Antigen

Publication

Pathogen Studied

Key Research Approach

Summarized Methodology of Publication

UniProt IDs & FASTA Sequences

19 kDa fibrinogen-binding protein (Fib)

Cloning of 19kDa fibrinogen-binding protein gene from Staphylococcus aureus

Staphylococcus aureus

Gene Cloning

Cloning, sequencing, and expression analysis of the gene encoding a fibrinogen-binding protein.

19-kDa lipoprotein

Toll-Like Receptor 2-Dependent Inhibition of Macrophage Class II MHC Expression and Antigen Processing by 19-kDa Lipoprotein of Mycobacterium tuberculosis9

Mycobacterium tuberculosis

Flow cytometry & Immunoassays

Studied the effect of the 19-kDa lipoprotein on MHC class II expression and antigen processing in macrophages. They used flow cytometry and T cell hybridoma assays to assess the impact of the lipoprotein and the role of Toll-like receptor 2 in this process.

38-kDa glycolipoprotein

The 38-kDa Antigen of Mycobacterium tuberculosis Induced in Vitro Potent Activation of Human Monocytes3

Mycobacterium tuberculosis

Immunoassays

Investigated the activation of human monocytes by the 38-kDa glycolipoprotein, comparing it to the 19-kDa lipoprotein. They measured cytokine production and MAPK activation.

19-kDa lipoprotein

The 38-kDa Antigen of Mycobacterium tuberculosis Induced in Vitro Potent Activation of Human Monocytes

Mycobacterium tuberculosis

Immunoassays

Investigated the activation of human monocytes by the 38-kDa glycolipoprotein, comparing it to the 19-kDa lipoprotein. They measured cytokine production and MAPK activation.

ACME-arcA

Two novel arginine catabolic mobile elements in CA-MRSA

Staphylococcus aureus (CA-MRSA)

PCR and Genome Analysis

Characterization of ACME-SCCmec composite islands in MRSA via PCR and sequencing.

AcrB multidrug efflux pump

Structural Basis of Drug Export by the Escherichia coli RND Efflux Pump AcrB6

Escherichia coli

Structural Study

Studied the structure of the AcrB multidrug efflux pump using designed ankyrin repeat proteins (DARPins) as inhibitors. They determined the crystal structure of AcrB in complex with a DARPin inhibitor.

AdeFGH efflux pump

Overexpression of Resistance-Nodulation-Cell Division Pump AdeFGH Confers Multidrug Resistance in Acinetobacter baumannii

Acinetobacter baumannii

Genome and Transcriptome Analysis

Selection of MDR mutants, transcriptome analysis, efflux pump gene identification

ADP-ribosyltransferase toxins (ExoA, cholix toxin)

Characterization of Antivirulence Compounds Inhibiting mART Toxins (2011)

Pseudomonas aeruginosa, Vibrio cholerae

Antibacterials Screening & Structural Analysis

In silico screening, compound testing against bacterial toxins, and crystal structure analysis to develop antivirulence agents.

Arginine catabolic mobile element (ACME)

Parallel Epidemics of Community-Associated MRSA USA300

Staphylococcus aureus (MRSA)

Epidemiological Study

Genomic sequencing and phylogenetic analysis to compare USA300 MRSA clones across continents.

Ata (trimeric autotransporter adhesin)

The Acinetobacter trimeric autotransporter adhesin Ata

Acinetobacter baumannii

Virulence Factors Study

Generation of Ata deletion mutants to study adhesion and invasion in human cells.

CarO protein

Small-Molecule Transport by CarO, an Abundant Eight-Stranded β-Barrel Outer Membrane Protein from Acinetobacter baumannii

Acinetobacter baumannii

Structural analysis and Functional assays

Crystal structures of CarO isoforms determined and transport activity tested using molecular dynamics simulations.

Cytidine triphosphate synthetase (CTPS)

Crystal Structure of Escherichia coli Cytidine Triphosphate Synthetase, a Nucleotide-Regulated Glutamine Amidotransferase/ATP-Dependent Amidoligase Fusion Protein

Escherichia coli

Structural Determination and Regulatory Analysis

Crystal structure determination using Hg-MAD phasing to analyze nucleotide-binding and allosteric sites.

Efb-C

Electrostatic contributions in Staphylococcus aureus protein Efb-C

Staphylococcus aureus

Structural Analysis

Structural and computational analysis of binding interactions between Efb-C and C3d.

Exotoxin A

Biochemical and Immunochemical Studies of Proteolytic Fragments of Exotoxin A from Pseudomonas aeruginosa

Pseudomonas aeruginosa

Biochemical and Immunochemical assays

Studied proteolysis with different proteases, activity assays and antibody neutralization studies

Exotoxin A (ETA)

Cloning, nucleotide sequence, and expression in Escherichia coli of the exotoxin A structural gene of Pseudomonas aeruginosa

Pseudomonas aeruginosa

Gene cloning, Expression, and Sequence Analysis

Cloning and sequence analysis of ETA gene, followed by expression in E. coli to confirm ADP-ribosylation activity.

Exotoxin A (ExoA)

The nature and character of the transition state for the ADP-ribosyltransferase reaction

Pseudomonas aeruginosa

Structural and Mutational Analysis

Site-directed mutagenesis and crystallography to investigate ADP-ribosyltransferase reaction of ExoA.

Exotoxin A Domain III

The crystal structure of Pseudomonas aeruginosa exotoxin domain III with nicotinamide and AMP

Pseudomonas aeruginosa

Crystallographic Analysis

Crystallographic analysis of exotoxin domain III, with comparisons to diphtheria toxin structure.

Extracellular fibrinogen-binding protein (Efb)

Extracellular Fibrinogen-binding Protein from Staphylococcus aureus

Staphylococcus aureus

Binding Assays

Binding assays to determine Efb's role in platelet aggregation inhibition.

FtsH protease

Functional Characterization of AAA Family FtsH Protease of Mycobacterium tuberculosis

Mycobacterium tuberculosis

Functional Analysis via Assays

Complementation of lethality in E. coli, proteolytic activity assays on heat shock proteins

graR regulator in graSR system

Mutated Response Regulator graR in Staphylococcus aureus and its Role in Vancomycin Resistance

Staphylococcus aureus (MRSA)

Genetic Mutation and Resistance Mechanism Studies

Mutation introduction in graR, conversion studies from hetero-VISA to VISA phenotype

IsdA, IsdB, SdrD, SdrE

Vaccine assembly from surface proteins of Staphylococcus aureus

Staphylococcus aureus

Vaccine Development

Immunization with cell wall-anchored proteins in mice to test immune response and protection.

MdfA multidrug resistance protein

Substrate-bound structure of the E. coli multidrug resistance transporter MdfA

Escherichia coli

Gene and Protein Analysis

Identified and sequenced the mdfA gene, which encodes a multidrug resistance protein. Analyzed the predicted protein sequence and structure of MdfA.

MdtABC multidrug efflux pump

Identification and Characterization of the BaeSR Two-Component Regulatory System Required for Multidrug Resistance in Escherichia coli

Escherichia coli

Functional Analysis and Drug Susceptibility Testing

Identified a two-component regulatory system, BaeSR, involved in multidrug resistance. They investigated its role in regulating the expression of the MdtABC efflux pump and its effect on drug susceptibility.

O Antigen

Structure of the K-12 O Antigen and rfb Sequence1

Escherichia coli

Gene Analysis and Comparative Gene Study

Sequenced the rfb gene cluster, responsible for O antigen synthesis. They compared this sequence to those from other E. coli and Salmonella enterica strains.

O Antigen

Genetic Variation at the O-Antigen Biosynthetic Locus in Pseudomonas aeruginosa

Pseudomonas aeruginosa

Genome Analysis and PCR

Whole-genome sequencing and PCR methods were used to analyze the O-antigen biosynthetic gene cluster in 20 P. aeruginosa strains.

OmpK17

Molecular characterization of a 17-kDa outer-membrane protein from Klebsiella pneumoniae

Klebsiella pneumoniae

Immunological Study and Resistance Analysis

Tn5 insertions and immunoblotting to identify and characterize OmpK17 in relation to bacteriocin resistance.

OmpK36 porin protein

Crystal structure and functional characterization of OmpK36, the osmoporin of Klebsiella pneumoniae

Klebsiella pneumoniae

Structural Analysis and functional Assay

X-ray crystallography of OmpK36 and functional assays in lipid bilayers to measure permeability and cation selectivity.

Outer membrane porin protein OprD

Analysis of two gene regions involved in the expression of the imipenem-specific, outer membrane porin protein OprD of Pseudomonas aeruginosa

Pseudomonas aeruginosa

Gene Expression and Protein Analysis

Complementation and DNA sequencing to identify OprD gene regulation sites.

Outer membrane protein A (KpOmpA)

Solution State NMR Structure and Dynamics of KpOmpA, a 210 Residue Transmembrane Domain Possessing a High Potential for Immunological Applications

Klebsiella pneumoniae

Structural Analysis and Immunogenic Potential Assessment

NMR spectroscopy used to determine 3D structure and dynamics of transmembrane domain.

Outer membrane protein A (OmpA)

Chromosomal sequencing using a PCR-based biotin-capture method allowed isolation of the complete gene for the outer membrane protein A of Klebsiella pneumoniae

Klebsiella pneumoniae

Genome Sequencing and PCR

Biotin-capture and PCR-based sequencing of OmpA gene, followed by expression in E. coli for protein recovery.

Penicillin-binding protein 2a (PBP2a)

Conformational dynamics in penicillin-binding protein 2a of methicillin-resistant Staphylococcus aureus, allosteric communication network and enablement of catalysis

Staphylococcus aureus

Structural Analysis

Computational and crystallographic studies on PBP2a binding dynamics with β-lactam antibiotics and structural changes.

Penicillin-binding protein 2a (PBP2a)

Characterization of methicillin-resistant Staphylococcus aureus displaying increased MICs of ceftaroline

Staphylococcus aureus (MRSA)

Drug Resistance Analysis

Analysis of PBP2a binding affinity variations linked to ceftaroline resistance.

Penicillin-binding protein PBP2

Molecular cloning and nucleotide sequence determination of the regulator region of mecA gene in methicillin-resistant Staphylococcus aureus

Staphylococcus aureus

Gene Cloning and Regulatory Sequence Analysis

Sequencing of mecA regulatory region in MRSA to understand methicillin resistance.

PepN

Nucleotide sequence of the pepN gene encoding aminopeptidase N of Escherichia coli

Escherichia coli

Enzymatic Activity Study

Characterization of PepN substrate specificity and response to stress conditions.

Pks15/1 polyketide synthase

Development of Escherichia coli and Mycobacterium smegmatis recombinants expressing major Mycobacterium tuberculosis-specific antigenic proteins

Mycobacterium smegmatis

Gene Cloning, Chromatography and Mass Spectrometry

loned the Mycobacterium tuberculosis pks15/1 gene into Mycobacterium smegmatis and investigated the resulting glycolipid production using thin-layer chromatography and mass spectrometry.

PlpD lipase

Structural basis of lipid targeting and destruction by the Type V secretion system of Pseudomonas aeruginosa

Pseudomonas aeruginosa

Structural Analysis and Enzymatic Assays

Crystal structure analysis of PlpD, with lipid-binding studies and phospholipase activity assays.

Porin F

Sequence and Transcriptional Start of Porin F Gene in P. aeruginosa (1988)

Pseudomonas aeruginosa

Gene Sequencing & Expression Analysis

Isolation of Porin F gene, DNA sequencing, and transcription start site mapping to study antigenic cross-reactivity.

Protein D2 (OprD)

Nucleotide Sequence of the Protein D2 Gene of Pseudomonas aeruginosa

Pseudomonas aeruginosa

Gene Sequencing, Cloning and Immuno Blotting

Cloning and sequencing of oprD gene, Western blot for protein identification

Protein D2 (OprD) protease

Identification of the Catalytic Triad of the Protein D2 Protease in Pseudomonas aeruginosa

Pseudomonas aeruginosa

Protein Identification and Mutagenesis

Site-directed mutagenesis was used to confirm catalytic triad residues of OprD protease.

Protein D2 channel

Protein D2 channel of the Pseudomonas aeruginosa outer membrane has a binding site for basic amino acids and peptides

Pseudomonas aeruginosa

Inhibition assays

Inhibition assays with basic amino acids to characterize binding specificity of the D2 channel for imipenem transport.

Protein D2 porin

Protein D2 porin of the Pseudomonas aeruginosa outer membrane bears the protease activity

Pseudomonas aeruginosa

Inhibition and Activity Assays

Activity assays and inhibition studies to assess protease function of D2 porin.

Pseudomonas Exotoxin (PE)

Mutagenesis of Pseudomonas exotoxin in identification of sequences responsible for the animal toxicity

Pseudomonas aeruginosa

Mutagenesis and Functional Analysis

Constructed mutants of Pseudomonas Exotoxin to map toxicity-related sequences using a periplasmic expression system.

Pseudomonas Exotoxin A (PE)

The alpha 2-macroglobulin receptor/low density lipoprotein receptor-related protein binds and internalizes Pseudomonas exotoxin A

Pseudomonas aeruginosa

Receptor-ligand binding and toxicity assay

Affinity-purified a2MR/LRP shown to specifically bind and internalize PE, validated by SDS-PAGE and binding assays.

Pseudomonas Exotoxin A (PE)

Active Site of Pseudomonas aeruginosa Exotoxin A: Glutamic Acid 553 is Photolabeled by NAD and Shows Functional Homology with Glutamic Acid 148 of Diphtheria Toxin

Pseudomonas aeruginosa

Photoaffinity Labeling and Active Site Identification

Photolabeling with NAD to identify Glu-553, a catalytic residue homologous to diphtheria toxin Glu-148.

recA protein

Mycobacterium leprae RecA is structurally analogous but functionally distinct from Mycobacterium tuberculosis RecA protein

Mycobacterium leprae, Mycobacterium tuberculosis

Comparative Functional Assays

In vitro functional assays comparing DNA-binding, ATPase, and coprotease activities of RecA proteins.

SCCmec (mecA, PBP2a)

Structural Comparison of Staphylococcal Cassette Chromosome mec in Methicillin-Resistant Staphylococcus aureus

Staphylococcus aureus (MRSA)

Comparative Genome Study and PCR Analysis

Analysis of SCCmec variants in MRSA strains worldwide, PCR and sequence alignment

SCCmec (methicillin-resistance determinant)

The emergence and evolution of methicillin-resistant Staphylococcus aureus

Staphylococcus aureus

Genome Study and Evolutionary Analysis

Analysis of SCCmec integration into the S. aureus genome and evolution towards multi-drug resistance.

SCCmec element

Insights on antibiotic resistance of Staphylococcus aureus from its whole genome: genomic island SCC

Staphylococcus aureus

Genome Analysis and Comparative Study

Genomic sequencing and comparative analysis of MRSA strains to examine SCCmec and other resistance factors.

SCCmec type IVA

CA-MRSA SCCmec Type IVA in South Korea (2007)

Methicillin-resistant Staphylococcus aureus (MRSA)

Epidemiological Study & PCR Typing

Typing of SCCmec elements and PVL gene in MRSA isolates from community and hospital settings in South Korea.

Panton-Valentine leukocidin (pvl)

CA-MRSA SCCmec Type IVA in South Korea (2007)

Methicillin-resistant Staphylococcus aureus (MRSA)

Epidemiological Study & PCR Typing

Typing of SCCmec elements and PVL gene in MRSA isolates from community and hospital settings in South Korea.

SCCmec type Ivg

Genetic diversity of MRSA carrying type IV SCCmec in Sweden

Staphylococcus aureus (MRSA)

MLST and spa Typing

Multilocus sequence and spa typing to identify SCCmec subtypes in MRSA isolates.

SCCmec types I-VIII

Multiplex PCR for SCCmec Typing in MRSA (2009)

Methicillin-resistant Staphylococcus aureus (MRSA)

PCR Assay and Molecular Epidemiology

Developed a multiplex PCR assay for rapid SCCmec typing across various MRSA strains.

SCCmec

Novel SCCmec Composite Island with Arginine Catabolic Mobile Element in MRSA (2013)

Methicillin-resistant Staphylococcus aureus (MRSA)

Genomic Analysis & Comparative Genome Study

Whole-genome sequencing and sequence comparison for novel genetic elements in MRSA from Dutch-German border area.

ACME

Novel SCCmec Composite Island with Arginine Catabolic Mobile Element in MRSA (2013)

Methicillin-resistant Staphylococcus aureus (MRSA)

Genomic Characterization & Comparative Genome Study

Whole-genome sequencing and sequence comparison for novel genetic elements in MRSA from Dutch-German border area.

SCCmec

Novel Staphylococcal Cassette Chromosome mec Type VIII in MRSA (2009)

Methicillin-resistant Staphylococcus aureus (MRSA)

Genome Analysis and PCR

Screening MRSA isolates for SCCmec types via PCR, sequence analysis to identify novel SCCmec Type VIII.

mecA

Novel Staphylococcal Cassette Chromosome mec Type VIII in MRSA (2009)

Methicillin-resistant Staphylococcus aureus (MRSA)

Genome Analysis and PCR

Screening MRSA isolates for SCCmec types via PCR, sequence analysis to identify novel SCCmec Type VIII.

ccr gene complexes

Novel Staphylococcal Cassette Chromosome mec Type VIII in MRSA (2009)

Methicillin-resistant Staphylococcus aureus (MRSA)

Genome Analysis and PCR

Screening MRSA isolates for SCCmec types via PCR, sequence analysis to identify novel SCCmec Type VIII.

ssl7 (Staphylococcal superantigen-like protein 7)

The Staphylococcal Superantigen-Like Protein 7 Binds IgA and Complement C5 and Inhibits IgA-FcαRI Binding and Serum Killing of Bacteria10

Staphylococcus aureus

Binding, Functional and Immuno Assays

The researchers characterized the function of SSL7, a staphylococcal superantigen-like protein. They used binding assays, complement hemolytic assays, and bacterial killing assays to determine SSL7's interactions with IgA, complement C5, and its effect on IgA-FcαRI binding and bacterial survival.

Staphylococcal cassette chromosome mec (SCCmec) type IVA

Two variants of SCCmec type IVA in CA-MRSA strains in South Korea

Staphylococcus aureus (CA-MRSA)

Comparative Genome Analysis and Molecular Typing

Comparison of SCCmec IVA subtypes using sequencing and molecular typing.

Translational initiation factor IF2

Identification, cloning and sequence of the Streptococcus faecium infB (translational initiation factor IF2) gene

Streptococcus faecium

Gene Cloning and Sequence Analysis

DNA cross-hybridization and sequence alignment with Bacillus stearothermophilus IF2 gene.

XcpQ

Structural Basis of Type 2 Secretion System in P. aeruginosa (2017)

Pseudomonas aeruginosa

Structural Study via Electron Microscopy

Cryo-electron microscopy to analyze the T2SS structure and mechanism for protein secretion.

Type 2 Secretion System (T2SS)

Structural Basis of Type 2 Secretion System in P. aeruginosa (2017)

Pseudomonas aeruginosa

Structural Study via Electron Microscopy

Cryo-electron microscopy to analyze the T2SS structure and mechanism for protein secretion.

mecA

Novel Type of Staphylococcal Cassette Chromosome mec in Community-Acquired Methicillin-Resistant Staphylococcus aureus

Staphylococcus aureus (Community-Acquired MRSA)

Comparative Genome Study and PCR

Characterization of SCCmec in community-acquired MRSA, PCR and sequence comparison

PBP2a

Novel Type of Staphylococcal Cassette Chromosome mec in Community-Acquired Methicillin-Resistant Staphylococcus aureus

Staphylococcus aureus (Community-Acquired MRSA)

Comparative Genome Study and PCR

Characterization of SCCmec in community-acquired MRSA, PCR and sequence comparison

VanN ligase (D-Ala-D-Ser type)

VanN-Type Transferable Vancomycin Resistance in Enterococcus faecium

Enterococcus faecium

PCR

PCR for vanN detection, conjugation to test transferability, resistance phenotype analysis

VanN ligase (D-Ala-D-Ser type)

Identification of VanN-Type Vancomycin Resistance in Enterococcus faecium from Chicken Meat in Japan

Enterococcus faecium

Epidemiological Study and Genome Analysis

PFGE for epidemiology, conjugation studies, sequence alignment of resistance operon

XcpP

Cloning of xcp Genes Possibly Involved in Protein Secretion in Pseudomonas Aeruginosa

Pseudomonas aeruginosa

Genetic Mapping and Mutants Analysis

Identification and functional analysis of xcp mutants involved in secretion.

YopD

Dissection of homologous translocon operons reveals role for YopD in Yersinia pseudotuberculosis

Yersinia pseudotuberculosis

Recombinant DNA Techniques and Cytotoxicity Analysis

Complementation experiments to assess YopD's role in secretion and regulation.