Week 6 Flashcards
What environmental conditons vary over 24 hours?
Temperature
Light intensity
Humidity
Predator behaviour
What is the example of extreme day-night temperature change?
57 degrees c
Montana, 1972 -48 to 9
What is a more typical day-night fluctuation?
10 degrees celcius each day (seen in central japan)
What is the mechanism for circadian clocks?
Biological oscillators with a rough 24 hour period
What did they find when the kept mice in constant darkness?
Continous darkness rhythms persist but with a 23 hour period
Most wheel running at night
When was the circadian rhythm first discorvered in plants?
1729 by Jean-Jacques d’Ortous de Mairan in Mimosa pudica
What is the stages of time course analysis?
First plant is grown in cycles of light and dark (this can be drawn in a graph with light and time on x axis and biological process on the y)
What happens to a plant grown in light and dark cycles when moved into continous light?
In constant light and temperature conditions the circadian rhythm will form whats called a ‘free run’
What is ‘free run’?
Circadian rhythm continous but elevated graph ie still running but with a peak and trough
The period that would have been night is subjective night
The period that would have been day is subjective day
What is a period?
Time to complete one full cycle
What is a phase?
The time at which a particular point of cycle occurs (e.g peak)
What is the amplitude?
The displacement of the oscillation from the centre point
What is the advantage of a functioning circadian clock?
Plants with functioning circadian clock grow larger
What plant activities are controlled by the circadian clocks?
In Arabidopsis thaliana around 30% of genes oscillates with a 24 period
Stomatal opening and closing are under the controle of the circadian oscillator
Hypocotyl elongation is clock controlled
Photoperiod is one of the environmental factors controlling flowering
In competition experiments what are the benefits of functioning circadian clock?
Higher:
Survivial
Biomass (dry and fresh rate)
Chlorophyll content
What was the experiement and result of changing the circadian cock period?
toc1-2 (20 hour day) ztl-27 (28 hour day)
toc1-2 was bigger in the 20 hour day compared to other plant and the same plant in the 28 hour day
ztl-27 was bigger in the 28 hour day compared to other plant and the same plant in the 20 hour day
What is the circadian oscillator?
Generate a rhythm with a ~24 hour period within the cell
What is the entrainment pathways?
Synchronise the oscillator with the external time of day so that the clock stays accurate
What is the output pathway?
Communicate temporal information form the oscillator to other parts of the cell
What is the circadian gating?
Adjust the sensitivity of entrainment and output pathways depending on the time of day
What is the pathway of the circadian system of plants?
Envrironemental inputs –> Entrainment pathways –> Circadian oscillator –> Output pathways –> Rhythms in transctiption, physiology and biochemistry
What is the system that oscillates for the circadian clock?
Transcription-translation feedback loop
What is the rough transcription-translation feedback loop?
Protein encoded by Gene A activates Gene B
Protein encoded by Gene B supresses Gene A
What are the key points of a simple biological oscillator?
Reciprocal feedback loop
Negative feedback step
Speed of biochemical reaction adds a rate constant
Who were the scientist who identify the genes forming the circadian clock?
Prof Steve Kay FRS (Uni of Southurn California)
Prof Andrew Millar FRS (Uni of Edinburgh)
What is the first step in identify genes forming circadian clock?
Made a transgenic Arabidopsis expressing a promoter-luciferase reporter for a circadian regulated gene
(CAB2 promoter, chlorphyll A/B binding protein2)
Just need to measure bioluminescence controlled by CAB2 promoter
What is the second step in identify genes forming circadian clock?
Mutagenise enormous number of seeds of CAB2:Luciferase transgenic plants, and screened the mutant population for changes in the circadian rhythm of CAB2:LUCIFERASE
(Some mutations fall within genes forming parts of the circadian clock, so disrupting the rhythm of CAB2:LUCIFERASE)
What was the early model for the functioning of the circadian clock in Arabidopsis?
Oscillator with acitvation with supression feedback
Main genes involved TOC1, LHY and CCA1
Why is the early model for circadian clock in Arabidopsis out of date?
TOC1 supresses CCA1, though this is a good example of oscillator structure
What is reciprocal repression between CCA1 and TOC1 at the core of the circadian clock?
Overexpression of CCA1 supresses circadian oscillation of TOC1 (CCA1 and LHY bind to the promoter of TOC1)
Overexpression of TOC1 supresses circadian oscillation of CCA1 (The CCT domain of TOC1 is required for it to bind the CCA1 promoter)
What are the two major loops in the circadian clocks?
Morning loops and Evening complex
What do Network modles indicate?
Connections between components but lack temporal information about clock function for example 3 genes CCA1, PRR9 and Lux all changing throughout the day
Why is entrainment required?
As dawn and dusk is different everyday
The period of the circadian oscillator is approximately 24h and there is natural variation between plants
How do circadian clocks regulate plant cells by controlling gene expressions?
Some circadian clock proteins are transcription factors that regulate sets of genes with a circadian rhythm
What is an example of clock regulating plant cells?
Daytime transcription factors –> transcription factors are active and genes transcribed during the day but are doesnt happen during the night
How can you analyse the extent of circadian regulation?
Sample RNA over a 24h or 48h period then analyse transcripts from all genes using microarray or RNA sequencing methods
What did early studies find about the importance of the circadian rhythms?
Found 6% of transcipts have circadian rhythms –> many photosynthesis genes have circadian rhythms (e.g photosystem 1 and 2)
What underlines specific circadian phases of transcription?
‘cis elements’ (short, specific sequences)
Where do cis elements appear in high frequency?
They appear frequently in promoters of transcripts which can be used to identify time of day of transcripting at certain circadian phases
What do cis elements do?
Indicates when the circadian clock regulates different circadian phases through particular clock-controlled promoter motifs
How wide spread are circadian controlled genes?
Almost all metabolic pathways include at least one enzyme that is under circadian transcriptional control
When is chlorophyll biosynthesis peak?
Just before dawn to anticipate light avaliability
When does starch catabolism genes peak?
Around dusk
What does the mutant called prr9/7/5 do?
Increase in shikimate suggests changes in secondary metabolism and increase in Citric Acid cycle intermediates
How did scientists find out the impact for the mutant prr/9/7/5?
Metabolomics
How does a plant make sure it doesnt deplete starch reserves before dawn?
The rate of starch degradation is related to the length of night so that the plant only exhausts starch reserves just before the end of the night
What does the cca1/Ihy mutation do?
Causes the plant to exhaust starch reserves at night
What is the impact to the plant with the cca1/Ihy mutation?
Accumulates 20% less starch than wildtypes
Degrade starch 35% faster than wildtypes at night
Exhaust starch reserves 3-4 hours before the end of the night
Express starvation genes before the end of night
Where does the gene controlling chloroplasts circadian rhythm?
The gene SIG5 is made in the nucleus which is then imported into the chloroplast
What is the overall factors for controlling the circadian rhythm?
Environmental signalling, central oscillator and metabolism all impact each other
What is circadian gating?
The regulaiton of other cell signalling pathways by the circadian clock
What is the importance of circadian gating?
Fundamental way that circadian clocks regulate plant cells
What happens during gating?
The clock acts as a valve on the response of the plant to the environment, so the same environmental cue causes a different strength response depending ont he time of day
What is the general principle of light gating?
Light stimulus –> gate open –> strong response to light
No light –> gate closed –> weak response to light