Research

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15 pages, 1392 KiB

Open AccessArticle

The Arabidopsis JMJ29 Protein Controls Circadian Oscillation through Diurnal Histone Demethylation at the CCA1 and PRR9 Loci

by Hong Gil Lee and Pil Joon Seo

Genes 2021, 12(4), 529; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12040529 - 05 Apr 2021

Cited by 2 | Viewed by 2485

Abstract

The circadian clock matches various biological processes to diurnal environmental cycles, such as light and temperature. Accumulating evidence shows that chromatin modification is crucial for robust circadian oscillation in plants, although chromatin modifiers involved in regulating core clock gene expression have been limitedly [...] Read more.

The circadian clock matches various biological processes to diurnal environmental cycles, such as light and temperature. Accumulating evidence shows that chromatin modification is crucial for robust circadian oscillation in plants, although chromatin modifiers involved in regulating core clock gene expression have been limitedly investigated. Here, we report that the Jumonji C domain-containing histone demethylase JMJ29, which belongs to the JHDM2/KDM3 group, shapes rhythmic changes in H3K4me3 histone marks at core clock loci in Arabidopsis. The evening-expressed JMJ29 protein interacts with the Evening Complex (EC) component EARLY FLOWERING 3 (ELF3). The EC recruits JMJ29 to the CCA1 and PRR9 promoters to catalyze the H3K4me3 demethylation at the cognate loci, maintaining a low-level expression during the evening time. Together, our findings demonstrate that interaction of circadian components with chromatin-related proteins underlies diurnal fluctuation of chromatin structures to maintain circadian waveforms in plants. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Circadian Clock Function in Plants)

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18 pages, 2726 KiB

Open AccessArticle

Characterization of the Ghd8 Flowering Time Gene in a Mini-Core Collection of Miscanthus sinensis

by Zhihui Guo, Meilan Xu, Hironori Nagano, Lindsay V. Clark, Erik J. Sacks and Toshihiko Yamada

Genes 2021, 12(2), 288; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12020288 - 19 Feb 2021

Viewed by 2515

Abstract

The optimal flowering time for bioenergy crop Miscanthus is essential for environmental adaptability and biomass accumulation. However, little is known about how genes controlling flowering in other grasses contribute to flowering regulation in Miscanthus. Here, we report on the sequence characterization and [...] Read more.

The optimal flowering time for bioenergy crop Miscanthus is essential for environmental adaptability and biomass accumulation. However, little is known about how genes controlling flowering in other grasses contribute to flowering regulation in Miscanthus. Here, we report on the sequence characterization and gene expression of Miscanthus sinensisGhd8, a transcription factor encoding a HAP3/NF-YB DNA-binding domain, which has been identified as a major quantitative trait locus in rice, with pleiotropic effects on grain yield, heading date and plant height. In M. sinensis, we identified two homoeologous loci, MsiGhd8A located on chromosome 13 and MsiGhd8B on chromosome 7, with one on each of this paleo-allotetraploid species’ subgenomes. A total of 46 alleles and 28 predicted protein sequence types were identified in 12 wild-collected accessions. Several variants of MsiGhd8 showed a geographic and latitudinal distribution. Quantitative real-time PCR revealed that MsiGhd8 expressed under both long days and short days, and MsiGhd8B showed a significantly higher expression than MsiGhd8A. The comparison between flowering time and gene expression indicated that MsiGhd8B affected flowering time in response to day length for some accessions. This study provides insight into the conserved function of Ghd8 in the Poaceae, and is an important initial step in elucidating the flowering regulatory network of Miscanthus. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Circadian Clock Function in Plants)

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Review

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19 pages, 1604 KiB

Open AccessReview

Cryptochromes and the Circadian Clock: The Story of a Very Complex Relationship in a Spinning World

by Loredana Lopez, Carlo Fasano, Giorgio Perrella and Paolo Facella

Genes 2021, 12(5), 672; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12050672 - 29 Apr 2021

Cited by 21 | Viewed by 6872

Abstract

Cryptochromes are flavin-containing blue light photoreceptors, present in most kingdoms, including archaea, bacteria, plants, animals and fungi. They are structurally 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 [...] Read more.

Cryptochromes are flavin-containing blue light photoreceptors, present in most kingdoms, including archaea, bacteria, plants, animals and fungi. They are structurally 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 light–dark daily cycles. Here, we review the molecular mechanisms by which plant cryptochromes control the synchronisation of the clock with the environmental light. Furthermore, we summarise the circadian clock-mediated changes in cell cycle regulation and chromatin organisation and, finally, we discuss a putative role for plant cryptochromes in the epigenetic regulation of genes. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Circadian Clock Function in Plants)

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11 pages, 988 KiB

Open AccessReview

Spatial Organization and Coordination of the Plant Circadian System

by Maria A. Nohales

Genes 2021, 12(3), 442; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12030442 - 20 Mar 2021

Cited by 9 | Viewed by 3412

Abstract

The plant circadian clock has a pervasive influence on many aspects of plant biology and is proposed to function as a developmental manager. To do so, the circadian oscillator needs to be able to integrate a multiplicity of environmental signals and coordinate an [...] Read more.

The plant circadian clock has a pervasive influence on many aspects of plant biology and is proposed to function as a developmental manager. To do so, the circadian oscillator needs to be able to integrate a multiplicity of environmental signals and coordinate an extensive and diverse repertoire of endogenous rhythms accordingly. Recent studies on tissue-specific characteristics and spatial structure of the plant circadian clock suggest that such plasticity may be achieved through the function of distinct oscillators, which sense the environment locally and are then coordinated across the plant through both intercellular coupling and long-distance communication. This review summarizes the current knowledge on tissue-specific features of the clock in plants and their spatial organization and synchronization at the organismal level. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Circadian Clock Function in Plants)

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22 pages, 1000 KiB

Open AccessEditor’s ChoiceReview

Circadian Clock Components Offer Targets for Crop Domestication and Improvement

by C. Robertson McClung

Genes 2021, 12(3), 374; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12030374 - 06 Mar 2021

Cited by 23 | Viewed by 4145

Abstract

During plant domestication and improvement, farmers select for alleles present in wild species that improve performance in new selective environments associated with cultivation and use. The selected alleles become enriched and other alleles depleted in elite cultivars. One important aspect of crop improvement [...] Read more.

During plant domestication and improvement, farmers select for alleles present in wild species that improve performance in new selective environments associated with cultivation and use. The selected alleles become enriched and other alleles depleted in elite cultivars. One important aspect of crop improvement is expansion of the geographic area suitable for cultivation; this frequently includes growth at higher or lower latitudes, requiring the plant to adapt to novel photoperiodic environments. Many crops exhibit photoperiodic control of flowering and altered photoperiodic sensitivity is commonly required for optimal performance at novel latitudes. Alleles of a number of circadian clock genes have been selected for their effects on photoperiodic flowering in multiple crops. The circadian clock coordinates many additional aspects of plant growth, metabolism and physiology, including responses to abiotic and biotic stresses. Many of these clock-regulated processes contribute to plant performance. Examples of selection for altered clock function in tomato demonstrate that with domestication, the phasing of the clock is delayed with respect to the light–dark cycle and the period is lengthened; this modified clock is associated with increased chlorophyll content in long days. These and other data suggest the circadian clock is an attractive target during breeding for crop improvement. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Circadian Clock Function in Plants)

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19 pages, 1076 KiB

Open AccessEditor’s ChoiceReview

Post-Translational Mechanisms of Plant Circadian Regulation

by Jiapei Yan, Yeon Jeong Kim and David E. Somers

Genes 2021, 12(3), 325; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12030325 - 24 Feb 2021

Cited by 24 | Viewed by 3919

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. [...] Read more.

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 has 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. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Circadian Clock Function in Plants)

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13 pages, 443 KiB

Open AccessReview

The Transcriptional Network in the Arabidopsis Circadian Clock System

by Norihito Nakamichi

Genes 2020, 11(11), 1284; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11111284 - 29 Oct 2020

Cited by 39 | Viewed by 6684

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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14 pages, 542 KiB

Open AccessReview

Chromatin Dynamics and Transcriptional Control of Circadian Rhythms in Arabidopsis

by Aida Maric and Paloma Mas

Genes 2020, 11(10), 1170; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11101170 - 06 Oct 2020

Cited by 9 | Viewed by 3565

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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15 pages, 1644 KiB

Open AccessReview

Gigantea: Uncovering New Functions in Flower Development

by Claudio Brandoli, Cesar Petri, Marcos Egea-Cortines and Julia Weiss

Genes 2020, 11(10), 1142; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11101142 - 28 Sep 2020

Cited by 17 | Viewed by 4866

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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