ActinoMation: a literate programming approach for medium-throughput robotic conjugation of Streptomyces spp. DOI Creative Commons

Tenna Alexiadis Møller,

Thomas Booth, Simon J. Shaw

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 9, 2024

Abstract The genus Streptomyces are valuable producers of antibiotics and other pharmaceutically important bioactive compounds. Advances in molecular engineering tools, such as CRISPR, has provided some access to the metabolic potential , but efficient genetic strains is hindered by laborious slow manual transformation protocols. In this paper, we present a semi-automated medium-throughput workflow for introduction recombinant DNA into spp. using affordable open-sourced Opentrons (OT-2) robotics platform. To increase accessibility provide an open-source protocol-creator, ActinoMation. ActinoMation literate programming environment Python Jupyter Notebook. We validated method transforming coelicolor (M1152 M1146), S. albidoflavus (J1047), venezuelae (DSM40230) with plasmids pSETGUS pIJ12551. demonstrate conjugation efficiencies 3.33*10 −3 M1152 pIJ12551; 2.96*10 M1146 1.21*10 −5 J1047 4.70*10 −4 pIJ12551, 4.97*10 −2 DSM40230 6.13*10 pIJ12551 false positive rate between 8.33% 54.54%. Automation improves consistency when handling large sample sizes that facilitates easy reproducibility on larger scale.

Language: Английский

ActinoMation: a literate programming approach for medium-throughput robotic conjugation of Streptomyces spp. DOI Creative Commons

Tenna Alexiadis Møller,

Thomas Booth, Simon J. Shaw

et al.

Synthetic and Systems Biotechnology, Journal Year: 2025, Volume and Issue: 10(2), P. 667 - 676

Published: March 11, 2025

The genus Streptomyces are valuable producers of antibiotics and other pharmaceutically important bioactive compounds. Advances in molecular engineering tools, such as CRISPR, have provided some access to the metabolic potential Streptomyces, but efficient genetic strains is hindered by laborious slow manual transformation protocols. In this paper, we present a semi-automated medium-throughput workflow for introduction recombinant DNA into spp. using affordable open-sourced Opentrons (OT-2) robotics platform. To increase accessibility provide an open-source protocol-creator, ActinoMation. ActinoMation literate programming environment Python Jupyter Notebook. We validated method transforming coelicolor (M1152 M1146), S. albidoflavus (J1047), venezuelae (DSM40230) with plasmids pSETGUS pIJ12551. demonstrate conjugation efficiencies 3.33∗10-3/0.33 % M1152 pIJ12551; 2.96∗10-3/0.29 M1146 1.21∗10-5/0.0012 J1047 4.70∗10-4/0.047 pIJ12551, 4.97∗10-2/4.97 DSM40230 6.13∗10-2/6.13 pIJ12551 false positive rate between 8.33 54.54 %. Automation facilitates streamlined on larger scale without any evident loss efficiency.

Language: Английский

Citations

0
ActinoMation: a literate programming approach for medium-throughput robotic conjugation of Streptomyces spp. DOI Creative Commons

Tenna Alexiadis Møller,

Thomas Booth, Simon J. Shaw

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 9, 2024

Abstract The genus Streptomyces are valuable producers of antibiotics and other pharmaceutically important bioactive compounds. Advances in molecular engineering tools, such as CRISPR, has provided some access to the metabolic potential , but efficient genetic strains is hindered by laborious slow manual transformation protocols. In this paper, we present a semi-automated medium-throughput workflow for introduction recombinant DNA into spp. using affordable open-sourced Opentrons (OT-2) robotics platform. To increase accessibility provide an open-source protocol-creator, ActinoMation. ActinoMation literate programming environment Python Jupyter Notebook. We validated method transforming coelicolor (M1152 M1146), S. albidoflavus (J1047), venezuelae (DSM40230) with plasmids pSETGUS pIJ12551. demonstrate conjugation efficiencies 3.33*10 −3 M1152 pIJ12551; 2.96*10 M1146 1.21*10 −5 J1047 4.70*10 −4 pIJ12551, 4.97*10 −2 DSM40230 6.13*10 pIJ12551 false positive rate between 8.33% 54.54%. Automation improves consistency when handling large sample sizes that facilitates easy reproducibility on larger scale.

Language: Английский

Citations

0