biostudies-literatureGeissler ASInnovation Fund Denmarkkuac028https://www.ebi.ac.uk/biostudies/studies/S-EPMC9936203biostudies-literatureUnknown50(1)Yield improvements in cell factories can potentially be obtained by fine-tuning the regulatory mechanisms for gene candidates. In pursuit of such candidates, we performed RNA-sequencing of two α-amylase producing Bacillus strains and predict hundreds of putative novel non-coding transcribed regions. Surprisingly, we found among hundreds of non-coding and structured RNA candidates that non-coding genomic regions are proportionally undergoing the highest changes in expression during fermentation. Since these classes of RNA are also understudied, we targeted the corresponding genomic regions with CRIPSRi knockdown to test for any potential impact on the yield. From differentially expression analysis, we selected 53 non-coding candidates. Although CRISPRi knockdowns target both the sense and tJournal of industrial microbiology & biotechnologyCRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis.PMC99362035163-00010BKallehauge TBAlkan FRasmussen MDHjort CGorodkin JGonzalez-Tortuero EVinther JBreuner AFehler AOAnthon CPoulsen LDGeissler ASSeemann SEfalseCRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis.Yield improvements in cell factories can potentially be obtained by fine-tuning the regulatory mechanisms for gene candidates. In pursuit of such candidates, we performed RNA-sequencing of two α-amylase producing Bacillus strains and predict hundreds of putative novel non-coding transcribed regions. Surprisingly, we found among hundreds of non-coding and structured RNA candidates that non-coding genomic regions are proportionally undergoing the highest changes in expression during fermentation. Since these classes of RNA are also understudied, we targeted the corresponding genomic regions with CRIPSRi knockdown to test for any potential impact on the yield. From differentially expression analysis, we selected 53 non-coding candidates. Although CRISPRi knockdowns target both the sense and t2023-01-01T00:00:00Z2023 Feb2025-04-19T07:25:33.451Z2025-02-19T02:56:14.69ZS-EPMC99362033656402510.1093/jimb/kuac028