SEVA 4.0: an update of the Standard European Vector
Architecture database for advanced analysis and programming of
bacterial phenotypes

J 2023

SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes

MARTÍNEZ-GARCÍA, Esteban; Sofía FRAILE; Elena ALGAR; Tomás APARICIO; Elena VELÁZQUEZ et al.

Základní údaje

Originální název

SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes

Autoři

Vydání

Nucleic Acids Research, Oxford University Press, 2023, 0305-1048

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

20801 Environmental biotechnology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 16.700

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/23:00134022

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

Plasmid; database; standardization; synthetic biology

Štítky

14314010, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 12. 7. 2023 11:31, Mgr. Marie Novosadová Šípková, DiS.

Anotace

V originále

The SEVA platform (https://seva-plasmids.com) was launched one decade ago, both as a database (DB) and as a physical repository of plasmid vectors for genetic analysis and engineering of Gram-negative bacteria with a structure and nomenclature that follows a strict, fixed architecture of functional DNA segments. While the current update keeps the basic features of earlier versions, the platform has been upgraded not only with many more ready-to-use plasmids but also with features that expand the range of target species, harmonize DNA assembly methods and enable new applications. In particular, SEVA 4.0 includes (i) a sub-collection of plasmids for easing the composition of multiple DNA segments with MoClo/Golden Gate technology, (ii) vectors for Gram-positive bacteria and yeast and [iii] off-the-shelf constructs with built-in functionalities. A growing collection of plasmids that capture part of the standard—but not its entirety—has been compiled also into the DB and repository as a separate corpus (SEVAsib) because of its value as a resource for constructing and deploying phenotypes of interest. Maintenance and curation of the DB were accompanied by dedicated diffusion and communication channels that make the SEVA platform a popular resource for genetic analyses, genome editing and bioengineering of a large number of microorganisms.

Návaznosti

GA22-12505S, projekt VaV

Název: Syntetické konsorcium kmenů Pseudomonas putida pro biodegradaci a ko-utilizaci (hemi)celulózových polymerů

Investor: Grantová agentura ČR, Syntetické konsorcium kmenů Pseudomonas putida pro biodegradaci a ko-utilizaci (hemi)celulózových polymerů

Citovat

MARTÍNEZ-GARCÍA, Esteban; Sofía FRAILE; Elena ALGAR; Tomás APARICIO; Elena VELÁZQUEZ; Belén CALLES; Huseyin TAS; Blas BLÁZQUEZ; Bruno MARTÍN; Clara PRIETO; Lucas SÁNCHEZ-SAMPEDRO; Morten H H NØRHOLM; Daniel C VOLKE; Nicolas T WIRTH; Pavel DVOŘÁK; Lorea ALEJALDRE; Lewis GROZINGER; Matthew CROWTHER; Angel GOÑI-MORENO; Pablo I NIKEL; Juan NOGALES a Víctor DE LORENZO. SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes. Nucleic Acids Research. Oxford University Press, 2023, roč. 51, D1, s. "D1558"-"D1567", 10 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkac1059.

@article{2237497,
   author = {MartínezandGarcía, Esteban and Fraile, Sofía and Algar, Elena and Aparicio, Tomás and Velázquez, Elena and Calles, Belén and Tas, Huseyin and Blázquez, Blas and Martín, Bruno and Prieto, Clara and SánchezandSampedro, Lucas and Nørholm, Morten H H and Volke, Daniel C and Wirth, Nicolas T and Dvořák, Pavel and Alejaldre, Lorea and Grozinger, Lewis and Crowther, Matthew and GoñiandMoreno, Angel and Nikel, Pablo I and Nogales, Juan and de Lorenzo, Víctor},
   article_number = {D1},
   doi = {https://doi.org/10.1093/nar/gkac1059},
   keywords = {Plasmid; database; standardization; synthetic biology},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes},
   url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1059/6845432},
   volume = {51},
   year = {2023}
}

TY  - JOUR
ID  - 2237497
AU  - Martínez-García, Esteban - Fraile, Sofía - Algar, Elena - Aparicio, Tomás - Velázquez, Elena - Calles, Belén - Tas, Huseyin - Blázquez, Blas - Martín, Bruno - Prieto, Clara - Sánchez-Sampedro, Lucas - Nørholm, Morten H H - Volke, Daniel C - Wirth, Nicolas T - Dvořák, Pavel - Alejaldre, Lorea - Grozinger, Lewis - Crowther, Matthew - Goñi-Moreno, Angel - Nikel, Pablo I - Nogales, Juan - de Lorenzo, Víctor
PY  - 2023
TI  - SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes
JF  - Nucleic Acids Research
VL  - 51
IS  - D1
SP  - "D1558"-"D1567"
EP  - "D1558"-"D1567"
PB  - Oxford University Press
SN  - 03051048
KW  - Plasmid
KW  - database
KW  - standardization
KW  - synthetic biology
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1059/6845432
N2  - The SEVA platform (https://seva-plasmids.com) was launched one decade ago, both as a database (DB) and as a physical repository of plasmid vectors for genetic analysis and engineering of Gram-negative bacteria with a structure and nomenclature that follows a strict, fixed architecture of functional DNA segments. While the current update keeps the basic features of earlier versions, the platform has been upgraded not only with many more ready-to-use plasmids but also with features that expand the range of target species, harmonize DNA assembly methods and enable new applications. In particular, SEVA 4.0 includes (i) a sub-collection of plasmids for easing the composition of multiple DNA segments with MoClo/Golden Gate technology, (ii) vectors for Gram-positive bacteria and yeast and [iii] off-the-shelf constructs with built-in functionalities. A growing collection of plasmids that capture part of the standard—but not its entirety—has been compiled also into the DB and repository as a separate corpus (SEVAsib) because of its value as a resource for constructing and deploying phenotypes of interest. Maintenance and curation of the DB were accompanied by dedicated diffusion and communication channels that make the SEVA platform a popular resource for genetic analyses, genome editing and bioengineering of a large number of microorganisms.
ER  -

MARTÍNEZ-GARCÍA, Esteban; Sofía FRAILE; Elena ALGAR; Tomás APARICIO; Elena VELÁZQUEZ; Belén CALLES; Huseyin TAS; Blas BLÁZQUEZ; Bruno MARTÍN; Clara PRIETO; Lucas SÁNCHEZ-SAMPEDRO; Morten H H NØRHOLM; Daniel C VOLKE; Nicolas T WIRTH; Pavel DVOŘÁK; Lorea ALEJALDRE; Lewis GROZINGER; Matthew CROWTHER; Angel GOÑI-MORENO; Pablo I NIKEL; Juan NOGALES a Víctor DE LORENZO. SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes. \textit{Nucleic Acids Research}. Oxford University Press, 2023, roč.~51, D1, s.~''D1558''-''D1567'', 10 s. ISSN~0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkac1059.

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