CRISPRi-TnSeq maps genome-wide interactions between essential and non-essential genes in bacteria.

Autor: Jana B; Department of Biology, Boston College, Chestnut Hill, MA, USA.; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA., Liu X; Department of Pathogen Biology, Base for International Science and Technology Cooperation: Carson Cancer Stem Cell Vaccines R&D Center, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, China.; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland., Dénéréaz J; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland., Park H; Department of Biology, Boston College, Chestnut Hill, MA, USA., Leshchiner D; Department of Biology, Boston College, Chestnut Hill, MA, USA., Liu B; Department of Biology, Boston College, Chestnut Hill, MA, USA., Gallay C; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland., Zhu J; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China., Veening JW; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland. jan-willem.veening@unil.ch., van Opijnen T; Broad Institute of MIT and Harvard, Cambridge, MA, USA. tim.vanopijnen@childrens.harvard.edu.; Boston Children's Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, MA, USA. tim.vanopijnen@childrens.harvard.edu.
Jazyk: angličtina
Zdroj: Nature microbiology [Nat Microbiol] 2024 Sep; Vol. 9 (9), pp. 2395-2409. Date of Electronic Publication: 2024 Jul 19.
DOI: 10.1038/s41564-024-01759-x
Abstrakt: 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.
(© 2024. The Author(s).)
Databáze: MEDLINE
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