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Quendera AP, Pinto SN, Pobre V, Antunes W, Bonifácio VDB, Arraiano CM, Andrade JM. The ribonuclease PNPase is a key regulator of biofilm formation in Listeria monocytogenes and affects invasion of host cells. NPJ Biofilms Microbiomes 2023; 9:34. [PMID: 37286543 DOI: 10.1038/s41522-023-00397-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/18/2023] [Indexed: 06/09/2023] Open
Abstract
Biofilms provide an environment that protects microorganisms from external stresses such as nutrient deprivation, antibiotic treatments, and immune defences, thereby creating favorable conditions for bacterial survival and pathogenesis. Here we show that the RNA-binding protein and ribonuclease polynucleotide phosphorylase (PNPase) is a positive regulator of biofilm formation in the human pathogen Listeria monocytogenes, a major responsible for food contamination in food-processing environments. The PNPase mutant strain produces less biofilm biomass and exhibits an altered biofilm morphology that is more susceptible to antibiotic treatment. Through biochemical assays and microscopical analysis, we demonstrate that PNPase is a previously unrecognized regulator of the composition of the biofilm extracellular matrix, greatly affecting the levels of proteins, extracellular DNA, and sugars. Noteworthy, we have adapted the use of the fluorescent complex ruthenium red-phenanthroline for the detection of polysaccharides in Listeria biofilms. Transcriptomic analysis of wild-type and PNPase mutant biofilms reveals that PNPase impacts many regulatory pathways associated with biofilm formation, particularly by affecting the expression of genes involved in the metabolism of carbohydrates (e.g., lmo0096 and lmo0783, encoding PTS components), of amino acids (e.g., lmo1984 and lmo2006, encoding biosynthetic enzymes) and in the Agr quorum sensing-like system (lmo0048-49). Moreover, we show that PNPase affects mRNA levels of the master regulator of virulence PrfA and PrfA-regulated genes, and these results could help to explain the reduced bacterial internalization in human cells of the ΔpnpA mutant. Overall, this work demonstrates that PNPase is an important post-transcriptional regulator for virulence and adaptation to the biofilm lifestyle of Gram-positive bacteria and highlights the expanding role of ribonucleases as critical players in pathogenicity.
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Affiliation(s)
- Ana Patrícia Quendera
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-901, Oeiras, Portugal
| | - Sandra Nunes Pinto
- Institute for Bioengineering and Biosciences (IBB) and Associate Laboratory-Institute for Health and Bioeconomy (i4HB), Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
| | - Vânia Pobre
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-901, Oeiras, Portugal
| | - Wilson Antunes
- Laboratório de Imagem, Nanomorfologia e Espectroscopia de Raios-X (Linx) da Unidade Militar Laboratorial de Defesa Biológica e Química (UMLDBQ), Instituto Universitário Militar, Centro de Investigação, Inovação e Desenvolvimento da Academia Militar, Av. Dr Alfredo Bensaúde, 1100-471, Lisboa, Portugal
| | - Vasco D B Bonifácio
- Institute for Bioengineering and Biosciences (IBB) and Associate Laboratory-Institute for Health and Bioeconomy (i4HB), Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
- Bioengineering Department, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
| | - Cecília Maria Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-901, Oeiras, Portugal
| | - José Marques Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-901, Oeiras, Portugal.
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Raimundo AF, Ferreira S, Pobre V, Lopes-da-Silva M, Brito JA, dos Santos DJVA, Saraiva N, dos Santos CN, Menezes R. Urolithin B: Two-way attack on IAPP proteotoxicity with implications for diabetes. Front Endocrinol (Lausanne) 2022; 13:1008418. [PMID: 36589826 PMCID: PMC9797523 DOI: 10.3389/fendo.2022.1008418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 11/15/2022] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION Diabetes is one of the major metabolic diseases worldwide. Despite being a complex systemic pathology, the aggregation and deposition of Islet Amyloid Polypeptide (IAPP), or amylin, is a recognized histopathological marker of the disease. Although IAPP proteotoxicity represents an important trigger of β-cell dysfunction and ultimately death, its exploitation as a therapeutic tool remains underdeveloped. The bioactivity of (poly)phenols towards inhibition of pathological protein aggregation is well known, however, most of the identified molecules have limited bioavailability. METHODS Using a strategy combining in silico, cell-free and cell studies, we scrutinized a unique in-house collection of (poly)phenol metabolites predicted to appear in the human circulation after (poly)phenols ingestion. RESULTS We identified urolithin B as a potent inhibitor of IAPP aggregation and a powerful modulator of cell homeostasis pathways. Urolithin B was shown to affect IAPP aggregation pattern, delaying the formation of amyloid fibrils and altering their size and morphology. The molecular mechanisms underlying urolithin B-mediated protection include protein clearance pathways, mitochondrial function, and cell cycle ultimately rescuing IAPP-mediated cell dysfunction and death. DISCUSSION In brief, our study uncovered urolithin B as a novel small molecule targeting IAPP pathological aggregation with potential to be exploited as a therapeutic tool for mitigating cellular dysfunction in diabetes. Resulting from the colonic metabolism of dietary ellagic acid in the human body, urolithin B bioactivity has the potential to be explored in nutritional, nutraceutical, and pharmacological perspectives.
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Affiliation(s)
- Ana F. Raimundo
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA Lisboa, Oeiras, Portugal
- iNOVA4Health, NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Sofia Ferreira
- iNOVA4Health, NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal
- CBIOS – Universidade Lusófona’s Research Center for Biosciences & Health Technologies, Lisboa, Portugal
- Universidad de Alcalá, Escuela de Doctorado, Departamento de Ciencias Biomédicas, Madrid, Spain
| | - Vânia Pobre
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA Lisboa, Oeiras, Portugal
| | - Mafalda Lopes-da-Silva
- iNOVA4Health, NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal
| | - José A. Brito
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA Lisboa, Oeiras, Portugal
| | | | - Nuno Saraiva
- CBIOS – Universidade Lusófona’s Research Center for Biosciences & Health Technologies, Lisboa, Portugal
| | - Cláudia N. dos Santos
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- iNOVA4Health, NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Regina Menezes
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- iNOVA4Health, NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal
- CBIOS – Universidade Lusófona’s Research Center for Biosciences & Health Technologies, Lisboa, Portugal
- *Correspondence: Regina Menezes,
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Defining the impact of exoribonucleases in the shift between exponential and stationary phases. Sci Rep 2019; 9:16271. [PMID: 31700028 PMCID: PMC6838162 DOI: 10.1038/s41598-019-52453-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 10/12/2019] [Indexed: 01/26/2023] Open
Abstract
The transition between exponential and stationary phase is a natural phenomenon for all bacteria and requires a massive readjustment of the bacterial transcriptome. Exoribonucleases are key enzymes in the transition between the two growth phases. PNPase, RNase R and RNase II are the major degradative exoribonucleases in Escherichia coli. We analysed the whole transcriptome of exponential and stationary phases from the WT and mutants lacking these exoribonucleases (Δpnp, Δrnr, Δrnb, and ΔrnbΔrnr). When comparing the cells from exponential phase with the cells from stationary phase more than 1000 transcripts were differentially expressed, but only 491 core transcripts were common to all strains. There were some differences in the number and transcripts affected depending on the strain, suggesting that exoribonucleases influence the transition between these two growth phases differently. Interestingly, we found that the double mutant RNase II/RNase R is similar to the RNase R single mutant in exponential phase while in stationary phase it seems to be closer to the RNase II single mutant. This is the first global transcriptomic work comparing the roles of exoribonucleases in the transition between exponential and stationary phase.
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