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. 2012 Jul 25;3:266. doi: 10.3389/fmicb.2012.00266

Table 4.

Transcription of genes involved in nitrogen fixation in “Ca. M. fumariolicum” strain SolV.

Enzyme Gene name GenBank identifier Expression level (RPKM)
Cells at μmax N2 fixing cells O2 limited cells
Nitrogenase iron protein nifH Mfum_690040 69 22651 80
Nitrogenase molybdenum-iron protein alpha chain nifD Mfum_690039 87 14359 65
Nitrogenase molybdenum-iron protein beta chain nifK Mfum_690038 35 3348 34
Nitrogenase Mo/Fe cofactor biosynthesis protein NifE nifE Mfum_690037 77 5370 67
Nitrogenase Mo/Fe cofactor biosynthesis protein NifN nifN Mfum_690036 64 3677 52
Protein NifX nifX Mfum_690035 100 2831 26
Nif-specific regulatory protein nifA Mfum_690018 123 1080 109
Nitrogenase Mo/Fe cofactor biosynthesis protein NifB nifB Mfum_690029 19 3316 14
Pyruvate-flavodoxin oxidoreductase nifJ Mfum_940083 149 133 185
NifQ family protein nifQ Mfum_690020 65 270 22
Cysteine desulfurase nifS1 Mfum_690022 93 801 87
nifS2 Mfum_90010 159 133 116
nifS3 Mfum_190023 681 491 486
nifS4 Mfum_970062 162 275 145
nifS5 Mfum_310028 226 151 264
NifU-like protein involved in FeS cluster formation nifU Mfum_310029 54 16 79
Nitrogenase-stabilizing/protective protein NifW nifW Mfum_690011 62 2260 43
NifZ domain protein nifZ Mfum_690023 158 1373 50
Electron transfer flavoprotein beta chain fixA Mfum_690010 60 3311 73
Electron transfer flavoprotein alpha chain fixB Mfum_690009 81 3043 69
Flavoprotein-ubiquinone oxidoreductase fixC Mfum_690008 101 3632 100
Ferredoxin-like protein fixX Mfum_690007 126 2917 135
Nitrogen fixation protein FixU fixU Mfum_690015 164 2265 91
FeS cluster assembly scaffold protein, HesB/SufA family sufA1 Mfum_690026 40 2301 22
sufA2 Mfum_810040 149 43 71
sufA3 Mfum_1020116 214 143 183
FeS cluster assembly protein SufB sufB Mfum_970056 1099 2409 622
FeS cluster assembly protein SufD sufD Mfum_970057 663 2169 279
FeS cluster assembly protein SufE family sufE Mfum_110022 375 209 219
FeS4 cluster protein with leucine rich repeats Mfum_690024 88 1884 61
Ferredoxin-like protein in nif region frxA Mfum_690027 112 7892 46
Uptake hydrogenase large subunit hupB Mfum_50004 92 372 1840
Uptake hydrogenase small subunit hupS Mfum_50003 186 997 2955
Nickel/iron-hydrogenase I, small subunit hyaA Mfum_870019 2380 4157 4280
Nickel/iron-hydrogenase I, large subunit hyaB Mfum_870018 2566 1879 3595
Ni,Fe-hydrogenase I cytochrome b subunit hyaC Mfum_50005 122 593 984
[NiFe] hydrogenase Ni incorporation protein HypA hypA Mfum_730023 119 110 95
[NiFe] hydrogenase Ni incorporation-associated protein HypB hypB Mfum_870009 421 335 692
[NiFe] hydrogenase metallocenter assembly protein HypC hypC Mfum_870006 830 600 321
[NiFe] hydrogenase expression/formation protein HypD hypD Mfum_870005 1159 893 1246
[NiFe] hydrogenase metallocenter assembly protein HypE hypE Mfum_870004 424 476 759
[NiFe] hydrogenase metallocenter assembly protein HypF hypF Mfum_870007 92 81 167
Hydrogenase expression protein HupH hupH Mfum_50006 160 631 879
Hydrogenase expression/formation protein HoxQ hoxQ Mfum_730017 177 169 136
Hydrogenase maturation protease hycI Mfum_730022 69 44 89

The mRNA expression is expressed as RPKM according to Mortazavi et al. (2008). Changes in expression in the chemostat cultures (N2 fixing cells or O2 limited cells) compared to batch culture cells growing at μmax are indicated by shading: up regulation >2 times (dark gray), down regulation <0.5 (light gray).