title: Dynamics of the Escherichia coli proteome in response to nitrogen starvation and entry into the stationary phase.
abstract: Nitrogen is needed for the biosynthesis of biomolecules including proteins and nucleic acids. In the absence of fixed nitrogen prokaryotes such as E. coli immediately ceases growth. Ammonium is the preferred nitrogen source for E. coli supporting the fastest growth rates. Under conditions of ammonium limitation, E. coli can use alternative nitrogen sources to supply ammonium ions and this reprogramming is led by the induction of the NtrC regulon. Here we used label free proteomics to determine the dynamics of E. coli proteins expression in response to ammonium starvation in both the short (30min) and the longer (60min) starvation. Protein abundances and post-translational modifications confirmed that activation of the NtrC regulon acts as the first line of defense against nitrogen starvation. The ribosome inactivating protein Rmf was induced shortly after ammonium exhaustion and this was preceded by induction of other ribosome inactivating proteins such as Hpf and RaiA supporting the hypothesis that ribosome shut-down is a key process during nitrogen limitation stress. The proteomic data revealed that growth arrest due to nitrogen starvation correlates with the accumulation of proteins involved in DNA condensation, RNA and protein catabolism and ribosome hibernation. Collectively, these proteome adaptations will result in metabolic inactive cells which are likely to exhibit multidrug tolerance.
authors.affiliation: Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil.
authors.forename: Heloisa B S
authors.initials: HB
authors.lastname: Sanchuki
authors.affiliation: Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil.
authors.forename: Fernanda
authors.initials: F
authors.lastname: Gravina
authors.affiliation: Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil.
authors.forename: Thiago E
authors.initials: TE
authors.lastname: Rodrigues
authors.affiliation: Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil.
authors.forename: Edileusa C M
authors.initials: EC
authors.lastname: Gerhardt
authors.affiliation: Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil.
authors.forename: Fábio O
authors.initials: FO
authors.lastname: Pedrosa
authors.affiliation: Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil.
authors.forename: Emanuel M
authors.initials: EM
authors.lastname: Souza
authors.affiliation: Setor de Educação Profissional e Tecnológica, UFPR, Curitiba, PR, Brazil.
authors.forename: Roberto T
authors.initials: RT
authors.lastname: Raittz
authors.affiliation: Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil; Departamento de Análises Clínicas, UFPR, Curitiba, PR, Brazil.
authors.forename: Glaucio
authors.initials: G
authors.lastname: Valdameri
authors.affiliation: Department of Immunology, University of Oslo and Oslo University Hospital, The Proteomics Core Facility, Rikshospitalet, Oslo, Norway; Instituto do Cérebro, UFRN, Natal, RN, Brazil.
authors.forename: Gustavo A
authors.initials: GA
authors.lastname: de Souza
authors.affiliation: Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil; Setor Litoral, UFPR, Matinhos, PR, Brazil. Electronic address: huergo@ufpr.br.
authors.forename: Luciano F
authors.initials: LF
authors.lastname: Huergo
mesh_terms: D064751:Ammonium Compounds / Q000378:metabolism; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology; D009584:Nitrogen / Q000378:metabolism*; D011499:Protein Processing, Post-Translational / Q000502:physiology; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics / Q000379:methods; D012269:Ribosomal Proteins / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism
chemical_list: D064751:Ammonium Compounds; D029968:Escherichia coli Proteins; D020543:Proteome; D012269:Ribosomal Proteins; D009584:Nitrogen
keywords: Nitrogen; Ntr; PII; Persister; RelE; Ribosome; Rmf