Molecular and transcriptional structure of the petal and leaf circadian clock in Petunia hybrida

AbstractThe plant circadian clock coordinates environmental signals with internal processes. We characterized the genomic and transcriptomic structure of the Petunia hybrida W115 clock in leaves and petals. We found three levels of evolutionary differences. First, PSEUDO-RESPONSE REGULATORS PhPRR5a, PhPRR5b, PhPRR7a, PhPRR7b, and GIGANTEA PhGI1 and PhGI2, differed in gene structure including exon number and deletions including the CCT domain of the PRR family. Second, leaves showed preferential day expression while petals tended to display night expression. Under continuous dark, most genes were delayed in leaves and petals. Importantly, photoperiod sensitivity of gene expression was tissue specific as TIMING OF CAB EXPRESSION PhNTOC1 was affected in leaves but not in petals, and PhPRR5b, PhPRR7b and the ZEITLUPE ortholog CHANEL, PhCHL, were modified in petals but not leaves. Third, we identified a strong transcriptional noise at different times of the day, and high robustness at dawn in leaves and dusk in petals, coinciding with the coordination of photosynthesis and scent emission. Our results indicate multilayered evolution of the Petunia clock including gene structure, number of genes and transcription patterns. The major transcriptional reprogramming of the clock in petals, with night expression may be involved in controlling scent emission in the dark.HighlightThe petunia leaf circadian clock shows maxima during the day while petal clock does it during the night. Reaction to dark is organ specific.

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The Circadian Clock inArabidopsisRoots Is a Simplified Slave Version of the Clock in Shoots

Science ◽

10.1126/science.1161403 ◽

2008 ◽

Vol 322 (5909) ◽

pp. 1832-1835 ◽

Cited By ~ 156

Author(s):

Allan B. James ◽

José A. Monreal ◽

Gillian A. Nimmo ◽

Ciarán L. Kelly ◽

Pawel Herzyk ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Circadian Clock ◽

Clock Genes ◽

Plant Cells ◽

Feedback Loops ◽

Circadian Oscillator ◽

Inhibit Gene Expression ◽

Organ Specific ◽

Plant Clock

The circadian oscillator in eukaryotes consists of several interlocking feedback loops through which the expression of clock genes is controlled. It is generally assumed that all plant cells contain essentially identical and cell-autonomous multiloop clocks. Here, we show that the circadian clock in the roots of matureArabidopsisplants differs markedly from that in the shoots and that the root clock is synchronized by a photosynthesis-related signal from the shoot. Two of the feedback loops of the plant circadian clock are disengaged in roots, because two key clock components, the transcription factors CCA1 and LHY, are able to inhibit gene expression in shoots but not in roots. Thus, the plant clock is organ-specific but not organ-autonomous.

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Distinct Signaling Pathways from the Circadian Clock Participate in Regulation of Rhythmic Conidiospore Development in Neurospora crassa

Eukaryotic Cell ◽

10.1128/ec.1.2.273-280.2002 ◽

2002 ◽

Vol 1 (2) ◽

pp. 273-280 ◽

Cited By ~ 20

Author(s):

Alejandro Correa ◽

Deborah Bell-Pedersen

Keyword(s):

Gene Expression ◽

Circadian Clock ◽

Neurospora Crassa ◽

Mutant Strain ◽

Specific Gene ◽

Developmentally Regulated ◽

Environmental Signals ◽

Endogenous Clock ◽

Environmental Induction ◽

High Level

ABSTRACT Several different environmental signals can induce asexual spore development (conidiation) and expression of developmentally regulated genes in Neurospora crassa. However, under constant conditions, where no environmental cues for conidiation are present, the endogenous circadian clock in N. crassa promotes daily rhythms in expression of known developmental genes and of conidiation. We anticipated that the same pathway of gene regulation would be followed during clock-controlled conidiation and environmental induction of conidiation and that the circadian clock would need only to control the initial developmental switch. Previous experiments showed that high-level developmental induction of the clock-controlled genes eas (ccg-2) and ccg-1 requires the developmental regulatory proteins FL and ACON-2, respectively, and normal developmental induction of fl mRNA expression requires ACON-2. We demonstrate that the circadian clock regulates rhythmic fl gene expression and that fl rhythmicity requires ACON-2. However, we find that clock regulation of eas (ccg-2) is normal in an fl mutant strain and ccg-1 expression is rhythmic in an acon-2 mutant strain. Together, these data point to the endogenous clock and the environment following separate pathways to regulate conidiation-specific gene expression.

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The hrcA and hspR regulons of Campylobacter jejuni

Microbiology ◽

10.1099/mic.0.031708-0 ◽

2010 ◽

Vol 156 (1) ◽

pp. 158-166 ◽

Cited By ~ 15

Author(s):

Christopher W. Holmes ◽

Charles W. Penn ◽

Peter A. Lund

Keyword(s):

Gene Expression ◽

Heat Shock ◽

Campylobacter Jejuni ◽

Growth Temperature ◽

Heat Shock Response ◽

Human Pathogen ◽

Response Regulators ◽

Heat Shock Genes ◽

Shock Response ◽

Number Of Genes

The human pathogen Campylobacter jejuni has a classic heat shock response, showing induction of chaperones and proteases plus several unidentified proteins in response to a small increase in growth temperature. The genome contains two homologues to known heat shock response regulators, HrcA and HspR. Previous work has shown that HspR controls several heat-shock genes, but the hrcA regulon has not been defined. We have constructed single and double deletions of C. jejuni hrcA and hspR and analysed gene expression using microarrays. Only a small number of genes are controlled by these two regulators, and the two regulons overlap. Strains mutated in hspR, but not those mutated in hrcA, showed enhanced thermotolerance. Some genes previously identified as being downregulated in a strain lacking hspR showed no change in expression in our experiments.

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A Circadian Oscillator in Aspergillus spp. Regulates Daily Development and Gene Expression

Eukaryotic Cell ◽

10.1128/ec.2.2.231-237.2003 ◽

2003 ◽

Vol 2 (2) ◽

pp. 231-237 ◽

Cited By ~ 52

Author(s):

Andrew V. Greene ◽

Nancy Keller ◽

Hubertus Haas ◽

Deborah Bell-Pedersen

Keyword(s):

Gene Expression ◽

Circadian Rhythms ◽

Circadian Clock ◽

Neurospora Crassa ◽

Aspergillus Nidulans ◽

Aspergillus Flavus ◽

Environmental Conditions ◽

Environmental Signals ◽

Molecular Assays ◽

Free Running

ABSTRACT We have established the presence of a circadian clock in Aspergillus flavus and Aspergillus nidulans by morphological and molecular assays, respectively. In A. flavus, the clock regulates an easily assayable rhythm in the development of sclerotia, which are large survival structures produced by many fungi. This developmental rhythm exhibits all of the principal clock properties. The rhythm is maintained in constant environmental conditions with a period of 33 h at 30°C, it can be entrained by environmental signals, and it is temperature compensated. This endogenous 33-h period is one of the longest natural circadian rhythms reported for any organism, and this likely contributes to some unique responses of the clock to environmental signals. In A. nidulans, no obvious rhythms in development are apparent. However, a free running and entrainable rhythm in the accumulation of gpdA mRNA (encoding glyceraldehyde-3-phosphate dehydrogenase) is observed, suggesting the presence of a circadian clock in this species. We are unable to identify an Aspergillus ortholog of frequency, a gene required for normal circadian rhythmicity in Neurospora crassa. Together, our data indicate the existence of an Aspergillus circadian clock, which has properties that differ from that of the well-described clock of N. crassa.

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Cross-talk and regulatory interactions between the essential response regulator RpaB and cyanobacterial circadian clock output

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1424632112 ◽

2015 ◽

Vol 112 (7) ◽

pp. 2198-2203 ◽

Cited By ~ 35

Author(s):

Javier Espinosa ◽

Joseph S. Boyd ◽

Raquel Cantos ◽

Paloma Salinas ◽

Susan S. Golden ◽

...

Keyword(s):

Gene Expression ◽

Circadian Clock ◽

Cross Talk ◽

Molecular Mechanisms ◽

Target Genes ◽

Response Regulator ◽

Control Of Gene Expression ◽

Environmental Signals ◽

Regulatory Interactions ◽

Intracellular Signals

The response regulator RpaB (regulator of phycobilisome associated B), part of an essential two-component system conserved in cyanobacteria that responds to multiple environmental signals, has recently been implicated in the control of cell dimensions and of circadian rhythms of gene expression in the model cyanobacteriumSynechococcus elongatusPCC 7942. However, little is known of the molecular mechanisms that underlie RpaB functions. In this study we show that the regulation of phenotypes by RpaB is intimately connected with the activity of RpaA (regulator of phycobilisome associated A), the master regulator of circadian transcription patterns. RpaB affects RpaA activity both through control of gene expression, a function requiring an intact effector domain, and via altering RpaA phosphorylation, a function mediated through the N-terminal receiver domain of RpaB. Thus, both phosphorylation cross-talk and coregulation of target genes play a role in the genetic interactions between the RpaA and RpaB pathways. In addition, RpaB∼P levels appear critical for survival under light:dark cycles, conditions in which RpaB phosphorylation is environmentally driven independent of the circadian clock. We propose that the complex regulatory interactions between the essential and environmentally sensitive NblS-RpaB system and the SasA-RpaA clock output system integrate relevant extra- and intracellular signals to the circadian clock.

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Age-related Gene Expression Signatures (AGES) in rats demonstrate early, late, and linear transcriptional changes from multiple tissues

10.1101/717835 ◽

2019 ◽

Author(s):

Tea Shavlakadze ◽

Melody Morris ◽

Jian Fang ◽

Sharon X. Wang ◽

Weihua Zhou ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Signature ◽

Chronological Age ◽

Related Gene ◽

Age Related ◽

Number Of Genes ◽

Organ Specific ◽

Transcriptional Changes ◽

Effects Of Aging ◽

Early Late

SUMMARYIn order to understand changes in gene expression that occur as a result of age, which might create a permissive or causal environment for age-related diseases, we produced a multi-timepoint Age-related Gene Expression Signature (AGES) from liver, kidney, skeletal muscle and hippocampus of rats, comparing 6, 9, 12, 18, 21, 24 and 27-month old animals. We focused on genes that changed in one direction throughout the lifespan of the animal, either early in life (early logistic changes); at mid-age (mid-logistic); late in life (late-logistic); or linearly, throughout the lifespan. The pathways perturbed as a result of chronological age demonstrate organ-specific and more global effects of aging, and point to mechanisms that might be counter-regulated pharmacologically in order to treat age-associated diseases. A small number of genes were regulated by aging in the same manner in every tissue, suggesting they may be more universal markers of aging.

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Arabidopsis thaliana PRR7 Provides Circadian Input to the CCA1 Promoter in Shoots but not Roots

Frontiers in Plant Science ◽

10.3389/fpls.2021.750367 ◽

2021 ◽

Vol 12 ◽

Author(s):

Hugh G. Nimmo ◽

Janet Laird

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Circadian Clock ◽

Constant Light ◽

Circadian Period ◽

The Core ◽

Specific Effects ◽

Organ Specific

The core of the plant circadian clock involves multiple interlocking gene expression loops and post-translational controls along with inputs from light and metabolism. The complexity of the interactions is such that few specific functions can be ascribed to single components. In previous work, we reported differences in the operation of the clocks in Arabidopsis shoots and roots, including the effects of mutations of key clock components. Here, we have used luciferase imaging to study prr7 mutants expressing CCA1::LUC and GI::LUC markers. In mature shoots expressing CCA1::LUC, loss of PRR7 radically altered behaviour in light:dark cycles and caused loss of rhythmicity in constant light but had little effect on roots. In contrast, in mature plants expressing GI::LUC, loss of PRR7 had little effect in light:dark cycles but in constant light increased the circadian period in shoots and reduced it in roots. We conclude that most or all of the circadian input to the CCA1 promoter in shoots is mediated by PRR7 and that loss of PRR7 has organ-specific effects. The results emphasise the differences in operation of the shoot and root clocks, and the importance of studying clock mutants in both light:dark cycles and constant light.

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