Serine, a signal molecule

Modified E.coli strains we used for this part of the project were designed and constructed as follows:

• The SdaB gene encoding a Serine transporter was deleted,
• The SdaC gene encoding for a protein able to degrade Serine into 3-PG was deleted.
• The CheA gene (BBa_K1349006) was fused with a (SH3)₄ module was expressed, and the native CheA gene was deleted. The (SH3)₄ module is to allow a synthetic interaction with the response regulator, see below.
• A truncated SerA gene (BBa_K1349000) was expressed: the mutated SerA is no longer sensitive to feedback inhibition by serine. Expression of this gene leads to accumulation of high concentrations of serine.

The truncated SerA gene is controlled by CusR promoter which is activated by the accumulation of phosphorylated CusR protein.

CheA‐SH3, modified chemotaxis signalling

This regulatory circuit is designed as follows. A change in the extracellular Serine concentration is detected by Tsr receptor. The Tsr inhibits the constitutive activity of the CheA (Histidine kinase) and reduces auto-phosphorylation. This natural circuit is modified so that CheA transfers phosphate groups not only to CheB and CheY as usual but also to CusR. Consequently, the CusR transcription factor is less phosphorylated and binds less well to its DNA recognition sequence.

When extracellular Serine concentration is stabilized, Tsr is not stimulated anymore and stops inhibiting CheA. As a consequence, CheA becomes activated again and phosphorylates CusR.

In order to modify the phosphorylation patern of CheA we have used the synthetic protein interaction modules developped by Whitaker et al. 2012 (PNAS 109: 18090-18095). The CheA (BBa_K1349006) is fused to a (SH3)₄ module (BBa_K1349005) and CusR to a LZa leucine zipper (BBa_K1349007), these two proteins will then interact in the presence of the adaptor module an SH3-pep-LZA protein (Bba_K1349008).

The combination of these first two parts defines an culture wide oscilatory control circuit that responds through changing extracellular serine levels.

Regulation of intracellular ppGpp concentration; green light, go !

To make the oscillator do something we have devised two reporter modules that respond to the level of CusR phosphorylation. The first modulating cellular levels of ppGpp the secondary messanger responsible for the stringent response, and the second leading to green or red cells.

In the first reporter module the phosphorylated CusR transcription factor binds to the CusR promoter (BBa_K1349003) and activates RelA (BBa_K1349001) expression. RelA is an enzyme that synthesises ppGpp increasing the intracellular concentration. It is known that ppGpp blocks the initiation of S phase in the bacterial cell cycle, leading to the arrest of cell division. At the same time, phosphorylated CusR attaches to the CusR-Box (BBa_K1349002) between a promoter and the Mesh1 gene (BBa_K1349004), inhibiting synthesis of the Mesh1 enzyme. Mesh1 is an enzyme from Drosophila melanogaster that hydrolyses ppGpp. Thus in the presence of phosphorylated CusR this module ensures the presence of RelA and the absence of Mesh1 resulting in the accumulation of ppGpp. In the absence of phosphorylated CusR, the regulator is unable to bind to either the promoter or the binding site upstream of the Mesh1 gene. Consequently RelA is not synthsised, but the Mesh1 protein can be synthesised resulting in the hydrolysis of ppGpp. This reporter module constitutes a two way switch synthesising either RelA, in the presence of phosphorylated CusR, or Mesh1, in the presence of unphosphorylated CusR.

The second reported module follows the same logic but RelA is replaced with RFP and Mesh1 with GFP. Thus changing levels of CusR phosphorylation can drive red/green color changes.

References

Pertinent articles related to our project:

Top Papers

• Gudipaty SA1, Larsen AS, Rensing C, McEvoy MM. Regulation of Cu(I)/Ag(I) efflux genes in Escherichia coli by the sensor kinase CusS. FEMS Microbiol Lett. 2012 May;330(1):30-7.
• Rudd KE, Bochner BR, Cashel M, Roth JR. Mutations in the spoT gene of Salmonella typhimurium: effects on his operon expression. J Bacteriol. ;163(2):534-42, 1985.
• Whitaker WR1, Davis SA, Arkin AP, Dueber JE. Engineering robust control of two-component system phosphotransfer using modular scaffolds. Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):18090-5.
• Ferullo DJ, Cooper DL, Moore HR, Lovett ST. Cell cycle synchronization of Escherichia coli using the stringent response, with fluorescence labeling assays for DNA content and replication. Methods. 2009 May;48(1):8-13.
• Peters-Wendisch P1, Stolz M, Etterich H, Kennerknecht N, Sahm H, Eggeling L. Metabolic engineering of Corynebacterium glutamicum for L-serine production. Appl Environ Microbiol. 2005 Nov;71(11):7139-44.

Related Papers

• Wahl A, My L, Dumoulin R, Sturgis JN, Bouveret E.Antagonistic regulation of dgkA and plsB genes of phospholipid synthesis by multiple stress responses in Escherichia coli. Mol Microbiol. 80(5):1260-75, 2011.
• Collins CH. Cell-cell communication special issue. ACS Synth Biol. 2014 Apr 18;3(4):1978.
• Hsiao V, de Los Santos EL, Whitaker WR, Dueber JE, Murray RM. Design and Implementation of a Biomolecular Concentration Tracker. ACS Synth Biol. 2014 May 15.
• Park JH, Oh JE, Lee KH, Kim JY, Lee SY. Rational design of Escherichia coli for L-isoleucine production. ACS Synth Biol. 2012 Nov 16;1(11):532-40.
• Tan MH1, Kozdon JB, Shen X, Shapiro L, McAdams HH. An essential transcription factor, SciP, enhances robustness of Caulobacter cell cycle regulation. Proc Natl Acad Sci U S A. 2010 Nov 2;107(44):18985-90.
• Park H, Saha SK, Inouye M. Two-domain reconstitution of a functional protein histidine kinase. Proc Natl Acad Sci U S A. 1998 Jun 9;95(12):6728-32.
• Porter SL, Wadhams GH, Armitage JP. Signal processing in complex chemotaxis pathways.Nat Rev Microbiol. 2011 Mar;9(3):153-65.
• Olson EJ, Hartsough LA, Landry BP, Shroff R, Tabor JJ. Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals. Nat Methods. 2014 Apr;11(4):449-55.
• Skerker JM1, Perchuk BS, Siryaporn A, Lubin EA, Ashenberg O, Goulian M, Laub MT. Rewiring the specificity of two-component signal transduction systems. Cell. 2008 Jun 13;133(6):1043-54.
• Skerker JM1, Prasol MS, Perchuk BS, Biondi EG, Laub MT. Two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis. PLoS Biol. 2005 Oct;3(10):e334.
• Gonzalez D, Collier J. Effects of (p)ppGpp on the progression of the cell cycle of Caulobacter crescentus. J Bacteriol. 2014 Jul;196(14):2514-25.
• Thanbichler M. Synchronization of chromosome dynamics and cell division in bacteria. Cold Spring Harb Perspect Biol. 2010 Jan;2(1):a000331.
• Wang X, Vallurupalli P, Vu A, Lee K, Sun S, Bai WJ, Wu C, Zhou H, Shea JE, Kay LE, Dahlquist FW. The linker between the dimerization and catalytic domains of the CheA histidine kinase propagates changes in structure and dynamics that are important for enzymatic activity. Biochemistry. 2014 Feb 11;53(5):855-61.
• Eggeling L, Sahm H. New ubiquitous translocators: amino acid export by Corynebacterium glutamicum and Escherichia coli. Arch Microbiol. 2003 Sep;180(3):155-60.
• Laub MT, Goulian M. Specificity in two-component signal transduction pathways. Annu Rev Genet. 2007;41:121-45.
• Alon U, Camarena L, Surette MG, Aguera y Arcas B, Liu Y, Leibler S, Stock JB. Response regulator output in bacterial chemotaxis. EMBO J. 1998 Aug 3;17(15):4238-48.
• Chang YC, Armitage JP, Papachristodoulou A, Wadhams GH. A single phosphatase can convert a robust step response into a graded, tunable or adaptive response. Microbiology. 2013 Jul;159(Pt 7):1276-85.
• Ganesh I, Ravikumar S, Lee SH, Park SJ, Hong SH. Engineered fumarate sensing Escherichia coli based on novel chimeric two-component system. J Biotechnol. 2013 Dec;168(4):560-6.
• Jonas K. To divide or not to divide: control of the bacterial cell cycle by environmental cues. Curr Opin Microbiol. 2014 Apr;18:54-60.

Strains used in the project

• Escherichia coli W3110 was used for chassis construction.
• Escherichia coli DH5alpha and TG1 strains were used for regular cloning.

Strain storage

For long-term conservation, 750 μL of an exponentially grown strain were mixed with 250 μL of glycerol 80%, and at -80°c in a cryotube.

Culture medium

• Regular bacterial growth was performed in LB medium or LB-agar plates (DIFCO) supplemented with the appropriated antibiotics if necessary: ampicillin 100 μM, kanamycin 50 μM, chloramphenicol 30 μM. When required, IPTG (Isopropyl β-D-1-thiogalactopyranoside ) was added to the final concentration of 500 μM to induce gene expression from Plac promoters.

  Growth was conducted at 37°C for regular experiments, and at 30°C when carrying temperature sensitive plasmids.

• The SMG medium used to characterize the BBa_K1349001 part was prepared based on the work of (Rudd et al.,1985).

  SMG plate composition:

  M9 salts	1X
  MgSO4	1mM
  CaCl2	0.1mM
  VitB1	0.5µg/ml
  Glucose	0.2%
  Serine	1mM
  Methionine	1mM
  Glycine	1mM
  Bactoagar	15g/L

References:

Rudd KE, Bochner BR, Cashel M, Roth JR. Mutations in the spoT gene of Salmonella typhimurium: effects on his operon expression. J Bacteriol. ;163(2):534-42, 1985.

Plasmid extraction

Performed with the Macherey-Nagel Kit, following the manufacturer instructions.

PCR clean-up

Performed with the Promega Kit, following the manufacturer instructions.

Competent cells

Cells were grown in LB medium as a starter O/N. The day after, the culture was back diluted in 100 mL of LB to reach an OD600=0.05.

When the culture reached and OD600 of 0.4 to 0.6, cells were centrifuged at 5000 rpm during 10 min. The cell pellet was carefully re-suspended in 1/2V of CaCl2 50 mM at 4°C. After an incubation of 10 min on ice, the cells were pelleted by centrifugation. The pellet was re-suspended in 1/20V of CaCl2 50 mM, Glycerol 15%. Aliquots of competent cells were stored at -80°C.

Transformation

Performed following the protocol published on the iGEM website : here

Lambda Red mutant construction

This protocol was adapted from the initial protocol published by Datsenko and Wanner (2000).

Reference:
Datsenko KA1, Wanner BL. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A. 2000 6;97(12):6640-5.

• Day 1:

  • Transform W3110 competent cells with the pKOBEG plasmid (cmR). Grow at 30°C o/n
  • PCR-amplify the FRT-kan-FRT cassette from the pKD4 plasmid (AmpR) using the set of primers targeting the gene to be deleted. Check the PCR product on an agarose gel. Then digest the pKD4 matrix plasmid with 1uL DpnI enzyme, and incubate at 37°C during 2 hrs. Clean-up the PCR product with the promega kit.

• Day 2:

  From one isolated W3110 pKOBEG clone, grow the cells at 30°C. When the culture reach an OD of 2.2, add arabinose to a final concentration of 0.05% and incubate 2 hrs at 30°C or until OD600=1. Switch the temperature to 42°C to get rid off the pKOBEG plasmid. Centrifuge the culture at 4°C and prepare a stock of electrocompetent cells.

  Electroporate 10 ul of purified PCR product into 50 ul of electrocompetent cells. Grow the transformed cells on LB+kan 50uM plates, and incubate at 37°C o/n.

• Day 3:

  Restreak 25 clones on LB+Kan plates and Lb+Cm plates, incubate at 37°C O/N.

• Day 4:

  Select 8 clones resistant to Kan but sensitive to Cm. Check the correct replacement of the targeted gene by the FRT-Kan-FRT cassette with primers exterior to the gene.

• Day 5:

  Cultivate and freeze 2 independent clones.

To flip the FRT-KAN-FRT cassette

• Day 6:

  Prepare a stock of electrocompetent W3110 mutant.

  Electroporate the pCP20 plasmid (CmR, ApR) encoding the flipase and spread the cells on LB+Ap+Cm. Incubate at 30°C O/N

• Day 7:

  To prepare a culture starter, inoculate 1 clone in LB at 30°c O/N

• Day 8:

  Back-dilute the culture 100x in LB without antibiotics. Grow at 30°c until you reach an OD600=0.3. Switch the temperature to 37°C until OD600= 0.8. Back-dilute the culture 100x in LB for 5 hrs. Spread 10 ul of the culture in LB plate without antibiotics to get isolated colonies.

• Day 9:

  Select 20 isolated clones and re-patch on LB, LB+Kan, LB+AP+CM.

• Day 10:

  Select 8 clones sensitive to Kan, Ap and Cm. Check by colony-PCR that the FRT-KAN-FRT cassette was truly deleted.

SLIC cloning

One-step sequence- and ligation-independent cloning (SLIC) was performed following the protocol published as supplemental data in the original manuscript of Jeong and collaborators. This protocol can be found here

References
Jeong JY1, Yim HS, Ryu JY, Lee HS, Lee JH, Seen DS, Kang SG. One-step sequence- and ligation-independent cloning as a rapid and versatile cloning method for functional genomics studies. Appl Environ Microbiol. 2012 ; 78(15):5440-3.

3A cloning

Performed following the protocol published on the iGEM website : here

Growth and fluorescence measurements in M9 medium

An overnight culture of TG1 strain carrying the plasmid of interest was back diluted 100x in modified M9 medium supplemented with casaminoacids, glycerol 0.4% and 10% of LB.

Strains were cultivated at 37°C with continuous shaking in 10 mL of M9 medium, until they reached an OD600nm=0,4 to 0,6. Then, a 5 mL aliquot of each culture was treated with a sub-lethal concentration of AgNO3 (5 μM, see reference Gudipaty SA et al., 2012) while a second untreated aliquot of 5 mL was used as a control. After Ag treatment, all the cultures were incubated in the dark at 37°C with continuous shaking. Then, cell growth and GFP fluorescence were determined over time by reading the OD at 600 nm and 530 nm, respectively. To do so, 150 μL aliquots were transferred into wells of a black 96-well plate (Greiner), and the absorbance at 600 nm and fluorescence (excitation, 485 nm; emission, 530 nm) were measured with a Tecan Infinite M200 microplate reader.

Result 1: validation of the RelA part: BBa_K1349001

The relA gene encodes a ppGpp synthetase. In bacteria, ppGpp (guanosine 3'-diphosphate 5-' diphosphate) acts as a signaling molecule that regulates a variety of cellular metabolisms in response to changes in the nutritional state of the cells.

This part was designed to allow the rapid synthesis of the alarmone ppGpp, responsible for the stringent response in E. coli. In the context of our project ppGpp is accumulation used to stop initiation of cell division.

How we tested the BBa_K1349001 part:

Expression of the BBa_K1349001 part is expected to cause accumulation of ppGpp and so reduce growth rate of a wild-type cell. At the opposite, expression of this part in a MG1655∆relA mutant unable to make ppGpp is expected to complement the mutant.

As seen on the figure below, our part is functional as it is able to fully complement the MG1655∆relA mutant. See lab-book for details on the experimental procedure.

Attribution of the figure: Dr. Emmanuelle Bouveret.

Result 2: validation of the CusR box: BBa_K1349002

In E. coli, the CusR/CusS two-component system induces expression of genes involved in metal efflux under condition of elevated Cu or Ag concentrations. Phosphorylated CusR specifically bind to CusR-dependent promoters. The CusR box is the recognition sequence for the protein CusR.

We designed a Part corresponding to the CusR box to be inserted downstream of a promoter to allow negative regulation of transcription by CusR phosphorylation. In common with many response regulators we expect over-expression of CusR to result in binding and so negative regulation of an upstream promoter. These negative effects are expected through bound CusR physically blocking RNA polymerase.

How we tested the BBa_K1349002 part:

Insertion of the BBa_K1349002 part downstream of a promoter is expected to allow the binding of the CusR regulator in response to metal (Cu or Ag) availability in the medium. While different in their biological role and cellular targets, these metals share very similar chemical and ligand- binding properties.

To test this part, we inserted the CusR box (BBa_K1349002) in a pLac vector (AmpR) downstream of the Lac dependent promoter, followed by the GFP coding sequence. The Lac promoter is leaky enough to allow GFP synthesis without the addition of inducer to the culture medium. As our final objective a fine-tuning of our modified CurR regulatory cascade, we also tested the effect of multiple CusR-boxes insertion in our assay (1 box, 2 boxes and 3 boxes). As a control, the Plac promoter was fused to the GFP coding sequence without any CusR box. Strains were cultivated at 37°C in M9 medium until they reached an OD600nm=0,4 to 0,6. Then, an aliquot of each culture was treated with a sub-lethal concentration of AgNO3 (5 μM, see reference Gudipaty SA et al., 2012) while a second untreated aliquot was used as a control. The two series of experiments presented here were performed twice and showed similar results.

• Growth was determined overtime by following the culture OD at 600 nm on a TECAN instrument (Figure A).
• GFP synthesis was quantified by measuring the OD at 530 nm on a TECAN instrument. Then, fluorescence was normalized by dividing the results with the OD at 600 nm (Figure B).

Figure A: The presence of cusR boxes on a pLac vector affects cell growth in the presence of a sub-lethal dose of AgNO3.

Attribution of the figure: L.Houot, S. Michel, G. Chambonnier, J. Sturgis.

As seen on figure A, the introduction of a unique CusR box in our test vector (P-cusB1-GFP) has no effect on growth compared to the control vector (P-GFP), with or without Ag supplementation to the medium. At the opposite the presence of 2 CusR boxes (P-cusBx2-GFP) or 3 CusR boxes (P-cusBx3-GFP) in our test vector has a very strong effect on growth when AgNO3 is added to the medium.

Conclusion:
Even if these are very preliminary results, our data suggest that the CusR-box part that we designed (BBa_K1349002) might be able to titrate the endogenous CusR regulator in the cells, preventing a correct stress response when E. coli is exposed to sub-lethal concentrations of Ag.

Figure B: The insertion of 2 or 3 CusR boxes downstream of the Plac promoter allow negative regulation of gene expression in response to of a sub-lethal dose of AgNO3.

Attribution of the figure: L.Houot, S. Michel, G. Chambonnier, J. Sturgis.

As seen on figure B, expression of GFP from our test pLac plasmid can be down regulated by Ag addition to the medium. The regulatory effect is only seen when at least 2 boxes were inserted downstream of the Plac promoter, and appears even stronger with 3 boxes inserted in our test vector.

Conclusion:
Our results show that the CusR-box part that we designed (BBa_K1349002) is functional, as it allows the control of gene expression in response to the presence of a sub lethal concentration of Ag to the medium. In this case, Ag is supposed to induce the phosphorylation of CusR, allowing its binding to the CusR box, and consequently the transcriptional down-regulation of the following gene. Interestingly, our data suggest that the insertion of 2 or 3 CusR-boxes is optimal to allow the binding of the CusR regulator.

Reference
Gudipaty SA, Larsen AS, Rensing C, McEvoy MM. Regulation of Cu(I)/Ag(I) efflux genes in Escherichia coli by the sensor kinase CusS. FEMS Microbiol Lett. 2012 May;330(1):30-7.