UC Davis Home | Students | Faculty | Alumni & Friends | Giving
Picture of J. Clark Lagarias


J. Clark Lagarias

Distinguished Professor of Biochemistry

Molecular & Cellular Biology

31A Briggs Hall

31 Briggs


1979 PhD University of California, Berkeley Chemistry
1975 BA University of California, Berkeley Botany and Chemistry

Research Contribution to Society:

Modern agriculture relies on crops that have been carefully tailored for environments by selective breeding. Phytochromes are attractive targets for crop improvement efforts aimed to enhance seed germination, seedling establishment, plant architecture and flowering time. The overall goal of this research is to understand the structural basis of both photosensory and regulatory functions of phytochromes from cyanobacteria to plants. Such basic knowledge will be leveraged for development of new strategies to alter the light responsiveness of agriculturally significant plant species. For example, our discovery of dominant photochemically uncoupled phytochrome alleles holds significant promise for crop improvement. Such plant-derived reagents may overcome environmental concerns while addressing the pressing need for increased food production on a finite amount of arable land needed to nourish the growing world population.

Research Interests:

Molecular Photobiology
Research in my laboratory focuses on the phytochrome superfamily, light sensing biliproteins that are widespread in eukaryotes (plants, algae, fungi, oomycetes and diatoms) and prokaryotes (both photosynthetic and non-photosynthetic species). Phytochromes and cyanobacteriochromes are light-switches whose function depends on the light color. Plants, algae and cyanobacteria use these pigmented protein sensors to regulate photosynthesis-associated gene expression for optimum photosynthesis under the ambient light conditions and for regulation of growth, movement or reproduction to avoid suboptimal light conditions. Our studies utilize representative species from all lineages of oxygenic photosynthetic organisms, including cyanobacteria, green alga and plants. Mainly biochemical in nature, our research focuses on structure-function and molecular evolution of these optogenetic light sensors. Ongoing research seeks to leverage this knowledge for optimizing yield and agronomic performance of photosynthetic species used for food, fiber and energy production.


2001 Elected to the National Academy of Sciences
1999-2006 Paul K. and Ruth R. Stumpf Professor of Plant Biochemistry

Department and Center Affiliations:

Department of Plant Biology Secondary Member (http://www-plb.ucdavis.edu/)

Professional Societies:

American Society of Plant Biologists
American Chemical Society

CBS Graduate Group Affiliations:

Biochemistry, Molecular, Cellular and Developmental Biology  
Plant Biology  

Specialties / Focus:

Biochemistry, Molecular, Cellular and Developmental Biology
Plant Biochemistry and Molecular Biology
Signal Transduction and Gene Regulation
Structural and Mechanistic Biochemistry

Plant Biology
Cell and Developmental Biology
Environmental and Integrative Biology
Molecular Biology, Biochemistry, and Genomics

Graduate Groups not Housed in CBS:



Last updated 8/27/2014
Chen*, A, Li*, C, Hu*, W, Lau, MY, Lin, H, Rockwell, NC, Martin, SS, Jernstedt, JA Lagarias, JC and Dubcovsky, J (2014) PHYTOCHROME C plays a major role in the acceleration of wheat flowering under long day photoperiod. Proc. Natl. Acad. Sci. (USA) 111(28), 10037-10044 (*co-first authors)

Rockwell NC, Duanmu D, Martin SS. Bachy C, Price DC, Bhattacharya D, Worden AZ and Lagarias JC Eukaryotic Algal Phytochromes Span the Visible Spectrum (2014) Proc. Natl. Acad. Sci. (USA) 111(10), 3871-3876.

Rockwell, NC, Martin, SS, Gulevich, AG and Lagarias, JC (2014) Conserved phenylalanine residues are required for blue shifting of cyanobacteriochrome photoproducts, Biochemistry 53(19), 3118-3130.

Lim S, Rockwell, NC, Martin, SS, Dallas, JL, Lagarias, JC and Ames, JB (2014) Photoconversion changes bilin chromophore conjugation and protein secondary structure in the violet/orange cyanobacteriochrome NpF2164g3. Photochem. Photobiol. Sci. 13(6), 951-962.

Kim, PW, Rockwell, NC, Martin, SS, Lagarias, JC and Larsen, DS (2014) Dynamic Inhomogeneity in the Cyanobacterial Phytochrome Cph1. Biochemistry 53(17), 2818-2826.

Gottlieb, SM, Chang, C-W, Martin, SS, Rockwell, Lagarias, JC, and Larsen, DS (2014) Optically Guided Photoactivity: Coordinating Tautomerization, Photoisomerization, Inhomogeneity, and Reactive Intermediates within the RcaE Cyanobacteriochrome. Journal of Physical Chemistry Letters 5(9), 1527-1533.

Kim, PW, Rockwell, NC, Martin, SS, Lagarias, JC, and Larsen, DS (2014) Heterogeneous Photodynamics of the Pfr State in the Cyanobacterial Phytochrome Cph1. Biochemistry 53(26), 4601–4611.

Hirose Y, Rockwell NC, Martin SS, Narikawa R, Inomata K, Lagarias JC and Ikeuchi M (2013) Green/red cyanobacteriochromes regulate complementary chromatic acclimation via a protochromic photocycle, Proceedings of the National Academy of Sciences (USA) 110, 4974-4979.

Duanmu D, Casero D, Dent RM, Gallaher S, Yang W, Rockwell NC, Martin SS, Pellegrini M, Niyogi KK, Merchant SS, Grossman AR and Lagarias JC Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival. (2013) Proceedings of the National Academy of Sciences (USA) 110, 3621-3626.

Hu W, Franklin KA, Sharrock RA, Jones MA, Harmer SL and Lagarias JC (2013) Unanticipated regulatory roles for Arabidopsis phytochromes revealed by null mutant analysis. Proceedings of the National Academy of Sciences (USA) 110, 1542-1547.

Kim PW, Rockwell NC, Freer LH, Chang CW, Martin SS, Lagarias JC and Larsen DS (2013) Unraveling the Primary Isomerization Dynamics in Cyanobacterial Phytochrome Cph1 with Multi-pulse Manipulations. Journal of Physical Chemistry Letters 4, 2605-2609.

Lim S, Rockwell NC, Martin SS, Lagarias JC and Ames JB (2013) 1H, 15N, and 13C chemical shift assignments of cyanobacteriochrome NpF2164g3 in the photoproduct state. Biomolecular NMR Assignments, DOI 10.1007/s12104-013-9496-0.

Gottlieb SM, Kim PW, Rockwell NC, Hirose Y, Ikeuchi M, Lagarias JC and Larsen DS (2013). Primary Photodynamics of the Green/Red-Absorbing Photoswitching Regulator of the Chromatic Adaptation E Domain from Fremyella diplosiphon. Biochemistry 52, 8198-8208.

Park E, Park J, Kim J, Nagatani A, Lagarias JC and Choi G (2012) Phytochrome inhibits binding of Phytochrome-Interacting Factors to their target promoters. Plant Journal 72, 537-546.

Kim PW, Pan J, Rockwell NC, Chang C-W, Taylor KC, Lagarias JC and Larsen DS (2012) Ultrafast E to Z Photoisomerization Dynamics of Phytochrome Cph1, Chemical Physics Letters 549, 86-92.

Rockwell NC, Martin SS, Gulevich AG and Lagarias JC (2012) Phycoviolobilin formation and spectral tuning in DXCF cyanobacteriochromes, Biochemistry, 51, 1449-1463.

Rockwell NC, Martin SS, Feoktistova K and Lagarias JC (2011) J.C. Diverse two-cysteine photocycles in phytochromes and cyanobacteriochromes Proceedings of the National Academy of Sciences (USA) 108, 11854-11859.

Song J-Y, Cho HS, Cho J-I, Jeon JS, Lagarias JC and Park Y-I (2011) A near ultraviolet cyanobacteriochrome signaling system elicits negative phototaxis in the cyanobacterium Synechocystis sp. PCC 6803 Proceedings of the National Academy of Sciences (USA) 108, 10780-10785.

Shang, L, Rockwell, NC, Martin SS and Lagarias, JC (2010) Biliverdin amides reveal roles for propionate side chains in bilin reductase recognition and in holophytochrome assembly and photoconversion. Biochemistry 49, 6070-6082

Rockwell, NC and Lagarias, JC (2010) A brief history of phytochromes. ChemPhysChem 11, 1172-1180.

Kohler, AC, Gae, DD, Richley, MA, Stoll, S, Gunn, A, Lim, S, Martin, SS, Doukov, TI, Britt, RD, Ames, JB, Lagarias, JC and Fisher, AJ (2010) Structural basis for hydration dynamics in radical stabilization of bilin reductase mutants. Biochemistry 49, 6206-6218.

Rockwell, NC, Shang, L, Martin, SS and Lagarias, JC (2009) J.C. Distinct classes of red/far-red photochemistry within the phytochrome superfamily. Proceedings of the National Academy of Sciences (USA) 106, 6123-6127

Stoll, S, Gunn, A, Brynda, M, Sughrue, W, Kohler, A, Ozarowski, A, Fisher, A, Lagarias, JC and Britt, RD (2009) The structure of the biliverdin radical intermediate in phycocyanobilin:ferredoxin oxidoreductase identified by high-field EPR and DFT. Journal of the American Chemical Society 131, 1986-1995.

Dasgupta, J, Frontiera, RR, Taylor, KC, Lagarias, JC and Mathies, R A (2009) Ultrafast Excited state isomerization in phytochrome revealed by femtosecond stimulated Raman spectroscopy. Proceedings of the National Academy of Sciences (USA) 106, 1784-1789

Hu, W, Su, Y-S and Lagarias, JC (2009) A light-independent allele of phytochrome B faithfully recapitulates photomorphogenic transcriptional networks. Molecular Plant, 2, 166-182; doi:10.1093/mp/ssn086

Su Y-S. and Lagarias JC (2007) Light independent phytochrome signaling mediated by dominant GAF-domain tyrosine mutants of Arabidopsis phytochromes in transgenic plants, Plant Cell (USA) 19, 2124-2139.

Laboratory Personnel:

31 Briggs Hall
Alexander G. Gulevich and Matthew Blain-Hartung; BMCDB Graduate Students; Nathan Rockwell, Project Scientist; Wei Hu, Project Scientist; Deqiang Duanmu, Postdoc; Shelley Martin, SRA; Crystal Liu, Lab Assistant

Teaching Interests:

Biochemistry laboratory. Bioinformatics. Signal transduction in plants.


MCB 120L Biochemistry Laboratory

Key Words:

photobiology, photochemistry, photomorphogenesis, signal transduction, photoreceptors, tetrapyrrole metabolism, light harvesting, photosynthesis, cyanobacteria, green algae, plants, Chlamydomonas, Arabidopsis