Synthetic Biology:Vectors/Single copy plasmid

Goal

Design and fabricate a single copy vector in which BioBricks devices can be characterized. To date most characterization work has been done in low or high copy vectors which have several issues including

1. Copy number is uncertain or variable making it difficult to infer PoPS per DNA copy.
2. At high copy, devices place a high metabolic load on the cell thereby altering host physiology and observed device behavior.

The proposed solution to these two problems is to characterize devices at single copy in the cell. Obviously, such a vector will vary between 1 and 2 copies per cell over the cell cycle but nevertheless will hopefully present an improvement over the current situation. The advantage of using a single copy plasmid rather than simply integrating the device into the genome is that a separate plasmid offers some isolation from the host and makes moving the device between different host strains slightly easier.

Design

5' BBa_P1010 -- BBa_I50020 --

BBsuffix -- TOPO site -- translational stop sequence -- plasmid barcode -- BBa_B0054 -- VR -- BBa_I50000 -- <BBa_B0056 or BBa_B0057< -- <antibiotic resistance cassette< --

VF2 -- BBa_B0055 -- plasmid barcode -- translational stop sequence -- TOPO site -- BB prefix 3'

Proposed features

• F plasmid backbone
• positive selection marker (i.e. ccdB or sacB) in between BioBricks restrictions sites to facilitate cloning
• a high copy origin in the multiple cloning site to enable easy purification of the vector
• strong terminators flanking the BioBricks insertion site
• no loxP or cos insertion sites or Tn7 attachment sites?
  • I can't think of an obvious use of these sites unless we want to build in the capability for integrating onto the genome. However, wouldn't it make more sense to build in recombination capabilities onto a higher copy number vector than this?
• no blue-white screening?
  • inclusion of a lacZα fragment would restrict its use as a part
• multiple versions with different antibiotic resistance markers
• no selection system for mammalian cells
• VF2 and VR sites
• Unique tag near but outside the cloning sites for identification during sequencing. (from Randy)
• orient the antibiotic resistance cassette on the reverse strand from the BioBricks insertion site
• Topoisomerase I mediated TA cloning
• include a sequence with translational stops in all frames flanking each side of the MCS
• need to include a terminator downstream of the antibiotic resistance cassette (use a terminator from the original BioBricks plasmids)
• Every plasmid should have AmpR plus another resistance marker.
• Apparently when you sequence, the first 30 bp or so are really bad (see also the talk page) but there can also be a bad spot at around base pair 80. So the verification primers should be about 100bp away from the multiple cloning site.

Drawbacks

• Can only be used in F^- strains
• Should likely be used in recA^- strains to avoid integration onto the genome and ensure plasmid stability.
• It is unclear whether this vector would truly be operating at single copy. If it is not, perhaps it is easier to stick with the pSB2* plasmids.

Planning

Current status

The following parts have been designed

• <bbpart>BBa_I50000</bbpart>: F plasmid backbone with BioBricks restriction sites removed
• <bbpart>BBa_I50020</bbpart>: high copy origin from pSB1A3
• <bbpart>BBa_B0055</bbpart>: upstream flanking terminator
• <bbpart>BBa_B0054</bbpart>: downstream flanking terminator
• <bbpart>BBa_B0056</bbpart>: bidirectional terminator from E. coli his operon
• <bbpart>BBa_B0057</bbpart>: forward terminator
• <bbpart>BBa_P1002</bbpart>: cassette providing ampicillin resistance (from Tom Knight)
• <bbpart>BBa_P1003</bbpart>: cassette providing kanamycin resistance (from Tom Knight)

The following parts have been designed, fabricated and tested

• <bbpart>BBa_P1001</bbpart>: cassette providing tetracycline resistance (from Austin Che)
• <bbpart>BBa_P1000</bbpart>: cassette providing chloramphenicol resistance (from Austin Che)
• <bbpart>BBa_I1000</bbpart> or <bbpart>BBa_P1010</bbpart>: ccd operon in BioBricks format (from Leon Chan)

Additional sequence upstream of prefix (see Non-functional DNA sequences and Topoisomerase I mediated TA cloning)

   Translational stop       TOPO site
5' T T A G T T A G T T A G  C C C T T N N N G A C T C 3'
3' A A T C A A T C A A T C  G G G A A N N N C T G A G 5'

Additional sequence downstream of suffix (see Non-functional DNA sequences and Topoisomerase I mediated TA cloning)

   TOPO site                  Translational stop
5' G A G T C N N N A A G G G  T T A G T T A G T T A G 3'
3' C T C A G N N N T T C C C  A A T C A A T C A A T C 5'

To do list

• Design unique identifiers for vectors: a plasmid barcode.
• Design a pSC101 origin.
• Design a pBR322 origin.
• Design a R6K origin. EZ-Tn5™ <R6Kγori /KAN-2> Sequence general information
• Possibly need to reorient antibiotic sequences.

To be decided

• Choose between manual assembly of vector modules or direct synthesis of all plasmid variants
  • Can we get a price break for synthesizing multiple plasmid variants?
  • How many assemblies would we need to do?
  • Is there a hybrid approach? Could we PCR the F plasmid backbone since its long and then have the collection of smaller parts (that would otherwise involve several assemblies) synthesized? Maybe a partial synthesis approach would help get around the issue of constructing a BioBricks insertion site?--BC
    • PCR'ing the F plasmid backbone is not very practical since there are several BioBricks sites in the backbone each of which would need to be individually mutated out. It is unlikely that there is anyone who is willing to do this much work. Therefore, the current plan is to synthesize the backbone. -- RS
• If all the vector components are specified in BioBricks format, how do we construct a BioBricks insertion site?
  • Blunt-end ligation?
  • Other restriction enzyme sites?
  • PCR
  • Use special restriction sites for vector construction (Austin's idea). Expanding on this, we could define a new idempotent assembly standard for exclusive use for vector components.

To be determined

• Are we sure that F plasmids are really at 1-2 copies per cell? Why was pSB2K3-1 measured to be higher than that?
  • From Johann Paulsson: it is unclear how tight of control F plasmid based vectors have over copy number fluctuation. Having the vector exist at single copy strongly depends on generation time. Faster growing cells are more likely to have multiple overlapping rounds of replications occurring simultaneously.
• What parts of the F plasmid are responsible for integration onto the genome? Can we omit them?
  • cos and/or loxP sites are generally used for integration in the genome. Currently, I have no plans to include them in this vector.
• Many of the existing BACs only seem to have a partial sopC CDS, do we want the rest?
  • pSMART VC vector appears to have a more complete sopC region. This may lead to tighter control of copy number.
• A set of orthogonal single copy replication origins to allow multiple vectors to be maintained in a cell. Can we have a set of vectors with F and P1 origins?--BC 17:36, 31 Oct 2005 (EST)
  • Not sure this is possible. I believe the P1 origins use the par set of genes to maintain single copy whereas the F origins use the sop set of genes. The two sets are pretty homologous to eachother and therefore likely incompatible. I need to check on this more. -- RS
  • Perhaps derivatives from the two plasmids the Berkeley iGEM team used might permit two single copy vectors to be used simultaneously. -- RS
• Should the flanking terminators be placed outside the VF2 and VR primer binding sites? Is it useful to have them within? Moving the flanking terminators outside the primer binding sites means fewer bases to sequence through before hitting the part. Alternatively, we could move the terminators to just inside the primers since anyway ~40bp are needed before sequence data is of high quality.
  • Tom thinks this doesn't matter but suggests including some translational stops around the multiple cloning site

Notes

See the list of parts for plasmid engineering.

See notes on bacterial artificial chromosomes.

See Synthetic Biology:Vectors for information on vector nomenclature, existing vectors and vectors that we would like constructed.

Vectors has a lot of general information on vectors.