L36 Circadian clocks 2

Question 1

Antisense ncRNA regulates neurospora clock

Answer 1

see onenote slides

frq = frequency gene

qrf transcription anti-phased with frq transcription

qrf and frq form double negative feedback loop - how?

Question 2

RNA pol collision

Answer 2

see onenote slides

inhibits transcription

Question 3

Translational control of mammalian clock by mTOR

Answer 3

see onenote slides

4E-BP phosphorylation is rhythmic
- Amount of 4E-BP is constant but its phosphorylation is rhythmic

4E-BP1 knock out mice = short-circadian period

reduced mTOR function => lengthens circadian rhythm in mice

Question 4

Translational control of mammalian clock by uORFs - DENR

Answer 4

see onenote slides

uORFs in circadian clock genes in mouse

DENR promotes ribosome initiation of mORF

denr RNAi => reduced mORF translation => shorter period

We uncover here the non-canonical initiation factors = Density Regulated Protein (DENR)

Question 5

Plant circadian clock regulates…

Answer 5

metabolism and physiology

Question 6

Circadian clock directly regulates transcriptional network

Answer 6

see onenote

CCA1 is a TF, binds to promoter regions of ~1700 genes

TOC1, PRR5, PRR7 are transcriptional repressors => bind to distinct set of gene promoters

Question 7

Protein folding and degradation in plant circadian rhythm

Answer 7

see onenote slides

• light-dependent post-translational control

Question 8

ZTL

Answer 8

see onenote slides

F-box protein that targets TOC1 for degradation

ztl mutants have a long period, due to slower TOC1 degradation

Question 9

Circadian oscillator in cyanobacteria - post-translational oscillator (PTO) in cyanobacteria

Answer 9

see onenote

Photosynthetic bacteria

KaiC = very slow autokinase and autophosphatase

KaiI promtoes KaiC autokinase activity

KaiB inhibits KaiA

KaiC activates SasA (a kinase) => phosphorylates RpaA => RpaA activates gene expression

Question 10

PTO can be reconstituted in vitro

KaiC mutations

Answer 10

Mutate KaiC in particular ways, can modify the circadian rhythm e.g. point mutations => long/short period mutants

Similar rhythm in vivo and in vitro imply that PTO is the core oscillator that drives circadian rhythm in this bacteria

generate similar rhythm in vivo and in vitro => PTO is core oscillator in cyanobacteria

Question 11

Post-translational oscillator in RBC

Answer 11

see onenote slides

RBC are anucleate, no transcription

Peroxiredoxins (PRX) conserved antioxidant enzymes

Can measure the rhythm of PRX in RBC via PRX’s oxidations states, there is an independent circadian rhythm in these RBC

circadian rhythms of PRX oxidation in all kingdoms of life

PRX PTO does not require functional TTFL - is it an independent oscillator?

Question 12

How does a circadian clock detect seasons?

Answer 12

see onenote slides

FT = flowering time gene

Photoperiodic flowering pathway

• day length detected in leaves
• activates FT gene exp
• FT protein moves through the phloem to the apical meristem => flowering initiated

Question 13

Alternative models for detecting daylength

Answer 13

see onenote slides

1. hourglass
2. external coincidence
3. internal coincidence