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Radka CD, Labiuk SL, DeLucas LJ, Aller SG. Structures of the substrate-binding protein YfeA in apo and zinc-reconstituted holo forms. Acta Crystallogr D Struct Biol 2019; 75:831-840. [PMID: 31478906 PMCID: PMC6719664 DOI: 10.1107/s2059798319010866] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/02/2019] [Indexed: 12/23/2022] Open
Abstract
In the structural biology of bacterial substrate-binding proteins (SBPs), a growing number of comparisons between substrate-bound and substrate-free forms of metal atom-binding (cluster A-I) SBPs have revealed minimal structural differences between forms. These observations contrast with SBPs that bind substrates such as amino acids or nucleic acids and may undergo >60° rigid-body rotations. Substrate transfer in these SBPs is described by a Venus flytrap model, although this model may not apply to all SBPs. In this report, structures are presented of substrate-free (apo) and reconstituted substrate-bound (holo) YfeA, a polyspecific cluster A-I SBP from Yersinia pestis. It is demonstrated that an apo cluster A-I SBP can be purified by fractionation when co-expressed with its cognate transporter, adding an alternative strategy to the mutagenesis or biochemical treatment used to generate other apo cluster A-I SBPs. The apo YfeA structure contains 111 disordered protein atoms in a mobile helix located in the flexible carboxy-terminal lobe. Metal binding triggers a 15-fold reduction in the solvent-accessible surface area of the metal-binding site and reordering of the 111 protein atoms in the mobile helix. The flexible lobe undergoes a 13.6° rigid-body rotation that is driven by a spring-hammer metal-binding mechanism. This asymmetric rigid-body rotation may be unique to metal atom-binding SBPs (i.e. clusters A-I, A-II and D-IV).
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Affiliation(s)
- Christopher D. Radka
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shaunivan L. Labiuk
- Canadian Macromolecular Crystallography Facility, Canadian Light Source, Saskatoon, SK S7N 2V3, Canada
| | - Lawrence J. DeLucas
- Division of Human Exploration and Spaceflight, Aerospace Corporation, El Segundo, CA 90245, USA
| | - Stephen G. Aller
- Department of Pharmacology and Toxicology, Birmingham, AL 35294, USA
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Immunoproteomic analyses of outer membrane antigens of Actinobacillus pleuropneumoniae grown under iron-restricted conditions. Vet Microbiol 2012; 159:187-94. [DOI: 10.1016/j.vetmic.2012.03.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 03/30/2012] [Accepted: 03/31/2012] [Indexed: 11/18/2022]
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Wu Z, Zhang W, Shao J, Wang Y, Lu Y, Lu C. Immunoproteomic assay of secreted proteins of Streptococcus suis serotype 9 with convalescent sera from pigs. Folia Microbiol (Praha) 2011; 56:423-30. [DOI: 10.1007/s12223-011-0065-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 08/25/2011] [Indexed: 10/17/2022]
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Xu Z, Chen H, Zhou R. Genome-wide evidence for positive selection and recombination in Actinobacillus pleuropneumoniae. BMC Evol Biol 2011; 11:203. [PMID: 21749728 PMCID: PMC3146884 DOI: 10.1186/1471-2148-11-203] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 07/13/2011] [Indexed: 11/10/2022] Open
Abstract
Background Actinobacillus pleuropneumoniae is an economically important animal pathogen that causes contagious pleuropneumonia in pigs. Currently, the molecular evolutionary trajectories for this pathogenic bacterium remain to require a better elucidation under the help of comparative genomics data. For this reason, we employed a comparative phylogenomic approach to obtain a comprehensive understanding of roles of natural selective pressure and homologous recombination during adaptation of this pathogen to its swine host. Results In this study, 12 A. pleuropneumoniae genomes were used to carry out a phylogenomic analyses. We identified 1,587 orthologous core genes as an initial data set for the estimation of genetic recombination and positive selection. Based on the analyses of four recombination tests, 23% of the core genome of A. pleuropneumoniae showed strong signals for intragenic homologous recombination. Furthermore, the selection analyses indicated that 57 genes were undergoing significant positive selection. Extensive function properties underlying these positively selected genes demonstrated that genes coding for products relevant to bacterial surface structures and pathogenesis are prone to natural selective pressure, presumably due to their potential roles in the avoidance of the porcine immune system. Conclusions Overall, substantial genetic evidence was shown to indicate that recombination and positive selection indeed play a crucial role in the adaptive evolution of A. pleuropneumoniae. The genome-wide profile of positively selected genes and/or amino acid residues will provide valuable targets for further research into the mechanisms of immune evasion and host-pathogen interactions for this serious swine pathogen.
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Affiliation(s)
- Zhuofei Xu
- Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
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Zhang W, Shao J, Liu G, Tang F, Lu Y, Zhai Z, Wang Y, Wu Z, Yao H, Lu C. Immunoproteomic analysis of bacterial proteins of Actinobacillus pleuropneumoniae serotype 1. Proteome Sci 2011; 9:32. [PMID: 21703014 PMCID: PMC3148531 DOI: 10.1186/1477-5956-9-32] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Accepted: 06/26/2011] [Indexed: 11/10/2022] Open
Abstract
Background Actinobacillus pleuropneumoniae (APP) is one of the most important swine pathogens worldwide. Identification and characterization of novel antigenic APP vaccine candidates are underway. In the present study, we use an immunoproteomic approach to identify APP protein antigens that may elicit an immune response in serotype 1 naturally infected swine and serotype 1 virulent strain S259-immunized rabbits. Results Proteins from total cell lysates of serotype 1 APP were separated by two-dimensional electrophoresis (2DE). Western blot analysis revealed 21 immunoreactive protein spots separated in the pH 4-7 range and 4 spots in the pH 7-11 range with the convalescent sera from swine; we found 5 immunoreactive protein spots that separated in the pH 4-7 range and 2 in the pH 7-11 range with hyperimmune sera from S259-immunized rabbits. The proteins included the known antigens ApxIIA, protective surface antigen D15, outer membrane proteins P5, subunit NqrA. The remaining antigens are being reported as immunoreactive proteins in APP for the first time, to our knowledge. Conclusions We identified a total of 42 immunoreactive proteins of the APP serotype 1 virulent strain S259 which represented 32 different proteins, including some novel immunoreactive factors which could be researched as vaccine candidates.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Shao
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Guangjin Liu
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Fang Tang
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Lu
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhipeng Zhai
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Wang
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zongfu Wu
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Huochun Yao
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Chengping Lu
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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Müller A, León-Kempis MDR, Dodson E, Wilson KS, Wilkinson AJ, Kelly DJ. A Bacterial Virulence Factor with a Dual Role as an Adhesin and a Solute-binding Protein: The Crystal Structure at 1.5 Å Resolution of the PEB1a Protein from the Food-borne Human Pathogen Campylobacter jejuni. J Mol Biol 2007; 372:160-71. [PMID: 17631313 DOI: 10.1016/j.jmb.2007.06.041] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Revised: 06/13/2007] [Accepted: 06/14/2007] [Indexed: 12/20/2022]
Abstract
The PEB1a protein is an antigenic factor exposed on the surface of the food-borne human pathogen Campylobacter jejuni, which has a major role in adherence and host colonisation. PEB1a is also the periplasmic binding protein component of an aspartate/glutamate ABC transporter essential for optimal microaerobic growth on these dicarboxylic amino acids. Here, we report the crystal structure of PEB1a at 1.5 A resolution. The protein has a typical two-domain alpha/beta structure, characteristic of periplasmic extracytoplasmic solute receptors and a chain topology related to the type II subfamily. An aspartate ligand, clearly defined by electron density in the interdomain cleft, forms extensive polar interactions with the protein, the majority of which are made with the larger domain. Arg89 and Asp174 form ion-pairing interactions with the main chain alpha-carboxyl and alpha-amino-groups, respectively, of the ligand, while Arg67, Thr82, Lys19 and Tyr156 co-ordinate the ligand side-chain carboxyl group. Lys19 and Arg67 line a positively charged groove, which favours binding of Asp over the neutral Asn. The ligand-binding cleft is of sufficient depth to accommodate a glutamate. This is the first structure of an ABC-type aspartate-binding protein, and explains the high affinity of the protein for aspartate and glutamate, and its much weaker binding of asparagine and glutamine. Stopped-flow fluorescence spectroscopy indicates a simple bimolecular mechanism of ligand binding, with high association rate constants. Sequence alignments and phylogenetic analyses revealed PEB1a homologues in some Gram-positive bacteria. The alignments suggest a more distant homology with GltI from Escherichia coli, a known glutamate and aspartate-binding protein, but Lys19 and Tyr156 are not conserved in GltI. Our results provide a structural basis for understanding both the solute transport and adhesin/virulence functions of PEB1a.
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Affiliation(s)
- Axel Müller
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK
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Müller A, Thomas GH, Horler R, Brannigan JA, Blagova E, Levdikov VM, Fogg MJ, Wilson KS, Wilkinson AJ. An ATP-binding cassette-type cysteine transporter in Campylobacter jejuni inferred from the structure of an extracytoplasmic solute receptor protein. Mol Microbiol 2005; 57:143-55. [PMID: 15948956 DOI: 10.1111/j.1365-2958.2005.04691.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Campylobacter jejuni is a Gram-negative food-borne pathogen associated with gastroenteritis in humans as well as cases of the autoimmune disease Guillain-Barré syndrome. C. jejuni is asaccharolytic because it lacks an active glycolytic pathway for the use of sugars as a carbon source. This suggests an increased reliance on amino acids as nutrients and indeed the genome sequence of this organism indicates the presence of a number of amino acid uptake systems. Cj0982, also known as CjaA, is a putative extracytoplasmic solute receptor for one such uptake system as well as a major surface antigen and vaccine candidate. The crystal structure of Cj0982 reveals a two-domain protein with density in the enclosed cavity between the domains that clearly defines the presence of a bound cysteine ligand. Fluorescence titration experiments were used to demonstrate that Cj0982 binds cysteine tightly and specifically with a K(d) of approximately 10(-7) M consistent with a role as a receptor for a high-affinity transporter. These data imply that Cj0982 is the binding protein component of an ABC-type cysteine transporter system and that cysteine uptake is important in the physiology of C. jejuni.
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Affiliation(s)
- Axel Müller
- Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5YW, UK
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Garmory HS, Titball RW. ATP-binding cassette transporters are targets for the development of antibacterial vaccines and therapies. Infect Immun 2004; 72:6757-63. [PMID: 15557595 PMCID: PMC529116 DOI: 10.1128/iai.72.12.6757-6763.2004] [Citation(s) in RCA: 222] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Helen S Garmory
- Department of Biomedical Sciences, Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, United Kingdom.
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Baltes N, Gerlach GF. Identification of genes transcribed by Actinobacillus pleuropneumoniae in necrotic porcine lung tissue by using selective capture of transcribed sequences. Infect Immun 2004; 72:6711-6. [PMID: 15501809 PMCID: PMC523062 DOI: 10.1128/iai.72.11.6711-6716.2004] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Genes expressed by Actinobacillus pleuropneumoniae in necrotic porcine lung tissue were identified by selective capture of transcribed sequences analysis. In total, 46 genes were identified, 20 of which have been previously reported to be associated with in vivo expression or virulence in A. pleuropneumoniae or in other organisms.
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Affiliation(s)
- Nina Baltes
- Department of Infectious Diseases, Institute for Microbiology, University of Veterinary Medicine Hannover, Germany.
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Pawelec DP, Korsak D, Wyszyńska AK, Rozynek E, Popowski J, Jagusztyn-Krynicka EK. Genetic diversity of the Campylobacter genes coding immunodominant proteins. FEMS Microbiol Lett 2000; 185:43-9. [PMID: 10731605 DOI: 10.1111/j.1574-6968.2000.tb09038.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Three Campylobacter jejuni 72Dz/92 genes (cjaA (ompH1), cjaC (hisJ) and cjaD (omp18)) encoding immunodominant proteins are considered to be potential chicken vaccine candidates. The presence and conservation of cjaA, cjaC and cjaD genes among different Campylobacter clinical isolates were determined. The genes were detected in thirty Campylobacter strains using hybridization as well as Western blot analysis. However, PCR products of the predicted size were amplified only from ten out of thirty examined strains regardless of the employed primer pair. The nucleotide sequence of the C. jejuni 72Dz/92 genes was compared with the nucleotide sequences of their homologs cloned from other Campylobacter strains as well as with the whole genome sequence of C. jejuni NCTC 11168. The examined sequences revealed 0 to 16% divergence. Strain-dependent levels of divergence were observed. The polymorphism detected in cjaC was mainly within the 5' region of the gene, while the nucleotide substitutions in cjaA and cjaD are distributed uniformly along the whole genes. Most of the observed nucleotide substitutions occurred at the third base of the codons. This observation is consistent with the results of Western blot experiments.
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Affiliation(s)
- D P Pawelec
- Institute of Microbiology, Warsaw University, Nowy OEwiat 67, 00-046, Warsaw, Poland
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