SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes
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Oxford University Press
2023-01-06
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| Online Access: | http://hdl.handle.net/10261/330806 http://dx.doi.org/10.13039/501100004837 http://dx.doi.org/10.13039/100012818 http://dx.doi.org/10.13039/501100000780 https://api.elsevier.com/content/abstract/scopus_id/85147543065 |
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Ministerio de Ciencia e Innovación (España) Martínez-García, Esteban Fraile, Sofía Algar, Elena Aparicio, Tomás Velázquez, Elena Calles, Belén Tas, Huseyin Blázquez, Blas Martín, Bruno Prieto, Clara Sánchez-Sampedro, Lucas Norholm, Morten H.H. Volke, Daniel C. Wirth, Nicolas T. Dvorak, Pavel Alejaldre, Lorea Grozinger, Lewis Crowther, Matthew Goñi-Moreno, Ángel Nikel, Pablo I. Nogales, Juan de Lorenzo, Victor |
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artículo |
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Martínez-García, Esteban Fraile, Sofía Algar, Elena Aparicio, Tomás Velázquez, Elena Calles, Belén Tas, Huseyin Blázquez, Blas Martín, Bruno Prieto, Clara Sánchez-Sampedro, Lucas Norholm, Morten H.H. Volke, Daniel C. Wirth, Nicolas T. Dvorak, Pavel Alejaldre, Lorea Grozinger, Lewis Crowther, Matthew Goñi-Moreno, Ángel Nikel, Pablo I. Nogales, Juan de Lorenzo, Victor |
| spellingShingle |
Martínez-García, Esteban Fraile, Sofía Algar, Elena Aparicio, Tomás Velázquez, Elena Calles, Belén Tas, Huseyin Blázquez, Blas Martín, Bruno Prieto, Clara Sánchez-Sampedro, Lucas Norholm, Morten H.H. Volke, Daniel C. Wirth, Nicolas T. Dvorak, Pavel Alejaldre, Lorea Grozinger, Lewis Crowther, Matthew Goñi-Moreno, Ángel Nikel, Pablo I. Nogales, Juan de Lorenzo, Victor SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes |
| author_sort |
Martínez-García, Esteban |
| title |
SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes |
| title_short |
SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes |
| title_full |
SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes |
| title_fullStr |
SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes |
| title_full_unstemmed |
SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes |
| title_sort |
seva 4.0: an update of the standard european vector architecture database for advanced analysis and programming of bacterial phenotypes |
| publisher |
Oxford University Press |
| publishDate |
2023-01-06 |
| url |
http://hdl.handle.net/10261/330806 http://dx.doi.org/10.13039/501100004837 http://dx.doi.org/10.13039/100012818 http://dx.doi.org/10.13039/501100000780 https://api.elsevier.com/content/abstract/scopus_id/85147543065 |
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dig-inia-es-10261-3308062024-10-24T20:35:39Z SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes Martínez-García, Esteban Fraile, Sofía Algar, Elena Aparicio, Tomás Velázquez, Elena Calles, Belén Tas, Huseyin Blázquez, Blas Martín, Bruno Prieto, Clara Sánchez-Sampedro, Lucas Norholm, Morten H.H. Volke, Daniel C. Wirth, Nicolas T. Dvorak, Pavel Alejaldre, Lorea Grozinger, Lewis Crowther, Matthew Goñi-Moreno, Ángel Nikel, Pablo I. Nogales, Juan de Lorenzo, Victor Ministerio de Ciencia e Innovación (España) European Commission Comunidad de Madrid Novo Nordisk Foundation Martínez-García, Esteban [0000-0001-8475-7286] Fraile, Sofía [0000-0002-6476-7513] Algar, Elena [0000-0002-0178-3153] Aparicio, Tomás [0000-0002-0133-0461] Velázquez, Elena [0000-0001-6648-1634] Calles, Belén [0000-0003-0603-0115] Tas, Huseyin [0000-0003-4804-2237] Blázquez, Blas [0000-0003-4099-6909] Sánchez-Sampedro, Lucas [0000-0001-9602-2762] Norholm, Morten H.H. [0000-0002-7871-5191] Volke, Daniel C. [0000-0003-0244-2534] Wirth, Nicolas T. [0000-0003-0799-1321] Alejaldre, Lorea [0000-0003-3086-5446] Grozinger, Lewis [0000-0002-9024-701X] Goñi-Moreno, Ángel [0000-0002-2097-2507] Nikel, Pablo I. [0000-0002-9313-7481] Nogales, Juan [0000-0002-4961-0833] de Lorenzo, Victor [0000-0002-6041-2731] Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72] 10 Pág. 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. The SEVA repository has been developed and maintained with funds of the SYCOLIM [ERA-COBIOTECH 2018-PCI2019-111859-2] Project of the Spanish Ministry of Science and Innovation, SYNBIO4FLAV [H2020-NMBP-TR-IND/H2020-NMBP-BIO-2018-814650]; MIX-UP [MIX-UP H2020-BIO-CN-2019-870294] Contracts of the European Union; BIOSINT-CM [Y2020/TCS-6555] Project of the Comunidad de Madrid-European Structural and Investment Funds (FSE, FECER); P.I.N. acknowledges financial support by the Novo Nordisk Foundation [NNF20CC0035580, TARGET (NNF21OC0067996]; European Union's Horizon 2020 Research and Innovation Programme [814418 (SinFonia)]; M.H.H.N. acknowledges funding by the Novo Nordisk Foundation [NNF20CC0035580]; P.D. was funded by Czech Science Foundation Project 22-12505S; A.G.M. was supported by the Grants BioSinT-CM [Y2020/TCS-6555]; CONTEXT (Atracción de Talento Program) [2019-T1/BIO-14053] Projects of the Comunidad de Madrid, MULTI-SYSBIO [PID2020-117205GA-I00]; Severo Ochoa Program for Centres of Excellence in R&D [CEX2020-000999-S] funded by MCIN/AEI/10.13039/501100011033 and the ECCO (ERC-2021-COG-101044360) Contract of the EU. Funding for open access charge: European Commission Grant SYNBIO4FLAV [H2020-NMBP-TR-IND/H2020-NMBP-BIO-2018-814650]. With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2020‐000999‐S) . Peer reviewed 2023-07-11T08:41:28Z 2023-07-11T08:41:28Z 2023-01-06 artículo http://purl.org/coar/resource_type/c_6501 Nucleic Acids Research 51(D1): D1558–D1567(2023) 0305-1048 CEX2020-000999-S http://hdl.handle.net/10261/330806 10.1093/nar/gkac1059 1362-4962 http://dx.doi.org/10.13039/501100004837 http://dx.doi.org/10.13039/100012818 http://dx.doi.org/10.13039/501100000780 36420904 2-s2.0-85147543065 https://api.elsevier.com/content/abstract/scopus_id/85147543065 en #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PCI2019-111859-2/ES/COMUNIDADES MICROBIANAS SINTETICAS PARA LA PRODUCCION DE PRODUCTOS DERIVADOS DEL LIMONENO/ info:eu-repo/grantAgreement/EC/H2020/814650 info:eu-repo/grantAgreement/EC/H2020/870294 S2020/TCS-6555 info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-117205GA-I00/ES/IMPLEMENTAR RELACIONES SOCIALES EN SISTEMAS MULTICELULARES SINTETICOS PARA ALCANZAR BIOCOMPUTACIONES ROBUSTAS Y FIABLES / Centro de Biotecnología y Genómica de Plantas (CBGP) Publisher's version https://doi.org/10.1093/nar/gkac1059 Sí open application/pdf Oxford University Press |