title: Consensus computational network analysis for identifying candidate outer membrane proteins from Borrelia spirochetes.
abstract: Similar to Gram-negative organisms, Borrelia spirochetes are dual-membrane organisms with both an inner and outer membrane. Although the outer membrane contains integral membrane proteins, few of the borrelial outer membrane proteins (OMPs) have been identified and characterized to date. Therefore, we utilized a consensus computational network analysis to identify novel borrelial OMPs.
  
  
  
  Using a series of computer-based algorithms, we selected all protein-encoding sequences predicted to be OM-localized and/or to form β-barrels in the borrelial OM. Using this system, we identified 41 potential OMPs from B. burgdorferi and characterized three (BB0838, BB0405, and BB0406) to confirm that our computer-based methodology did, in fact, identify borrelial OMPs. Triton X-114 phase partitioning revealed that BB0838 is found in the detergent phase, which would be expected of a membrane protein. Proteolysis assays indicate that BB0838 is partially sensitive to both proteinase K and trypsin, further indicating that BB0838 is surface-exposed. Consistent with a prior study, we also confirmed that BB0405 is surface-exposed and associates with the borrelial OM. Furthermore, we have shown that BB0406, the product of a co-transcribed downstream gene, also encodes a novel, previously uncharacterized borrelial OMP. Interestingly, while BB0406 has several physicochemical properties consistent with it being an OMP, it was found to be resistant to surface proteolysis. Consistent with BB0405 and BB0406 being OMPs, both were found to be capable of incorporating into liposomes and exhibit pore-forming activity, suggesting that both proteins are porins. Lastly, we expanded our computational analysis to identify OMPs from other borrelial organisms, including both Lyme disease and relapsing fever spirochetes.
  
  
  
  Using a consensus computer algorithm, we generated a list of candidate OMPs for both Lyme disease and relapsing fever spirochetes and determined that three of the predicted B. burgdorferi proteins identified were indeed novel borrelial OMPs. The combined studies have identified putative spirochetal OMPs that can now be examined for their roles in virulence, physiology, and disease pathogenesis. Importantly, the studies described in this report provide a framework by which OMPs from any human pathogen with a diderm ultrastructure could be cataloged to identify novel virulence factors and vaccine candidates.
authors.affiliation: Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA.
authors.forename: Melisha R
authors.initials: MR
authors.lastname: Kenedy
authors.affiliation: Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA.
authors.forename: Edgar J
authors.initials: EJ
authors.lastname: Scott
authors.affiliation: Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA.
authors.forename: Binu
authors.initials: B
authors.lastname: Shrestha
authors.affiliation: Department of Medicine, University of Connecticut Health Center, Farmington, Connecticut, 06030, USA.
authors.forename: Arvind
authors.initials: A
authors.lastname: Anand
authors.affiliation: Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA.
authors.forename: Henna
authors.initials: H
authors.lastname: Iqbal
authors.affiliation: Department of Medicine, University of Connecticut Health Center, Farmington, Connecticut, 06030, USA.|Department of Pediatrics, University of Connecticut Health Center, Farmington, Connecticut, 06030, USA.|Department of Genetics and Genomic Science, University of Connecticut Health Center, Farmington, Connecticut, 06030, USA.|Department of Immunology, University of Connecticut Health Center, Farmington, Connecticut, 06030, USA.|Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, 06030, USA.
authors.forename: Justin D
authors.initials: JD
authors.lastname: Radolf
authors.affiliation: Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA.
authors.forename: David W
authors.initials: DW
authors.lastname: Dyer
authors.affiliation: Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA. darrin-akins@ouhsc.edu.
authors.forename: Darrin R
authors.initials: DR
authors.lastname: Akins
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D025065:Borrelia burgdorferi / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D003195:Computer Communication Networks; D003205:Computing Methodologies; D032921:Consensus; D016680:Genome, Bacterial; D006801:Humans; D008081:Liposomes / Q000378:metabolism; D008193:Lyme Disease / Q000382:microbiology; D009876:Operon; D018272:Porins / Q000378:metabolism; D064166:Vaccine Potency; D037521:Virulence Factors / Q000378:metabolism
chemical_list: D001425:Bacterial Outer Membrane Proteins; D008081:Liposomes; D018272:Porins; D037521:Virulence Factors
keywords: Borrelia; Lyme disease; Outer membrane proteins; Relapsing fever