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SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities.

Martínez-García E, Aparicio T, Goñi-Moreno A, Fraile S, de Lorenzo V - Nucleic Acids Res. (2014)

Bottom Line: By adopting simple compositional rules, the SEVA standard facilitates combinations of functional DNA segments that ease both the analysis and the engineering of diverse Gram-negative bacteria for fundamental or biotechnological purposes.The large number of users of the SEVA-DB during its first two years of existence has resulted in a valuable feedback that we have exploited for fixing DNA sequence errors, improving the nomenclature of the SEVA plasmids, expanding the vector collection, adding new features to the web interface and encouraging contributions of materials from the community of users.The SEVA platform is also adopting the Synthetic Biology Open Language (SBOL) for electronic-like description of the constructs available in the collection and their interfacing with genetic devices developed by other Synthetic Biology communities.

View Article: PubMed Central - PubMed

Affiliation: Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain.

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Expanded SEVA nomenclature. Vectors include four modules (antibiotic resistance marker, replication origin, cargo and gadget), which are represented in a code with four unequivocal positions. The first position is for antibiotic resistance markers, numbered 1 to 9 for the first nine and then 9B to 9Z for the next ones. The second position (the plasmid origin of replication) also receive a 1 to 9 code for the first variants and 9B to 9Z for those that follow. The cargo (third position), each cargo is assigned a sole number 1 to n, but the figure can be added with a capital letter in cases of variants of the same module. The fourth position is kept for the gadgets, which receive Greek letters (α to ω). See text for rationale and detailed explanation.
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Figure 2: Expanded SEVA nomenclature. Vectors include four modules (antibiotic resistance marker, replication origin, cargo and gadget), which are represented in a code with four unequivocal positions. The first position is for antibiotic resistance markers, numbered 1 to 9 for the first nine and then 9B to 9Z for the next ones. The second position (the plasmid origin of replication) also receive a 1 to 9 code for the first variants and 9B to 9Z for those that follow. The cargo (third position), each cargo is assigned a sole number 1 to n, but the figure can be added with a capital letter in cases of variants of the same module. The fourth position is kept for the gadgets, which receive Greek letters (α to ω). See text for rationale and detailed explanation.

Mentions: As shown in Figure 2, we consider each plasmid to be composed of four functional modules (antibiotic resistance marker, replication origin, cargo and gadget), which correspond to a code of four unequivocal positions in a cipher. Each position can have one or more numeric symbols as follows. The first position is for the antibiotic resistance marker, the first series of which received a sole numeric code (1 to 9). Beyond that number, a capital letter will be added to ‘9’, starting with an A (9A) and following with 9B, 9C etc. We avoid increasing the numeral beyond 9, as this may cause confusion with the rest of the code. It is unlikely that the new antibiotic resistances will exceed the capacity of such a numbering. Similarly, for the second position, the first nine origins of replication receive a sole numeric code 1 to 9. As before, beyond that figure, a capital letter will be added to ‘9’, starting with an A (9A) and following with 9B, 9C etc. The number of novel origins of replication is implausible to surpass that account. In the third position, each cargo is assigned a sole ordinal numeric code 1 to n (n being unlimited). This is because the number of cargoes will surely grow much faster than the other functional modules and thus this position of the code is not to be restrained. In the cases where there is a variant of the same cargo type (e.g. a new version of a promoterless fluorescent protein gene) we then add a capital letter to the numeral. For example, 7R is a variant of cargo #7 (GFP) that encodes the gene of the mCherry protein. Finally, the fourth position is for the gadgets, which are designated by lower case Greek letters (α to ω). This gives 24 possibilities that in case of completion can similarly be extended with capital Greek letters. For example: a pSEVA code 9C-9E-13-α (abridged: 9C9E13α) means a vector with a 9C antibiotic resistance marker, a 9E origin of replication, bearing cargo #13 and endowed with α gadget. To facilitate the coding and de-coding of the different plasmid ciphers, the SEVA web page includes a tab for generating vector codes and, if such a code is available, to disclose the structure and components of the cognate plasmid to potential users. Since the release of the 1.0 version of the database, the collection has increased the number of origins of replication, cargoes and gadgets (see plasmid list), while the antibiotic resistance markers have remained at the figure of 6.


SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities.

Martínez-García E, Aparicio T, Goñi-Moreno A, Fraile S, de Lorenzo V - Nucleic Acids Res. (2014)

Expanded SEVA nomenclature. Vectors include four modules (antibiotic resistance marker, replication origin, cargo and gadget), which are represented in a code with four unequivocal positions. The first position is for antibiotic resistance markers, numbered 1 to 9 for the first nine and then 9B to 9Z for the next ones. The second position (the plasmid origin of replication) also receive a 1 to 9 code for the first variants and 9B to 9Z for those that follow. The cargo (third position), each cargo is assigned a sole number 1 to n, but the figure can be added with a capital letter in cases of variants of the same module. The fourth position is kept for the gadgets, which receive Greek letters (α to ω). See text for rationale and detailed explanation.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383931&req=5

Figure 2: Expanded SEVA nomenclature. Vectors include four modules (antibiotic resistance marker, replication origin, cargo and gadget), which are represented in a code with four unequivocal positions. The first position is for antibiotic resistance markers, numbered 1 to 9 for the first nine and then 9B to 9Z for the next ones. The second position (the plasmid origin of replication) also receive a 1 to 9 code for the first variants and 9B to 9Z for those that follow. The cargo (third position), each cargo is assigned a sole number 1 to n, but the figure can be added with a capital letter in cases of variants of the same module. The fourth position is kept for the gadgets, which receive Greek letters (α to ω). See text for rationale and detailed explanation.
Mentions: As shown in Figure 2, we consider each plasmid to be composed of four functional modules (antibiotic resistance marker, replication origin, cargo and gadget), which correspond to a code of four unequivocal positions in a cipher. Each position can have one or more numeric symbols as follows. The first position is for the antibiotic resistance marker, the first series of which received a sole numeric code (1 to 9). Beyond that number, a capital letter will be added to ‘9’, starting with an A (9A) and following with 9B, 9C etc. We avoid increasing the numeral beyond 9, as this may cause confusion with the rest of the code. It is unlikely that the new antibiotic resistances will exceed the capacity of such a numbering. Similarly, for the second position, the first nine origins of replication receive a sole numeric code 1 to 9. As before, beyond that figure, a capital letter will be added to ‘9’, starting with an A (9A) and following with 9B, 9C etc. The number of novel origins of replication is implausible to surpass that account. In the third position, each cargo is assigned a sole ordinal numeric code 1 to n (n being unlimited). This is because the number of cargoes will surely grow much faster than the other functional modules and thus this position of the code is not to be restrained. In the cases where there is a variant of the same cargo type (e.g. a new version of a promoterless fluorescent protein gene) we then add a capital letter to the numeral. For example, 7R is a variant of cargo #7 (GFP) that encodes the gene of the mCherry protein. Finally, the fourth position is for the gadgets, which are designated by lower case Greek letters (α to ω). This gives 24 possibilities that in case of completion can similarly be extended with capital Greek letters. For example: a pSEVA code 9C-9E-13-α (abridged: 9C9E13α) means a vector with a 9C antibiotic resistance marker, a 9E origin of replication, bearing cargo #13 and endowed with α gadget. To facilitate the coding and de-coding of the different plasmid ciphers, the SEVA web page includes a tab for generating vector codes and, if such a code is available, to disclose the structure and components of the cognate plasmid to potential users. Since the release of the 1.0 version of the database, the collection has increased the number of origins of replication, cargoes and gadgets (see plasmid list), while the antibiotic resistance markers have remained at the figure of 6.

Bottom Line: By adopting simple compositional rules, the SEVA standard facilitates combinations of functional DNA segments that ease both the analysis and the engineering of diverse Gram-negative bacteria for fundamental or biotechnological purposes.The large number of users of the SEVA-DB during its first two years of existence has resulted in a valuable feedback that we have exploited for fixing DNA sequence errors, improving the nomenclature of the SEVA plasmids, expanding the vector collection, adding new features to the web interface and encouraging contributions of materials from the community of users.The SEVA platform is also adopting the Synthetic Biology Open Language (SBOL) for electronic-like description of the constructs available in the collection and their interfacing with genetic devices developed by other Synthetic Biology communities.

View Article: PubMed Central - PubMed

Affiliation: Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain.

Show MeSH