Targeted and high-throughput gene knockdown in diverse bacteria using synthetic sRNAs.
Jae Sung ChoDongsoo YangCindy Pricilia Surya PrabowoMohammad Rifqi GhiffaryTaehee HanKyeong Rok ChoiCheon Woo MoonHengrui ZhouJae Yong RyuHyun Uk KimSang Yup LeePublished in: Nature communications (2023)
Synthetic sRNAs allow knockdown of target genes at translational level, but have been restricted to a limited number of bacteria. Here, we report the development of a broad-host-range synthetic sRNA (BHR-sRNA) platform employing the RoxS scaffold and the Hfq chaperone from Bacillus subtilis. BHR-sRNA is tested in 16 bacterial species including commensal, probiotic, pathogenic, and industrial bacteria, with >50% of target gene knockdown achieved in 12 bacterial species. For medical applications, virulence factors in Staphylococcus epidermidis and Klebsiella pneumoniae are knocked down to mitigate their virulence-associated phenotypes. For metabolic engineering applications, high performance Corynebacterium glutamicum strains capable of producing valerolactam (bulk chemical) and methyl anthranilate (fine chemical) are developed by combinatorial knockdown of target genes. A genome-scale sRNA library covering 2959 C. glutamicum genes is constructed for high-throughput colorimetric screening of indigoidine (natural colorant) overproducers. The BHR-sRNA platform will expedite engineering of diverse bacteria of both industrial and medical interest.
Keyphrases
- high throughput
- genome wide
- escherichia coli
- genome wide identification
- biofilm formation
- klebsiella pneumoniae
- bacillus subtilis
- staphylococcus aureus
- wastewater treatment
- pseudomonas aeruginosa
- healthcare
- dna methylation
- genome wide analysis
- copy number
- single cell
- gold nanoparticles
- multidrug resistant
- heavy metals
- antimicrobial resistance
- bioinformatics analysis
- nitric oxide
- hydrogen peroxide
- cancer therapy
- air pollution
- oxidative stress
- living cells
- heat shock
- genetic diversity