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. 2016 Dec 9;11(4):945–958. doi: 10.1038/ismej.2016.171

Table 2. The transcriptome profile of the genes involved in H2 metabolism and CO2 fixation of Methylacidiphilum fumariolicum SolV.

Protein annotation Gene Gene IDa Expression level (RPKM)b
      H2 culturec CH4 cultured Cells at μmaxe
Hydrogenase expression/formation protein hoxQ hoxQ MfumV2_0886 269 112 157
Putative hydrogenase maturation protease hycL MfumV2_0891 191 184 160
[NiFe] hydrogenase nickel insertion protein hypA MfumV2_892 145 137 156
[NiFe] hydrogenase Group 1h/5 small subunit hhyS MfumV2_978 3449 1853 2076
[NiFe] hydrogenase Group 1h/5 large subunit hhyL MfumV2_979 2233 803 1746
Putative maturation protein hupD MfumV2_980 328 388 580
[NiFe] hydrogenase Ni-incorporation protein hhaB MfumV2_988 613 543 480
High affinity Ni transporter   MfumV2_989 325 218 230
[NiFe] hydrogenase metallocenter assembly protein HhaF hhaF MfumV2_990 77 43 92
[NiFe] hydrogenase metallocenter assembly protein HhaC hhaC MfumV2_991 240 353 524
[NiFe] hydrogenase metallocenter assembly protein HhaD hhaD MfumV2_992 727 483 948
[NiFe] hydrogenase metallocenter assembly protein HhaE hhaE MfumV2_993 843 734 560
Hydrogenase expression protein HupH hupH MfumV2_1562 608 247 27
[NiFe] hydrogenase cytochrome b subunit hupZ MfumV2_1563 818 266 36
[NiFe] hydrogenase Group 1d large subunit hupL MfumV2_1564 1596 751 239
[NiFe] hydrogenase Group 1d small subunit hupS MfumV2_1565 3219 1370 47
RuBisCOf small subunit cbbS Mfumv2_1495 6826 3456 8520
RuBisCO large subunit cbbL Mfumv2_1496 7576 4028 6419
a

Available at the MicroScope annotation platform (https://www.genoscope.cns.fr/agc/microscope/home/).

b

The mRNA expression is shown as RPKM according to Mortazavi et al (Saitou and Nei, 1987). Changes in expression in the continuous cultures (substrates H2 or CH4) compared to batch culture cells growing at μmax are demonstrated by shading (up-regulation>twofold, dark grey, downregulation<0.5, light grey).

c

Continuous culture using H2 as an electron donor.

d

Continuous culture using CH4 as an electron donor.

e

Batch culture using CH4 as an electron donor to obtain μmax=0.07 h−1.

f

Ribulose-1,5-bisphosphate carboxylase/oxygenase.