Special Issue "Molecular Mechanisms of Circadian Clock Function 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: 31 January 2021.

Special Issue Editor

Prof. Dr. Paloma Mas
Website
Guest Editor
Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Spain
Consejo Superior de Investigaciones Científicas (CSIC), Spain
Interests: plant circadian clock; circadian rhythms; circadian regulatory networks; circadian outputs

Special Issue Information

Dear Colleagues,

Over the past several years, it has become increasingly clear that the circadian function pervades practically every aspect of the plant life cycle. A comprehensive understanding of the plant circadian system, its connection with other signaling pathways, and the circadian processes that are temporally and spatially controlled by the clock are currently the main foci of attention within the plant circadian clock field. Circadian function relies on an intricate regulatory network in which essential clock components rhythmically regulate the expression and function of each other, and generate rhythms in multiple biological activities. Initial mechanistic studies on Arabidopsis thaliana have rapidly expanded to other crops of agronomic interest, opening interesting possibilities of translating the circadian knowledge into changes in crop productivity and resilience. New perspectives are also arising from studies on clock natural variation and evolution as well as on the specificities of the circadian function in cells, organs, and the circadian connection within the whole plant.

This Special Issue invites research articles, reviews, and short communications related but not limited to: transcriptional, post-transcriptional, and epigenetic mechanisms of clock regulation; processes regulated by the clock; and their connection with the predictable changes in light and temperature using Arabidopsis and other plant species, including crops of agronomic interest.

Prof. Dr. Paloma Mas
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Plant circadian clock 
  • Circadian rhythms 
  • Signal transduction 
  • Regulatory networks 
  • Light signaling 
  • Transcriptional regulation 
  • Post-translational regulation 
  • Chromatin 
  • Flowering

Published Papers (3 papers)

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Review

Open AccessReview
The Transcriptional Network in the Arabidopsis Circadian Clock System
Genes 2020, 11(11), 1284; https://doi.org/10.3390/genes11111284 - 29 Oct 2020
Abstract
The circadian clock is the biological timekeeping system that governs the approximately 24-h rhythms of genetic, metabolic, physiological and behavioral processes in most organisms. This oscillation allows organisms to anticipate and adapt to day–night changes in the environment. Molecular studies have indicated that [...] Read more.
The circadian clock is the biological timekeeping system that governs the approximately 24-h rhythms of genetic, metabolic, physiological and behavioral processes in most organisms. This oscillation allows organisms to anticipate and adapt to day–night changes in the environment. Molecular studies have indicated that a transcription–translation feedback loop (TTFL), consisting of transcriptional repressors and activators, is essential for clock function in Arabidopsis thaliana (Arabidopsis). Omics studies using next-generation sequencers have further revealed that transcription factors in the TTFL directly regulate key genes implicated in clock-output pathways. In this review, the target genes of the Arabidopsis clock-associated transcription factors are summarized. The Arabidopsis clock transcriptional network is partly conserved among angiosperms. In addition, the clock-dependent transcriptional network structure is discussed in the context of plant behaviors for adapting to day–night cycles. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Circadian Clock Function in Plants)
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Open AccessReview
Chromatin Dynamics and Transcriptional Control of Circadian Rhythms in Arabidopsis
Genes 2020, 11(10), 1170; https://doi.org/10.3390/genes11101170 - 06 Oct 2020
Abstract
Circadian rhythms pervade nearly all aspects of plant growth, physiology, and development. Generation of the rhythms relies on an endogenous timing system or circadian clock that generates 24-h oscillations in multiple rhythmic outputs. At its bases, the plant circadian function relies on dynamic [...] Read more.
Circadian rhythms pervade nearly all aspects of plant growth, physiology, and development. Generation of the rhythms relies on an endogenous timing system or circadian clock that generates 24-h oscillations in multiple rhythmic outputs. At its bases, the plant circadian function relies on dynamic interactive networks of clock components that regulate each other to generate rhythms at specific phases during the day and night. From the initial discovery more than 13 years ago of a parallelism between the oscillations in chromatin status and the transcriptional rhythms of an Arabidopsis clock gene, a number of studies have later expanded considerably our view on the circadian epigenome and transcriptome landscapes. Here, we describe the most recent identification of chromatin-related factors that are able to directly interact with Arabidopsis clock proteins to shape the transcriptional waveforms of circadian gene expression and clock outputs. We discuss how changes in chromatin marks associate with transcript initiation, elongation, and the rhythms of nascent RNAs, and speculate on future interesting research directions in the field. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Circadian Clock Function in Plants)
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Open AccessReview
Gigantea: Uncovering New Functions in Flower Development
Genes 2020, 11(10), 1142; https://doi.org/10.3390/genes11101142 - 28 Sep 2020
Abstract
GIGANTEA (GI) is a gene involved in multiple biological functions, which have been analysed and are partially conserved in a series of mono- and dicotyledonous plant species. The identified biological functions include control over the circadian rhythm, light signalling, cold tolerance, hormone signalling [...] Read more.
GIGANTEA (GI) is a gene involved in multiple biological functions, which have been analysed and are partially conserved in a series of mono- and dicotyledonous plant species. The identified biological functions include control over the circadian rhythm, light signalling, cold tolerance, hormone signalling and photoperiodic flowering. The latter function is a central role of GI, as it involves a multitude of pathways, both dependent and independent of the gene CONSTANS(CO), as well as on the basis of interaction with miRNA. The complexity of the gene function of GI increases due to the existence of paralogs showing changes in genome structure as well as incidences of sub- and neofunctionalization. We present an updated report of the biological function of GI, integrating late insights into its role in floral initiation, flower development and volatile flower production. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Circadian Clock Function in Plants)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Transcriptional network in Arabidopsis circadian clock
Authors: Norihito Nakamichi
Affiliation: Nagoya University
Abstract: The circadian clock is the biological timekeeping system that governs the approximately 24-h rhythms of genetic, metabolic, physiological, and behavioral processes in most organisms. This oscillation allows organisms to anticipate and adapt to the day-night changes in the environment. Molecular studies indicated that the transcription-translation feedback loop (TTFL) consisted of transcriptional repressors and activators, is essential for the clock function in plants. Omics studies using next generation sequencers further revealed that transcription factors in the TTFL directly regulate key genes implicated in clock-output pathways. In this review, target genes of clock-associated transcription factors are summarized. In addition, the clock-dependent transcriptional network structure is discussed in line with for plant behaviors to adapt to day-night cycles.

Title: Cryptochromes and the circadian clock: story of a very complex relationship in a spinning world
Authors: Lopez L.; Fasano C.; Perrella G.; Facella P.
Affiliation: Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), TERIN-BBC-BBE, Trisaia Research Center, 75026, Rotondella (Matera),Italy.
Abstract: Cryptochromes are flavin-containing blue light photoreceptors, present in most of the kingdoms, including archea, bacteria, plants, animals and fungi. Structurally they are similar to photolyases, a class of flavoproteins involved in light-dependent repair of UV-damaged DNA. Cryptochromes were first discovered in Arabidopsis thaliana in which they control many light-regulated physiological processes like seed germination, de-etiolation, photoperiodic control of the flowering time, cotyledon opening and expansion, anthocyanin accumulation, chloroplast development and root growth. They also regulate the entrainment of plant circadian clock to the phase of daily light/dark cycles. Here, we review the molecular mechanisms by which plant cryptochromes control the synchronization of the clock with the environmental light, with a specific focus on the cryptochromes-mediated changes in the chromatin organisation and the cell cycle regulation.

Title: The Arabidopsis EC-JMJ29 complex facilitates diurnal histone demethylation at the PRR7 and PRR9 loci in the control of circadian oscillation
Authors: Hong Gil Lee; Pil Joon Seo
Affiliation: 1. Department of Chemistry, Seoul National University, Seoul 08826, Korea 2. Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
Abstract: The circadian clock synchronizes a majority of biological processes with daily environmental fluctuations, such as light and temperatures. Chromatin modification is emerging as key regulatory mechanism for shaping circadian oscillation in plants, although chromatin modifiers responsible for core clock gene expression remain to be fully elucidated. Here, we report that the Jumonji C domain-containing histone demethylase JMJ29, which belongs to the JHDM2/KDM3 group, refines rhythmic changes in histone marks at core clock loci in Arabidopsis. The evening-expressed JMJ29 protein interacts with the Evening Complex (EC) component EARLY FLOWEING 3 (ELF3). The EC-JMJ29 complex binds to the PRR7 and PRR9 promoters and catalyzes the H3K4me3 demethylation at the PRR7 and PRR9 loci, maintaining their expression at low levels during the night. Together, our findings indicate that interaction of circadian components with chromatin modifiers allows diurnal fluctuation of histone landscapes to shape circadian waveforms in plants.

Title: Chromatin dynamics and transcriptional control of circadian rhythms in Arabidopsis
Authors: Aida Maric; Paloma Mas
Affiliation: Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain. Consejo Superior de Investigaciones Científicas (CSIC), 08028 Barcelona, Spain.
Abstract: Circadian rhythms pervade nearly all aspects of plant growth, physiology and development. Generation of the rhythms relies on an endogenous timing system or circadian clock that generates 24-hour oscillations in multiple rhythmic outputs. At its bases, the plant circadian function relies on dynamic interactive networks of clock components that regulate each other to generate rhythms at specific phases during the day and night. From the initial discovery more than 13 years ago of a parallelism between the oscillations in chromatin status and the transcriptional rhythms of an Arabidopsis clock gene, a number of studies have later expanded considerably our view on the circadian epigenome and transcriptome landscapes. Here, we describe the most recent identification of chromatin-related factors that are able to directly interact with Arabidopsis clock proteins to shape the transcriptional waveforms of circadian gene expression and clock outputs. We discuss how changes in chromatin marks associate with transcript initiation, elongation and the rhythms of nascent RNAs, and speculate on future interesting research directions in the field.

Title: Post-translational mechanisms of plant circadian regulation
Authors: Jiapei Yan; Yeon Jeong Kim; David E Somers
Affiliation: Department of Molecular Genetics, The Ohio State University, Columbus Ohio, USA
Abstract: The molecular components of the circadian system possess the interesting feature of acting together to create a self-sustaining oscillator, while at the same time acting individually, and in complexes, to confer phase-specific circadian control over a wide range of physiological and developmental outputs. This means that many circadian oscillator proteins are simultaneously also part of the circadian output pathway. Most studies have focused on transcriptional control of circadian rhythms, but work in plants and metazoans have shown the importance of post-transcriptional and post-translational processes within the circadian system. Here we highlight recent work describing post-translational mechanisms that impact both the function of the oscillator and the clock-controlled outputs.

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