Hugh G. Nimmo

The Arabidopsis CDPK-SnRK Superfamily of Protein Kinases

The CDPK-SnRK superfamily consists of seven types of serine-threonine protein kinases: calcium-dependent protein kinase (CDPKs), CDPK-related kinases (CRKs), phosphoenolpyruvate carboxylase kinases (PPCKs), PEP carboxylase kinase-related kinases (PEPRKs), calmodulin-dependent protein kinases (CaMKs), calcium and calmodulin-dependent protein kinases (CCaMKs), and SnRKs. Within this superfamily, individual isoforms and subfamilies contain distinct regulatory domains, subcellular targeting information, and substrate specificities. Our analysis of the Arabidopsis genome identified 34 CDPKs, eight CRKs, two PPCKs, two PEPRKs, and 38 SnRKs. No definitive examples were found for a CCaMK similar to those previously identified in lily (Lilium longiflorum) and tobacco (Nicotiana tabacum) or for a CaMK similar to those in animals or yeast. CDPKs are present in plants and a specific subgroup of protists, but CRKs, PPCKs, PEPRKs, and two of the SnRK subgroups have been found only in plants. CDPKs and at least one SnRK have been implicated in decoding calcium signals in Arabidopsis. Analysis of intron placements supports the hypothesis that CDPKs, CRKs, PPCKs and PEPRKs have a common evolutionary origin; however there are no conserved intron positions between these kinases and the SnRK subgroup. CDPKs and SnRKs are found on all five Arabidopsis chromosomes. The presence of closely related kinases in regions of the genome known to have arisen by genome duplication indicates that these kinases probably arose by divergence from common ancestors. The PlantsP database provides a resource of continuously updated information on protein kinases from Arabidopsis and other plants.

The regulation of phosphoenolpyruvate carboxylase in CAM plants

Phosphoenolpyruvate carboxylase catalyses the primary assimilation of CO(2) in Crassulacean acid metabolism plants. It is activated by phosphorylation, and this plays a major role in setting the day-night pattern of metabolism in these plants. The key factor that controls the phosphorylation state of phosphoenolpyruvate carboxylase is the activity of phosphoenolpyruvate carboxylase kinase. Recent work on Crassulacean acid metabolism plants has established this enzyme as a novel protein kinase and has provided new insights into the regulation of protein phosphorylation. Phosphoenolpyruvate carboxylase kinase is controlled by synthesis and degradation in response to a circadian oscillator. The circadian control of phosphoenolpyruvate carboxylase kinase can be overridden by changes in metabolite levels. The primary effect of the circadian oscillator in this system may be at the level of the tonoplast, and changes in kinase expression may be secondary to circadian changes in the concentration of a metabolite, perhaps cytosolic malate.

Alternative Splicing Mediates Responses of the Arabidopsis Circadian Clock to Temperature Changes

The circadian clock is a timing device that allows plants to anticipate environmental changes rather than just respond to them. This work demonstrates that alternative splicing of clock gene transcripts is one of the mechanisms that regulate the clock, particularly in response to changes in temperature. Alternative splicing plays crucial roles by influencing the diversity of the transcriptome and proteome and regulating protein structure/function and gene expression. It is widespread in plants, and alteration of the levels of splicing factors leads to a wide variety of growth and developmental phenotypes. The circadian clock is a complex piece of cellular machinery that can regulate physiology and behavior to anticipate predictable environmental changes on a revolving planet. We have performed a system-wide analysis of alternative splicing in clock components in Arabidopsis thaliana plants acclimated to different steady state temperatures or undergoing temperature transitions. This revealed extensive alternative splicing in clock genes and dynamic changes in alternatively spliced transcripts. Several of these changes, notably those affecting the circadian clock genes LATE ELONGATED HYPOCOTYL (LHY) and PSEUDO RESPONSE REGULATOR7, are temperature-dependent and contribute markedly to functionally important changes in clock gene expression in temperature transitions by producing nonfunctional transcripts and/or inducing nonsense-mediated decay. Temperature effects on alternative splicing contribute to a decline in LHY transcript abundance on cooling, but LHY promoter strength is not affected. We propose that temperature-associated alternative splicing is an additional mechanism involved in the operation and regulation of the plant circadian clock.

The Circadian Clock in Arabidopsis Roots Is a Simplified Slave Version of the Clock in Shoots

The circadian oscillator in eukaryotes consists of several interlocking feedback loops through which the expression of clock genes is controlled. It is generally assumed that all plant cells contain essentially identical and cell-autonomous multiloop clocks. Here, we show that the circadian clock in the roots of mature Arabidopsis plants differs markedly from that in the shoots and that the root clock is synchronized by a photosynthesis-related signal from the shoot. Two of the feedback loops of the plant circadian clock are disengaged in roots, because two key clock components, the transcription factors CCA1 and LHY, are able to inhibit gene expression in shoots but not in roots. Thus, the plant clock is organ-specific but not organ-autonomous.

Circadian rhythms in the activity of a plant protein kinase.

Bryophyllum fedtschenkoi is a Crassulacean acid metabolism plant whose phosphoenolpyruvate carboxylase is regulated by reversible phosphorylation in response to a circadian rhythm. A partially purified protein kinase phosphorylated phosphoenolpyruvate carboxylase in vitro with a stoichiometry approaching one per subunit and caused a concomitant 5‐ to 10‐fold decrease in the sensitivity of the carboxylase to inhibition by malate. The sites phosphorylated in vitro were identical to those phosphorylated in intact tissue. The activity of the protein kinase was controlled in a circadian fashion. During normal diurnal cycles, kinase activity appeared between 4 and 5 h after the onset of darkness and disappeared 2‐‐‐‐3 h before the end of darkness. Kinase activity displayed circadian oscillations in constant environmental conditions. The activity of protein phosphatase 2A, which dephosphorylates phosphoenolpyruvate carboxylase, did not oscillate. Treatment of detached leaves with the protein synthesis inhibitors puromycin and cycloheximide blocked the nocturnal appearance of the protein kinase activity, maintained phosphoenolypyruvate carboxylase in the dephosphorylated state and blocked the circadian rhythms of CO2 output that is observed in constant darkness and CO2‐free air. The simplest explanation of the data is that there is a circadian rhythm in the synthesis of phosphoenolpyruvate carboxylase kinase.

BHLH32 modulates several biochemical and morphological processes that respond to Pi starvation in Arabidopsis

P(i) (inorganic phosphate) limitation severely impairs plant growth and reduces crop yield. Hence plants have evolved several biochemical and morphological responses to P(i) starvation that both enhance uptake and conserve use. The mechanisms involved in P(i) sensing and signal transduction are not completely understood. In the present study we report that a previously uncharacterized transcription factor, BHLH32, acts as a negative regulator of a range of P(i) starvation-induced processes in Arabidopsis. In bhlh32 mutant plants in P(i)-sufficient conditions, expression of several P(i) starvation-induced genes, formation of anthocyanins, total P(i) content and root hair formation were all significantly increased compared with the wild-type. Among the genes negatively regulated by BHLH32 are those encoding PPCK (phosphoenolpyruvate carboxylase kinase), which is involved in modifying metabolism so that P(i) is spared. The present study has shown that PPCK genes are rapidly induced by P(i) starvation leading to increased phosphorylation of phosphoenolpyruvate carboxylase. Furthermore, several Arabidopsis proteins that regulate epidermal cell differentiation [TTG1 (TRANSPARENT TESTA GLABRA1), GL3 (GLABRA3) and EGL3 (ENHANCER OF GL3)] positively regulate PPCK gene expression in response to P(i) starvation. BHLH32 can physically interact with TTG1 and GL3. We propose that BHLH32 interferes with the function of TTG1-containing complexes and thereby affects several biochemical and morphological processes that respond to P(i) availability.

Changes in the kinetic properties and phosphorylation state of phosphoenolpyruvate carboxylase in Zea mays leaves in reponse to light and dark

In plants such as Zea mays that carry out C4 metabolism, phosphoenolpyruvate carboxylase catalyses the primary fixation of atmospheric CO2. The properties of this enzyme from Z. mays leaves kept in light and in darkness are different. In brightly illuminated leaves, which are actively fixing CO2, the enzyme is less sensitive to feedback inhibition by malate and is phosphorylated on one or more serine residues. In darkened leaves, which are not photosynthesising, the enzyme is more sensitive to inhibition by malate and is much less phosphorylated. This indicates that the activity of the enzyme is controlled by a reversible phosphorylation.

Diurnal changes in the properties of phosphoenolpyruvate carboxylase in Bryophyllum leaves: a possible co valent modification

In plants that show Crassulacean acid metabolism, phosphoenolpyruvate carboxylase catalyses the key step of CO2 fixation at night. We show here that the properties of this enzyme from Bryophyllum fedtschenkoi undergo marked changes between night and day; the night form is much less sensitive to feedback inhibition by malate than is the day form. Incubation of leaves with 32Pi followed by extraction and immunoprecipitation of phosphoenolpyruvate carboxylase showed that only the night form contained 32P. This suggests that the activity of the enzyme is controlled by a covalent modification mechanism.

Bryophyllum fedtschenkoi protein phosphatase type 2A can dephosphorylate phosphoenolpyruvate carboxylase

Phosphoenolpyruvate carboxylase, which catalyses the nocturnal fixation of CO2 in Crassulacean acid metabolism (CAM) plants, is regulated by reversible phosphorylation. The phosphorylated ‘night’ form of the enzyme is ten‐fold less sensitive to inhibition by malate than is the dephosphorylated ‘day’ form. The phosphoenolpyruvate carboxylase of the CAM plant Bryophyllum fedtschenkoi can be dephosphorylated by rabbit muscle protein phosphatase type 2A but not by type 1. B. fedtschenkoi leaves contain protein phosphatase activity that can dephosphorylate phosphoenolpyruvate carboxylase. Inhibitor studies show that this enzyme is a type 2A protein phosphatase.

Persistent circadian rhythms in the phosphorylation state of phosphoenolpyruvate carboxylase from Bryophyllum fedtschenkoi leaves and in its sensitivity to inhibition by malate

Phosphoenolpyruvate carboxylase (EC 4.1.1.31; PEPCase) from Bryophyllum fedtschenkoi leaves has previously been shown to exist in two forms in vivo. During the night the enzyme is phosphorylated and relatively insensitive to feedback inhibition by malate whereas during the day the enzyme is dephosphorylated and more sensitive to inhibition by malate. These properties of PEPCase have now been investigated in leaves maintained under constant conditions of temperature and lighting. When leaves were maintained in continuous darkness and CO2-free air at 15°C, PEPCase exhibited a persistent circadian rhythm of interconversion between the two forms. There was a good correlation between periods during which the leaves were fixing respiratory CO2 and periods during which PEPCase was in the form normally observed at night. When leaves were maintained in continuous light and normal air at 15°C, starting at the end of a night or the end of a day, a circadian rhythm of net uptake of CO2 was observed. Only when these constant conditions were applied at the end of a day was a circadian rhythm of interconversions between the two forms of PEPCase observed and the rhythms of enzyme interconversion and CO2 uptake did not correlate in phase or period.