Recent publications


de Lima, L.A., Reinmets, K., Nielsen, L.K., Marcellin, E., Harris, A., Köpke, M. & Valgepea, K. RNA-seq Sample Preparation Kits Strongly Affect Transcriptome Profiles of a Gas-Fermenting Bacterium. Microbiology Spectrum, 31; 10(4):e0230322; doi:; Preprint.

Im, C., Valgepea, K., Modin, O. & Nygård, Y. Clostridium ljungdahlii as a biocatalyst in microbial electrosynthesis – Effect of culture conditions on product formation. Biotechnology Resource Reports, 19, 101156; doi:

de Lima, L.A., Ingelman, H., Brahmbhatt, K., Reinmets, K., Barry, C., Harris, A., Marcellin, E., Köpke, M. & Valgepea, K. Faster Growth Enhances Low Carbon Fuel and Chemical Production Through Gas Fermentation. Frontiers in Bioengineering and Biotechnology, 879578; doi: 10.3389/fbioe.2022.879578; Preprint.

Valgepea, K., Talbo, G., Takemori, N., Takemori, A., Ludwig, C., Mahamkali, V., Mueller, A.P., Tappel, R., Köpke, M., Simpson, S.D., Nielsen, L.K. & Marcellin, E. Absolute Proteome Quantification in the Gas-Fermenting Acetogen Clostridium autoethanogenum. mSystems, doi: 10.1128/msystems.00026-22; Preprint.

Heffernan, J.K., Mahamkali, V., Valgepea, K., Marcellin, E., Nielsen, L.K. Analytical tools for unravelling the metabolism of gas-fermenting Clostridia. Current Opinion in Biotechnology, 28;75:102700;

Pavan, M., Reinmets, K., Garg, S., Mueller, A.P., Marcellin, E., Köpke, M., Valgepea, K. Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy. Metabolic Engineering, S1096-7176(22)00021-0; doi:

Doddapaneni, T.R.K.C., Ahmad, F., Valgepea, K., Kikas, T. Integrated thermochemical and biochemical processes for the production of biofuels and biochemicals, In: Biomass, Biofuels, Biochemicals. Elsevier. 67–105. doi:


Espinosa, M.I., Gonzalez-Garcia, R.A., Valgepea, K., Plan, M.R., Scott, C., Pretorius, I.S., Marcellin, E., Paulsen, I.T. & Williams, T.C. Adaptive laboratory evolution of native methanol assimilation in Saccharomyces cerevisiae. Nature Communications, 11:5564. doi:; Preprint.

Mahamkali, V.*, Valgepea, K.*, Lemgruber, R.d.S.P., Plan, M., Tappel, R., Köpke, M., Simpson, S.D., Nielsen, L.K. & Marcellin, E. Redox controls metabolic robustness in the gas-fermenting acetogen Clostridium autoethanogenum. Proceedings of the National Academy of Sciences of U.S.A., doi: 10.1073/pnas.1919531117

Heffernan, J.K.*, Valgepea, K.*, Lemgruber, R.d.S.P., Casini, I., Plan, M., Tappel, R., Simpson, S.D., Köpke, M., Nielsen, L.K. & Marcellin, E. Enhancing CO2-valorization using Clostridium autoethanogenum for sustainable fuel and chemicals production. Frontiers in Bioengineering and Biotechnology, 8:204. doi:; Preprint.


Lemgruber, R.d.S.P., Valgepea, K., Gonzalez Garcia, R.A., de Bakker, C., Palfreyman, R.W., Tappel, R., Köpke, M., Simpson, S.D., Nielsen, L.K. & Marcellin, E. A TetR-Family Protein (CAETHG_0459) Activates Transcription From a New Promoter Motif Associated With Essential Genes for Autotrophic Growth in Acetogens. Frontiers in Microbiology 10:2549; doi:; Preprint.

Lemgruber, R.d.S.P.*, Valgepea*, K., Tappel, R., Behrendorff, J.B., Palfreyman, R.W., Plan, M., Hodson, M.P., Simpson, S.D., Nielsen, L.K., Köpke, M. & Marcellin, E. Systems-level engineering and characterization of Clostridium autoethanogenum through heterologous production of poly-3-hydroxybutyrate (PHB). Metabolic Engineering, 53: 14-23; doi:


Valgepea, K., Lemgruber, R.d.S.P., Abdalla, T., Binos, S., Takemori, N., Takemori, A., Tanaka, Y., Tappel, R., Köpke, M., Simpson, S.D., Nielsen, L.K. & Marcellin, E. H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum. Biotechnology for Biofuels, 11:55; doi:

Lemgruber, R.d.S.P., Valgepea, K., Hodson, M.P., Tappel, R., Köpke, M., Simpson, S.D., Nielsen, L.K. & Marcellin, E. Quantitative analysis of tetrahydrofolate metabolites from Clostridium autoethanogenum. Metabolomics, 14:35; doi:


Valgepea, K., Lemgruber, R.d.S.P., Meaghan, K., Palfreyman, R.W., Abdalla, T., Heijstra, B., Behrendorff, J.B., Tappel, R., Köpke, M., Simpson, S.D., Nielsen, L.K. & Marcellin, E. Maintenance of ATP homeostasis triggers metabolic shifts in gas-fermenting acetogens. Cell Systems, 4: 505-515; doi:

Valgepea, K., Loi, K.Q., Behrendorff, J.B., Lemgruber, R.d.S.P., Plan, M., Hodson, M.P., Köpke, M., Nielsen, L.K. & Marcellin, E. Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenum. Metabolic Engineering, 41: 202-211; doi:

*joint first author