title: Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli.
abstract: In recent years, Escherichia coli has served as one of a few model bacterial species for studying cyclic di-GMP (c-di-GMP) signaling. The widely used E. coli K-12 laboratory strains possess 29 genes encoding proteins with GGDEF and/or EAL domains, which include 12 diguanylate cyclases (DGC), 13 c-di-GMP-specific phosphodiesterases (PDE), and 4 "degenerate" enzymatically inactive proteins. In addition, six new GGDEF and EAL (GGDEF/EAL) domain-encoding genes, which encode two DGCs and four PDEs, have recently been found in genomic analyses of commensal and pathogenic E. coli strains. As a group of researchers who have been studying the molecular mechanisms and the genomic basis of c-di-GMP signaling in E. coli, we now propose a general and systematic dgc and pde nomenclature for the enzymatically active GGDEF/EAL domain-encoding genes of this model species. This nomenclature is intuitive and easy to memorize, and it can also be applied to additional genes and proteins that might be discovered in various strains of E. coli in future studies.
authors.affiliation: Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Berlin, Germany regine.hengge@hu-berlin.de.
authors.forename: Regine
authors.initials: R
authors.lastname: Hengge
authors.affiliation: NCBI, NLM, National Institutes of Health, Bethesda, Maryland, USA.
authors.forename: Michael Y
authors.identifier: http://orcid.org/0000-0002-2265-5572
authors.initials: MY
authors.lastname: Galperin
authors.affiliation: Département de Microbiologie, Institut Pasteur, Paris, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Ghigo
authors.affiliation: Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Gomelsky
authors.affiliation: Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Green
authors.affiliation: Department of Biology, University of Utah, Salt Lake City, Utah, USA.
authors.forename: Kelly T
authors.initials: KT
authors.lastname: Hughes
authors.affiliation: Biozentrum, Universität Basel, Basel, Switzerland.
authors.forename: Urs
authors.initials: U
authors.lastname: Jenal
authors.affiliation: Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Landini
mesh_terms: D006152:Cyclic GMP / Q000031:analogs & derivatives* / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000145:classification* / Q000235:genetics / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D015398:Signal Transduction; D009626:Terminology as Topic
chemical_list: D029968:Escherichia coli Proteins; C062025:bis(3',5')-cyclic diguanylic acid; D006152:Cyclic GMP