Colony-live —a high-throughput method for measuring microbial colony growth kinetics— reveals diverse growth effects of gene knockouts in Escherichia coli

BMC Microbiology

Hirotada Mori²  Barry L Wanner³  Ai Muto²  Yuichirou Tanaka²  Toru Nakayashiki¹  Takeyuki Tamura⁴  Rikiya Takeuchi² 

[1] Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan;Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan;Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA;Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan

关键词: Saturation point growth (SPG);    Maximum growth rate (MGR);    Lag time of growth (LTG);    Keio collection;    Single-gene knockout;    High-throughput;    Phenotype screening;    Growth kinetics;   

Others  :  1140856
DOI  :  10.1186/1471-2180-14-171

 received in 2014-01-20, accepted in 2014-06-06,  发布年份 2014

【 摘 要 】

Background

Precise quantitative growth measurements and detection of small growth changes in high-throughput manner is essential for fundamental studies of bacterial cell. However, an inherent tradeoff for measurement quality in high-throughput methods sacrifices some measurement quality. A key challenge has been how to enhance measurement quality without sacrificing throughput.

Results

We developed a new high-throughput measurement system, termed Colony-live. Here we show that Colony-live provides accurate measurement of three growth values (lag time of growth (LTG), maximum growth rate (MGR), and saturation point growth (SPG)) by visualizing colony growth over time. By using a new normalization method for colony growth, Colony-live gives more precise and accurate growth values than the conventional method. We demonstrated the utility of Colony-live by measuring growth values for the entire Keio collection of Escherichia coli single-gene knockout mutants. By using Colony-live, we were able to identify subtle growth defects of single-gene knockout mutants that were undetectable by the conventional method quantified by fixed time-point camera imaging. Further, Colony-live can reveal genes that influence the length of the lag-phase and the saturation point of growth.

Conclusions

Measurement quality is critical to achieving the resolution required to identify unique phenotypes among a diverse range of phenotypes. Sharing high-quality genome-wide datasets should benefit many researchers who are interested in specific gene functions or the architecture of cellular systems. Our Colony-live system provides a new powerful tool to accelerate accumulation of knowledge of microbial growth phenotypes.

【 授权许可】

   
2014 Takeuchi et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Babu M, Diaz-Mejia JJ, Vlasblom J, Gagarinova A, Phanse S, Graham C, Yousif F, Ding H, Xiong X, Nazarians-Armavil A, Alamgir M, Ali M, Pogoutse O, Pe'er A, Arnold R, Michaut M, Parkinson J, Golshani A, Whitfield C, Wodak SJ, Moreno-Hagelsieb G, Greenblatt JF, Emili A: Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. PLoS Genet 2011, 7(11):e1002377.
• [2]Butland G, Babu M, Diaz-Mejia JJ, Bohdana F, Phanse S, Gold B, Yang W, Li J, Gagarinova AG, Pogoutse O, Mori H, Wanner BL, Lo H, Wasniewski J, Christopolous C, Ali M, Venn P, Safavi-Naini A, Sourour N, Caron S, Choi JY, Laigle L, Nazarians-Armavil A, Deshpande A, Joe S, Datsenko KA, Yamamoto N, Andrews BJ, Boone C, Ding H, et al.: eSGA: E. coli synthetic genetic array analysis. Nat Methods 2008, 5(9):789-795.
• [3]Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, et al.: The genetic landscape of a cell. Science 2010, 327(5964):425-431.
• [4]Typas A, Nichols RJ, Siegele DA, Shales M, Collins SR, Lim B, Braberg H, Yamamoto N, Takeuchi R, Wanner BL, Mori H, Weissman JS, Krogan NJ, Gross CA: High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods 2008, 5(9):781-787.
• [5]Nichols RJ, Sen S, Choo YJ, Beltrao P, Zietek M, Chaba R, Lee S, Kazmierczak KM, Lee KJ, Wong A, Shales M, Lovett S, Winkler ME, Krogan NJ, Typas A, Gross CA: Phenotypic landscape of a bacterial cell. Cell 2011, 144(1):143-156.
• [6]Blomberg A: Measuring growth rate in high-throughput growth phenotyping. Curr Opin Biotechnol 2011, 22(1):94-102.
• [7]Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boone C, Myers CL: Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods 2010, 7(12):1017-1024.
• [8]Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C: Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 2001, 294(5550):2364-2368.
• [9]Zwietering MH, Jongenburger I, Rombouts FM, van ’t Riet K: Modeling of the bacterial growth curve. Appl Environ Microbiol 1990, 56(6):1875-1881.
• [10]Warringer J, Ericson E, Fernandez L, Nerman O, Blomberg A: High-resolution yeast phenomics resolves different physiological features in the saline response. Proc Natl Acad Sci U S A 2003, 100(26):15724-15729.
• [11]Warringer J, Zorgo E, Cubillos FA, Zia A, Gjuvsland A, Simpson JT, Forsmark A, Durbin R, Omholt SW, Louis EJ, Liti G, Moses A, Blomberg A: Trait variation in yeast is defined by population history. PLoS Genet 2011, 7(6):e1002111.
• [12]Levin-Reisman I, Gefen O, Fridman O, Ronin I, Shwa D, Sheftel H, Balaban NQ: Automated imaging with ScanLag reveals previously undetectable bacterial growth phenotypes. Nat Methods 2010, 7(9):737-739.
• [13]Ernebjerg M, Kishony R: Distinct growth strategies of soil bacteria as revealed by large-scale colony tracking. Appl Environ Microbiol 2012, 78(5):1345-1352.
• [14]Addinall SG, Holstein EM, Lawless C, Yu M, Chapman K, Banks AP, Ngo HP, Maringele L, Taschuk M, Young A, Ciesiolka A, Lister AL, Wipat A, Wilkinson DJ, Lydall D: Quantitative fitness analysis shows that NMD proteins and many other protein complexes suppress or enhance distinct telomere cap defects. PLoS Genet 2011, 7(4):e1001362.
• [15]Shah NA, Laws RJ, Wardman B, Zhao LP, Hartman JL: Accurate, precise modeling of cell proliferation kinetics from time-lapse imaging and automated image analysis of agar yeast culture arrays. BMC Syst Biol 2007, 1:3.
• [16]Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H: Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2006, 2:2006-0008.
• [17]Yamamoto N, Nakahigashi K, Nakamichi T, Yoshino M, Takai Y, Touda Y, Furubayashi A, Kinjyo S, Dose H, Hasegawa M, Datsenko KA, Nakayashiki T, Tomita M, Wanner BL, Mori H: Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol Syst Biol 2009, 5:335.
• [18]Pellis L, Franssen-van Hal NL, Burema J, Keijer J: The intraclass correlation coefficient applied for evaluation of data correction, labeling methods, and rectal biopsy sampling in DNA microarray experiments. Physiol Genomics 2003, 16(1):99-106.
• [19]Erhardt H, Steimle S, Muders V, Pohl T, Walter J, Friedrich T: Disruption of individual nuo-genes leads to the formation of partially assembled NADH:ubiquinone oxidoreductase (complex I) in Escherichia coli. Biochim Biophys Acta 2012, 1817(6):863-871.
• [20]Gulmezian M, Hyman KR, Marbois BN, Clarke CF, Javor GT: The role of UbiX in Escherichia coli coenzyme Q biosynthesis. Arch Biochem Biophys 2007, 467(2):144-153.
• [21]Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T: Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol Cell 2006, 21(1):97-108.
• [22]Yim L, Moukadiri I, Bjork GR, Armengod ME: Further insights into the tRNA modification process controlled by proteins MnmE and GidA of Escherichia coli. Nucleic Acids Res 2006, 34(20):5892-5905.
• [23]Paek KH, Walker GC: Escherichia coli dnaK null mutants are inviable at high temperature. J Bacteriol 1987, 169(1):283-290.
• [24]Baranyi J: Comparison of Stochastic and Deterministic Concepts of Bacterial Lag. J Theor Biol 1998, 192(3):403-408.
• [25]Pirt SJ: The maintenance energy of bacteria in growing cultures. Proc R Soc Lond B Biol Sci 1965, 163(991):224-231.
• [26]Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martinez C, Fulcher C, Huerta AM, Kothari A, Krummenacker M, Latendresse M, Muniz-Rascado L, Ong Q, Paley S, Schroder I, Shearer AG, Subhraveti P, Travers M, Weerasinghe D, Weiss V, Collado-Vides J, Gunsalus RP, Paulsen I, Karp PD: EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res 2013, 41(Database issue):D605-D612.
• [27]Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28(1):27-30.
• [28]Jensen PR, Michelsen O: Carbon and energy metabolism of atp mutants of Escherichia coli. J Bacteriol 1992, 174(23):7635-7641.
• [29]Bekker M, de Vries S, Ter Beek A, Hellingwerf KJ, de Mattos MJ: Respiration of Escherichia coli can be fully uncoupled via the nonelectrogenic terminal cytochrome bd-II oxidase. J Bacteriol 2009, 191(17):5510-5517.
• [30]Sezonov G, Joseleau-Petit D, D’Ari R: Escherichia coli physiology in Luria-Bertani broth. J Bacteriol 2007, 189(23):8746-8749.
• [31]Pirt SJ: A kinetic study of the mode of growth of surface colonies of bacteria and fungi. J Gen Microbiol 1967, 47(2):181-197.
• [32]McKay AL, Peters AC, Hann AC: The growth of Salmonella typhimurium on irradiated, raw, skinless chicken breast. Int J Food Microbiol 1997, 37(2–3):121-129.
• [33]Agris PF, Vendeix FA, Graham WD: tRNA’s wobble decoding of the genome: 40 years of modification. J Mol Biol 2007, 366(1):1-13.
• [34]Selinger DW, Cheung KJ, Mei R, Johansson EM, Richmond CS, Blattner FR, Lockhart DJ, Church GM: RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol 2000, 18(12):1262-1268.
• [35]Ohtsu I, Wiriyathanawudhiwong N, Morigasaki S, Nakatani T, Kadokura H, Takagi H: The L-cysteine/L-cystine shuttle system provides reducing equivalents to the periplasm in Escherichia coli. J Biol Chem 2010, 285(23):17479-17487.
• [36]Imlay JA: Cellular defenses against superoxide and hydrogen peroxide. Annu Rev Biochem 2008, 77:755-776.
• [37]Nakahigashi K, Miyamoto K, Nishimura K, Inokuchi H: Isolation and characterization of a light-sensitive mutant of Escherichia coli K-12 with a mutation in a gene that is required for the biosynthesis of ubiquinone. J Bacteriol 1992, 174(22):7352-7359.
• [38]Tschowri N, Busse S, Hengge R: The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli. Genes Dev 2009, 23(4):522-534.
• [39]Bradski G: The OpenCV Library. Dr Dobb’s J Softw Tools 2000, 25(11):122-125.
• [40]Lawless C, Wilkinson DJ, Young A, Addinall SG, Lydall DA: Colonyzer: automated quantification of micro-organism growth characteristics on solid agar. BMC Bioinformatics 2010, 11:287.
• [41]Liao P, Chen T, Chung P: A fast algorithm for multilevel thresholding. J Inform Sci Eng 2001, 17:713-727.
• [42]Russell JB, Cook GM: Energetics of bacterial growth: balance of anabolic and catabolic reactions. Microbiol Rev 1995, 59(1):48-62.
• [43]Todorov V, Filzmoser P: An object-oriented framework for robust multivariate analysis. J Stat Softw 2009, 32(3):1-47.
• [44]Gamer M, Lemon J, Fellows I, Sing P: irr: Various coefficients of interrater reliability and agreement (Version 0.83). Available from http://CRANR-projectorg/package=irr webcite 2010
• [45]Breitling R, Armengaud P, Amtmann A, Herzyk P: Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett 2004, 573(1–3):83-92.
• [46]Hong F, Breitling R, McEntee CW, Wittner BS, Nemhauser JL, Chory J: RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics 2006, 22(22):2825-2827.