Journal of Basic Microbiology 2012, 52, 1 – 16 1 © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.jbm-journal.com Research Paper New insights on transcriptional responses of genes involved in carbon central metabolism, respiration and fermentation to low ATP levels in Escherichia coli Sandra Soria 1 , Ramón de Anda 2 , Noemí Flores 2 , Susana Romero-Garcia 3 , Guillermo Gosset 2 , Francisco Bolívar 2 and José Luis Báez-Viveros 1 1 Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos (UAEM), Cuernavaca, Morelos, México 2 Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México 3 Departamento de Enfermedades Crónico-Degenerativas, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosio Villegas”, Tlalpan, Ciudad de México, México Adenosine-5-triphosphate (ATP) plays a fundamental role in many cellular processes such as trans- port, central carbon metabolism, biosynthetic reactions, macromolecular synthesis, signal trans- duction and cellular division. In addition, the intracellular [ATP]/[ADP] ratio in Escherichia coli plays an important role in controlling the specific rates of growth (µ), glucose consumption (q Glc ) and oxygen uptake (q O2 ), as well as the transcriptome pattern in the cell, as was recently reported. In the current study, the energetic level (expressed as [ATP]/[ADP] ratio) was substantially reduced in E. coli strains by either over-expressing the F 1 -ATPase activity (JMAGD + ) or inactivating ATP syn- thase (JMat – ). The physiological characterization of the wild-type JM101 strain and its derivative JMAGD + and JMatp – strains was conducted in bioreactors containing minimal medium with glu- cose. The inactivation of the atp operon and F 1 -ATPase overexpression significantly diminished the energetic level and cAMP concentration in derivative strains. Relative transcription levels of 105 genes involved in glucose transport, glycolysis, tricarboxylic acid (TCA) cycle, fermentation, respi- ration, transcriptional regulators, transcription and genes involved in stress were determined by using qPCR. Interestingly, in the JMAGD + and JMatp – strains, having a reduced energetic level, many transcripts of glycolysis, TCA cycle and respiratory genes were down-regulated when com- pared to wild type JM101. The transcriptional responses, detected in the strains with reduced ener- getic level show down-regulation of genes involved in central carbon metabolism and respiration, these results are apposite to the observed trends of increased metabolic fluxes in glucose consump- tion, glycolysis, acetate synthesis, TCA cycle and respiration. Regulation mediated by CRP-cAMP complex may explain some observed transcriptional responses of TCA cycle genes, since cAMP concentration and crp transcript level were significant reduced in the JMatp – mutant. Therefore, the substantial reduction of [ATP]/[ADP] ratio had a relevant effect on the CRP-cAMP regulatory system (among other global regulators), which may trigger an extensive transcriptional response. Keywords: ATPase / Transcriptional responses / Escherichia coli / Carbon central metabolism / qPCR Received: November 03, 2011; accepted: February 03, 2012 DOI 10.1002/jobm.201100525 Introduction * Adenosine-5-triphosphate (ATP) plays a fundamental role in all cells, providing Gibbs free energy for many Correspondence: José Luis Báez-Viveros, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos (UAEM), Av. Universidad 1001, C.P. 62209. Cuernavaca, Morelos, México E-mail: jlbaez@uaem.mx cellular processes such as active transport [1], peptide folding [2], central carbon metabolism [3], biosynthetic reactions, macromolecular synthesis (DNA, RNA and protein), signal transduction [4], motility, cellular divi- sion [5, 6], and stress responses [4, 7]. ATP synthesis in prokaryotic organisms takes place mainly in glycolysis by substrate-level phosphorylation [3] and in the tricarb-