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Sarshar M, Scribano D, Palamara AT, Ambrosi C, Masotti A. The Acinetobacter baumannii model can explain the role of small non-coding RNAs as potential mediators of host-pathogen interactions. Front Mol Biosci 2022; 9:1088783. [PMID: 36619166 PMCID: PMC9810633 DOI: 10.3389/fmolb.2022.1088783] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Bacterial small RNAs (sRNAs) research has accelerated over the past decade, boosted by advances in RNA-seq technologies and methodologies for capturing both protein-RNA and RNA-RNA interactions. The emerging picture is that these regulatory sRNAs play important roles in controlling complex physiological processes and are required to survive the antimicrobial challenge. In recent years, the RNA content of OMVs/EVs has also gained increasing attention, particularly in the context of infection. Secreted RNAs from several bacterial pathogens have been characterized but the exact mechanisms promoting pathogenicity remain elusive. In this review, we briefly discuss how secreted sRNAs interact with targets in infected cells, thus representing a novel perspective of host cell manipulation during bacterial infection. During the last decade, Acinetobacter baumannii became clinically relevant emerging pathogens responsible for nosocomial and community-acquired infections. Therefore, we also summarize recent findings of regulation by sRNAs in A. baumannii and discuss how this emerging bacterium utilizes many of these sRNAs to adapt to its niche and become successful human pathogen.
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Affiliation(s)
- Meysam Sarshar
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,*Correspondence: Meysam Sarshar, ; Andrea Masotti,
| | - Daniela Scribano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Anna Teresa Palamara
- Laboratory Affiliated to Institute Pasteur Italia-Cenci Bolognetti Foundation, Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy,Department of Infectious Diseases, National Institute of Health, Rome, Italy
| | - Cecilia Ambrosi
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, Rome, Italy,IRCCS San Raffaele Roma, Rome, Italy
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,*Correspondence: Meysam Sarshar, ; Andrea Masotti,
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2
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Rodríguez-Mera IB, Carrasco-Yépez MM, Vásquez-Moctezuma I, Correa-Basurto J, Salinas GR, Castillo-Ramírez DA, Rosales-Cruz É, Rojas-Hernández S. Role of cathepsin B of Naegleria fowleri during primary amebic meningoencephalitis. Parasitol Res 2022; 121:3287-3303. [PMID: 36125528 PMCID: PMC9485797 DOI: 10.1007/s00436-022-07660-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022]
Abstract
Naegleria fowleri causes primary amoebic meningoencephalitis in humans and experimental animals. It has been suggested that cysteine proteases of parasites play key roles in metabolism, nutrient uptake, host tissue invasion, and immune evasion. The aim of this work was to evaluate the presence, expression, and role of cathepsin B from N. fowleri in vitro and during PAM. Rabbit-specific polyclonal antibodies against cathepsin B were obtained from rabbit immunization with a synthetic peptide obtained by bioinformatic design. In addition, a probe was designed from mRNA for N. fowleri cathepsin B. Both protein and messenger were detected in fixed trophozoites, trophozoites interacted with polymorphonuclear and histological sections of infected mice. The main cathepsin B distribution was observed in cytoplasm or membrane mainly pseudopods and food-cups while messenger was in nucleus and cytoplasm. Surprisingly, both the messenger and enzyme were observed in extracellular medium. To determine cathepsin B release, we used trophozoites supernatant recovered from nasal passages or brain of infected mice. We observed the highest release in supernatant from recovered brain amoebae, and when we analyzed molecular weight of secreted proteins by immunoblot, we found 30 and 37 kDa bands which were highly immunogenic. Finally, role of cathepsin B during N. fowleri infection was determined; we preincubated trophozoites with E-64, pHMB or antibodies with which we obtained 60%, 100%, and 60% of survival, respectively, in infected mice. These results suggest that cathepsin B plays a role during pathogenesis caused by N. fowleri mainly in adhesion and contributes to nervous tissue damage.
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Affiliation(s)
- Itzel Berenice Rodríguez-Mera
- Laboratorio de Inmunología Molecular, Instituto Politécnico Nacional, Escuela Superior de Medicina, Salvador Díaz Mirón Esq. Plan de San Luis S/N, Miguel Hidalgo, Casco de Santo Tomas, Ciudad de México, CDMX, 11340, México
| | - María Maricela Carrasco-Yépez
- Laboratorio de Microbiología Ambiental, Estado de México, Universidad Nacional Autónoma de México, Grupo CyMA, UIICSE, FES Iztacala, Tlalnepantla de Baz, México
| | - Ismael Vásquez-Moctezuma
- Laboratorio de Bioquímica, Instituto Politécnico Nacional, Escuela Superior de Medicina, Ciudad de Mexico, México
| | - José Correa-Basurto
- Laboratorio de Modelado Molecular y Diseño de Fármacos, Instituto Politécnico Nacional, Escuela Superior de Medicina, Ciudad de Mexico, México
| | - Gema Ramírez- Salinas
- Laboratorio de Modelado Molecular y Diseño de Fármacos, Instituto Politécnico Nacional, Escuela Superior de Medicina, Ciudad de Mexico, México
| | - Diego Arturo Castillo-Ramírez
- Laboratorio de Inmunología Molecular, Instituto Politécnico Nacional, Escuela Superior de Medicina, Salvador Díaz Mirón Esq. Plan de San Luis S/N, Miguel Hidalgo, Casco de Santo Tomas, Ciudad de México, CDMX, 11340, México
| | - Érika Rosales-Cruz
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Ciudad de Mexico, México
| | - Saúl Rojas-Hernández
- Laboratorio de Inmunología Molecular, Instituto Politécnico Nacional, Escuela Superior de Medicina, Salvador Díaz Mirón Esq. Plan de San Luis S/N, Miguel Hidalgo, Casco de Santo Tomas, Ciudad de México, CDMX, 11340, México.
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3
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Díez-Sainz E, Lorente-Cebrián S, Aranaz P, Riezu-Boj JI, Martínez JA, Milagro FI. Potential Mechanisms Linking Food-Derived MicroRNAs, Gut Microbiota and Intestinal Barrier Functions in the Context of Nutrition and Human Health. Front Nutr 2021; 8:586564. [PMID: 33768107 PMCID: PMC7985180 DOI: 10.3389/fnut.2021.586564] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 02/15/2021] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding single-stranded RNA molecules from 18 to 24 nucleotides that are produced by prokaryote and eukaryote organisms, which play a crucial role in regulating gene expression through binding to their mRNA targets. MiRNAs have acquired special attention for their potential in cross kingdom communication, notably food-derived microRNAs (xenomiRs), which could have an impact on microorganism and mammal physiology. In this review, we mainly aim to deal with new perspectives on: (1) The mechanism by which food-derived xenomiRs (mainly dietary plant xenomiRs) could be incorporated into humans through diet, in a free form, associated with proteins or encapsulated in exosome-like nanoparticles. (2) The impact of dietary plant-derived miRNAs in modulating gut microbiota composition, which in turn, could regulate intestinal barrier permeability and therefore, affect dietary metabolite, postbiotics or food-derived miRNAs uptake efficiency. Individual gut microbiota signature/composition could be also involved in xenomiR uptake efficiency through several mechanisms such us increasing the bioavailability of exosome-like nanoparticles miRNAs. (3) Gut microbiota dysbiosis has been proposed to contribute to disease development by affecting gut epithelial barrier permeability. For his reason, the availability and uptake of dietary plant xenomiRs might depend, among other factors, on this microbiota-related permeability of the intestine. We hypothesize and critically review that xenomiRs-microbiota interaction, which has been scarcely explored yet, could contribute to explain, at least in part, the current disparity of evidences found dealing with dietary miRNA uptake and function in humans. Furthermore, dietary plant xenomiRs could be involved in the establishment of the multiple gut microenvironments, in which microorganism would adapt in order to optimize the resources and thrive in them. Additionally, a particular xenomiR could preferentially accumulate in a specific region of the gastrointestinal tract and participate in the selection and functions of specific gut microbial communities.
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Affiliation(s)
- Ester Díez-Sainz
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
| | - Silvia Lorente-Cebrián
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - Paula Aranaz
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
| | - José I. Riezu-Boj
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - J. Alfredo Martínez
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Fermín I. Milagro
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
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Kiselev S, Markelova N, Masulis I. Divergently Transcribed ncRNAs in Escherichia coli: Refinement of the Transcription Starts Assumes Functional Diversification. Front Mol Biosci 2021; 8:610453. [PMID: 33748186 PMCID: PMC7967276 DOI: 10.3389/fmolb.2021.610453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/07/2021] [Indexed: 02/05/2023] Open
Abstract
Non-coding regulatory RNAs (ncRNAs) comprise specialized group of essential genetically encoded biological molecules involved in the wide variety of cellular metabolic processes. The progressive increase in the number of newly identified ncRNAs and the defining of their genome location indicate their predominant nesting in intergenic regions and expression under the control of their own regulatory elements. At the same time, the regulation of ncRNA's transcription cannot be considered in isolation from the processes occurring in the immediate genetic environment. A number of experimental data indicate the notable impact of positional regulation of gene expression mediated by dynamic temporal DNA rearrangements accompanying transcription events in the vicinity of neighboring genes. This issue can be perceived as particularly significant for divergently transcribed ncRNAs being actually subjected to double regulatory pressure. Based on available results of RNAseq experiments for Escherichia coli, we screened out divergent ncRNAs and the adjacent genes for the exact positions of transcription start sites (TSSs) and relative efficiency of RNA production. This analysis revealed extension or shortening of some previously annotated ncRNAs resulting in modified secondary structure, confirmed stable expression of four ncRNAs annotated earlier as putative, and approved the possibility of expression of divergently transcribed ncRNAs containing repetitive extragenic palindromic (REP) elements. The biogenesis of secreted ncRNAs from divergently transcribed ffs, chiX, ralA, and ryhB is discussed taking into account positions of TSSs. Refinement of TSSs for the neighboring genes renders some ncRNAs as true antisense overlapping with 5'UTR of divergently transcribed mRNAs.
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Extracellular RNAs in Bacterial Infections: From Emerging Key Players on Host-Pathogen Interactions to Exploitable Biomarkers and Therapeutic Targets. Int J Mol Sci 2020; 21:ijms21249634. [PMID: 33348812 PMCID: PMC7766527 DOI: 10.3390/ijms21249634] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/04/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are key regulators of post-transcriptional gene expression in prokaryotic and eukaryotic organisms. These molecules can interact with mRNAs or proteins, affecting a variety of cellular functions. Emerging evidence shows that intra/inter-species and trans-kingdom regulation can also be achieved with exogenous RNAs, which are exported to the extracellular medium, mainly through vesicles. In bacteria, membrane vesicles (MVs) seem to be the more common way of extracellular communication. In several bacterial pathogens, MVs have been described as a delivery system of ncRNAs that upon entry into the host cell, regulate their immune response. The aim of the present work is to review this recently described mode of host-pathogen communication and to foster further research on this topic envisaging their exploitation in the design of novel therapeutic and diagnostic strategies to fight bacterial infections.
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6
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Ozoline ON, Jass J. Editorial: Secretion and signalling of bacterial RNAs. FEMS Microbiol Lett 2019; 366:5230856. [PMID: 30517616 DOI: 10.1093/femsle/fny281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 11/26/2018] [Indexed: 12/11/2022] Open
Affiliation(s)
- Olga N Ozoline
- Institute of Cell Biophysics, RAS, Pushchino Research Center, RAS, Pushchino, Moscow Region, Russia
| | - Jana Jass
- The Life Science Centre - Biology, School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
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7
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Alikina OV, Glazunova OA, Bykov AA, Kiselev SS, Tutukina MN, Shavkunov KS, Ozoline ON. A cohabiting bacterium alters the spectrum of short RNAs secreted by Escherichia coli. FEMS Microbiol Lett 2018; 365:5146451. [PMID: 30376063 DOI: 10.1093/femsle/fny262] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/28/2018] [Indexed: 02/07/2023] Open
Abstract
Recently, it has been found that bacteria secrete short RNAs able to affect gene expression in eukaryotic cells, while certain mammalian microRNAs shape the gut microbiome altering bacterial transcriptome. The involvement of bacterial RNAs in communication with other bacteria is also expected, but has not been documented yet. Here, we compared the fractions of extremely short (12-22 nucleotides) RNAs secreted by Escherichia coli grown in a pure culture and jointly with bacteria of the Paenibacillus genus. Besides fragments of rRNAs and tRNAs, abundant in all samples, secreted oligonucleotides (exoRNAs) predominantly contained GC-rich fragments of messenger and antisense RNAs processed from regions with stable secondary structures. They differed in composition from oligonucleotides of intracellular fraction, where fragments of small regulatory RNAs were prevalent. Both fractions contained RNAs capable of forming complementary duplexes, while for exoRNA samples a higher percentage of 3΄-end modified RNAs and different endonuclease cleavage were detected. The presence of a cohabiting bacterium altered the spectrum of E. coli exoRNAs, indicating a population-dependent control over their composition. Possible mechanisms of this effect are discussed.
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MESH Headings
- Biological Transport
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Genome, Bacterial
- Nucleic Acid Conformation
- RNA, Antisense/chemistry
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
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Affiliation(s)
- Olga V Alikina
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Olga A Glazunova
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
- Pushchino Research Center of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Alexandr A Bykov
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Sergey S Kiselev
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Maria N Tutukina
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
- Pushchino Research Center of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Konstantin S Shavkunov
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
- Pushchino Research Center of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Olga N Ozoline
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
- Pushchino Research Center of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
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