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

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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%.

Original languageEnglish
Article numberkuac028
JournalJournal of Industrial Microbiology and Biotechnology
Volume50
Issue number1
Number of pages16
ISSN1367-5435
DOIs
Publication statusPublished - 2023

Bibliographical note

Erratum: https://academic.oup.com/jimb/article/50/1/kuad003/7080731?login=true

    Research areas

  • Transcriptomics, alpha-amylase, fermentation, screening, CRISPRi, SEQUENCE-SPECIFIC CONTROL, PROTEIN SECRETION, REGULATORY RNAS, ELEMENT ICEBS1, IN-VIVO, IDENTIFICATION, ENZYMES, LEVEL, GROWTH, PRSA

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