Team:DTU-Denmark/Project

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{{:Team:DTU-Denmark/Templates/Standard_page_begin|Project}}
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{{:Team:DTU-Denmark/Templates/Standard_page_begin|Overview}}
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<iframe style="float: right; margin: 15px 0 20px 10px; border: 4px solid white; outline: 1px solid #CCCCCC;" width="440" height="350" src="http://www.youtube.com/embed/dtleYPzOg-Y" frameborder="0" allowfullscreen></iframe>
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== Abstract ==
== Abstract ==
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Small regulatory RNA is an active area of research with untapped possibilities for application in biotechnology. Such applications include convenient gene silencing and fine-tuning of synthetic biological circuits, which are currently cumbersome processes restricted to well studied bacteria. We have investigated a novel type of RNA regulation<span class="superscript">[[#References|[2]]]</span><span class="superscript">[[#References|[5]]]</span>, where the inhibition caused by a small regulatory RNA is relieved by another RNA called trap-RNA. The system displays a large dynamic range and can uniquely target and repress any gene of interest providing unprecedented flexibility. We suspect that any level of repression is achievable by simply altering the sequences of the involved RNAs. Multiple such systems can coexist without interfering and are thus compatible with more complex designs.
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Small regulatory RNA is an active area of research with untapped possibilities for application in biotechnology. Such applications include convenient gene silencing and fine-tuning of gene expression, which are currently cumbersome processes restricted to well studied bacteria. We have investigated a novel type of RNA regulation based on the [[Team:DTU-Denmark/Background_the_natural_system|chitobiose system]], where the inhibition caused by a small RNA is relieved by another small RNA called trap-RNA.[[File:DTU2011_project_fig1.png|100px|frameless|right|Two-level sRNA regulation. Blue is any target mRNA, red is sRNA and green is trap-RNA.]] We explore the possibility of using the system to uniquely target and repress any gene of interest, potentially providing unprecedented specificity and control of gene silencing. We furthermore constructed araBAD promoters with varying promoter activities using synthetic promoter libraries.
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== Experiment: Testing sRNA ==
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[[File:DTU1_Redswap.png|200px|frameless|right|link=Team:DTU-Denmark/Project_experiment|Chromosomal knockout]]
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Experiments were performed to verify that the envisioned small RNA based gene silencing is possible. Plasmids containing and strains deleted for the components were constructed providing a biological model.
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[[Team:DTU-Denmark/Project_experiment|Read more...]]
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== The natural system ==
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== Bioinformatics ==
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[[File:DTU_Chitobiose.png|200px|thumb|right|Chitobiose]]
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[[File:DTU1 Sequence logo.png|200px|frameless|right|link=Team:DTU-Denmark/Bioinformatic]]
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The project is inspired by the regulation of chitobiose uptake and metabolism in E. coli. Especially the three components: '''a chitoporin''' that transports chitosugars into cells; '''a sRNA''' which regulates the chitoporin post-transcriptionally; and '''a trap-RNA''' which is transcribed from intergenic region in the chitobiose operon. The sRNA regulates chitobiose expression through binding to the Shine_Dalgarno sequence on the chitobiose mRNA inhibiting recruitment of the 30S ribosome and altering RNA stability. When chitobiose is present trap-RNA is transcribed and its transcript binds sRNA, relieving chitoporin repression.
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== The idea ==
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A bioinformatics study was performed to investigate the possibilities of engineering the trap-RNA system to target any gene. The study elucidates interesting features of sequence and secondary structure conservation guiding future application.
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[[File:DTU2011_project_fig1.png|200px|thumb|right|Schematic representation of RNA interactions in trap-RNA system. Blue is any target mRNA. Red is sRNA. Green is trap-RNA.]]
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[[Team:DTU-Denmark/Bioinformatic|Read more...]]
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The natural system is exploited to target any mRNA (m) by altering the sequences responsible for base-pairing in the sRNA (s) and the trap-RNA (r). Because these sequences are short the wild type function of the sRNA and the trap-RNA is maintained.
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== The experiments ==
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The experiments are a proof of concept, showing that the sRNA and the trap-RNA can be used to silence and control gene expression by targeting the chitoporin Shine-Dalgarno. Furthermore it is shown that sRNA and trap-RNA can be rationally designed to target any Shine-Dalgarno. The experiments fall into '''three parts'''. For full description go to [[Team:DTU-Denmark/Project_experiment|experiments]].
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'''Construction of plasmids''' necessary for testing our system involves taking the native system from ''E. coli'', as well as a slightly modified system and putting them on plasmids that let us both control the expression of these components and measure the output of the system.
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'''Strain construction''' involves deleting the original genes from the chromosome of a ''E. coli'' W3110 strain. Since we use the original genes, these need to be deleted from the chromosome to prevent them from interfering with our measurements.
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'''Improving the ''araBAD'' promoter''' entails expanding the dynamic range of this promoter by modifying the -10 and -35 sequence of the promoter, as well as randomly changing the nucleotide sequence around and in between these sequences. Since the ''araBAD'' promoter is used in our project improving this promoter could lead to even finer control of our system.
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== Modeling ==
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[[File:DTU2011_modeling_fig.png|200px|frameless|right|link=Team:DTU-Denmark/Modeling|'''Kinetic models''' of the system are the basis for modeling. Blue is target mRNA, red is small RNA and green is trap-RNA]]
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== The models ==
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A framework for characterization of gene silencing was developed to guide rational design and test hypotheses. Steady state analysis revealed that each trap-RNA system has a characteristic fold repression.
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[[File:DTU2011_modeling_fig.png|200px|thumb|right|'''Kinetic models''' of the system are the basis for modeling. Blue is target mRNA, red is small RNA and green is trap-RNA]]
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[[Team:DTU-Denmark/Modeling|Read more...]]
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Models are developed to provide a '''framework''' for characterization and the means to incorporate the system into larger models.
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A '''steady state analysis''' revealed that each system has a characteristic '''fold repression'''. The influence of parameters on the fold repression was investigated to help guide the design of the trap-RNA system. Temporal '''simulation''' provides additional tools for characterization and design. For more information got to [[Team:DTU-Denmark/Modeling|modeling]].
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== Bioinformatic ==
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== Experiment: Improving araBAD ==
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[[File:DTU-Relative_promoter_activity.png|200px|right|link=Team:DTU-Denmark/Project_improving_araBAD]]
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The dynamic range of the araBAD promoter was expanded by either changing the -10 and -35 elements or randomly changing the promoter using a synthetic promoter library. Experiments were performed characterizing the constructed promoters.
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[[Team:DTU-Denmark/Project_improving_araBAD|Read more..]]
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A bioinformatic study was performed to investigate the flexibility when engineering sRNA regulation genetically. For full analysis go to [[Team:DTU-Denmark/Bioinformatic|bioinformatic]].
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== Data page ==
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[[File:DTU1_Data_page-figure1.png|200px|right|link=Team:DTU-Denmark/Data]]
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The data page provides a description of the constructed BioBricks and how they work. It furthermore provides full links to the iGEM parts registry enabling easy retrieval of each submitted part.
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[[Team:DTU-Denmark/Data|Read more...]]
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==References==
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[1] Datsenko, K.A. & Wanner, B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proceedings of the National Academy of Sciences 97, 6640-6645(2000).
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[2] Figueroa-Bossi, Nara, Martina Valentini, Laurette Malleret, and Lionello Bossi. “Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target.” Genes & Development 23, no. 17 (2009): 2004 -2015.  
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== Results ==
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The '''bioinformatic study''' revealed some interesting constrains for engineering novel sRNAs with our gene silencing tool; a terminal poly-U tail, a putative Hfq binding site, a stemloop without sequence constrains, and a terminal stemloop with high sequence conservation. See the results [[Team:DTU-Denmark/Bioinformatic#Results|here]].
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[3] Hayashi, K. et al. Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Molecular Systems Biology 2, 2006.0007(2006).
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'''Testing sRNA''' we were able to show that the target gene chiP can be placed on a plasmid and be regulated by a small RNA. Changing the complementary sequence removes this regulation. See the results [[Team:DTU-Denmark/Project_testing_sRNA#Results_and_Conclusions|here]].
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[4] Lambert, J.M., Bongers, R.S. & Kleerebezem, M. Cre-lox-based system for multiple gene deletions and selectable-marker removal in Lactobacillus plantarum. Applied and environmental microbiology 73, 1126-35(2007).
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Through rational design of the '''araBAD promoter''' we managed to reach a higher level of expression from that promoter. Also, we proved that Synthetic Promoter Library can be created for an inducible promoter to expand its dynamic range. See the results [[Team:DTU-Denmark/Project_improving_araBAD#Results|here]].
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[5] Overgaard, Martin, Jesper Johansen, Jakob Møller‐Jensen, and Poul Valentin‐Hansen. “Switching off small RNA regulation with trap‐mRNA.” Molecular Microbiology 73, no. 5 (September 2009): 790-800.  
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The '''modeling''' provides a guideline for [[Team:DTU-Denmark/Modeling#Parameters_and_proposed_experiments|determining parameters]] and design of [[Team:DTU-Denmark/Modeling#Design_of_dynamic_range|dynamic range]] of our gene silencing tool. A simulation revealed fast dynamics of gene silencing. See the results [[Team:DTU-Denmark/Modeling#Dynamics|here]].
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Latest revision as of 03:41, 22 September 2011

Overview

Abstract

Small regulatory RNA is an active area of research with untapped possibilities for application in biotechnology. Such applications include convenient gene silencing and fine-tuning of gene expression, which are currently cumbersome processes restricted to well studied bacteria. We have investigated a novel type of RNA regulation based on the chitobiose system, where the inhibition caused by a small RNA is relieved by another small RNA called trap-RNA.
Two-level sRNA regulation. Blue is any target mRNA, red is sRNA and green is trap-RNA.
We explore the possibility of using the system to uniquely target and repress any gene of interest, potentially providing unprecedented specificity and control of gene silencing. We furthermore constructed araBAD promoters with varying promoter activities using synthetic promoter libraries.

Experiment: Testing sRNA

Chromosomal knockout

Experiments were performed to verify that the envisioned small RNA based gene silencing is possible. Plasmids containing and strains deleted for the components were constructed providing a biological model. Read more...

Bioinformatics

DTU1 Sequence logo.png

A bioinformatics study was performed to investigate the possibilities of engineering the trap-RNA system to target any gene. The study elucidates interesting features of sequence and secondary structure conservation guiding future application. Read more...

Modeling

Kinetic models of the system are the basis for modeling. Blue is target mRNA, red is small RNA and green is trap-RNA

A framework for characterization of gene silencing was developed to guide rational design and test hypotheses. Steady state analysis revealed that each trap-RNA system has a characteristic fold repression. Read more...

Experiment: Improving araBAD

DTU-Relative promoter activity.png

The dynamic range of the araBAD promoter was expanded by either changing the -10 and -35 elements or randomly changing the promoter using a synthetic promoter library. Experiments were performed characterizing the constructed promoters. Read more..

Data page

DTU1 Data page-figure1.png

The data page provides a description of the constructed BioBricks and how they work. It furthermore provides full links to the iGEM parts registry enabling easy retrieval of each submitted part. Read more...

Results

The bioinformatic study revealed some interesting constrains for engineering novel sRNAs with our gene silencing tool; a terminal poly-U tail, a putative Hfq binding site, a stemloop without sequence constrains, and a terminal stemloop with high sequence conservation. See the results here.

Testing sRNA we were able to show that the target gene chiP can be placed on a plasmid and be regulated by a small RNA. Changing the complementary sequence removes this regulation. See the results here.

Through rational design of the araBAD promoter we managed to reach a higher level of expression from that promoter. Also, we proved that Synthetic Promoter Library can be created for an inducible promoter to expand its dynamic range. See the results here.

The modeling provides a guideline for determining parameters and design of dynamic range of our gene silencing tool. A simulation revealed fast dynamics of gene silencing. See the results here.

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