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A Synthetic Biology Approach to Discerning Circadian Output Pathways in Cyanobacteria
Zhipeng SunMCB186 Final ProjectDecember 13, 2006
PPP
P PP
The Kai Clock in Cyanobacteria•KaiC autophosphorylates and dephosphorylates•KaiA promotes phosphorylation•KaiB inhibits KaiA•Transcription-translation independent•Period: 14-60 h
Time
Phos
phor
ylati
on o
f Kai
C
b
Nakajima et al. (2005)
Question
• By what molecular mechanism does KaiC phosphorylation drive clock output?
P
P?
SasA? RpaA?
PpsbAI::luxABreporter
Hypothesis: SasA-RpaA complex as intermediary (Takai et al. 2006)
Hypothesis: SasA-RpaA complex as intermediary (Smith and Williams 2006)
Synthetic Approach: Pathway Reconstitution in E. coli
• Traditional CoIP vs. proposed reconstitution• Tools– Lambda-red recombination (Court et al. 2002)– Conjugation (Li and Elledge 2006)– Cloning– In-vitro transcription (Melton et. al 1984)
http://www.igmors.u-psud.fr/images/Coli.gifhttp://www.abc.net.au/science/news/img/environment/cyanobacteria220805.jpg
Synechococcus PCC7942
E. Coli ECNR1
Cyanobacteria PCC6803 genome cloned into B. subtilis
•“Megacloning,” or mass horizontal gene transfer
•Cyanobacteria rRNA operon genes induced cell death
•Resulting cell contained cyanobacteria mRNA transcripts
Itaya et al. (2005)
Step 1: Reconstitute transcription pathway
1. Clone RNAP α1α2, β, β‘, ω, σ subunits into vector containing lac promoter + RBS +antibiotic– PubMed Entrez Protein entries for PCC7942:
• 24 sigma factors• 1 ea. α1α2, β, β‘ subunits
2. Lambda-red recombination into E. coli, antibiotic selection
Cat/Kanvector
E. Coli genome
Selection and screening
LB-MIN+MARKER PlateE. Coli colony
α1α2, β, β‘, ω, σ
Lambda-red Recombination
lac
Step 1: Reconstitute transcription pathway
3. Clone and transform PsbAI::luxAB from cyanobacteria α1α2, β, β‘, ω, σ
E-coli RNAP
CyanoRNAP
psbAI
PpsbAI
luxAB
output
Transcription/translation
lac
Verification•Bioluminescence should be constant over time•Western blot with anti-cyanobacteria-RNAP antibody
Step 2: Reconstitute circadian control
1. Clone and transform KaiA, KaiB, and KaiC under inducible e. coli promoter to express in 1:1:4 ratio by molar mass
VerificationWestern Blot KaiC over circadian cycle
2. Compare KaiC expression through anti-KaiC Western Blot:• With KaiA, B, C under e. coli promoter• With KaiA, B, C under cyanobacteria promoter(If the expression level is similar, do not put subsequent cyanobacteria
genes under e. coli promoters to save time)
Nakajima et al. (2005)
Proof of PrincipleKai Proteins Interact in E. coli
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Hsieh, Lau, Ramos, and Sun (unpublished, 2006)
Step 3: Screen for pathway components
1. Reconstitute SasA and RpaA and observe bioluminescence
2. Horizontal gene transfer from cyanobacteria to e. coli until bioluminescence is oscillatory
3. Selectively knockout genes until bioluminescence is constant
4. Repeat 2-3 for other proteins5. Label e. coli DNA with DAPI
and visualize over circadian cycle to test Smith and Williams (2006) hypothesis
Verification
P
P
output
ConclusionsIn case of failure…• Change promoters and RBS
to inducible or low expression
• Change promoter system from cyanobacteria to e. coli
• Use different reporter systems from cyanobacteria (eg. PKaiBC)
• Create a cDNA library from extracted cyanobacteria genes and conduct microarray analysis
Versatility of Approach• Can be modified for other
pathways in cyanobacteria– Light-input pathway– Biochemistry of phase shift
and resetting• Can be genearlized for
simple prokaryotes• Can be automated
ReferencesCourt DL, Sawitzke JA, and Thomason LC. Genetic engineering using
homologous recombination. Annu Rev Genet 2002; 36 361-88. Hsieh H, Lau J, Ramos D, Sun Z. Reconstitution of the cyanobacteria
oscillator in E. coli. iGEM 2006, unpub.Itaya M, Tsuge K, Koizumi M, and Fujita K. Combining two genomes in
one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. Proc Natl Acad Sci U S A 2005 Nov 1; 102(44) 15971-6.
Li MZ and Elledge SJ. MAGIC, an in vivo genetic method for the rapid construction of recombinant DNA molecules. Nat Genet 2005 Mar; 37(3) 311-9.
Melton DA, Krieg PA, Rebagliati MR, Maniatis T, Zinn K, and Green MR. Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Res 1984 Sep 25; 12(18) 7035-56.
Nakajima M, Imai K, Ito H, Nishiwaki T, Murayama Y, Iwasaki H, Oyama T, and Kondo T. Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro. Science 2005 Apr 15; 308(5720) 414-5.
Smith RM and Williams SB. Circadian rhythms in gene transcription imparted by chromosome compaction in the cyanobacterium Synechococcus elongatus. Proc Natl Acad Sci U S A 2006 May 30; 103(22) 8564-9.
Takai N, Nakajima M, Oyama T, Kito R, Sugita C, Sugita M, Kondo T, and Iwasaki H. A KaiC-associating SasA-RpaA two-component regulatory system as a major circadian timing mediator in cyanobacteria. Proc Natl Acad Sci U S A 2006 Aug 8; 103(32) 12109-14.
Thanks for listening, and thanks for a great semester!