Specific Features of the Proteomic Response of Thermophilic Bacterium Geobacillus icigianus to Terahertz Irradiation
Abstract
:1. Introduction
2. Results
2.1. Changes in the Proteomic Profile of the Thermophilic Bacterium G. icigianus in Response to Irradiation with THz Electromagnetic Waves (2.3 THz) for 15 Min
Protein/Reaction | Gene/Locus | Process/Function | ∆ |
---|---|---|---|
Electron transfer flavoprotein subunit beta/FixA family protein (ETFb) Electron transfer flavoprotein subunit alpha/FixB family protein (ETFa) | EP10_09770 EP10_09765 | ETF:heterodimer, a key component of the electron transfer chain | 1.7 1.4 |
NADH dehydrogenase (EC 7.1.1.2), NADH:ubiquinone reductase (H+-translocating) NADH + Q + 5H+-> QH2 + NAD +4H+ | EP10_04625 | Respiration, generates PMF | 1.6 |
D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) G3P + NAD+ -> 3-phosphooxypyruvate + NADH + H+ | EP10_12110 | NADH synthesis, serine biosynthesis | 1.8 |
Type I glyceraldehyde-3-phosphate dehydrogenase (NAD+), (EC 1.2.1.12) G3P + Pi + NAD -> NADH + 1, 3PDG | gap/ EP10_12960 | Key enzyme of the glycolytic pathway, NADH synthesis | 1.2 |
Class II fructose-bisphosphatase Fructose-1,6-bisphosphatase (FBPase) (EC 3.1.3.11) FDP+ H2O + ADP -> F6P + ATP | glpX/ EP10_10310 | ATP biosynthesis, peptidoglycan biosynthesis | 1.2 |
Elongation factor Tu | tuf/ EP10_11775 | Translation elongation factor, GTPase | 1.6 |
Ribosome recycling factor | frr/EP10_17125 | Translation | 1.4 |
Cysteine-tRNA ligase (EC:6.1.1.16) | CysS/ EP10_11880 | Translation | 1.35 |
Transcription elongation factor GreA | EP10_01545 | Transcription, chaperone activity | 1.8 |
Bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase (EC 4.1.99.12)/GTP cyclohydrolase II (EC 3.5.4.25) | EP10_18260 | Riboflavin biosynthesis, protects DNA from oxygen radicals | 1.4 |
Thioredoxin reductase (EC 1.8.1.9) Thr + NADP+ -> Thr disulfide + NADPH + H+ | EP10_04630 | Antioxidant system, NADPH synthesis | 1.6 |
Thiol peroxidase, Tpx-type (EC:1.11.1.24) [thioredoxin]-dithiol + a hydroperoxide -> [thioredoxin]-disulfide + alcohol + H2O | EP10_18085 | Thiol peroxidase is part of an oxidative stress defense system | 1.6 |
Deacetylase BshB2 (deacetylase of the LmbE family protein) | bshB2/ EP10_10565 | Bacillithiol synthesis, resistance during oxidative stress | 1.55 |
Pantoate-beta-alanine ligase (EC 6.3.2.1) ATP + pantoate + alanine -> AMP + diphosphate + pantothenate | EP10_07480 | Synthesis of pantothenate from alanine | 1.3 |
L-serine deaminase, L-serine ammonia-lyase, iron-sulfur-dependent, subunit beta (EC 4.3.1.17) L-serine -> pyruvate + NH3 | sdaAB/ EP10_16780 | Pyruvate synthesis | 1.4 |
Acetyl-CoA acetyltransferase (EC 2.3.1.9) 2 Acetyl-CoA -> CoA + acetoacetyl-CoA | thlA/ EP10_03775 | CoA biosynthesis | 1.7 |
Acetate kinase (EC 2.7.2.1) ATP + acetate -> ADP + acetyl phosphate | ackA/EP10_18095 | АсСоА biosynthesis | 1.4 |
Pyridoxal 5′-phosphate synthase (PLP synthase) Glutaminase subunit PdxT (EC 2.4.2.-) | pdxT/ EP10_02655 | De novo pyridoxal 5′-phosphate biosynthesis | 1.5 |
Inorganic pyrophosphatase (EC 3.6.1.1) Diphosphate + H2O <-> 2 phosphate | EP10_12120 | Cell growth | 1.3 |
Protein/Reaction | Gene/Locus | Process/Function | ∆ |
---|---|---|---|
ATP synthase alpha chain (EC 7.1.2.2) ADP + PI + [H+]ex <-> ATP + H2O + [H+]in | atpA/ EP10_10185 | ATP biosynthesis; when the PMF is decreased, ATP synthase catalyzes the reverse reaction, working as an ATP-dependent proton pump | 1.3 |
Predicted L-lactate dehydrogenase (multisubunits, lldEFG, syn ykgEFG), PYR + NAD+ <-> LAC + NADH + H+ | EP10_13275 | NADH and lactate biosynthesis; iron–sulfur cluster-binding subunit YkgF [51] | 1.6 |
Malic enzyme, NAD-dependent Mal + NAD -> Pyr + NADH + CO2 | EP10_15870 | NADH and pyruvate biosynthesis | 1.8 |
Oxidoreductase, aldo/keto reductase family | EP10_11090 | NADH and NADPH biosynthesis | 1.55 |
2-Oxo acid dehydrogenase complex subunit E2 Dihydrolipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (EC 2.3.1.168) | EP10_06390 | Complex catalyze-irreversible oxidation of 2-oxoacids with production of acyl-CoA and NADH | 2.15 |
Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) L-aspartate 4-semialdehyde + phosphate + NADP+ -> L-4-aspartyl phosphate + NADPH + H+ | Asd/ EP10_17245 | NADPH biosynthesis | 2.0 |
Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) ICIT + NADP -> AKG + CO2 + NADPH | EP10_07280 | NADPH biosynthesis | 2.2 |
HslU—subunit of the ATP-dependent HslUV protease | EP10_16935 | Molecular chaperone | 1.3 |
Trehalose-6-phosphate hydrolase (EC 3.2.1.93) Trehalose 6-phosphate + H2O -> glucose + glucose 6-phosphate | EP10_08195/treA | Trehalose—osmoprotectant and carbon source [52] | 2.0 |
Tyrosine-tRNA ligase (EC 6.1.1.1) | EP10_13885 | Translation | 1.9 |
Tripeptide aminopeptidase (EC 3.4.11.4) | pepT EP10_11320 | Protease | 1.6 |
Excinuclease ABC subunit UvrB, ATP-dependent | EP10_00715 | DNA reparation | 3.3 |
Cysteine methyltransferase Methylated-DNA-protein-cysteine methyltransferase (EC 2.1.1.63) | EP10_00085 | Repair of methylated DNA | 5.4 |
Flagellar motor switch phosphatase FliY | EP10_17020 | Chemotaxis disorder | 1.8 |
2.2. The Reaction of G. icigianus Cells 10 Min after the End of the THz Irradiation (2.3 THz)
3. Discussion
4. Materials and Methods
4.1. Cell Culture Conditions
4.2. Irradiation Conditions
- Wavelength, mm 0.05–0.340
- Pulse duration, ps 50
- Pulse repetition frequency, MHz 2.8–11.2
- Average power, W up to 400
- Peak power, MW up to 1
- Minimum relative line width 3 × 10−3
4.3. Two-Dimensional Electrophoresis of Proteins
4.4. Determination of the Proteomic Profile
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Protein/Reaction | Gene/Locus | Process/Function | ∆ |
---|---|---|---|
Electron transfer flavoprotein subunit alpha/FixB family protein ETFb Electron transfer flavoprotein subunit beta/FixA family protein, ETFa | EP10_09770 EP10_09765 | ETF—heterodimer, a key component of the electron transfer chain | 1.7 1.3 |
Elongation factor Tu | tuf/EP10_11775 | Translation elongation factor, GTPase | 1.4 |
DNA-directed RNA polymerase subunit alpha | rpoA/EP10_11630 | Transcription | 2.2 * |
NAD-dependent malic enzyme Mal + NAD -> Pyr + NADH + CO2 | EP10_15870 | NADH and pyruvate biosynthesis | 1.3 * |
Acetyl-CoA acetyltransferase (EC 2.3.1.9) 2 Acetyl-CoA -> CoA + acetoacetyl-CoA | thlA/EP10_03775 | Acetyl-CoA degradation | 1.5 * |
Molecular chaperone DnaK | EP10_05360 | Molecular chaperone | 1.35 * |
Phosphopentomutase (EC 5.4.2.7) (2-Deoxy)-alpha-D-ribose 1-phosphate -> (2-deoxy)-D-ribose 5-phosphate | EP10_18365 | Ribonucleoside catabolism | 1.6 |
Methionine adenosyltransferase (EC 2.5.1.6) ATP + L-methionine + H2O -> phosphate + diphosphate + S-adenosyl-L-methionine | metK/EP10_09910 | S-Adenosyl-L-methionine biosynthesis, SAM—methyl donor | 1.4 |
Acid sugar phosphatase (TIGR01457 family HAD-type hydrolase) | EP10_04705 | 1.5 | |
Amino acid ABC transporter ATP-binding protein | EP10_06290 | Amino acid transport | 1.5 |
Bifunctional 3,4-dihydroxy-2-butanone 4-phosphate (DHBP) synthase (EC 4.1.99.12)/GTP cyclohydrolase II (EC 3.5.4.25) | EP10_18260 | Riboflavin biosynthesis, protects DNA from oxygen radicals | 2.1 * |
Protein/Reaction | Gene/Locus | Process/Function | ∆ |
---|---|---|---|
ATP synthase alpha chain (EC 7.1.2.2) ADP + PI + [H+]ex <-> ATΦ + H2O + [H+]in | atpA/EP10_10185 | ATP biosynthesis | 1.1 ± 0.04 |
Type I glyceraldehyde-3-phosphate dehydrogenase (NAD+), EC 1.2.1.12 G3P + PI + NAD -> NADH + 1, 3PDG | gapA/ EP10_12960 | NADH synthesis | 1.3 |
Pyruvate dehydrogenase (Acetyl-transferring) E1 component subunit alpha (EC 1.2.4.1) PYR + NAD + COA -> ACCOA + NADH + CO2 | pdhA/EP10_14290 | Complex production of NADH and AcCoA | 2.5 |
Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, subunit E2 (EC 2.3.1.12) ACLIPO + COA -> ACCOA + DLIPO | EP10_14300 | Complex production of NADH and AcCoA | 2.8 |
2-Oxo acid dehydrogenase complex subunit E2 Dihydrolipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (EC 2.3.1.168) | EP10_06390 | Complex production of acyl-CoA and NADH | 1.6 |
Leucine dehydrogenase, NAD (+)-dependent (EC 1.4.1.9) L-leucine + H2O + NAD+ -> 4-methyl-2-oxopentanoate + NH3 + NADH + H+ | EP10_06415 | NADH biosynthesis | 1.3 |
Glutamate dehydrogenase, NAD-specific (EC 1.4.1.2) L-glutamate + H2O + NAD+ -> 2-oxoglutarate + NH3 + NADH + H+. | EP10_12170 | NADH biosynthesis | 1.3 |
Glycine dehydrogenase (decarboxylating) (glycine cleavage system P1 protein) (EC 1.4.4.2) Gly + THF + NAD+ -> MetTHF + CO2 + NH3 + NADH | EP10_05755 | NADH biosynthesis | 1.6 |
Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) L-aspartate 4-semialdehyde + phosphate + NADP+ -> L-4-aspartyl phosphate + NADPH + H+ | Asd/EP10_17245 | NADPH biosynthesis | 1.2 |
6-Phosphogluconate dehydrogenase, NADP (+)-dependent (EC 1.1.1.44) 6PG + NADP -> D-ribulose 5-phosphate + CO2 + NADPH | EP10_18520 | PPP, NADPH biosynthesis | 2.2 |
Phosphoenolpyruvate carboxykinase (ATP) (EC 4.1.1.49) ATP + oxaloacetate -> ADP + phosphoenolpyruvate + CO2 | pckA/EP10_09915 | Enhances pyruvate pool | 1.3 |
Serine hydroxymethyltransferase (EC 2.1.2.1) MetTHF + glycine + H2O -> THF + L-serine | EP10_10230 | L-serine biosynthesis | 1.8 |
UDP-N-acetylmuramoyl(AM)-tripeptide-D-alanyl-D-alanine ligase, ATP-dependent (EC 6.3.2.10) ATΦ + UDP-N-AM-tripeptide + D-alanyl-D-alanine -> ADP + Pi + N-AM-pentapeptide | MurF/EP10_18840 | Peptidoglycan biosynthesis | 1.4 |
Arginase (L-arginine amidinohydrolase, EC 3.5.3.1) L-arginine + H2O -> L-ornithine + urea | rocF/EP10_17840 | Urea and ornithine can be further utilized as nitrogen and carbon sources | 1.3 |
Aspartate-tRNA ligase, Aspartyl-tRNA synthetase (EC 6.1.1.12) | EP10_01675 | Translation | 1.3 |
Proline-tRNA ligase, Prolyl-tRNA synthetase (EC 6.1.1.15) | EP10_17150 | Translation | 1.7 |
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Bannikova, S.; Khlebodarova, T.; Vasilieva, A.; Mescheryakova, I.; Bryanskaya, A.; Shedko, E.; Popik, V.; Goryachkovskaya, T.; Peltek, S. Specific Features of the Proteomic Response of Thermophilic Bacterium Geobacillus icigianus to Terahertz Irradiation. Int. J. Mol. Sci. 2022, 23, 15216. https://doi.org/10.3390/ijms232315216
Bannikova S, Khlebodarova T, Vasilieva A, Mescheryakova I, Bryanskaya A, Shedko E, Popik V, Goryachkovskaya T, Peltek S. Specific Features of the Proteomic Response of Thermophilic Bacterium Geobacillus icigianus to Terahertz Irradiation. International Journal of Molecular Sciences. 2022; 23(23):15216. https://doi.org/10.3390/ijms232315216
Chicago/Turabian StyleBannikova, Svetlana, Tamara Khlebodarova, Asya Vasilieva, Irina Mescheryakova, Alla Bryanskaya, Elizaveta Shedko, Vasily Popik, Tatiana Goryachkovskaya, and Sergey Peltek. 2022. "Specific Features of the Proteomic Response of Thermophilic Bacterium Geobacillus icigianus to Terahertz Irradiation" International Journal of Molecular Sciences 23, no. 23: 15216. https://doi.org/10.3390/ijms232315216