A tool named Iris for versatile high-throughput phenotyping in microorganisms

Nature Microbiology

Volumn 2, Issue , 2017, Pages

  Kritikos, George ^a   Banzhaf, Manuel ^a   Herrera Dominguez, Lucia ^a   Koumoutsi, Alexandra ^a   Wartel, Morgane ^a   Zietek, Matylda ^a   Typas, Athanasios ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PHENOMENA AND FUNCTIONS; BACTERIUM; BIOFILM; CANDIDA ALBICANS; CLASSIFICATION; DEVICES; ESCHERICHIA COLI; GENETICS; GENOMICS; HIGH THROUGHPUT SCREENING; HUMAN; IMAGE PROCESSING; PHENOTYPE; PROCEDURES; SOFTWARE;

BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; BIOFILMS; CANDIDA ALBICANS; ESCHERICHIA COLI; GENOMICS; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; PHENOTYPE; SOFTWARE;

EID: 85013328480     PISSN: None     EISSN: 20585276     Source Type: Journal    
DOI: 10.1038/nmicrobiol.2017.14     Document Type: Article

References (63)

1. Brochado, A. R. & Typas, A. High-throughput approaches to understanding gene function and mapping network architecture in bacteria. Curr. Opin. Microbiol. 16, 199-206 (2013).
2. Gray, A. N. et al. High-throughput bacterial functional genomics in the sequencing era. Curr. Opin. Microbiol. 27, 86-95 (2015).
3. Auer, G. K. et al. Mechanical genomics identifies diverse modulators of bacterial cell stiffness. Cell Syst. 2, 402-411 (2016).
4. Collins, S. R., Schuldiner, M., Krogan, N. J. & Weissman, J. S. A strategy for extracting and analyzing large-scale quantitative epistatic interaction data. Genome Biol. 7, R63 (2006).
5. Lawless, C., Wilkinson, D. J., Young, A., Addinall, S. G. & Lydall, D. A. Colonyzer: automated quantification of micro-organism growth characteristics on solid agar. BMC Bioinformatics 11, 287 (2010).
6. Dittmar, J. C., Reid, R. J. D. & Rothstein, R. Screenmill: a freely available software suite for growth measurement, analysis and visualization of high-throughput screen data. BMC Bioinformatics 11, 353 (2010).
7. Young, B. P. & Loewen, C. J. R. Balony: a software package for analysis of data generated by synthetic genetic array experiments. BMC Bioinformatics 14, 354 (2013).
8. Wagih, O. & Parts, L. gitter: a robust and accurate method for quantification of colony sizes from plate images. G3 (Bethesda) 4, 547-552 (2014).
9. Takeuchi, R. et al. Colony-live-a high-throughput method for measuring microbial colony growth kinetics-reveals diverse growth effects of gene knockouts in Escherichia coli. BMC Microbiol. 14, 171 (2014).
10. Noble, S. M., French, S., Kohn, L. A., Chen, V. & Johnson, A. D. Systematic screens of a Candida albicans homozygous deletion library decouple morphogenetic switching and pathogenicity. Nat. Genet. 42, 590-598 (2010).
11. Ryan, O. et al. Global gene deletion analysis exploring yeast filamentous growth. Science 337, 1353-1356 (2012).
12. Cabeen, M. T., Leiman, S. A. & Losick, R. Colony-morphology screening uncovers a role for the Pseudomonas aeruginosa nitrogen-related phosphotransferase system in biofilm formation. Mol. Microbiol. 99, 557-570 (2016).
13. Paradis-Bleau, C., Kritikos, G., Orlova, K., Typas, A. & Bernhardt, T. G. A genomewide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism. PLoS Genet. 10, e1004056 (2014).
14. Peters, J. M. et al. A comprehensive, CRISPR-based functional analysis of essential genes in bacteria. Cell 165, 1493-1506 (2016).
15. Shiver, A. L. et al. A chemical-genomic screen of neglected antibiotics reveals illicit transport of kasugamycin and blasticidin S. PLoS Genet. 12, e1006124 (2016).
16. Koo, B. M. et al. Construction and analysis of two genome-scale deletion libraries for Bacillus subtilis (in the press).
17. Schuldiner, M., Collins, S. R., Weissman, J. S. & Krogan, N. J. Quantitative genetic analysis in Saccharomyces cerevisiae using epistatic miniarray profiles (E-MAPs) and its application to chromatin functions. Methods 40, 344-352 (2006).
18. Costanzo, M. et al. The genetic landscape of a cell. Science 327, 425-431 (2010).
19. Nichols, R. J. et al. Phenotypic landscape of a bacterial cell. Cell 144, 143-156 (2011).
20. Ryan, C. J. et al. Hierarchical modularity and the evolution of genetic interactomes across species. Mol. Cell 46, 691-704 (2012).
21. Brown, J. C. et al. Unraveling the biology of a fungal meningitis pathogen using chemical genetics. Cell 159, 1168-1187 (2014).
22. Serra, D. O., Richter, A. M. & Hengge, R. Cellulose as an architectural element in spatially structured Escherichia coli biofilms. J. Bacteriol. 195, 5540-5554 (2013).
23. Ha, D. G., Richman, M. E. & O'Toole, G. A. Deletion mutant library for investigation of functional outputs of cyclic diguanylate metabolism in Pseudomonas aeruginosa PA14. Appl. Environ. Microbiol. 80, 3384-3393 (2014).
24. Okegbe, C., Price-Whelan, A. & Dietrich, L. E. Redox-driven regulation of microbial community morphogenesis. Curr. Opin. Microbiol. 18, 39-45 (2014).
25. Hoffman, L. R. et al. Aminoglycoside antibiotics induce bacterial biofilm formation. Nature 436, 1171-1175 (2005).
26. Cho, S. H. et al. Detecting envelope stress by monitoring β-barrel assembly. Cell 159, 1652-1664 (2014).
27. Majdalani, N. & Gottesman, S. The Rcs phosphorelay: a complex signal transduction system. Annu. Rev. Microbiol. 59, 379-405 (2005).
28. Serra, D. O. & Hengge, R. Stress responses go three dimensional-the spatial order of physiological differentiation in bacterial macrocolony biofilms. Environ. Microbiol. 16, 1455-1471 (2014).
29. 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).
30. Liberati, N. T. et al. An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants. Proc. Natl Acad. Sci. USA 103, 2833-2838 (2006).
31. Zogaj, X., Nimtz, M., Rohde, M., Bokranz, W. & Romling, U. The multicellular morphotypes of Salmonella typhimurium and Escherichia coli produce cellulose as the second component of the extracellular matrix. Mol. Microbiol. 39, 1452-1463 (2001).
32. Evans, M. L. et al. The bacterial curli system possesses a potent and selective inhibitor of amyloid formation. Mol. Cell 57, 445-455 (2015).
33. Hover, B. M., Tonthat, N. K., Schumacher, M. A. & Yokoyama, K. Mechanism of pyranopterin ring formation in molybdenum cofactor biosynthesis. Proc. Natl Acad. Sci. USA 112, 6347-6352 (2015).
34. Kozmin, S. G. & Schaaper, R. M. Genetic characterization of moaB mutants of Escherichia coli. Res. Microbiol. 164, 689-694 (2013).
35. Hengge, R. Principles of c-di-GMP signalling in bacteria. Nat. Rev. Microbiol. 7, 263-273 (2009).
36. Wolska, K. I., Grudniak, A. M., Rudnicka, Z. & Markowska, K. Genetic control of bacterial biofilms. J. Appl. Genet. 57, 225-238 (2016).
37. D'Argenio, D. A., Calfee, M. W., Rainey, P. B. & Pesci, E. C. Autolysis and autoaggregation in Pseudomonas aeruginosa colony morphology mutants. J. Bacteriol. 184, 6481-6489 (2002).
38. Dietrich, L. E., Teal, T. K., Price-Whelan, A. & Newman, D. K. Redox-active antibiotics control gene expression and community behavior in divergent bacteria. Science 321, 1203-1206 (2008).
39. Recinos, D. A. et al. Redundant phenazine operons in Pseudomonas aeruginosa exhibit environment-dependent expression and differential roles in pathogenicity. Proc. Natl Acad. Sci. USA 109, 19420-19425 (2012).
40. Dietrich, L. E. et al. Bacterial community morphogenesis is intimately linked to the intracellular redox state. J. Bacteriol. 195, 1371-1380 (2013).
41. Mann, E. E. & Wozniak, D. J. Pseudomonas biofilm matrix composition and niche biology. FEMS Microbiol. Rev. 36, 893-916 (2012).
42. Burrows, L. L. Pseudomonas aeruginosa twitching motility: type IV pili in action. Annu. Rev. Microbiol. 66, 493-520 (2012).
43. Persat, A., Inclan, Y. F., Engel, J. N., Stone, H. A. & Gitai, Z. Type IV pili mechanochemically regulate virulence factors in Pseudomonas aeruginosa. Proc. Natl Acad. Sci. USA 112, 7563-7568 (2015).
44. Oliveira, N. M., Foster, K. R. & Durham, W. M. Single-cell twitching chemotaxis in developing biofilms. Proc. Natl Acad. Sci. USA 113, 6532-6537 (2016).
45. Kazmierczak, B. I., Lebron, M. B. & Murray, T. S. Analysis of FimX, a phosphodiesterase that governs twitching motility in Pseudomonas aeruginosa. Mol. Microbiol. 60, 1026-1043 (2006).
46. Sampedro, I., Parales, R. E., Krell, T. & Hill, J. E. Pseudomonas chemotaxis. FEMS Microbiol. Rev. 39, 17-46 (2015).
47. Typas, A. & Sourjik, V. Bacterial protein networks: properties and functions. Nat. Rev. Microbiol. 13, 559-572 (2015).
48. Kuchma, S. L., Griffin, E. F. & O'Toole, G. A. Minor pilins of the type IV pilus system participate in the negative regulation of swarming motility. J. Bacteriol. 194, 5388-5403 (2012).
49. Asally, M. et al. Localized cell death focuses mechanical forces during 3D patterning in a biofilm. Proc. Natl Acad. Sci. USA 109, 18891-18896 (2012).
50. Homann, O. R., Dea, J., Noble, S. M. & Johnson, A. D. A phenotypic profile of the Candida albicans regulatory network. PLoS Genet. 5, e1000783 (2009).
51. Nobile, C. J. et al. A recently evolved transcriptional network controls biofilm development in Candida albicans. Cell 148, 126-138 (2012).
52. Fox, E. P. et al. An expanded regulatory network temporally controls Candida albicans biofilm formation. Mol. Microbiol. 96, 1226-1239 (2015).
53. Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH image to ImageJ 25 years of image analysis. Nat. Methods 9, 671-675 (2012).
54. Typas, A. et al. Regulation of peptidoglycan synthesis by outer membrane proteins. Cell 143, 1097-1109 (2010).
55. Porwollik, S. et al. Defined single-gene and multi-gene deletion mutant collections in Salmonella enterica sv Typhimurium. PLoS ONE 9, e99820 (2014).
56. Takhar, H. K., Kemp, K., Kim, M., Howell, P. L. & Burrows, L. L. The platform protein is essential for type IV pilus biogenesis. J. Biol. Chem. 288, 9721-9728 (2013).
57. Baryshnikova, A. et al. Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat. Methods 7, 1017-1024 (2010).
58. Wagih, O. et al. SGAtools: one-stop analysis and visualization of array-based genetic interaction screens. Nucleic Acids Res. 41, W591-W596 (2013).
59. Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. & Tanabe, M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457-D462 (2016).
60. Mao, F., Dam, P., Chou, J., Olman, V. & Xu, Y. DOOR: a database for prokaryotic operons. Nucleic Acids Res. 37, D459-D463 (2009).
61. Marchler-Bauer, A. et al. CDD: NCBI's conserved domain database. Nucleic Acids Res. 43, D222-D226 (2015).
62. Inglis, D. O. et al. The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata. Nucleic Acids Res. 40, D667-D674 (2012).
63. Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57, 289-300 (1995).