CRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis

Autor: Adrian Sven Geissler, Annaleigh Ohrt Fehler, Line Dahl Poulsen, Enrique González-Tortuero, Thomas Beuchert Kallehauge, Ferhat Alkan, Christian Anthon, Stefan Ernst Seemann, Michael Dolberg Rasmussen, Anne Breüner, Carsten Hjort, Jeppe Vinther, Jan Gorodkin
Rok vydání: 2022
Předmět:
Zdroj: Geissler, A S, Fehler, A O, Poulsen, L D, Gonzalez-Tortuero, E, Kallehauge, T B, Alkan, F, Anthon, C, Seemann, S E, Rasmussen, M D, Breuener, A, Hjort, C, Vinther, J & Gorodkin, J 2023, ' CRISPRi screen for enhancing heterologous alpha-amylase yield in Bacillus subtilis ', Journal of Industrial Microbiology and Biotechnology, vol. 50, no. 1, kuac028 . https://doi.org/10.1093/jimb/kuac028
ISSN: 1476-5535
1367-5435
DOI: 10.1093/jimb/kuac028
Popis: 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 the antisense strand, the CRISPRi experiment cannot link causes for yield changes to the sense or antisense disruption. Nevertheless, we observed on several instances with strong changes in enzyme yield. The knockdown targeting the genomic region for a putative antisense RNA of the 3′ UTR of the skfA-skfH operon led to a 21% increase in yield. In contrast, the knockdown targeting the genomic regions of putative antisense RNAs of the cytochrome c oxidase subunit 1 (ctaD), the sigma factor sigH, and the uncharacterized gene yhfT decreased yields by 31 to 43%. 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 alpha-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 the antisense strand, the CRISPRi experiment cannot link causes for yield changes to the sense or antisense disruption. Nevertheless, we observed on several instances with strong changes in enzyme yield. The knockdown targeting the genomic region for a putative antisense RNA of the 3 ' UTR of the skfA-skfH operon led to a 21% increase in yield. In contrast, the knockdown targeting the genomic regions of putative antisense RNAs of the cytochrome c oxidase subunit 1 (ctaD), the sigma factor sigH, and the uncharacterized gene yhfT decreased yields by 31 to 43%.
Databáze: OpenAIRE
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