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J Bacteriol. 2015 Jul 6;198(1):7-11. doi: 10.1128/JB.00424-15. Print 2016 Jan 1.

Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli.

Author information

1
Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Berlin, Germany regine.hengge@hu-berlin.de.
2
NCBI, NLM, National Institutes of Health, Bethesda, Maryland, USA.
3
Département de Microbiologie, Institut Pasteur, Paris, France.
4
Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA.
5
Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom.
6
Department of Biology, University of Utah, Salt Lake City, Utah, USA.
7
Biozentrum, Universität Basel, Basel, Switzerland.
8
Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.

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.

PMID:
26148715
PMCID:
PMC4686207
DOI:
10.1128/JB.00424-15
[Indexed for MEDLINE]
Free PMC Article

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