Much of the ingenuity of life has revolved around the evolution of metabolic pathways, which has unlocked novel chemistries and expanded the molecular repertoire of nature. In particular, plants have been especially successful through the evolution of many unique and relevant metabolisms, ranging from synthesis of specialized compounds that can be used as pharmaceuticals (e.g., morphine, artemisinin) to broad processes that drive our planet’s elemental cycles (e.g., photosynthesis). As a result, life as we know it could not exist without plants. Given the scale and utility of agriculture, plants offer a unique platform to address many imminent challenges facing society. The Shih lab focuses on developing the foundational knowledge needed to innovate, deploy, and engineer new traits in plants using synthetic biology. Beyond biotechnological applications, we are intereseted in using these approaches to study how diverse metabolisms evolved in both plants and microbes and their impact on the environment.
1) Developing synthetic biology approaches to enable complex engineering efforts in plant systems for applications in agriculture, sustainability, human health, and bioenergy
2) Leveraging genomics and molecular biology to investigate how the evolution of early microbial metabolisms (e.g., photosynthesis) shaped our planet over geological timescales.
Banda DM, Pereira JH, Liu AK, Orr DJ, Hammel M, He C, Parry MAJ, Carmo-Silva E., Adams PD, Banfield JF‡, and Shih PM‡. (2020) Novel bacterial clade reveals origin of Form I Rubisco. Nature Plants, 6(9), 1158-1166.
Calgaro-Kozina A, Vuu KM, Keasling JD, Loque D, Sattely ES‡, Shih PM‡. (2020) Engineering plant synthetic pathways for the biosynthesis of novel antifungals. ACS Central Science, 6(8):1394–1400.
Belcher MS, Vuu KM, Zhou A, Mansoori N, Agosto Ramos A, Thompson MG, Scheller HV, Loque D, Shih PM. (2020) Design of orthogonal regulatory systems for modulating gene expression in plants. Nature Chemical Biology, 16(8):857-865.
Yang M, Baral NR, Simmons BA, Mortimer JC, Shih PM‡, Scown CD‡. (2020) Accumulation of high-value bioproducts in planta can improve the economics of advanced biofuels, Proceedings of the National Academy of Sciences, 117(50):8639-8648.
Ward LM, Shih PM. (2019) The evolution and productivity of carbon fixation pathways in response to changes in oxygen concentration over geological time. Free Radical Biology and Medicine, 140:188-199.
Shih PM. (2018) Towards a sustainable bio-based economy: Redirecting primary metabolism to new products with plant synthetic biology. Plant Science, 273:84-91.
Shih PM, Ward LM, Fischer WW. (2017) Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi. Proceedings of the National Academy of Sciences, 114(40):10749-10754.
Shih PM, Vuu K, Mansoori N, Ayad L, Louie K, Bowen BP, Northen TR, Loqué D. (2016) A robust gene stacking method utilizing yeast assembly for plant synthetic biology. Nature Communications, 7:13215.
Shih PM, Occhialini A, Cameron JC, Andralojc PJ, Parry MAJ, Kerfeld CA. (2016) Biochemical characterization of predicted Precambrian RuBisCO. Nature Communications, 7:10382.
Shih PM, Zarzycki J, Niyogi KK, Kerfeld CA. (2014) Introduction of a synthetic CO2-fixing photorespiratory bypass into a cyanobacterium. Journal of Biological Chemistry, 289(14): 9493-500.
Shih PM and Matzke NM. (2013) Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins. Proceedings of the National Academy of Sciences, 110 (30): 12355-360.
Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, Talla E, Calteau A, Cai F, Tandeau de Marsac N, Rippka R, Herdman M, Sivonen K, Coursin T, Laurent T, Goodwin L, Nolan M, Davenport KW, Han CS, Rubin EM, Eisen JA, Woyke T, Gugger M, Kerfeld CA. (2013) Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proceedings of the National Academy of Sciences, 110 (3): 1053-58.
Honors and Awards:
Katherine Esau Junior Faculty Fellow Award
Alfred P. Sloan Fellowship in Computational & Evolutionary Molecular Biology
NIH K99 Award
Branco Weiss Fellowship
Life Sciences Research Foundation Fellowship
Lawrence Berkeley National Lab Director’s Award for Exceptional Early Scientific Career Achievement
Ph.D. Plant Biology UC Berkeley
B.S. Microbiology UC San Diego
B.A. Political Science UC San Diego