J. Clark Lagarias
Professor
jclagarias@ucdavis.edu
Molecular & Cellular Biology
Office
31A Briggs Hall
530-752-1865
Lab
31 Briggs
530-752-7026
Degrees:
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 lab focuses on phytochromes, a family of light sensing biliproteins found in plants, photosynthetic bacteria and even nonphotosynthetic eubacteria and fungi, and cyanobacteriochromes, phytochrome-related biliprotein sensors that have proliferated in cyanobacteria. Phytochromes mediate responses mainly to red and far-red light in the environment that are particularly important to shade sensing. Cyanobacteriochromes sense light from the near UV to red region to optimize light energy conversion by the oxygenic photosynthetic apparatus. Our investigations are biochemical in nature focusing on structure-function and evolutionary relationships of these light sensors and the enzymes responsible for the synthesis of their linear tetrapyrrole (bilin) prosthetic groups. The long-term goal of these investigations is to rationally alter the natural responses of plants and cyanobacteria to their light environment for optimum biomass yield and/or light energy conversion.
http://www.mcb.ucdavis.edu/faculty-labs/lagarias/
Awards:
2001 Elected to the National Academy of Sciences
1999-2006 Paul K. and Ruth R. Stumpf Professor of Plant Biochemistry
Department and Center Affiliations:
NSF Center for Biophotonics Science and Technology (http://biophotonics.ucdavis.edu/)
NEAT ORU (http://neat.ucdavis.edu/)
PARSEC
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:
Chemistry
Publications:
Last updated 3/25/2013
Hirose Y, Rockwell NC, Martin SS, Narikawa R, Inomata K, Lagarias JC and Ikeuchi M (2012) Green/red cyanobacteriochromes regulate complementary chromatic acclimation via a protochromic photocycle, Proceedings of the National Academy of Sciences (USA) 110, in press
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.
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.
Freer LH, Kim PW, Corley SC, Rockwell NC, Zhao, L, Thibert AJ, Lagarias JC and Larsen DS (2012) Chemical Inhomogeneity in the Ultrafast Dynamics of the DXCF Cyanobacteriochrome Tlr0924. Journal of Physical Chemistry 116, 10571-10581.
Rockwell NC, Martin SS, Gulevich AG and Lagarias JC (2012) Phycoviolobilin formation and spectral tuning in DXCF cyanobacteriochromes, Biochemistry, 51, 1449-1463.
Kim PW, Freer LH, Rockwell NC, Martin SS, Lagarias JC and Larsen DS (2012) Femtosecond Photodynamics of the Red/Green Absorbing NpR6012g4 Photoswitching Cyanobacteriochrome Domain from Nostoc punctiforme: 2. Reverse Dynamics. Biochemistry 51, 619-630.
Kim PW, Freer LH, Rockwell NC, Martin SS, Lagarias JC and Larsen DS (2012) Femtosecond Photodynamics of the Red/Green Cyanobacteriochrome NpR6012g4 from Nostoc punctiforme. 1. Forward Dynamics. Biochemistry 51, 608-618.
Kim PW, Freer LH, Rockwell NC, Martin SS, Lagarias JC and Larsen DS (2012) Second-Chance Forward Isomerization Dynamics of the Red/Green Cyanobacteriochrome NpR6012g4 from Nostoc punctiforme. J. Am. Chem. Soc. 134, 130-133.
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
Rockwell, NC, Njuguna, SL, Dwojak, S, Castillo, E, Roberts, L, Parson, VL, Lagarias, JC, and Spiller, SS (2008) A second conserved GAF domain cysteine is required for the blue/green photoreversibility of cyanobacteriochrome Tlr0924 from Thermosynechococcus elongatus. Biochemistry, 47, 7304-7316.
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.
Tu SL, Rockwell NC, Lagarias, JC and Fisher AJ (2007). Insight into the radical mechanism of phycocyanobilin:ferredoxin oxidoreductase (PcyA) revealed by x-ray crystallography and biochemical analysis. Biochemistry 46, 1484-1494.
Miller AE, Fischer AJ, Laurence T, Hollars C, Saykally R, Lagarias JC and Huser T (2006) Single molecule dynamics of phytochrome-bound fluorophores probed by fluorescence correlation spectroscopy. Proceedings of the National Academy of Sciences (USA) 103, 11136-11141.
Rockwell NC, Su Y-S and Lagarias JC (2006) Phytochrome structure and signaling mechanisms. Annual Review of Plant Biology 57, 837-858.
Fischer AJ, Rockwell NC, Jang A, Ernst L, Waggoner A, Duan Y, Lei H-X and Lagarias JC (2005) Multiple roles of a conserved GAF domain tyrosine residue in cyanobacterial and plant phytochromes. Biochemistry 44, 15203-15215.
Tu S-L, Sughrue WL, Britt RD and Lagarias JC (2006) A Catalytic Histidine-Aspartate Pair in Exo-Vinyl Reduction of Biliverdin by Phycocyanobilin:Ferredoxin Oxidoreductase (PcyA). Journal of Biological Chemistry 281, 3127-3136.
Laboratory Personnel:
31 Briggs Hall
http://www.mcb.ucdavis.edu/faculty-labs/lagarias/
Nathan Rockwell, Project Scientist; Wei Hu, Project Scientist; Deqiang Duanmu, Postdoc; Shelley Martin, SRA; Alexander G. Gulevich and Matthew Blaine-Hartung; BMCDB Graduate Students; Daniel Mendoza, undergrad; Simon Au, undergrad; Crystal Liu, Lab Assistant
Teaching Interests:
Biochemistry laboratory. Bioinformatics. Signal transduction in plants.
Courses:
MCB
120L
Biochemistry Laboratory
Key Words:
photobiology, photochemistry, photomorphogenesis, signal transduction, photoreceptors, tetrapyrrole metabolism, light harvesting, photosynthesis, cyanobacteria, green algae, plants, Chlamydomonas, Arabidopsis