Transcriptomics and Functional Analysis of Copper Stress Response in the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20
Abstract
:1. Introduction
2. Results
2.1. DA-G20 Growth under Cu(II) Stress
2.2. Differential Gene Expression Analysis during Cu(II) Stress
2.3. Gene Ontology Analyses of DEGs
2.3.1. Biological Process, Molecular Function, and Cellular Component Enrichment Analyses
2.3.2. Association between Genes and Enriched GO Terms
2.3.3. Network Analysis of the DEGs and Identification of Clusters
2.3.4. Metabolomic Profile of Control and Test Samples
3. Discussion
3.1. Downregulation of Translation Machinery
3.2. Modulation in Transporter Related Activity
3.3. Regulation of Oxidative Stress Response
3.4. Impact on Chemotaxis and Signal Transduction System
3.5. Some Atypical Transcriptional Changes Induced by Cu(II) Ions
3.5.1. Significant Upregulation of ApbE Family Lipoprotein
3.5.2. Differential Expression of DNA Repair Genes
3.5.3. Modulation of Methylation Related Activity
3.5.4. Regulation of Genes Associated with Cell Division and Cell Wall Organization
3.5.5. Role of Ascorbic Acid and Alkaline Phosphatase
4. Materials and Methods
4.1. Bacterial Strain and Growth Conditions
4.2. Copper Toxicity Experimental Setup
4.3. Determination of Total Cell Protein and SEM Analysis
4.4. RNA Isolation
4.5. Complementary DNA (cDNA) Library Preparation and Sequencing
4.6. QC of Raw RNA Sequencing Reads and Data Analysis
4.7. RT-qPCR Validation
4.8. Network Analysis Using Cytoscape
4.9. Bioinformatics Analysis
4.10. Targeted Metabolomics Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene ID | Protein Name | log2FC | Standard Error |
---|---|---|---|
Dde_2535 * | ApbE family lipoprotein | 3.95 | ±0.37 |
Dde_2958 * | Flagellar basal body rod protein | 3.12 | ±0.31 |
Dde_3047 * | Protein serine/threonine phosphatase | 3.08 | ±1.19 |
Dde_1981 * | Uncharacterized protein | 3.05 | ±0.93 |
Dde_0899 * | Uncharacterized protein | 2.98 | ±0.48 |
Dde_1205 * | Uncharacterized protein | 2.96 | ±0.44 |
Dde_2895 * | Teichoic-acid-transporting ATPase | 2.85 | ±0.96 |
Dde_1929 * | Uncharacterized protein | 2.82 | ±0.49 |
Dde_2799 * | Phage regulatory protein, Rha family | 2.81 | ±0.63 |
Dde_0900 * | RNA polymerase sigma factor, sigma-70 family | 2.77 | ±0.54 |
Dde_0111 # | Zinc resistance-associated protein | −8.56 | ±0.30 |
Dde_4025 # | Uncharacterized protein | −7.07 | ±0.64 |
Dde_2170 # | UPF0235 protein Dde_2170 | −6.48 | ±0.39 |
Dde_2819 # | Uncharacterized protein | −6.11 | ±0.27 |
Dde_3737 # | Putative GAF sensor protein | −5.98 | ±0.77 |
Dde_2991 # | Transcription termination/antitermination protein, NusG | −5.97 | ±0.36 |
Dde_3226 # | Phage shock protein A, PspA | −5.68 | ±0.27 |
Dde_1010 # | Uncharacterized protein | −5.52 | ±0.22 |
Dde_0221 # | Response regulator receiver protein | −5.51 | ±0.41 |
Dde_0715 # | Uncharacterized protein | −5.46 | ±0.35 |
Dde_3047 ** | Protein serine/threonine phosphatase | 3.05 | ±1.03 |
Dde_2958 ** | Flagellar basal body rod protein | 2.48 | ±0.36 |
Dde_0959 ** | AIG2 family protein | 2.04 | ±0.60 |
Dde_3729 ** | ABC transporter related protein | 2.01 | ±0.55 |
Dde_4035 ** | Uncharacterized protein | 1.87 | ±0.60 |
Dde_1264 ** | PAS modulated sigma54 specific transcriptional regulator, Fis family | 1.82 | ±0.67 |
Dde_3378 ** | Uncharacterized protein | 1.80 | ±0.61 |
Dde_0930 ** | Uncharacterized protein | 1.70 | ±0.53 |
Dde_3061 ** | M18 family aminopeptidase | 1.68 | ±0.69 |
Dde_0925 ** | Uncharacterized protein | 1.67 | ±0.62 |
Dde_0715 ## | Uncharacterized protein | −5.93 | ±0.32 |
Dde_2170 ## | UPF0235 protein Dde_2170 | −5.72 | ±0.37 |
Dde_4025 ## | Uncharacterized protein | −5.58 | ±0.63 |
Dde_0356 ## | Flagellar basal body rod protein FlgB | −5.34 | ±0.35 |
Dde_0221 ## | Response regulator receiver protein | −5.17 | ±0.42 |
Dde_0563 ## | Uncharacterized protein | −5.10 | ±0.37 |
Dde_1010 ## | Uncharacterized protein | −4.88 | ±0.23 |
Dde_2560 ## | Thioredoxin peroxidase | −4.84 | ±0.29 |
Dde_1689 ## | OmpA/MotB domain protein | −4.78 | ±0.25 |
Dde_0283 ## | Uncharacterized protein | −4.64 | ±0.26 |
Enriched GO Terms in SP1 (0 vs. 5 µM Cu) | ||||
---|---|---|---|---|
Gene Ontology (GO) Term | GO ID | Total Gene Count | −Log10 (p-Value) | z-Score * |
Regulation of transcription, DNA-templated (BP) | GO:0006355 | 34 | 16.5 | 0 |
Phosphorelay signal transduction system (BP) | GO:0000160 | 29 | 2.60 | −1.29 |
Translation (BP) | GO:0006412 | 27 | 48.14 | −4.81 |
Chemotaxis (BP) | GO:0006935 | 19 | 2.74 | −2.98 |
Signal transduction (BP) | GO:0007165 | 18 | 2.73 | −1.88 |
ATP binding (MF) | GO:0005524 | 114 | 16.55 | 2.06 |
Metal ion binding (MF) | GO:0046872 | 97 | 2.97 | −2.94 |
Hydrolase activity (MF) | GO:0016787 | 54 | 1.96 | 0 |
4 iron, 4 sulfur cluster binding (MF) | GO:0051539 | 28 | 2.32 | −0.75 |
ATPase-coupled transmembrane transporter activity (MF) | GO:0042626 | 25 | 1.64 | 3.40 |
Integral component of membrane (CC) | GO:0016021 | 212 | 3.38 | −0.41 |
Plasma membrane (CC) | GO:0005886 | 99 | 1.94 | −0.90 |
Cytoplasm (CC) | GO:0005737 | 76 | 1.77 | −2.52 |
ATP-binding cassette (ABC) transporter complex (CC) | GO:0043190 | 15 | 1.58 | 2.32 |
Bacterial-type flagellum basal body (CC) | GO:0009425 | 9 | 5.05 | −3.00 |
Enriched GO terms in SP2 (0 vs. 15 µM Cu) | ||||
Translation (BP) | GO:0006412 | 54 | 51.75 | −7.07 |
Regulation of transcription, DNA-templated (BP) | GO:0006355 | 45 | 3.59 | 1.5 |
Phosphorelay signal transduction system (BP) | GO:0000160 | 45 | 2.30 | 0.15 |
Signal transduction (BP) | GO:0007165 | 22 | 5.76 | −0.85 |
Methylation (BP) | GO:0032259 | 20 | 4.26 | 0 |
ATP binding (MF) | GO:0005524 | 194 | 72.25 | 1.29 |
Metal ion binding (MF) | GO:0046872 | 152 | 3.30 | −1.13 |
Hydrolase activity (MF) | GO:0016787 | 81 | 4.37 | 1.22 |
Transmembrane transporter activity (MF) | GO:0022857 | 47 | 3.20 | 4.23 |
4 iron, 4 sulfur cluster binding (MF) | GO:0051539 | 42 | 2.33 | 0.3 |
Integral component of membrane (CC) | GO:0016021 | 346 | 17.47 | 4.3 |
Plasma membrane (CC) | GO:0005886 | 160 | 1.66 | 1.42 |
Cytoplasm (CC) | GO:0005737 | 149 | 1.52 | −5.65 |
ATP-binding cassette (ABC) transporter complex (CC) | GO:0043190 | 34 | 1.73 | 4.11 |
Bacterial-type flagellum basal body (CC) | GO:0009425 | 6 | 2.76 | −0.81 |
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Tripathi, A.K.; Saxena, P.; Thakur, P.; Rauniyar, S.; Samanta, D.; Gopalakrishnan, V.; Singh, R.N.; Sani, R.K. Transcriptomics and Functional Analysis of Copper Stress Response in the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20. Int. J. Mol. Sci. 2022, 23, 1396. https://doi.org/10.3390/ijms23031396
Tripathi AK, Saxena P, Thakur P, Rauniyar S, Samanta D, Gopalakrishnan V, Singh RN, Sani RK. Transcriptomics and Functional Analysis of Copper Stress Response in the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20. International Journal of Molecular Sciences. 2022; 23(3):1396. https://doi.org/10.3390/ijms23031396
Chicago/Turabian StyleTripathi, Abhilash Kumar, Priya Saxena, Payal Thakur, Shailabh Rauniyar, Dipayan Samanta, Vinoj Gopalakrishnan, Ram Nageena Singh, and Rajesh Kumar Sani. 2022. "Transcriptomics and Functional Analysis of Copper Stress Response in the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20" International Journal of Molecular Sciences 23, no. 3: 1396. https://doi.org/10.3390/ijms23031396