Difference between revisions of "Help:Plasmid backbones/Nomenclature"

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Plasmids in the Registry of Standard Biological parts adhere to a particular naming convention.  This page describes the details of this naming scheme. 
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[[Help:Plasmid backbones|< Back to Plasmid Help]]
  
−
If you are interested in designing and/or constructing a new BioBricks compatible plasmid and are submitting it to the Registry, please follow this naming convention.  Questions or comments can be directed to [[User:Rshetty|Reshma Shetty]].
+
==Overview==
 +
BioBrick [[Help:Plasmid backbones/Glossary#Plasmid_backbone|plasmid backbone names]] take the form pSB#X#. The letters pSB are an acronym for '''p'''lasmid '''S'''ynthetic '''B'''iology. 
  
−
==pSBxyz-a==
+
*The first number denotes the origin of replication. 
 +
*The letter X identifies the antibiotic resistance marker(s) present in the vector.  Plasmid backbones with multiple resistance markers have multiple, successive letters. 
 +
*The last number in the plasmid backbone name is a version number to differentiate between the various implementations of the pSB series of plasmid backbones. 
  
−
pSB = plasmid Synthetic Biology<br>
+
When referring to both a BioBrick standard biological part and the plasmid backbone in which it is cloned, the convention is to use the form [plasmid backbone name]-[part number] like pSB4K5-T9003.  To refer to BioBrick standard plasmid backbones to be used for construction of BioBrick parts, use the full plasmid backbone name and default cloned part.  For example, [[Part:pSB4A3|pSB4A3]]-[[Part:BBa_P1010|P1010]], [[Part:pSB1A10|pSB1A10]]-[[Part:BBa_P1010|P1010]], [[Part:pSB4K5|pSB4K5]]-[[Part:BBa_I52002|I52002]] and [[Part:pSB3T5|pSB3T5]]-[[Part:BBa_I52001|I52001]] are all available construction plasmids from the Registry of Standard Biological Parts.  However, for convenience, these [[Help:Plasmids/Glossary#Construction_plasmid|construction plasmid]] names are often abbreviated to pSB4A3, pSB1A10, pSB4K5 and pSB3T5, respectively. 
−
x = origin of replication<br>
+
−
y = selection marker<br>
+
−
z = version number<br>
+
−
-a = insert
+
  
−
===Origin of replication===
+
New plasmid-based vectors [[Help:Plasmid backbones/Construction|constructed]] from [[Part:BBa_I51020|BBa_I51020]] should be named pSB#X5-I52002 where the # is determined by the identity of the replication origin and the letter X is determined by the antibiotic resistance marker(s) present.  To expand the BioBrick vector nomenclature, submit new vectors or vector parts to the Registry of Standard Biological Parts and then document any new annotation needed here.  [http://biobricks.org The BioBricks Foundation] will lead the standards setting process should any revisions to the BioBrick plasmid backbone nomenclature beyond addition of new replication origins, antibiotic resistance markers and version numbers be needed.
−
*1= pUC19-derived pMB1 (in pSB series)
+
−
*2 = pSCANS-derived
+
−
*3 = p15A pMR101-derived
+
−
*4 = rep101, repA pSC101-derived
+
−
*5 = F plasmid
+
−
*6 = pBR322
+
  
−
===Selection marker===
+
==Origin of replication==
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*X = none
+
BioBrick plasmid backbone names take the form pSB#X#.  The first number indicates the identity of the origin of replication.  The number, corresponding replication origin, expected plasmid copy number and typical purpose of that origin are listed.  To expand this list to include additional replication origins, obtain an account with the Registry of Standard Biological Parts and edit this page.
−
*A = ampicillin
+
−
*C = chloramphenicol
+
−
*E = erythromycin
+
−
*G = gentamycin
+
−
*K = kanamycin
+
−
*N = neomycin
+
−
*Na = nalidixic acid
+
−
*R = rifampicin
+
−
*S = spectinomycin
+
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*St = streptomycin
+
−
*T = tetracycline
+
−
*Tm = trimethoprim
+
−
*Z = zeocin
+
−
*AK = kanamycin and ampicillin
+
−
*KT = kanamycin and tetracycline
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*AKT = ampicillin and kanamycin and tetracycline
+
−
*AC = ampicillin and chloramphenicol
+
−
… etc
+
  
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===Version number===
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{| border="1" cellpadding="4" cellspacing="0" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" <!-- This line here formats your table for you.  Change the code to change the formatting of your table.-->
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(used to indicate miscellaneous interesting changes to backbone)
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! align="left" style="background:#f0f0f0;"| Number
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*0 = nothing
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! align="left" style="background:#f0f0f0;"| Replication origin
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*1 = complete Biobricks insertion site
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! align="left" style="background:#f0f0f0;"| [http://openwetware.org/wiki/Molecular_Cloning Copy number]
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*2 = 5’ terminator and complete Biobricks insertion site
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! align="left" style="background:#f0f0f0;"| Purpose
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*3 = 5’ terminator and complete Biobricks insertion site and 3’ terminator
+
|-
−
*4 = misc restriction sites removed for the T7 project
+
| 1
−
*5 = Held for next generation of cloning plasmid.  See [http://openwetware.org/wiki/Synthetic_Biology:Vectors/Parts].
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| modified pMB1 derived from pUC19
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*10 = Held for a version of Jason's measurement plasmid
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| 500-700
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*11 = Held for a version of Jason's measurement plasmid
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| Easy plasmid DNA purification
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*12 = Held for a version of Jason's measurement plasmid
+
|-
 +
| 2
 +
| F and P1 lytic derived from [http://www.genome.bnl.gov/Vectors/pscans.php pSCANS-1-BNL]
 +
| 1-2 inducible to high copy
 +
| Inducible copy number
 +
|-
 +
| 3
 +
| p15A derived from pMR101
 +
| 10-12
 +
| Multi-plasmid engineered systems
 +
|-
 +
| 4
 +
| rep101, repA derived from pSC101
 +
| ~5
 +
| Small cell to cell copy number variation
 +
|-
 +
| 5
 +
| derived from F plasmid
 +
| 1-2
 +
| Improved plasmid stability
 +
|-
 +
| 6
 +
| pMB1 derived from pBR322
 +
| 15-20
 +
| Multi-plasmid engineered systems
 +
|-
 +
| 7
 +
| broad host range origin
 +
|
 +
| by Ichiro et al.
 +
|-
 +
| 8
 +
| pSC101TS
 +
|
 +
| temperature sensitive origin, only propagates at 30C
 +
|-
 +
| 9
 +
|
 +
|
 +
|
 +
|}
  
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===Insert===
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==Selection marker==
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*generally a BioBricks part number where multiple parts are separated by periods
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BioBrick plasmid backbone names take the form pSB#X#.  The letter X indicates the antibiotic to which the plasmid backbone confers resistance.  The letter code and corresponding antibiotic resistance marker are listed.  The absence of a letter indicates that no antibiotic resistance marker is present.  Multiple resistance markers in a vector are indicated by successive codes in alphabetical order e.g., AK, StT, AC and AKT.  To expand this list to include additional antibiotic resistance markers, obtain an account with the Registry of Standard Biological Parts and edit this page.
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*no dash = no insert
+
 
−
*-P1010 = ccd operon insert
+
{| border="1" cellpadding="4" cellspacing="0" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" <!-- This line here formats your table for you.  Change the code to change the formatting of your table.-->
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**-1 = ccdB <-- this has now become legacy nomenclature.
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! align="left" style="background:#f0f0f0;"| Code
 +
! align="left" style="background:#f0f0f0;"| Antibiotic
 +
|-
 +
| A
 +
| ampicillin
 +
|-
 +
| C
 +
| chloramphenicol
 +
|-
 +
| E
 +
| erythromycin
 +
|-
 +
| G
 +
| gentamycin
 +
|-
 +
| K
 +
| kanamycin
 +
|-
 +
| N
 +
| neomycin
 +
|-
 +
| Na
 +
| nalidixic acid
 +
|-
 +
| R
 +
| rifampicin
 +
|-
 +
| S
 +
| spectinomycin
 +
|-
 +
| St
 +
| streptomycin
 +
|-
 +
| T
 +
| tetracycline
 +
|-
 +
| Tm
 +
| trimethoprim
 +
|-
 +
| Z
 +
| zeocin
 +
|}
 +
 
 +
==Version number==
 +
BioBrick vector names take the form pSB#X#.  The second number indicates the BioBrick plasmid backbone version number.  The version number, key features, purpose for which that version was designed, example vector and vector designer(s) are listed.  To expand this list to assign new vector version numbers, obtain an account with the Registry of Standard Biological Parts and edit this page.
 +
 
 +
{| border="1" cellpadding="4" cellspacing="0" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" <!-- This line here formats your table for you. Change the code to change the formatting of your table.-->
 +
! align="left" style="background:#f0f0f0;"| Number
 +
! align="left" style="background:#f0f0f0;"| Key features
 +
! align="left" style="background:#f0f0f0;"| Purpose
 +
! align="left" style="background:#f0f0f0;"| Example
 +
! align="left" style="background:#f0f0f0;"| Designer
 +
|-
 +
| 0
 +
| absent or incomplete BioBrick cloning site
 +
|                         
 +
| [[Part:pSB2K0|pSB2K0]]
 +
| Brookhaven National Lab
 +
|-
 +
| 1
 +
| complete BioBrick cloning site (BCS) 
 +
| assembly of BioBrick parts
 +
| [[Part:pSB4A1|pSB4A1]]
 +
| Reshma Shetty
 +
|-
 +
| 2
 +
| 5' terminator and BCS
 +
| transcriptional insulation of plasmid backbone upstream of cloned BioBrick part
 +
| [[Part:pSB1A2|pSB1A2]]
 +
| Tom Knight
 +
|-
 +
| 3
 +
| 5' terminator and BCS and 3' terminator
 +
| transcriptional insulation of plasmid backbone downstream of cloned BioBrick part
 +
| [[Part:pSB1AC3|pSB1AC3]]
 +
| Reshma Shetty & Tom Knight
 +
|-
 +
| 4
 +
| pSB2K3-derived plasmid backbone free of many restriction sites
 +
| Genome refactoring<cite>Chan-Mol-Syst-Biol-2005</cite>
 +
| [[Part:pSB2K4|pSB2K4]]
 +
| Leon Chan
 +
|-
 +
| 5
 +
| constructed from BioBrick base vector
 +
|  standardized BioBrick vector design
 +
| [[Part:pSB4K5|pSB4K5]]
 +
| Reshma Shetty
 +
|-
 +
| 6
 +
| Reserved for some plasmid backbone versions that the Berkeley iGEM team has made
 +
|
 +
|
 +
|
 +
|-
 +
| 7
 +
| BCS flanked by terminator [[Part:BBa_B0015|BBa_B0015]]         
 +
| transcriptional insulation of cloned BioBrick part
 +
| [[Part:pSB1A7|pSB1A7]]
 +
| Karmella Haynes
 +
|-
 +
| 8
 +
| BCS followed by eukaryotic terminator
 +
| for cloning of eukaryotic composite parts
 +
| [[Part:pSB1AK8|pSB1AK8]]
 +
| Monika Ciglic and the 2007 Slovenian iGEM team
 +
|-
 +
| 9
 +
|
 +
||
 +
| 
 +
|-
 +
| 10
 +
| [http://openwetware.org/index.php?title=Endy:Screening_plasmid/v1.0 Screening plasmid v1.0]
 +
| characterization of single input, single output transcriptional devices
 +
| [[Part:pSB1A10|pSB1A10]]
 +
| Josh Michener  & Jason Kelly
 +
|-
 +
| 11
 +
| Reserved for a version of Jason's measurement plasmid
 +
|
 +
|
 +
|
 +
|-
 +
| 12
 +
| Reserved for a version of Jason's measurement plasmid
 +
|
 +
|
 +
|
 +
|-
 +
| 13
 +
| Reserved for a version of Reshma's measurement plasmid
 +
|
 +
|
 +
|
 +
|-
 +
| 15-19
 +
| Reserved for new lambda red compatible BioBrick backbones.
 +
| For chromosomal integration of single gene and operon of BioBricks.
 +
|
 +
| Erik Lundin
 +
|-
 +
| 20-29
 +
| Reserved for a version of Berkeley iGEM team's plasmids
 +
|
 +
|
 +
|
 +
|-
 +
| 30
 +
| Expression Plasmid Backbone harbouring a LacI repressible T7 Promotor right in front of the BB prefix based on pSBXX3 backbones.
 +
|
 +
| [[Part:BBa_K1362091|pSB1A30]]
 +
| iGEM team Heidelberg 2014
 +
|-
 +
| 50
 +
| Expression Plasmid Backbone harbouring a LacI repressible T7 Promotor right in front of the BB prefix based on pSBXX5 backbones.
 +
|
 +
| [[Part:BBa_K1362095|pSB1A50]]
 +
|iGEM team Heidelberg 2014
 +
|-
 +
| 51
 +
|  pBAD plasmid vector with an AraC operon with D family cameleon (D4) inserted in
 +
|  pBAD was used as vector backbone for construct for the TPHS_San_Diego 2018 iGEM team
 +
| pSB4K5
 +
|  Allison Bien
 +
|}
  
 
==Contact==
 
==Contact==
  
 
Questions or comments can be directed to [[User:Rshetty|Reshma Shetty]].
 
Questions or comments can be directed to [[User:Rshetty|Reshma Shetty]].
 +
 +
==References==
 +
<biblio>
 +
#Chan-Mol-Syst-Biol-2005 pmid=16729053
 +
</biblio>
 +
 +
'''Engineering BioBrick vectors from BioBrick parts'''<br>
 +
''Journal of Biological Engineering,'' 2008 Apr 14;2:5<br>
 +
Reshma Shetty, Drew Endy, Tom Knight<br>
 +
[http://www.jbioleng.org/content/2/1/5 URL]

Latest revision as of 11:05, 10 October 2018

< Back to Plasmid Help

Overview

BioBrick plasmid backbone names take the form pSB#X#. The letters pSB are an acronym for plasmid Synthetic Biology.

  • The first number denotes the origin of replication.
  • The letter X identifies the antibiotic resistance marker(s) present in the vector. Plasmid backbones with multiple resistance markers have multiple, successive letters.
  • The last number in the plasmid backbone name is a version number to differentiate between the various implementations of the pSB series of plasmid backbones.

When referring to both a BioBrick standard biological part and the plasmid backbone in which it is cloned, the convention is to use the form [plasmid backbone name]-[part number] like pSB4K5-T9003. To refer to BioBrick standard plasmid backbones to be used for construction of BioBrick parts, use the full plasmid backbone name and default cloned part. For example, pSB4A3-P1010, pSB1A10-P1010, pSB4K5-I52002 and pSB3T5-I52001 are all available construction plasmids from the Registry of Standard Biological Parts. However, for convenience, these construction plasmid names are often abbreviated to pSB4A3, pSB1A10, pSB4K5 and pSB3T5, respectively.

New plasmid-based vectors constructed from BBa_I51020 should be named pSB#X5-I52002 where the # is determined by the identity of the replication origin and the letter X is determined by the antibiotic resistance marker(s) present. To expand the BioBrick vector nomenclature, submit new vectors or vector parts to the Registry of Standard Biological Parts and then document any new annotation needed here. [http://biobricks.org The BioBricks Foundation] will lead the standards setting process should any revisions to the BioBrick plasmid backbone nomenclature beyond addition of new replication origins, antibiotic resistance markers and version numbers be needed.

Origin of replication

BioBrick plasmid backbone names take the form pSB#X#. The first number indicates the identity of the origin of replication. The number, corresponding replication origin, expected plasmid copy number and typical purpose of that origin are listed. To expand this list to include additional replication origins, obtain an account with the Registry of Standard Biological Parts and edit this page.

Number Replication origin [http://openwetware.org/wiki/Molecular_Cloning Copy number] Purpose
1 modified pMB1 derived from pUC19 500-700 Easy plasmid DNA purification
2 F and P1 lytic derived from [http://www.genome.bnl.gov/Vectors/pscans.php pSCANS-1-BNL] 1-2 inducible to high copy Inducible copy number
3 p15A derived from pMR101 10-12 Multi-plasmid engineered systems
4 rep101, repA derived from pSC101 ~5 Small cell to cell copy number variation
5 derived from F plasmid 1-2 Improved plasmid stability
6 pMB1 derived from pBR322 15-20 Multi-plasmid engineered systems
7 broad host range origin by Ichiro et al.
8 pSC101TS temperature sensitive origin, only propagates at 30C
9

Selection marker

BioBrick plasmid backbone names take the form pSB#X#. The letter X indicates the antibiotic to which the plasmid backbone confers resistance. The letter code and corresponding antibiotic resistance marker are listed. The absence of a letter indicates that no antibiotic resistance marker is present. Multiple resistance markers in a vector are indicated by successive codes in alphabetical order e.g., AK, StT, AC and AKT. To expand this list to include additional antibiotic resistance markers, obtain an account with the Registry of Standard Biological Parts and edit this page.

Code Antibiotic
A ampicillin
C chloramphenicol
E erythromycin
G gentamycin
K kanamycin
N neomycin
Na nalidixic acid
R rifampicin
S spectinomycin
St streptomycin
T tetracycline
Tm trimethoprim
Z zeocin

Version number

BioBrick vector names take the form pSB#X#. The second number indicates the BioBrick plasmid backbone version number. The version number, key features, purpose for which that version was designed, example vector and vector designer(s) are listed. To expand this list to assign new vector version numbers, obtain an account with the Registry of Standard Biological Parts and edit this page.

Number Key features Purpose Example Designer
0 absent or incomplete BioBrick cloning site pSB2K0 Brookhaven National Lab
1 complete BioBrick cloning site (BCS) assembly of BioBrick parts pSB4A1 Reshma Shetty
2 5' terminator and BCS transcriptional insulation of plasmid backbone upstream of cloned BioBrick part pSB1A2 Tom Knight
3 5' terminator and BCS and 3' terminator transcriptional insulation of plasmid backbone downstream of cloned BioBrick part pSB1AC3 Reshma Shetty & Tom Knight
4 pSB2K3-derived plasmid backbone free of many restriction sites Genome refactoringChan-Mol-Syst-Biol-2005 pSB2K4 Leon Chan
5 constructed from BioBrick base vector standardized BioBrick vector design pSB4K5 Reshma Shetty
6 Reserved for some plasmid backbone versions that the Berkeley iGEM team has made
7 BCS flanked by terminator BBa_B0015 transcriptional insulation of cloned BioBrick part pSB1A7 Karmella Haynes
8 BCS followed by eukaryotic terminator for cloning of eukaryotic composite parts pSB1AK8 Monika Ciglic and the 2007 Slovenian iGEM team
9
10 [http://openwetware.org/index.php?title=Endy:Screening_plasmid/v1.0 Screening plasmid v1.0] characterization of single input, single output transcriptional devices pSB1A10 Josh Michener & Jason Kelly
11 Reserved for a version of Jason's measurement plasmid
12 Reserved for a version of Jason's measurement plasmid
13 Reserved for a version of Reshma's measurement plasmid
15-19 Reserved for new lambda red compatible BioBrick backbones. For chromosomal integration of single gene and operon of BioBricks. Erik Lundin
20-29 Reserved for a version of Berkeley iGEM team's plasmids
30 Expression Plasmid Backbone harbouring a LacI repressible T7 Promotor right in front of the BB prefix based on pSBXX3 backbones. pSB1A30 iGEM team Heidelberg 2014
50 Expression Plasmid Backbone harbouring a LacI repressible T7 Promotor right in front of the BB prefix based on pSBXX5 backbones. pSB1A50 iGEM team Heidelberg 2014
51 pBAD plasmid vector with an AraC operon with D family cameleon (D4) inserted in pBAD was used as vector backbone for construct for the TPHS_San_Diego 2018 iGEM team pSB4K5 Allison Bien

Contact

Questions or comments can be directed to Reshma Shetty.

References

<biblio>

  1. Chan-Mol-Syst-Biol-2005 pmid=16729053

</biblio>

Engineering BioBrick vectors from BioBrick parts
Journal of Biological Engineering, 2008 Apr 14;2:5
Reshma Shetty, Drew Endy, Tom Knight
[http://www.jbioleng.org/content/2/1/5 URL]