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A genome-wide screen for identifying all regulators of a target gene

Guillaume Baptist 1, 2 Corinne Pinel 1, 2 Caroline Ranquet 2, 1 Jérôme Izard 1, 2 Delphine Ropers 1 Hidde de Jong 1 Johannes Geiselmann 1, 2, * 
* Corresponding author
1 IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks
LAPM - Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble], Inria Grenoble - Rhône-Alpes, Institut Jean Roget
Abstract : We have developed a new screening methodology for identifying all genes that control the expression of a target gene through genetic or metabolic interactions. The screen combines mutant libraries with luciferase reporter constructs, whose expression can be monitored in vivo and over time in different environmental conditions. We apply the method to identify the genes that control the expression of the gene acs, encoding the acetyl coenzyme A synthetase, in Escherichia coli. We confirm most of the known genetic regulators, including CRP-cAMP, IHF and components of the phosphotransferase system. In addition, we identify new regulatory interactions, many of which involve metabolic intermediates or metabolic sensing, such as the genes pgi, pfkA, sucB and lpdA, encoding enzymes in glycolysis and the TCA cycle. Some of these novel interactions were validated by quantitative reverse transcriptase-polymerase chain reaction. More generally, we observe that a large number of mutants directly or indirectly influence acs expression, an effect confirmed for a second promoter, sdhC. The method is applicable to any promoter fused to a luminescent reporter gene in combination with a deletion mutant library.
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Submitted on : Tuesday, September 3, 2013 - 1:02:59 PM
Last modification on : Thursday, January 20, 2022 - 4:16:16 PM

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Guillaume Baptist, Corinne Pinel, Caroline Ranquet, Jérôme Izard, Delphine Ropers, et al.. A genome-wide screen for identifying all regulators of a target gene. Nucleic Acids Research, Oxford University Press, 2013, 41 (17), pp.e164. ⟨10.1093/nar/gkt655⟩. ⟨hal-00857345⟩



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