Transcriptome Profiling Analysis of Phosphate-Solubilizing Mechanism of Pseudomonas Strain W134
Abstract
:1. Introduction
2. Materials and Methods
2.1. Strain and Culture Conditions
2.2. RNA Extraction and Library Construction
2.3. Clean Reads Filtering and Differentially Expressed Genes Analysis
2.4. qRT-PCR Analysis
2.5. Determination of Organic Acids
2.6. Statistical Analysis
3. Results
3.1. Transcriptome Sequence Analysis of PSB W134
3.2. Statistics of DEGs
3.3. GO Analysis of DEGs
3.4. KEGG Analysis of DEGs
3.5. Genes Expression in the Citrate Cycle Pathway
3.6. qRT-PCR Validation
3.7. Determination of Organic Acids Contents
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Three Different Media | Medium Formulation | pH |
---|---|---|
Soluble P (Group A) | Glucose 10 g, KH2PO4 4.3874 g, (NH4)2SO4 0.5 g, NaCl 0.3 g, KCl 0.3 g, MgSO4 • 7H2O 0.03 g, FeSO4 • 7H2O 0.03 g, MnSO4 • H2O 0.03 g, aseptic water 1000 mL | 7.80 |
Insoluble P (Group B) | Glucose 10 g, Ca3(PO4)2 5 g, (NH4)2SO4 0.5 g, NaCl 0.3 g, KCl 0.3 g, MgSO4 • 7H2O 0.03 g, FeSO4 • 7H2O 0.03 g, MnSO4 • H2O 0.03 g, aseptic water 1000 mL | 7.80 |
Lacking P (Group C) | Glucose 10 g, CaCl2 5.3678 g, (NH4)2SO4 0.5 g, NaCl 0.3 g, KCl 0.3 g, MgSO4 • 7H2O 0.03 g, FeSO4 • 7H2O 0.03 g, MnSO4 • H2O 0.03 g, aseptic water 1000 mL | 7.80 |
Unigene | Forward Primer | Reverse Primer |
---|---|---|
BLU65_RS00705 | 5′-ACAGATCAGCGAATCCCAA-3′ | 5′-GGAAGTGCTGCATGAAGTC-3′ |
BLU65_RS03630 | 5′-CCGTTACCTGATCGGTGAC-3′ | 5′-GTCGATGCACTTGGCATAG-3′ |
BLU65_RS11635 | 5′-GTGATCAAGCAAGACGACC-3′ | 5′-CCTGGATGAAATCCACGG-3′ |
BLU65_RS15190 | 5′-CCCGCTCGAAGATCATCTATAC-3′ | 5′-AAAGCCTCTACGATAGGCA-3′ |
BLU65_RS26350 | 5′-CTCTACCTGCACGACCCTAA-3′ | 5′-CGAAACATCGGTGACAGT-3′ |
BLU65_RS26355 | 5′-GTTGATACCGGTGGTAAAGAC-3′ | 5′-GAGCGACGATAGGAGAAAC-3′ |
BLU65_RS26360 | 5′-TGCCGATCCGAACGATGA-3′ | 5′-ATGTACTCGATAGCGTCCT-3′ |
aceE | 5′-CAAAGAAGGCGAAGACCG-3′ | 5′-TGGTGATGGCGTAAGGGA-3′ |
acnB | 5′-GGTGGCTACAACATCGTG-3′ | 5′-GTGGAAGGCATCGAACATCA-3′ |
16S rRNA | 5′-GGGGAGTACGGTCGCAAGAT-3′ | 5′-CATGTCAAGGGTAGGTAAGGTTT-3′ |
Gene ID | Log2 FC | Significant | FDR | Description | |||
---|---|---|---|---|---|---|---|
B/A | C/A | B/A | C/A | B/A | C/A | ||
BLU65_RS00350 | −1.64 | −1.53 | yes | no | 1.41 × 10−2 | 1.16 × 10−1 | alpha-ketoacid dehydrogenase subunit beta |
BLU65_RS00705 | 1.87 | 5.13 | yes | yes | 1.83 × 10−4 | 2.28 × 10−5 | class II fumarate hydratase |
BLU65_RS03630 | 1.56 | 1.80 | yes | yes | 4.94 × 10−6 | 4.69 × 10−3 | phosphoenolpyruvate carboxykinase (ATP) |
BLU65_RS05250 | 1.53 | 0.15 | yes | no | 3.40 × 10−7 | 9.61 × 10−1 | pyruvate carboxylase subunit A |
BLU65_RS11635 | 2.24 | 1.66 | yes | yes | 4.63 × 10−9 | 9.35 × 10−3 | fumarate hydratase |
BLU65_RS15190 | 2.41 | 2.09 | yes | yes | 2.70 × 10−14 | 6.88 × 10−4 | isocitrate dehydrogenase |
BLU65_RS26350 | 2.11 | 2.32 | yes | yes | 1.28 × 10−9 | 4.87 × 10−5 | 2-oxoglutarate dehydrogenase |
BLU65_RS26355 | 1.64 | 1.49 | yes | yes | 5.02 × 10−8 | 3.97 × 10−3 | succinate dehydrogenase |
BLU65_RS26360 | 1.45 | 1.55 | yes | yes | 8.56 × 10−6 | 7.68 × 10−3 | succinate dehydrogenase |
aceE | 1.18 | 2.39 | yes | yes | 2.94 × 10−3 | 1.41 × 10−4 | pyruvate dehydrogenase (acetyl-transferring), homodimeric type |
aceF | 0.61 | 1.56 | no | yes | 1.01 × 10−1 | 3.16 × 10−2 | dihydrolipoyllysine-residue acetyltransferase |
acnB | 2.56 | 2.42 | yes | yes | 5.15 × 10−14 | 1.12 × 10−5 | aconitase |
gltA | 1.82 | 1.11 | yes | no | 2.48 × 10−6 | 8.55 × 10−2 | citrate synthase I, hexameric type |
oadA | 2.32 | 0.86 | yes | no | 1.76 × 10−14 | 1.66 × 10−1 | pyruvate carboxylase subunit B |
odhB | 1.69 | 1.53 | yes | yes | 2.38 × 10−7 | 9.35 × 10−3 | 2-oxoglutarate dehydrogenase complex dihydrolipoamide succinyltransferase |
sdhC | 1.50 | 1.58 | yes | yes | 1.89 × 10−5 | 5.42 × 10−3 | succinate dehydrogenase |
sucC | 1.78 | 1.78 | yes | yes | 4.87 × 10−6 | 2.97 × 10−3 | Succinyl-CoA ligase [ADP-forming] subunit beta |
sucD | 2.48 | 2.12 | yes | yes | 5.97 × 10−13 | 2.99 × 10−4 | succinyl-CoA synthetase, alpha subunit |
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Wang, S.; Li, Y.; Zhang, J.; Wang, X.; Hong, J.; Qiu, C.; Meng, H. Transcriptome Profiling Analysis of Phosphate-Solubilizing Mechanism of Pseudomonas Strain W134. Microorganisms 2022, 10, 1998. https://doi.org/10.3390/microorganisms10101998
Wang S, Li Y, Zhang J, Wang X, Hong J, Qiu C, Meng H. Transcriptome Profiling Analysis of Phosphate-Solubilizing Mechanism of Pseudomonas Strain W134. Microorganisms. 2022; 10(10):1998. https://doi.org/10.3390/microorganisms10101998
Chicago/Turabian StyleWang, Shuaibing, Yi Li, Jie Zhang, Xiangying Wang, Jianping Hong, Chen Qiu, and Huisheng Meng. 2022. "Transcriptome Profiling Analysis of Phosphate-Solubilizing Mechanism of Pseudomonas Strain W134" Microorganisms 10, no. 10: 1998. https://doi.org/10.3390/microorganisms10101998