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Shavkunov KS, Markelova NY, Glazunova OA, Kolzhetsov NP, Panyukov VV, Ozoline ON. The Fate and Functionality of Alien tRNA Fragments in Culturing Medium and Cells of Escherichia coli. Int J Mol Sci 2023; 24:12960. [PMID: 37629141 PMCID: PMC10455298 DOI: 10.3390/ijms241612960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Numerous observations have supported the idea that various types of noncoding RNAs, including tRNA fragments (tRFs), are involved in communications between the host and its microbial community. The possibility of using their signaling function has stimulated the study of secreted RNAs, potentially involved in the interspecies interaction of bacteria. This work aimed at identifying such RNAs and characterizing their maturation during transport. We applied an approach that allowed us to detect oligoribonucleotides secreted by Prevotella copri (Segatella copri) or Rhodospirillum rubrum inside Escherichia coli cells. Four tRFs imported by E. coli cells co-cultured with these bacteria were obtained via chemical synthesis, and all of them affected the growth of E. coli. Their successive modifications in the culture medium and recipient cells were studied by high-throughput cDNA sequencing. Instead of the expected accidental exonucleolysis, in the milieu, we observed nonrandom cleavage by endonucleases continued in recipient cells. We also found intramolecular rearrangements of synthetic oligonucleotides, which may be considered traces of intermediate RNA circular isomerization. Using custom software, we estimated the frequency of such events in transcriptomes and secretomes of E. coli and observed surprising reproducibility in positions of such rare events, assuming the functionality of ring isoforms or their permuted derivatives in bacteria.
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Affiliation(s)
- Konstantin S. Shavkunov
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Natalia Yu. Markelova
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Olga A. Glazunova
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Nikolay P. Kolzhetsov
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Valery V. Panyukov
- Institute of Mathematical Problems of Biology RAS—The Branch of Keldysh Institute of Applied Mathematics of the Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Olga N. Ozoline
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia
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2
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Castaño C, Novials A, Párrizas M. An Overview of Inter-Tissue and Inter-Kingdom Communication Mediated by Extracellular Vesicles in the Regulation of Mammalian Metabolism. Int J Mol Sci 2023; 24:2071. [PMID: 36768391 PMCID: PMC9916451 DOI: 10.3390/ijms24032071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Obesity and type 2 diabetes are associated with defects of insulin action in different tissues or alterations in β-cell secretory capacity that may be triggered by environmental challenges, inadequate lifestyle choices, or an underlying genetic predisposition. In addition, recent data shows that obesity may also be caused by perturbations of the gut microbiota, which then affect metabolic function and energy homeostasis in the host. Maintenance of metabolic homeostasis in complex organisms such as mammals requires organismal-level communication, including between the different organs and the gut microbiota. Extracellular vesicles (EVs) have been identified in all domains of life and have emerged as crucial players in inter-organ and inter-kingdom crosstalk. Interestingly, EVs found in edible vegetables or in milk have been shown to influence gut microbiota or tissue function in mammals. Moreover, there is a multidirectional crosstalk mediated by EVs derived from gut microbiota and body organs that has implications for host health. Untangling this complex signaling network may help implement novel therapies for the treatment of metabolic disease.
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Affiliation(s)
- Carlos Castaño
- Pathogenesis and Prevention of Diabetes Group, Instituto de Investigaciones Biomédicas August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Pathogenesis and Prevention of Diabetes Group, Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas (CIBERDEM), 08036 Barcelona, Spain
| | - Anna Novials
- Pathogenesis and Prevention of Diabetes Group, Instituto de Investigaciones Biomédicas August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Pathogenesis and Prevention of Diabetes Group, Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas (CIBERDEM), 08036 Barcelona, Spain
| | - Marcelina Párrizas
- Pathogenesis and Prevention of Diabetes Group, Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas (CIBERDEM), 08036 Barcelona, Spain
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3
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Antoniêto ACC, Nogueira KMV, Mendes V, Maués DB, Oshiquiri LH, Zenaide-Neto H, de Paula RG, Gaffey J, Tabatabaei M, Gupta VK, Silva RN. Use of carbohydrate-directed enzymes for the potential exploitation of sugarcane bagasse to obtain value-added biotechnological products. Int J Biol Macromol 2022; 221:456-471. [PMID: 36070819 DOI: 10.1016/j.ijbiomac.2022.08.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 11/15/2022]
Abstract
Microorganisms, such as fungi and bacteria, are crucial players in the production of enzymatic cocktails for biomass hydrolysis or the bioconversion of plant biomass into products with industrial relevance. The biotechnology industry can exploit lignocellulosic biomass for the production of high-value chemicals. The generation of biotechnological products from lignocellulosic feedstock presents several bottlenecks, including low efficiency of enzymatic hydrolysis, high cost of enzymes, and limitations on microbe metabolic performance. Genetic engineering offers a route for developing improved microbial strains for biotechnological applications in high-value product biosynthesis. Sugarcane bagasse, for example, is an agro-industrial waste that is abundantly produced in sugar and first-generation processing plants. Here, we review the potential conversion of its feedstock into relevant industrial products via microbial production and discuss the advances that have been made in improving strains for biotechnological applications.
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Affiliation(s)
- Amanda Cristina Campos Antoniêto
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Karoline Maria Vieira Nogueira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Vanessa Mendes
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - David Batista Maués
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Letícia Harumi Oshiquiri
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Hermano Zenaide-Neto
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Renato Graciano de Paula
- Department of Physiological Sciences, Health Sciences Centre, Federal University of Espirito Santo, Vitória, ES 29047-105, Brazil
| | - James Gaffey
- Circular Bioeconomy Research Group, Shannon Applied Biotechnology Centre, Munster Technological University, Kerry, Ireland; BiOrbic, Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland
| | - Meisam Tabatabaei
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK; Center for Safe and Improved Food, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK.
| | - Roberto Nascimento Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil.
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4
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Xiang Q, Zhao Y, Lin J, Jiang S, Li W. Epigenetic modifications in spinal ligament aging. Ageing Res Rev 2022; 77:101598. [PMID: 35218968 DOI: 10.1016/j.arr.2022.101598] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 02/07/2023]
Abstract
Spinal stenosis is a common degenerative spine disorder in the aged population and the spinal ligament aging is a main contributor to this chronic disease. However, the underlying mechanisms of spinal ligament aging remain unclear. Epigenetics is the study of heritable and reversible changes in the function of a gene or genome that occur without any alteration in the primary DNA sequence. Epigenetic alterations have been demonstrated to play crucial roles in age-related diseases and conditions, and they are recently studied as biomarkers and therapeutic targets in the field of cancer research. The main epigenetic modifications, including DNA methylation alteration, histone modifications as well as dysregulated noncoding RNA modulation, have all been implicated in spinal ligament aging diseases. DNA methylation modulates the expression of critical genes including WNT5A, GDNF, ACSM5, miR-497 and miR-195 during spinal ligament degeneration. Histone modifications widely affect gene expression and obvious histone modification abnormalities have been found in spinal ligament aging. MicroRNAs (miRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) exert crucial regulating effects on spinal ligament aging conditions via targeting various osteogenic or fibrogenic differentiation related genes. To our knowledge, there is no systematic review yet to summarize the involvement of epigenetic mechanisms of spinal ligament aging in degenerative spinal diseases. In this study, we systematically discussed the different epigenetic modifications and their potential functions in spinal ligament aging process.
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Díez-Sainz E, Milagro FI, Riezu-Boj JI, Lorente-Cebrián S. Effects of gut microbiota-derived extracellular vesicles on obesity and diabetes and their potential modulation through diet. J Physiol Biochem 2022; 78:485-499. [PMID: 34472032 PMCID: PMC8410452 DOI: 10.1007/s13105-021-00837-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022]
Abstract
Obesity and diabetes incidence rates are increasing dramatically, reaching pandemic proportions. Therefore, there is an urgent need to unravel the mechanisms underlying their pathophysiology. Of particular interest is the close interconnection between gut microbiota dysbiosis and obesity and diabetes progression. Hence, microbiota manipulation through diet has been postulated as a promising therapeutic target. In this regard, secretion of gut microbiota-derived extracellular vesicles is gaining special attention, standing out as key factors that could mediate gut microbiota-host communication. Extracellular vesicles (EVs) derived from gut microbiota and probiotic bacteria allow to encapsulate a wide range of bioactive molecules (such as/or including proteins and nucleic acids) that could travel short and long distances to modulate important biological functions with the overall impact on the host health. EV-derived from specific bacteria induce differential physiological responses. For example, a high-fat diet-induced increase of the proteobacterium Pseudomonas panacis-derived EV is closely associated with the progression of metabolic dysfunction in mice. In contrast, Akkermansia muciniphila EV are linked with the alleviation of high-fat diet-induced obesity and diabetes in mice. Here, we review the newest pieces of evidence concerning the potential role of gut microbiota and probiotic-derived EV on obesity and diabetes onset, progression, and management, through the modulation of inflammation, metabolism, and gut permeability. In addition, we discuss the role of certain dietary patterns on gut microbiota-derived EV profile and the clinical implication that dietary habits could have on metabolic diseases progression through the shaping of gut microbiota-derived EV.
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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
| | - 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 (CIBERobn), Instituto de Salud Carlos III, Madrid, 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
| | - Silvia Lorente-Cebrián
- Department of Pharmacology, Physiology and Legal and Forensic Medicine, Faculty of Health and Sport Science, University of Zaragoza, Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Zaragoza, Spain
- Aragón Health Research Institute (IIS-Aragon), Zaragoza, Spain
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6
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Kazimierczyk M, Wojnicka M, Biała E, Żydowicz-Machtel P, Imiołczyk B, Ostrowski T, Kurzyńska-Kokorniak A, Wrzesinski J. Characteristics of Transfer RNA-Derived Fragments Expressed during Human Renal Cell Development: The Role of Dicer in tRF Biogenesis. Int J Mol Sci 2022; 23:ijms23073644. [PMID: 35409004 PMCID: PMC8998818 DOI: 10.3390/ijms23073644] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/04/2023] Open
Abstract
tRNA-derived fragments participate in the regulation of many processes, such as gene silencing, splicing and translation in many organisms, ranging from bacteria to humans. We were interested to know how tRF abundance changes during the different stages of renal cell development. The research model used here consisted of the following human renal cells: hESCs, HEK-293T, HK-2 and A-489 kidney tumor cells, which, together, mimic the different stages of kidney development. The characteristics of the most abundant tRFs, tRFGly(CCC), tRFVal(AAC) and tRFArg(CCU), were presented. It was found that these parental tRNAs present in cells are the source of many tRFs, thus increasing the pool of potential regulatory RNAs. Indeed, a bioinformatic analysis showed the possibility that tRFGly(CCC) and tRRFVal(AAC) could regulate the activity of a range of kidney proteins. Moreover, the distribution of tRFs and the efficiency of their expression is similar in adult and embryonic stem cells. During the formation of tRFs, HK-2 cells resemble A-498 cancer cells more than other cells. Additionally, we postulate the involvement of Dicer nuclease in the formation of tRF-5b in all the analyzed tRNAs. To confirm this, 293T NoDice cells, which in the absence of Dicer activity do not generate tRF-5b, were used.
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7
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Wortelboer K, Bakker GJ, Winkelmeijer M, van Riel N, Levin E, Nieuwdorp M, Herrema H, Davids M. Fecal microbiota transplantation as tool to study the interrelation between microbiota composition and miRNA expression. Microbiol Res 2022; 257:126972. [DOI: 10.1016/j.micres.2022.126972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 02/07/2023]
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8
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Legüe M, Aguila B, Calixto A. Interspecies RNA Interactome of Pathogen and Host in a Heritable Defensive Strategy. Front Microbiol 2021; 12:649858. [PMID: 34367078 PMCID: PMC8334366 DOI: 10.3389/fmicb.2021.649858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022] Open
Abstract
Communication with bacteria deeply impacts the life history traits of their hosts. Through specific molecules and metabolites, bacteria can promote short- and long-term phenotypic and behavioral changes in the nematode Caenorhabditis elegans. The chronic exposure of C. elegans to pathogens promotes the adaptive behavior in the host’s progeny called pathogen-induced diapause formation (PIDF). PIDF is a pathogen avoidance strategy induced in the second generation of animals infected and can be recalled transgenerationally. This behavior requires the RNA interference machinery and specific nematode and bacteria small RNAs (sRNAs). In this work, we assume that RNAs from both species co-exist and can interact with each other. Under this principle, we explore the potential interspecies RNA interactions during PIDF-triggering conditions, using transcriptomic data from the holobiont. We study two transcriptomics datasets: first, the dual sRNA expression of Pseudomonas aeruginosa PAO1 and C. elegans in a transgenerational paradigm for six generations and second, the simultaneous expression of sRNAs and mRNA in intergenerational PIDF. We focus on those bacterial sRNAs that are systematically overexpressed in the intestines of animals compared with sRNAs expressed in host-naïve bacteria. We selected diverse in silico methods that represent putative mechanisms of RNA-mediated interspecies interaction. These interactions are as follows: heterologous perfect and incomplete pairing between bacterial RNA and host mRNA; sRNAs of similar sequence expressed in both species that could mimic each other; and known or predicted eukaryotic motifs present in bacterial transcripts. We conclude that a broad spectrum of tools can be applied for the identification of potential sRNA and mRNA targets of the interspecies RNA interaction that can be subsequently tested experimentally.
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Affiliation(s)
- Marcela Legüe
- Centro Interdisciplinario de Neurociencia de Valparaíso, Instituto de Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaiso, Chile
| | - Blanca Aguila
- Centro Interdisciplinario de Neurociencia de Valparaíso, Instituto de Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaiso, Chile.,Programa de Doctorado en Microbiología, Universidad de Chile, Santiago, Chile
| | - Andrea Calixto
- Centro Interdisciplinario de Neurociencia de Valparaíso, Instituto de Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaiso, Chile
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Extracellular Vesicles and Host-Pathogen Interactions: A Review of Inter-Kingdom Signaling by Small Noncoding RNA. Genes (Basel) 2021; 12:genes12071010. [PMID: 34208860 PMCID: PMC8303656 DOI: 10.3390/genes12071010] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
The focus of this brief review is to describe the role of noncoding regulatory RNAs, including short RNAs (sRNA), transfer RNA (tRNA) fragments and microRNAs (miRNA) secreted in extracellular vesicles (EVs), in inter-kingdom communication between bacteria and mammalian (human) host cells. Bacteria secrete vesicles that contain noncoding regulatory RNAs, and recent studies have shown that the bacterial vesicles fuse with and deliver regulatory RNAs to host cells, and similar to eukaryotic miRNAs, regulatory RNAs modulate the host immune response to infection. Recent studies have also demonstrated that mammalian cells secrete EVs containing miRNAs that regulate the gut microbiome, biofilm formation and the bacterial response to antibiotics. Thus, as evidence accumulates it is becoming clear that the secretion of noncoding regulatory RNAs and miRNAs in extracellular vesicles is an important mechanism of bidirectional communication between bacteria and mammalian (human) host cells. However, additional research is necessary to elucidate how noncoding regulatory RNAs and miRNA secreted in extracellular vesicles mediate inter-kingdom communication.
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10
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Kazimierczyk M, Wrzesinski J. Long Non-Coding RNA Epigenetics. Int J Mol Sci 2021; 22:6166. [PMID: 34200507 PMCID: PMC8201194 DOI: 10.3390/ijms22116166] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs exceeding a length of 200 nucleotides play an important role in ensuring cell functions and proper organism development by interacting with cellular compounds such as miRNA, mRNA, DNA and proteins. However, there is an additional level of lncRNA regulation, called lncRNA epigenetics, in gene expression control. In this review, we describe the most common modified nucleosides found in lncRNA, 6-methyladenosine, 5-methylcytidine, pseudouridine and inosine. The biosynthetic pathways of these nucleosides modified by the writer, eraser and reader enzymes are important to understanding these processes. The characteristics of the individual methylases, pseudouridine synthases and adenine-inosine editing enzymes and the methods of lncRNA epigenetics for the detection of modified nucleosides, as well as the advantages and disadvantages of these methods, are discussed in detail. The final sections are devoted to the role of modifications in the most abundant lncRNAs and their functions in pathogenic processes.
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Affiliation(s)
| | - Jan Wrzesinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland;
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Bancroft AJ, Grencis RK. Immunoregulatory molecules secreted by Trichuris muris. Parasitology 2021; 148:1-7. [PMID: 34075864 PMCID: PMC8660643 DOI: 10.1017/s0031182021000846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 12/19/2022]
Abstract
Trichuris, whipworm nematode infections are prevalent in humans, domestic livestock and mammals. All share an epithelial dwelling niche and similar life cycle with the chronic infections that follow implying that immune evasion mechanisms are operating. Nematode excretory secretory (ES) products have been shown to be a rich source of immunomodulatory molecules for many species. The Trichuris muris model is a natural parasite of mice and has been used extensively to study host–parasite interactions and provides a tractable platform for investigation of the immunoregulatory capacity of whipworm ES. The present review details progress in identification of the composition of T. muris ES, immunomodulatory components and their potential mechanisms of action. The adult T. muris secretome is dominated by one protein with modulatory capacity although remains to be completely characterized. In addition, the secretome contains multiple other proteins and small molecules that have immunomodulatory potential, certainly by comparison to other Trichuris species. Moreover, T. muris-derived exosomes/exosome-like vesicles contain both protein and multiple miRNAs providing an alternate delivery process for molecules with the potential to modulate host immunity.
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Affiliation(s)
- Allison J. Bancroft
- Lydia Becker Institute for Immunology and Inflammation, ManchesterM13 9PT, UK
- Wellcome Trust Centre for Cell Matrix Research, Manchester M13 9PT, UK
- Division of Infection, Immunity and Respiratory Medicine, ManchesterM13 9PT, UK
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, ManchesterM13 9PL, UK
| | - Richard K. Grencis
- Lydia Becker Institute for Immunology and Inflammation, ManchesterM13 9PT, UK
- Wellcome Trust Centre for Cell Matrix Research, Manchester M13 9PT, UK
- Division of Infection, Immunity and Respiratory Medicine, ManchesterM13 9PT, UK
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, ManchesterM13 9PL, UK
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12
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Sirufo M, Ginaldi L, De Martinis M. Non-coding RNAs, osteoarthritis and the microbiome: new therapeutic targets? Arthritis Rheumatol 2021; 73:2146. [PMID: 33982882 DOI: 10.1002/art.41795] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 04/12/2021] [Indexed: 11/07/2022]
Abstract
we read with great interest the article by J Wei et al. "Association between gut microbiota and symptomatic hand osteoarthritis: data from the Xiangya Osteoarthritis Study" recently published in the Journal and shedding light on the association between gut microbiome and the presence of symptomatic hand osteoarthritis (OA). Their findings help understand the role of microbiome in the development of SHOA and [1] could became the target of emerging therapies [2].
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Affiliation(s)
- Maddalena Sirufo
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Italy.,Allergy and Clinical Immunology Unit, Center for the diagnosis and treatment of Osteoporosis, AUSL 04 Teramo, Italy
| | - Lia Ginaldi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Italy.,Allergy and Clinical Immunology Unit, Center for the diagnosis and treatment of Osteoporosis, AUSL 04 Teramo, Italy
| | - Massimo De Martinis
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Italy.,Allergy and Clinical Immunology Unit, Center for the diagnosis and treatment of Osteoporosis, AUSL 04 Teramo, Italy
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13
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Cánovas-Márquez JT, Navarro-Mendoza MI, Pérez-Arques C, Lax C, Tahiri G, Pérez-Ruiz JA, Lorenzo-Gutiérrez D, Calo S, López-García S, Navarro E, Nicolás FE, Garre V, Murcia L. Role of the Non-Canonical RNAi Pathway in the Antifungal Resistance and Virulence of Mucorales. Genes (Basel) 2021; 12:genes12040586. [PMID: 33920552 PMCID: PMC8072676 DOI: 10.3390/genes12040586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/19/2022] Open
Abstract
Mucorales are the causal agents for the lethal disease known as mucormycosis. Mortality rates of mucormycosis can reach up to 90%, due to the mucoralean antifungal drug resistance and the lack of effective therapies. A concerning urgency among the medical and scientific community claims to find targets for the development of new treatments. Here, we reviewed different studies describing the role and machinery of a novel non-canonical RNAi pathway (NCRIP) only conserved in Mucorales. Its non-canonical features are the independence of Dicer and Argonaute proteins. Conversely, NCRIP relies on RNA-dependent RNA Polymerases (RdRP) and an atypical ribonuclease III (RNase III). NCRIP regulates the expression of mRNAs by degrading them in a specific manner. Its mechanism binds dsRNA but only cuts ssRNA. NCRIP exhibits a diversity of functional roles. It represses the epimutational pathway and the lack of NCRIP increases the generation of drug resistant strains. NCRIP also regulates the control of retrotransposons expression, playing an essential role in genome stability. Finally, NCRIP regulates the response during phagocytosis, affecting the multifactorial process of virulence. These critical NCRIP roles in virulence and antifungal drug resistance, along with its exclusive presence in Mucorales, mark this pathway as a promising target to fight against mucormycosis.
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Affiliation(s)
- José Tomás Cánovas-Márquez
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - María Isabel Navarro-Mendoza
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; (M.I.N.-M.); (C.P.-A.)
| | - Carlos Pérez-Arques
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; (M.I.N.-M.); (C.P.-A.)
| | - Carlos Lax
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - Ghizlane Tahiri
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - José Antonio Pérez-Ruiz
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - Damaris Lorenzo-Gutiérrez
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - Silvia Calo
- School of Natural and Exact Sciences, Pontificia Universidad Católica Madre y Maestra, Santiago de los Caballeros 51033, Dominican Republic;
| | - Sergio López-García
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - Eusebio Navarro
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - Francisco Esteban Nicolás
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - Victoriano Garre
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - Laura Murcia
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
- Correspondence:
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14
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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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15
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Research on Transboundary Regulation of Plant-Derived Exogenous MiRNA Based on Biological Big Data. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:6656763. [PMID: 33604010 PMCID: PMC7868139 DOI: 10.1155/2021/6656763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/06/2021] [Accepted: 01/13/2021] [Indexed: 11/17/2022]
Abstract
In recent years, researchers have discovered plant miRNA (plant xenomiR) in mammalian samples, but it is unclear whether it exists stably and participates in regulation. In this paper, a cross-border regulation model of plant miRNAs based on biological big data is constructed to study the possible cross-border regulation of plant miRNAs. Firstly, a variety of human edible plants were selected, and based on the miRNA data detected in human experimental studies, screening was performed to obtain the plant xenomiR that may stably exist in the human body. Then, we use plant and animal target gene prediction methods to obtain the mRNAs of animals and plants that may be regulated, respectively. Finally, we use GO (Gene Ontology) and the Multiple Dimensional Scaling (MDS) algorithm to analyze the biological processes regulated by plants and animals. We obtain the relationship between different biological processes and explore the regulatory commonality and individuality of plant xenomiR in plants and humans. Studies have shown that the development and metabolic functions of the human body are affected by daily eating habits. Soybeans, corn, and rice can not only affect the daily development and metabolism of the human body but also regulate biological processes such as protein modification and mitosis. This conclusion explains the reasons for the different physiological functions of the human body. This research is an important meaning for the design of small RNA drugs in Chinese herbal medicine and the treatment of human nutritional diseases.
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