Comprehensive Genomics and Proteomics Analysis Reveals the Multiple Response Strategies of Endophytic Bacillus sp. WR13 to Iron Limitation
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacteria Growth and Treatment
2.2. Draft Genome Sequencing of WR13
2.3. Siderophore Determination
2.4. RNA Isolation and qPCR Assay
2.5. Total Protein Extraction, Digestion and iTRAQ Labeling
2.6. High pH Reverse Phase Separation and LC-MS/MS Analysis
2.7. Protein Identification and Differentially Abundant Protein (DAP) Screening
2.8. Statistical Analysis
3. Results
3.1. The Growth of WR13 under Different Fe Conditions
3.2. Genome Analysis of WR13
3.3. Siderophore Production and Siderophore-Related Genes Expression in WR13 under Fe Limitation
3.4. Quantification of Total Proteins and Protein Differential Analysis by iTRAQ-Labeled Proteomics
3.5. Functional Annotation of DAPs
3.6. The Key DAPs Involved in Carbohydrate Metabolism, Amino Acid Metabolism, Lipid Metabolism, and Fe-Containing Proteins
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Accession | Description | FC (Fe−/Fe+) | p Value | Regulate |
---|---|---|---|---|
Carbohydrate metabolism | ||||
gene1651 | pyruvate dehydrogenase E1 component beta subunit (PDHB) | 0.718 | 0.006 | down |
gene4021 | aconitase (ACO) | 0.747 | 0.036 | down |
gene2203 | phosphoglycerate kinase (PGK) | 0.749 | 0.030 | down |
gene2204 | type I glyceraldehyde-3-phosphate dehydrogenase (GAPDH) | 0.660 | 0.008 | down |
gene4010 | transketolase (TKT) | 0.367 | 0.017 | down |
gene2263 | beta-phosphoglucomutase (PGMB) | 0.501 | 0.028 | down |
Amino acid metabolism | ||||
gene1700 | Asparaginase (ANS) | 0.572 | 0.007 | down |
gene0508 | ω-amidase | 0.816 | 0.022 | down |
gene0981 | methionine adenosyltransferase (MAT) | 0.723 | 0.022 | down |
gene0743 | L-serine ammonia-lyase, iron-sulfur-dependent subunit beta (SDH) | 0.729 | 0.038 | down |
Lipid metabolism | ||||
gene3591 | glycerophosphodiester phosphodiesterase (GDPD) | 0.810 | 0.039 | down |
gene0063 | glycerol-3-phosphate dehydrogenase (GPD) | 0.725 | 0.044 | down |
Fe-containing proteins | ||||
gene2592 | heme-dependent peroxidase HemQ | 0.549 | 0.028 | down |
gene1752 | ferredoxin | 0.348 | 0.040 | down |
gene0858 | 2′,3′-cyclic-nucleotide 2′-phosphodiesterase (CNP) | 0.537 | 0.002 | down |
gene2067 | Fe-S cluster assembly protein SufD | 0.741 | 0.039 | down |
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Yue, Z.; Liu, Y.; Chen, Y.; Chen, C.; Zhang, J.; He, L.; Ma, K. Comprehensive Genomics and Proteomics Analysis Reveals the Multiple Response Strategies of Endophytic Bacillus sp. WR13 to Iron Limitation. Microorganisms 2023, 11, 367. https://doi.org/10.3390/microorganisms11020367
Yue Z, Liu Y, Chen Y, Chen C, Zhang J, He L, Ma K. Comprehensive Genomics and Proteomics Analysis Reveals the Multiple Response Strategies of Endophytic Bacillus sp. WR13 to Iron Limitation. Microorganisms. 2023; 11(2):367. https://doi.org/10.3390/microorganisms11020367
Chicago/Turabian StyleYue, Zonghao, Yongchuang Liu, Yanjuan Chen, Can Chen, Ju Zhang, Le He, and Keshi Ma. 2023. "Comprehensive Genomics and Proteomics Analysis Reveals the Multiple Response Strategies of Endophytic Bacillus sp. WR13 to Iron Limitation" Microorganisms 11, no. 2: 367. https://doi.org/10.3390/microorganisms11020367
APA StyleYue, Z., Liu, Y., Chen, Y., Chen, C., Zhang, J., He, L., & Ma, K. (2023). Comprehensive Genomics and Proteomics Analysis Reveals the Multiple Response Strategies of Endophytic Bacillus sp. WR13 to Iron Limitation. Microorganisms, 11(2), 367. https://doi.org/10.3390/microorganisms11020367