Special Issue "Genetic Regulation of Circadian Rhythm in Plants"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (15 October 2018)

Special Issue Editor

Guest Editor
Prof. László Kozma-Bognár

Biological Research Center at Hungarian Academy of Sciences, Szeged, Hungary
Website | E-Mail
Interests: Arabidopsis; circadian clock; photoreceptors; light signaling; flowering; regulation of gene expression; luciferase imaging

Special Issue Information

Dear Colleagues,

Circadian rhythms are endogenous 24-h oscillations in molecular and physiological processes in living organisms. They are controlled by circadian clocks, built on gene networks, where clock genes and the encoded proteins form interlocked regulatory loops capable of oscillations primarily at the level of gene expression. This oscillation is synchronized to the day/night cycles via light and temperature (called entrainment). Although circadian rhythms were first discovered in plants centuries ago, clock genes and their regulatory links were revealed in the last two decades. Results accumulated so far indicate that the complexity of the plant oscillator exceeds that of the insect and mammalian circadian oscillators in terms of the number of components and the regulatory loops. This probably reflects the fact that vital signaling systems are usually over-secured in the sessile plants in order to provide mutation-proof and reliable adaptation to the environment. The aim of this Special Issue is to publish original research papers reporting identification of novel clock genes or novel functions/connections of/among clock components in plants. Studies on the genetic background of entrainment and review papers on these topics are also invited. We believe that this collection of papers will contribute to a better understanding of the fascinating machinery of plant circadian clocks and rhythms.

Prof. László Kozma-Bognár
Guest Editor

Manuscript Submission Information

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Keywords

  • plant
  • circadian
  • clock gene/protein
  • regulation of gene expression
  • mechanisms of entrainment

Published Papers (7 papers)

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Research

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Open AccessArticle A Magnesium Transport Protein Related to Mammalian SLC41 and Bacterial MgtE Contributes to Circadian Timekeeping in a Unicellular Green Alga
Received: 7 January 2019 / Revised: 29 January 2019 / Accepted: 12 February 2019 / Published: 19 February 2019
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Abstract
Circadian clocks in eukaryotes involve both transcriptional-translational feedback loops, post-translational regulation, and metabolic, non-transcriptional oscillations. We recently identified the involvement of circadian oscillations in the intracellular concentrations of magnesium ions ([Mg2+]i) that were conserved in three eukaryotic kingdoms. [Mg [...] Read more.
Circadian clocks in eukaryotes involve both transcriptional-translational feedback loops, post-translational regulation, and metabolic, non-transcriptional oscillations. We recently identified the involvement of circadian oscillations in the intracellular concentrations of magnesium ions ([Mg2+]i) that were conserved in three eukaryotic kingdoms. [Mg2+]i in turn contributes to transcriptional clock properties of period and amplitude, and can function as a zeitgeber to define phase. However, the mechanism—or mechanisms—responsible for the generation of [Mg2+]i oscillations, and whether these are functionally conserved across taxonomic groups, remain elusive. We employed the cellular clock model Ostreococcus tauri to provide a first study of an MgtE domain-containing protein in the green lineage. OtMgtE shares homology with the mammalian SLC41A1 magnesium/sodium antiporter, which has previously been implicated in maintaining clock period. Using genetic overexpression, we found that OtMgtE contributes to both timekeeping and daily changes in [Mg2+]i. However, pharmacological experiments and protein sequence analyses indicated that critical differences exist between OtMgtE and either the ancestral MgtE channel or the mammalian SLC41 antiporters. We concluded that even though MgtE domain-containing proteins are only distantly related, these proteins retain a shared role in contributing to cellular timekeeping and the regulation of [Mg2+]i. Full article
(This article belongs to the Special Issue Genetic Regulation of Circadian Rhythm in Plants)
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Open AccessArticle Transcriptome Analysis of Diurnal Gene Expression in Chinese Cabbage
Received: 16 December 2018 / Revised: 31 January 2019 / Accepted: 4 February 2019 / Published: 11 February 2019
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Abstract
Plants have developed timing mechanisms that enable them to maintain synchrony with daily environmental events. These timing mechanisms, i.e., circadian clocks, include transcriptional/translational feedback loops that drive 24 h transcriptional rhythms, which underlie oscillations in protein abundance, thus mediating circadian rhythms of behavior, [...] Read more.
Plants have developed timing mechanisms that enable them to maintain synchrony with daily environmental events. These timing mechanisms, i.e., circadian clocks, include transcriptional/translational feedback loops that drive 24 h transcriptional rhythms, which underlie oscillations in protein abundance, thus mediating circadian rhythms of behavior, physiology, and metabolism. Circadian clock genes have been investigated in the diploid model plant Arabidopsis thaliana. Crop plants with polyploid genomes—such as Brassica species—have multiple copies of some clock-related genes. Over the last decade, numerous studies have been aimed at identifying and understanding the function of paralogous genes with conserved sequences, or those that diverged during evolution. Brassica rapa’s triplicate genomes retain sequence-level collinearity with Arabidopsis. In this study, we used RNA sequencing (RNAseq) to profile the diurnal transcriptome of Brassica rapa seedlings. We identified candidate paralogs of circadian clock-related genes and assessed their expression levels. These genes and their related traits that modulate the diurnal rhythm of gene expression contribute to the adaptation of crop cultivars. Our findings will contribute to the mechanistic study of circadian clock regulation inherent in polyploidy genome crops, which differ from those of model plants, and thus will be useful for future breeding studies using clock genes. Full article
(This article belongs to the Special Issue Genetic Regulation of Circadian Rhythm in Plants)
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Open AccessArticle The LNK Gene Family: At the Crossroad between Light Signaling and the Circadian Clock
Received: 14 November 2018 / Revised: 13 December 2018 / Accepted: 17 December 2018 / Published: 20 December 2018
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Abstract
Light signaling pathways interact with the circadian clock to help organisms synchronize physiological and developmental processes to periodic environmental cycles. The plant photoreceptors responsible for clock resetting have been characterized, but signaling components that link the photoreceptors to the clock remain to be [...] Read more.
Light signaling pathways interact with the circadian clock to help organisms synchronize physiological and developmental processes to periodic environmental cycles. The plant photoreceptors responsible for clock resetting have been characterized, but signaling components that link the photoreceptors to the clock remain to be identified. Members of the family of NIGHT LIGHT–INDUCIBLE AND CLOCK-REGULATED (LNK) genes play key roles linking light regulation of gene expression to the control of daily and seasonal rhythms in Arabidopsis thaliana. Particularly, LNK1 and LNK2 were shown to control circadian rhythms, photomorphogenic responses, and photoperiod-dependent flowering time. Here we analyze the role of the four members of the LNK family in Arabidopsis in these processes. We found that depletion of the closely related LNK3 and LNK4 in a lnk1;lnk2 mutant background affects circadian rhythms, but not other clock-regulated processes such as flowering time and seedling photomorphogenesis. Nevertheless, plants defective in all LNK genes (lnkQ quadruple mutants) display developmental alterations that lead to increased rosette size, biomass, and enhanced phototropic responses. Our work indicates that members of the LNK family have both distinctive and partially overlapping functions, and are an essential link to orchestrate light-regulated developmental processes. Full article
(This article belongs to the Special Issue Genetic Regulation of Circadian Rhythm in Plants)
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Open AccessArticle PIF-Mediated Sucrose Regulation of the Circadian Oscillator is Light Quality and Temperature Dependent
Genes 2018, 9(12), 628; https://doi.org/10.3390/genes9120628
Received: 19 October 2018 / Revised: 26 November 2018 / Accepted: 10 December 2018 / Published: 13 December 2018
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Abstract
Studies are increasingly showing that metabolic and circadian (~24 h) pathways are strongly interconnected, with the circadian system regulating the metabolic state of the cell, and metabolic products feeding back to entrain the oscillator. In plants, probably the most significant impact of the [...] Read more.
Studies are increasingly showing that metabolic and circadian (~24 h) pathways are strongly interconnected, with the circadian system regulating the metabolic state of the cell, and metabolic products feeding back to entrain the oscillator. In plants, probably the most significant impact of the circadian system on metabolism is in its reciprocal regulation of photosynthesis; however, the pathways by which this occurs are still poorly understood. We have previously shown that members of the basic helix-loop-helix (bHLH) transcription factor PHYTOCHROME INTERACTING FACTOR (PIF) family are involved in the photosynthate entrainment of the circadian oscillator. In this paper, using Arabidopsis mutants and overexpression lines, we examine how temperature and light quality affect PIF-mediated sucrose signaling to the oscillator and examine the contributions of individual PIF members. Our results also show that the quality of light is important for PIF signaling, with red and blue lights having the opposite effects, and that temperature affects PIF-mediated sucrose signaling. We propose the light sensitivity of PIF-mediated sucrose entrainment of the oscillator may be important in enabling plants to distinguish between sucrose produced de novo from photosynthesis during the day and the sucrose products of starch degradation at the end of the night. Full article
(This article belongs to the Special Issue Genetic Regulation of Circadian Rhythm in Plants)
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Review

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Open AccessReview Beyond Transcription: Fine-Tuning of Circadian Timekeeping by Post-Transcriptional Regulation
Genes 2018, 9(12), 616; https://doi.org/10.3390/genes9120616
Received: 6 November 2018 / Revised: 29 November 2018 / Accepted: 3 December 2018 / Published: 10 December 2018
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Abstract
The circadian clock is an important endogenous timekeeper, helping plants to prepare for the periodic changes of light and darkness in their environment. The clockwork of this molecular timer is made up of clock proteins that regulate transcription of their own genes with [...] Read more.
The circadian clock is an important endogenous timekeeper, helping plants to prepare for the periodic changes of light and darkness in their environment. The clockwork of this molecular timer is made up of clock proteins that regulate transcription of their own genes with a 24 h rhythm. Furthermore, the rhythmically expressed clock proteins regulate time-of-day dependent transcription of downstream genes, causing messenger RNA (mRNA) oscillations of a large part of the transcriptome. On top of the transcriptional regulation by the clock, circadian rhythms in mRNAs rely in large parts on post-transcriptional regulation, including alternative pre-mRNA splicing, mRNA degradation, and translational control. Here, we present recent insights into the contribution of post-transcriptional regulation to core clock function and to regulation of circadian gene expression in Arabidopsis thaliana. Full article
(This article belongs to the Special Issue Genetic Regulation of Circadian Rhythm in Plants)
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Open AccessReview A Functional Connection between the Circadian Clock and Hormonal Timing in Arabidopsis
Genes 2018, 9(12), 567; https://doi.org/10.3390/genes9120567
Received: 15 October 2018 / Revised: 20 November 2018 / Accepted: 20 November 2018 / Published: 23 November 2018
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Abstract
The rotation of the Earth entails changes in environmental conditions that pervasively influence an organism’s physiology and metabolism. An internal cellular mechanism known as the circadian clock acts as an internal timekeeper that is able to perceive the changes in environmental cues to [...] Read more.
The rotation of the Earth entails changes in environmental conditions that pervasively influence an organism’s physiology and metabolism. An internal cellular mechanism known as the circadian clock acts as an internal timekeeper that is able to perceive the changes in environmental cues to generate 24-h rhythms in synchronization with daily and seasonal fluctuations. In plants, the circadian clock function is particularly important and regulates nearly every aspect of plant growth and development as well as proper responses to stresses. The circadian clock does not function in isolation but rather interconnects with an intricate network of different pathways, including those of phytohormones. Here, we describe the interplay of the circadian clock with a subset of hormones in Arabidopsis. The molecular components directly connecting the circadian and hormone pathways are described, highlighting the biological significance of such connections in the control of growth, development, fitness, and survival. We focus on the overlapping as well as contrasting circadian and hormonal functions that together provide a glimpse on how the Arabidopsis circadian system regulates hormone function in response to endogenous and exogenous cues. Examples of feedback regulation from hormone signaling to the clock are also discussed. Full article
(This article belongs to the Special Issue Genetic Regulation of Circadian Rhythm in Plants)
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Open AccessReview The Plant Circadian Clock and Chromatin Modifications
Genes 2018, 9(11), 561; https://doi.org/10.3390/genes9110561
Received: 3 October 2018 / Revised: 27 October 2018 / Accepted: 5 November 2018 / Published: 20 November 2018
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Abstract
The circadian clock is an endogenous timekeeping network that integrates environmental signals with internal cues to coordinate diverse physiological processes. The circadian function depends on the precise regulation of rhythmic gene expression at the core of the oscillators. In addition to the well-characterized [...] Read more.
The circadian clock is an endogenous timekeeping network that integrates environmental signals with internal cues to coordinate diverse physiological processes. The circadian function depends on the precise regulation of rhythmic gene expression at the core of the oscillators. In addition to the well-characterized transcriptional feedback regulation of several clock components, additional regulatory mechanisms, such as alternative splicing, regulation of protein stability, and chromatin modifications are beginning to emerge. In this review, we discuss recent findings in the regulation of the circadian clock function in Arabidopsis thaliana. The involvement of chromatin modifications in the regulation of the core circadian clock genes is also discussed. Full article
(This article belongs to the Special Issue Genetic Regulation of Circadian Rhythm in Plants)
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