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Table 6 Genes encoding putative hydrogenases, sensory hydrogenases, and NADH:Fd oxidoreductases using ferredoxin, coenzyme F 420 , and NAD(P)H as electron carriers

From: Linking genome content to biofuel production yields: a meta-analysis of major catabolic pathways among select H2and ethanol-producing bacteria

Organism

Hydrogenase and NADH:Fd oxidoreductase classification and corresponding genes

 

[NiFe] H2ase

[FeFe] H2ase

NFO

 

Fd-dependent echand mbhG4

F420-dependentG3 and otherG1

Bifurcating

SensoryA

NAD(P)H-dependent

Fd-dependent

rnf-type

Standard free energy (ΔG°’)*

−3.0

11

+7.5**

NA

18.1

18.1

−21.1***

Ca. bescii DSM 6725

Athe_1082-Athe_1087

 

Athe_1297- Athe_1299 A1 TR(M3)

Athe_1292 D M2e

   

Ca. saccharolyticus DSM 8903

Csac_1534-Csac_1539

 

Csac_1862- Csac_1864 A1 TR(M3)

Csac_1857 D M2e

   

P. furiosus DSM 3638

PF1423- PF1436

PF0891- PF0894 G3

     
  

PF1329- PF1332 G3

     

Th. kodakaraensis KOD1

TK2080- TK2093

TK2069-TK2072 G3

     

T. neapolitana DSM 4359

  

CTN_1067- CTN1069 TTH

CTN_1071- CTN_1072 CD(M2f)

CTN_0485 TTH

 

CTN_0437-CTN_0442

T. petrophila RKU-1

  

Tpet_1367- Tpet_1369 TTH

Tpet_1371- Tpet_1372 CD(M2f)

Tpet_0723 TTH

 

Tpet_0675-Tpet_0680

T. maritima MSB8

  

TM1424- TM1426 TTH

TM1420- TM1422 CD(M2f)

TM0201 TTH

 

TM0244- TM0249

Cal.subterraneus subsp. tengcongensis MB4

TTE0123- TTE0134

 

TTE0892- TTE0894 A1 TR(M3)

TTE0887 D M2e

   
    

TTE0697 CD(M2f)

   

E. harbinense YUAN-3 T

  

Ethha_2614- Ethha_2616 A8 TR(M3)

Ethha_0052 CD(M2f)

Ethha_2293 A7 D(M3)

Ethha_0031 B2 M2a

 

C. cellulolyticum H10

Ccel_1686- Ccel_1691

Ccel_1070-Ccel_1071 G1

Ccel_2303- Ccel_2305 A8 TR(M3)

Ccel_2300- Ccel_2301 CD(M2f)

 

Ethha_2695 B3 M3a

 
 

Ccel_3363- Ccel_3371

 

Ccel_2232- Ccel_2234 A1 TR(M3)

    
   

Ccel_2467- Ccel_2468 A1 TR(M3)

    

C. phytofermentans ISDg

Cphy_1730-Cphy_1735

 

Cphy_0087- Cphy_0089 A8 TR(M3)

Cphy_0092- Cphy_0093 CD(M2f)

 

Cphy_2056 A5 M2c

Cphy_0211-Cphy_0216

   

Cphy_3803- Cphy_3805 A1 TR(M3)

Cphy_3798 D M2e

Cthe_3003-Cthe_3004

Cphy_0090 B1 M3a

 

C. thermocellum ATCC 27405

Cthe_3013-Cthe_3024

 

Cthe_0428- Cthe_0430 A8 TR(M3)

Cthe_0425- Cthe_0426 CD(M2f)

  

Cthe_2430-Cthe_2435

   

Cthe_0340- Cthe_0342 A1 TR(M3)

Cthe_0335 D M2e

   

C. thermocellum DSM 4150

CtherDRAFT_2162-CtherDRAFT_2173

 

CtherDRAFT_1101-CtherDRAFT_1103 A8 TR(M3)

CtherDRAFT_1098-CtherDRAFT_1099 CD(M2f)

YesB

 

CtherDRAFT_0369-CtherDRAFT_0375

   

CtherDRAFT_2978 A1 TR(M3)

    

Ta. pseudethanolicus 39E

   

Teth39_0221 CD(M2f)

  

Teth39_2119-Teth39_2124

   

Teth39_1456- Teth39_1458 A1 TR(M3)

Teth39_1463 D M2e

   

G. thermoglucosidasius C56-YS93

B. cereus ATCC 14579

       
  1. AGroup D M2e hydrogenases are poorly characterized and do not contain a PAS/PAC-sensory domain. However, given their proximity to protein kinases and bifurcating hydrogenases, and their phylogenetic proximity to group C D(M2f) sensory hydrogenases (Additional file 3) we have classified them as sensory hydrogenases.
  2. BVerified by microarray and proteomic analysis (unpublished).
  3. Characterization of hydrogenase specificity was based metallocenter composition ([NiFe] or [FeFe]), modular structure, subunit composition, and large (catalytic) subunit phylogeny according to Vignais et al. and Calusinska et al. [16, 95, 96]. Phylogenetic cluster groupings are indicated in superscript, and corresponding phylogenetic trees are provided in Additional file 1 and Additional file 2. Abbreviations: H 2 ase, hydrogenase; NFO, NADH:ferredoxin oxidoreductase; ech, energy conserving hydrogenase; mbh, membrane bound hydrogenase; rnf, Rhodobacter nitrogen fixation.