Detection of Antagonistic Compounds Synthesized by Bacillus velezensis against Xanthomonas citri subsp. citri by Metabolome and RNA Sequencing
Abstract
:1. Introduction
2. Materials and Methods
2.1. Strains and Culture Conditions
2.2. Antibacterial Activity of Ethyl Acetate Extracts of Bv-25 and Ba-2 in Landy Broth and YNB
2.3. Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC) of Bv-25 and Ba-2 Extracts Cultured in Landy Broth and YNB
2.4. HPLC-MS Analysis of Ethyl Acetate Extracts from Bv-25 and Ba-2
2.5. Differential Gene Expression Analysis of Bv-25 Grown in Landy Broth and YNB
2.6. Antibacterial Activity Assay of Pure Surfactin and Fengycin against Xcc
3. Results
3.1. Antibacterial Activity of Ethyl Acetate Extracts of Bv-25 in Landy and YNB
3.2. Determination of MIC and MBC of the Ethyl Acetate Extracts of Bv-25 and Ba-2 Incubated in Landy Broth and YNB
3.3. Detection of Antimicrobial Compounds by HPLC-MS Analysis
3.4. Differential Gene Expression Analysis of Bv-25 Grown in Landy and YNB Media
3.5. Antibacterial Activity Assay of Pure Surfactin and Fengycin against Xcc
4. Discussion
5. Conclusions
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Xcc Strains | Extract of Bv-25 Using Landy Broth | Extract of Bv-25 Using YNB | Streptomycin | |||
---|---|---|---|---|---|---|
MIC (µg mL−1) | MBC (µg mL−1) | MIC (µg mL−1) | MBC (µg mL−1) | MIC (µg mL−1) | MBC (µg mL−1) | |
XccW1 | 31.25 | 62.5 | 62.5 | 125.0 | 1.25 | 2.5 |
XccM4 | 31.25 | 62.5 | 62.5 | 125.0 | >500 | >1000 |
Compound Name | M/Z | RT (min) | Ba-2 | Bv-25 | Fold Change (Bv-25/Ba-2) | p-Value |
---|---|---|---|---|---|---|
Oxydifficidin | 559.0 | 43.3 | 216,380.3 | 30,417,069.1 | 140.6 | 0.0027 |
Bacillaene | 582.2 | 31.3 | 291,622.7 | 2,774,552.5 | 9.5 | 0.0001 |
Macrolactin | 524.2 | 38.6 | 308,031.1 | 2,211,408.9 | 7.2 | 0.0046 |
Surfactin | 1036.6 | 27.0 | 93,166.2 | 1,420,585.5 | 15.2 | 0.0000 |
Fengycin A | 1475.9 | 30.5 | 128,474.2 | 1,092,443.5 | 8.5 | 0.0006 |
Fengycin B | 1489.3 | 31.3 | 158,266.9 | 983,475.3 | 6.2 | 0.0005 |
Bacillomycin D | 1118.6 | 40.5 | 92,804.4 | 19,132,037.6 | 206.2 | 0.0031 |
Iturin | 1083.7 | 29.3 | 272,286.6 | 2,513,178.3 | 9.2 | 0.0036 |
Active Compound | Gene | UniProt ID | Product |
---|---|---|---|
Bacilysin | bacA | Q8KWT6 | Prephenate decarboxylase |
bacB | Q8KWT5 | 3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate isomerase | |
bacC | Q8KWT4 | Dihydroanticapsin dehydrogenase | |
bacD | Q8KWT3 | L-alanine-anticapsin ligase | |
bacE | Q8KWT2 | Putative bacilysin exporter | |
ywfG | P39643 | Probable aspartate aminotransferase | |
ywfH | P39644 | Bacilysin biosynthesis oxidoreductase | |
Plipastatin or Fengycin | ppsA | P39845 | Plipastatin synthase subunit A |
ppsB | P39846 | Plipastatin synthase subunit B | |
ppsC | P39847 | Plipastatin synthase subunit C | |
ppsD | P94459 | Plipastatin synthase subunit D | |
ppsE | O31827 | Plipastatin synthase subunit E | |
Mycosubtilin | fenF | Q9R9J2 | Malonyl CoA-acyl carrier protein transacylase |
mycA | Q9R9J1 | Mycosubtilin synthase subunit A | |
mycB | Q9R9J0 | Mycosubtilin synthase subunit B | |
mycC | Q9R9I9 | Mycosubtilin synthase subunit C | |
Surfactin | srfAD | Q08788 | Surfactin synthase thioesterase subunit |
srfAC | Q08787 | Surfactin synthase subunit 3 | |
srfAB | Q04747 | Surfactin synthase subunit 2 | |
srfAA | P27206 | Surfactin synthase subunit 1 |
Bioactivity | Gene | Product | Log2 FC |
---|---|---|---|
Biofilm formation (Exopolysaccharide component) | epsC | Probable polysaccharide biosynthesis protein | −3.17 |
epsD | Putative glycosyltransferase | −2.08 | |
epsE | Putative glycosyltransferase | −4.00 | |
epsF | Putative glycosyltransferase | −0.45 | |
epsG | Transmembrane protein | 0.04 | |
epsH | Putative glycosyltransferase | −1.25 | |
epsI | Putative pyruvyl transferase | −0.85 | |
epsJ | Uncharacterized glycosyltransferase | 0.51 | |
epsK | Uncharacterized membrane protein | 0.20 | |
epsL | Uncharacterized sugar transferase | −0.88 | |
epsM | Putative acetyltransferase EpsM | −1.37 | |
epsN | Putative pyridoxal phosphate-dependent aminotransferase | −0.55 | |
Plant growth promotion and ISR induction (3- hydroxy-2-butanone) | alsR | HTH-type transcriptional regulator | 2.77 |
alsS | Acetolactate synthase | −3.58 | |
alsD | Alpha-acetolactate decarboxylase | −7.67 | |
Plant growth promotion (Indole acetic acid) | ysnE | Uncharacterized N-acetyltransferase | inf |
yhcX | Hydrolase | −0.48 | |
Plant growth promotion (Trehalose) | treR | Trehalose operon transcriptional repressor | 1.91 |
treA | Trehalose-6-phosphate hydrolase | 1.32 | |
treP | PTS system trehalose-specific EIIBC component | 0.72 |
Bioactivity | Gene | Product | Log2 FC |
---|---|---|---|
Bacillibactin for iron (Fe2+) assimilation | dhbA | 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase | 0.80 |
dhbC | Isochorismate synthase | −1.52 | |
dhbE | 2,3-dihydroxybenzoate-AMP ligase | −2.45 | |
dhbB | Isochorismatase | −3.08 | |
dhbF | Dimodular nonribosomal peptide synthase | −1.32 | |
Manganese (Mn2+) assimilation | mntH | Divalent metal cation transporter | 3.71 |
mntP | Putative manganese efflux pump | 0.69 | |
mntR | Transcriptional regulator | −0.75 | |
Magnesium (Mg2+) assimilation | mgtE | Magnesium transporter | 2.19 |
corA | Magnesium transport protein | −2.66 | |
Potassium (K) assimilation | ktrD | Ktr system potassium uptake protein D | 1.06 |
ktrC | Ktr system potassium uptake protein C | −2.75 | |
Nitrogen (N) assimilation | moaA | Cyclic pyranopterin monophosphate synthase | −1.03 |
moaB | Molybdenum cofactor biosynthesis protein B | 1.59 | |
moaC | Cyclic pyranopterin monophosphate synthase | 0.79 | |
moaD | Molybdopterin synthase sulfur carrier subunit | 0.00 | |
nasB | Assimilatory nitrate reductase electron transfer subunit | 1.34 | |
nasD | Nitrite reductase [NAD(P)H] | 2.82 | |
nasF | Uroporphyrinogen-III C-methyltransferase | 0.41 | |
nrgB | Nitrogen regulatory PII-like protein | −3.03 | |
narK | Nitrite extrusion protein | 3.04 |
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Rabbee, M.F.; Baek, K.-H. Detection of Antagonistic Compounds Synthesized by Bacillus velezensis against Xanthomonas citri subsp. citri by Metabolome and RNA Sequencing. Microorganisms 2023, 11, 1523. https://doi.org/10.3390/microorganisms11061523
Rabbee MF, Baek K-H. Detection of Antagonistic Compounds Synthesized by Bacillus velezensis against Xanthomonas citri subsp. citri by Metabolome and RNA Sequencing. Microorganisms. 2023; 11(6):1523. https://doi.org/10.3390/microorganisms11061523
Chicago/Turabian StyleRabbee, Muhammad Fazle, and Kwang-Hyun Baek. 2023. "Detection of Antagonistic Compounds Synthesized by Bacillus velezensis against Xanthomonas citri subsp. citri by Metabolome and RNA Sequencing" Microorganisms 11, no. 6: 1523. https://doi.org/10.3390/microorganisms11061523
APA StyleRabbee, M. F., & Baek, K.-H. (2023). Detection of Antagonistic Compounds Synthesized by Bacillus velezensis against Xanthomonas citri subsp. citri by Metabolome and RNA Sequencing. Microorganisms, 11(6), 1523. https://doi.org/10.3390/microorganisms11061523