Genomic and Transcriptomic Analysis Reveal Multiple Strategies for the Cadmium Tolerance in Vibrio parahaemolyticus N10-18 Isolated from Aquatic Animal Ostrea gigas Thunberg
Abstract
:1. Introduction
2. Materials and Methods
2.1. V. parahaemolyticus Strain and Cultural Conditions
2.2. Genomic DNA Preparation, Sequencing, Assembly, and Annotation
2.3. Comparative Genome Analysis
2.4. Phylogenetic Tree Analysis
2.5. Determination of Minimum Inhibitory Concentrations (MICs) of Antibiotics and Heavy Metals
2.6. Stress Conditions
2.7. Cell Membrane Permeability, Fluidity, and Surface Hydrophobicity Assays
2.8. Scanning Electron Microscope (SEM) Assay
2.9. Illumina RNA Sequencing and Analysis
2.10. Statistical Analysis
3. Results
3.1. Genotype and Phenotype of V. parahaemolyticus N10-18
3.2. Genome Features of V. parahaemolyticus N10-18
3.3. Serotype and ST of V. parahaemolyticus N10-18
3.4. Phylogenetic Relatedness of V. parahaemolyticus N10-18
3.5. MGEs in the V. parahaemolyticus N10-18 Genome
3.5.1. GIs
3.5.2. INs
3.5.3. ISs
3.6. Putative Virulence-Associated Genes
3.7. Heavy Metal and Antibiotic Resistance-Associated Genes
3.8. Survival of V. parahaemolyticus N10-18 under the Cd2+ (50 μg/mL) Stress
3.9. Changes in Cell Membrane Permeability and Fluidity and Cell Surface Hydrophobicity of V. parahaemolyticus N10-18 under the Cd2+ (50 μg/mL) Stress
3.10. The Major Changed Metabolic Pathways Medicated by the Cd2+ (50 μg/mL) Stress in V. parahaemolyticus N10-18
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Genome Feature | V. parahaemolyticus N10-18 |
---|---|
Genome size (bp) | 4,910,080 |
G + C (%) | 45.46 |
DNA Scaffold | 70 |
Total predicted gene | 4653 |
Protein-coding gene | 4565 |
RNA gene | 143 |
Genes assigned to COG | 3843 |
Genes with unknown function | 722 |
Transposase gene | 10 |
GI | 2 |
Prophage | 0 |
IN | 8 |
IS | 1 |
Heavy Metal and Antibiotic Agent | Resistance Gene | Reference |
---|---|---|
Heavy metal | ||
As | arsCR, pstABCS | [65] |
Cu | actP, copAB, corC, cueR, cusABRS, cutAC | [65,73] |
Cr | nfsA | [65,74] |
Ni | nirBD | [65,75] |
Zn | zntAR, znuABC, zur | [66,67] |
Zn, Hg | smtA | [65] |
Cr, Fe | chrAR | [65,76] |
W, Mo | modABC | [65] |
Cr, Te, Se | recG, ruvB | [65] |
Cd, Zn, Pb | cadC | [65,77] |
Cd, Zn, Hg, Cu | dsbABC | [65] |
Antimicrobial agent | ||
Beta-lactamases | blaCARB-21 | [78] |
Elfamycin | tuf | [68] |
Fluoroquinolone | crp | [69] |
Fosfomycin | UhpT | [71] |
Peptide, rifamycin | rpoB | [70] |
Tetracycline | Tet (34), Tet (35) | [72,79] |
Metabolic Pathway | Gene | Gene ID | Fold Change | Description |
---|---|---|---|---|
ABC transporters | livH | Vp_N10_18_2959 | 0.061 | Branched-chain amino acid ABC transporter permease |
znuB | Vp_N10_18_4101 | 0.081 | Metal ABC transporter permease | |
malE | Vp_N10_18_1557 | 0.252 | Maltose ABC transporter substrate-binding protein MalE | |
malK | Vp_N10_18_1556 | 0.263 | Maltose/maltodextrin import ATP-binding protein MalK | |
rbsB | Vp_N10_18_3026 | 0.325 | Ribose ABC transporter substrate-binding protein RbsB | |
aapP | Vp_N10_18_2527 | 0.355 | Arginine ABC transporter ATP-binding protein | |
rbsD | Vp_N10_18_3023 | 0.378 | D-ribose pyranase | |
rbsC | Vp_N10_18_3025 | 0.428 | Ribose ABC transporter permease | |
aapJ | Vp_N10_18_2530 | 0.441 | Amino acid ABC transporter substrate-binding protein | |
oppF | Vp_N10_18_2154 | 0.478 | Hypothetical protein VIBHAR_00643 | |
yejA | Vp_N10_18_2156 | 0.494 | Extracellular solute-binding protein | |
aapQ | Vp_N10_18_2529 | 0.496 | Amino acid ABC transporter permease | |
mlaF | Vp_N10_18_2720 | 0.500 | ATP-binding cassette domain-containing protein | |
proV | Vp_N10_18_0094 | 2.147 | Glycine betaine/L-proline transport ATP binding subunit | |
afuA | Vp_N10_18_1887 | 2.243 | Iron ABC transporter substrate-binding protein | |
fhuB | Vp_N10_18_1520 | 2.270 | Fe3+-hydroxamate ABC transporter permease FhuB | |
thiY | Vp_N10_18_1092 | 2.400 | Hypothetical protein | |
oppB | Vp_N10_18_3430 | 2.402 | Oligopeptide ABC transporter permease OppB | |
znuA | Vp_N10_18_4099 | 2.594 | Metal ABC transporter substrate-binding protein | |
artI | Vp_N10_18_0733 | 3.101 | Arginine ABC transporter substrate-binding protein | |
artM | Vp_N10_18_0735 | 3.204 | Arginine transporter permease subunit ArtM | |
thiZ | Vp_N10_18_1090 | 3.271 | Hydrogenase expression protein | |
thiX | Vp_N10_18_1091 | 3.567 | ABC transporter permease | |
- | Vp_N10_18_1522 | 3.891 | Iron (III) ABC transporter ATP-binding protein | |
artP | Vp_N10_18_0732 | 4.015 | Arginine ABC transporter ATP-binding protein ArtP | |
znuB | Vp_N10_18_1681 | 6.403 | Zinc ABC transporter permease subunit ZnuB | |
znuC | Vp_N10_18_1680 | 9.190 | Zinc ABC transporter ATP-binding protein ZnuC | |
znuA | Vp_N10_18_1679 | 11.609 | Zinc ABC transporter substrate-binding protein ZnuA | |
Propanoate metabolism | puuE | Vp_N10_18_2902 | 0.069 | Aspartate aminotransferase family protein |
prpE | Vp_N10_18_0011 | 0.330 | AMP-binding protein | |
acnD | Vp_N10_18_0013 | 0.370 | Fe/S-dependent 2-methylisocitrate dehydratase AcnD | |
pdhB | Vp_N10_18_0742 | 0.382 | Alpha-ketoacid dehydrogenase subunit beta | |
prpF | Vp_N10_18_0012 | 0.431 | 2-Methylaconitate cis-trans isomerase PrpF | |
gabT | Vp_N10_18_0139 | 0.432 | 4-Aminobutyrate--2-oxoglutarate transaminase | |
prpC | Vp_N10_18_0015 | 0.438 | 2-Methylcitrate synthase | |
Benzoate degradation | pcaH | Vp_N10_18_0737 | 0.49 | Dioxygenase family protein |
pcaC | Vp_N10_18_2971 | 2.003 | Carboxymuconolactone decarboxylase family protein | |
Thiamine metabolism | thiC | Vp_N10_18_4412 | 2.116 | Phosphomethylpyrimidine synthase ThiC |
thiE | Vp_N10_18_4413 | 2.247 | Thiamine phosphate synthase | |
thiD | Vp_N10_18_1089 | 2.555 | Bifunctional hydroxymethylpyrimidine Kinase/phosphomethylpyrimidine kinase | |
tenA | Vp_N10_18_1094 | 2.615 | Thiaminase II | |
thiE | Vp_N10_18_1096 | 2.740 | Thiamine phosphate synthase | |
Fat digestion and absorption | atoB | Vp_N10_18_3849 | 0.371 | 3-Ketoacyl-CoA thiolase @ Acetyl-CoA Acetyltransferase |
atoB | Vp_N10_18_2988 | 4.215 | Thiolase family protein | |
Quorum sensing | - | Vp_N10_18_2155 | 0.424 | ABC transporter ATP-binding protein |
ribA | Vp_N10_18_1217 | 0.453 | GTP cyclohydrolase II | |
- | Vp_N10_18_1879 | 0.472 | ABC transporter ATP-binding protein | |
- | Vp_N10_18_2632 | 0.486 | Sigma 54-interacting transcriptional regulator | |
- | Vp_N10_18_1219 | 2.140 | Sugar ABC transporter ATP-binding protein | |
- | Vp_N10_18_0181 | 2.378 | Polyamine ABC transporter substrate-binding protein | |
ribA | Vp_N10_18_2468 | 2.675 | GTP cyclohydrolase II | |
- | Vp_N10_18_1876 | 2.918 | ABC transporter permease | |
- | Vp_N10_18_2783 | 9.727 | ABC transporter permease | |
Pathogenic Escherichia coli infection | gapA | Vp_N10_18_3876 | 2.086 | Glyceraldehyde-3-phosphate dehydrogenase |
yscF | Vp_N10_18_0060 | 5.836 | Type III secretion system needle filament protein VscF |
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Yu, P.; Yang, L.; Wang, J.; Su, C.; Qin, S.; Zeng, C.; Chen, L. Genomic and Transcriptomic Analysis Reveal Multiple Strategies for the Cadmium Tolerance in Vibrio parahaemolyticus N10-18 Isolated from Aquatic Animal Ostrea gigas Thunberg. Foods 2022, 11, 3777. https://doi.org/10.3390/foods11233777
Yu P, Yang L, Wang J, Su C, Qin S, Zeng C, Chen L. Genomic and Transcriptomic Analysis Reveal Multiple Strategies for the Cadmium Tolerance in Vibrio parahaemolyticus N10-18 Isolated from Aquatic Animal Ostrea gigas Thunberg. Foods. 2022; 11(23):3777. https://doi.org/10.3390/foods11233777
Chicago/Turabian StyleYu, Pan, Lianzhi Yang, Juanjuan Wang, Chenli Su, Si Qin, Chaoxi Zeng, and Lanming Chen. 2022. "Genomic and Transcriptomic Analysis Reveal Multiple Strategies for the Cadmium Tolerance in Vibrio parahaemolyticus N10-18 Isolated from Aquatic Animal Ostrea gigas Thunberg" Foods 11, no. 23: 3777. https://doi.org/10.3390/foods11233777