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Sánchez-Arroyo A, Plaza-Vinuesa L, de Las Rivas B, Mancheño JM, Muñoz R. Aspergillus niger Ochratoxinase Is a Highly Specific, Metal-Dependent Amidohydrolase Suitable for OTA Biodetoxification in Food and Feed. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18658-18669. [PMID: 39110482 DOI: 10.1021/acs.jafc.4c02944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Microbial enzymes can be used as processing aids or additives in food and feed industries. Enzymatic detoxification of ochratoxin A (OTA) is a promising method to reduce OTA content. Here, we characterize the full-length enzyme ochratoxinase (AnOTA), an amidohydrolase from Aspergillus niger. AnOTA hydrolyzes OTA and ochratoxin B (OTB) mycotoxins efficiently and also other substrates containing phenylalanine, alanine, or leucine residues at their C-terminal position, revealing a narrow specificity profile. AnOTA lacks endopeptidase or aminoacylase activities. The structural basis of the molecular recognition by AnOTA of OTA, OTB, and a wide array of model substrates has been investigated by molecular docking simulation. AnOTA shows maximal hydrolytic activity at neutral pH and high temperature (65 °C) and retained high activity after prolonged incubation at 45 °C. The reduction of OTA levels in food products by AnOTA has been investigated using several commercial plant-based beverages. The results showed complete degradation of OTA with no detectable modification of beverage proteins. Therefore, the addition of AnOTA seems to be a useful procedure to eliminate OTA in plant-based beverages. Moreover, computational predictions of in vivo characteristics indicated that AnOTA is neither an allergenic nor antigenic protein. All characteristics found for AnOTA supported the suitability of its use for OTA detoxification in food and feed.
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Affiliation(s)
- Ana Sánchez-Arroyo
- Bacterial Biotechnology, Institute of Food Science, Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - Laura Plaza-Vinuesa
- Bacterial Biotechnology, Institute of Food Science, Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - Blanca de Las Rivas
- Bacterial Biotechnology, Institute of Food Science, Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - José Miguel Mancheño
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera (IQF), CSIC, Serrano 119, 28006 Madrid, Spain
| | - Rosario Muñoz
- Bacterial Biotechnology, Institute of Food Science, Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
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Haltom J, Trovao NS, Guarnieri J, Vincent P, Singh U, Tsoy S, O'Leary CA, Bram Y, Widjaja GA, Cen Z, Meller R, Baylin SB, Moss WN, Nikolau BJ, Enguita FJ, Wallace DC, Beheshti A, Schwartz R, Wurtele ES. SARS-CoV-2 Orphan Gene ORF10 Contributes to More Severe COVID-19 Disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.27.23298847. [PMID: 38076862 PMCID: PMC10705665 DOI: 10.1101/2023.11.27.23298847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
The orphan gene of SARS-CoV-2, ORF10, is the least studied gene in the virus responsible for the COVID-19 pandemic. Recent experimentation indicated ORF10 expression moderates innate immunity in vitro. However, whether ORF10 affects COVID-19 in humans remained unknown. We determine that the ORF10 sequence is identical to the Wuhan-Hu-1 ancestral haplotype in 95% of genomes across five variants of concern (VOC). Four ORF10 variants are associated with less virulent clinical outcomes in the human host: three of these affect ORF10 protein structure, one affects ORF10 RNA structural dynamics. RNA-Seq data from 2070 samples from diverse human cells and tissues reveals ORF10 accumulation is conditionally discordant from that of other SARS-CoV-2 transcripts. Expression of ORF10 in A549 and HEK293 cells perturbs immune-related gene expression networks, alters expression of the majority of mitochondrially-encoded genes of oxidative respiration, and leads to large shifts in levels of 14 newly-identified transcripts. We conclude ORF10 contributes to more severe COVID-19 clinical outcomes in the human host.
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Affiliation(s)
- Jeffrey Haltom
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Nidia S Trovao
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Joseph Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Pan Vincent
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Urminder Singh
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
| | - Sergey Tsoy
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Collin A O'Leary
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Gabrielle A Widjaja
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Zimu Cen
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Robert Meller
- Morehouse School of Medicine, Atlanta, GA , 30310-1495, USA
| | - Stephen B Baylin
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231
- Van Andel Research Institute, Grand Rapids, MI 49503
| | - Walter N Moss
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Basil J Nikolau
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA 02155, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Blue Marble Space Institute of Science, Seattle, WA, 98104 USA
| | - Robert Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
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Artime O, De Domenico M. From the origin of life to pandemics: emergent phenomena in complex systems. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20200410. [PMID: 35599559 PMCID: PMC9125231 DOI: 10.1098/rsta.2020.0410] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 05/31/2023]
Abstract
When a large number of similar entities interact among each other and with their environment at a low scale, unexpected outcomes at higher spatio-temporal scales might spontaneously arise. This non-trivial phenomenon, known as emergence, characterizes a broad range of distinct complex systems-from physical to biological and social-and is often related to collective behaviour. It is ubiquitous, from non-living entities such as oscillators that under specific conditions synchronize, to living ones, such as birds flocking or fish schooling. Despite the ample phenomenological evidence of the existence of systems' emergent properties, central theoretical questions to the study of emergence remain unanswered, such as the lack of a widely accepted, rigorous definition of the phenomenon or the identification of the essential physical conditions that favour emergence. We offer here a general overview of the phenomenon of emergence and sketch current and future challenges on the topic. Our short review also serves as an introduction to the theme issue Emergent phenomena in complex physical and socio-technical systems: from cells to societies, where we provide a synthesis of the contents tackled in the issue and outline how they relate to these challenges, spanning from current advances in our understanding on the origin of life to the large-scale propagation of infectious diseases. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.
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Affiliation(s)
- Oriol Artime
- Fondazione Bruno Kessler, Via Sommarive 18, Povo, TN 38123, Italy
| | - Manlio De Domenico
- Department of Physics and Astronomy ‘Galileo Galilei’, University of Padua, Padova, Veneto, Italy
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