Macarena Varas1, Camilo Valdivieso2, Cecilia Mauriaca3, Javiera Ortíz-Severín4, Alberto Paradela5, Ignacio Poblete-Castro6, Ricardo Cabrera7, Francisco P Chávez8. 1. Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile. Electronic address: mvaras26@gmail.com. 2. Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile; Department of Ecology, Faculty of Science, University of Chile, Chile. Electronic address: c.valdivieso.guerrero@gmail.com. 3. Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile. Electronic address: cmauriaca@gmail.com. 4. Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile. Electronic address: javiera.o.s@gmail.com. 5. Proteomic Service, CNB CSIC, Spain. Electronic address: alberto.paradela@cnb.csic.es. 6. Facultad de Ciencias Biológicas, Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Universidad Andrés Bello, Chile. Electronic address: ignacio.poblete@unab.cl. 7. Department of Biology, Faculty of Sciences, University of Chile, Chile. Electronic address: rcabrer@uchile.cl. 8. Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile. Electronic address: fpchavez@uchile.cl.
Abstract
BACKGROUND: 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. METHODS: 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. RESULTS: 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. CONCLUSIONS: 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. GENERAL SIGNIFICANCE: Understanding the interplay of polyP in bacterial metabolism using a systems biology approach can help to improve design of novel antimicrobials toward pathogens.
BACKGROUND: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. METHODS: By integrating different omics levels (transcriptome, proteome and phenome), we described the functioning of various metabolic pathways among Escherichia colipolyphosphate mutant strains (Δppk1, Δppx, and ΔpolyP). Bioinformatic analyses reveal the complex metabolic and regulatory bases of the phenotypes unique to polyP mutants. RESULTS: 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. CONCLUSIONS: 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. GENERAL SIGNIFICANCE: Understanding the interplay of polyP in bacterial metabolism using a systems biology approach can help to improve design of novel antimicrobials toward pathogens.
Authors: Macarena A Varas; Sebastián Riquelme-Barrios; Camila Valenzuela; Andrés E Marcoleta; Camilo Berríos-Pastén; Carlos A Santiviago; Francisco P Chávez Journal: Front Cell Infect Microbiol Date: 2018-01-30 Impact factor: 5.293
Authors: Alejandra Recalde; Marleen van Wolferen; Shamphavi Sivabalasarma; Sonja-Verena Albers; Claudio A Navarro; Carlos A Jerez Journal: Microorganisms Date: 2021-01-18