Abstract
Formate is a promising energy carrier that could be used to transport renewable electricity. Some acetogenic bacteria, such as Eubacterium limosum, have the native ability to utilise formate as a sole substrate for growth, which has sparked interest in the biotechnology industry. However, formatotrophic metabolism in acetogens is poorly understood, and a systems-level characterization in continuous cultures is yet to be reported. Here we present the first steady-state dataset for E. limosum formatotrophic growth. At a defined dilution rate of 0.4 d-1, there was a high specific uptake rate of formate (280±56 mmol/gDCW/d), however, most carbon went to CO2 (150±11 mmol/gDCW/d). Compared to methylotrophic growth, protein differential expression data and intracellular metabolomics revealed several key features of formate metabolism. Upregulation of pta appears to be a futile attempt of cells to produce acetate as the major product. Instead, a cellular energy limitation resulted in the accumulation of intracellular pyruvate and upregulation of Pfl to convert formate to pyruvate. Therefore, metabolism is controlled, at least partially, at the protein expression level, an unusual feature for an acetogen. We anticipate that formate could be an important one-carbon substrate for acetogens to produce chemicals rich in pyruvate, a metabolite generally in low abundance during syngas growth.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Cross referencing of comparison methanol dataset.
Abbreviations
- D
- Dilution rate
- LLOQ
- Lower Limit of Quantification
- OD
- Optical Density
- WLP
- Wood-Ljungdahl Pathway
- 2PG
- 2-phosphoglycerate
- 3DHQ
- 3-dehydroquinate
- 3DHSA
- 3-dehydroshikimate
- 3PG
- 3-phosphoglycerate
- Ac-CoA
- acetyl-CoA
- BPG
- 1,3-biphosphoglycerate
- DAHP
- 3-deoxy-arabino-heptulonate 7-phosphate
- DHAP
- Dihydroxy acetone phosphate
- E4P
- Erythrose 4-phosphate
- EPSP
- 3-enolpyruvyl-shikimate 5-phosphate
- F6P
- Fructose 6-hosphate
- FBP
- Fructose 1,6-biphosphate
- G3P
- Glyceraldehyde 3-phosphate
- G6P
- Glucose 6-phosphate
- Glc
- Glucose
- PEP
- Phosphoenolpyruvate
- PRPP
- 5-phosphoribosyl diphosphate
- PYR
- Pyruvate
- R5P
- Ribose 5-phosphate
- RL5P
- Ribulose 5-phosphate
- S3P
- Shikimate 3-phosphate
- S7P
- Sedoheptulose 7-phosphate
- THF
- tetrahydrofolate
- X5P
- Xylulose 5-phosphate
- ALD
- aldehyde dehydrogenase
- ACK
- acetate kinase
- ACN
- anonitase
- ACS
- acetyl-CoA synthase
- ADH
- alcohol dehydrogenase
- AOR
- aldehyde:ferredoxin oxidoreductase
- aroA
- DAHP synthase
- aroA
- 3-phosphoshikimate 1-carboxyvinyltransferase
- aroB
- 3-dehydroquinate synthase
- aroC
- chorismate synthase
- aroD
- 3-dehydroquinate dehydratase
- aroKL
- shikimate kinase
- BK
- butyrate kinase
- cimA
- citramalate synthase
- CODH
- CO dehydrogenase
- crt
- crotonase
- CS
- citrate synthase
- ENO
- enolase
- Etf-Bcd
- butyryl-CoA dehydrogenase
- FBA
- Fructose biphosphate aldose
- FBP
- fructose 1
- FDH
- formate dehydrogenase
- FTHFS
- formyl-THF synthetase
- FUM
- fumarase
- GAD
- glutamate decarboxylase
- GAPDH
- glyceraldehyde 3-phosphate dehydrogenase
- GDH
- glutamate dehydrogenase
- GLK
- Glucokinase
- hbd
- 3-hydroxybutyryl-CoA dehydrogenase
- IDH
- isocitrate dehydrogenase
- ilvBN
- pyruvate:2-oxobutanoate acetaldehydetransferase
- ilvC
- 2-aceto-2hydroxy-butanoate:NADP+ oxidoreductase
- ilvD
- dihydroxy acid dehydratase
- ilvE
- branched chain amino acid aminotransferase
- KOR
- oxoglutarate ferredoxin oxidoreductase
- leuB
- methylmalate dehydrogenase
- leuCD
- methylmalate hydrolase
- LeuDH
- leucine dehydrogenase
- MDH
- malate dehydrogenase
- MtaABC
- methanol dependent methyl transferase
- MTHFC
- methenyl-THF cylcohydrolase
- MTHFD
- methylene-THF dehydrogenase
- MTHFR
- methyltransferase/methylene-THF reductase
- PC
- pyruvate carboxylase
- PD
- pyruvate dehydrogenase
- PFKA
- Phosphofructose kinase
- PFL
- pyruvate formate ligase
- PFOR
- pyruvate ferredoxin oxidoreductase
- PGAM
- phosphoglycerate mutase
- PGI
- Glucose 6-phosphate isomerase
- PGK
- phosphoglycerate kinase
- PK
- pyruvate kinase
- PPDK
- phosphoenolpyruvate synthetase
- PRPS
- Ribose phosphat epyrophosphokinase
- PTA
- phosphotransacetylase
- PTB
- phosphotransbutyrylase
- PTS
- phosphotransferase system
- RPE
- Ribulose phosphate epimerase
- RPI
- Ribose phosphate isomerase
- Stn
- Sporomusa type Nfn transhydrogenase
- TAL
- Transaldolase
- thl
- thiolase
- TKT
- Transketolase
- TPI
- Trisephosphate isomerase
- trpE
- anthranilate synthase
- ydiB
- shikimate dehydrogenase