Impact of Hydrogen on the Transcriptome of Sinorhizobium meliloti 1021 Using RNA-sequencing Technology

LIU, RUIRUI; LI, LULU; LI, ZHIYING; WANG, WEIWEI

doi:10.33073/pjm-2020-006

Figures & Tables

Differential gene clustering. Red dots indicate downregulated genes and blue dots indicate upregulated genes in comparison with the control.

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.

Differential gene bubble map in the KEGG metabolic pathway.

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.

The oxidative phosphorylation complex activity map. Each experiment was performed three times.

The content of amino acids after hydrogen treatment_

Amino acid	Concentration (mg/g)
	Control group	Test group
	Control 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

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

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

Impact of Hydrogen on the Transcriptome of Sinorhizobium meliloti 1021 Using RNA-sequencing Technology

Figures & Tables

Fig. 1.

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Fig. 4.

Fig. 5.

The content of amino acids after hydrogen treatment_

Differentially expressed genes – change with hydrogen treatment_

Hydrogenases involved in arginine and proline metabolism_

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