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Falchi FA, Forti F, Carnelli C, Genco A, Pizzoccheri R, Manzari C, Pavesi G, Briani F. Human PNPase causes RNA stabilization and accumulation of R-loops in the Escherichia coli model system. Sci Rep 2023; 13:11771. [PMID: 37479726 PMCID: PMC10362022 DOI: 10.1038/s41598-023-38924-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023] Open
Abstract
Polyribonucleotide phosphorylase (PNPase) is a phosphorolytic RNA exonuclease highly conserved throughout evolution. In Escherichia coli, PNPase controls complex phenotypic traits like biofilm formation and growth at low temperature. In human cells, PNPase is located in mitochondria, where it is implicated in the RNA import from the cytoplasm, the mitochondrial RNA degradation and the processing of R-loops, namely stable RNA-DNA hybrids displacing a DNA strand. In this work, we show that the human PNPase (hPNPase) expressed in E. coli causes oxidative stress, SOS response activation and R-loops accumulation. Hundreds of E. coli RNAs are stabilized in presence of hPNPase, whereas only few transcripts are destabilized. Moreover, phenotypic traits typical of E. coli strains lacking PNPase are strengthened in presence of the human enzyme. We discuss the hypothesis that hPNPase expressed in E. coli may bind, but not degrade, the RNA, in agreement with previous in vitro data showing that phosphate concentrations in the range of those found in the bacterial cytoplasm and, more relevant, in the mitochondria, inhibit its activity.
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Affiliation(s)
- Federica A Falchi
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milan, Italy
| | - Francesca Forti
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milan, Italy
| | - Cristina Carnelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milan, Italy
| | - Aurelia Genco
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milan, Italy
| | - Roberto Pizzoccheri
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milan, Italy
| | - Caterina Manzari
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari "Aldo Moro", 70121, Bari, Italy
| | - Giulio Pavesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milan, Italy.
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milan, Italy.
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Falchi FA, Pizzoccheri R, Briani F. Activity and Function in Human Cells of the Evolutionary Conserved Exonuclease Polynucleotide Phosphorylase. Int J Mol Sci 2022; 23:ijms23031652. [PMID: 35163574 PMCID: PMC8836086 DOI: 10.3390/ijms23031652] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
Polynucleotide phosphorylase (PNPase) is a phosphorolytic RNA exonuclease highly conserved throughout evolution. Human PNPase (hPNPase) is located in mitochondria and is essential for mitochondrial function and homeostasis. Not surprisingly, mutations in the PNPT1 gene, encoding hPNPase, cause serious diseases. hPNPase has been implicated in a plethora of processes taking place in different cell compartments and involving other proteins, some of which physically interact with hPNPase. This paper reviews hPNPase RNA binding and catalytic activity in relation with the protein structure and in comparison, with the activity of bacterial PNPases. The functions ascribed to hPNPase in different cell compartments are discussed, highlighting the gaps that still need to be filled to understand the physiological role of this ancient protein in human cells.
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Abstract
The term Long COVID (or Post COVID) describes a condition characterized by persistence of symptoms for at least 12 weeks after the onset of COVID-19. It may last several months but the duration is still matter of observation. The symptoms and the clinical manifestations are clinically heterogeneous and suggesting involvement of multi-organs/systems, including the cardiovascular system. The general recurrent symptoms include fatigue, breathlessness, myalgia, headache, loss of memory, and impaired concentration. Patients report loss of their previous psychophysical performance. Cardiovascular involvement manifests with common symptoms such as palpitations and chest pain, and, less commonly, with events such as late arterial and venous thromboembolisms, heart failure episodes, strokes or transient ischaemic attack, 'myo-pericarditis'. The diagnostic criteria are mainly based on the narrative of the patients. Measurable biomarkers or instrumental findings or clinical events are not yet framed in a shared diagnostic framework. The open question for clinicians and researchers is whether biomarkers, electrocardiogram, non-invasive imaging, and clinical monitoring should be included in a shared diagnostic protocol aimed at defining the diagnostic path and protecting patients at risk of unexpected events.
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Affiliation(s)
- Alessandro Di Toro
- Department of Medical Sciences and Infectious Diseases, Transplant Research Area and Centre for Inherited Cardiovascular Diseases, Fondazione IRCCS Policlinico San Matteo, Piazzale Camillo Golgi 19, 27100 Pavia, Italy
| | - Antonio Bozzani
- Department of Surgical Science, Vascular and Endovascular Surgery Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Guido Tavazzi
- Anaesthesia and Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Mario Urtis
- Department of Medical Sciences and Infectious Diseases, Transplant Research Area and Centre for Inherited Cardiovascular Diseases, Fondazione IRCCS Policlinico San Matteo, Piazzale Camillo Golgi 19, 27100 Pavia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Lorenzo Giuliani
- Department of Medical Sciences and Infectious Diseases, Transplant Research Area and Centre for Inherited Cardiovascular Diseases, Fondazione IRCCS Policlinico San Matteo, Piazzale Camillo Golgi 19, 27100 Pavia, Italy
| | - Roberto Pizzoccheri
- Department of Medical Sciences and Infectious Diseases, Transplant Research Area and Centre for Inherited Cardiovascular Diseases, Fondazione IRCCS Policlinico San Matteo, Piazzale Camillo Golgi 19, 27100 Pavia, Italy
| | - Flaminia Aliberti
- Department of Medical Sciences and Infectious Diseases, Transplant Research Area and Centre for Inherited Cardiovascular Diseases, Fondazione IRCCS Policlinico San Matteo, Piazzale Camillo Golgi 19, 27100 Pavia, Italy
| | - Viola Fergnani
- Department of Medical Sciences and Infectious Diseases, Transplant Research Area and Centre for Inherited Cardiovascular Diseases, Fondazione IRCCS Policlinico San Matteo, Piazzale Camillo Golgi 19, 27100 Pavia, Italy
| | - Eloisa Arbustini
- Department of Medical Sciences and Infectious Diseases, Transplant Research Area and Centre for Inherited Cardiovascular Diseases, Fondazione IRCCS Policlinico San Matteo, Piazzale Camillo Golgi 19, 27100 Pavia, Italy
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Di Toro A, Urtis M, Giuliani L, Pizzoccheri R, Aliberti F, Smirnova A, Grasso M, Disabella E, Arbustini E. Spectrum of phenotype of ventricular noncompaction in adults. Progress in Pediatric Cardiology 2021. [DOI: 10.1016/j.ppedcard.2021.101416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Falchi FA, Di Lorenzo F, Pizzoccheri R, Casino G, Paroni M, Forti F, Molinaro A, Briani F. Overexpression of lpxT Gene in Escherichia coli Inhibits Cell Division and Causes Envelope Defects without Changing the Overall Phosphorylation Level of Lipid A. Microorganisms 2020; 8:E826. [PMID: 32486329 PMCID: PMC7356881 DOI: 10.3390/microorganisms8060826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/20/2022] Open
Abstract
LpxT is an inner membrane protein that transfers a phosphate group from the essential lipid undecaprenyl pyrophosphate (C-55PP) to the lipid A moiety of lipopolysaccharide, generating a lipid A tris-phosphorylated species. The protein is encoded by the non-essential lpxT gene, which is conserved in distantly related Gram-negative bacteria. In this work, we investigated the phenotypic effect of lpxT ectopic expression from a plasmid in Escherichia coli. We found that lpxT induction inhibited cell division and led to the formation of elongated cells, mostly with absent or altered septa. Moreover, the cells became sensitive to detergents and to hypo-osmotic shock, indicating that they had cell envelope defects. These effects were not due to lipid A hyperphosphorylation or C-55PP sequestering, but most likely to defective lipopolysaccharide transport. Indeed, lpxT overexpression in mutants lacking the L,D-transpeptidase LdtD and LdtE, which protect cells with outer membrane defects from osmotic lysis, caused cell envelope defects. Moreover, we found that pyrophosphorylated lipid A was also produced in a lpxT deletion mutant, indicating that LpxT is not the only protein able to perform such lipid A modification in E. coli.
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Affiliation(s)
- Federica A. Falchi
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy; (F.A.F.); (R.P.); (G.C.); (M.P.); (F.F.)
| | - Flaviana Di Lorenzo
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy; (F.D.L.); (A.M.)
| | - Roberto Pizzoccheri
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy; (F.A.F.); (R.P.); (G.C.); (M.P.); (F.F.)
| | - Gianluca Casino
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy; (F.A.F.); (R.P.); (G.C.); (M.P.); (F.F.)
| | - Moira Paroni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy; (F.A.F.); (R.P.); (G.C.); (M.P.); (F.F.)
| | - Francesca Forti
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy; (F.A.F.); (R.P.); (G.C.); (M.P.); (F.F.)
| | - Antonio Molinaro
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy; (F.D.L.); (A.M.)
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy; (F.A.F.); (R.P.); (G.C.); (M.P.); (F.F.)
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