Guide Sequences for Mobile-CRISPRi Knockdown in Pseudomonas

Using sgRNA design scripts, we have identified sequences to knock down genes in Green Star Pseudomonas strains.

Comprehensive list of guides targeting genes in popular strains

Pseudomonas aeruginosa LESB58

Pseudomonas aeruginosa PA7

Pseudomonas aeruginosa PAK (Cain et al., 2019)

Pseudomonas aeruginosa PAK - Assembly GCF_000568855.2

Pseudomonas aeruginosa PAO1

Pseudomonas aeruginosa UCBPP-PA14

Pseudomonas fluorescens SBW25

Pseudomonas protegens Pf-5

Pseudomonas putida F1

Pseudomonas putida KT2440 (TIGR)

Pseudomonas savastanoi pv. phaseolicola 1448A

Pseudomonas stutzeri A1501

Pseudomonas syringae pv. tomato DC3000

Notes

• Generally, guides with the lowest offset result in a superior knockdown.
• Since optimal guides are found on the strand opposite to coding sequence, directionality is anti-parallel to the direction of RNA polymerase readthrough.
• Guides are described using a valid bed format.

Chromosome	Left	Right	Locus Tag	Gene Name	Direction (Anti)	PAM	Offset	Target	Top Oligo	Bottom Oligo	NCBI Track URL

NCBI Track Links

In the last column for each guide, the links to NCBI demonstrate the location of the guide in green, with other guides targeting the same gene in grey.

Special thanks

• https://www.ncbi.nlm.nih.gov/home/tools/
• https://bedtools.readthedocs.io/en/latest/
• https://github.com/vividvilla/csvtotable
• https://github.com/traeki/sgrna_design