T7.1: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
No edit summary |
No edit summary |
||
(3 intermediate revisions by the same user not shown) | |||
Line 1: | Line 1: | ||
{{Rebuilding T7 | {{Rebuilding T7}} | ||
==Background== | ==Background== | ||
Line 20: | Line 20: | ||
#[[T7.1/Reannotation|Reannotation of the T7 Genome]] -- The wild-type T7 genome is a 39,937 base pair linear double-stranded DNA molecule. We annotated the genome by specifying the boundaries of the following functional genetic elements: 57 open reading frames, 57 putative RBSs encoding 60 proteins, and 51 regulatory elements controlling phage gene expression, DNA replication, and genome packaging. A genbank file of the reannotation can be found [http://web.mit.edu/endy/www/ncbi/T7.1/T7.WT.gb here]. | #[[T7.1/Reannotation|Reannotation of the T7 Genome]] -- The wild-type T7 genome is a 39,937 base pair linear double-stranded DNA molecule. We annotated the genome by specifying the boundaries of the following functional genetic elements: 57 open reading frames, 57 putative RBSs encoding 60 proteins, and 51 regulatory elements controlling phage gene expression, DNA replication, and genome packaging. A genbank file of the reannotation can be found [http://web.mit.edu/endy/www/ncbi/T7.1/T7.WT.gb here]. | ||
#[[T7.1/Specification|Specification of T7.1 genome]] -- The designed sequence of T7.1 can be found [http://web.mit.edu/endy/www/ncbi/T7.1/T7.1.gb here]. [[Image:T7-1-sections_alpha-beta.jpg|thumb|T7.1 genome design (sections ''alpha'' and ''beta'').]] | #[[T7.1/Specification|Specification of T7.1 genome]] -- The designed sequence of T7.1 can be found [http://web.mit.edu/endy/www/ncbi/T7.1/T7.1.gb here]. [[Image:T7-1-sections_alpha-beta.jpg|thumb|T7.1 genome design (sections ''alpha'' and ''beta'').]] | ||
#[[T7.1/Construction|Contructing the T7.1 Genome]] | #[[T7.1/Construction|Contructing the T7.1 Genome]] -- We constructed sections ''alpha'' and ''beta''; the as built sequences can be found [[T7.1/Construction#Sequences|here]] | ||
#[[T7.1/Evolution|Evolution of the T7.1 Genome]] -- We are starting to evolve the T7.1 genome to regain some fitness lost during the refactoring. | |||
==References== | ==References== | ||
'''Refactoring bacteriophage T7'''<br> | |||
''Nature/EMBO Molecular Systems Biology'' 13 September 2005 DOI:10.1038/msb4100025<br> | |||
[[Leon Chan|Leon Y. Chan]], [[Sriram Kosuri]] and [[Drew Endy]]<br> | |||
[http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html URL] | |||
[http://openwetware.mit.edu/images/e/ef/Msb4100025.pdf PDF reprint] | |||
[http://www.nature.com/msb/journal/v1/n1/full/msb4100028.html News & Views] | |||
[https://dspace.mit.edu/handle/1721.1/27501 October 2004 version] |
Latest revision as of 10:07, 8 December 2005
Project pages on Rebuilding T7 | |
back to Endy Lab |
Background
Wild-type T7 is a superb organism for discovering the primary components of a natural biological system. However, our experience indicates that the original T7 isolate is not best suited for understanding how all the parts of the phage are arganized to encode a functioning whole. We decided to engineer a surrogate genome, which we designated T7.1, that would be easier to study and extend.
Goals
- We wanted to insulate and enable independent manipulation of all identified genetic elements.
- We wanted the T7.1 genome to encode a viable bacteriophage; at the start of this work, we were uncertain how many simultaneous changes the wild-type genome could tolerate.
Method
- Reannotation of the wild-type T7 genome, thus defining the functional genetic elements
- Specification of T7.1 genome design and sequence
- Construct sections individually
- Construct chimeric phages that contain replace a single wild-type section with a rebuit section
- Combine sections of rebuilt phage into a single rebuilt phage
- Characterize chimeric phage
Progress
- Reannotation of the T7 Genome -- The wild-type T7 genome is a 39,937 base pair linear double-stranded DNA molecule. We annotated the genome by specifying the boundaries of the following functional genetic elements: 57 open reading frames, 57 putative RBSs encoding 60 proteins, and 51 regulatory elements controlling phage gene expression, DNA replication, and genome packaging. A genbank file of the reannotation can be found here.
- Specification of T7.1 genome -- The designed sequence of T7.1 can be found here.
- Contructing the T7.1 Genome -- We constructed sections alpha and beta; the as built sequences can be found here
- Evolution of the T7.1 Genome -- We are starting to evolve the T7.1 genome to regain some fitness lost during the refactoring.
References
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