Rob McClung

215 Gilman Hall

Genetics And Molecular Genetics Of Plant Circadian Rhythms

 

The ability of an organism to measure time is the product of a cellular biological clock.  Many phenomena controlled by the biological clock cycle on a daily basis and are called circadian rhythms.  My goal is to understand the genetic and biochemical mechanisms by which an organism measures time and uses that temporal information to regulate gene expression and cellular physiology.  The circadian clock is an endogenous oscillator that drives rhythms with periods of approximately 24 hours.  By definition, these circadian (from the Latin, circa, approximately; dies, day) rhythms persist in constant conditions and reflect the activity of an endogenous biological clock.  Plants are richly rhythmic and the circadian clock regulates a number of key metabolic pathways and stress responses.  In addition, the circadian clock plays a critical role in the photoperiodic regulation of the transition to flowering in many species.  Circadian rhythms in plants have been the subject of a number of recent reviews, including several from my lab (SalomŽ and McClung, 2004, 2005a; McClung, 2006).  It is worth noting that two of these were largely taken from the introduction to Patrice SalomŽÕs Ph.D. thesis.

 

POTENTIAL THESIS PROJECTS

1.  Mutational Analysis of the Arabidopsis Circadian Clock.  We have identified a number of loci which, when mutated, alter circadian rhythmicity (period or phase is altered, or the plants are arrhythmic).  These studies include novel genes identified in forward genetic screens as well as defined genes identified through a candidate gene (reverse genetics) approach.  The genetic and molecular biological analysis of these mutations offers a number of thesis projects (Michael et al., 2003; SalomŽ and McClung, 2005b, a).

 

2. Post-transcriptional Regulation by the Arabidopsis Circadian Clock.  The biochemical function of the PRR proteins is not yet understood.  However, it has become clear that the stability of each is tightly regulated.  For example, TOC1 and PRR5 are targeted for proteasomal degradation through interaction with the F-box protein ZTL.  Each PRR is phosphorylated and this phosphorylation is implicated in their regulated stability (Fujiwara et al., 2008). For example, the more highly phosphorylated forms of PRR5 and TOC1 interact best with ZTL.  This suggests that phosphorylation may be an important step in the regulated proteolysis of the PRRs.  What kinases are important for clock function?  We have recently identified several kinases important for proper clock function and experiments are in progress to identify the targets of these kinases and the biochemical mechanisms by which phosphorylation contributes to clock function.

 

3. Evolutionary and Quantitative Genetic Analysis of the Arabidopsis Circadian Clock.  PSEUDO-RESPONSE REGULATOR 7 (PRR7) is a gene that plays a role in the Arabidopsis thaliana circadian clock, because eliminating function of the PRR7 gene results in a lengthening of the circadian period. Also, we have mapped a number of loci (Quantitative Trait Loci; QTL) that contribute incrementally to the definition of period length and one of the QTLÕs mapped near PRR7 (Michael et al., 2003). We wish to determine whether PRR7 encodes a period QTL.  If it does, we would predict there to be different PRR7 alleles among multiple accessions (natural populations). Sequence analysis confirms this prediction; most simply these can be divided into two clades that show distinct geographic distributions, with one clade in southwestern Europe and North Africa and the second clade in central and northeastern Europe.  Excitingly, the distribution of mutations among these PRR7 alleles suggests that PRR7 is undergoing strong diversifying selection, consistent with the hypothesis that selection is acting to enrich multiple PRR7 forms, each of which is suited to a particular geographic habitat.  Flanking genes fail to show similar distributions of mutations, consistent with natural selection acting on PRR7.  We are extending this analysis to other Òclock genes,Ó including PRR9 and PRR1 (TOC1). 

 

We intend to take two additional approaches concerning the identity of PRR7 as the QTL we identified.  The first is a genetic approach in which we generate two sets of Near Isogenic Lines (NILs), in which the PRR7 allele from one Arabidopsis accession, Col, is introduced into a second accession, Ler and vice versa.  One would predict that the Col and Ler PRR7 alleles would result in distinct periods.  The second approach is more molecular biological.  We would introduce the PRR7 alleles from several different accessions into a loss-of-function prr7 prr9 double mutant and ask whether each of the different alleles can restore PRR7 function equally well.

 

4. Evolutionary and Quantitative Genetic Analysis of the Brassica rapa Circadian Clock. We have started a new collaboration to look at clocks in a crop species, Brassica rapa (Chinese cabbage, turnip). We are measuring clock parameters (again, by leaf movement) in order to map QTLs that contribute to period, phase and amplitude.  The study is ongoing, but we already have identified multiple QTLs, one of which maps near a B. rapa PRR7 ortholog.  In addition, we will map genes that contribute to temperature entrainment and temperature compensation.  Besides the QTL mapping, we will identify B. rapa orthologs of Arabidopsis clock genes and test whether they play similar roles in the B. rapa clock.

 

 

RECENT LAB PUBLICATIONS

Fujiwara, S., Wang, L., Han, L., Suh, S.S., SalomŽ, P.A., McClung, C.R., and Somers, D.E. (2008). Post-translational regulation of the circadian clock through selective proteolysis and phosphorylation of pseudo-response regulator proteins. J. Biol Chem. 283, 23073-23083.

GutiŽrrez, R.A., Stokes, T.L., Thum, K., Xu, X., Obertello, M., Katari, M.S., Tanurdzic, M., Dean, A., Nero, D.C., McClung, C.R., and Coruzzi, G.M. (2008). Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc. Natl. Acad. Sci. USA 105, 4939-4944.

McClung, C.R. (2006). Plant circadian rhythms. Plant Cell 18, 792-803.

Michael, T.P., SalomŽ, P.A., Yu, H.J., Spencer, T.R., Sharp, E.L., Alonso, J.M., Ecker, J.R., and McClung, C.R. (2003). Enhanced fitness conferred by naturally occurring variation in the circadian clock. Science 302, 1049-1053.

SalomŽ, P.A., and McClung, C.R. (2004). The Arabidopsis thaliana clock. J. Biol. Rhythms 19, 425-435.

SalomŽ, P.A., and McClung, C.R. (2005a). What makes Arabidopsis tick: Light and temperature entrainment of the circadian clock. Plant Cell Environ. 28, 21-38.

SalomŽ, P.A., and McClung, C.R. (2005b). PRR7 and PRR9 are partially redundant genes essential for the temperature responsiveness of the Arabidopsis circadian clock. Plant Cell 17, 791-803.

SalomŽ, P.A., Xie, Q., and McClung, C.R. (2008). Circadian timekeeping during early Arabidopsis development. Plant Physiol. 147, 1110-1125.

 

updated October 22, 2008