Shota Atsumi

image of Shota Atsumi




Offices and Labs

Chemistry 218


2002 Ph.D Chemistry Kyoto University

Research Interests

Synthetic biology for biofuel production

An increased understanding of system properties underlying cellular networks enables us to construct novel systems by assembling the components and the control systems into new combinations. We are applying this approach to the field of metabolic engineering, which strives for the optimization of desired properties and functions, such as the production of valuable biochemicals. The production of valuable chemicals from microorganisms suites to solve some significant challenges, such as converting renewable feedstocks into energy-rich biofuels. Currently, our main focus is developing synthetic organisms capable of converting CO2 directly to biofuels.


2012 UCD Hellman Fellowship
2014 NSF CAREER Award

Department and Center Affiliations

Department of Chemistry


American Chemical Society
American Society for Microbiology
Society for industrial microbiology

CBS Grad Group Affiliations

Biochemistry, Molecular, Cellular and Developmental Biology

Graduate Groups not Housed in CBS



Atsumi Research Group website
  • (Postdocs) Christy R-Deere, (Visiting Researcher) Masahiro Kanno, (Graduate Students) Jordan McEwen, Shuchi Desai, Nicole Nozzi, Anna Case, Austin Carroll, Neal Oliver, and Yuki Soma


CHE 298 Chemical Biology for Energy and Environment
CHE 105 Anal & Phys Chem Methods
CHE 2C General Chemistry
CHE 135 Adv Bio-organic Chem Lab


7/15/2015 7:34:47 PM
  • (42) Tashiro, Y., Desai, S.H. & Atsumi, S.
    Two-dimensional isobutyl acetate production pathways to improve carbon yield
    Nat Commun. 6: 7488 (2015) [Pudmed]

  • (41) Nozzi, N.E. & Atsumi, S.
    Genome engineering of the 2,3-butanediol biosynthetic pathway for tight regulation in cyanobacteria
    ACS Synth Biol. DOI: 10.1021/acssynbio.5b00057  (2015) [Pudmed]

  • (40) Desai, S.H., Rabinovitch-Deere, C.A., Fan, Z. & Atsumi, S.
    Isobutanol production from cellobionic acid in Escherichia coli
    Microb Cell Fact. 14: 52 (2015) [Pudmed]

  • (39) Oliver, J.W.K. & Atsumi, S.
    A carbon sink pathway increases carbon productivity in cyanobacteria
    Metab Eng. 29: 106-112 (2015) [Pudmed]

  • (38) Tashiro, Y.,  Rodriguez, G.M. & Atsumi, S.
    2-Keto acids based biosynthesis pathways for renewable fuels and chemicals
    J Ind Microbiol Biotechnol. 42(3): 361-373 (2015) [Pudmed]

  • (37) Rodriguez, G.M. & Atsumi, S.
    Toward aldehyde and alkane production by removing aldehyde reductase activity in Escherichia coli
    Metab Eng. 25: 227-237 (2014) [Pudmed]

  • (36)  Nozzi, N.E., Desai, S.H., Case, A.N., & Atsumi, S.
    Metabolic engineering for Higher alcohol produciton
    Metab Eng25: 174-182 (2014) [Pudmed]

  • (35)  McEwen, J.T. & Atsumi, S.
    Engineering trophic diversity into photosynthetic microbes
    Biofuels 5(3): 199-201 (2014) [Link]

  • (34) Oliver, J.W.K. & Atsumi, S.
    Metabolic design for cyanobacterial chemical synthesis
    Photosynth Res. 120(3): 249-261 (2014) [Pudmed]

  • (33) Rodriguez, G.M.*, Tashiro, Y.*, & Atsumi, S. Expanding ester biosynthesis in Escherichia coli Nat Chem Biol. 10: 259-265 (2014) *Contributed equally to this work
  • (32) Oliver, J.W.K.*, Machado, I.M.P.*, Yoneda, H., & Atsumi, S. Combinatorial optimization of cyanobacterial 2,3-butanediol production Metab Eng. 22: 76-82 (2014) *Contributed equally to this work
  • (31) Desai, S.H., Rabinovitch-Deere, C.A., Tashiro, Y., & Atsumi, S. Isobutanol production from cellobiose in Escherichia coli Appl Microbiol Biotechnol. 98(8): 3727-3736 (2014)
  • (30) Kusakabe, T., Tatsuke, T., Tsuruno, K., Hirokawa, Y., Atsumi, S., Liao, J.C., & Hanai, T. Engineering a synthetic pathway in cyanobacteria for isopropanol production directly from carbon dioxide and light Metab. Eng. 20: 101-108 (2013)
  • (29) Yoneda, H., Tantillo, D.J., & Atsumi, S. Biological production of 2-butanone in Escherichia coli ChemSusChem 7(1): 92-95. (2014)
  • (28) Nozzi, N.E., Oliver, J.W.K. & Atsumi, S. Photosynthetic approaches to chemical biotechnology Front. Bioeng. Biotechnol. 1:7. (2013)
  • (27) Desai, S.H. & Atsumi, S. Photosynthetic approaches to chemical biotechnology Curr Opin Biotechnol. 14(6): 1031-1036 (2013)
  • (26) Rabinovitch-Deere, C.A., Oliver, J.W.K, Rodriguez, G.M., & Atsumi, S. Synthetic Biology and Metabolic Engineering Approaches to Produce Biofuels Chem Rev. 113(7): 4611-4632 (2013)
  • (25) McEwen, J.T., Machado, I.M.P, Connor, M.R., & Atsumi, S. Engineering Synechococcus elongatus PCC 7942 to grow continuously in diurnal conditions Appl Environ Microbiol. 79(5):1668-1675 (2013)
  • (24) Oliver, J.W.K.*, Machado, I.M.P.*, Yoneda, H., & Atsumi, S. Cyanobacterial conversion of carbon dioxideto 2,3-butanediol Proc. Natl. Acad. Sci. USA 110(4): 1249-1254 (2013) *Contributed equally to this work
  • (23) Rodriguez, G.M. & Atsumi, S. Isobutyraldehyde production from Escherichia coli by removing aldehyde reductase activity Microbial Cell Factories 11:90 (2012)
  • (22) Lamsen, E.N. & Atsumi, S. Recent progress in synthetic biology for microbialproduction of C3–C10 alcohols Frontiers in Microbiology 3:196 (2012)
  • (21) Machado, I.M.P. & Atsumi, S. Cyanobacterial biofuel production J Biotechnol 162: 50-56 (2012)
  • (20) Rodriguez, G.M. & Atsumi, S. Synthetic biology approaches to produce C3-C6 alcohols from microorganisms Curr Chem Biol 6: 32-41 (2012)
  • (19) McEwen, J.T. & Atsumi, S. Alternative biofuel production in non-natural hosts Curr Opin Biotechnol. 23: 744-750 (2012)
  • (18) Atsumi, S.*, Wu, T.*, Machado, I.M.P., Huang, W., Chen, P., Pellegrini, M. & Liao, J.C. Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli Mol Syst Biol. 6: 449 (2010) Contributed equally to this work
  • (17) Connor, M.R. & Atsumi, S. Synthetic Biology Guides Biofuel Production J Biomed Biotechnol. 2010:541698 doi: 10.1155/2010/541698 (2010)
  • (16) Wong, I., Atsumi, S., Huang, W., Wu, T., Hanai, T., Lam, M., Tang, P., Yang, J., Liao, J.C. & Ho, C. An agar gel membrane-PDMS hybrid microfluidic device for long term single cell dynamic study Lab Chip 10: 2710-2719 (2010)
  • (15) Atsumi, S., Higashide, W. & Liao, J.C. Direct recycling of carbon dioxide to isobutyraldehyde using photosynthesis Nat Biotechnol. 27: 1177-1180 (2009)
  • (14) Atsumi, S., Li, Z. & Liao, J.C. Acetolactate synthase from Bacillus subtilis serves as a 2-ketoisovalerate decarboxylase for isobutanol biosynthesis in Escherichia coli Appl Environ Microbiol. 75: 6306-6311 (2009)
  • (13) Atsumi, S., Wu, T., Eckl, E., Hawkins, S.D., Buelter, T. & Liao, J.C. Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes Appl Microbiol Biotechnol. 85:651-657. (2010)
  • (12) Atsumi, S. & Liao, J.C. Directed evolution of thermophilic citramalate synthase for 1-propanol and 1-butanol biosynthesis from Escherichia coli Appl Environ Microbiol. 74: 7802-7808 (2008)
  • (11) Atsumi, S. & Liao, J.C. Metabolic Engineering for Advanced Biofuels Production from Escherichia coli Curr Opin Biotechnol. 19: 414-419 (2008)
  • (10) Atsumi, S., Hanai, T. & Liao, J.C. Non-Fermentative Pathways for Synthesis of Branched-Chain Higher Alcohols as Biofuels Nature 451: 86-89 (2008)
  • (9) Hanai, T., Atsumi, S. & Liao, J.C. Engineered synthetic pathway for isopropanol production in Escherichia coli Appl Environ Microbiol. 73: 7814-7818 (2007)
  • (8) Atsumi, S., Can, A.F., Connor, M.R., Shen, C.R., Smith, K.M., Brynildsen, M.P., Chou, K.J., Hanai, T & Liao, J.C. Metabolic engineering of Escherichia coli for 1-butanol production Metab. Eng. 10: 305–311 (2008)
  • (7) Atsumi, S. & Little, J.W. A synthetic phage lambda regulatory circuit Proc. Natl. Acad. Sci. USA. 103: 19045-19050 (2006)
  • (6) Atsumi, S. & Little, J.W. Role of the lytic repressor in prophage induction of phage lambda analyzed by a module-replacement approach Proc. Natl. Acad. Sci. USA. 103: 4558-4563 (2006)
  • (5) Atsumi, S. & Little, J.W. Regulatory circuit design and evolution using phage lambda Genes Dev 18: 2086-2094 (2004)
  • (4) Ikawa, Y., Tsuda, K., Matsumura, S., Atsumi, S. & Inoue, T. Putative intermediary stages for the molecular evolution from a ribozyme to a catalytic RNP Nucleic Acids Res 31: 1488-1496 (2003)
  • (3) Atsumi, S., Ikawa, Y., Shiraishi, H. & Inoue, T. Selections for constituting new RNA-protein interactions in catalytic RNP Nucleic Acids Res, 31: 661-669 (2003)
  • (2) Atsumi, S., Ikawa, Y., Shiraishi, H. & Inoue, T. Design and development of a catalytic ribonucleoprotein EMBO.J, 20: 5453-5460 (2001)
  • (1) Ikawa, Y., Nohmi, K., Atsumi, S., Shiraishi, H. & Inoue, T. A comparative study on two GNRA-tetraloop receptors: 11-nt and IC3 motif J. Biochem. (Tokyo) 130: 251-255 (2001)