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

RUIRUI LIU

RUIRUI LIU

  • The College of Life Sciences, Northwest UniversityXi’an, P.R. China
  • Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest UniversityXi’an, P.R. China
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LIU, RUIRUI
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LULU LI

LULU LI

  • The College of Life Sciences, Northwest UniversityXi’an, P.R. China
  • Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest UniversityXi’an, P.R. China
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LI, LULU
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ZHIYING LI

ZHIYING LI

  • The College of Life Sciences, Northwest UniversityXi’an, P.R. China
  • Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest UniversityXi’an, P.R. China
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LI, ZHIYING
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WEIWEI WANG

WEIWEI WANG

  • The College of Life Sciences, Northwest UniversityXi’an, P.R. China
  • Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest UniversityXi’an, P.R. China
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WANG, WEIWEI
  
18. Feb. 2020
Impact of Hydrogen on the Transcriptome of Sinorhizobium meliloti 1021 Using RNA-sequencing Technology's Cover Image
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Artikel-Kategorie: original-paper
Online veröffentlicht: 18. Feb. 2020
Seitenbereich: 39 - 48
Eingereicht: 29. Aug. 2019
Akzeptiert: 12. Jan. 2020
DOI: https://doi.org/10.33073/pjm-2020-006
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© 2020 Ruirui Liu et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Fig. 1.

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

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.
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.
Differential gene bubble map in the KEGG metabolic pathway.

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.
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.
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
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
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