Fig. 1.
Differential gene clustering. Red dots indicate downregulated genes and blue dots indicate upregulated genes in comparison with the control.
Table I
Differentially expressed genes – change with hydrogen treatment.
| Gene ID | Gene name | Change with hydrogen treatment | Gene description |
|---|---|---|---|
| Gene1418 | sugE | Down | Quaternary ammonium compound efflux SMR transporter SugE |
| Gene1984 | msbB | Down | Lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase |
| Gene2119 | SMc04350 | Down | Multidrug efflux system transmembrane protein |
| Gene2120 | SMc04351 | Down | Transmembrane ATP-binding ABC transporter protein |
| Gene2494 | mtlK | Down | Oxygen-independent coproporphyrinogen III oxidase |
| Gene2940 | SMc02983 | Down | Arginine decarboxylase |
| Gene3019 | SMc03139 | Ups | Hypothetical protein |
| Gene3089 | SMc02519 | Down | ABC transporter ATP-binding protein |
| Gene3090 | SMc02518 | Down | ABC transporter ATP-binding protein |
| Gene3090 | SMc02518 | Down | ABC transporter ATP-binding protein |
| Gene3091 | SMc02517 | Down | ABC transporter permease |
| Gene3471 | SMa0081 | Ups | ABC transporter permease |
| Gene361 | iolB | Down | 5-deoxy-glucuronate isomerase |
| Gene362 | iolE | Down | Myo-inosose-2 dehydratase |
| Gene4065 | SMa1163 | Down | Cation transport P-type ATPase |
| Gene4073 | SMa1176 | Down | Hypothetical protein |
| Gene4075 | nosR | Down | NosR regulatory protein for N2O reductase |
| Gene4076 | nosZ | Down | Nitrous-oxide reductase |
| Gene4078 | nosF | Down | NosF ATPase |
| Gene4079 | nosY | Down | NosY permease |
| Gene4082 | fhp | Down | Nitric oxide dioxygenase |
| Gene4092 | fixI1 | Down | ATPase |
| Gene4093 | fixH | Down | Nitrogen fixation protein FixH |
| Gene4094 | fixG | Down | FixG iron sulfur membrane protein |
| Gene4095 | fixP1 | Down | FixP1 di-heme cytochrome c |
| Gene4097 | fixO1 | Down | Cbb3-type cytochrome c oxidase subunit II |
| Gene4123 | hemN | Down | Oxygen-independent coproporphyrinogen III oxidase |
| Gene4550 | SMa2051 | Down | Desaturase |
| Gene4551 | SMa2053 | Down | MocE-like protein |
| Gene5192 | SM_b20487 | Down | Sugar ABC transporter permease |
| Gene5193 | SM_b20488 | Down | Hypothetical protein |
| Gene5194 | SM_b20489 | Down | Carbohydrate kinase |
| Gene5727 | groEL | Down | Chaperonin GroEL |
| Gene5728 | groES5 | Down | Molecular chaperone GroES |
| Gene6038 | cyoB | Down | Cytochrome O ubiquinol oxidase subunit I |
| Gene6039 | cyoC | Down | Cytochrome O ubiquinol oxidase subunit III |
| Gene6040 | cyoD | Down | Cytochrome O ubiquinol oxidase CyoD |
| Gene6083 | SM_b20654 | Ups | Hypothetical protein |
| Gene6166 | SM_b20753 | Ups | Acyl-CoA dehydrogenase |
| Gene6288 | agaL1 | Down | Alpha-galactosidase (melibiase) protein |
| Gene811 | groES | Down | Co-chaperone GroES (Cpn10) binds to Cpn60 in the presence of Mg-ATP and suppresses the ATPase activity of the latte |
| Gene968 | betA | Down | Choline dehydrogenase |
| Gene969 | betB | Down | Betaine aldehyde dehydrogenase |
| Gene970 | betC | Down | Choline-sulfatase |
Fig. 2.
Histogram of GO terms associated with differentially expressed genes; the GO term is on the ordinate; the number of differentially expressed genes associated with each term is on the abscissa.
Fig. 3.
Differential gene bubble map in the KEGG metabolic pathway.
Table II
Hydrogenases involved in arginine and proline metabolism.
| EC number | Name |
|---|---|
| 1.2.1.19 | Aminobutyraldehyde dehydrogenase |
| 1.2.1.3 | Aldehyde dehydrogenase (NAD+) |
| 1.4.3.22 | Diamine oxidase |
| 1.2.1.71 | Succinylglutamate-semialdehyde dehydrogenase |
| 1.2.1.88 | L-glutamate gamma-semialdehyde dehydrogenase |
| 1.5.1.19 | D-nopaline dehydrogenase |
| 1.5.1.11 | D-octopine dehydrogenase |
Table III
The content of amino acids after hydrogen treatment.
| Amino acid | Concentration (mg/g) | |||
|---|---|---|---|---|
| Control group | Test group | |||
| 24 h | 48 h | 72 h | ||
| Alanine | 0.32 ± 0.012 | 0.292 ± 0.03 | 0.342 ± 0.011 | 0.372 ± 0.05 |
| Arginine | 0.0842 ± 0.006 | 0.0682 ± 0.002 | 0.0622 ± 0008 | 0.0372 ± 0.004 |
| Aspartic acid | 1.822 ± 0.015 | 1.862 ± 0.3 | 1.882 ± 0.29 | 1.772 ± 0.24 |
| Cysteine | 0.182 ± 0.07 | 0.152 ± 0.04 | 0.222 ± 0.06 | 0.142 ± 0.03 |
| Glutamic acid | 2.12 ± 0.25 | 2.252 ± 0.16 | 2.242 ± 0.19 | 2.22 ± 0.11 |
| Glycine | 0.0772 ± 0.004 | 0.0742 ± 0.006 | 0.0712 ± 0.003 | 0.0682 ± 0.009 |
| Histidine | 0.162 ± 0.07 | 0.182 ± 0.09 | 0.172 ± 0.05 | 0.152 ± 0.02 |
| Isoleucine | 0.72 ± 0.037 | 0.682 ± 0.02 | 0.772 ± 0.03 | 0.732 ± 0.08 |
| Leucine | 0.252 ± 0.022 | 0.222 ± 0.03 | 0.262 ± 0.04 | 0.292 ± 0.05 |
| Lysine | 3.62 ± 0.17 | 3.42 ± 0.11 | 3.32 ± 0.2 | 3.72 ± 0.19 |
| Methionine | 0.092 ± 0.003 | 0.062 ± 0.001 | 0.092 ± 0.004 | 0.0122 ± 0.002 |
| Phenylalanine | 1.52 ± 0.08 | 1.72 ± 0.05 | 1.622 ± 0.07 | 1.582 ± 0.03 |
| Proline | 0.0732 ± 0.002 | 0.0642 ± 0.008 | 0.0262 ± 0.002 | 0.0222 ± 0.004 |
| Serine | 0.0652 ± 0.007 | 0.0612 ± 0.002 | 0.062 ± 0.008 | 0.0552 ± 0.007 |
| Threonine | 0.0782 ± 0.005 | 0.0772 ± 0.005 | 0.0542 ± 0.007 | 0.0582 ± 0.003 |
| Tyrosine | None | None | None | None |
| Valine | 0.062 ± 0.003 | 0.0622 ± 0.007 | 0.0642 ± 0.004 | 0.0672 ± 0.008 |
Fig. 4.
Fold change in the expression levels of SMc02983, SMc01578, SMc01656, SMc02677, SM_b20752, cyoD, cyoB, and cyoC after the hydrogen treatment as determined by real-time quantitative PCR.
Fig. 5.
The oxidative phosphorylation complex activity map. Each experiment was performed three times.