Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering

Tellechea‐Luzardo, Jonathan; Winterhalter, Charles; Widera, Paweł; Kozyra, Jerzy; Krasnogor, Natalio

doi:10.1021/acssynbio.9b00400

Cited by 24 publications

(27 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…CellRepo is a version control system for cell engineering that integrates a new cloud-based version control software for cell lines' digital footprint tracking and molecular barcoding of living samples. CellRepo, which substantially improves our earlier work (35), relies on two fundamental pillars. Firstly, during the process of engineering a new strain, changes introduced to the cell line are recorded in "commits" that include information such as the genotype, phenotype, author of the modifications, laboratory protocols, characterization profiles, etc.…”

Section: Main Textmentioning

confidence: 84%

Versioning Biological Cells for Trustworthy Cell Engineering

Tellechea‐Luzardo

Velázquez

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

Abstract“Full-stack”biotechnology platforms for cell line (re)programming are on the horizon, due mostly to (a) advances in gene synthesis and editing techniques as well as (b) the growing integration with informatics, the internet of things and automation. These emerging platforms will accelerate the production and consumption of biological products. Hence, transparency, traceability and -ultimately-trustworthiness is required -from cradle to grave- for engineered cell lines and their engineering processes. We report here the first version control system for cell engineering that integrates a new cloud-based version control software for cell lines’ digital footprint with molecular barcoding of living samples. We argue that version control for cell engineering marks a significant step towards more open, reproducible, easier to trace and share, and more trustworthy engineering biology.One Sentence SummaryWe demonstrate a transparent and open way of engineering and sharing cell lines.

show abstract

Section: Main Textmentioning

confidence: 84%

Versioning Biological Cells for Trustworthy Cell Engineering

Tellechea‐Luzardo

Velázquez

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…So far, the concept of genetic barcoding is based on incorporation of specific genetic “watermark” sequences into the genome that could later be sequenced to identify the strain. These barcoding sequences, however, might get lost due to mutation and selection pressure [50] . For what we know, genetic code seems highly conserved and extremely stable over long evolutionary timescales, certainly more stable and long‐lasting than a genetic sequence.…”

Section: Resultsmentioning

confidence: 99%

How To Quantify a Genetic Firewall? A Polarity‐Based Metric for Genetic Code Engineering

Schmidt

Kubyshkin

2020

ChemBioChem

View full text Add to dashboard Cite

Genetic code engineering aims to produce organisms that translate genetic information in a different way from that prescribed by the standard genetic code. This endeavor could eventually lead to genetic isolation, where an organism that operates under a different genetic code will not be able to transfer functional genes with other living species, thereby standing behind a genetic firewall. It is not clear however, how distinct the code should be, or how to measure the distance. We have developed a metric (Δcode) where we assigned polarity indices (clog D7) to amino acids to calculate the distances between pairs of genetic codes. We then calculated the distance between a set of 204 genetic codes, including the 24 known distinct natural codes, 11 extreme‐distance codes created computationally, nine theoretical special purpose codes from literature and 160 codes in which canonical amino acids were replaced by noncanonical chemical analogues. The metric can be used for building strategies towards creating semantically alienated organisms, and testing the strength of genetic firewalls. This metric provides the basis for a map of the genetic codes that could guide future efforts towards novel biochemical worlds, biosafety and deep barcoding applications.

show abstract

“…By introducing these barcodes in the genomes of modified cells, we can create a physical link between this engineered organism and its digital counterpart. This idea has been described previously along with a version control system for microbial strains (named CellRepo) where all important information about barcoded strains can be archived and consulted in repositories 34,54 . In this way, after barcoding one strain, one only needs to sequence the barcode to retrieve all the available information about that strain on the website, including laboratory of origin, developer, modifications, resistances, etc.…”

Section: Application Of Llltrb For the Delivery Of Small Genetic Fragments That Can Be Used As Traceable Barcodesmentioning

confidence: 99%

Targetron-assisted delivery of exogenous DNA sequences intoPseudomonas putidathrough CRISPR-aided counterselection

Velázquez

Al‐Ramahi

Tellechea‐Luzardo

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

Genome editing methods based on Group II introns (known as Targetron technology) have been long used as a gene knock-out strategy in a wide range of organisms in a fashion independent of homologous recombination. Yet, their utility as delivery systems has been typically suboptimal because of their reduced efficiency of insertion when they carry exogenous sequences. We show that this limitation can be tackled and Targetron adapted as a general tool in Gram-negative bacteria. To this end, a set of broad host range standardized vectors were designed for conditional expression of the Ll.LtrB intron. After testing the correct functionality of these plasmids in Escherichia coli and Pseudomonas putida, we created a library of Ll.LtrB variants carrying cargo DNA sequences of different lengths to benchmark the capacity of intron-mediated delivery in these bacteria. Next, we combined CRISPR/Cas9-facilitated counterselection to increase the chances of finding genomic sites inserted with the thereby engineered introns. By following this pipeline, we were able to insert exogenous sequences of up to 600 bp at specific genomic locations in wild-type P. putida KT2440 and its ΔrecA derivative. Finally, we were able to apply this technology to successfully tag this strain with an orthogonal short sequence (barcode) that acts as a unique identifier for tracking this microorganism in biotechnological settings. The results with P. putida exemplified the value of the Targetron approach for unrestricted delivery of small DNA fragments to the genomes of Gram-negative bacteria for a suite of genome editing endeavours.

show abstract

Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering

Cited by 24 publications

References 36 publications

Versioning Biological Cells for Trustworthy Cell Engineering

Versioning Biological Cells for Trustworthy Cell Engineering

How To Quantify a Genetic Firewall? A Polarity‐Based Metric for Genetic Code Engineering

Targetron-assisted delivery of exogenous DNA sequences intoPseudomonas putidathrough CRISPR-aided counterselection

Contact Info

Product

Resources

About