SynbiSTRAIN: strain and natural bioPart discovery resources of exploitable bacterial species for synthetic biology

SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts

Nucleic Acids Research ◽

10.1093/nar/gkz1024 ◽

2019 ◽

Vol 48 (D1) ◽

pp. D1164-D1170 ◽

Cited By ~ 17

Author(s):

Esteban Martínez-García ◽

Angel Goñi-Moreno ◽

Bryan Bartley ◽

James McLaughlin ◽

Lucas Sánchez-Sampedro ◽

...

Keyword(s):

Synthetic Biology ◽

Bacterial Species ◽

Web Based ◽

Genomic Engineering ◽

Bioinformatic Tools ◽

Synthetic Biology Open Language ◽

User Friendly ◽

Machine Readable ◽

Genetic Constructs

Abstract The Standard European Vector Architecture 3.0 database (SEVA-DB 3.0, http://seva.cnb.csic.es) is the update of the platform launched in 2013 both as a web-based resource and as a material repository of formatted genetic tools (mostly plasmids) for analysis, construction and deployment of complex bacterial phenotypes. The period between the first version of SEVA-DB and the present time has witnessed several technical, computational and conceptual advances in genetic/genomic engineering of prokaryotes that have enabled upgrading of the utilities of the updated database. Novelties include not only a more user-friendly web interface and many more plasmid vectors, but also new links of the plasmids to advanced bioinformatic tools. These provide an intuitive visualization of the constructs at stake and a range of virtual manipulations of DNA segments that were not possible before. Finally, the list of canonical SEVA plasmids is available in machine-readable SBOL (Synthetic Biology Open Language) format. This ensures interoperability with other platforms and affords simulations of their behaviour under different in vivo conditions. We argue that the SEVA-DB will remain a useful resource for extending Synthetic Biology approaches towards non-standard bacterial species as well as genetically programming new prokaryotic chassis for a suite of fundamental and biotechnological endeavours.

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Inducible Plasmid Self-Destruction (IPSD) assisted genome engineering in lactobacilli and bifidobacteria

10.1101/649921 ◽

2019 ◽

Author(s):

Fanglei Zuo ◽

Zhu Zeng ◽

Lennart Hammarström ◽

Harold Marcotte

Keyword(s):

Synthetic Biology ◽

Homologous Recombination ◽

Genetic Engineering ◽

Genome Editing ◽

Genome Engineering ◽

Bacterial Species ◽

Knock Out ◽

Recombination System ◽

A Genome ◽

Selection Of

ABSTRACTGenome engineering is essential for application of synthetic biology in probiotics including lactobacilli and bifidobacteria. Several homologous recombination system-based mutagenesis tools have been developed for these bacteria but still, have many limitations in different species or strains. Here we developed a genome engineering method based on an inducible self-destruction plasmid delivering homologous DNA into bacteria. Excision of the replicon by induced recombinase facilitates selection of homologous recombination events. This new genome editing tool called Inducible Plasmid Self-Destruction (IPSD) was successfully used to perform gene knock-out and knock-in in lactobacilli and bifidobacteria. Due to its simplicity and universality, the IPSD strategy may provide a general approach for genetic engineering of various bacterial species.

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Bacteria-Based Microdevices for the Oral Delivery of Macromolecules

Pharmaceutics ◽

10.3390/pharmaceutics13101610 ◽

2021 ◽

Vol 13 (10) ◽

pp. 1610

Author(s):

Zhenping Cao ◽

Sisi Lin ◽

Jinyao Liu

Keyword(s):

Synthetic Biology ◽

Half Life ◽

Oral Delivery ◽

Biomedical Applications ◽

Bacterial Species ◽

Disease Diagnosis ◽

Review Article ◽

Gi Tract ◽

Oral Ingestion ◽

Engineered Bacteria

The oral delivery of macromolecules is quite challenging due to environmental insults and biological barriers encountered along the gastrointestinal (GI) tract. Benefiting from their living characteristics, diverse bacterial species have been engineered as intelligent platforms to deliver various therapeutics. To tackle difficulties in oral delivery, innovative bacteria-based microdevices have been developed by virtue of advancements in synthetic biology and nanotechnology, with aims to overcome the instability and short half-life of macromolecules in the GI tract. In this review, we summarize the main classes of macromolecules that are produced and delivered through the oral ingestion of bacteria and bacterial derivatives. Furtherly, we discuss the engineering strategies and biomedical applications of these living microdevices in disease diagnosis, bioimaging, and treatment. Finally, we highlight the advantages as well as the limitations of these engineered bacteria used as platforms for the oral delivery of macromolecules and also propose their potential for clinical translation. The results summarized in this review article would contribute to the invention of next-generation bacteria-based systems for the oral delivery of macromolecules.

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Structural analysis of the photosynthetic membrane from Ectothiorhodospira halochloris

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010007727x ◽

1983 ◽

Vol 41 ◽

pp. 740-741

Author(s):

H. Engelhardt ◽

R. Guckenberger ◽

W. Baumeister

Keyword(s):

Lattice Structure ◽

Bacterial Species ◽

Hexagonal Lattice ◽

Reaction Centre ◽

Photosynthetic Membrane ◽

Rhodopseudomonas Viridis ◽

Photosynthetic Membranes ◽

Ectothiorhodospira Halochloris ◽

Main Components

Bacterial photosynthetic membranes contain, apart from lipids and electron transport components, reaction centre (RC) and light harvesting (LH) polypeptides as the main components. The RC-LH complexes in Rhodopseudomonas viridis membranes are known since quite seme time to form a hexagonal lattice structure in vivo; hence this membrane attracted the particular attention of electron microscopists. Contrary to previous claims in the literature we found, however, that 2-D periodically organized photosynthetic membranes are not a unique feature of Rhodopseudomonas viridis. At least five bacterial species, all bacteriophyll b - containing, possess membranes with the RC-LH complexes regularly arrayed. All these membranes appear to have a similar lattice structure and fine-morphology. The lattice spacings of the Ectothiorhodospira haloohloris, Ectothiorhodospira abdelmalekii and Rhodopseudomonas viridis membranes are close to 13 nm, those of Thiocapsa pfennigii and Rhodopseudomonas sulfoviridis are slightly smaller (∼12.5 nm).

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