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

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.

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

Science ◽  
2008 ◽  
Vol 322 (5909) ◽  
pp. 1832-1835 ◽  
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.

scholarly journals Rhizosphere microbes influence host circadian clock function

2021 ◽  
Author(s):  
Charley Hubbard ◽  
Robby McMinn ◽  
Cynthia Weinig
Keyword(s):  
Arabidopsis Thaliana ◽  
Circadian Clock ◽  
Microbial Communities ◽  
Abiotic Factors ◽  
Circadian Period ◽  
Local Conditions ◽  
Mutant Genotype ◽  
Short Period ◽  
Clock Mutant ◽  
Boechera Stricta

The circadian clock is an important determinant of fitness that is entrained by local conditions. Aside from abiotic factors, individual pathogenic soil bacteria affect circadian clock function in plant hosts. Yet, in nature, plants interact with diverse microbial communities, and the effect of complex communities on clock function remains unclear. In Arabidopsis thaliana and its wild relative, Boechera stricta, we used diverse rhizosphere inoculates and host genotypes to test the effect of complex rhizosphere microbial communities on the host circadian clock. Arabidopsis thaliana plants with an intact rhizosphere microbiome expressed a circadian period closer to 24h in duration and significantly shorter (by 48 minutes on average) relative to plants grown with a disrupted microbiome. Wild-type host genotypes of A. thaliana differed in clock sensitivity to microbes, with one genotype (Landsberg erecta) expressing a 119-minute difference in circadian period length across rhizosphere microbial treatments. A similar pattern of clock sensitivity to soil microbes was observed in B. stricta. Finally, rhizosphere microbes collected from the mutant genotype toc1-21 of A. thaliana with a short-period phenotype and used as inoculate significantly shortened the long-period phenotype of the clock mutant genotype ztl-1. The results indicate that complex rhizosphere microbial communities affect host clock function.

Coxsackievirus B3 infection and PBDE exposure causes organ-specific effects on CYP-gene expression in the mouse

Toxicology ◽  
2007 ◽  
Vol 242 (1-3) ◽  
pp. 91-99 ◽  
Author(s):  
Magnus Lundgren ◽  
Per Ola Darnerud ◽  
Ylva Molin ◽  
Hellmuth Lilienthal ◽  
Jonas Blomberg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Coxsackievirus B3 ◽  
Specific Effects ◽  
Organ Specific

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

2019 ◽  
Author(s):  
Marta I. Terry ◽  
Marta Carrera-Alesina ◽  
Julia Weiss ◽  
Marcos Egea-Cortines
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Gene Structure ◽  
Petunia Hybrida ◽  
Photoperiod Sensitivity ◽  
Response Regulators ◽  
Environmental Signals ◽  
Transcriptional Reprogramming ◽  
Number Of Genes ◽  
Organ Specific

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.

scholarly journals Global View on the Cytokinin Regulatory System in Potato

2020 ◽  
Vol 11 ◽  
Author(s):  
Sergey N. Lomin ◽  
Yulia A. Myakushina ◽  
Oksana O. Kolachevskaya ◽  
Irina A. Getman ◽  
Ekaterina M. Savelieva ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulatory System ◽  
Potato Research ◽  
Tuber Initiation ◽  
Future Directions ◽  
The Core ◽  
Global View ◽  
Transcriptome Database ◽  
Organ Specific ◽  
Potato Tuberization

Cytokinins (CKs) were earlier shown to promote potato tuberization. Our study aimed to identify and characterize CK-related genes which constitute CK regulatory system in the core potato (Solanum tuberosum) genome. For that, CK-related genes were retrieved from the sequenced genome of the S. tuberosum doubled monoploid (DM) Phureja group, classified and compared with Arabidopsis orthologs. Analysis of selected gene expression was performed with a transcriptome database for the S. tuberosum heterozygous diploid line RH89-039-16. Genes responsible for CK signaling, biosynthesis, transport, and metabolism were categorized in an organ-specific fashion. According to this database, CK receptors StHK2/3 predominate in leaves and flowers, StHK4 in roots. Among phosphotransmitters, StHP1a expression largely predominates. Surprisingly, two pseudo-phosphotransmitters intended to suppress CK effects are hardly expressed in studied organs. Among B-type RR genes, StRR1b, StRR11, and StRR18a are actively expressed, with StRR1b expressing most uniformly in all organs and StRR11 exhibiting the highest expression in roots. By cluster analysis four types of prevailing CK-signaling chains were identified in (1) leaves and flowers, StHK2/3→StHP1a→StRR1b/+; (2) shoot apical meristems, stolons, and mature tubers, StHK2/4→StHP1a→StRR1b/+; (3) stems and young tubers, StHK2/4→StHP1a→StRR1b/11/18a; and (4) roots and tuber sprouts, StHK4→StHP1a→StRR11/18a. CK synthesis genes StIPT3/5 and StCYP735A are expressed mainly in roots followed by tuber sprouts, but rather weakly in stolons and tubers. By contrast, CK-activation genes StLOGs are active in stolons, and StLOG3b expression is even stolon-confined. Apparently, the main CK effects on tuber initiation are realized via activity of StLOG1/3a/3b/7c/8a genes in stolons. Current advances and future directions in potato research are discussed.

scholarly journals Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator

Science ◽  
2012 ◽  
Vol 336 (6077) ◽  
pp. 75-79 ◽  
Author(s):  
W. Huang ◽  
P. Pérez-García ◽  
A. Pokhilko ◽  
A. J. Millar ◽  
I. Antoshechkin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Interference ◽  
Circadian Clock ◽  
Network Structure ◽  
The Core

In many organisms, the circadian clock is composed of functionally coupled morning and evening oscillators. In Arabidopsis, oscillator coupling relies on a core loop in which the evening oscillator component TIMING OF CAB EXPRESSION 1 (TOC1) was proposed to activate a subset of morning-expressed oscillator genes. Here, we show that TOC1 does not function as an activator but rather as a general repressor of oscillator gene expression. Repression occurs through TOC1 rhythmic association to the promoters of the oscillator genes. Hormone-dependent induction of TOC1 and analysis of RNA interference plants show that TOC1 prevents the activation of morning-expressed genes at night. Our study overturns the prevailing model of the Arabidopsis circadian clock, showing that the morning and evening oscillator loops are connected through the repressing activity of TOC1.

scholarly journals period-1 encodes an ATP-dependent RNA helicase that influences nutritional compensation of the Neurospora circadian clock

2015 ◽  
Vol 112 (51) ◽  
pp. 15707-15712 ◽  
Author(s):  
Jillian M. Emerson ◽  
Bradley M. Bartholomai ◽  
Carol S. Ringelberg ◽  
Scott E. Baker ◽  
Jennifer J. Loros ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Ribosome Biogenesis ◽  
Sufficient Conditions ◽  
Rna Helicase ◽  
Period Length ◽  
Circadian Oscillator ◽  
Developmental Cycle ◽  
Circadian Period ◽  
The Core ◽  
Long Period

Mutants in the period-1 (prd-1) gene, characterized by a recessive allele, display a reduced growth rate and period lengthening of the developmental cycle controlled by the circadian clock. We refined the genetic location of prd-1 and used whole genome sequencing to find the mutation defining it, confirming the identity of prd-1 by rescuing the mutant circadian phenotype via transformation. PRD-1 is an RNA helicase whose orthologs, DDX5 [DEAD (Asp-Glu-Ala-Asp) Box Helicase 5] and DDX17 in humans and DBP2 (Dead Box Protein 2) in yeast, are implicated in various processes, including transcriptional regulation, elongation, and termination, ribosome biogenesis, and mRNA decay. Although prd-1 mutants display a long period (∼25 h) circadian developmental cycle, they interestingly display a WT period when the core circadian oscillator is tracked using a frq-luciferase transcriptional fusion under conditions of limiting nutritional carbon; the core oscillator in the prd-1 mutant strain runs with a long period under glucose-sufficient conditions. Thus, PRD-1 clearly impacts the circadian oscillator and is not only part of a metabolic oscillator ancillary to the core clock. PRD-1 is an essential protein, and its expression is neither light-regulated nor clock-regulated. However, it is transiently induced by glucose; in the presence of sufficient glucose, PRD-1 is in the nucleus until glucose runs out, which elicits its disappearance from the nucleus. Because circadian period length is carbon concentration-dependent, prd-1 may be formally viewed as a clock mutant with defective nutritional compensation of circadian period length.

scholarly journals Organ-specific NLR resistance gene expression varies with plant symbiotic status

2017 ◽  
Author(s):  
David Munch ◽  
Vikas Gupta ◽  
Asger Bachmann ◽  
Wolfgang Busch ◽  
Simon Kelly ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Plant Species ◽  
Meta Analysis ◽  
Expression Patterns ◽  
Expression Data ◽  
Leucine Rich Repeat ◽  
Root Infection ◽  
Organ Specific ◽  
Specific Receptors

AbstractNucleotide-binding site leucine-rich repeat resistance genes (NLRs) allow plants to detect microbial effectors. We hypothesized that NLR expression patterns would reflect organ-specific differences in effector challenge and tested this by carrying out a meta-analysis of expression data for 1,235 NLRs from 9 plant species. We found stable NLR root/shoot expression ratios within species, suggesting organ-specific hardwiring of NLR expression patterns in anticipation of distinct challenges. Most monocot and dicot plant species preferentially expressed NLRs in roots. In contrast, Brassicaceae species, including oilseed rape and the model plant Arabidopsis thaliana, were unique in showing NLR expression skewed towards the shoot across multiple phylogenetically distinct groups of NLRs. The Brassicaceae NLR expression shift coincides with loss of the endomycorrhization pathway, which enables intracellular root infection by symbionts. We propose that its loss offer two likely explanations for the unusual Brassicaceae NLR expression pattern: loss of NLR-guarded symbiotic components and elimination of constraints on general root defences associated with exempting symbionts from targeting. This hypothesis is consistent with the existence of Brassicaceae-specific receptors for conserved microbial molecules and suggests that Brassicaceae species are rich sources of unique antimicrobial root defences.

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