Frank Harmon
Frank G. Harmon
Circadian Clock
Adjunct Associate Professor
800 Buchanan St
Albany, California 94710
Phone 510.559.5939
Lab Phone 510.559.6089
Fax 510.559.5678

Ph.D.  Microbiology    University of California, Davis, 1999
B.S.   Microbiology    Idaho State University, 1990

The circadian clock is a key adaptation for life on earth, since it lets organisms coordinate internal physiological activities with daily and seasonal environmental changes. The Harmon lab investigates the plant circadian oscillator's molecular mechanism, using Arabidopsis as a model system. We apply genetic, biochemical, molecular, and genomic approaches to identify and characterize proteins contributing the plant clockworks. We seek to integrate their function into current clock models.


Circadian clocks in Arabidopsis and maize

Circadian rhythms are physiological processes with an approximately 24 hour periodicity that persist in the absence of environmental cues. These rhythms are ubiquitous in nature, found in higher eukaryotes as well as in many lower eukaryotic and some prokaryotic organisms. These rhythmic processes are driven by the circadian clock, an endogenous timekeeper responsible for generating and maintaining 24 hour rhythms. The clock is a key adaptation for life on earth since it allows an organism to coordinate its internal activities with daily and seasonal changes in the environment. Clock-regulated phenomena are not only widespread among all major groups of organisms but are pervasive within an organism, occurring within most cell types and tissues.

Intense study of the circadian systems in several model organisms, including Arabidopsis, has revealed that the oscillator influences major aspects of physiology. In plants, the circadian clock contributes to photoperiodic control over growth and development, responses to cold stress and shading, as well as coordinating genome-wide changes in transcription. Recent work in Arabidopsis has demonstrated that plants having a circadian oscillator matched to the environmental period exhibit higher overall biomass, elevated rates of photosynthesis, and improved chances of survival in a mixed population. Thus, the presence of a robust circadian clock elevates plant fitness.

The circadian clock plays an important role in daily plant physiology as well as in seasonal responses. At the molecular level, the oscillator's influence is mediated through both direct transcriptional and post-transcriptional regulation of large networks of genes and proteins. Much remains to discover about the signaling network that contributes to these massive changes in message and protein levels. In addition, the vast majority of plant oscillator work has been done with Arabidopsis. The use of this model species has been very productive. But, the details of circadian systems signaling networks in other species will be important to understand the relationship between the clock and plant physiology.

Understanding the circadian clock in crop plants is vital not only for basic biology, but also because the oscillator influences traits like flowering and stress responses that have direct agronomic importance.

Recent Publications

Peer-reviewed articles

Thines B, Harmon FG. Four easy pieces: mechanisms underlying circadian regulation of growth and development. 2011 Curr Opin Plant Biol 14:31
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Khan S, Rowe SC, Harmon FG. Coordination of the maize transcriptome by a conserved circadian clock. 2010 BMC Plant Biology 10:126
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Thines B, Harmon FG. Ambient temperature response establishes ELF3 as a required component of the core Arabidopsis circadian clock. 2010 PNAS 107(7) 3257-62
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International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon. 2010 Nature 463(7282):763-8

*Harmon FG, Imaizumi T, Gray W. CUL1 regulates TOC1 protein stability in the Arabidopsis circadian clock. 2008 Plant Journal 55(4):568-579 *Corresponding author
link to full text
Faculty of 1000 Biology recommendation of this paper

Para A, Farré EM, Imaizumi T, Pruneda-Paz JL, Harmon FG, Kay SA. PRR3 Is a vascular regulator of TOC1 stability in the Arabidopsis circadian clock. 2007 Plant Cell 19(11):3462-73

Faigón-Soverna A, Harmon FG, Storani L, Karayekov E, Staneloni RJ, Gassmann W, Más P, Casal JJ, Kay SA, Yanovsky MJ. Constitutive shade-avoidance mutant implicates TIR-NBS-LRR proteins in Arabidopsis photomorphogenic development. 2006 Plant Cell 18(11):2919-28

Imaizumi T, Schultz TF, Harmon FG, Ho LA, Kay SA. FKF1 F-box protein mediates cyclic degradation of a repressor of CONSTANS in Arabidopsis. 2005 Science 309(5732):293-7.

Hazen SP, Borevitz JO, Harmon FG, Pruneda-Paz JL, Schultz TF, Yanovsky MJ, Liljegren SJ, Ecker JR, Kay SA. Rapid array mapping of circadian clock and developmental mutations in Arabidopsis. 2005 Plant Physiology 138(2):990-7. Epub 2005 May 20.

Farre EM, Harmer SL, Harmon FG, Yanovsky MJ, Kay SA. Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock. 2005 Current Biology 15(1):47-54.

Harmon FG, Kay SA. The F box protein AFR is a positive regulator of phytochrome A-mediated light signaling. 2003 Current Biology 13(23):2091-6.

Harmon FG, Brockman JP, Kowalczykowski SC. RecQ helicase stimulates both DNA catenation and changes in DNA topology by topoisomerase III. 2003 Journal of Biological Chemistry 278(43):42668-78. Epub 2003 Aug 8.

Alabadi D, Oyama T, Yanovsky MJ, Harmon FG, Mas P, Kay SA. Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. 2001 Science 293(5531):880-3.

Harmon FG, Kowalczykowski SC. Biochemical characterization of the DNA helicase activity of the escherichia coli RecQ helicase. 2001 Journal of Biological Chemistry 276(1):232-43.

Harmon FG, DiGate RJ, Kowalczykowski SC. RecQ helicase and topoisomerase III comprise a novel DNA strand passage function: a conserved mechanism for control of DNA recombination. 1999 Molecular Cell 3(5):611-20.

Harmon FG, Kowalczykowski SC. RecQ helicase, in concert with RecA and SSB proteins, initiates and disrupts DNA recombination. 1998 Genes and Development 12(8):1134-44.

Harmon FG, Rehrauer WM, Kowalczykowski SC. Interaction of Escherichia coli RecA protein with LexA repressor. II. Inhibition of DNA strand exchange by the uncleavable LexA S119A repressor argues that recombination and SOS induction are competitive processes. 1996 Journal of Biological Chemistry 271(39):23874-83.

Book Chapters

Harmon FG, Imaizumi T, Kay SA. The plant circadian clock: review of a clockwork Arabidopsis. 2005 Annual Plant Reviews 20;1-23.

Harmon FG, Kowalczykowski SC. Coupling of DNA helicase function to DNA strand exchange activity. 2000 Methods in Molecular Biology 152:75-89.