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Personal profile

Personal profile

My lab focuses on the interaction between plants and their environment. The work falls under three specific areas:

1. Light input to the plant circadian clock

2. Light signalling in the shade avoidance response

3. The interaction between plants and their microbiome

Our current projects all involve the use of bioinformatic approaches to analyse high throughput data and we have particularly developed expertise in the analysis of microarrays, RNA sequencing data, and next generation DNA sequencing data.

1. Light input to the plant circadian clock

 The circadian clock controls a wide range of processes many organisms, synchronising their physiology and metabolism with the daily light / dark cycle. An internal rhythm maintains an approximate 24 hour cycle ensuring an anticipation of diurnal fluctuations and allowing the organism to take maximum advantage of its environment. Daily entrainment by light allows the clock to keep the correct time but this clock will continue to run even in the absence of any environmental cues (McWatters and Devlin, 2011, FEBS Lett.). Plants are no exception to this. All aspects of a plant’s physiology and metabolism show rhythmicity. In plants a number of clock genes maintain this rhythm and, in collaboration with Yale University, we have shown that a key part of that mechanism involves the activation of a gene called EARLY FLOWERING 4 (ELF4) by two transcription factors, FHY3 and FAR1 (Li et al., 2011, Nature Cell Biology). These transcription factors directly bind to the promoter of one of the ELF4 gene and, since light regulates the stability of FHY3, this mediates a light-dependent activation of ELF4 expression (Siddiqui et al., 2016, Front. Plant Sci.). We are now using a bioinformatic approach to look at wider roles for FHY3 and FAR1 in the way that the clock responds to light using global gene expression data obtained from fhy3 and far1 mutant plants.

(Funded by BBSRC grant: BB/F02116X/1). 

FHY3 and FAR1 transcription factors regulate central clock gene expression. (Video generated using time lapse images from seedlings expressing a firefly luciferase reporter gene under the control of the clock).. 


We have also used bioinformatic approaches to look at how the clock regulates its target genes. Using a novel machine learning approach we carried out a meta-analysis of high-throughput global gene expression data to show that the target genes regulated by the clock show an overlapping progression of promoter sequences which corresponds to their peak time of expression. This project was a collaboration with Prof Alberto Paccanaro in the Department of Computer Science. Morning, noon, evening and night-time modules were identified but genes peaking between these times showed a combination of promoter sequences associated with the preceding and following modules. The final time of the peak expression of a gene seems to depend on the additive effect of these various sequences (Smieszek et al., 2014, Roy. Soc. Interface).

(Funded by a Crosslands studentship).

Genes regulated by the clock show an overlapping progression of promoter sequences which corresponds to their peak time of expression.. 


In a further collaboration with the Kunming Institute of Botany we are currently carrying out a high-throughput “RNA-sequencing” analysis of global circadian gene expression patterns in Setaria italica to establish a definitive circadian transcriptome in this novel model crop plant. Ultimately, it is hoped that the patterns of expression revealed by this analysis will yield new insights into the importance of the clock in agricultural yield in grain crops.

(Funded by the Royal Holloway University of London Research Strategy Fund).


2. Light signalling in the shade avoidance response

A second aspect of my work involves analysis of the shade avoidance syndrome. Many plants adapted to growth in open canopies show a dramatic increase in elongation growth in response to competition for light with neighbouring plants. The phytochrome photoreceptors detect red-depleted light (low red:far-red ratio light) reflected from neighbouring vegetation which induces this shade avoidance response. The shade avoidance syndrome can have a tremendous negative impact upon agricultural yield if resources are reallocated to elongation rather than biomass growth (Devlin 2016, PNAS). In collaboration with the Centre for Research in Agricultural Genomics, Barcelona we are currently characterising a number of novel “dracula” mutants identified as showing no avoidance of shade. We identified these using a luciferase reporter screen. We are able to follow shade responsive gene expression using a firefly luciferase reporter gene engineered so that plants glow when subjected to simulated vegetative shade. The dra1 mutant is the result of a novel mutation in a phytochrome gene that causes disruption of shade signalling. It allowed us to identify a key amino acid in phytochrome protein which determines the specificity of different members of the phytochrome gene family (Wang et al., 2011, J. Ex. Bot.). The dra2 mutant is the result of a mutation in a nuclear pore complex which is important in exporting messenger RNA out from the nucleus. This work revealed a novel mechanism by which shade signalling is mediated in plants (Gallemí et al., 2016, Development).

(Funded by the Royal Society and The KC Wong Foundation).

Low red to far red ratio light reflected from vegetation when plants are grown in close proximity causes shade avoidance responses, reducing yield. (Photographs by James Gillies (Left) and Sandra Smith (Centre)).

In collaboration with Vitacress and the labs of Tony Stead and Alan Gange at RHUL, we have also been examining the importance of light in the regulation of metabolism in potted herbs. We have demonstrated that shade treatment can improve cold tolerance in potted basil allowing it to better survive the transport chain to the supermarket shelf. Using high-throughput “RNA-sequencing” technology we are now examining the effect of simulated shade on the expression patterns of genes involved in cold tolerance in basil but we are also examining whether light treatment can also lengthen shelf life of basil once it reaches the supermarket.

(Funded by Vitacress).