scholarly journals Sequence variation of rare outer membrane protein β-barrel domains in clinical strains provides insights into the evolution ofTreponema pallidumsubsp.pallidum, the syphilis spirochete

2018 ◽  
Author(s):  
Sanjiv Kumar ◽  
Melissa J. Caimano ◽  
Arvind Anand ◽  
Abhishek Dey ◽  
Kelly L. Hawley ◽  
...  
Keyword(s):  
Outer Membrane ◽  
Evolutionary Biology ◽  
Sequence Variation ◽  
Vaccine Development ◽  
Outer Membrane Proteins ◽  
Treponema Pallidum ◽  
Clinical Strains ◽  
Extracellular Loops ◽  
Reference Strains ◽  
Reference Genomes

ABSTRACTIn recent years, considerable progress has been made in topologically and functionally characterizing integral outer membrane proteins (OMPs) ofTreponema pallidumsubspeciespallidum(TPA), the syphilis spirochete, and identifying its surface-exposed β-barrel domains. Extracellular loops in OMPs of Gram-negative bacteria are known to be highly variable. We examined the sequence diversity of β-barrel-encoding regions oftprC,tprD, andbamA, in 31 specimens from Cali, Colombia; San Francisco, California; and the Czech Republic and compared them to allelic variants in the 41 reference genomes in the NCBI database. To establish a phylogenetic framework, we usedtp0548genotyping andtp0558sequences to assign strains to the Nichols or SS14 clades. We found that (i) β-barrels in clinical strains could be grouped according to allelic variants inTPAreference genomes; (ii) for all three OMP loci, clinical strains within the Nichols or SS14 clades often harbored β-barrel variants that differed from the Nichols and SS14 reference strains; and (iii) OMP variable regions often reside in predicted extracellular loops containing B-cell epitopes. Based upon structural models, non-conservative amino acid substitutions in predicted transmembrane β-strands of TprC and TprD2 could give rise to functional differences in their porin channels. OMP profiles of some clinical strains were mosaics of different reference strains and did not correlate with results from enhanced molecular typing. Our observations suggest that human host selection pressures driveTPAOMP diversity and that genetic exchange contributes to the evolutionary biology ofTPA. They also set the stage for topology-based analysis of antibody responses against OMPs and help frame strategies for syphilis vaccine development.IMPORTANCEDespite recent progress characterizing outer membrane proteins (OMPs) ofTreponema pallidum(TPA), little is known about how their surface-exposed, β-barrel-forming domains vary among strains circulating within high-risk populations. In this study, sequences for the β-barrel-encoding regions of three OMP loci,tprC,tprD, andbamA,inTPAfrom a large number of patient specimens from geographically disparate sites were examined. Structural models predict that sequence variation within β-barrel domains occurred predominantly within predicted extracellular loops. Amino acid substitutions in predicted transmembrane strands that could potentially affect porin channel function also were noted. Our findings suggest that selection pressures exerted by human populations driveTPAOMP diversity and that recombination at OMP loci contributes to the evolutionary biology of syphilis spirochetes. These results also set the stage for topology-based analysis of antibody responses that promote clearance ofTPAand frame strategies for vaccine development based upon conserved OMP extracellular loops.

scholarly journals Sequence Variation of Rare Outer Membrane Protein β-Barrel Domains in Clinical Strains Provides Insights into the Evolution ofTreponema pallidumsubsp.pallidum, the Syphilis Spirochete

mBio ◽  
2018 ◽  
Vol 9 (3) ◽  
Author(s):  
Sanjiv Kumar ◽  
Melissa J. Caimano ◽  
Arvind Anand ◽  
Abhishek Dey ◽  
Kelly L. Hawley ◽  
...  
Keyword(s):  
Outer Membrane ◽  
Evolutionary Biology ◽  
Vaccine Development ◽  
Outer Membrane Proteins ◽  
Treponema Pallidum ◽  
Content Type ◽  
Clinical Strains ◽  
Extracellular Loops ◽  
Reference Strains ◽  
Reference Genomes

ABSTRACTIn recent years, considerable progress has been made in topologically and functionally characterizing integral outer membrane proteins (OMPs) ofTreponema pallidumsubspeciespallidum, the syphilis spirochete, and identifying its surface-exposed β-barrel domains. Extracellular loops in OMPs of Gram-negative bacteria are known to be highly variable. We examined the sequence diversity of β-barrel-encoding regions oftprC,tprD, andbamAin 31 specimens from Cali, Colombia; San Francisco, California; and the Czech Republic and compared them to allelic variants in the 41 reference genomes in the NCBI database. To establish a phylogenetic framework, we usedT. pallidum0548 (tp0548) genotyping andtp0558sequences to assign strains to the Nichols or SS14 clades. We found that (i) β-barrels in clinical strains could be grouped according to allelic variants inT. pallidumsubsp.pallidumreference genomes; (ii) for all three OMP loci, clinical strains within the Nichols or SS14 clades often harbored β-barrel variants that differed from the Nichols and SS14 reference strains; and (iii) OMP variable regions often reside in predicted extracellular loops containing B-cell epitopes. On the basis of structural models, nonconservative amino acid substitutions in predicted transmembrane β-strands ofT. pallidumrepeat C (TprC) and TprD2 could give rise to functional differences in their porin channels. OMP profiles of some clinical strains were mosaics of different reference strains and did not correlate with results from enhanced molecular typing. Our observations suggest that human host selection pressures driveT. pallidumsubsp.pallidumOMP diversity and that genetic exchange contributes to the evolutionary biology ofT. pallidumsubsp.pallidum. They also set the stage for topology-based analysis of antibody responses to OMPs and help frame strategies for syphilis vaccine development.IMPORTANCEDespite recent progress characterizing outer membrane proteins (OMPs) ofTreponema pallidum, little is known about how their surface-exposed, β-barrel-forming domains vary among strains circulating within high-risk populations. In this study, sequences for the β-barrel-encoding regions of three OMP loci,tprC,tprD, andbamA, inT. pallidumsubsp.pallidumisolates from a large number of patient specimens from geographically disparate sites were examined. Structural models predict that sequence variation within β-barrel domains occurs predominantly within predicted extracellular loops. Amino acid substitutions in predicted transmembrane strands that could potentially affect porin channel function were also noted. Our findings suggest that selection pressures exerted within human populations driveT. pallidumsubsp.pallidumOMP diversity and that recombination at OMP loci contributes to the evolutionary biology of syphilis spirochetes. These results also set the stage for topology-based analysis of antibody responses that promote clearance ofT. pallidumsubsp.pallidumand frame strategies for vaccine development based upon conserved OMP extracellular loops.

scholarly journals Simultaneous detection of LipL32 and LipL21 genes of pathogenic leptospira from serum samples of bovines by multiplex PCR

2011 ◽  
Vol 1 (1) ◽  
pp. 15
Author(s):  
Timiri V. Meenambigai ◽  
Gopalakrishnan Ravikumar ◽  
Andy Srithar ◽  
Govindan Balakrishnan ◽  
Chidambaram Saranya ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Multiplex Pcr ◽  
Outer Membrane ◽  
Vaccine Development ◽  
Outer Membrane Proteins ◽  
Simultaneous Detection ◽  
Serum Samples ◽  
Pathogenic Leptospira ◽  
Annealing Conditions ◽  
Reference Strains

<p>Leptospirosis is a worldwide zoonotic disease of cattle associated with pathogenic leptospiral infection. This study focuses in the use of a molecular tool to detect pathogenic leptospiral infection in bovines by targeting the outer membrane proteins LipL32 and LipL21 simultaneously in a multiplex PCR. Sixteen pathogenic reference strains and 10 bovine serum samples were analyzed for simultaneous detection of both genes at appropriate annealing conditions. These findings are suggestive of the fact that multiplex PCR can be used to detect major outer membrane proteins of pathogenic leptospira from serum samples. Further it aided in the differentiation of pathogenic and non-pathogenic species of leptospires too. This study will definitely serve as a valuable tool, as it suggests the importance of <em>LipL32</em> genes as potential candidates for vaccine development to control animal Leptospirosis.</p>

scholarly journals Transcriptional and immunological analysis of the putative outer membrane protein and vaccine candidate TprL of Treponema pallidum

2021 ◽  
Vol 15 (1) ◽  
pp. e0008812
Author(s):  
Austin M. Haynes ◽  
Mark Fernandez ◽  
Emily Romeis ◽  
Oriol Mitjà ◽  
Kelika A. Konda ◽  
...  
Keyword(s):  
Outer Membrane ◽  
Vaccine Development ◽  
Vaccine Candidate ◽  
Transcriptional Start Site ◽  
Outer Membrane Proteins ◽  
Treponema Pallidum ◽  
Phase Variation ◽  
Laboratory Animals ◽  
Transcriptional Level ◽  
Development Effort

Background An effective syphilis vaccine should elicit antibodies to Treponema pallidum subsp. pallidum (T. p. pallidum) surface antigens to induce pathogen clearance through opsonophagocytosis. Although the combination of bioinformatics, structural, and functional analyses of T. p. pallidum genes to identify putative outer membrane proteins (OMPs) resulted in a list of potential vaccine candidates, still very little is known about whether and how transcription of these genes is regulated during infection. This knowledge gap is a limitation to vaccine design, as immunity generated to an antigen that can be down-regulated or even silenced at the transcriptional level without affecting virulence would not induce clearance of the pathogen, hence allowing disease progression. Principal findings We report here that tp1031, the T. p. pallidum gene encoding the putative OMP and vaccine candidate TprL is differentially expressed in several T. p. pallidum strains, suggesting transcriptional regulation. Experimental identification of the tprL transcriptional start site revealed that a homopolymeric G sequence of varying length resides within the tprL promoter and that its length affects promoter activity compatible with phase variation. Conversely, in the closely related pathogen T. p. subsp. pertenue, the agent of yaws, where a naturally-occurring deletion has eliminated the tprL promoter region, elements necessary for protein synthesis, and part of the gene ORF, tprL transcription level are negligible compared to T. p. pallidum strains. Accordingly, the humoral response to TprL is absent in yaws-infected laboratory animals and patients compared to syphilis-infected subjects. Conclusion The ability of T. p. pallidum to stochastically vary tprL expression should be considered in any vaccine development effort that includes this antigen. The role of phase variation in contributing to T. p. pallidum antigenic diversity should be further studied.

scholarly journals Tight Turns of Outer Membrane Proteins: An Analysis of Sequence, Structure, and Hydrogen Bonding

2018 ◽  
Author(s):  
Meghan Whitney Franklin ◽  
Joanna S.G. Slusky
Keyword(s):  
Hydrogen Bonding ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Soluble Protein ◽  
Structure Prediction ◽  
Outer Membrane Proteins ◽  
Sequence Structure ◽  
Structural Class ◽  
Future Design ◽  
Extracellular Loops

I.AbstractAs a structural class, tight turns can control molecular recognition, enzymatic activity, and nucleation of folding. They have been extensively characterized in soluble proteins but have not been characterized in outer membrane proteins (OMPs), where they also support critical functions. We clustered the 4-6 residue tight turns of 110 OMPs to characterize the phi/psi angles, sequence, and hydrogen bonding of these structures. We find significant differences between reports of soluble protein tight turns and OMP tight turns. Since OMP strands are less twisted than soluble strands they favor different turn structures types. Moreover, the membrane localization of OMPs yields different sequence hallmarks for their tight turns relative to soluble protein turns. We also characterize the differences in phi/psi angles, sequence, and hydrogen bonding between OMP extracellular loops and OMP periplasmic turns. As previously noted, the extracellular loops tend to be much longer than the periplasmic turns. We find that this difference in length is due to the broader distribution of lengths of the extracellular loops not a large difference in the median length. Extracellular loops also tend to have more charged residues as predicted by the charge-out rule. Finally, in all OMP tight turns, hydrogen bonding between the sidechain and backbone two to four residues away plays an important role. These bonds preferentially use an Asp, Asn, Ser or Thr residue in a beta or pro phi/psi conformation. We anticipate that this study will be applicable to future design and structure prediction of OMPs.

scholarly journals Modification of Outer Membrane Protein Profile and Evidence Suggesting an Active Drug Pump in Enterobacter aerogenes Clinical Strains

2003 ◽  
Vol 47 (5) ◽  
pp. 1555-1559 ◽  
Author(s):  
Stéphane Gayet ◽  
Renaud Chollet ◽  
Gérard Molle ◽  
Jean-Marie Pagès ◽  
Jacqueline Chevalier
Keyword(s):  
Outer Membrane ◽  
Protein Profile ◽  
Outer Membrane Proteins ◽  
Enterobacter Aerogenes ◽  
Normal Structure ◽  
Clinical Strains ◽  
Resistance Strategies ◽  
Carbonyl Cyanide ◽  
Energy Dependent ◽  
Drug Pump

ABSTRACT Two clinical strains of Enterobacter aerogenes that exhibited phenotypes of multiresistance to β-lactam antibiotics, fluoroquinolones, chloramphenicol, tetracycline, and kanamycin were investigated. Both strains showed a porin pattern different from that of a susceptible strain, with a drastic reduction in the amount of the major porin but with an apparently conserved normal structure (size and immunogenicity), together with overproduction of two known outer membrane proteins, OmpX and LamB. In addition, the full-length O-polysaccharide phenotype was replaced by a semirough Ra phenotype. Moreover, in one isolate the intracellular accumulation of chloramphenicol was increased in the presence of the energy uncoupler carbonyl cyanide m-chlorophenylhydrazone, suggesting an energy-dependent efflux of chloramphenicol in this strain. The resistance strategies used by these isolates appear to be similar to that induced by stress in Escherichia coli cells.

scholarly journals Antigenic Organization of the N-Terminal Part of the Polymorphic Outer Membrane Proteins 90, 91A, and 91B of Chlamydophilaabortus

2003 ◽  
Vol 71 (6) ◽  
pp. 3240-3250 ◽  
Author(s):  
Evangelia Vretou ◽  
Panagiota Giannikopoulou ◽  
David Longbottom ◽  
Evgenia Psarrou
Keyword(s):  
Outer Membrane ◽  
Binding Sites ◽  
Outer Membrane Proteins ◽  
Single Amino Acid ◽  
Antigenic Peptides ◽  
Terminal Part ◽  
Passenger Domain ◽  
Recombinant Peptides ◽  
Type V ◽  
Reference Strains

ABSTRACT A series of overlapping recombinant antigens, 61 to 74 residues in length, representing polymorphic outer membrane protein 90 (POMP90) of Chlamydophila abortus and two recombinant peptides spanning gene fragment p91Bf99 of POMP91B were assessed by immunoblotting to determine the antigen-binding sites of 20 monoclonal antibodies to POMP90, -91A, and -91B. The epitopes were further restricted by scanning 52 overlapping synthetic 12-mer peptides representing the N-terminal part of POMP90, and the 12-mer epitopes were then analyzed by using hexapeptides to the resolution of a single amino acid. Ten epitopes were defined: 1, TSEEFQVKETSSGT; 2, SGAIYTCEGNVCISYAGKDSPL; 3, SLVFHKNCSTAE; 4, AIYADKLTIVSGGPTLFS; 5, SPKGGAISIKDS; 6, ITFDGNKIIKTS; 7, LRAKDGFGIFFY; 7a, DGFGIF; 7b, GIFFYD; 8, IFFYDPITGGGS; 8a, FFYDPIT; 9, GKIVFSGE; and 10, DLGTTL. The 20-mer peptide LRAKDGFGIFFYDPITGGGS was a major epitope that was recognized by seven antibodies. Epitopes 7 to 10 were conserved in reference strains of the former species C. psittaci, whereas the strong antigenic peptides FYDPIT and IVFSGE were conserved among members of the genus Chlamydophila. Epitopes 3 to 8 were located within the best-scoring beta-helical wrap (residues 148 to 293) predicted for POMP91B by the program BETAWRAP. Other studies have suggested an association of the POMPs with type V secretory autotransporter proteins. The results presented in this study provide some evidence for a passenger domain that is folded as a beta-helix pyramid with compact antigenic organization.

scholarly journals TP0453, a Concealed Outer Membrane Protein of Treponema pallidum, Enhances Membrane Permeability

2005 ◽  
Vol 187 (18) ◽  
pp. 6499-6508 ◽  
Author(s):  
Karsten R. O. Hazlett ◽  
David L. Cox ◽  
Marc Decaffmeyer ◽  
Michael P. Bennett ◽  
Daniel C. Desrosiers ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Outer Membrane ◽  
Outer Membrane Protein ◽  
Outer Membrane Proteins ◽  
Nutrient Transport ◽  
Treponema Pallidum ◽  
Protein S ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Membrane Spanning

ABSTRACT The outer membrane of Treponema pallidum, the noncultivable agent of venereal syphilis, contains a paucity of protein(s) which has yet to be definitively identified. In contrast, the outer membranes of gram-negative bacteria contain abundant immunogenic membrane-spanning β-barrel proteins mainly involved in nutrient transport. The absence of orthologs of gram-negative porins and outer membrane nutrient-specific transporters in the T. pallidum genome predicts that nutrient transport across the outer membrane must differ fundamentally in T. pallidum and gram-negative bacteria. Here we describe a T. pallidum outer membrane protein (TP0453) that, in contrast to all integral outer membrane proteins of known structure, lacks extensive β-sheet structure and does not traverse the outer membrane to become surface exposed. TP0453 is a lipoprotein with an amphiphilic polypeptide containing multiple membrane-inserting, amphipathic α-helices. Insertion of the recombinant, nonlipidated protein into artificial membranes results in bilayer destabilization and enhanced permeability. Our findings lead us to hypothesize that TP0453 is a novel type of bacterial outer membrane protein which may render the T. pallidum outer membrane permeable to nutrients while remaining inaccessible to antibody.

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