From 2009.igem.org

Revision as of 02:42, 22 October 2009

Jammer Overview

A general explanation of the Jammer component of the E. coli Traffic Light Biosensor.

“Jammer”: Modular Gene Regulation (and Binary Logic) using Reverse Antisense Transcription

SECTION 1: STATEMENT OF RESEARCH PROBLEM

Description of Biological Phenomenon and General Aims of Project

A fundamental goal of synthetic biology is the construction of modular parts that form genetic circuits, which perform tasks akin to electronic devices. Control of these genetic elements is essential for their effectual performance. Although means of controlling gene expression via inhibition exist, such methods require well-characterized and effective pathways on the part of the biological chassis (e.g. Dicer in RNAi), and exogenous amplification is necessary preparation for their use (e.g. exogenously produced RNA for siRNA).

J23100-Jammer works as expected. Arabinose induces near-total knockdown of GFP expression.

The forward terminator is necessary for proper functioning of the Jammer. Arabinose induction shows no significant effects on GFP expression.

SECTION 2: RESEARCH OBJECTIVES AND SPECIFIC METHODS

Here, we aim to develop an endogenous system to control gene expression using antisense-based inhibition. A BioBrick containing a reverse promoter and terminator is assembled downstream of the transcript before its terminator. Another terminator is assembled upstream of this transcript, so that the completed assembly has a terminator-promoter-transcript-promoter-terminator motif.

Composite BioBrick parts are assembled using the standard three-antibiotics method. B0014 and J23100/101/105 were assembled as part of the terminator and promoter parts respectively (i.e. three strengths of forward constitutive promoters; inducible forward promoters may enable binary logic if used with an inducible reverse promoter). B0034 and K145015 were assembled as part of the fast-degrading GFP_LVA reporter transcript. J44002, an arabinose-inducible reverse promoter and B0014 functioned as part of the promoter-terminator.

The intended conditions of the completed BioBrick part are constitutively expressed GFP in LB without arabinose. In presence of arabinose, the reverse promoter is induced thus reducing the amount of reporter transcript available for transcription, leading to reduced levels of GFP. Flow cytometry analysis will primarily determine the efficacy of the device. Results, time and material-permitting, quantitative dot blot and RT-PCR may be used for further verification of results.

SECTION 3: SUMMARY OF RESULTS

GFP expression will be analyzed by flow cytometry to determine if a detectable shift exists. Quantitative dot blot analysis may be used for absolute quantification. If results can be reproduced, RT-PCR may be used for additional verification of the production of an anti-sense RNA transcript.

The reverse promoter is expected to exert genetic control when induced through two mechanisms: 1) it recruits RNA polymerase to transcribe in the reverse direction, thus colliding polymerases inhibit transcription, and 2) the reverse transcript is complementary to the coding transcript, thus they form a dsRNA duplex, which solicits anti-sense mediated blocking of the ribosome for the translation of RNA and related bacterial degradosome machinery (e.g. RNase II, III).

SECTION 4: SUMMARY OF PROPOSED FUTURE EXPERIMENTS AND TIMELINE OF COMPLETION

One assembly remains until the final device is complete. Sequence verification of the pre-complete assembly should arrive by Monday, Sept. 21. Final assembly should be complete by Friday, Sept. 25. Flow cytometry analysis will begin immediately and is expected to yield final results by Wednesday, Sept. 30. Concurrent quantitative dot blot analysis will be complete by that date, if materials exist.

Preliminary Results for Immediate Release ­- 11:48pm October 14, 2009

• Alex Ng and Amelia Hardjasa

Summary of Results

BW27783 cells containing Jammer plasmids grown overnight show GFP_LVA knockdown in the presence of arabinose. Although these results are very preliminary (e.g. without replicates), they suggest that arabinose is inducing the production of an anti-sense transcript that causes knockdown of GFP_LVA expression.

Methods

BW27783 cells with the following plasmids were inoculated and grown overnight in 15mL LB with or without 0.5% arabinose: Constitutive GFP_LVA, Jammer-100, Jammer-101, Jammer-105, and Empty Cells (no plasmids). FACS data was taken at approximately 18 hours and 24 hours post-inoculation. 18-hour data is shown. ODs were taken at 24 hours to verify similar growth. Jammer constructs: Terminator- Constitutive Promoter (J23100 or J23101 or J23105)-RBS-GFP_LVA-Pbad_reverse- Terminator. *Note that J23100 Jammer has not been sequence verified, only length and fluorescence verified.

Results

Astonishingly, Jammer-100 cells grown in presence of arabinose show fluorescence almost identical to cells without GFP_LVA plasmids, implying near total knockdown levels of GFP_LVA fluorescence. Note that the plasmid is not sequence verified; however, failed assemblies should only be missing the reverse-strand terminator.

Cells containing Jammer-101 plasmids show 101 knockdown in the presence of arabinose. Uninduced populations show two peaks of GFP_LVA expression, one at constitutive levels and another at no fluorescence. It is possible that weak transcription of the promoter and rapid LVA degradation tags may contribute to non-fluorescent cells.

Cells containing Jammer-105 plasmids show no apparent GFP_LVA fluorescence. It is surprising that arabinose-induced cells have measurable fluorescence.

OD data do not suggest significant differences in viability from potential toxicity in LB containing 0.5% arabinose, suggesting observed knockdowns are unlikely to result from dead cells with dysfunctional translational machinery for GFP_LVA production.

Conclusions

FACS data of three independent constructs and ODs taken together strongly suggest an observable knockdown of GFP_LVA from arabinose induction. Although these results are very preliminary and require additional verification, they are exciting results that an endogenous, modular method of knockdown at the RNA level is possible, thus potentially enabling elegant and rapid constructs of auto-regulation at the RNA-level that is independent of the biological chassis.

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