Applications of imaging for bacterial systems biology

Current Opinion in Microbiology

Volumn 27, Issue , 2015, Pages 114-120

  Huang, Kerwyn Casey ^a,b  

^a Stanford University   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL CELL; BACTERIAL SYSTEMS BIOLOGY; BIOFILM; FLUORESCENCE IMAGING; HIGH THROUGHPUT FLUORESCENCE IMAGING; INTESTINE FLORA; MICROBIAL COMMUNITY; NONHUMAN; SINGLE CELL ANALYSIS; SYSTEMS BIOLOGY; TIME LAPSE IMAGING; BACTERIUM; DEVICES; GENETICS; METABOLISM; MICROBIAL CONSORTIUM; MOLECULAR IMAGING; MOLECULARLY TARGETED THERAPY; PHYSIOLOGY; PROCEDURES; ULTRASTRUCTURE;

BACTERIA; BIOFILMS; GASTROINTESTINAL MICROBIOME; MICROBIAL CONSORTIA; MOLECULAR IMAGING; MOLECULAR TARGETED THERAPY; SYSTEMS BIOLOGY;

EID: 84941199253     PISSN: 13695274     EISSN: 18790364     Source Type: Journal    
DOI: 10.1016/j.mib.2015.08.003     Document Type: Review

References (48)

1. Holtje J.V. Growth of the stress-bearing and shape-maintaining murein sacculus of Escherichia coli. Microbiol Mol Biol Rev 1998, 62:181-203.
2. Brochado A.R., Typas A. High-throughput approaches to understanding gene function and mapping network architecture in bacteria. Curr Opin Microbiol 2013, 16:199-206.
3. Nichols R.J., Sen S., Choo Y.J., Beltrao P., Zietek M., Chaba R., Lee S., Kazmierczak K.M., Lee K.J., Wong A., et al. Phenotypic landscape of a bacterial cell. Cell 2011, 144:143-156.
4. Schaechter M., Maaloe O., Kjeldgaard N.O. Dependency on medium and temperature of cell size and chemical composition during balanced grown of Salmonella typhimurium. J Gen Microbiol 1958, 19:592-606.
5. Lenski R.E., Travisano M. Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proc Natl Acad Sci U S A 1994, 91:6808-6814.
6. Monds R.D., Lee T.K., Colavin A., Ursell T., Quan S., Cooper T.F., Huang K.C. Systematic perturbation of cytoskeletal function reveals a linear scaling relationship between cell geometry and fitness. Cell Rep 2014, 9:1528-1537.
7. Ouzounov N., Nguyen J., Bratton B., Jacobowitz D., Gitai Z., Shaevitz J.W. MreB helical pitch angle determines cell diameter in Escherichia coli 2015, arxiv:1503.07789.
8. Levy S.F., Siegal M.L. Network hubs buffer environmental variation in Saccharomyces cerevisiae. PLoS Biol 2008, 6:e264.
9. Helaine S., Cheverton A.M., Watson K.G., Faure L.M., Matthews S.A., Holden D.W. Internalization of Salmonella by macrophages induces formation of nonreplicating persisters. Science 2014, 343:204-208.
10. Goshima G., Wollman R., Goodwin S.S., Zhang N., Scholey J.M., Vale R.D., Stuurman N. Genes required for mitotic spindle assembly in Drosophila S2 cells. Science 2007, 316:417-421.
11. Chong Y.T., Koh J.L., Friesen H., Duffy K., Cox M.J., Moses A., Moffat J., Boone C., Andrews B.J. Yeast proteome dynamics from single cell imaging and automated analysis. Cell 2015, 161:1413-1424.
12. Werner J.N., Chen E.Y., Guberman J.M., Zippilli A.R., Irgon J.J., Gitai Z. Quantitative genome-scale analysis of protein localization in an asymmetric bacterium. Proc Natl Acad Sci U S A 2009, 106:7858-7863.
13. Ingerson-Mahar M., Briegel A., Werner J.N., Jensen G.J., Gitai Z. The metabolic enzyme CTP synthase forms cytoskeletal filaments. Nat Cell Biol 2010, 12:739-746.
14. Castellana M., Wilson M.Z., Xu Y., Joshi P., Cristea I.M., Rabinowitz J.D., Gitai Z., Wingreen N.S. Enzyme clustering accelerates processing of intermediates through metabolic channeling. Nat Biotechnol 2014, 32:1011-1018.
15. Christian J., Scott W. Water relations of salmonellae at 30°C. Aust J Biol Sci 1953, 6:565-573.
16. Rojas E., Theriot J.A., Huang K.C. Response of Escherichia coli growth rate to osmotic shock. Proc Natl Acad Sci U S A 2014, 111:7807-7812.
17. Kentner D., Sourjik V. Dynamic map of protein interactions in the Escherichia coli chemotaxis pathway. Mol Syst Biol 2009, 5:238.
18. Sourjik V., Berg H.C. Binding of the Escherichia coli response regulator CheY to its target measured in vivo by fluorescence resonance energy transfer. Proc Natl Acad Sci U S A 2002, 99:12669-12674.
19. Ogura T.B.P., Niki H., D'Ari R., Hiraga S., Jaffé A. Penicillin-binding protein 2 is essential in wild-type Escherichia coli but not in lov or cya mutants. J Bacteriol 1989, 171:3025-3030.
20. Teeffelen S.v., Wang S., Furchtgott L., Huang K.C., Wingreen N.S., Shaevitz J.W., Gitai Z. The bacterial actin MreB rotates and rotation depends on cell-wall assembly. Proc Natl Acad Sci U S A 2011, 108:15822-15827.
21. Lee T.K., Tropini C., Hsin J., Desmarais S.M., Ursell T.S., Gong E., Gitai Z., Monds R.D., Huang K.C. A dynamically assembled cell wall synthesis machinery buffers cell growth. Proc Natl Acad Sci U S A 2014, 111:4554-4559.
22. Arifuzzaman M., Maeda M., Itoh A., Nishikata K., Takita C., Saito R., Ara T., Nakahigashi K., Huang H.C., Hirai A., et al. Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res 2006, 16:686-691.
23. Kuwada N.J., Traxler B., Wiggins P.A. Genome-scale quantitative characterization of bacterial protein localization dynamics throughout the cell cycle. Mol Microbiol 2015, 95:64-79.
24. Cotsonas King A., Wu L. Macromolecular synthesis and membrane perturbation assays for mechanisms of action studies of antimicrobial agents. Curr Protoc Pharmacol 2009, 13A:17.11-17.23.
25. Nonejuie P., Burkart M., Pogliano K., Pogliano J. Bacterial cytological profiling rapidly identifies the cellular pathways targeted by antibacterial molecules. Proc Natl Acad Sci U S A 2013, 110:16169-16174.
26. Whitney J.C., Howell P.L. Synthase-dependent exopolysaccharide secretion in Gram-negative bacteria. Trends Microbiol 2013, 21:63-72.
27. Serra D.O., Richter A.M., Hengge R. Cellulose as an architectural element in spatially structured Escherichia coli biofilms. J Bacteriol 2013, 195:5540-5554.
28. Romling U., Sierralta W.D., Eriksson K., Normark S. Multicellular and aggregative behaviour of Salmonella Typhimurium strains is controlled by mutations in the agfD promoter. Mol Microbiol 1998, 28:249-264.
29. Hengge R. Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol 2009, 7:263-273.
30. Kashyap P.C., Marcobal A., Ursell L.K., Smits S.A., Sonnenburg E.D., Costello E.K., Higginbottom S.K., Domino S.E., Holmes S.P., Relman D.A., et al. Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota. Proc Natl Acad Sci U S A 2013, 110:17059-17064.
31. Dominguez-Bello M.G., Costello E.K., Contreras M., Magris M., Hidalgo G., Fierer N., Knight R. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A 2010, 107:11971-11975.
32. Spor A., Koren O., Ley R. Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol 2011, 9:279-290.
33. Turnbaugh P.J., Ridaura V.K., Faith J.J., Rey F.E., Knight R., Gordon J.I. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 2009, 1:6ra14.
34. Turnbaugh P.J., Ley R.E., Mahowald M.A., Magrini V., Mardis E.R., Gordon J.I. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006, 444:1027-1031.
35. Frank D.N., St Amand A.L., Feldman R.A., Boedeker E.C., Harpaz N., Pace N.R. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A 2007, 104:13780-13785.
36. Lee S.M., Donaldson G.P., Mikulski Z., Boyajian S., Ley K., Mazmanian S.K. Bacterial colonization factors control specificity and stability of the gut microbiota. Nature 2013, 501:426-429.
37. Vaishnava S., Yamamoto M., Severson K.M., Ruhn K.A., Yu X., Koren O., Ley R., Wakeland E.K., Hooper L.V. The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine. Science 2011, 334:255-258.
38. Scheffers D.J., Pinho M.G. Bacterial cell wall synthesis: new insights from localization studies. Microbiol Mol Biol Rev 2005, 69:585-607.
39. Qi L.S., Larson M.H., Gilbert L.A., Doudna J.A., Weissman J.S., Arkin A.P., Lim W.A. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 2013, 152:1173-1183.
40. Biteen J.S., Moerner W.E. Single-molecule and superresolution imaging in live bacteria cells. Cold Spring Harb Perspect Biol 2010, 2:a000448.
41. Furchtgott L., Wingreen N.S., Huang K.C. Mechanisms for maintaining cell shape in rod-shaped Gram-negative bacteria. Mol Microbiol 2011, 81:340-353.
42. Huang K.C., Mukhopadhyay R., Wen B., Gitai Z., Wingreen N.S. Cell shape and cell-wall organization in Gram-negative bacteria. Proc Natl Acad Sci U S A 2008, 105:19282-19287.
43. Wang S., Furchtgott L., Huang K.C., Shaevitz J.W. Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall. Proc Natl Acad Sci U S A 2012, 109:E595-E604.
44. Tropini C., Lee T.K., Hsin J., Desmarais S.M., Ursell T., Monds R.D., Huang K.C. Principles of bacterial cell-size determination revealed by cell-wall synthesis perturbations. Cell Rep 2014, 9:1520-1527.
45. Dye N.A., Pincus Z., Fisher I.C., Shapiro L., Theriot J.A. Mutations in the nucleotide binding pocket of MreB can alter cell curvature and polar morphology in Caulobacter. Mol Microbiol 2011, 81:368-394.
46. Pincus Z., Theriot J.A. Comparison of quantitative methods for cell-shape analysis. J Microsc 2007, 227:140-156.
47. Fridman O., Goldberg A., Ronin I., Shoresh N., Balaban N.Q. Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations. Nature 2014, 513:418-421.
48. Agaisse H., Burrack L.S., Philips J.A., Rubin E.J., Perrimon N., Higgins D.E. Genome-wide RNAi screen for host factors required for intracellular bacterial infection. Science 2005, 309:1248-1251.