Assistant Professor
The Shih lab focuses on engineering plants, microbes, and proteins for novel applications in agriculture, sustainability, human health, and bioenergy. We utilize a blend of synthetic biology, biochemistry, functional genomics, and evolutionary biology to better understand plant and microbial systems.
Research Interests:
Plant Synthetic Biology: Plants are essential to our societal infrastructure as the starting point for our food, raw material, and bioenergy economies. Given the scale and utility of agriculture, plants offer a unique platform to address many imminent challenges facing society. Our group focuses on developing the foundational knowledge and technologies needed to innovate, deploy, and engineer new traits into plants using synthetic biology approaches. In order to efficiently engineer plants, tools and techniques will need to be developed to expedite and implement biotechnological applications in agriculturally relevant crops. Beyond biotechnological applications, these approaches will also be utilized to provide more sophisticated tools to improve our basic understanding of plant systems.
Plant Metabolic Biochemistry and Engineering: 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 evolved a multitude of metabolic pathways, enabling the production of a wealth of chemically diverse compounds. Many of these pathways are responsible for various traits relevant to human health and agricultural sustainability. Our group is interested in understanding core principles of plant metabolism for the ultimate goal of metabolic engineering for specific applications.
Evolution of Photosynthesis and Carbon Fixation: Photosynthesis drives nearly all global carbon fixation and thus sustains nearly all of life on Earth. The enzyme at the center of this metabolism is rubisco, which fixes CO2 into organic carbon. This process constitutes the largest flux in the carbon cycle, and has sourced nearly all the organic carbon present on Earth – most notably sustaining our entire food supply. Rubisco has evolved over billions of years under a wide range of atmospheric conditions, as prehistoric CO2 levels were higher and O2 levels much lower than those of today’s environment. Our group utilizes a combination of evolutionary biology, biochemistry, and synthetic biology to understand how rubisco shaped our planet’s carbon cycle over geological timescales, which may provide novel insight to drive future engineering endeavors.
Selected Publications:
Hummel NFC, Zhou A, Li B, Markel K, Ornelas IJ, Shih PM. (2023) Trans-regulatory landscape of gene networks in plants. Cell Systems. 14 (6), 501-511. e4.
Liu AK, Pereira JH, Kehl AJ, Rosenberg DJ, Orr DJ, Chu SKS, Banda DM, Hammel M, Adams PD, Siegel JB, Shih PM. (2022) Structural plasticity enables evolution and innovation of rubisco assemblies. Science Advances, 8 (34), eadc9440.
Banda DM, Pereira JH, Liu AK, Orr DJ, Hammel M, He C, Parry MAJ, Carmo-Silva E., Adams PD, Banfield JF, 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, 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, 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.
Honors and Awards:
Packard Fellowship
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
Education:
Ph.D. Plant Biology UC Berkeley
B.S. Microbiology UC San Diego
B.A. Political Science UC San Diego
