Rebuilding T7

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{{EndyLab}}
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{{Rebuilding T7}}
== Summary ==  
== Summary ==  
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The rebuilding T7 project is an effort to construct a more modelable version of the T7 genome that we can study.  These efforts began with our first designs and testing in [[T7.1]], and are now continuing with the [[T7.2]] project.
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Wild-type T7 is a superb organism for discovering the primary components of a biological system [Studier, 1972].  However, is the original T7 isolate also best suited for understanding how all parts of the phage are organized to encode a functioning whole?
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== People ==
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[[Leon Chan]], [[Drew Endy]], [[Sriram Kosuri]]
==Motivations==
==Motivations==
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We are interested in questions of how the genetic components of an organism are organized on the genome to carryout functions such as development even in the face of significant environmental variations.  However, to rigorously answer these questions, we need to first understand how changes in genome organization lead to changes in the timing and level of gene expression.  However our efforts to create empirical computational models based on observations of the primary genetic elements and mechanisms governing gene expression have fallen short of providing system-level predictive capacity.  It is unclear whether the differences between our measurements and models are due to our inability to parameterize and simulate the complex biophysical processes involved, or our understanding of the biophysical processes is just incorrect or incomplete.  Moving forward, instead of further studying wild-type T7, we can try encoding our understanding of the biophysical processes onto a new genome.  We will try to only encode those functions which we understand, while actively removing those that we don't.  Differences between the behavior of the engineered and wild-type phage will highlight gaps in our understanding, and will lead to follow-on science.
We are interested in questions of how the genetic components of an organism are organized on the genome to carryout functions such as development even in the face of significant environmental variations.  However, to rigorously answer these questions, we need to first understand how changes in genome organization lead to changes in the timing and level of gene expression.  However our efforts to create empirical computational models based on observations of the primary genetic elements and mechanisms governing gene expression have fallen short of providing system-level predictive capacity.  It is unclear whether the differences between our measurements and models are due to our inability to parameterize and simulate the complex biophysical processes involved, or our understanding of the biophysical processes is just incorrect or incomplete.  Moving forward, instead of further studying wild-type T7, we can try encoding our understanding of the biophysical processes onto a new genome.  We will try to only encode those functions which we understand, while actively removing those that we don't.  Differences between the behavior of the engineered and wild-type phage will highlight gaps in our understanding, and will lead to follow-on science.
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===New Model Organism===
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===New Model Organism===
On the other hand, our interest in T7 is somewhat arbitrary.  If we can construct a better model organism that will let us study hypotheses of how the organization of genetic components make up a biophysical system, it may not be necessary to relate that back to the wild type.   
On the other hand, our interest in T7 is somewhat arbitrary.  If we can construct a better model organism that will let us study hypotheses of how the organization of genetic components make up a biophysical system, it may not be necessary to relate that back to the wild type.   
== T7 Versions ==
== T7 Versions ==
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<big>'''[[T7.1]]'''</big> -- Our initial attempt to rebuild the T7 genome.
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=== T7.1 ===
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<big>'''[[T7.2]]'''</big> -- A more ambitious effort that revisits some of our initial ideas that were tabled in T7.1.
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At the start of this work, we were uncertain how many simultaneous changes the wild-type genome could tolerate. Hence we were conservative with our original design. Two goals drove our design of T7.1. ''First'', we wanted to insulate and enable independent manipulation of all identified genetic elements. ''Second'', we wanted the T7.1 genome to encode a viable bacteriophage.   
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== T7 Family ==
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The following phages are the ones most closely related to T7. They have a similar genome organization and mainly differ in presence or absence of non-essential genes, many of which are homologous to homing endonucleases or other parasitic elements.
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* T3 -- see [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12079351&itool=iconabstr&query_hl=13&itool=pubmed_docsum "Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3."]
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* Yersiniophage &phi;A122 -- see [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12923098&itool=iconpmc&query_hl=11&itool=pubmed_docsum "The genome sequence of Yersinia pestis bacteriophage phiA1122 reveals an intimate history with the coliphage T3 and T7 genomes"]
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* Yersiniophage &phi;Ye03-12 -- see [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11222590&itool=iconpmc&query_hl=17&itool=pubmed_docsum "Complete genomic sequence of the lytic bacteriophage phiYeO3-12 of Yersinia enterocolitica serotype O:3"]
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* Pseudomonas putida phage gh-1 -- see [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12842620&itool=iconabstr&query_hl=8&itool=pubmed_docsum "The complete genomic sequence of lytic bacteriophage gh-1 infecting Pseudomonas putida--evidence for close relationship to the T7 group"]
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=== T7.2 ===
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* [[T7_Feature_Conservation|Table showing genomic feature conservation]]
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Five goals will drive our design of T7.2; the first four goals revisit or extend those used in the design of T7.1.  ''First'', we will specify a genome that only includes elements that webelieve contribute to phage gene expression.  Moving beyond our design of T7.1, we will actively erase or delete elements of unknown function.  ''Second'', we will specify a genome that does not include any functions that might be encoded via the physical coupling of multiple genetic elements. ''Third'', our design of T7.2 will enable the unique and selection-independent manipulation of each genetic element via restriction enzymes. ''Fourth'', for practical reasons, our design of T7.2 must encode a viable bacteriophage.  Fifth, to attempt to make our modeling of gene expression easier, we will use standard synthetic elements in place of the natural elements that regulate transcription and translation. Taken together, our design of T7.2 should specify a genome that is simpler to model andmanipulate, in which we have a putative function for each base pair of DNA involved in phage gene expression. Thus, we hypothesize that T7.2 will also encode a dynamicsystem that is easier to model and interact with, relative to the wild type.
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== People ==
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A more distant relative is the marine phage Roseophage SIO1. See [http://aslo.org/lo/toc/vol_45/issue_2/0408.pdf "The complete genomic sequence of the marine phage Roseophage SIO1 shares homology with nonmarine phages"].
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[[Leon Chan]], [[Sriram Kosuri]], [[Drew Endy]]
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[Based on Ian Molineux's chapter in Calendar's "The Bacteriophages" book.]
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==Publications==
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'''Refactoring bacteriophage T7'''<br>
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''Nature/EMBO Molecular Systems Biology'' 13 September 2005 DOI:10.1038/msb4100025<br>
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[[Leon Chan|Leon Y. Chan]], [[Sriram Kosuri]] and [[Drew Endy]]<br>
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[http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html URL]
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[http://openwetware.mit.edu/images/e/ef/Msb4100025.pdf PDF reprint]
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[http://www.nature.com/msb/journal/v1/n1/full/msb4100028.html News & Views]
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[https://dspace.mit.edu/handle/1721.1/27501 October 2004 version]

Current revision

Project pages on
Rebuilding T7

T7.1
Reannotation
Specification
Construction
Evolution

T7.2
Design

back to Endy Lab

Contents

Summary

The rebuilding T7 project is an effort to construct a more modelable version of the T7 genome that we can study. These efforts began with our first designs and testing in T7.1, and are now continuing with the T7.2 project.

People

Leon Chan, Drew Endy, Sriram Kosuri

Motivations

Physical Model to further understand biology

We are interested in questions of how the genetic components of an organism are organized on the genome to carryout functions such as development even in the face of significant environmental variations. However, to rigorously answer these questions, we need to first understand how changes in genome organization lead to changes in the timing and level of gene expression. However our efforts to create empirical computational models based on observations of the primary genetic elements and mechanisms governing gene expression have fallen short of providing system-level predictive capacity. It is unclear whether the differences between our measurements and models are due to our inability to parameterize and simulate the complex biophysical processes involved, or our understanding of the biophysical processes is just incorrect or incomplete. Moving forward, instead of further studying wild-type T7, we can try encoding our understanding of the biophysical processes onto a new genome. We will try to only encode those functions which we understand, while actively removing those that we don't. Differences between the behavior of the engineered and wild-type phage will highlight gaps in our understanding, and will lead to follow-on science.

New Model Organism

On the other hand, our interest in T7 is somewhat arbitrary. If we can construct a better model organism that will let us study hypotheses of how the organization of genetic components make up a biophysical system, it may not be necessary to relate that back to the wild type.

T7 Versions

T7.1 -- Our initial attempt to rebuild the T7 genome.

T7.2 -- A more ambitious effort that revisits some of our initial ideas that were tabled in T7.1.

T7 Family

The following phages are the ones most closely related to T7. They have a similar genome organization and mainly differ in presence or absence of non-essential genes, many of which are homologous to homing endonucleases or other parasitic elements.

A more distant relative is the marine phage Roseophage SIO1. See "The complete genomic sequence of the marine phage Roseophage SIO1 shares homology with nonmarine phages".

[Based on Ian Molineux's chapter in Calendar's "The Bacteriophages" book.]

Publications

Refactoring bacteriophage T7
Nature/EMBO Molecular Systems Biology 13 September 2005 DOI:10.1038/msb4100025
Leon Y. Chan, Sriram Kosuri and Drew Endy
URL PDF reprint News & Views October 2004 version

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