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Jay Dunlap KITP UC Santa Barbara July, 2007 Circadian The Neurospora Circadian System - some new tools and new insights Jay Dunlap KITP UC Santa Barbara July, 2007 Circadian. Systems in the Universal Tree of Life Brown Algae Ciliates PLANTAE Diatoms TetrahymenaExcellent genetics Arabidopsis Paramecium Chlamydomonas Tractable molecular genetics Dinoflagellates Insects - Antheraea, - genome of 43 Mb fully sequenced Drosophila Gonyaulax ANIMALIA ~10,000 genes annotated Mammals- - ongoing curation mouse, human FUNGI Neurospora - numerousBrown Algaeregulatable promoters Diatoms Ciliates Protista - targetedPLANTAE replacements @98% efficiency EUKARYOTA ~2500Sponges genes knockedDinoflagellates out + ~200/month Red Algae ANIMALIA Dictyostelium discoideum - wholeFUNGI genome microarrays Neurospora Entamoebae invadens Typical eukaryotic gene structureAmoebamastigote Plant Chloroplasts Synechococcus Mycoplasma-multiple introns Bodonids Cyanobacteria capricolum- combinatorial gene regulationKinetoplastids EUBACTERIA Euglenoids Physarum polycephalum Agrobacterium 28 cell types tumefaciens Plant Mitochondria Real world biology - photobiology Vairimorpha necatrix Pseudomonas testosteroni Trichomonas foetus - developmentGiardia lamblia Escherichia coli-cell/environmental interaction - circadian rhythms ARCHAEBACTERIA Dunlap, Cell, 1999 LIGHT P NeurosporaNeurosporaP P P LIGHTLIGHTLIGHT FRH FRQ P WC-2 WC-1LIGHT FRQ NucleusWC-1NucleusWC-2LightLIGHT - P P P Nucleus - WC-2PWC-2P WC-1 LIGHTP + ubiquitinationmodifications & by FRQFRQ WC-2 WC-1 modifications by WC-1P WC-2::WC-1 productsturnoverproducts of other of other FRQ P nucleus WCC clock genes? WC-2WC-2 / nucleus WC-1WCC / WC-1 clock genes? ? WCCfrqWCCnucleusWC-1Nucleus / WC-2 turnoverP P Productsproducts ? transcription turnover productsProductsProductsProductsofproductsCCRE ? frqon/off ? PFRQPofof of frq clock controlledfrq of of frqCCREgenes PFRQ PclockProductsclockclockof FRQ/clock frqfrqfrq vvd gene CCRE FRQturnoverofclockgenes clockWCCgenesclockprocessingCCREclock-controlledclockCCREfrq genesWCCturnovergenesFRQ/ CCREfrq genes frq ? WC-1 genesclockgenesgenes controlledfrq Nucleus P CCRE(ccg-1 frq toccg-14) ? Nucleus kinaseP genesFRQ ccggenes Nucleus FRQ FRQ ? ? (ccg-1wc-2 toccg-14) Nucleus FRQ ? rhythmicccg'swc-2 process vvd kinaseFRQ FRQprotein?FRQWCC CCRE on/off proteinsFRQprotein or ccg'sccg's FRQ FRQ? ? CCREwc-1ccg ccg'swc-1 kinase+proteinsFRQprotein? ccg'sCCRE up/downwc-1ccgccg's FRH FRQ PproteinsPproteins+ ? CCRE CCRE P P proteinother clock? CCRE CCRE ccg ccg regulatedother clock ccg ccgfrq caseinkinaseWC-2 regulatedprocessingTHEfrq CELL P Clock-controlledClock-controlledprocessesprocessesprocessingwc-2 ccg’s kinase II processesFRQ Clock-controlledprocessesWCCccg's Clock-controlledprocesses translationprocesses: ccg's Clock-controlledproteinstranslation processes:THE CELL Clock-controlledFRQ stressstress responses responses+ Cell proteins processesdevelopmentaldevelopmentalThe regulationregulation Cell intermediaryClock-controlled metabolism processes: 1/99 Schematic Clock-controlled viewintermediary of a circadian system. processes: metabolism Bold black lines trace the oscillator, aCell kinases: feedback loop comprised stress of the products responses of clock genes. With the exception of nucleus FRQ stress developmental responses regulation Cell CK-1, CK-2 FRQ, nothing is known about where in the cell these might frqact. Light actsCell through Review the wc genes anddevelopmental resetsintermediary the clock by inducing regulation metabolism frq ; the wc genes are also required CAMK-1, PRD-4for rhythmicity in intermediarythe dark. ccg's are metabolism output genes, regulated by the clockCell but not part of the feedback loop. CCRE = clock-control regulatory element. Cell Cell Simplified elements and dynamics of the N. crassa clock CK2, CK1 pro Andte arepeats every 22.5 h … ome H R FWD F FRQ WC-2 WC-1 frq RNA animation by Arun Mehra Known Molecular Components of the Neurospora clock •WC-1 and WC-2 act positively on the production of frq transcript. P P P •FRQ makes a trimer with itself and FRQ P FRH WC-2 P the FRH helicase, acting negatively WC-2WC-1 FRQ WC-1 on the production of its own - WC-2 + - ubiquitination WC-1 transcript. (negative feedback loop) & turnover •FRQ acts positively on the production of wc-2 transcript WC-1 and WC-1. (positive feedback loops) P P FRQ vvd •FRQ promotes phosphorylation of wc-1 FRH FRQ + + WC-1 and WC-2, inactivating them. WC-2 P wc-2 ccg’s •FRQ becomes phosphorylated which leads to its turnover, + releasing WC-1 and WC-2. kinases: nucleus FRQ •These interactions lead to CK-1, CK-2 frq oscillations in levels of frq/FRQ that CAMK-1, PRD-4 are essential for all true circadian Cell rhythms in Neurospora, including FRQ frq nested loops affecting input. •Changes in frq/FRQ levels are directly translated into changes in circadian rhythms in Neurospora. day night The Cellular Circadian System in Neurospora input Cell cycle DNA damage output PRD-4 FLO(s) LMO VVD FRQ/ NRO WCC CRY, PHY1, PHY2, output and other WC-1 CDO photoreceptors WC-2 ult WC/FLO clock-independent light effects ccg-16 FGO cno cel CLO Outline - I’m going to cover (or attempt to cover) three topics that are linked by the fact that their resolution was made possible by technical improvements in the system. 1. A role for chromatin remodeling in the FRQ-WCC circadian feedback loop. 2. A role for casein kinase 2 in circadian temperature compensation. 3. A method for simultaneous analysis of multiple oscillators in a single cell, and its use in establishing regulatory relationships between and among separate oscillators within the circadian system. Rhythms in frq mRNA and FRQ protein 20 20 + frq mRNA 15 15 FRQ rRNA 10 10 5 5 0 11 15 18 22 25 29 33 36 40 43 47 51 0 Hours in Constant Darkness frq + frq10 CT 041220041220 8 16 8 16 4 8 DD 1115 18 22 25 2933 36 40 4347 5115 18 hours 203 FRQ 118 + frq mRNA from Garceau et al, Cell, 1997 Expression of frq is surprisingly complex long FRQ intron 1 short FRQ * eliminates 5 of 6 upstream ATG’s eliminates 5 of 6 upstream ATG’s and ATGL frq mRNA is spliced to yield several transcripts; splicing of intron 2 is enhanced at low temperatures; uORFs reduce FRQ expression at lower temperatures by occupying ribosomes. Colot et al. 2005, MBoC Two sites in the frq promoter are bound by WC-1/WC-2 ER45 KO KO WC-2 FRQ WC-1 self non-self mut.self wc-1 frq α α α wc-2 WC-1 WC-2 FAD FAD +1 frq promoter distal proximal LRE LRE Allan Froehlich A distal WC binding site is necessary for rhythmicity Light Dark wt ∆ distal frq RNA FRQ protein 0212 436 0212 436 hours in dark hours in dark wt ∆ distal 425oC wt ∆ distal Therefore, important regulatory factors bind to that DNA, and it is now called the Clock-Box or C-Box. Chromatin Immunoprecipitation assays show rhythmic association of WC-2 with the Clock-Box but no rhythmic changes in binding at the PLRE, TSS or FCR. C-box 3.303: loading control of nontranscribed DNA Bill Belden Additional data suggested that chromatin remodeling was happening at frq. (Chromatin-immunoprecipitation assay - proteins normally bound to DNA are chemically cross-linked to the DNA, which is then isolated, sheared to a smaller size, and immunoprecipitated with antisera to the specific transcription factors bound to the DNA. The cross links are reversed and the IP’d DNA is used in PCR to see what regions are enriched, that is, where the transcription factors were binding) Limited digestion with micrococcal nuclease confirms light- and clock-associated changes in chromatin structure. Light causes chromatin to close The Clock Box is generally bound or be inaccessible at the Clock during periods of clock-associated frq Box and to open up at the PLRE. transcription and opens up as frq expression declines. An enzyme is doing this - But there are 19 SWI/SNF-like homologs to chromatin remodeling enzymes in Neurospora. Which one(s) are important? MmeI MmeI hph X X ORF The selectable marker hph is used to replace the ORF by homologous recombination Mme I sites are inserted at the ends of hph to provide molecular barcoding capabilities • The knockout procedure overcomes three traditional roadblocks to knockout creation in Neurospora: Techniques for making deletion cassetcassettestes were cumbersome. Long stretches of homology (2-3 kb) were required for reasonable efficiency of homologous recombination. EctopiEctopicc integration was frequent. www.dartmouth.edu/~neurosporagenome/ Knockout cassettes were assembled using recombination cloning in yeast Synthesize 4 primers for each gene 5f 3f 5r 3r (An algorithm analyzes each ORF and picks a gene-specific 20 nt sequence as the 3’ end of each primer. It then adds one of four generic 29 nt sequences that has homology to the vector or hph, as appropriate.) PCR flank fragments from genomic DNA ORF ORF (PCR then generates 1- 1.3 kb flank fragments within the 1500 bases 5’ flank on 5’ or 3’ side of ORF.) 3’ flank www.dartmouth.edu/~neurosporagenome/ The two flanks from the PCR are mixed with the generic selectable marker (hph) and with the vector, and the 4 components cotransformed into yeast. MmeI MmeI hph 5’ flank 3’ flank vector recombine in yeast X X X X www.dartmouth.edu/~neurosporagenome/ Yeast DNA is prepared from the mixed pool of transformants. PCR directly from the mixed pool of DN using the outside primers generates the knockout cassette which can be used without purification. 5f PCR 3r transform into Neurospora www.dartmouth.edu/~neurosporagenome/ SouthernSouthern blotblot analysisanalysis ofof primaryprimary transformantstransformants Transformations
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