A Night-Time Edge Site Intermediate in the Cyanobacterial Circadian Clock Identified by EPR Spectroscopy

Abstract Background In soybean, some circadian clock genes have been identified as loci for maturity traits. However, the effects of these genes on soybean circadian rhythmicity and their impacts on maturity are unclear. Results We used two geographically, phenotypically and genetically distinct cultivars, conventional juvenile Zhonghuang 24 (with functional J/GmELF3a, a homolog of the circadian clock indispensable component EARLY FLOWERING 3) and long juvenile Huaxia 3 (with dysfunctional j/Gmelf3a) to dissect the soybean circadian clock with time-series transcriptomal RNA-Seq analysis of unifoliate leaves on a day scale. The results showed that several known circadian clock components, including RVE1, GI, LUX and TOC1, phase differently in soybean than in Arabidopsis, demonstrating that the soybean circadian clock is obviously different from the canonical model in Arabidopsis. In contrast to the observation that ELF3 dysfunction results in clock arrhythmia in Arabidopsis, the circadian clock is conserved in soybean regardless of the functional status of J/GmELF3a. Soybean exhibits a circadian rhythmicity in both gene expression and alternative splicing. Genes can be grouped into six clusters, C1-C6, with different expression profiles. Many more genes are grouped into the night clusters (C4-C6) than in the day cluster (C2), showing that night is essential for gene expression and regulation. Moreover, soybean chromosomes are activated with a circadian rhythmicity, indicating that high-order chromosome structure might impact circadian rhythmicity. Interestingly, night time points were clustered in one group, while day time points were separated into two groups, morning and afternoon, demonstrating that morning and afternoon are representative of different environments for soybean growth and development. However, no genes were consistently differentially expressed over different time-points, indicating that it is necessary to perform a circadian rhythmicity analysis to more thoroughly dissect the function of a gene. Moreover, the analysis of the circadian rhythmicity of the GmFT family showed that GmELF3a might phase- and amplitude-modulate the GmFT family to regulate the juvenility and maturity traits of soybean. Conclusions These results and the resultant RNA-seq data should be helpful in understanding the soybean circadian clock and elucidating the connection between the circadian clock and soybean maturity.

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The plant circadian clock influences rhizosphere community structure and function

10.1101/158576 ◽

2017 ◽

Cited By ~ 1

Author(s):

Charley J. Hubbard ◽

Marcus T. Brock ◽

Linda T.A. van Diepen ◽

Loïs Maignien ◽

Brent E. Ewers ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Circadian Clock ◽

Structure And Function ◽

Plant Performance ◽

Wild Type ◽

Night Time ◽

History Of ◽

And Function ◽

Rhizosphere Community

AbstractPlants alter chemical and physical properties of soil, and thereby influence rhizosphere microbial community structure. The structure of microbial communities may in turn affect plant performance. Yet, outside of simple systems with pairwise interacting partners, the plant genetic pathways that influence microbial community structure remain largely unknown, as are the performance feedbacks of microbial communities selected by the host plant genotype. We investigated the role of the plant circadian clock in shaping rhizosphere community structure and function. We performed 16S rRNA gene sequencing to characterize rhizosphere bacterial communities of Arabidopsis thaliana between day and night time points, and tested for differences in community structure between wild-type (Ws) vs. clock mutant (toc1-21, ztl-30) genotypes. We then characterized microbial community function, by growing wild-type plants in soils with an overstory history of Ws, toc1-21 or ztl-30 and measuring plant performance. We observed that rhizosphere community structure varied between day and night time points, and clock misfunction significantly altered rhizosphere communities. Finally, wild-type plants germinated earlier and were larger when inoculated with soils having an overstory history of wild-type in comparison to clock mutant genotypes. Our findings suggest the circadian clock of the plant host influences rhizosphere community structure and function.

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Abstract 130: Modulation of Salt and Mineralocorticoid Sensitivity of Blood Pressure by the Circadian Clock Protein Per1

Hypertension ◽

10.1161/hyp.68.suppl_1.130 ◽

2016 ◽

Vol 68 (suppl_1) ◽

Author(s):

Kristen Solocinski ◽

Xuerong Wen ◽

Kit-Yan Cheng ◽

Jeanette Lynch ◽

Brian D Cain ◽

...

Keyword(s):

Blood Pressure ◽

Circadian Clock ◽

Clock Gene ◽

Salt Intake ◽

Disease Risk ◽

Male Mice ◽

Night Time ◽

Increased Risk ◽

Time Map ◽

Clock Protein

The circadian clock is important for maintaining rhythms in physiological functions including blood pressure (BP). Circadian disruption leads to increased disease risk. The clock has also been implicated in the maintenance of a normal dip in BP at night. In humans, non-dipping (night/day difference in BP<10%) is associated with an increased risk of cardiovascular and kidney disease. Dipping status can also be affected by salt intake and by hormones such as the mineralocorticoid aldosterone. The goal of this study was to determine the effects of a high salt (HS, 4% NaCl) diet plus mineralocorticoid (deoxycorticosterone pivalate (DOCP)) on BP regulation by the circadian clock protein Per1 in C57BL/6J mice. BP was monitored in conscious, unrestrained male mice by radiotelemetry and values are reported as mean arterial pressure (MAP) ± SEM. Under control conditions, MAP in male WT mice was 112.5 ± 1.08 mmHg during the night when mice are active and decreased to 102.1 ± 1.7 mmHg during the day, a “dip” in MAP of 9.2 ± 1.3%. Similarly, Per1 KO mice dip 14 ± 1.4%, with night time MAP of 119.8 ± .9 mmHg which decreased to 103 ± 1.4 mmHg during the day. On HS/DOCP, WT mice MAP decreased from 114.5 ± 1.1 mmHg to 101.5 ± 1.92 mmHg (night indicated by shaded bars in figure). This 11.4 ± 1.9% dip in WT mice was not significantly different from what was observed under control conditions. In contrast, Per1 KO mice display a significantly attenuated dip of 5.7 ± 1.4% with night time MAP of 125.3 ± 1.5 mmHg dropping to 118.1 ± 1 mmHg during the inactive day period (p<0.05). Thus, HS/DOCP treatment in Per1 KO mice leads to non-dipping hypertension. This is the first report of this phenotype in a single clock gene KO.

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Faculty Opinions recommendation of Ambient temperature signal feeds into the circadian clock transcriptional circuitry through the EC night-time repressor in Arabidopsis thaliana.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718267558.793493660 ◽

2014 ◽

Author(s):

Stacey Harmer

Keyword(s):

Arabidopsis Thaliana ◽

Ambient Temperature ◽

Circadian Clock ◽

Night Time ◽

Temperature Signal

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Temperature but not the circadian clock determines nocturnal carbohydrate availability for growth in cereals

10.1101/363218 ◽

2018 ◽

Cited By ~ 3

Author(s):

Lukas M. Müller ◽

Leonard Gol ◽

Jong-Seong Jeon ◽

Andreas P.M. Weber ◽

Seth J. Davis ◽

...

Keyword(s):

Circadian Clock ◽

Vegetative Growth ◽

Degradation Rate ◽

Crop Improvement ◽

External Factors ◽

Cereal Crops ◽

Starch Degradation ◽

Night Time ◽

Carbohydrate Source ◽

Carbohydrate Availability

AbstractThe circadian clock is considered a key target for crop improvement because it controls metabolism and growth in Arabidopsis. Here, we show that the clock gene EARLY FLOWERING 3 (ELF3) controls vegetative growth in Arabidopsis but not in the cereal crop barley. Growth in Arabidopsis is determined by the degradation of leaf starch reserves at night, which is controlled by ELF3. The vegetative growth of barley, however, is determined by the depletion of leaf sucrose stores through an exponential kinetics, presumably catalyzed by the vacuolar sucrose exporter SUCROSE TRANSPORTER 2 (SUT2). This process depends on the sucrose content and the nighttime temperature but not on ELF3. The regulation of starch degradation and sucrose depletion in barley ensures efficient growth at favorable temperature as stores become exhausted at dawn. On cool nights, however, only the starch degradation rate is compensated against low nighttime temperatures, whereas the sucrose depletion rate is reduced. This coincides with reduced biomass in barley but not in Arabidopsis after growth in consecutive cool nights. The sucrose depletion metabolism determines growth in the cereal crops barley, wheat, and rice but is not generally conserved in monocot species and is not a domestication-related trait. Therefore, the control of growth by endogenous (clock) versus external factors (temperature) is species-specific and depends on the predominant carbohydrate store. Our results give new insights into the physiology of growth in cereals and provide a basis for studying the genetics and evolution of different carbohydrate stores and their contribution to plant productivity and adaptation.Significance StatementThe circadian clock controls growth in the model plant Arabidopsis thaliana by regulating the starch degradation rate so that reserves last until dawn. This prevents nocturnal starvation until photosynthesis resumes. The cereal crops barley, wheat and rice, however, predominantly consume sucrose instead of starch as carbohydrate source. We find that carbohydrate supply from sucrose at night is regulated by enzyme kinetics and night-time temperature, but not the circadian clock. We postulate that the regulation of growth depends on the predominant carbohydrate store, where starch degradation is controlled by endogenous cues (clock) and sucrose depletion by external factors (temperature). These differences in the regulation of carbohydrate availability at night may have important implications for adapting crops yields to climate change.

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The day/night difference in the circadian clock’s response to acute lipopolysaccharide and the rhythmic Stat3 expression in the rat suprachiasmatic nucleus

10.1101/342568 ◽

2018 ◽

Author(s):

Simona Moravcová ◽

Dominika Pačesová ◽

Barbora Melkes ◽

Hana Kyclerová ◽

Veronika Spišská ◽

...

Keyword(s):

Locomotor Activity ◽

Circadian Clock ◽

Suprachiasmatic Nucleus ◽

Clock Genes ◽

Activity Patterns ◽

Night Time ◽

Male Wistar Rats ◽

And Function ◽

External Signals

AbstractThe circadian clock in the suprachiasmatic nucleus (SCN) regulates daily rhythms in physiology and behaviour and is an important part of the mammalian homeostatic system. Previously, we have shown that systemic inflammatory stimulation with lipopolysaccharide (LPS) induced the daytime-dependent phosphorylation of STAT3 in the SCN. Here, we demonstrate the LPS-induced Stat3 mRNA expression in the SCN and show also the circadian rhythm in Stat3 expression in the SCN, with high levels during the day. Moreover, we examined the effects of LPS (1mg/kg), applied either during the day or the night, on the rhythm in locomotor activity of male Wistar rats. We observed that recovery of normal locomotor activity patterns took longer when the animals were injected during the night. The clock genes Per1, Per2 and Nr1d1, and phosphorylation of kinases ERK1/2 and GSK3β are sensitive to external cues and function as the molecular entry for external signals into the circadian clockwork. We also studied the immediate changes in these clock genes expressions and the phosphorylation of ERK1/2 and GSK3β in the suprachiasmatic nucleus in response to daytime or night-time inflammatory stimulation. We revealed mild and transient changes with respect to the controls. Our data stress the role of STAT3 in the circadian clock response to the LPS and provide further evidence of the interaction between the circadian clock and immune system.

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Ambient Temperature Signal Feeds into the Circadian Clock Transcriptional Circuitry Through the EC Night-Time Repressor in Arabidopsis thaliana

Plant and Cell Physiology ◽

10.1093/pcp/pcu030 ◽

2014 ◽

Vol 55 (5) ◽

pp. 958-976 ◽

Cited By ~ 90

Author(s):

Takeshi Mizuno ◽

Yuji Nomoto ◽

Haruka Oka ◽

Miki Kitayama ◽

Aya Takeuchi ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Ambient Temperature ◽

Circadian Clock ◽

Night Time ◽

Temperature Signal

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Insight into a Physiological Role for the EC Night-Time Repressor in the Arabidopsis Circadian Clock

Plant and Cell Physiology ◽

10.1093/pcp/pcv094 ◽

2015 ◽

Vol 56 (9) ◽

pp. 1738-1747 ◽

Cited By ~ 10

Author(s):

Takeshi Mizuno ◽

Miki Kitayama ◽

Chieko Takayama ◽

Takafumi Yamashino

Keyword(s):

Circadian Clock ◽

Physiological Role ◽

Night Time ◽

Insight Into

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Speed breeding: a space inspired technology.

CAB Reviews Perspectives in Agriculture Veterinary Science Nutrition and Natural Resources ◽

10.1079/pavsnnr202116004 ◽

2021 ◽

Vol 16 (004) ◽

Author(s):

Mohanlal Vijaya Amalraj

Keyword(s):

Circadian Clock ◽

Clock Genes ◽

Functional Expression ◽

Space Mission ◽

Wheat Crop ◽

Breeding Cycle ◽

Night Time ◽

Short Period ◽

Rapid Generation ◽

Crop Research

Abstract Speed breeding technology reduces the breeding cycle and fastens crop research by producing many generations within a short period of time. In this technology, plants are exposed to an extended light and reduced night time for rapid generation advancement. For instance, wheat crop can be cultivated for 2-3 generations per year under normal glass house conditions but employing speed breeding, it can be cultivated up to 6 generations per year. Speed breeding approach is inspired by NASA experiments conducted on a space mission where wheat crops were grown inside small chambers exposed to a continuous source of light. The basic principal underlying this technique is optimization of photosynthetic activity to promote rapid growth of crops, whereas the extended photoperiod with a short dark period supports functional expression of circadian clock genes. The circadian clock coordinates the biological processes with changing external environment and acts as an internal timekeeper. Under controlled environment of growth chambers, speed breeding can accelerate plant development phase which will be useful for variety development and crop research purposes including phenotyping, mutant studies and transformation. In the process of variety development, conventional breeding approaches take 7-10 years for crossing and inbreeding to develop genetically stable lines, while speed breeding takes only 2 years for crossing and inbreeding. Moreover, this technology can speed up genomic selection and can be integrated with other advanced techniques like genome editing and high throughput genotyping.

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Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA

10.1101/283812 ◽

2018 ◽

Cited By ~ 1

Author(s):

David G. Welkie ◽

Benjamin E. Rubin ◽

Yong-Gang Chang ◽

Spencer Diamond ◽

Scott A. Rifkin ◽

...

Keyword(s):

Circadian Clock ◽

Environmental Changes ◽

Time Of Day ◽

Negative Regulator ◽

Starvation Period ◽

Night Time ◽

Photosynthetic Organisms ◽

Genetic Components ◽

Clock Protein

AbstractThe recurrent pattern of light and darkness generated by Earth’s axial rotation has profoundly influenced the evolution of organisms, selecting for both biological mechanisms that respond acutely to environmental changes and circadian clocks that program physiology in anticipation of daily variations. The necessity to integrate environmental responsiveness and circadian programming is exemplified in photosynthetic organisms such as cyanobacteria, which depend on light-driven photochemical processes. The cyanobacterium Synechococcus elongatus PCC 7942 is an excellent model system for dissecting these entwined mechanisms. Its core circadian oscillator, consisting of three proteins KaiA, KaiB, and KaiC, transmits time-of-day signals to clock-output proteins, which reciprocally regulate global transcription. Research performed under constant light facilitates analysis of intrinsic cycles separately from direct environmental responses, but does not provide insight into how these regulatory systems are integrated during light-dark cycles. Thus, we sought to identify genes that are specifically necessary in a day-night environment. We screened a dense bar-coded transposon library in both continuous light and daily cycling conditions and compared the fitness consequences of loss of each nonessential gene in the genome. Although the clock itself is not essential for viability in light-dark cycles, the most detrimental mutations revealed by the screen were those that disrupt KaiA. The screen broadened our understanding of light-dark survival in photosynthetic organisms, identified unforeseen clock-protein interaction dynamics, and reinforced the role of the clock as a negative regulator of a night-time metabolic program that is essential for S. elongatus to survive in the dark.SignificanceUnderstanding how photosynthetic bacteria respond to and anticipate natural light–dark cycles is necessary for predictive modeling, bioengineering, and elucidating metabolic strategies for diurnal growth. Here, we identify the genetic components that are important specifically under light-dark cycling conditions and determine how a properly functioning circadian clock prepares metabolism for darkness, a starvation period for photoautotrophs. This study establishes that the core circadian clock protein KaiA is necessary to enable rhythmic de-repression of a night-time circadian program.

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