Multi-level evaluation of Escherichia coli polyphosphate related mutants using global transcriptomic, proteomic and phenomic analyses

• Published in: Biochimica et biophysica acta. General subjects Vol. 1861; no. 4; pp. 871 - 883
• Main Authors: Varas, Macarena, Valdivieso, Camilo, Mauriaca, Cecilia, Ortíz-Severín, Javiera, Paradela, Alberto, Poblete-Castro, Ignacio, Cabrera, Ricardo, Chávez, Francisco P.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.04.2017
• Subjects: anti-infective agents; Antitoxins - genetics; bacteria; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; biochemical pathways; bioinformatics; biopolymers; Cell Respiration - genetics; energy; Escherichia coli; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins - genetics; fermentation; Fermentation - genetics; gene expression regulation; Metabolic Networks and Pathways - genetics; microarray technology; mutants; Mutation - genetics; Omics; pathogens; phenotype; Phenotypic microarray; Phosphotransferases (Alcohol Group Acceptor) - genetics; PolyP-dependent proteolysis; Polyphosphate; Polyphosphates - metabolism; proteolysis; proteome; Proteome - genetics; proteomics; Proteomics - methods; Q-proteomics; Sigma Factor - genetics; Systems Biology; transcriptome; Transcriptome - genetics; transcriptomics; Up-Regulation - genetics; Q-proteomics; Phenotypic microarray; Polyphosphate; Systems Biology; PolyP-dependent proteolysis; Omics
• ISSN: 0304-4165; 1872-8006
• DOI: 10.1016/j.bbagen.2017.01.007

Polyphosphate (polyP) is a linear biopolymer found in all living cells. In bacteria, mutants lacking polyphosphate kinase 1 (PPK1), the enzyme responsible for synthesis of most polyP, have many structural and functional defects. However, little is known about the causes of these pleiotropic alterations. The link between ppk1 deletion and those numerous phenotypes observed can be the result of complex molecular interactions that can be elucidated via a systems biology approach. By integrating different omics levels (transcriptome, proteome and phenome), we described the functioning of various metabolic pathways among Escherichia coli polyphosphate mutant strains (Δppk1, Δppx, and ΔpolyP). Bioinformatic analyses reveal the complex metabolic and regulatory bases of the phenotypes unique to polyP mutants. Our results suggest that during polyP deficiency (Δppk1 mutant), metabolic pathways needed for energy supply are up-regulated, including fermentation, aerobic and anaerobic respiration. Transcriptomic and q-proteomic contrasting changes between Δppk1 and Δppx mutant strains were observed in those central metabolic pathways and confirmed by using Phenotypic microarrays. In addition, our results suggest a regulatory connection between polyP, second messenger metabolism, alternative Sigma/Anti-Sigma factors and type-II toxin-antitoxin (TA) systems. We suggest a broader role for polyP via regulation of ATP-dependent proteolysis of type II toxin-antitoxin system and alternative Sigma/Anti-Sigma factors, that could explain the multiple structural and functional deficiencies described due to alteration of polyP metabolism. Understanding the interplay of polyP in bacterial metabolism using a systems biology approach can help to improve design of novel antimicrobials toward pathogens. [Display omitted] •The results showed contrasting changes between Δppk1 and Δppx mutant strains in central metabolic pathways using multi-level omics.•Alteration of polyphosphate content affect second messenger metabolism, alternative Sigma/Anti-Sigma factors and type-II toxin-antitoxin (TA) systems.•E. coli cells without both genes (Δppk1 and Δppx) phenotypically behave like the polyP synthesis mutant Δppk1.