J. Clark Lagarias

image of J. Clark Lagarias

Distinguished Professor of Biochemistry


Molecular & Cellular Biology

Offices and Labs

31A Briggs Hall
31 Briggs


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

Research Contribution

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/)


American Society of Plant Biologists
American Chemical Society

CBS Grad Group Affiliations

Biochemistry, Molecular, Cellular and Developmental Biology
Plant Biology

Specialties / Focus

Plant Biology
  • Cell and Developmental Biology
  • Molecular Biology, Biochemistry, and Genomics
  • Environmental and Integrative Biology
Biochemistry, Molecular, Cellular and Developmental Biology
  • Signal Transduction and Gene Regulation
  • Structural and Mechanistic Biochemistry
  • Plant Biochemistry and Molecular Biology

Graduate Groups not Housed in CBS



10/22/2014 12:40:18 PM
  • Gottlieb SM, Kim PW, Chang C-W, Hanke S, Hayer R, Rockwell NC, Martin SS, Lagarias JC and Larsen DS  (2015) Conservation and diversity in the primary forward photodynamics of red/green cyanobacteriochromes. Biochemistry 54, 1028-1042 

  • Rockwell NC, Martin SS, Gan F, Bryant DA, and Lagarias JC (2015) NpR3784 is the prototype for a distinctive group of red/green cyanobacteriochromes using alternative Phe residues for photoproduct tuning. Photochem. Photobiol. Sci. 14, 258 - 269

  • Rockwell NC, Lagarias JC and Bhattacharya D (2014) Primary endosymbiosis and the evolution of light and oxygen sensing in photosynthetic eukaryotes. Front. Ecol. Evol. 2, doi:10.3389/fevo.2014.00066

  • Duanmu* D, Bachy* C, Sudek S, Wong C-H, Jimenez V, Rockwell NC, Martin SS, Ngan CY, Reistetter E, van Baren MJ, Price DC, Wei C-L, Reyes-Prieto A, Lagarias JC and Worden AZ (2014) Marine algae and land plants share conserved phytochrome signaling systems. Proc. Natl. Acad. Sci. (USA) 111 (44), 5827–15832 (*co-first authors)

  • Gan F, Zhang S, Rockwell NC, Martin SS, Lagarias JC and Bryant DA (2014) Extensive remodeling of a cyanobacterial photosynthetic apparatus in far-red light. Science 345(6202), 1312-1317

  • 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

  • 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

  • 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

  • Kim, PW, Rockwell, NC, Martin, SS, Lagarias, JC and Larsen, DS (2014) Dynamic Inhomogeneity in the Cyanobacterial Phytochrome Cph1. Biochemistry 53(17), 2818-2826.
  • 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, Proc. Natl. Acad. Sci. (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) Proc. Natl. Acad. Sci. (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. Proc. Natl. Acad. Sci. (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. J. Phys. Chem. Lett. 4, 2605-2609

  • 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

  • Rockwell NC, Martin SS and Lagarias JC (2012) Red/green cyanobacteriochromes: sensors of color and power. Biochemistry 51(48):9667-9677

  • 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 J. 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, Chem. Phys. Lett. 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 Proc. Natl. Acad. Sci. (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. Proc. Natl. Acad. Sci. (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. Proc. Natl. Acad. Sci. (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. J. Am. Chem. Soc. 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. Proc. Natl. Acad. Sci. (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

  • 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


31 Briggs Hall website
  • 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