Genome-scale cis-acting catabolite-responsive element editing confers Bacillus pumilus LG3145 plant-beneficial functions

Rhizosphere dwelling microorganism such as Bacillus spp. are helpful for crop growth. However, these functions are adversely affected by long-term synthetic fertilizer application. We developed a modified CRISPR/Cas9 system using non-specific single-guide RNAs to disrupt the genome-wide cis-acting c...

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Bibliographic Details
Published in:iScience 2024-02, Vol.27 (2), p.108983, Article 108983
Main Authors: Bi, Meiying, Li, Mingkun, Wei, Jiaxun, Meng, Ziwen, Wang, Zhaoyang, Ying, Ming, Yang, Xiurong, Huang, Lei
Format: Article
Language:English
Subjects:
Biological sciences
Genetics
Interaction of plants with organisms
Microbiology
Techniques in genetics
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Summary:Rhizosphere dwelling microorganism such as Bacillus spp. are helpful for crop growth. However, these functions are adversely affected by long-term synthetic fertilizer application. We developed a modified CRISPR/Cas9 system using non-specific single-guide RNAs to disrupt the genome-wide cis-acting catabolite-responsive elements (cres) in a wild-type Bacillus pumilus strain, which conferred dual plant-benefit properties. Most of the mutations occurred around imperfectly matched cis-acting elements (cre-like sites) in genes that are mainly involved in carbon and secondary metabolism pathways. The comparative metabolomics and transcriptome results revealed that carbon is likely transferred to some pigments, such as riboflavin, carotenoid, and lycopene, or non-ribosomal peptides, such as siderophore, surfactin, myxochelin, and bacilysin, through the pentose phosphate and amino acid metabolism pathways. Collectively, these findings suggested that the mutation of global cre-like sequences in the genome might alter carbon flow, thereby allowing beneficial biological interactions between the rhizobacteria and plants. [Display omitted] •B. pumilus acquired disease resistance via non-specific cis-acting element editing•Cis-acting element editing caused carbon source utilization changes in B. pumilus•Cis-acting element editing allowed B. pumilus to promote plant growth•Cre-like sequence mutation induced B. pumilus activity against plant pathogens Biological sciences; Genetics; Interaction of plants with organisms; Microbiology; Techniques in genetics
ISSN:2589-0042
2589-0042
DOI:10.1016/j.isci.2024.108983