CRISPRi-TnSeq maps genome-wide interactions between essential and non-essential genes in bacteria.
Nat Microbiol
; 9(9): 2395-2409, 2024 Sep.
Article
em En
| MEDLINE
| ID: mdl-39030344
ABSTRACT
Genetic interactions identify functional connections between genes and pathways, establishing gene functions or druggable targets. Here we use CRISPRi-TnSeq, CRISPRi-mediated knockdown of essential genes alongside TnSeq-mediated knockout of non-essential genes, to map genome-wide interactions between essential and non-essential genes in Streptococcus pneumoniae. Transposon-mutant libraries constructed in 13 CRISPRi strains enabled screening of ~24,000 gene pairs. This identified 1,334 genetic interactions, including 754 negative and 580 positive interactions. Network analyses show that 17 non-essential genes pleiotropically interact with more than half the essential genes tested. Validation experiments confirmed that a 7-gene subset protects against perturbations. Furthermore, we reveal hidden redundancies that compensate for essential gene loss, relationships between cell wall synthesis, integrity and cell division, and show that CRISPRi-TnSeq identifies synthetic and suppressor-type relationships between both functionally linked and disparate genes and pathways. Importantly, in species where CRISPRi and Tn-Seq are established, CRISPRi-TnSeq should be straightforward to implement.
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Base de dados:
MEDLINE
Assunto principal:
Streptococcus pneumoniae
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Elementos de DNA Transponíveis
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Genoma Bacteriano
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Genes Essenciais
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Sistemas CRISPR-Cas
Idioma:
En
Ano de publicação:
2024
Tipo de documento:
Article