Phytochromes measure photoperiod in Brachypodium

SummaryDaylength is a key seasonal cue for animals and plants. In cereals, photoperiodic responses are a major adaptive trait, and alleles of clock genes such as PHOTOPERIOD DEPENDENT1 (PPD1) and EARLY FLOWERING3 (ELF3) have been selected for in breeding barley and wheat for more northern latitudes (Faure et al., 2012; Turner, Beales, Faure, Dunford, & Laurie, 2005). How monocot plants sense photoperiod and integrate this information into growth and development is not well understood. We show that in Brachypodium distachyon, phytochrome C (phyC) acts as a molecular timer, directly communicating information to the circadian clock protein ELF3. In this way, ELF3 levels integrate night length information. ELF3 is a central regulator of photoperiodism in Brachypodium, and elf3 mutants display a constitutive long day transcriptome. Conversely, conditions that result in higher levels of ELF3 suppress long day responses. We are able to show that these effects are direct, as ELF3 and phyC occur in a common complex, and they associate with the promoters of a number of conserved regulators of photoperiodism, including PPD1. Consistent with observations in barley, we are able to show that PPD1 overexpression accelerates flowering in SD and is necessary for rapid flowering in response to LD. These findings provide a conceptual framework for understanding observations in the photoperiodic responses of key crops, including wheat, barley and rice.

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Into the Evening: Complex Interactions in the Arabidopsis circadian clock

10.1101/068460 ◽

2016 ◽

Cited By ~ 1

Author(s):

He Huang ◽

Dmitri A. Nusinow

Keyword(s):

Arabidopsis Thaliana ◽

Circadian Clock ◽

Growth And Development ◽

Clock Genes ◽

Day Length ◽

Interacting Proteins ◽

Plant Growth And Development ◽

Complex Interactions ◽

New Findings ◽

Direct Regulation

AbstractIn Arabidopsis thaliana, an assembly of proteins named the evening complex (EC) has been established as an essential component of the circadian clock with conserved functions in regulating plant growth and development. Recent studies identifying EC-regulated genes and EC-interacting proteins have expanded our understanding of EC function. In this review, we focus on new progress uncovering how the EC contributes to the circadian network through the integration of environmental inputs and the direct regulation of key clock genes. We also summarize new findings of how the EC directly regulates clock outputs, such as day-length dependent and thermoresponsive growth, and provide new perspectives on future experiments to address unsolved questions related to the EC.

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An NF-κB–driven lncRNA orchestrates colitis and circadian clock

Science Advances ◽

10.1126/sciadv.abb5202 ◽

2020 ◽

Vol 6 (42) ◽

pp. eabb5202

Author(s):

Shuai Wang ◽

Yanke Lin ◽

Feng Li ◽

Zifei Qin ◽

Ziyue Zhou ◽

...

Keyword(s):

Circadian Clock ◽

Clock Gene ◽

Clock Genes ◽

Experimental Colitis ◽

Circadian Clock Gene ◽

Its Gene ◽

E Box ◽

Direct Binding ◽

Central Clock ◽

Clock Protein

We uncover a cycling and NF-κB–driven lncRNA (named Lnc-UC) that epigenetically modifies transcription of circadian clock gene Rev-erbα, thereby linking circadian clock to colitis. Cycling expression of Lnc-UC is generated by the central clock protein Bmal1 via an E-box element. NF-κB activation in experimental colitis transcriptionally drives Lnc-UC through direct binding to two κB sites. Lnc-UC ablation disrupts colonic expressions of clock genes in mice; particularly, Rev-erbα is down-regulated and its diurnal rhythm is blunted. Consistently, Lnc-UC promotes expression of Rev-erbα (a known dual NF-κB/Nlrp3 repressor) to inactivate NF-κB signaling and Nlrp3 inflammasome in macrophages. Furthermore, Lnc-UC ablation sensitizes mice to experimental colitis and abolishes the diurnal rhythmicity in disease severity. Mechanistically, Lnc-UC physically interacts with Cbx1 protein to reduce its gene silencing activity via H3K9me3, thereby enhancing Rev-erbα transcription and expression. In addition, we identify a human Lnc-UC that has potential to promote Rev-erbα expression and restrain inflammations.

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Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation

10.1101/762021 ◽

2019 ◽

Cited By ~ 1

Author(s):

Kirk J-M. MacKinnon ◽

Benjamin J. Cole ◽

Chang Yu ◽

Joshua H. Coomey ◽

Nolan T. Hartwick ◽

...

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Circadian Clock ◽

Clock Genes ◽

Brachypodium Distachyon ◽

Regulation Of Gene Expression ◽

Enrichment Analysis ◽

Grass Species ◽

List Type ◽

Sequence Motifs

SUMMARYPlants are continuously exposed to diurnal fluctuations in light and temperature, and spontaneous changes in their physical or biotic environment. The circadian clock coordinates regulation of gene expression with a 24-hour period, enabling the anticipation of these events.We used RNA sequencing to characterize the Brachypodium distachyon transcriptome under light and temperature cycles, as well as under constant conditions.Approximately 3% of the transcriptome was regulated by the circadian clock, a smaller proportion reported in most other species. For most transcripts that were rhythmic under all conditions, including many known clock genes, the period of gene expression lengthened from 24 to 27 h in the absence of external cues. To functionally characterize the cyclic transcriptome in B. distachyon, we used Gene Ontology enrichment analysis, and found several terms significantly associated with peak expression at particular times of the day. Furthermore we identified sequence motifs enriched in the promoters of similarly-phased genes, some potentially associated with transcription factors.When considering the overlap in rhythmic gene expression and specific pathway behavior, thermocycles was the prevailing cue that controlled diurnal gene regulation. Taken together, our characterization of the rhythmic B. distachyon transcriptome represents a foundational resource with implications in other grass species.

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Clock proteins regulate spatiotemporal organization of clock genes to control circadian rhythms

10.1101/2020.10.09.333732 ◽

2020 ◽

Author(s):

Yangbo Xiao ◽

Ye Yuan ◽

Mariana Jimenez ◽

Neeraj Soni ◽

Swathi Yadlapalli

Keyword(s):

Gene Expression ◽

Circadian Rhythms ◽

Nuclear Envelope ◽

Circadian Clock ◽

Clock Genes ◽

Circadian Clocks ◽

Spatiotemporal Organization ◽

Clock Proteins ◽

Expression Behavior ◽

Clock Protein

ABSTRACTCircadian clocks regulate ∼24 hour oscillations in gene expression, behavior, and physiology. While the molecular and neural mechanisms of circadian rhythms are well characterized, how cellular organization of clock components controls circadian clock regulation remains poorly understood. Here, we elucidate how clock proteins regulate circadian rhythms by controlling the spatiotemporal organization of clock genes. Using high-resolution live imaging techniques we demonstrate that Drosophila clock proteins are concentrated in a few discrete foci and are organized at the nuclear envelope; these results are in contrast to longstanding expectations that clock proteins are diffusely distributed in the nucleus. We also show that clock protein foci are highly dynamic and change in number, size, and localization over the circadian cycle. Further, we demonstrate that clock genes are positioned at the nuclear periphery by the clock proteins precisely during the circadian repression phase, suggesting that subnuclear localization of clock genes plays an important role in the control of rhythmic gene expression. Finally, we show that Lamin B receptor, a nuclear envelope protein, is required for peripheral localization of clock protein foci and clock genes and for normal circadian rhythms. These results reveal that clock proteins form dynamic nuclear foci and play a hitherto unexpected role in the subnuclear reorganization of clock genes to control circadian rhythms, identifying a novel mechanism of circadian regulation. Our results further suggest a new role for clock protein foci in the clustering of clock-regulated genes during the repression phase to control gene co-regulation and circadian rhythms.SIGNIFICANCEAlmost all living organisms have evolved circadian clocks to tell time. Circadian clocks regulate ∼24-hour oscillations in gene expression, behavior and physiology. Here, we reveal the surprisingly sophisticated spatiotemporal organization of clock proteins and clock genes and its critical role in circadian clock function. We show, in contrast to current expectations, that clock proteins are concentrated in a few discrete, dynamic nuclear foci at the nuclear envelope during the repression phase. Further, we uncovered several unexpected features of clock protein foci, including their role in positioning the clock genes at the nuclear envelope precisely during the repression phase to enable circadian rhythms. These studies provide fundamental new insights into the cellular mechanisms of circadian rhythms and establish direct links between nuclear organization and circadian clocks.

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Oviposition-promoting pars intercerebralis neurons show period-dependent photoperiodic changes in their firing activity in the bean bug

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2018823118 ◽

2021 ◽

Vol 118 (9) ◽

pp. e2018823118

Author(s):

Masaharu Hasebe ◽

Sakiko Shiga

Keyword(s):

Rna Interference ◽

Circadian Clock ◽

Ovarian Development ◽

Clock Genes ◽

Neuronal Response ◽

Photoperiodic Response ◽

Firing Activity ◽

Pars Intercerebralis ◽

Photoperiodic Responses ◽

Bean Bug

Animals show photoperiodic responses in physiology and behavior to adapt to seasonal changes. Recent genetic analyses have demonstrated the significance of circadian clock genes in these responses. However, the importance of clock genes in photoperiodic responses at the cellular level and the physiological roles of the cellular responses are poorly understood. The bean bug Riptortus pedestris shows a clear photoperiodic response in its reproduction. In the bug, the pars intercerebralis (PI) is an important brain region for promoting oviposition. Here, we analyzed the role of the photoperiodic neuronal response and its relationship with clock genes, focusing on PI neurons. Large PI neurons exhibited photoperiodic firing changes, and high firing activities were primarily found under photoperiodic conditions suitable for oviposition. RNA interference-mediated knockdown of the clock gene period abolished the photoperiodic response in PI neurons, as well as the response in ovarian development. To clarify whether the photoperiodic response in the PI was dependent on ovarian development, we performed an ovariectomy experiment. Ovariectomy did not have significant effects on the firing activity of PI neurons. Finally, we identified the output molecules of the PI neurons and analyzed the relevance of the output signals in oviposition. PI neurons express multiple neuropeptides—insulin-like peptides and diuretic hormone 44—and RNA interference of these neuropeptides reduced oviposition. Our results suggest that oviposition-promoting peptidergic neurons in the PI exhibit a circadian clock-dependent photoperiodic firing response, which contributes to the photoperiodic promotion of oviposition.

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Deubiquitinating enzyme USP9X regulates cellular clock function by modulating the ubiquitination and degradation of a core circadian protein BMAL1

Biochemical Journal ◽

10.1042/bcj20180005 ◽

2018 ◽

Vol 475 (8) ◽

pp. 1507-1522 ◽

Cited By ~ 7

Author(s):

Yang Zhang ◽

Chunyan Duan ◽

Jing Yang ◽

Suping Chen ◽

Qing Liu ◽

...

Keyword(s):

Circadian Rhythm ◽

Circadian Clock ◽

Clock Genes ◽

Affinity Purification ◽

Mass Spectrometry Analysis ◽

Regulatory Function ◽

Spectrometry Analysis ◽

The Core ◽

Clock Proteins ◽

Clock Protein

Living organisms on the earth maintain a roughly 24 h circadian rhythm, which is regulated by circadian clock genes and their protein products. Post-translational modifications of core clock proteins could affect the circadian behavior. Although ubiquitination of core clock proteins was studied extensively, the reverse process, deubiquitination, has only begun to unfold and the role of this regulation on circadian function is not completely understood. Here, we use affinity purification and mass spectrometry analysis to identify probable ubiquitin carboxyl-terminal hydrolase FAF-X (USP9X) as an interacting protein of the core clock protein aryl hydrocarbon receptor nuclear translocator-like protein 1 (ARNTL or BMAL1). Through biochemical experiments, we discover that USP9X reduces BMAL1 ubiquitination, enhances its stability, and increases its protein level, leading to the elevated transcriptional activity. Bioluminescence measurement reveals that USP9X knockdown decreases the amplitude of the cellular circadian rhythm but the period and phase are not affected. Our experiments find a new regulator for circadian clock at the post-translational level and demonstrate a different regulatory function for the circadian clock through the deubiquitination and the up-regulation of the core clock protein BMAL1 in the positive limb of the transcription–translation feedback loop.

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Photoperiodic and clock regulation of the vitamin A pathway in the brain mediates seasonal responsiveness in the monarch butterfly

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1913915116 ◽

2019 ◽

Vol 116 (50) ◽

pp. 25214-25221 ◽

Cited By ~ 4

Author(s):

Samantha E. Iiams ◽

Aldrin B. Lugena ◽

Ying Zhang ◽

Ashley N. Hayden ◽

Christine Merlin

Keyword(s):

Vitamin A ◽

Circadian Clock ◽

Environmental Changes ◽

Clock Genes ◽

Monarch Butterfly ◽

Genetic Evidence ◽

Mammalian Brain ◽

Loss Of Function ◽

Photoperiodic Responses ◽

The Brain

Seasonal adaptation to changes in light:dark regimes (i.e., photoperiod) allows organisms living at temperate latitudes to anticipate environmental changes. In nearly all animals studied so far, the circadian system has been implicated in measurement and response to the photoperiod. In insects, genetic evidence further supports the involvement of several clock genes in photoperiodic responses. Yet, the key molecular pathways linking clock genes or the circadian clock to insect photoperiodic responses remain largely unknown. Here, we show that inactivating the clock in the North American monarch butterfly using loss-of-function mutants for the circadian activators CLOCK and BMAL1 and the circadian repressor CRYPTOCHROME 2 abolishes photoperiodic responses in reproductive output. Transcriptomic approaches in the brain of monarchs raised in long and short photoperiods, summer monarchs, and fall migrants revealed a molecular signature of seasonal-specific rhythmic gene expression that included several genes belonging to the vitamin A pathway. We found that the rhythmic expression of these genes was abolished in clock-deficient mutants, suggesting that the vitamin A pathway operates downstream of the circadian clock. Importantly, we showed that a CRISPR/Cas9-mediated loss-of-function mutation in the gene encoding the pathway’s rate-limiting enzyme, ninaB1, abolished photoperiod responsiveness independently of visual function in the compound eye and without affecting circadian rhythms. Together, these results provide genetic evidence that the clock-controlled vitamin A pathway mediates photoperiod responsiveness in an insect. Given previously reported seasonal changes associated with this pathway in the mammalian brain, our findings suggest an evolutionarily conserved function of vitamin A in animal photoperiodism.

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Cross-species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots

10.1101/131185 ◽

2017 ◽

Author(s):

He Huang ◽

Malia A. Gehan ◽

Sarah E. Huss ◽

Sophie Alvarez ◽

Cesar Lizarraga ◽

...

Keyword(s):

Circadian Clock ◽

Clock Genes ◽

Expression Profiles ◽

Affinity Purification ◽

Brachypodium Distachyon ◽

Sequence Divergence ◽

Plant Responses ◽

Crop Species ◽

Physiological Level ◽

High Sequence Divergence

ABSTRACTPlant responses to the environment are shaped by external stimuli and internal signaling pathways. In both the model plant Arabidopsis thaliana and crop species, circadian clock factors have been identified as critical for growth, flowering and circadian rhythms. Outside of A. thaliana, however, little is known about the molecular function of clock genes. Therefore, we sought to compare the function of Brachypodium distachyon and Seteria viridis orthologs of EARLY FLOWERING3, a key clock gene in A. thaliana. To identify both cycling genes and putative ELF3 functional orthologs in S. viridis, a circadian RNA-seq dataset and online query tool (Diel Explorer) was generated as a community resource to explore expression profiles of Setaria genes under constant conditions after photo- or thermo-entrainment. The function of ELF3 orthologs from A. thaliana, B. distachyon, and S. viridis were tested for complementation of an elf3 mutation in A. thaliana. Despite comparably low sequence identity versus AtELF3 (less than 37%), both monocot orthologs were capable of rescuing hypocotyl elongation, flowering time and arrhythmic clock phenotypes. Molecular analysis using affinity purification and mass spectrometry to compare physical interactions also found that BdELF3 and SvELF3 could be integrated into similar complexes and networks as AtELF3, including forming a composite evening complex. Thus, we find that, despite 180 million years of separation, BdELF3 and SvELF3 can functionally complement loss of ELF3 at the molecular and physiological level.One Sentence SummaryOrthologs of a key circadian clock component ELF3 from grasses functionally complement the Arabidopsis counterpart at the molecular and physiological level, in spite of high sequence divergence.

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