Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance-net

Nature Communications

Volumn 9, Issue 1, 2018, Pages

  Wang, Tianmin ^a   Guan, Changge ^a   Guo, Jiahui ^a   Liu, Bing ^b   Wu, Yinan ^a   Xie, Zhen ^a   Zhang, Chong ^a   Xing, Xin Hui ^a  

^a TSINGHUA UNIVERSITY   (China)

^b Beijing Engineering Consultants Ltd   (China)

Author keywords

[No Author keywords available]

Indexed keywords

GUIDE RNA; UNTRANSLATED RNA; BACTERIAL RNA; BUTANOL; FURFURAL; ISOBUTANOL; TRANSCRIPTOME;

BACTERIUM; DETECTION METHOD; GENE; GENETIC ANALYSIS; GENOME; GENOMICS; PERFORMANCE ASSESSMENT; PHENOTYPE;

ARTICLE; BACTERIAL GENOME; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CONTROLLED STUDY; ESCHERICHIA COLI; FUNCTIONAL GENOMICS; GENE LIBRARY; GENE REPRESSION; MICROBIAL GENOME; NONHUMAN; PHENOTYPE; TRANSCRIPTION TERMINATION; TRANSPOSON; BACTERIUM; CHROMOSOMAL MAPPING; COMPARATIVE STUDY; CRISPR CAS SYSTEM; DRUG EFFECT; ESSENTIAL GENE; EVALUATION STUDY; GENE REGULATORY NETWORK; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; INDEL MUTATION; METABOLISM;

PROKARYOTA;

BACTERIA; BUTANOLS; CHROMOSOME MAPPING; CRISPR-CAS SYSTEMS; ESCHERICHIA COLI; FURALDEHYDE; GENE LIBRARY; GENE REGULATORY NETWORKS; GENES, ESSENTIAL; GENOME, BACTERIAL; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INDEL MUTATION; METABOLIC NETWORKS AND PATHWAYS; RNA, BACTERIAL; RNA, GUIDE; RNA, UNTRANSLATED; TRANSCRIPTOME;

EID: 85049243694     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/s41467-018-04899-x     Document Type: Article

References (70)

1. Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006.0008 (2006).
2. Koo, B.-M. et al. Construction and analysis of two genome-scale deletion libraries for Bacillus subtilis. Cell Syst. 4, 291 (2017).
3. Freed, E. F. et al. Genome-wide tuning of protein expression levels to rapidly engineer microbial traits. ACS Synth. Biol. 4, 1244-1253 (2015).
4. Garst, A. D. et al. Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering. Nat. Biotechnol. 35, 48-55 (2016).
5. Van Opijnen, T., Bodi, K. L. & Camilli, A. Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nat. Methods 6, 767-772 (2009).
6. Barquist, L. et al. A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium. Nucleic Acids Res. 41, 4549-4564 (2013).
7. Lluch-Senar, M. et al. Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium. Mol. Syst. Biol. 11, 780-780 (2015).
8. Ibberson, C. B. et al. Co-infecting microorganisms dramatically alter pathogen gene essentiality during polymicrobial infection. Nat. Microbiol. 2, 17079 (2017).
9. Wagner, E. G. H. & Romby, P. Small RNAs in bacteria and archaea: who they are, what they do, and how they do it. Adv. Genet. 90, 133-208 (2015).
10. Frohlich, K. S. & Vogel, J. Activation of gene expression by small RNA. Curr. Opin. Microbiol. 12, 674-682 (2009).
11. Cong, L. et al. Multiplex genome engineering using CRISPR-Cas systems. Science 339, 819-823 (2013).
12. DiCarlo, J. E. et al. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 41, 4336-4343 (2013).
13. Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L.A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 31, 233-239 (2013).
14. Choudhary, E., Thakur, P., Pareek, M. & Agarwal, N. Gene silencing by CRISPR interference in mycobacteria. Nat. Commun. 6, 6267 (2015).
15. Yao, L., Cengic, I., Anfelt, J. & Hudson, E. P. Multiple gene repression in cyanobacteria using CRISPRi. ACS Synth. Biol. 5, 207-212 (2016).
16. Xu, T. et al. Efficient genome editing in Clostridium cellulolyticum via CRISPR-Cas9 nickase. Appl. Environ. Microbiol. 81, 4423-4431 (2015).
17. Peters, J. M. et al. A comprehensive, CRISPR-based functional analysis of essential genes in bacteria. Cell 165, 1493-1506 (2016).
18. Nayak, D. D. & Metcalf, W. W. Cas9-mediated genome editing in the methanogenic archaeon Methanosarcina acetivorans. Proc. Natl Acad. Sci. USA 114, 2976-2981 (2017).
19. Shalem, O., Sanjana, N. E. & Zhang, F. High-throughput functional genomics using CRISPR-Cas9. Nat. Rev. Genet. 16, 299-311 (2015).
20. Kuzminov, A. The precarious prokaryotic chromosome. J. Bacteriol. 196, 1793-1806 (2014).
21. Struhl, K. Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 98, 1-4 (1999).
22. Doench, J. G. et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34, 184-191 (2016).
23. Horlbeck, M. A. et al. Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. eLife 5, 339-350 (2016).
24. Qi, L. S. et al. Repurposing CRISPR as an RNA-guided platform for sequencespecific control of gene expression. Cell 152, 1173-1183 (2013).
25. Wetmore, K. M. et al. Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. mBio 6, e00306-e00315 (2015).
26. Gallagher, L. A. et al. Sequence-defined transposon mutant library of Burkholderia thailandensis. mBio 4, e00604-e00613 (2013).
27. Yamamoto, N. et al. Update on the Keio collection of Escherichia coli singlegene deletion mutants. Mol. Syst. Biol. 5, 335 (2009).
28. Gerdes, S. Y. et al. Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J. Bacteriol. 185, 5673-5684 (2003).
29. Goodall, E. C. A. et al. The essential genome of Escherichia coli K-12. mBio 9, e02096-17 (2018).
30. Zuurmond, A. M., Rundlöf, A. K. & Kraal, B. Either of the chromosomal tuf genes of E. coli K-12 can be deleted without loss of cell viability. Mol. Gen. Genet. 260, 603-607 (1999).
31. Kacar, B., Garmendia, E., Tuncbag, N., Andersson, D. I. & Hughes, D. Functional constraints on replacing an essential gene with its ancient and modern homologs. mBio 8, e01276-17 (2017).
32. Gilbert, L. A. et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159, 647-661 (2014).
33. Wong, A. S. L., Choi, G. C. G., Cheng, A. A., Purcell, O. & Lu, T. K. Massively parallel high-order combinatorial genetics in human cells. Nat. Biotechnol. 33, 952-961 (2015).
34. Kato, J. I. & Hashimoto, M. Construction of consecutive deletions of the Escherichia coli chromosome. Mol. Syst. Biol. 3, 1-7 (2007).
35. Rousset, F., Cui, L., Siouve, E., Depardieu, F. & Bikard, D. Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors. Preprint at https://doi.org/10.1101/308916 (2018).
36. Crick, F. H. C. Codon-anticodon pairing: the wobble hypothesis. J. Mol. Biol. 19, 548-555 (1966).
37. Nasvall, S. J., Chen, P. & Bjork, G. R. The modified wobble nucleoside uridine-5-oxyacetic acid in tRNAPro(cmo5UGG) promotes reading of all four proline codons in vivo. RNA 10, 1662-1673 (2004).
38. Christen, B. et al. The essential genome of a bacterium. Mol. Syst. Biol. 7, 528-528 (2014).
39. Nichols, R. J. et al. Phenotypic landscape of a bacterial cell. Cell 144, 143-156 (2011).
40. Fang, M. et al. Intermediate-sensor assisted push-pull strategy and its application in heterologous deoxyviolacein production in Escherichia coli. Metab. Eng. 33, 41-51 (2016).
41. Pu, Y. et al. Enhanced efflux activity facilitates drug tolerance in dormant bacterial cells. Mol. Cell 62, 284-294 (2016).
42. Bloom-Ackermann, Z. et al. A comprehensive tRNA deletion library unravels the genetic architecture of the tRNA pool. PLoS. Genet. 10, e1004084 (2014).
43. Vega, N. M., Allison, K. R., Khalil, A. S. & Collins, J. J. Signaling-mediated bacterial persister formation. Nat. Chem. Biol. 8, 431-433 (2012).
44. Hu, Y., Kwan, B. W., Osbourne, D. O., Benedik, M. J. & Wood, T. K. Toxin YafQ increases persister cell formation by reducing indole signalling. Environ. Microbiol. 17, 1275-1285 (2015).
45. Liu, S.-D., Wu, Y.-N., Wang, T.-M., Zhang, C. & Xing, X.-H. Maltose utilization as a novel selection strategy for continuous evolution of microbes with enhanced metabolite production. ACS Synth. Biol. 6, 2326-2338 (2017).
46. Morgens, D. W., Deans, R. M., Li, A. & Bassik, M. C. Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes. Nat. Biotechnol. 34, 634-636 (2016).
47. Abudayyeh, O. O. et al. RNA targeting with CRISPR-Cas13. Nature 550, 280-284 (2017).
48. Kleinstiver, B. P. et al. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523, 481-485 (2015).
49. Kim, S. K. et al. Efficient transcriptional gene repression by type V-A CRISPRCpf1 from Eubacterium eligens. ACS Synth. Biol. 6, 1273-1282 (2017).
50. Konermann, S. et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517, 583-588 (2014).
51. Bikard, D. et al. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. 41, 7429-7437 (2013).
52. Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343-345 (2009).
53. Neidhardt, F. C., Bloch, P. L. & Smith, D. F. Culture medium for enterobacteria. J. Bacteriol. 119, 736-747 (1974).
54. Lv, L., Ren, Y.-L., Chen, J.-C., Wu, Q. & Chen, G.-Q. Application of CRISPRi for prokaryotic metabolic engineering involving multiple genes, a case study: controllable P(3HB-co-4HB) biosynthesis. Metab. Eng. 29, 160-168 (2015).
55. Murphy, K. C., Campellone, K. G. & Poteete, A. R. PCR-mediated gene replacement in Escherichia coli. Gene. 246, 321-330 (2000).
56. Zhang, Y., Buchholz, F., Muyrers, J. P. P. & Stewart, A. F. A new logic for DNA engineering using recombination in Escherichia coli. Nature 20, 123-128 (1998).
57. Jiang, Y. et al. Multigene editing in the Escherichia coli genome using the CRISPR-Cas9 system. Appl. Environ. Microbiol. 81, 2506-2514 (2015).
58. Zhao, J. et al. Engineering central metabolic modules of Escherichia coli for improving β-carotene production. Metab. Eng. 17, 42-50 (2013).
59. Amann, E., Ochs, B. & Abel, K. J. Tightly regulated tac promoter vectors useful for the expression of unfused and fused proteins in Escherichia coli. Gene. 69, 301-315 (1988).
60. Lutz, R. & Bujard, H. Independent and tight regulation of transcriptional units in escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. 25, 1203-1210 (1997).
61. Ronda, C., Pedersen, L. E., Sommer, M. O. A. & Nielsen, A. T. CRMAGE: CRISPR optimized MAGE recombineering. Sci. Rep. 6, 19452 (2016).
62. Jiang, H. & Wong, W. H. SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 24, 2395-2396 (2008).
63. Hsu, P. D. et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 31, 827-832 (2013).
64. Sander, J. D. & Joung, J. K. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol. 32, 347-355 (2014).
65. Gama-Castro, S. et al. RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. Nucleic Acids Res. 44, D133-D143 (2016).
66. Engler, C., Gruetzner, R., Kandzia, R. & Marillonnet, S. Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes. PLoS ONE 4, e5553 (2009).
67. Kampmann, M., Bassik, M. C. & Weissman, J. S. Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells. Proc. Natl Acad. Sci. USA 110, E2317-E2326 (2013).
68. Magoč, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957-2963 (2011).
69. Liu, S. J. et al. CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Science 355, eaah7111 (2017).
70. Storey, J. D. & Tibshirani, R. Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA 100, 9440-9445 (2003).