pLannotate: engineered plasmid annotation

Barrick, Jeffrey E.

doi:10.1093/nar/gkab374

Cited by 28 publications

(22 citation statements)

References 27 publications

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“…To deal with such features and constraints, cMatch adopts a very different strategy to recent annotation tools such as pLannotate, which rely on BLAST for matching and do not use any positional and combinatorial information. First, cMatch uses the highly validated Smith–Waterman algorithm, , instead of BLAST, which is better suited to genome length sequences.…”

Section: Resultsmentioning

confidence: 99%

PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies

et al. 2022

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We present here a newly developed workflow—which we have called PASIV—designed to provide a solution to a practical problem with design of experiments (DoE) methodology: i.e., what can be done if the scoping phase of the DoE cycle is severely hampered by burden and toxicity issues (caused by either the metabolite or an intermediary), making it unreliable or impossible to proceed to the screening phase? PASIV—standing for pooled approach, screening, identification, and visualization—was designed so the (viable) region of interest can be made to appear through an interplay between biology and software. This was achieved by combining multiplex construction in a pooled approach (one-pot reaction) with a viability assay and with a range of bioinformatics tools (including a novel construct matching tool). PASIV was tested on the exemplar of the lycopene pathway—under stressful constitutive expression—yielding a region of interest with comparatively stronger producers.

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Section: Resultsmentioning

confidence: 99%

PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies

et al. 2022

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“…Recently, McGuffie et al developed an open source web server to help annotate plasmids automatically. 10 BLAST has been integrated with ICE to allow users to automatically annotate a sequence of interest, based on publicly accessible annotated sequences that are available in the web of registries and other data sources, to increase the quantity, accuracy and quality of available annotations.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…Annotating a DNA sequence is, therefore, an essential step in research activity, but manual sequence annotation is still a very tedious and time-consuming activity, subject to the potential errors of any “by hand” process and creating a bottleneck for high-throughput workflows and pipelines. Recently, McGuffie et al developed an open source web server to help annotate plasmids automatically . BLAST has been integrated with ICE to allow users to automatically annotate a sequence of interest, based on publicly accessible annotated sequences that are available in the web of registries and other data sources, to increase the quantity, accuracy and quality of available annotations.…”

Section: Results and Discussionmentioning

confidence: 99%

BioParts—A Biological Parts Search Portal and Updates to the ICE Parts Registry Software Platform

et al. 2021

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Capturing, storing, and sharing biological DNA parts data are integral parts of synthetic biology research. Here, we detail updates to the ICE biological parts registry software platform that enable these processes, describe our implementation of the Web of Registries concept using ICE, and establish Bioparts, a search portal for biological parts available in the public domain. The Web of Registries enables standalone ICE installations to securely connect and form a distributed parts database. This distributed database allows users from one registry to query and access plasmid, strain, (DNA) part, plant seed, and protein entry types in other connected registries. Users can also transfer entries from one ICE registry to another or make them publicly accessible. Bioparts, the new search portal, combines the ease and convenience of modern web search engines with the capabilities of bioinformatics search tools such as BLAST. This portal, available at , allows anyone to search for publicly accessible biological part information (e.g., NCBI, iGEM, SynBioHub, Addgene), including parts publicly accessible through ICE Registries. Additionally, the portal offers a REST API that enables third-party applications and tools to access the portal’s functionality programmatically.

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“…Plasmids were verified for sequencing by Sanger Sequencing (University of Texas GSAF core) and Plasmidsaurus (https://www.plasmidsaurus.com/). Plasmids derived from previous work was sequence confirmed and analyzed by both Plasmidsaurus and Plannotate (McGuffie,M.J. and Barrick,J.E.…”

Section: Methodsmentioning

confidence: 99%

Rewiring native post-transcriptional carbon regulators to build multi-layered genetic circuits and optimize engineered microbes for bioproduction

Simmons,

Partipilo,

Stankes

et al. 2023

Preprint

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As the bioprocessing and synthetic biology spaces rapidly expand, post-transcriptional regulation is emerging as driver for maximizing signal response rate and for minimizing cost per protein within cells. Designing robust post-transcriptional control systems that have precise tunability and can achieve diverse regulatory outcomes are paramount to advance the field. Herein, we develop a new approach for engineered post-transcriptional control in bacteria by rewiring a native regulatory system inEscherichia coli, the Carbon Storage Regulatory (Csr) Network, to create tunable, complex genetic circuits. First, by co-opting native components of the Csr Network to regulate translation of a target mRNA transcript, we establish a Csr-regulated Buffer Gate. Next, by rationally engineering the interactions between our synthetic construct and the native components of the Csr Network, we expand our original design into a genetic toolbox of 12 Buffer Gates that achieve precise tunability across a 10-fold range of target gene expression. Subsequently, to further regulatory capabilities using this approach, we develop a Csr-regulated NOT Gate through engineering a Csr-activated sequence into our synthetic constructs. We then build upon the Csr Buffer and Not Gates to create post-transcriptional dual input Boolean OR, NOR, AND and NAND Logic Gates, as well as a genetic pulse circuit. As a third step, we demonstrate portability of our Csr-regulated Buffer Gates into three industrially relevant bacteria by recapitulating Buffer Gate activity simply by leveraging the conserved homologous Csr Network in each species. Lastly, as a demonstration of downstream application, we apply our system to a proof-of-concept synthetic mevalonate pathway. Using our engineered constructs, we optimize mevalonate production inE.coli resulting in a three-fold increase in production relative to a transcriptionally controlled mevalonate pathway. As a whole, we establish a novel approach to rewire post-transcriptional regulatory networks for complex bacterial computation that can be utilized for efficient bioproduction in engineered microbes.

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pLannotate: engineered plasmid annotation

Cited by 28 publications

References 27 publications

PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies

PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies

BioParts—A Biological Parts Search Portal and Updates to the ICE Parts Registry Software Platform

Rewiring native post-transcriptional carbon regulators to build multi-layered genetic circuits and optimize engineered microbes for bioproduction

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