Publications
Synthetic Biology and Metabolic Engineering at UCD
(67) Pressley, S.R., McGill, A.S., Luu, B., & Atsumi, S.
Recent advances in the microbial production of human milk oligosaccharides.
Curr Opin Food Sci. 57:101154 (2024) [Link]

(66) Taylor, J.E., Palur, D.S.K., Zhang, A., Gonzales, J.N., Arredondo, A., Coulther, T.A., Lechner, A.B.J., Rodriguez, E.P., Fiehn, O., Didzbalis, J., Siegel, J.B., & Atsumi, S.
Awakening the natural capability of psicose production in Escherichia coli.
npj Sci Food 7:54 (2023) [Pudmed] (UC Davis Press Release)

(65) Gonzales, J.N., Treece, T.R., Mayfield, S.P., Simkovsky, R., & Atsumi, S.
Utilization of lignocellulosic hydrolysates for photomixotrophic chemical production in Synechococcus elongatus PCC 7942.
Commun Biol. 6: 1022 (2023) [Pudmed]

(64) Treece, T.R.^#, Pattanayak, S.^#, Matson, M.M., Cepeda, M.M., Berben, L.A.*, & Atsumi, S.* ^#contributed equally *co-corresponding author
Electrorical-biological hybrid system for carbon efficient isobutanol production.
Metab Eng. 80: 142-150 (2023) [Pudmed]

(63) Treece, T.R., Tessman, M., Pomeroy, R.S., Mayfield, S.P., Simkovsky, R., & Atsumi, S.
Fluctuating pH for efficient photomixotrophic succinate production.
Metab Eng. 79: 118-129 (2023) [Pudmed]

(62) François, J.M. & Atsumi, S.
Editorial: Insights into synthetic biology 2021: Novel developments, current challenges, and future perspectives.
Front Bioeng Biotehnology 11:1200227 (2023) [Pudmed]

(61) Palur D.S.K., Pressley S.R., & Atsumi S.
Microbial Production of Human Milk Oligosaccharides.
Molecules. 28: 1491 (2023) [Pudmed]

(60) Treece, T.R., Gonzales, J.N., Pressley, J.R., & Atsumi, S.
Synthetic Biology Approaches for Improving Chemical Production in Cyanobacteria.
Front Bioeng Biotehnology. 10:869195 (2022) [Pudmed]

(59) Kobayashi, S., Atsumi, S., Ikebukuro, K., Sode, K, and Asano, R.
Light-induced production of isobutanol and 3-methyl-1-butanol by metabolically engineered cyanobacteria.
Microb Cell Fact. 21: 7 (2022) [Pudmed]

(58) Matson, M.M., Cepeda, M.M., Zhang, A., Case, A.E., Kavvas, E., Wang, X., Carroll, A.L., Tagkopoulos, I., & Atsumi S.
Adaptive laboratory evolution for improved tolerance of isobutyl acetate in Escherichia coli.
Metab Eng. 69: 50-58 (2022) [Pudmed]

(57) Zhang, A., Sun, L., Bai, Y., Yu, H., McArthur, J.B., Chen, X., & Atsumi, S.
Microbial production of human milk oligosaccharide lactodifucotetraose.
Metab Eng. 66: 12-20 (2021) [Pudmed]

(56) Kobayashi, S., Nakajima, M., Asano, R., Ferreira, E.A., Abe, K., Tamagnini, P., Atsumi, S., & Sode, K.
Application of an engineered chromatic acclimation sensor for red-light-regulated gene expression in cyanobacteria.
Algal Res. 44: 101691 (2019) [Link]

(55) Gonzales, J.N., Matson M.M., & Atsumi S.
Nonphotosynthetic Biological CO₂ Reduction.
Biochemistry 58: 1470-1477 (2019) [Pudmed]

(54) Tashiro, Y., Hirano, S., Matson, M.M., Atsumi, S*., & Kondo, A*. *co-corresponding author
Electrical-biological hybrid system for CO₂ reduction.
Metab Eng. 47: 211-218 (2018) [Pudmed]
 
(53) Carroll, A.L., Case, A.E., Zhang, A., & Atsumi S.
Metabolic engineering tools in model cyanobacteria.
Metab Eng. 50: 47-56 (2018) [Pudmed]

(52) Matson, M.M. & Atsumi, S.
Photomixotrophic chemical production in cyanobacteria
Curr Opin Biotechnol. 50: 65-71 (2018). [Pudmed]

(51) Zhang, A., Carroll, A.L., & Atsumi, S.
Carbon recycling by cyanobacteria: improving CO₂-fixation through chemcial production
FEMS Microbiol Lett. 364: fnx165 (2017) [Pudmed]

(50) Nozzi, N.E., Case, A.E., Caroll, A.L. & Atsumi, S.
Systematic approaches to efficiently produce 2,3-butanediol in a marine cyanobacterium
ACS Synth Biol. 6: 2136-2144 (2017) [Pudmed]

(49) Kanno, M., Carroll, A.L. & Atsumi, S.
Global metabolic rewiring for improved CO₂ fixation and chemical production in cyanobacteria
Nat Commun. 8: 14724 (2017) [Pudmed]
(highlighted in UCD Egghead)

(48) Kanno, M. & Atsumi, S.
Engineering an obligate photoautotrophic cyanobacterium to utilize glycerol for growth and chemical production
ACS Synth Biol. 6: 69-75 (2017) [Pudmed]
(highlighted in C&EN)

(47) Oliver, N.J., Ribinovitch-Deere, C.A., Carroll, A.L., Nozzi, N.E., Case, A.E., & Atsumi, S.
Cyanobacterial metabolic engineering for biofuel and chemical production
Curr Opin Chem Biol. 35: 43-50 (2016) [Pudmed]

(46) Desai, S.H., Koryakina, I., Case, A.E., Toney, M.D. & Atsumi, S.
Biological conversion of gaseous alkenes to liquid chemicals
Metab Eng. 38: 98-104 (2016) [Pudmed]

(45) Case, A.E. & Atsumi, S.
Cyanobacterial chemical production
J Biotechnol. 231: 106-114 (2016) [Pudmed]

(44) McEwen, J.T., Kanno, M. & Atsumi, S.
2,3 Butanediol production in an obligate photoautotrophic cyanobacterium in dark conditions via diverse sugar consumption
Metab Eng. 36: 28-36 (2016) [Pudmed]

(43) Carroll, A.L., Desai, S.H. & Atsumi, S.
Microbial production of scent and flavor compounds
Curr Opin Biotechnol. 37: 8-15 (2016) [Pudmed]

(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. 4: 1197-1204 (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]

(Book Chapter 4) McEwen, J.T., & Atsumi, S.
Metabolic Engineering for the Biobased Conversion of CO₂ to Biofuels
In Industrial Biocatalysis
(ed. Grunwald, P., Pan Stanford Publishing) [Link][Google Books]

(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 production
Metab Eng. 25: 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) [Pudmed] *Contributed equally to this work
(News & Views by B. Barney)

(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) [Pudmed] *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) [Pudmed]

(Book Chapter 3) Nozzi, N.E., & Atsumi, S.
Biosynthesis of fuels
In McGraw-Hill Yearbook of Science & Technology 2014
(McGraw-Hill Professional Publishing)

(Book Chapter 2) McEwen, J.T., Tashiro, Y., & Atsumi, S.
Higher chain alcohols from non-fermentative pathways
In Biofuels: From microbes to molecules
(ed. Lu, X., Caister Academic Press) [Link]

(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) [Pudmed]

(Book Chapter 1) Oliver, J.W.K. & Atsum, S.
Cyanobacterial biofuel and chemical production for CO₂ sequestration.
In Natural and artificial photosynthesis: Solar power as an energy source
(ed. Razeghifard, R., John Wiley & Sons) [Link][Google Books]

(29) Yoneda, H., Tantillo, D.J., & Atsumi, S.
Biological production of 2-butanone in Escherichia coli 
ChemSusChem 7(1): 92-95 (2014) [Pudmed]

(28) Nozzi, N.E., Oliver, J.W.K. & Atsumi, S.
Cyanobacteria as a platform for biofuel production.
Front Bioeng Biotechnol. 1:7. (2013) [Link]

(27) Desai, S.H. & Atsumi, S.
Photosynthetic approaches to chemical biotechnology.
Curr Opin Biotechnol. 14(6): 1031-1036 (2013) [Pudmed]

(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) [Pudmed]

(25) McEwen, J.T., Machado, I.M.P, Connor, M.R., & Atsumi, S.
Engineering Synechococcus elongatus PCC7942 to grow continuously in diurnal conditions
Appl Environ Microbiol. 79(5): 1668-1675 (2013) [Pudmed] (selected for "Spotlight" by the Editors)

(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 [Pudmed]

(23) Rodriguez, G.M. & Atsumi, S.
Isobutyraldehyde production from Escherichia coli by removing aldehyde reductase activity
Microb Cell Fact. 11:90 (2012) [Pudmed] (qualified as "Highly accessed")

(22) Lamsen, E.N. & Atsumi, S.
Recent progress in synthetic biology for microbialproduction of C3–C10 alcohols
Front Microbiol. 3:196 (2012) [Pudmed]

(21) Machado, I.M.P. & Atsumi, S.
Cyanobacterial biofuel production
J Biotechnol. 162: 50-56 (2012) [Pudmed] (Most cited papers on rank 2)

(20) Rodriguez, G.M. & Atsumi, S.
Synthetic biology approaches to produce C3-C6 alcohols from microorganisms
Curr Chem Biol. 6: 32-41 (2012) [Link]

(19) McEwen, J.T. & Atsumi, S.
Alternative biofuel production in non-natural hosts
Curr Opin Biotechnol. 23: 744-750 (2012)[Pudmed]

(18) Connor, M.R. & Atsumi, S.
Synthetic Biology Guides Biofuel Production
J Biomed Biotechnol. doi: 10.1155/2010/541698 (2010) [Pudmed]

Biofuels and Metabolic Engineering at UCLA
(17) 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 [Pudmed]

(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) [Pudmed]

(15) Atsumi, S., Higashide, W. & Liao, J.C.
Direct recycling of carbon dioxide to isobutyraldehyde using photosynthesis
Nat Biotechnol. 27: 1177-1180 (2009) [PudMed] (News & Views by J. Sheehan)

(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) [PudMed]

(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) Epub 2009 [PudMed]

(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) [PudMed]

(11) Atsumi, S. & Liao, J.C.
Metabolic Engineering for Advanced Biofuels Production from Escherichia coli
Curr Opin Biotechnol. 19: 414-419 (2008) [PudMed] (Top 25 Hottest Articles)

(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) [PudMed] (News & Views by J. Keasling & H. Chou) (Faculty of 1000 biology, Must Read)

(9) Hanai, T., Atsumi, S. & Liao, J.C.
Engineered synthetic pathway for isopropanol production in Escherichia coli
Appl Environ Microbiol. 73: 7814-7818 (2007) [PudMed]

(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) [PudMed] (Top 25 Hottest Articles)

Gene Regulatory Circuits at U. Arizona
(7) Atsumi, S. & Little, J.W.
A synthetic phage lambda regulatory circuit
Proc Natl Acad Sci USA. 103: 19045-19050 (2006) [PudMed]

(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) [PudMed] (Dispatch by M. Ptashne)

(5) Atsumi, S. & Little, J.W.
Regulatory circuit design and evolution using phage lambda
Genes Dev. 18: 2086-2094 (2004) [PudMed]

RNA Synthetic Biology at Kyoto U.
(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) [PudMed]

(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) [PudMed]

(2) Atsumi, S., Ikawa, Y., Shiraishi, H. & Inoue, T.
Design and development of a catalytic ribonucleoprotein
EMBO J. 20: 5453-5460 (2001) [PudMed]

(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) [PudMed]