Oxidative Stress Response of Probiotic Strain Bifidobacterium longum subsp. longum GT15
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strains, Media, Culture Condition
2.2. Treatment of B. longum Culture by Oxidative Stress
2.3. Total RNA Isolation and Sequencing
2.4. Whole Transcriptome Analysis
2.5. Forming a Reference Catalog of Orthologs of Genes of Antioxidant Function
2.6. Genetic Analysis of Genomes of B. longum Genera
2.7. Analysis of Expression Levels of the Genes Responsible for Antioxidative Properties
2.8. Sample Preparation for Proteomic Analysis
2.9. Digestion of Proteins with Trypsin in Solution
2.10. Liquid Chromatography and Mass Spectrometry
2.11. Proteomic Data Analysis
2.12. DPPH• Radical Scavenging Assay
2.13. ABTS•+ Radical Scavenging Assay
2.14. Ferric-Reducing Antioxidant Power (FRAP) Assay
2.15. Cupric Ion-Reducing Antioxidant Capacity (CUPRAC) Assay
2.16. Determination of an Intracellular Metabolic Profile
3. Results and Discussion
3.1. Genomic and Transcriptomic Data of Antioxidative Response of B. longum GT15
3.1.1. Genes for Antioxidative Response of B. longum
3.1.2. Transcriptomic Data for Antioxidative Response of B. longum GT15
3.2. Proteomic Data for Antioxidative Response of B. longum GT15 in Comparison with Transcriptomics Data
3.3. Metabolomic Data for Antioxidative Response of B. longum GT15
3.3.1. Antioxidant Activity of B. longum GT15
3.3.2. Metabolic Fingerprinting and Data Analysis
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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No. | Product of the Gene | Locus_tag | * H2O2/ Control | O2 2 h/ Control | O2 4 h/ Control |
---|---|---|---|---|---|
1 | Glutaredoxin | BLGT_RS07125 | 3.5 | 11.4 | 28.6 |
2 | Thioredoxin | BLGT_RS02480 | 13.07 | 6.8 | 7.75 |
3 | DSBA_oxidoreductase | BLGT_RS00210 | 1.24 | 8.55 | 18.35 |
4 | Thioredoxin_reductase | BLGT_RS00265 | 5.47 | 4.35 | 4.35 |
5 | P-type_ATPase | BLGT_RS01395 | 18.11 | 5.88 | 9.80 |
6 | Thioredoxin_domain_protein | BLGT_RS01710 | 1.42 | 2.48 | 8.05 |
7 | Thioredoxin_peroxidase | BLGT_RS04835 | 1.54 | 1.37 | 6.76 |
8 | Linoleic_acid_isomerase | BLGT_RS06870 | 3.61 | 0.99 | 1.88 |
9 | Class_I_pyridine_nucleotide-disulfideoxidoreductase | BLGT_RS08540 | 9.02 | 2.79 | 1.34 |
10 | NADH_oxidase | BLGT_RS09280 | 0.74 | 0.72 | 3.74 |
11 | Dihydroorotate dehydrogenase | BLGT_RS02540 | 6.59 | 9.02 | 8.68 |
No. | Product of the Gene | Locus_Tag | H2O2 2 h/ Control | O2 2 h/Control | O2 4 h/ Control | COG *** Category |
---|---|---|---|---|---|---|
Oxidative response | ||||||
1 | Glutaredoxin | BLGT_RS07125 | NS 3.5 | 2.89 * 11.4 ** | 2.15 28.6 | O |
2 | Thioredoxin | BLGT_RS02480 | NS 13.07 | 2.59 6.8 | 2.71 7.75 | O |
3 | Class_I pyridine nucleotide-disulfide oxidoreductase | BLGT_RS08540 | 2.17 9.01 | NS 2.79 | NS 1.32 | C |
4 | Ribonucleoside-triphosphate reductase | BLGT_RS07845 | NS 0.84 | 2.17 0.68 | NS 1.32 | H |
5 | P-type ATPase | BLGT_RS01395 | NS 17.40 | 2.24 5.65 | NS 9.48 | RP |
Stress response | ||||||
6 | Cystathionine gamma-synthase | BLGT_RS03020 | 2.63 11.43 | 5.78 2.86 | 5.74 2.96 | E |
7 | Co-chaperonin GroES | groES | NS 35.69 | NS 4.84 | 2.18 46.57 | O |
8 | Transcription elongation factor GreA | BLGT_RS03800 | NS 0.73 | 2.23 4.47 | NS 5.28 | K |
9 | DEAD/DEAH box helicase | BLGT_RS07930 | 2.63 2.7 | 2.27 1.26 | NS 1.04 | L |
10 | LexA repressor | BLGT_RS06740 | NS 1.19 | 2.33 1.38 | 2.93 3.21 | KT |
11 | General stress protein | BLGT_RS07865 | 2.77 1.89 | NS 1.27 | NS 2.3 | R |
12 | DNA topoisomerase | BLGT_RS06115 | 2.17 0.95 | NS 1.1 | NS 1.19 | L |
13 | Nucleotidyl transferase | BLGT_RS07810 | NS 3.5 | 4.65 3.9 | 3.25 5 | - |
14 | DNA polymerase sliding clamp subunit | BLGT_RS00420 | NS 7.84 | 7.47 11.32 | 14.46 43.6 | VP |
Nucleotide metabolism | ||||||
15 | Orotate phosphoribosyl transferase | BLGT_RS04975 | 2.27 0.77 | NS 1.02 | NS 1.23 | - |
16 | Multifunctional fusion protein cytidylate kinase | BLGT_RS05305 | 3.84 1.0 | NS 0.63 | NS 0.29 | J |
17 | Ribonucleoside-diphosphate reductase subunit beta | BLGT_RS00155 | NS 0.7 | 2.08 1.98 | NS 2.1 | F |
Amino acid metabolism and transport | ||||||
18 | Cystathionine beta-synthase | BLGT_RS03015 | 3.22 6.62 | 7.00 1.69 | 7.38 1.99 | E |
19 | Chorismate synthase | BLGT_RS04580 | 3.12 0.45 | 3.10 0.85 | NS 1.17 | E |
20 | Amino acid ABC transporter | BLGT_RS07135 | NS 3.6 | 3.96 11 | 3.89 3.6 | E |
Carbohydrate metabolism | ||||||
21 | Gluconate kinase | BLGT_RS06825 | 2.77 0.67 | NS 0.70 | NS 1.04 | G |
22 | Alpha-amylase | BLGT_RS00840 | 2.13 13.0 | NS 1.21 | NS 1.35 | G |
Regulation of transcription and biosynthesis | ||||||
23 | XRE family transcriptional regulator | BLGT_RS06195 | 7.14 17.1 | 11.55 6.1 | 14.17 25.9 | K |
24 | MerR family transcriptional regulator | BLGT_RS00895 | 2.08 9.34 | NS 1.72 | NS 4.81 | K |
Transport | ||||||
25 | Membrane protein | BLGT_RS07320 | NS 0.62 | 8.21 1.9 | 10.07 1.27 | H |
26 | Cation transporter | BLGT_RS06745 | NS 1.61 | NS 2.42 | 2.06 3.0 | P |
Uncharacterized proteins | ||||||
27 | Uncharacterized protein | BLGT_RS00505 | NS 1.05 | 3.02 2.42 | 2.31 4.12 | - |
28 | Uncharacterized protein | BLGT_RS06485 | NS 6.4 | 3.04 5.3 | 3.50 13 | - |
29 | Uncharacterized protein | BLGT_RS07070 | NS 5.4 | 3.58 7.7 | 3.94 17.8 | - |
Sample/Assay * | DPPH | ABTS | FRAP | CUPRAC |
---|---|---|---|---|
Culture liquid | ||||
Control **—0 h | 0.61 ± 0.01 | 6.50 ± 0.04 | 1.26 ± 0.03 | 2.04 ± 0.02 |
Control—2 h | 0.82 ± 0.00 | 7.30.03 | 1.94 ± 0.02 | 2.43 ± 0.04 |
Control—4 h | 0.75 ± 0.01 | 6.15 ± 0.07 | 0.92 ± 0.02 | 2.10 ± 0.02 |
O2—0 h | 0.61 ± 0.01 | 6.50 ± 0.04 | 1.26 ± 0.03 | 2.04 ± 0.02 |
O2—2 h | 0.81 ± 0.0 | 6.69 ± 0.02 | 1.44 ± 0.02 | 2.25 ± 0.01 |
O2—4 h | 0.63 ± 0.01 | 6.38 ± 0.08 | 1.33 ± 0.01 | 2.40 ± 0.06 |
H2O2—0 h | 0.53 ± 0.00 | 6.39 ± 0.04 | 0.74 ± 0.02 | 2.93 ± 0.05 |
H2O2—2 h | 0.50 ± 0.01 | 6.49 ± 0.08 | 0.92 ± 0.02 | 2.89 ± 0.04 |
Cell biomass | ||||
Control *—0 h | 0.06 ± 0.00 | 0.87 ± 0.02 | 0.084 ± 0.003 | 0.41 ± 0.01 |
Control—2 h | 0.08 ± 0.00 | 0.91 ± 0.01 | 0.048 ± 0.000 | 0.53 ± 0.01 |
Control—4 h | 0.07 ± 0.00 | 1.06 ± 0.016 | 0.09 ± 0.00 | 0.58 ± 0.02 |
O2—0 h | 0.06 ± 0.00 | 0.87 ± 0.02 | 0.084 ± 0.003 | 0.41 ± 0.01 |
O2—2 h | 0.10 ± 0.00 | 1.15 ± 0.03 | 0.08 ± 0.00 | 0.51 ± 0.01 |
O2—4 h | 0.08 ± 0.00 | 0.94 ± 0.02 | 0.21 ± 0.01 | 0.62 ± 0.01 |
H2O2—0 h | 0.06 ± 0.00 | 0.87 ± 0.02 | 0.084 ± 0.003 | 0.41 ± 0.01 |
H2O2—2 h | 0.06 ± 0.00 | 1.03 ± 0.02 | 0.09 ± 0.00 | 0.73 ± 0.02 |
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Averina, O.V.; Kovtun, A.S.; Mavletova, D.A.; Ziganshin, R.H.; Danilenko, V.N.; Mihaylova, D.; Blazheva, D.; Slavchev, A.; Brazkova, M.; Ibrahim, S.A.; et al. Oxidative Stress Response of Probiotic Strain Bifidobacterium longum subsp. longum GT15. Foods 2023, 12, 3356. https://doi.org/10.3390/foods12183356
Averina OV, Kovtun AS, Mavletova DA, Ziganshin RH, Danilenko VN, Mihaylova D, Blazheva D, Slavchev A, Brazkova M, Ibrahim SA, et al. Oxidative Stress Response of Probiotic Strain Bifidobacterium longum subsp. longum GT15. Foods. 2023; 12(18):3356. https://doi.org/10.3390/foods12183356
Chicago/Turabian StyleAverina, Olga V., Aleksey S. Kovtun, Dilara A. Mavletova, Rustam H. Ziganshin, Valery N. Danilenko, Dasha Mihaylova, Denica Blazheva, Aleksandar Slavchev, Mariya Brazkova, Salam A. Ibrahim, and et al. 2023. "Oxidative Stress Response of Probiotic Strain Bifidobacterium longum subsp. longum GT15" Foods 12, no. 18: 3356. https://doi.org/10.3390/foods12183356