The BioBricks Foundation:Standards/Technical/Formats

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(Expression / BioFusion format conversion strategies)
(Expression parts (Freiburg iGem2007 team))
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* N-parts are assembled with a different enzyme combination.
* N-parts are assembled with a different enzyme combination.
* not compatible to BioFusion protein parts (frame shift + stop codon), but see below!
* not compatible to BioFusion protein parts (frame shift + stop codon), but see below!
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====Expression / BioFusion format conversion strategies====
 
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====Expression / BioFusion format conversion strategies====
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Until recently, the Silver lab BioFusion format was the only well-described way to compose fusion proteins from (unofficial) BioBricks. Due to the frameshift, the Expression Part format cannot be made compatible to both BBa and BioFusion at the same time. Since I (Raik) am collaborating with BioFusion users, I am constructing a conversion vector that introduces a prefix and suffix that are compatible to both BioFusion and Expression Parts. I would not consider this a good candidate for a real format though.
Until recently, the Silver lab BioFusion format was the only well-described way to compose fusion proteins from (unofficial) BioBricks. Due to the frameshift, the Expression Part format cannot be made compatible to both BBa and BioFusion at the same time. Since I (Raik) am collaborating with BioFusion users, I am constructing a conversion vector that introduces a prefix and suffix that are compatible to both BioFusion and Expression Parts. I would not consider this a good candidate for a real format though.
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=====BioFusion --> Expression part conversion=====
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None really. Introducing the modified flanks by PCR seems the only way.
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=====BioFusion --> Expression part conversion=====
 
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None really. Introducing the modified flanks by PCR seems the only way.
 
== The Berkeley (BBb) Format ==
== The Berkeley (BBb) Format ==

Revision as of 11:23, 20 July 2008

Biobrick Formats: This working group aims to specify a new BioBrick DNA format.


Contents

Aim / Application scenarios for this standard

Formulate a successor to the current BBa physical assembly format of standard biological parts. [add further]

Overview over existing and proposed Biobrick formats

All biobrick formats proposed so far follow the same basic scheme where restriction and ligation of two biobricks forms a new biobrick:


classic Biobrick format (BBa)

This is the format used by most iGem teams and most BioBricks in the MIT registry.

prefix
suffix
5' GAATTC GCGGCCGC T TCTAGA G
   EcoRI    NotI      XbaI
...part...
T ACTAGT A GCGGCCG CTGCAG 3'
   SpeI     NotI    PstI 
Protein coding prefix
5' GAATTC GCGGCCGC T TCTAG
   EcoRI    NotI     XbaI 
ATG.part

Fusing two parts leaves the following scar:

5' ...part A...
TACTAGAG
 *  *
...part B... 3'


description at parts.mit.edu

Advantages

  • standard
  • well tested and documented
  • native protein start codon can be preserved while using RBS parts.
  • large and still growing set of parts

Disadvantages

  • no protein fusions (frame shift, stop codon)
  • a single mutation (at the fused region) can upset the setup?

Biofusion (Silver lab)

The Silver lab modified the classic 1.0 format to allow for protein fusions:

Prefix
Suffix
5' GAATTC GCGGCCGC T TCTAGA
   EcoRI    NotI      XbaI
...part...
ACTAGT A GCGGCCG CTGCAG 3'
 SpeI     NotI    PstI 

Fusing two parts now leaves the following scar:

5' ...part A...
ACTAGA
 T  R
...part B... 3'

description by Silver lab

Advantages

  • in-frame fusion of protein parts
  • restriction-compatible to 1.0 parts -- no new enzymes
  • also protein parts can, theoretically, be fused N-terminally to to BBa protein parts, as long as the frameshift is corrected by an adapter part
  • used by several iGem teams

Disadvantages

  • Arg in scar can be problematic
  • N-terminal Thr-Arg = destabilization signal (N-end rule)
  • Dam methylation blocks cloning when prefix is followed by "TC"
  • unexpected side-effects for users not aware of the shortened prefix/suffix
  • non-coding parts may be not functionally compatible due to the changed bp distance
  • frameshift with respect to what is expected from protein coding 1.0 parts
  • not possible to preserve native protein start (but equivalent to BBa coding part could be constructed)

Expression parts (Freiburg iGem2007 team)

The Freiburg iGem2007 team proposed a more radical modification or rather extension of BBa, which would enable protein fusions but alleviate the disadvantages of the Biofusion format:

Prefix
Suffix
5' GAATTC GCGGCCGC T TCTAGA GT GCCGGC
   EcoRI    NotI     XbaI  Met NgoMIV
...part...
ACCGGT TAAT ACTAGT A GCGGCCG CTGCAG 3'
 AgeI   *    SpeI     NotI    PstI 
"N-part" prefix
5' GAATTC GCGGCCGC T TCTAG
   EcoRI    NotI     XbaI 
ATG.part

Fusing two parts now leaves the following scar:

5' ...part A...
ACCGCC
 T  G
...part B... 3'


description by Freiburg iGem team

For cases where the native ATG needs to be conserved, the Freiburg team introduces an "N-part" which has the classic BBa coding part prefix and the Expression part suffix. N-parts would need to be cut with XbaI in place of NgoMIV.

Advantages

  • in-frame fusion of protein parts
  • benign protein scar
  • N-end rule safe (long protein half-life)
  • provision for preserving native N-terminal while using RBS parts
  • both new enzymes can be heat-inactivated
  • stand-alone protein expression (start + stop in prefix / suffix)
  • full BBa compatibility -- functionally & compositionally equivalent to BBa protein coding part
  • blunt-cutting isochizomer of NgoMIV (NaeI) -- possibility of directional cloning with two inner restriction sites enables part transfer between different formats and other potentially interesting transfer reactions.

Disadvantages

  • N-parts are assembled with a different enzyme combination.
  • not compatible to BioFusion protein parts (frame shift + stop codon), but see below!

Expression / BioFusion format conversion strategies

Until recently, the Silver lab BioFusion format was the only well-described way to compose fusion proteins from (unofficial) BioBricks. Due to the frameshift, the Expression Part format cannot be made compatible to both BBa and BioFusion at the same time. Since I (Raik) am collaborating with BioFusion users, I am constructing a conversion vector that introduces a prefix and suffix that are compatible to both BioFusion and Expression Parts. I would not consider this a good candidate for a real format though.

Expression -> BioFusion conversion vectors

Construction vectors with a modified Freiburg prefix / suffix could bring a protein part in frame with BioFusion parts and remove the STOP between the AgeI and SpeI site. Restriction / ligation with AgeI + NaeI can (theoretically) transfer Expression parts into this conversion vector which can then be used for normal BioFusion cloning (at the cost of adding a T G before and after the part). NaeI is an isoschizomer to NgoMIV but generates blunt ends which should allow for a directional transfer.

5' GAATTC GCGGCCGC T TCTAGA GCCGGC
   EcoRI    NotI     XbaI   NgoMIV
...part...
ACCGGT ACTAGT A GCGGCCG CTGCAG 3'
 AgeI   SpeI     NotI    PstI 
BioFusion --> Expression part conversion

None really. Introducing the modified flanks by PCR seems the only way.

The Berkeley (BBb) Format

BBb is used by several researchers at UC Berkeley and is based on idempotent assembly with BamHI and BglII restriction enzymes. In a nutshell, most plasmids look like this:

Prefix
Suffix
5' GAATTC atg AGATCT
   EcoRI      BglII
...part...
GGATCC taa CTCGAG 3'
BamHI   *   PstI 

Fusing two parts leaves the following scar:

5' ...part A...
GGATCT
 G  S
...part B... 3'

Note, however, that BBb is intended as a minimal physical assembly standard, and only those features needed for interconversion of BBb plasmids are formally defined. Therefore, "atg" and "taa" spacers are not core definitions of the standard.

Formal Definition:

  • A BBb part is a DNA sequence flanked on the 5' end by "GATCT" and on the 3' end by "G" lacking BglII, BamHI, EcoRI, and XhoI restriction sites
  • A BBb vector is a DNA sequence flanked on its 5' end by "GATCC" and on its 3' end by "A"
  • A BBb entry vector has a unique EcoRI site, no BamHI or BglII restriction sites, and at most one XhoI site 5' to the EcoRI site
  • A BBb plasmid is represented as <vector_name>-<part_name> and has the sequence obtained by concatenating the vector and part sequences
  • Further definition constraints are "sub-standards" of the BBb format

Advantages

  • in-frame fusion of protein parts
  • benign protein scar
  • enzymes selected for efficient cutting

Disadvantages

  • BglII cannot be heat-inactivated -- current 3A standard assembly won't work
  • incompatible to BBa format
  • incompatible to BioFusion format

Tom Knight's BBb proposal

Tom Knight has recently proposed to replace BBa by the following format:

Prefix
Suffix
5' GAATTC...ACTAGT
   EcoRI     SpeI
...part...
GCTAGC...CTCGAG 3'
 NheI     PstI 

Fusing two parts would then leave the following scar:

5' ...part A...
GCTAGT
 A  S
...part B... 3'

Advantages

  • in-frame fusion of protein parts
  • benign protein scar
  • N-end rule save
  • introduction of only one new enzyme
  • NheI is comparatively rare in the E. coli genome -- less background fragments from genomic DNA
  • NheI can be heat-inactivated
  • assembly scar ends in ATG
    • RBS parts could thus be redesigned to furnish (start-less) protein parts with the ATG
    • the native N-terminal of a protein part would then be automatically preserved

Disadvantages

  • incompatible to BBa format
  • incompatible to BioFusion format

Comparison of different format proposals

BBa Silver Freiburg Berkeley Knight
protein issues
(1) protein fusion? no yes yes yes yes
(2) good protein scar? n/a no yes yes yes
(3) N-end rule save? n/a no yes yes yes
(4a) native N' after RBS part? coding part no N-part no p-RBS
(4b) native N' after Kozak part? no no no no no
BBa compatibility
(5) same ass. enzymes? yes yes no no no
(6) restriction-compatible? yes yes yes no no
(7) ..side effects? none some none n/a n/a
(8) directional transfer with inner restr. sites? no no sticky/blunt ligation no no
standard assembly issues
(9) heat inactivation? yes yes yes no yes
(10)inner restr. site occurrence in E. coli 240 240 2100 1200 500
(11) enzyme efficiency? ok ok ? good ?
other issues
(12) current adoption? wide some some some none

Explanations:

(2) good meaning small and biochemically nonperturbing

(3) Some N-terminal amino acids are strong destabilization signals in both pro- and eucaryotes. The assembly scar turns into the protein N-terminal if a RBS+start part is coupled with the protein part -- the scar should hence not code for destabilizing residues.

(4a) Some protein parts, in particular signaling peptides, critically depend on preserving their sequence at the N-terminal. That means any additional scar residues between a "start" part and the old N-terminal would disrupt function. Procaryotic RBS tolerate a variable 6bp spacer between RBS and AUG and special parts-layout can shift the assembly scar into this spacer. BBa and Freiburg define a specialized sub-format where the ATG is shifted into the part and partly overlaps with the end of the scar. p-RBS: Tom's assembly scar ends in ATG and RBS parts could thus be redesigned to furnish (start-less) protein parts with the ATG. see: RBS, Kozak explanation

(4b) All bets are, apparently, off for eucaryotic proteins where the Kozak reaches 4 bp (ATG G) into the reading frame. Only a scar-less assembly method would allow us to freely combine special Kozak parts (lacking ATGG) with special N-term protein parts (starting with ATG). Kozak and N-terminal signaling peptides are thus not decomposable with any of the current schemes.

(5) Uses same restriction enzyme combination as the BBa assembly.

(6) The format allows to couple parts with "old" BBa parts using the BBa assembly.

(7) Side effects mean that parts in the new format do not behave exactly like BBa parts after assembly with "old" BBa parts.

(8) Can the part be directionally transferred into other vectors that introduce different flanking sequences (more or less) directly right and left of it? This may be critical for offsite-cutter (IIS) based or other future assembly schemes.

(9) Can all restriction enzymes used be heat-inactivated?

(10) Approximate combined occurrence of the two inner restriction sites in E. coli.

entirely different strategies

IIS restriction and multi-fragment ligation

The IIS restriction strategy from the UCSF iGem2007 team could probably be extended into a more general multi-ligation Biobrick system: UCSF 2007 cloning strategy

BioBrick ++

... was an early (2004) proposal for a more versatile BioBrick format, which somehow didn't catch on. BioBrick ++ is based on a sophisticated combination of IIS (offsite cutters) and nicking restriction enzymes, and was intended to allow both seamless and normal BioBrick assembly, flipping of BioBricks and other operations. There are some disadvantages though [Raik's opinion, add your own view]:

(1) the large combination of restriction sites makes the system not quite easy to understand. (2) ++ was designed without keeping protein fusions in mind -- the proposed standard assembly would again introduce a frameshift and a stop codon, although the more sophisticated blunt assembly would of course work for protein fragments. (3) the different assembly methods produce different frames. (4) Some of the proposed enzymes or ligation schemes may not behave as ideally as assumed (?) (5) Several of the proposed "operations" involve two sequential restriction/ligation/transformation cycles which, in practice, may amount to more work then a normal single step conversion by PCR.

Nevertheless, BioBrick ++ describes, at least, two core innovations that may be very helpful for a second (or third?) generation BioBrick format:

  1. IIS-restriction (offsite cutting) in prefix and suffix uncouples the cohesive ends from the enzyme recognition sites -- overhangs can therefore end directly at the part boundary (allowing for blunt ligation strategies and parts "upgrade")
  2. Construction plasmids can be created with any overhang by inside-out IIS restriction or with nicking enzymes.
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