Global responses of Escherichia coli to adverse conditions determined by microarrays and FT-IR spectroscopy Birgitte Moen, Astrid Oust Janbu, Solveig Langsrud, Øyvind Langsrud, Jon L. Hobman, Chrystala Constantinidou, Achim Kohler, and Knut Rudi Abstract: The global gene expression and biomolecular composition in an Escherichia coli model strain exposed to 10 ad- verse conditions (sodium chloride, ethanol, glycerol, hydrochloric and acetic acid, sodium hydroxide, heat (46 8C), and cold (15 8C), as well as ethidium bromide and the disinfectant benzalkonium chloride) were determined using DNA micro- arrays and Fourier transform infrared (FT-IR) spectroscopy. In total, approximately 40% of all investigated genes (1682/ 4279 genes) significantly changed expression, compared with a nonstressed control. There were, however, only 3 genes (ygaW (unknown function), rmf (encoding a ribosomal modification factor), and ghrA (encoding a glyoxylate/hydroxypyru- vate reductase)) that significantly changed expression under all conditions (not including benzalkonium chloride). The FT- IR analysis showed an increase in unsaturated fatty acids during ethanol and cold exposure, and a decrease during acid and heat exposure. Cold conditions induced changes in the carbohydrate composition of the cell, possibly related to the up- regulation of outer membrane genes (glgAP and rcsA). Although some covariance was observed between the 2 data sets, principle component analysis and regression analyses revealed that the gene expression and the biomolecular responses are not well correlated in stressed populations of E. coli, underlining the importance of multiple strategies to begin to under- stand the effect on the whole cell. Key words: Escherichia coli, global responses, microarray, FT-IR spectroscopy, multivariate data analysis. Re ´sume ´: L’expression ge ´nique globale et la composition biomole ´culaire d’une souche mode `le d’Escherichia coli soumise a ` 10 conditions de ´favorables (le chlorure de sodium, l’e ´thanol, le glyce ´rol, l’acide chlorhydrique, l’acide ace ´tique, l’hy- droxyde de sodium, la chaleur (46 8C) et le froid (15 8C) ainsi que le bromure d’e ´thidium et le chlorure de benzalkonium, un de ´sinfectant) ont e ´te ´ de ´termine ´es sur des puces a ` ADN et par spectroscopie infrarouge a ` transforme ´e de Fourier (IRTF). Au total, environ 40 % de tous les ge `nes examine ´s (1682/4279) changeaient de niveau d’expression de fac ¸on si- gnificative comparativement au contro ˆle non stresse ´. Il n’y avait cependant que 3 ge `nes (ygaW (fonction inconnue), rmf (codant un facteur de modification ribosomal) et ghrA (codant une glyoxylate/hydroxypyruvate re ´ductase)) dont le niveau d’expression changeait significativement sous toutes les conditions (sauf le chlorure de benzalkonium). L’analyse en IRTF a montre ´ une augmentation du contenu en acides gras insature ´s lors de l’exposition a ` l’e ´thanol et au froid, et une diminu- tion lors d’une exposition aux acides et a ` la chaleur. Le induisait des changements dans la composition en sucres de la cel- lule, possiblement en lien avec l’augmentation de l’expression de ge `nes codant des composantes membranaires (glgAP et rcsA). Me ˆme si une certaine covariance e ´tait observe ´e entre les 2 se ´ries de donne ´es, les analyses en composantes principa- les et de re ´gression ont re ´ve ´le ´ que l’expression ge ´nique et la re ´ponse biomole ´culaire n’e ´taient pas en corre ´lation chez les populations de E. coli stresse ´es, et mettent en e ´vidence l’importance d’adopter de multiples strate ´gies pour comprendre l’effet du stress sur la cellule entie `re. Mots-cle ´s : Escherichia coli, re ´ponse globale, puce d’ADN, spectroscopie IRTF, analyse multivarie ´e de donne ´es. [Traduit par la Re ´daction] Received 6 January 2009. Accepted 16 January 2009. Published on the NRC Research Press Web site at cjm.nrc.ca on 23 June 2009. B. Moen 1 and A.O. Janbu. 2 Nofima Mat, Osloveien 1, N-1430 A ˚ s, Norway; Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 A ˚ s, Norway. S. Langsrud, 3 Ø. Langsrud, and A. Kohler. Nofima Mat, Osloveien 1, N-1430 A ˚ s, Norway. J.L. Hobman 4 and C. Constantinidou. School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK. K. Rudi. Nofima Mat, Osloveien 1, N-1430 A ˚ s, Norway; Hedmark University College, Holsetgata 22, 2306 Hamar, Norway. 1 Corresponding author (e-mail: birgitte.moen@nofima.no). 2 Present address: Oslo University College, Post Box 4, ST. Olavs. plass, 0130 Oslo, Norway. 3 Corresponding author (e-mail: solveig.langsrud@nofima.no). 4 Present address: School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington LE12 5RD, UK. 714 Can. J. Microbiol. 55: 714–728 (2009) doi:10.1139/W09-016 Published by NRC Research Press