The Screening of the Protective Antigens of Aeromonas hydrophila Using the Reverse Vaccinology Approach: Potential Candidates for Subunit Vaccine Development
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Bioinformatic Analysis of the A. hydrophila Genome
2.2.1. Data Collection
2.2.2. Signal Peptide Prediction
2.2.3. Transmembrane Helical Structure Prediction
2.2.4. Prediction of the Subcellular Localization
2.2.5. Antigenicity and Adhesion Index Analysis of the TARGET Proteins
2.2.6. Homology Analysis of the Protein Sequences
2.3. Conservative Analysis of Candidate Proteins in Different Subtypes of A. hydrophila and Aeromonas Species
2.3.1. Sample Collection
2.3.2. Molecular Characterization of the A. hydrophila Strains
2.3.3. ERIC-PCR Analysis of A. hydrophila Strains
2.3.4. Cluster Analysis of A. hydrophila Strains
2.3.5. PCR Amplification of the CDS Regions of Candidate Proteins
2.3.6. Sequence Alignment Using BLAST
2.4. Statistical Analysis
3. Results
3.1. Bioinformatic Analysis of the A. hydrophila Genome
3.1.1. Signal Peptide Prediction
3.1.2. Transmembrane Helix Prediction
3.1.3. Prediction of the Subcellular Localization
3.1.4. Antigenicity and Adhesion Index Prediction of the Candidate Proteins
3.1.5. Homology Analysis of the Candidate Proteins
3.2. Molecular Identification of Strains
3.3. ERIC-PCR
3.3.1. ERIC-PCR Typing of A. hydrophila
3.3.2. Cluster Analysis of ERIC-PCR Fingerprints
3.4. Conservative Analysis of Candidate Proteins in Aeromonas and Different Subtypes of A. hydrophila
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Strain | Host Fish Species | Isolated Tissues | Location |
---|---|---|---|
A. hydrophila Ahp001 | Parabramis pekinensis | kidney | Nanjing |
A. hydrophila Ahp002 | Parabramis pekinensis | liver | Nanjing |
A. hydrophila Ahp003 | Parabramis pekinensis | gill | Huai’an |
A. hydrophila Ahp004 | Parabramis pekinensis | liver | Huai’an |
A. hydrophila Ahm001 | Megalobrama amblycephala | liver | Wuhan |
A. hydrophila Ahc001 | Carassius auratus gibelio | body surface | Hubei |
A. hydrophila Ahi001 | Ictalurus punctatus | kidney | Sichuan |
A. hydrophila Ahx001 | Ictalurus punctatus | body surface | Sichuan |
A. hydrophila Ahx002 | Ictalurus punctatus | body surface | Sichuan |
A. veronii Avc001 | Carassius auratus | gill | Lianyungang |
Protein Number | Protein Description | α-Helix | Adhesion | Antigenicity | Percentage of Occurrence (%) |
---|---|---|---|---|---|
AJE34457.1 | fimbrial biogenesis outer membrane usher protein | 0 | 0.715 | 0.6061 | 8 |
AJE34471.1 | TonB-dependent receptor | 0 | 0.555 | 0.6085 | 38 |
AJE34515.1 | porin OmpA | 0 | 0.715 | 0.6038 | 16 |
AJE34700.1 | ligand-gated channel protein | 0 | 0.616 | 0.6769 | 30 |
AJE34708.1 | outer membrane beta-barrel protein | 0 | 0.838 | 0.7068 | 30 |
AJE35401.1 | type IV pilus secretin PilQ | 0 | 0.565 | 0.6985 | 57 |
AJE35595.1 | carbohydrate porin | 0 | 0.663 | 0.7585 | 51 |
AJE35662.1 | efflux transporter outer membrane subunit | 0 | 0.539 | 0.6502 | 32 |
AJE35814.1 | MtrB/PioB family decaheme-associated outer membrane protein | 0 | 0.723 | 0.5953 | 11 |
AJE35877.1 | TolC family outer membrane protein | 0 | 0.535 | 0.6247 | 70 |
AJE36112.1 | siderophore amonabactin TonB-dependent receptor | 0 | 0.657 | 0.6506 | 41 |
AJE36246.1 | OmpP1/FadL family transporter | 0 | 0.71 | 0.5389 | 22 |
AJE36247.1 | outer membrane protein transport protein | 0 | 0.825 | 0.6604 | 11 |
AJE36909.1 | TonB-dependent hemoglobin/transferrin/lactoferrin family receptor | 0 | 0.525 | 0.7156 | 14 |
AJE37341.1 | OmpA family protein | 0 | 0.612 | 0.725 | 19 |
AJE37342.1 | porin OmpA | 0 | 0.625 | 0.6875 | 54 |
AJE37343.1 | OmpA family protein | 0 | 0.559 | 0.6993 | 24 |
AJE37434.1 | outer membrane protein assembly factor BamA | 0 | 0.637 | 0.6605 | 49 |
AJE37449.1 | maltoporin LamB | 0 | 0.774 | 0.6319 | 43 |
AJE37487.1 | outer membrane protein OmpK | 0 | 0.726 | 0.5222 | 41 |
AJE37516.1 | outer membrane beta-barrel protein | 0 | 0.764 | 0.6778 | 11 |
AJE37629.1 | TonB-dependent hemoglobin/transferrin/lactoferrin family receptor | 1 | 0.624 | 0.665 | 43 |
AJE37705.1 | LPS assembly protein LptD | 1 | 0.527 | 0.7443 | 32 |
AJE37778.1 | porin | 0 | 0.704 | 0.7588 | 19 |
AJE37804.1 | peptidoglycan DD-metalloendopeptidase family protein | 0 | 0.787 | 0.7381 | 14 |
AJE38163.1 | porin | 0 | 0.767 | 0.7306 | 54 |
AJE38201.1 | OmpA family protein | 0 | 0.611 | 0.7071 | 3 |
AJE38225.1 | porin | 0 | 0.811 | 0.748 | 16 |
AJE38562.1 | TonB-dependent siderophore receptor | 0 | 0.591 | 0.5896 | 62 |
AJE34456.1 | hypothetical protein | 1 | 0.667 | 0.5206 | 5 |
AJE34989.1 | TIGR04219 family outer membrane beta-barrel protein | 0 | 0.691 | 0.7105 | 24 |
AJE35148.1 | immune inhibitor A | 0 | 0.572 | 0.5513 | 41 |
AJE37118.1 | DUF1566 domain-containing protein | 0 | 0.605 | 0.6726 | 5 |
AJE37120.1 | outer membrane protein assembly factor BamE | 0 | 0.608 | 0.6881 | 46 |
AJE37322.1 | M23 family metallopeptidase | 0 | 0.74 | 0.5346 | 11 |
AJE37560.1 | OprD family outer membrane porin | 0 | 0.644 | 0.6276 | 19 |
AJE37735.1 | DUF2860 family protein | 0 | 0.673 | 0.5925 | 16 |
AJE37742.1 | outer membrane protein assembly factor BamC | 0 | 0.643 | 0.6185 | 57 |
AJE38071.1 | glycine zipper 2TM domain-containing protein | 0 | 0.815 | 0.8437 | 57 |
No. | Protein Number | NCBI NR Data Base | Sample Strains | |||
---|---|---|---|---|---|---|
A. caviae | A. salmonicida | A. veronii | A. hydrophila | |||
1 | AJE34457.1 | 67 | 50 | 50 | 100 | 50 |
2 | AJE34471.1 | 100 | 100 | 100 | 100 | 83 |
3 | AJE34515.1 | 100 | 100 | 100 | 100 | 50 |
4 | AJE34700.1 | 100 | 100 | 100 | 100 | 83 |
5 | AJE34708.1 | 100 | 83 | 100 | 100 | 100 |
6 | AJE35401.1 | 100 | 100 | 100 | 100 | 100 |
7 | AJE35595.1 | 100 | 100 | 100 | 100 | 50 |
8 | AJE35662.1 | 100 | 100 | 100 | 100 | 67 |
9 | AJE35814.1 | 0 | 0 | 0 | 100 | 50 |
10 | AJE35877.1 | 100 | 100 | 100 | 100 | 100 |
11 | AJE36112.1 | 100 | 100 | 100 | 100 | 83 |
12 | AJE36246.1 | 100 | 100 | 100 | 100 | 17 |
13 | AJE36247.1 | 100 | 100 | 100 | 100 | 100 |
14 | AJE36909.1 | 100 | 100 | 100 | 100 | 50 |
15 | AJE37341.1 | 100 | 100 | 100 | 100 | 83 |
16 | AJE37342.1 | 100 | 100 | 100 | 83 | 100 |
17 | AJE37343.1 | 100 | 100 | 100 | 100 | 100 |
18 | AJE37434.1 | 100 | 100 | 100 | 100 | 83 |
19 | AJE37449.1 | 100 | 83 | 100 | 100 | 50 |
20 | AJE37487.1 | 100 | 100 | 100 | 100 | 100 |
21 | AJE37516.1 | 100 | 100 | 100 | 100 | 83 |
22 | AJE37629.1 | 100 | 100 | 100 | 100 | 100 |
23 | AJE37705.1 | 100 | 100 | 100 | 100 | 100 |
24 | AJE37778.1 | 100 | 100 | 100 | 100 | 100 |
25 | AJE37804.1 | 100 | 100 | 100 | 100 | 100 |
26 | AJE38163.1 | 100 | 100 | 100 | 100 | 100 |
27 | AJE38201.1 | 100 | 100 | 100 | 83 | 83 |
28 | AJE38225.1 | 67 | 100 | 67 | 100 | 83 |
29 | AJE38562.1 | 100 | 100 | 100 | 100 | 100 |
30 | AJE34456.1 | 100 | 50 | 0 | 100 | 67 |
31 | AJE34989.1 | 100 | 100 | 100 | 100 | 100 |
32 | AJE35148.1 | 0 | 100 | 0 | 100 | 100 |
33 | AJE37118.1 | 83 | 100 | 67 | 100 | 83 |
34 | AJE37120.1 | 100 | 100 | 100 | 100 | 33 |
35 | AJE37322.1 | 0 | 100 | 0 | 100 | 0 |
36 | AJE37560.1 | 100 | 100 | 100 | 100 | 83 |
37 | AJE37735.1 | 100 | 100 | 100 | 100 | 100 |
38 | AJE37742.1 | 100 | 100 | 100 | 100 | 83 |
39 | AJE38071.1 | 100 | 100 | 100 | 100 | 67 |
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Zhang, T.; Zhang, M.; Xu, Z.; He, Y.; Zhao, X.; Cheng, H.; Chen, X.; Xu, J.; Ding, Z. The Screening of the Protective Antigens of Aeromonas hydrophila Using the Reverse Vaccinology Approach: Potential Candidates for Subunit Vaccine Development. Vaccines 2023, 11, 1266. https://doi.org/10.3390/vaccines11071266
Zhang T, Zhang M, Xu Z, He Y, Zhao X, Cheng H, Chen X, Xu J, Ding Z. The Screening of the Protective Antigens of Aeromonas hydrophila Using the Reverse Vaccinology Approach: Potential Candidates for Subunit Vaccine Development. Vaccines. 2023; 11(7):1266. https://doi.org/10.3390/vaccines11071266
Chicago/Turabian StyleZhang, Ting, Minying Zhang, Zehua Xu, Yang He, Xiaoheng Zhao, Hanliang Cheng, Xiangning Chen, Jianhe Xu, and Zhujin Ding. 2023. "The Screening of the Protective Antigens of Aeromonas hydrophila Using the Reverse Vaccinology Approach: Potential Candidates for Subunit Vaccine Development" Vaccines 11, no. 7: 1266. https://doi.org/10.3390/vaccines11071266