Insights into the Antimicrobial Mechanisms of a Scorpion Defensin on Staphylococcus aureus Using Transcriptomic and Proteomic Analyses
Abstract
1. Introduction
2. Results
2.1. Bactericidal Effect of BmKDfsin4 on S. aureus AB94004
2.2. Global Transcriptomic and Proteomic Analyses of BmKDfsin4-Treated S. aureus AB94004
2.3. Functional Enrichment Analysis of DEGs and DEPs
2.4. Effects of BmKDfsin4 on the Ribosome Assembly and Protein Synthesis of S. aureus
2.5. Reduction in Amino Acid Biosynthesis and Metabolism in S. aureus Due to BmKDfsin4 Treatment
2.6. Inhibition of Cell Wall Biosynthesis in S. aureus AB94004 Due to BmKDfsin4 Treatment
2.7. Inhibitory Effect of BmKDfsin4 on the Metabolism of S. aureus AB9004
3. Discussion
4. Materials and Methods
4.1. Bactericidal Kinetics
4.2. RNA Extraction
4.3. Transcriptomic Analysis
4.4. Protein Extraction and Proteomic Analysis
4.5. Bioinformatics and Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Pathway ID | KEGG Description | p Value | Rich Factor | Regulation |
---|---|---|---|---|
map00740 | Riboflavin metabolism | 5.42 × 10−6 | 0.90 | up |
map00240 | Pyrimidine metabolism | 2.39 × 10−5 | 0.42 | up |
map03010 | Ribosome | 3.20 × 10−5 | 0.48 | up |
map00030 | Pentose phosphate pathway | 1.69 × 10−4 | 0.62 | up |
map00270 | Cysteine and methionine metabolism | 5.95 × 10−4 | 0.57 | up |
map01240 | Biosynthesis of cofactor | 7.59 × 10−4 | 0.37 | up |
map00910 | Nitrogen metabolism | 1.14 × 10−3 | 0.46 | up |
map00230 | Purine metabolism | 2.65 × 10−3 | 0.43 | up |
map01232 | Nucleotide metabolism | 2.85 × 10−3 | 0.47 | up |
map01240 | Biosynthesis of cofactor | 5.21 × 10−3 | 0.31 | up |
map00730 | Thiamine metabolism | 7.60 × 10−3 | 0.60 | up |
map00360 | Phenylalanine metabolism | 8.93 × 10−3 | 1.00 | up |
map01502 | Vancomycin resistance | 1.93 × 10−2 | 0.67 | up |
map00983 | Drug metabolism—other enzyme | 2.06 × 10−2 | 0.63 | up |
map00350 | Tyrosine metabolism | 3.02 × 10−2 | 0.75 | up |
map00750 | Vitamin B6 metabolism | 3.02 × 10−2 | 0.75 | up |
map00362 | Benzoate degradation | 1.20 × 10−2 | 0.50 | down |
map03020 | RNA polymerase | 2.90 × 10−2 | 0.60 | down |
map00552 | Teichoic acid biosynthesis | 3.40 × 10−2 | 0.41 | down |
map02060 | Phosphotransferase system (PTS) | 3.40 × 10−2 | 0.41 | down |
Accession | Protein Name | Log2 FC | p Value | Regulation | GO Term |
---|---|---|---|---|---|
PR417_000186 | Ribosomal_S14 | 0.68 | 0.004935 | up | BP |
PR417_000260 | Ribosomal_S15 | 3.86 | 0.01018 | up | BP |
PR417_000310 | Ribosomal_L28 | 0.98 | 0.001746 | up | BP |
PR417_000560 | Ribosomal_S20p | 1.21 | 0.0006025 | up | BP |
PR417_000570 | Ribosomal_S21 | 2.01 | 0.004936 | up | BP |
PR417_001047 | Ribosomal_S10 | 0.88 | 0.0007706 | up | BP |
PR417_001051 | Ribosomal_L2 | 1.53 | 0.0000644 | up | BP |
PR417_001052 | Ribosomal_S19 | 2.92 | 0.0007064 | up | BP |
PR417_001054 | Ribosomal_S3_C | 0.70 | 0.0002152 | up | BP |
PR417_001055 | Ribosomal_L16 | 1.29 | 0.002452 | up | BP |
PR417_001057 | Ribosomal_S17 | 1.51 | 0.001027 | up | BP |
PR417_001059 | Ribosomal_L24 | 2.01 | 0.001125 | up | BP |
PR417_001064 | Ribosomal_L18p | 1.59 | 0.0003322 | up | BP |
PR417_001066 | Ribosomal_L30 | 1.65 | 0.0000517 | up | BP |
PR417_001067 | Ribosomal_L27A | 0.77 | 0.000431 | up | BP |
PR417_001073 | Ribosomal_S11 | 0.84 | 0.0000539 | up | BP |
PR417_001217 | Ribosomal_S4 | 0.75 | 0.001019 | up | BP |
PR417_001258 | Ribosomal_L35p | 3.92 | 0.0004422 | up | BP |
PR417_001259 | Ribosomal_L20 | 0.77 | 0.002422 | up | BP |
PR417_001303 | Ribosomal_S1 | 0.72 | 0.001404 | up | CC |
PR417_001445 | Ribosomal_L31 | 1.21 | 0.006626 | up | BP |
PR417_001541 | Ribosomal_S18 | 1.93 | 0.0001338 | up | BP |
PR417_001543 | Ribosomal_S6 | 2.54 | 0.0000811 | up | BP |
PR417_001894 | Ribosomal_L9 | 0.70 | 0.006551 | up | BP |
PR417_002081 | Ribosomal_L10 | 0.67 | 0.0001408 | up | BP |
PR417_002082 | Ribosomal_L12 | 1.68 | 0.0007194 | up | BP |
PR417_002088 | Ribosomal_S7 | 0.94 | 0.003338 | up | BP |
Gene ID | Gene Name | Gene Description | Log2 FC | p Value | Regulation |
---|---|---|---|---|---|
PR417_000270 | proS | proline–tRNA ligase | 1.05 | 1.01 × 10−34 | up |
PR417_000515 | hisS | histidine–tRNA ligase | 2.00 | 9.38 × 10−57 | up |
PR417_000530 | alaS | alanine–tRNA ligase | 0.95 | 4.72 × 10−16 | up |
PR417_000580 | glyS1 | glycine–tRNA ligase | 1.22 | 3.33 × 10−46 | up |
PR417_001207 | tyrS | tyrosine–tRNA ligase | 0.94 | 1.14 × 10−6 | up |
PR417_001255 | thrS | threonine–tRNA ligase | 1.03 | 1.54 × 10−9 | up |
PR417_001275 | valS | valine–tRNA ligase | 0.81 | 2.02 × 10−17 | up |
PR417_001324 | asnS | asparagine–tRNA ligase | 0.87 | 3.27 × 10−14 | up |
PR417_001745 | leuS | leucine–tRNA ligase | 1.18 | 5.81 × 10−26 | up |
PR417_001888 | serS | serine–tRNA ligase | 0.60 | 4.58 × 10−8 | up |
PR417_002019 | lysS | lysine–tRNA ligase | 0.63 | 4.96 × 10−11 | up |
PR417_002406 | ileS | isoleucine–tRNA ligase | 1.85 | 9.62 × 10−77 | up |
PR417_001117 | pheT | phenylalanine–tRNA ligase subunit beta | 1.39 | 2.01 × 10−26 | up |
PR417_001118 | pheS | phenylalanine–tRNA ligase subunit alpha | 1.05 | 9.27 × 10−17 | up |
Accession | Gene Name | Protein ID | Description | Log2 FC | |
---|---|---|---|---|---|
Gene | Protein | ||||
PR417_001228 | ald | HDK3247889.1 | Alanine dehydrogenase | −0.55 | −0.72 |
PR417_000076 | puuE | HDK3246759.1 | Aspartate aminotransferase family protein | −1.91 | −0.67 |
PR417_001891 | metX | HDK3248527.1 | Homoserine O-acetyltransferase | −0.07 | −0.60 |
PR417_001358 | argJ | HDK3248015.1 | Bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ | 0.86 | −16.61 |
PR417_000873 | argH | HDK3247540.1 | Argininosuccinate lyase | −3.66 | |
PR417_000874 | argG | HDK3247541.1 | Argininosuccinate synthase | −2.77 | |
PR417_001186 | purF | HDK3247847.1 | Amidophosphoribosyl transferase | −0.53 | - |
PR417_001184 | purN | HDK3247845.1 | Phosphoribosyl glycinamide formyl transferase | −0.41 | - |
PR417_000028 | pruA | HDK3246711.1 | L-glutamate gamma-semialdehyde dehydrogenase | −0.90 | - |
PR417_000076 | - | HDK3246759.1 | Aspartate aminotransferase family protein | −1.91 | −0.668 |
PR417_002017 | gltB | HDK3248649.1 | Glutamate synthase large subunit | −1.45 | |
PR417_002018 | gltD | HDK3248650.1 | Glutamate synthase subunit beta | −1.23 | |
PR417_000871 | - | HDK3247538.1 | Glu/Leu/Phe/Val dehydrogenase | −1.08 | |
PR417_000225 | glnA | HDK3246901.1 | Type I glutamate–ammonia ligase | −0.96 | - |
Accession | Protein Name | Protein ID | Description | Log2 FC |
---|---|---|---|---|
PR417_000847 | DltC | HDK3247514.1 | D-alanine-activating enzyme/D-alanine-D-alanyl | −0.84 |
PR417_000449 | LtaS | HDK3247125.1 | Polyglycerol-phosphate lipoteichoic acid synthase LtaS | −0.95 |
PR417_002396 | MurD | HDK3249008.1 | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase | −0.59 |
PR417_000273 | UppS | HDK3246949.1 | UDP pyrophosphate synthase UppS | −0.85 |
PR417_001798 | - | HDK3248439.1 | LCP protein family | −1.00 |
PR417_000593 | PBP | HDK3247268.1 | Penicillin-binding protein | −0.60 |
PR417_002630 | - | HDK3249238.1 | Polyisoprenyl-teichoic acid–peptidoglycan teichoic acid transferase | −0.62 |
PR417_000365 | TagA | HDK3247041.1 | Teichoic acid biosynthesis protein TagA | −0.74 |
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Yang, X.; Zhang, H.; Lu, S.; Guo, Y.; Li, Y.; Qin, C.; Zuo, Z.; Wu, Y.; Cao, Z. Insights into the Antimicrobial Mechanisms of a Scorpion Defensin on Staphylococcus aureus Using Transcriptomic and Proteomic Analyses. Molecules 2025, 30, 1542. https://doi.org/10.3390/molecules30071542
Yang X, Zhang H, Lu S, Guo Y, Li Y, Qin C, Zuo Z, Wu Y, Cao Z. Insights into the Antimicrobial Mechanisms of a Scorpion Defensin on Staphylococcus aureus Using Transcriptomic and Proteomic Analyses. Molecules. 2025; 30(7):1542. https://doi.org/10.3390/molecules30071542
Chicago/Turabian StyleYang, Xuhua, Haozhen Zhang, Sijia Lu, Yiyuan Guo, Yitong Li, Chenhu Qin, Zheng Zuo, Yingliang Wu, and Zhijian Cao. 2025. "Insights into the Antimicrobial Mechanisms of a Scorpion Defensin on Staphylococcus aureus Using Transcriptomic and Proteomic Analyses" Molecules 30, no. 7: 1542. https://doi.org/10.3390/molecules30071542
APA StyleYang, X., Zhang, H., Lu, S., Guo, Y., Li, Y., Qin, C., Zuo, Z., Wu, Y., & Cao, Z. (2025). Insights into the Antimicrobial Mechanisms of a Scorpion Defensin on Staphylococcus aureus Using Transcriptomic and Proteomic Analyses. Molecules, 30(7), 1542. https://doi.org/10.3390/molecules30071542