Our Work

Work published whilst at Essex is listed below. A complete list of work I've contributed to can be found here.

Using light to improve commercial value

Matt Jones

The plasticity of plant morphology has evolved to maximize reproductive fitness in response to prevailing environmental conditions. Leaf architecture elaborates to maximize light harvesting, while the transition to flowering can either be accelerated or delayed to improve an individual’s fitness. One of the most important environmental signals is light, with plants using light for both photosynthesis and as an environmental signal. Plants perceive different wavelengths of light using distinct photoreceptors. Recent advances in LED technology now enable light quality to be manipulated at a commercial scale, and as such opportunities now exist to take advantage of plants’ developmental plasticity to enhance crop yield and quality through precise manipulation of a crop's lighting regime. This review will discuss how plants perceive and respond to light, and consider how these specific signaling pathways can be manipulated to improve crop yield and quality

The published version can be found here- Horticulture Research.

SAL1-PAP retrograde signalling extends circadian period by reproducing the loss of exoribonuclease (XRN) activity

Suzanne Litthauer and Matt Jones

Plants have developed an internal timing mechanism, the circadian system, that serves to synchronise physiological and metabolic functions with daily cues such as dawn and dusk, and provides plants with an advantage in adapting to changing and challenging conditions. We have recently shown that the SAL1-PAP-XRN retrograde signalling pathway, which is proposed to regulate plant responses under stress conditions, also acts within the circadian system. Here we provide further evidence of circadian regulation by SAL1-PAP-XRN signalling, thereby affirming a link between molecular timekeeping and abiotic stress response mechanisms.

The published version can be found here- Plant Signalling & Behaviour.

Offprint copies of the final version are available on request, but cannot be posted online due to licensing restrictions- Contact me.

3'-Phosphoadenosine 5'-Phosphate Accumulation Delays the Circadian System

Suzanne Litthauer, Kai X Chan, and Matt Jones

The circadian system optimizes cellular responses to stress, but the signaling pathways that convey the metabolic consequences of stress into this molecular timekeeping mechanism remain unclear. Redox regulation of the SAL1 phosphatase during abiotic stress initiates a signaling pathway from chloroplast to nucleus by regulating the accumulation of a metabolite, 3'-phosphoadenosine 5'-phosphate (PAP). Consequently, PAP accumulates in response to redox stress and inhibits the activity of exoribonucleases (XRNs) in the nucleus and cytosol. We demonstrated that osmotic stress induces a lengthening of circadian period and that genetically inducing the SAL1-PAP-XRN pathway in plants lacking either SAL1 or XRNs similarly delays the circadian system. Exogenous application of PAP was also sufficient to extend circadian period. Thus, SAL1-PAP-XRN signaling likely regulates circadian rhythms in response to redox stress. Our findings exemplify how two central processes in plants, molecular timekeeping and responses to abiotic stress, can be interlinked to regulate gene expression.

The published version can be found here- Plant Physiology.

Interplay of Circadian Rhythms and Light in the Regulation of Photosynthesis-Derived Metabolism

Matt Jones

Alternating periods of day and night confer an environmental rhythm upon terrestrial plants. Seasonal changes in light intensity and duration (as well as integrals of temperature) inform developmental decisions that directly impact upon plant growth. In response to the selective pressure of these daily rhythms, plants have evolved an endogenous, biological oscillator that coincides with these patterns. These circadian rhythms allow plants to anticipate daily transitions and consequently allocate specific metabolic functions to certain times of day. The circadian system also has a dramatic effect upon development, with the external coincidence model describing how plants measure day length to induce flowering under inductive conditions. Plants’ responses to environmental change are therefore a distillation of direct responses to abiotic factors and moderating factors derived from endogenous biological rhythms. This review summarizes our understanding of how metabolic processes are governed by these interactions, with particular attention to carbon and redox metabolism, two processes derived from photosynthesis.

The published version can be found here- Springer.

Offprint copies of the final version are available on request, but cannot be posted online due to licensing restrictions- Contact me.

Natural Variation Of Circadian Rhythms In Kalanchoë Species

Kathryn Malpas and Matt Jones

Plants have evolved an internal body clock- the circadian system- that allows the optimization of behavior during the day by anticipating regular environmental change. This timing mechanism also serves as an internal reference to control flowering time. One observable consequence of the circadian system is the rhythmic regulation of processes that underlie photosynthesis, which persists after plants are transferred to constant conditions. Many cacti and succulents use Crassulacean Acid Metabolism (CAM) as a modification of the predominant C3 method of photosynthesis to limit water loss. CAM allows the temporal separation of carbon capture from the atmosphere and the Calvin-Benson cycle, and so separates stomatal opening from some of the biochemical aspects of photosynthesis. Here we document the diversity of circadian rhythms in several Kalanchoë species and reveal differences in the period, phase and amplitude of circadian outputs derived from regulation of the photosynthetic apparatus.

The published version can be found here- Haseltonia.

Offprint copies of the final version are available on request, but cannot be posted online due to licensing restrictions- Contact me.

Phototropins do not Alter Accumulation of Evening-phased Circadian Transcripts Under Blue Light

Suzanne Litthauer, Martin Battle and Matt Jones

A short addendum to our first phototropin paper (below). The circadian system induces rhythmic variation in a suite of biochemical and physiological processes that serves to optimise plant growth in diel cycles. To be of greatest utility, these rhythmic behaviours are coordinated with regular environmental changes such as the rising and setting of the sun. Photoreceptors, and metabolites produced during photosynthesis, act to synchronise the internal timing mechanism with lighting cues. We have recently shown that phototropins help maintain robust rhythms of photosynthetic operating efficiency (ϕPSII or Fq'/Fm') under blue light, although rhythmic accumulation of morning-phased circadian transcripts in the nucleus was unaffected. Here we report that evening-phased nuclear clock transcripts were also unaffected. We also observe that rhythms of nuclear clock transcript accumulation are maintained in phototropin mutant plants under a fluctuating lighting regime that induced a loss of Fq'/Fm' rhythms.

The published version can be found here- Plant Signalling & Behaviour.

Phototropins Maintain Robust Circadian Oscillation of PSII Operating Efficiency Under Blue Light

Suzanne Litthauer, Martin Battle, Tracy Lawson and Matt Jones

Measurement of circadian rhythms of PSII operating efficiency in the chloroplast reveals a distinct physiological circadian output compared to previously reported delayed fluorescence methods. Phototropins are required for the maintenance of these chlorophyll fluorescence rhythms under dim blue light (while not affecting rhythms of nuclear gene expression) via a signalling cascade independent of NPH3.

The published version can be found here- The Plant Journal.

A Constitutively Active Allele of Phytochrome B Maintains Circadian Robustness in the Absence of Light

Matt Jones, Wei Hu, Suzanne Litthauer, J. Clark Lagarias, Stacey Harmer

The sensitivity of the circadian system to light allows entrainment of the clock, permitting coordination of plant metabolic function and flowering time across seasons. Light affects the circadian system both via photoreceptors, such as phytochromes and cryptochromes, and sugar production by photosynthesis. In the present studies, we introduce a constitutively active version of phytochrome B (phyB-Y276H, YHB) into both wild-type and phytochrome null backgrounds of Arabidopsis thaliana to distinguish the effects of photoreceptor signalling on clock function from those of photosynthesis. We find that the YHB mutation is sufficient to phenocopy red light input into the circadian mechanism and to sustain robust rhythms in steady-state mRNA levels even in plants grown without light or exogenous sugars. The pace of the clock is insensitive to light intensity in YHB plants, indicating that light input to the clock is constitutively activated by this allele. Mutation of YHB so that it is retained in the cytoplasm abrogates its effects on clock function, indicating that nuclear localization of phytochrome is necessary for its clock regulatory activity. We also demonstrate a role for phytochrome C as part of the red light sensing network that modulates phytochrome B signalling input into the circadian system. Our findings indicate that phytochrome signaling in the nucleus plays a critical role in sustaining robust clock function under red light, even in the absence of photosynthesis or exogenous sources of energy.

The published version can be found here- Plant Physiology.

Mutation of Arabidopsis SPLICEOSOMAL TIMEKEEPER LOCUS1 Causes Circadian Clock Defects

Matt Jones, Brian Williams, Jim McNicol, Craig G. Simpson, John W. S. Brown, Stacey Harmer

The circadian clock plays a crucial role in coordinating plant metabolic and physiological functions with predictable environmental variables, such as dusk and dawn, while also modulating responses to biotic and abiotic challenges. Much of the initial characterization of the circadian system has focused on transcriptional initiation, but it is now apparent that considerable regulation is exerted after this key regulatory step. Transcript processing, protein stability, and cofactor availability have all been reported to influence circadian rhythms in a variety of species. We used a genetic screen to identify a mutation within a putative RNA binding protein (SPLICEOSOMAL TIMEKEEPER LOCUS1 [STIPL1]) that induces a long circadian period phenotype under constant conditions. STIPL1 is a homolog of the spliceosomal proteins TFP11 (Homo sapiens) and Ntr1p (Saccharomyces cerevisiae) involved in spliceosome disassembly. Analysis of general and alternative splicing using a high-resolution RT-PCR system revealed that mutation of this protein causes less efficient splicing of most but not all of the introns analyzed. In particular, the altered accumulation of circadian-associated transcripts may contribute to the observed mutant phenotype. Interestingly, mutation of a close homolog of STIPL1, STIP-LIKE2, does not cause a circadian phenotype, which suggests divergence in function between these family members. Our work highlights the importance of posttranscriptional control within the clock mechanism.

The published version can be found here- Plant Cell.