scholarly journals The Transcriptional Network in the Arabidopsis Circadian Clock System

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1284
Author(s):  
Norihito Nakamichi
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Circadian Clock ◽  
Feedback Loop ◽  
Target Genes ◽  
Transcriptional Network ◽  
Transcriptional Repressors ◽  
Clock System ◽  
Molecular Studies ◽  
Key Genes

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.

Evolution Analysis of the Circadian Clock Protein KaiB

2013 ◽  
Vol 647 ◽  
pp. 391-395
Author(s):  
Liu Sen ◽  
Song Liu
Keyword(s):  
Circadian Rhythms ◽  
Circadian Clock ◽  
Feedback Loop ◽  
Circadian System ◽  
Circadian Rhythmicity ◽  
Physiological Functions ◽  
Clock System ◽  
Evolution Analysis ◽  
Clock Protein

Regulation of daily physiological functions with approximate a 24-hour periodicity, or circadian rhythms, is a characteristic of eukaryotes. So far, cyanobacteria are only known prokaryotes reported to possess circadian rhythmicity. The circadian system in cyanobacteria comprises both a post-translational oscillator (PTO) and a transcriptional/translational feedback loop (TTFL). The PTO can be reconstituted in vitro with three purified proteins (KaiA, KaiB, and KaiC) with the existence of ATP. Phase of the nanoclockwork has been associated with the phosphorylation states of KaiC, with KaiA promoting the phosphorylation of KaiC, and KaiB de-phosphorylating KaiC. Here we studied the evolution of the KaiB protein. The result will be helpful in understanding the evolution of the circadian clock system.

scholarly journals A Global Search for novel Transcription Factors impacting the Neurospora crassa Circadian Clock

2021 ◽  
Author(s):  
Felipe Muñoz-Guzmán ◽  
Valeria Caballero ◽  
Luis F Larrondo
Keyword(s):  
Transcription Factors ◽  
Circadian Clock ◽  
Neurospora Crassa ◽  
Feedback Loop ◽  
Transcriptional Regulators ◽  
Positive Element ◽  
Reverse Genetic ◽  
Circadian Oscillators ◽  
Reverse Genetic Screen ◽  
Level Of Analysis

Abstract Eukaryotic circadian oscillators share a common circuit architecture, a negative feedback loop in which a positive element activates the transcription of a negative one that then represses the action of the former, inhibiting its own expression. While studies in mammals and insects have revealed additional transcriptional inputs modulating the expression of core clock components, this has been less characterized in the model Neurospora crassa, where the participation of other transcriptional components impacting circadian clock dynamics remains rather unexplored. Thus, we sought to identify additional transcriptional regulators modulating the N. crassa clock, following a reverse genetic screen based on luminescent circadian reporters and a collection of transcription factors knockouts, successfully covering close to 60% of them. Besides the canonical core clock components WC-1 and WC-2, none of the tested transcriptional regulators proved to be essential for rhythmicity. Nevertheless, we identified a set of 23 transcription factors that when absent lead to discrete, but significant, changes in circadian period. While the current level of analysis does not provide mechanistic information about how these new players modulate circadian parameters, the results of this screen reveal that an important number of light and clock-regulated transcription factors, involved in a plethora of processes, are capable of modulating the clockworks. This partial reverse genetic clock screen also exemplifies how the N. crassa knockout collection continues to serve as an expedite platform to address broad biological questions.

scholarly journals Synthetic hormone-responsive transcription factors can monitor and re-program plant development

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Arjun Khakhar ◽  
Alexander R Leydon ◽  
Andrew C Lemmex ◽  
Eric Klavins ◽  
Jennifer L Nemhauser
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Mathematical Models ◽  
Plant Development ◽  
Target Genes ◽  
Plant Morphology ◽  
Shoot Branching ◽  
Exogenous Hormone ◽  
Induced Expression ◽  
Auxin Transporter

Developmental programs sculpt plant morphology to meet environmental challenges, and these same programs have been manipulated to increase agricultural productivity (Doebley et al., 1997; Khush, 2001). Hormones coordinate these programs, creating chemical circuitry (Vanstraelen and Benková, 2012) that has been represented in mathematical models (Refahi et al., 2016; Prusinkiewicz et al., 2009); however, model-guided engineering of plant morphology has been limited by a lack of tools (Parry et al., 2009; Voytas and Gao, 2014). Here, we introduce a novel set of synthetic and modular hormone activated Cas9-based repressors (HACRs) in Arabidopsis thaliana that respond to three hormones: auxin, gibberellins and jasmonates. We demonstrate that HACRs are sensitive to both exogenous hormone treatments and local differences in endogenous hormone levels associated with development. We further show that this capability can be leveraged to reprogram development in an agriculturally relevant manner by changing how the hormonal circuitry regulates target genes. By deploying a HACR to re-parameterize the auxin-induced expression of the auxin transporter PIN-FORMED1 (PIN1), we decreased shoot branching and phyllotactic noise, as predicted by existing models (Refahi et al., 2016; Prusinkiewicz et al., 2009).

scholarly journals Cross-Species Root Transcriptional Network Analysis Highlights Conserved Modules in Response to Nitrate between Maize and Sorghum

2020 ◽  
Vol 21 (4) ◽  
pp. 1445
Author(s):  
Hongyang Du ◽  
Lihua Ning ◽  
Bing He ◽  
Yuancong Wang ◽  
Min Ge ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Network Analysis ◽  
Target Genes ◽  
Affinity Purification ◽  
Hormone Signaling ◽  
Transcriptional Repressors ◽  
Nutrient Metabolism ◽  
Available Nitrogen ◽  
Genetic Mechanisms ◽  
Root Morphogenesis

Plants have evolved complex mechanisms to respond to the fluctuation of available nitrogen (N) in soil, but the genetic mechanisms underlying the N response in crops are not well-documented. In this study, we generated a time series of NO3−-mediated transcriptional profiles in roots of maize and sorghum, respectively. Using weighted gene co-expression network analysis, we identified modules of co-expressed genes that related to NO3− treatments. A cross-species comparison revealed 22 conserved modules, of which four were related to hormone signaling, suggesting that hormones participate in the early nitrate response. Three other modules are composed of genes that are mainly upregulated by NO3− and involved in nitrogen and carbohydrate metabolism, including NRT, NIR, NIA, FNR, and G6PD2. Two G2-like transcription factors (ZmNIGT1 and SbNIGT1), induced by NO3− stimulation, were identified as hub transcription factors (TFs) in the modules. Transient assays demonstrated that ZmNIGT1 and SbNIGT1 are transcriptional repressors. We identified the target genes of ZmNIGT1 by DNA affinity-purification sequencing (DAP-Seq) and found that they were significantly enriched in catalytic activity, including carbon, nitrogen, and other nutrient metabolism. A set of ZmNIGT1 targets encode transcription factors (ERF, ARF, and AGL) that are involved in hormone signaling and root development. We propose that ZmNIGT1 and SbNIGT1 are negative regulators of nitrate responses that play an important role in optimizing nutrition metabolism and root morphogenesis. Together with conserved N responsive modules, our study indicated that, to encounter N variation in soil, maize and sorghum have evolved an NO3−-regulatory network containing a set of conserved modules and transcription factors.

scholarly journals TCP Transcription Factors Link the Regulation of Genes Encoding Mitochondrial Proteins with the Circadian Clock in Arabidopsis thaliana

2010 ◽  
Vol 22 (12) ◽  
pp. 3921-3934 ◽  
Author(s):  
Estelle Giraud ◽  
Sophia Ng ◽  
Chris Carrie ◽  
Owen Duncan ◽  
Jasmine Low ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Circadian Clock ◽  
Mitochondrial Proteins ◽  
Genes Encoding

A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana

2011 ◽  
Vol 65 (4) ◽  
pp. 634-646 ◽  
Author(s):  
Xiaofei Yu ◽  
Lei Li ◽  
Jaroslaw Zola ◽  
Maneesha Aluru ◽  
Huaxun Ye ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Target Genes ◽  
Transcriptional Network ◽  
Genome Wide

scholarly journals Casein kinase 1 family regulates PRR5 and TOC1 in the Arabidopsis circadian clock

2019 ◽  
Vol 116 (23) ◽  
pp. 11528-11536 ◽  
Author(s):  
Takahiro N. Uehara ◽  
Yoshiyuki Mizutani ◽  
Keiko Kuwata ◽  
Tsuyoshi Hirota ◽  
Ayato Sato ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Posttranslational Modifications ◽  
Posttranslational Modification ◽  
Target Genes ◽  
Casein Kinase ◽  
Transcriptional Repressors ◽  
Circadian Period ◽  
Casein Kinase 1 ◽  
Chemical Screening ◽  
Plant Clock

The circadian clock provides organisms with the ability to adapt to daily and seasonal cycles. Eukaryotic clocks mostly rely on lineage-specific transcriptional-translational feedback loops (TTFLs). Posttranslational modifications are also crucial for clock functions in fungi and animals, but the posttranslational modifications that affect the plant clock are less understood. Here, using chemical biology strategies, we show that the Arabidopsis CASEIN KINASE 1 LIKE (CKL) family is involved in posttranslational modification in the plant clock. Chemical screening demonstrated that an animal CDC7/CDK9 inhibitor, PHA767491, lengthens the Arabidopsis circadian period. Affinity proteomics using a chemical probe revealed that PHA767491 binds to and inhibits multiple CKL proteins, rather than CDC7/CDK9 homologs. Simultaneous knockdown of Arabidopsis CKL-encoding genes lengthened the circadian period. CKL4 phosphorylated transcriptional repressors PSEUDO-RESPONSE REGULATOR 5 (PRR5) and TIMING OF CAB EXPRESSION 1 (TOC1) in the TTFL. PHA767491 treatment resulted in accumulation of PRR5 and TOC1, accompanied by decreasing expression of PRR5- and TOC1-target genes. A prr5 toc1 double mutant was hyposensitive to PHA767491-induced period lengthening. Together, our results reveal posttranslational modification of transcriptional repressors in plant clock TTFL by CK1 family proteins, which also modulate nonplant circadian clocks.

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