCs). These membrane proteins consist of an amino-terminal cytosolic domain involved in protein interactions and a carboxyl-terminal membrane domain that carries out the transport function. Mutation of a conserved arginine residue (R298S) in the cytosolic domain of NBCe1 (SLC4A4) is linked to proximal renal tubular acidosis and results in impaired transport function, suggesting that the cytosolic domain plays a role in substrate permeation. Introduction of single and double mutations at the equivalent arginine (Arg(283)) and at an interacting glutamate (Glu(85)) in the cytosolic domain of human AE1 (cdAE1) had no effect on the cell surface expression or the transport activity of AE1 expressed in HEK-293 cells. In addition, the membrane domain of AE1 (mdAE1) efficiently mediated anion transport. A 2.1-Å resolution crystal structure of cdΔ54AE1 (residues 55-356 of cdAE1) lacking the amino-terminal and carboxyl-terminal disordered regions, produced at physiological pH, revealed an extensive hydrogen-bonded network involving Arg(283) and Glu(85). Mutations at these residues affected the pH-dependent conformational changes and stability of cdΔ54AE1. As these structural alterations did not impair functional expression of AE1, the cytosolic and membrane domains operate independently. A substrate access tunnel within the cytosolic domain is not present in AE1 and therefore is not an essential feature of the SLC4 family of bicarbonate transporters.
Collapse
Affiliation(s)
- Volodymyr Shnitsar
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jing Li
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Xuyao Li
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Charles Calmettes
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Arghya Basu
- Department of Biochemistry and Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Joseph R Casey
- Department of Biochemistry and Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | |
Collapse
|
34
|
Malott RJ, Keller BO, Gaudet RG, McCaw SE, Lai CCL, Dobson-Belaire WN, Hobbs JL, St. Michael F, Cox AD, Moraes TF, Gray-Owen SD. Neisseria gonorrhoeae-derived heptose elicits an innate immune response and drives HIV-1 expression. Proc Natl Acad Sci U S A 2013; 110:10234-9. [PMID: 23733950 PMCID: PMC3690901 DOI: 10.1073/pnas.1303738110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Clinical and epidemiological synergy exists between the globally important sexually transmitted infections, gonorrhea and HIV. Neisseria gonorrhoeae, which causes gonorrhea, is particularly adept at driving HIV-1 expression, but the molecular determinants of this relationship remain undefined. N. gonorrhoeae liberates a soluble factor that potently induces expression from the HIV-1 LTR in coinfected cluster of differentiation 4-positive (CD4(+)) T lymphocytes, but this factor is not a previously described innate effector. A genome-wide mutagenesis approach was undertaken to reveal which component(s) of N. gonorrhoeae induce HIV-1 expression in CD4(+) T lymphocytes. A mutation in the ADP-heptose biosynthesis gene, hldA, rendered the bacteria unable to induce HIV-1 expression. The hldA mutant has a truncated lipooligosaccharide structure, contains lipid A in its outer membrane, and remains bioactive in a TLR4 reporter-based assay but did not induce HIV-1 expression. Mass spectrometry analysis of extensively fractionated N. gonorrhoeae-derived supernatants revealed that the LTR-inducing fraction contained a compound having a mass consistent with heptose-monophosphate (HMP). Heptose is a carbohydrate common in microbes but is absent from the mammalian glycome. Although ADP-heptose biosynthesis is common among Gram-negative bacteria, and heptose is a core component of most lipopolysaccharides, N. gonorrhoeae is peculiar in that it effectively liberates HMP during growth. This N. gonorrhoeae-derived HMP activates CD4(+) T cells to invoke an NF-κB-dependent transcriptional response that drives HIV-1 expression and viral production. Our study thereby shows that heptose is a microbial-specific product that is sensed as an innate immune agonist and unveils the molecular link between N. gonorrhoeae and HIV-1.
Collapse
Affiliation(s)
- Rebecca J. Malott
- Departments of Molecular Genetics and
- Centre for Understanding and Preventing Infection in Children, Department of Pediatrics, and
| | - Bernd O. Keller
- Child and Family Research Institute, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada V5Z 4H4; and
| | | | | | | | | | - J. Leigh Hobbs
- Centre for Understanding and Preventing Infection in Children, Department of Pediatrics, and
| | - Frank St. Michael
- Vaccine Program, National Research Council, Ottawa, ON, Canada K1A 0R6
| | - Andrew D. Cox
- Vaccine Program, National Research Council, Ottawa, ON, Canada K1A 0R6
| | - Trevor F. Moraes
- Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | | |
Collapse
|
35
|
Moraes TF, Reithmeier RAF. Membrane transport metabolons. Biochim Biophys Acta 2012; 1818:2687-706. [PMID: 22705263 DOI: 10.1016/j.bbamem.2012.06.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 05/28/2012] [Accepted: 06/05/2012] [Indexed: 10/28/2022]
Abstract
In this review evidence from a wide variety of biological systems is presented for the genetic, functional, and likely physical association of membrane transporters and the enzymes that metabolize the transported substrates. This evidence supports the hypothesis that the dynamic association of transporters and enzymes creates functional membrane transport metabolons that channel substrates typically obtained from the extracellular compartment directly into their cellular metabolism. The immediate modification of substrates on the inner surface of the membrane prevents back-flux through facilitated transporters, increasing the efficiency of transport. In some cases products of the enzymes are themselves substrates for the transporters that efflux the products in an exchange or antiport mechanism. Regulation of the binding of enzymes to transporters and their mutual activities may play a role in modulating flux through transporters and entry of substrates into metabolic pathways. Examples showing the physical association of transporters and enzymes are provided, but available structural data is sparse. Genetic and functional linkages between membrane transporters and enzymes were revealed by an analysis of Escherichia coli operons encoding polycistronic mRNAs and provide a list of predicted interactions ripe for further structural studies. This article supports the view that membrane transport metabolons are important throughout Nature in organisms ranging from bacteria to humans.
Collapse
Affiliation(s)
- Trevor F Moraes
- Department of Biochemistry, University of Toronto, Ontario, Canada
| | | |
Collapse
|
36
|
Calmettes C, Alcantara J, Yu RH, Schryvers AB, Moraes TF. The structural basis of transferrin sequestration by transferrin-binding protein B. Nat Struct Mol Biol 2012; 19:358-60. [PMID: 22343719 PMCID: PMC3981719 DOI: 10.1038/nsmb.2251] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 01/19/2012] [Indexed: 12/14/2022]
Abstract
Neisseria meningitidis, the causative agent of bacterial meningitis, acquires the essential element iron from the host glycoprotein transferrin (Tf) during infection via a surface Tf receptor system composed of proteins TbpA and TbpB. Here in we present the crystal structures of TbpB from N. meningitidis, in its apo form and in complex with human Tf (hTf). The structure reveals how TbpB sequesters hTf and initiates iron release from hTf.
Collapse
Affiliation(s)
- Charles Calmettes
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | | |
Collapse
|
37
|
Yang X, Yu RH, Calmettes C, Moraes TF, Schryvers AB. Anchor peptide of transferrin-binding protein B is required for interaction with transferrin-binding protein A. J Biol Chem 2011; 286:45165-73. [PMID: 22069313 DOI: 10.1074/jbc.m110.214171] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gram-negative bacterial pathogens belonging to the Pasteurellaceae, Moraxellaceae, and Neisseriaceae families rely on an iron acquisition system that acquires iron directly from host transferrin (Tf). The process is mediated by a surface receptor composed of transferrin-binding proteins A and B (TbpA and TbpB). TbpA is an integral outer membrane protein that functions as a gated channel for the passage of iron into the periplasm. TbpB is a surface-exposed lipoprotein that facilitates the iron uptake process. In this study, we demonstrate that the region encompassing amino acids 7-40 of Actinobacillus pleuropneumoniae TbpB is required for forming a complex with TbpA and that the formation of the complex requires the presence of porcine Tf. These results are consistent with a model in which TbpB is responsible for the initial capture of iron-loaded Tf and subsequently interacts with TbpA through the anchor peptide. We propose that TonB binding to TbpA initiates the formation of the TbpB-TbpA complex and transfer of Tf to TbpA.
Collapse
Affiliation(s)
- Xue Yang
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary T2N 4N1 Alberta, Canada
| | | | | | | | | |
Collapse
|
38
|
Silva LP, Yu R, Calmettes C, Yang X, Moraes TF, Schryvers AB, Schriemer DC. Conserved interaction between transferrin and transferrin-binding proteins from porcine pathogens. J Biol Chem 2011; 286:21353-60. [PMID: 21487007 DOI: 10.1074/jbc.m111.226449] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gram-negative porcine pathogens from the Pasteurellaceae family possess a surface receptor complex capable of acquiring iron from porcine transferrin (pTf). This receptor consists of transferrin-binding protein A (TbpA), a transmembrane iron transporter, and TbpB, a surface-exposed lipoprotein. Questions remain as to how the receptor complex engages pTf in such a way that iron is positioned for release, and whether divergent strains present distinct recognition sites on Tf. In this study, the TbpB-pTf interface was mapped using a combination of mass shift analysis and molecular docking simulations, localizing binding uniquely to the pTf C lobe for multiple divergent strains of Actinobacillus plueropneumoniae and suis. The interface was further characterized and validated with site-directed mutagenesis. Although targeting a common lobe, variants differ in preference for the two sublobes comprising the iron coordination site. Sublobes C1 and C2 participate in high affinity binding, but sublobe C1 contributes in a minor fashion to the overall affinity. Further, the TbpB-pTf complex does not release iron independent of other mediators, based on competitive iron binding studies. Together, our findings support a model whereby TbpB efficiently captures and presents iron-loaded pTf to other elements of the uptake pathway, even under low iron conditions.
Collapse
Affiliation(s)
- Leslie P Silva
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | | | | | | | | | | | | |
Collapse
|
39
|
Calmettes C, Yu RH, Silva LP, Curran D, Schriemer DC, Schryvers AB, Moraes TF. Structural variations within the transferrin binding site on transferrin-binding protein B, TbpB. J Biol Chem 2011; 286:12683-92. [PMID: 21297163 DOI: 10.1074/jbc.m110.206102] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pathogenic bacteria acquire the essential element iron through specialized uptake pathways that are necessary in the iron-limiting environments of the host. Members of the Gram-negative Neisseriaceae and Pasteurellaceae families have adapted to acquire iron from the host iron binding glycoprotein, transferrin (Tf), through a receptor complex comprised of transferring-binding protein (Tbp) A and B. Because of the critical role they play in the host, these surface-exposed proteins are invariably present in clinical isolates and thus are considered prime vaccine targets. The specific interactions between TbpB and Tf are essential and ultimately might be exploited to create a broad-spectrum vaccine. In this study, we report the structure of TbpBs from two porcine pathogens, Actinobacillus pleuropneumoniae and suis. Paradoxically, despite a common Tf target, these swine related TbpBs show substantial sequence variation in their Tf-binding site. The TbpB structures, supported by docking simulations, surface plasmon resonance and hydrogen/deuterium exchange experiments with wild-type and mutant TbpBs, explain why there are structurally conserved elements within TbpB homologs despite major sequence variation that are required for binding Tf.
Collapse
Affiliation(s)
- Charles Calmettes
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | | | | | | | | | | | |
Collapse
|
40
|
Moraes TF, Yu RH, Strynadka NCJ, Schryvers AB. Insights into the bacterial transferrin receptor: the structure of transferrin-binding protein B from Actinobacillus pleuropneumoniae. Mol Cell 2009; 35:523-33. [PMID: 19716795 DOI: 10.1016/j.molcel.2009.06.029] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 05/09/2009] [Accepted: 06/11/2009] [Indexed: 11/17/2022]
Abstract
Pathogenic bacteria from the Neisseriaceae and Pasteurellacea families acquire iron directly from the host iron-binding glycoprotein, transferrin (Tf), in a process mediated by surface receptor proteins that directly bind host Tf, extract the iron, and transport it across the outer membrane. The bacterial Tf receptor is comprised of a surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), both of which are essential for survival in the host. In this study, we report the 1.98 A resolution structure of TbpB from the porcine pathogen Actinobacillus pleuropneumoniae, providing insights into the mechanism of Tf binding and the role of TbpB. A model for the complex of TbpB bound to Tf is proposed. Mutation of a single surface-exposed Phe residue on TbpB within the predicted interface completely abolishes binding to Tf, suggesting that the TbpB N lobe comprises the sole high-affinity binding region for Tf.
Collapse
Affiliation(s)
- Trevor F Moraes
- Department of Biochemistry and Molecular Biology, Center for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | | | | | | |
Collapse
|
41
|
Dalal K, Nguyen N, Alami M, Tan J, Moraes TF, Lee WC, Maurus R, Sligar SS, Brayer GD, Duong F. Structure, binding, and activity of Syd, a SecY-interacting protein. J Biol Chem 2009; 284:7897-902. [PMID: 19139097 PMCID: PMC2658082 DOI: 10.1074/jbc.m808305200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 12/19/2008] [Indexed: 01/20/2023] Open
Abstract
The Syd protein has been implicated in the Sec-dependent transport of polypeptides across the bacterial inner membrane. Using Nanodiscs, we here provide direct evidence that Syd binds the SecY complex, and we demonstrate that interaction involves the two electropositive and cytosolic loops of the SecY subunit. We solve the crystal structure of Syd and together with cysteine cross-link analysis, we show that a conserved concave and electronegative groove constitutes the SecY-binding site. At the membrane, Syd decreases the activity of the translocon containing loosely associated SecY-SecE subunits, whereas in detergent solution Syd disrupts the SecYEG heterotrimeric associations. These results support the role of Syd in proofreading the SecY complex biogenesis and point to the electrostatic nature of the Sec channel interaction with its cytosolic partners.
Collapse
Affiliation(s)
- Kush Dalal
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T1Z3, Canada
| | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Okon M, Moraes TF, Lario PI, Creagh AL, Haynes CA, Strynadka NC, McIntosh LP. Structural Characterization of the Type-III Pilot-Secretin Complex from Shigella flexneri. Structure 2008; 16:1544-54. [DOI: 10.1016/j.str.2008.08.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2008] [Revised: 08/08/2008] [Accepted: 08/15/2008] [Indexed: 02/02/2023]
|
43
|
Moraes TF, Spreter T, Strynadka NC. Piecing together the type III injectisome of bacterial pathogens. Curr Opin Struct Biol 2008; 18:258-66. [PMID: 18258424 DOI: 10.1016/j.sbi.2007.12.011] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Revised: 12/17/2007] [Accepted: 12/18/2007] [Indexed: 01/01/2023]
Abstract
The Type III secretion system is a bacterial 'injectisome' which allows Gram-negative bacteria to shuttle virulence proteins directly into the host cells they infect. This macromolecular assembly consists of more than 20 different proteins put together to collectively span three biological membranes. The recent T3SS crystal structures of the major oligomeric inner membrane ring, the helical needle filament, needle tip protein, the associated ATPase, and outer membrane pilotin together with electron microscopy reconstructions have dramatically furthered our understanding of how this protein translocator functions. The crucial details that describe how these proteins assemble into this oligomeric complex will need a hybrid of structural methodologies including EM, crystallography, and NMR to clarify the intra- and inter-molecular interactions between different structural components of the apparatus.
Collapse
Affiliation(s)
- Trevor F Moraes
- University of British Columbia, Biochemistry and Molecular Biology and the Center for Blood Research, Rm 4350 Life Sciences Center, 2350 Health Sciences Mall, Vancouver, Canada V6T 1Z3
| | | | | |
Collapse
|
44
|
Moraes TF, Bains M, Hancock REW, Strynadka NCJ. An arginine ladder in OprP mediates phosphate-specific transfer across the outer membrane. Nat Struct Mol Biol 2006; 14:85-7. [PMID: 17187075 DOI: 10.1038/nsmb1189] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 12/06/2006] [Indexed: 11/09/2022]
Abstract
The outer membrane protein OprP mediates the transport of essential phosphate anions into the pathogenic bacterium Pseudomonas aeruginosa. Here we report the crystallographic structure of trimeric OprP at 1.9-A resolution, revealing an unprecedented 9-residue arginine 'ladder' that spans from the extracellular surface down through a constriction zone where phosphate is coordinated. Lysine residues coat the inner periplasmic surface, creating an 'electropositive sink' that pulls the phosphates through the eyelet and into the cell.
Collapse
Affiliation(s)
- Trevor F Moraes
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | | | | | | |
Collapse
|
45
|
Pastushok L, Moraes TF, Ellison MJ, Xiao W. A single Mms2 "key" residue insertion into a Ubc13 pocket determines the interface specificity of a human Lys63 ubiquitin conjugation complex. J Biol Chem 2005; 280:17891-900. [PMID: 15749714 DOI: 10.1074/jbc.m410469200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human Ubc13 and Mms2 (or its homolog, Uev1) form a unique ubiquitin-conjugating enzyme (Ubc) complex that generates atypical Lys(63)-linked ubiquitin conjugates. Such conjugates are attached to specific targets that modulate the activity of various cellular processes including DNA repair, mitotic progression, and nuclear factor-kappaB signaling. Whereas Ubc13 is a typical Ubc, Mms2 is a non-catalytic Ubc variant. Substantial biochemical evidence has revealed a mechanism whereby Mms2 properly orients ubiquitin to allow for Lys(63) conjugation by Ubc13; however, how this specific Ubc13-Mms2 complex is formed and why Mms2 does not form a complex with other Ubcs have not been reported. In order to address these questions, we used a structure-based approach to design mutations and characterize the human Ubc13-Mms2 interface. We used the yeast two-hybrid assay, glutathione S-transferase pull-downs, and surface plasmon resonance to test in vivo and in vitro binding. These experiments were paired with functional complementation and ubiquitin conjugation studies to provide in vivo and in vitro functional data. The results in this study allowed us to identify important residues of the Ubc13-Mms2 interface, determine a correlation between heterodimer formation and function, and conclude why Mms2 forms a specific complex with Ubc13 but not other Ubc proteins.
Collapse
Affiliation(s)
- Landon Pastushok
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | | | | | | |
Collapse
|
46
|
Rivoal J, Smith CR, Moraes TF, Turpin DH, Plaxton WC. A method for activity staining after native polyacrylamide gel electrophoresis using a coupled enzyme assay and fluorescence detection: application to the analysis of several glycolytic enzymes. Anal Biochem 2002; 300:94-9. [PMID: 11743696 DOI: 10.1006/abio.2001.5445] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe a method for the detection of isoforms of several glycolytic enzymes by activity staining after native PAGE. The staining is based on coupled enzyme assays carried out on the gel after electrophoresis and is linked to the disappearance of NADH, which is visualized by fluorescence. This method offers reliable and sensitive detection for phosphoenolpyruvate carboxylase, PPi-dependent phosphofructokinase, and pyruvate kinase from plant tissues. It can be applied to the detection of all enzymes which are normally detected spectrophotometrically using coupled enzyme assays consuming NAD(P)H.
Collapse
Affiliation(s)
- Jean Rivoal
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada.
| | | | | | | | | |
Collapse
|
47
|
Moraes TF, Edwards RA, McKenna S, Pastushok L, Xiao W, Glover JN, Ellison MJ. Crystal structure of the human ubiquitin conjugating enzyme complex, hMms2-hUbc13. Nat Struct Biol 2001; 8:669-73. [PMID: 11473255 DOI: 10.1038/90373] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ubiquitin conjugating enzyme complex Mms2-Ubc13 plays a key role in post-replicative DNA repair in yeast and the NF-kappaB signal transduction pathway in humans. This complex assembles novel polyubiquitin chains onto yet uncharacterized protein targets. Here we report the crystal structure of a complex between hMms2 (Uev1) and hUbc13 at 1.85 A resolution and a structure of free hMms2 at 1.9 A resolution. These structures reveal that the hMms2 monomer undergoes a localized conformational change upon interaction with hUbc13. The nature of the interface provides a physical basis for the preference of Mms2 for Ubc13 as a partner over a variety of other structurally similar ubiquitin-conjugating enzymes. The structure of the hMms2-hUbc13 complex provides the conceptual foundation for understanding the mechanism of Lys 63 multiubiquitin chain assembly and for its interactions with the RING finger proteins Rad5 and Traf6.
Collapse
Affiliation(s)
- T F Moraes
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G-2H7, Canada
| | | | | | | | | | | | | |
Collapse
|
48
|
Moraes TF, Plaxton WC. Purification and characterization of phosphoenolpyruvate carboxylase from Brassica napus (rapeseed) suspension cell cultures: implications for phosphoenolpyruvate carboxylase regulation during phosphate starvation, and the integration of glycolysis with nitrogen assimilation. Eur J Biochem 2000; 267:4465-76. [PMID: 10880970 DOI: 10.1046/j.1432-1327.2000.01495.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) specific activity increased by 250% following 8 to 10 days of Pi starvation of Brassica napus suspension cells. Densitometric scanning of PEPC immunoblots revealed a close correlation between PEPC activity and the amount of the antigenic 104-kDa PEPC subunit. To further assess the influence of Pi deprivation on PEPC, the enzyme was purified from Pi-sufficient (+Pi) and Pi-starved (-Pi) cells to electrophoretic homogeneity and final specific activities of 37-40 micromol phosphoenolpyruvate utilized per min per mg protein. Gel filtration, SDS/PAGE, and CNBr peptide mapping indicated that the +Pi and -Pi PEPCs are both homotetramers composed of an identical 104-kDa subunit. Respective pH-activity profiles, phosphoenolpyruvate saturation kinetics, and sensitivity to L-malate inhibition were also indistinguishable. Kinetic studies and phosphatase treatments revealed that PEPC of the +Pi and -Pi cells exists mainly in its dephosphorylated (L-malate sensitive) form. Thus, up-regulation of PEPC activity in -Pi cells appears to be solely due to the accumulation of the same PEPC isoform being expressed in +Pi cells. PEPC activity was modulated by several metabolites involved in carbon and nitrogen metabolism. At pH 7.3, marked activation by glucose 6-phosphate and inhibition by L-malate, L-aspartate, L-glutamate, DL-isocitrate, rutin and quercetin was observed. The following paper provides a model for the coordinate regulation of B. napus PEPC and cytosolic pyruvate kinase by allosteric effectors. L-Aspartate and L-glutamate appear to play a crucial role in the control of the phosphoenolpyruvate branchpoint in B. napus, particularly with respect to the integration of carbohydrate partitioning with the generation of carbon skeletons required during nitrogen assimilation.
Collapse
Affiliation(s)
- T F Moraes
- Departments of Biochemistry and Biology, Queen's University, Kingston, Ontario, Canada
| | | |
Collapse
|