Plasmid Backbone

The colored arrows above the cargo and AbR modules represent the directionality of the transcription flow of that element

SEVA Plasmid Nomenclature

The figure sketches the expanded rules for naming each of the 4 positions available for composing a complete SEVA code. The first position identifies the antibiotic resistance. The second position is the origin of replication (a sole numeric code 1 to 9 and then a capital letter is added). In case of either variants or addition(s) of either the antibiotic marker or a second replication origin, a lower case letter is then inserted next. The third position is the cargo, which can be mono-function (named 1 to n) or variants/multi-function thereof (number followed by a capital letter). Finally, the fourth position is for the gadgets, which are designated by lowercase Greek letters (α to ω). For instance; pSEVA237M means a KmR plasmid with a pBBR1 origin of replication and a promoterless msfGFP reporter (mono-function). pSEVA2313R means KmR, pBBR1 origin and a PEM7–>mCherry cargo (bi-function). pSEVA 2a2b8Rα means KmR plasmid selectable in Gram-positive hosts with a double RK2-SCP2* replication origin, a bi-functional cargo xylS-Pm–> mCherry and a hok-sok gadget.

Glossary

  • oriV: vegetative origin of plasmid replication
  • oriT: origin of transfer
  • MCS: multiple cloning site
  • AbR: antibiotic resistance cassette
  • Gbk: Genbank file
  • SBOL: Synthetic Biology Open Language

  • Ap: ampicillin (150 ug ml-1 for E. coli and 500 ug ml-1 P. putida).
  • Km: kanamycin (50 ug ml-1 for E. coli and P. putida).
  • Cm: chloramphenicol (30 ug ml-1 for E. coli).
  • Sm: streptomycin (50 ug ml-1 for E. coli and 100 ug ml-1 P. putida).
  • Sp: spectinomycin (50 ug ml-1 for E. coli and 100 ug ml-1 P. putida).
  • Tc: tetracycline (10 ug ml-1 for E. coli and P. putida).
  • Gm: gentamicin (10 ug ml-1 for E. coli and 15-20 ug ml-1P. putida).
  • Tmp: trimethroprim (10 ug ml-1 for E. coli).
  • Am: apramycin (40 ug ml-1 for E. coli and P. putida and 100 ug ml-1 for S. albus)