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Cappelletto A, Alfì E, Volf N, Vu TVA, Bortolotti F, Ciucci G, Vodret S, Fantuz M, Perin M, Colliva A, Rozzi G, Rossi M, Ruozi G, Zentilin L, Vuerich R, Borin D, Lapasin R, Piazza S, Chiesa M, Lorizio D, Triboli L, Kumar S, Morello G, Tripodo C, Pinamonti M, Piperno GM, Benvenuti F, Rustighi A, Jo H, Piccolo S, Del Sal G, Carrer A, Giacca M, Zacchigna S. EMID2 is a novel biotherapeutic for aggressive cancers identified by in vivo screening. J Exp Clin Cancer Res 2024; 43:15. [PMID: 38195652 PMCID: PMC10777502 DOI: 10.1186/s13046-023-02942-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 12/22/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND New drugs to tackle the next pathway or mutation fueling cancer are constantly proposed, but 97% of them are doomed to fail in clinical trials, largely because they are identified by cellular or in silico screens that cannot predict their in vivo effect. METHODS We screened an Adeno-Associated Vector secretome library (> 1000 clones) directly in vivo in a mouse model of cancer and validated the therapeutic effect of the first hit, EMID2, in both orthotopic and genetic models of lung and pancreatic cancer. RESULTS EMID2 overexpression inhibited both tumor growth and metastatic dissemination, consistent with prolonged survival of patients with high levels of EMID2 expression in the most aggressive human cancers. Mechanistically, EMID2 inhibited TGFβ maturation and activation of cancer-associated fibroblasts, resulting in more elastic ECM and reduced levels of YAP in the nuclei of cancer cells. CONCLUSION This is the first in vivo screening, precisely designed to identify proteins able to interfere with cancer cell invasiveness. EMID2 was selected as the most potent protein, in line with the emerging relevance of the tumor extracellular matrix in controlling cancer cell invasiveness and dissemination, which kills most of cancer patients.
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Affiliation(s)
- Ambra Cappelletto
- Cardiovascular Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Edoardo Alfì
- Cardiovascular Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Nina Volf
- Cardiovascular Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Thi Van Anh Vu
- Cardiovascular Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Francesca Bortolotti
- Molecular Medicine, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Giulio Ciucci
- Cardiovascular Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Simone Vodret
- Cardiovascular Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Marco Fantuz
- Veneto Institute of Molecular Medicine, Padova, Italy
- University of Padova, Padova, Italy
| | - Martina Perin
- Cardiovascular Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Andrea Colliva
- Cardiovascular Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Giacomo Rozzi
- Cardiovascular Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Matilde Rossi
- Cardiovascular Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Giulia Ruozi
- Molecular Medicine, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Lorena Zentilin
- Molecular Medicine, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Roman Vuerich
- Cardiovascular Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Daniele Borin
- Department of Engineering and Architecture, University of Trieste, Trieste, Italy
| | - Romano Lapasin
- Department of Engineering and Architecture, University of Trieste, Trieste, Italy
| | - Silvano Piazza
- Bioinformatics, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- Bioinformatics Facility, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | | | | | - Luca Triboli
- Department of Life Sciences, University of Trieste, Trieste, Italy
- Cancer Cell Signaling, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Sandeep Kumar
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gaia Morello
- Tumor Immunology Unit, Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Claudio Tripodo
- Tumor Immunology Unit, Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
- Histopathology Unit, Institute of Molecular Oncology Foundation (IFOM), ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Maurizio Pinamonti
- Pathology Department Azienda Sanitaria Universitaria Giuliano-Isontina and University of Trieste, Trieste, Italy
| | - Giulia Maria Piperno
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Federica Benvenuti
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Alessandra Rustighi
- Department of Life Sciences, University of Trieste, Trieste, Italy
- Cancer Cell Signaling, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Hanjoong Jo
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Giannino Del Sal
- Department of Life Sciences, University of Trieste, Trieste, Italy
- Cancer Cell Signaling, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Alessandro Carrer
- Veneto Institute of Molecular Medicine, Padova, Italy
- University of Padova, Padova, Italy
| | - Mauro Giacca
- Molecular Medicine, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- King's College London, British Heart Foundation Centre of Research Excellence, London, UK
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Serena Zacchigna
- Cardiovascular Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.
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Tombari C, Zannini A, Bertolio R, Pedretti S, Audano M, Triboli L, Cancila V, Vacca D, Caputo M, Donzelli S, Segatto I, Vodret S, Piazza S, Rustighi A, Mantovani F, Belletti B, Baldassarre G, Blandino G, Tripodo C, Bicciato S, Mitro N, Del Sal G. Author Correction: Mutant p53 sustains serine-glycine synthesis and essential amino acids intake promoting breast cancer growth. Nat Commun 2023; 14:7129. [PMID: 37932286 PMCID: PMC10628279 DOI: 10.1038/s41467-023-43018-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Affiliation(s)
- Camilla Tombari
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy
| | - Alessandro Zannini
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy
| | - Rebecca Bertolio
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy
| | - Silvia Pedretti
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, University of Milan, Milan, Italy
| | - Matteo Audano
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, University of Milan, Milan, Italy
| | - Luca Triboli
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy
| | - Valeria Cancila
- Tumor Immunology Unit, Department of Health Science, Human Pathology Section, School of Medicine, University of Palermo, 90133, Palermo, Italy
| | - Davide Vacca
- Tumor Immunology Unit, Department of Health Science, Human Pathology Section, School of Medicine, University of Palermo, 90133, Palermo, Italy
| | - Manuel Caputo
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy
| | - Sara Donzelli
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Ilenia Segatto
- Unit of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081, Aviano, Italy
| | - Simone Vodret
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy
| | - Silvano Piazza
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy
| | - Alessandra Rustighi
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy
| | - Fiamma Mantovani
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Barbara Belletti
- Unit of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081, Aviano, Italy
| | - Gustavo Baldassarre
- Unit of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081, Aviano, Italy
| | - Giovanni Blandino
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Claudio Tripodo
- Tumor Immunology Unit, Department of Health Science, Human Pathology Section, School of Medicine, University of Palermo, 90133, Palermo, Italy
- IFOM ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Silvio Bicciato
- Center for Genome Research, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Nico Mitro
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, University of Milan, Milan, Italy
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Giannino Del Sal
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy.
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy.
- IFOM ETS, the AIRC Institute of Molecular Oncology, Milan, Italy.
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Tombari C, Zannini A, Bertolio R, Pedretti S, Audano M, Triboli L, Cancila V, Vacca D, Caputo M, Donzelli S, Segatto I, Vodret S, Piazza S, Rustighi A, Mantovani F, Belletti B, Baldassarre G, Blandino G, Tripodo C, Bicciato S, Mitro N, Del Sal G. Mutant p53 sustains serine-glycine synthesis and essential amino acids intake promoting breast cancer growth. Nat Commun 2023; 14:6777. [PMID: 37880212 PMCID: PMC10600207 DOI: 10.1038/s41467-023-42458-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/11/2023] [Indexed: 10/27/2023] Open
Abstract
Reprogramming of amino acid metabolism, sustained by oncogenic signaling, is crucial for cancer cell survival under nutrient limitation. Here we discovered that missense mutant p53 oncoproteins stimulate de novo serine/glycine synthesis and essential amino acids intake, promoting breast cancer growth. Mechanistically, mutant p53, unlike the wild-type counterpart, induces the expression of serine-synthesis-pathway enzymes and L-type amino acid transporter 1 (LAT1)/CD98 heavy chain heterodimer. This effect is exacerbated by amino acid shortage, representing a mutant p53-dependent metabolic adaptive response. When cells suffer amino acids scarcity, mutant p53 protein is stabilized and induces metabolic alterations and an amino acid transcriptional program that sustain cancer cell proliferation. In patient-derived tumor organoids, pharmacological targeting of either serine-synthesis-pathway and LAT1-mediated transport synergizes with amino acid shortage in blunting mutant p53-dependent growth. These findings reveal vulnerabilities potentially exploitable for tackling breast tumors bearing missense TP53 mutations.
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Affiliation(s)
- Camilla Tombari
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy
| | - Alessandro Zannini
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy
| | - Rebecca Bertolio
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy
| | - Silvia Pedretti
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, University of Milan, Milan, Italy
| | - Matteo Audano
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, University of Milan, Milan, Italy
| | - Luca Triboli
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy
| | - Valeria Cancila
- Tumor Immunology Unit, Department of Health Science, Human Pathology Section, School of Medicine, University of Palermo, 90133, Palermo, Italy
| | - Davide Vacca
- Tumor Immunology Unit, Department of Health Science, Human Pathology Section, School of Medicine, University of Palermo, 90133, Palermo, Italy
| | - Manuel Caputo
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy
| | - Sara Donzelli
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Ilenia Segatto
- Unit of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081, Aviano, Italy
| | - Simone Vodret
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy
| | - Silvano Piazza
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy
| | - Alessandra Rustighi
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy
| | - Fiamma Mantovani
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Barbara Belletti
- Unit of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081, Aviano, Italy
| | - Gustavo Baldassarre
- Unit of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081, Aviano, Italy
| | - Giovanni Blandino
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Claudio Tripodo
- Tumor Immunology Unit, Department of Health Science, Human Pathology Section, School of Medicine, University of Palermo, 90133, Palermo, Italy
- IFOM ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Silvio Bicciato
- Center for Genome Research, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Nico Mitro
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, University of Milan, Milan, Italy
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Giannino Del Sal
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy.
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park-Padriciano, 34149, Trieste, Italy.
- IFOM ETS, the AIRC Institute of Molecular Oncology, Milan, Italy.
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Mercatelli D, Triboli L, Fornasari E, Ray F, Giorgi FM. Coronapp: A web application to annotate and monitor SARS-CoV-2 mutations. J Med Virol 2020; 93:3238-3245. [PMID: 33205830 PMCID: PMC7753722 DOI: 10.1002/jmv.26678] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/16/2020] [Accepted: 11/13/2020] [Indexed: 01/15/2023]
Abstract
The avalanche of genomic data generated from the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) virus requires the development of tools to detect and monitor its mutations across the world. Here, we present a webtool, coronapp, dedicated to easily processing user‐provided SARS‐CoV‐2 genomic sequences and visualizing the current worldwide status of SARS‐CoV‐2 mutations. The webtool allows users to highlight mutations and categorize them by frequency, country, genomic location and effect on protein sequences, and to monitor their presence in the population over time. The tool is available at http://giorgilab.unibo.it/coronannotator/ for the annotation of user‐provided sequences. The full code is freely shared at https://github.com/federicogiorgi/giorgilab/tree/master/coronannotator.
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Affiliation(s)
- Daniele Mercatelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Luca Triboli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Eleonora Fornasari
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Forest Ray
- Department of Systems Biology, Columbia University Medical Center, New York City, New York, USA
| | - Federico M Giorgi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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Mercatelli D, Scalambra L, Triboli L, Ray F, Giorgi FM. Gene regulatory network inference resources: A practical overview. Biochim Biophys Acta Gene Regul Mech 2019; 1863:194430. [PMID: 31678629 DOI: 10.1016/j.bbagrm.2019.194430] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 02/08/2023]
Abstract
Transcriptional regulation is a fundamental molecular mechanism involved in almost every aspect of life, from homeostasis to development, from metabolism to behavior, from reaction to stimuli to disease progression. In recent years, the concept of Gene Regulatory Networks (GRNs) has grown popular as an effective applied biology approach for describing the complex and highly dynamic set of transcriptional interactions, due to its easy-to-interpret features. Since cataloguing, predicting and understanding every GRN connection in all species and cellular contexts remains a great challenge for biology, researchers have developed numerous tools and methods to infer regulatory processes. In this review, we catalogue these methods in six major areas, based on the dominant underlying information leveraged to infer GRNs: Coexpression, Sequence Motifs, Chromatin Immunoprecipitation (ChIP), Orthology, Literature and Protein-Protein Interaction (PPI) specifically focused on transcriptional complexes. The methods described here cover a wide range of user-friendliness: from web tools that require no prior computational expertise to command line programs and algorithms for large scale GRN inferences. Each method for GRN inference described herein effectively illustrates a type of transcriptional relationship, with many methods being complementary to others. While a truly holistic approach for inferring and displaying GRNs remains one of the greatest challenges in the field of systems biology, we believe that the integration of multiple methods described herein provides an effective means with which experimental and computational biologists alike may obtain the most complete pictures of transcriptional relationships. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.
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Affiliation(s)
- Daniele Mercatelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Laura Scalambra
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Luca Triboli
- Centre for Integrative Biology (CIBIO), University of Trento, Italy
| | - Forest Ray
- Department of Systems Biology, Columbia University Medical Center, New York, NY, United States
| | - Federico M Giorgi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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Esposito A, Tamburini S, Triboli L, Ambrosino L, Chiusano ML, Jousson O. Insights into the genome structure of four acetogenic bacteria with specific reference to the Wood-Ljungdahl pathway. Microbiologyopen 2019; 8:e938. [PMID: 31573151 PMCID: PMC6925170 DOI: 10.1002/mbo3.938] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/28/2019] [Accepted: 08/31/2019] [Indexed: 11/20/2022] Open
Abstract
Acetogenic bacteria are obligate anaerobes with the ability of converting carbon dioxide and other one‐carbon substrates into acetate through the Wood–Ljungdahl (WL) pathway. These substrates are becoming increasingly important feedstock in industrial microbiology. The main potential industrial application of acetogenic bacteria is the production of metabolites that constitute renewable energy sources (biofuel); such bacteria are of particular interest for this purpose thanks to their low energy requirements for large‐scale cultivation. Here, we report new genome sequences for four species, three of them are reported for the first time, namely Acetobacterium paludosum DSM 8237, Acetobacterium tundrae DSM 917, Acetobacterium bakii DSM 8239, and Alkalibaculum bacchi DSM 221123. We performed a comparative genomic analysis focused on the WL pathway's genes and their encoded proteins, using Acetobacterium woodii as a reference genome. The Average Nucleotide Identity (ANI) values ranged from 70% to 95% over an alignment length of 5.4–6.5 Mbp. The core genome consisted of 363 genes, whereas the number of unique genes in a single genome ranged from 486 in A. tundrae to 2360 in A.bacchi. No significant rearrangements were detected in the gene order for the Wood–Ljungdahl pathway however, two species showed variations in genes involved in formate metabolism: A. paludosum harbor two copies of fhs1, and A. bakii a truncated fdhF1. The analysis of protein networks highlighted the expansion of protein orthologues in A. woodii compared to A. bacchi, whereas protein networks involved in the WL pathway were more conserved. This study has increased our understanding on the evolution of the WL pathway in acetogenic bacteria.
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Affiliation(s)
- Alfonso Esposito
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
| | - Sabrina Tamburini
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, USA
| | - Luca Triboli
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
| | - Luca Ambrosino
- Research Infrastructures for Marine Biological Resources (RIMAR), Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Maria Luisa Chiusano
- Department of Agricultural sciences, University of Naples "Federico II", Portici, Italy
| | - Olivier Jousson
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
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Polsinelli I, Borruso L, Caliandro R, Triboli L, Esposito A, Benini S. A genome-wide analysis of desferrioxamine mediated iron uptake in Erwinia spp. reveals genes exclusive of the Rosaceae infecting strains. Sci Rep 2019; 9:2818. [PMID: 30808981 PMCID: PMC6391442 DOI: 10.1038/s41598-019-39787-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 01/29/2019] [Indexed: 11/17/2022] Open
Abstract
Erwinia amylovora is the etiological agent of fire blight, a devastating disease which is a global threat to commercial apple and pear production. The Erwinia genus includes a wide range of different species belonging to plant pathogens, epiphytes and even opportunistic human pathogens. The aim of the present study is to understand, within the Erwinia genus, the genetic differences between phytopathogenic strains and those strains not reported to be phytopathogenic. The genes related to the hydroxamate siderophores iron uptake have been considered due to their potential druggability. In E. amylovora siderophore-mediated iron acquisition plays a relevant role in the progression of Fire blight. Here we analyzed the taxonomic relations within Erwinia genus and the relevance of the genes related to the siderophore-mediated iron uptake pathway. The results of this study highlight the presence of a well-defined sub-group of Rosaceae infecting species taxonomically and genetically related with a high number of conserved core genes. The analysis of the complete ferrioxamine transport system has led to the identification of two genes exclusively present in the Rosaceae infecting strains.
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Affiliation(s)
- Ivan Polsinelli
- Bioorganic Chemistry and Bio-Crystallography laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Luigimaria Borruso
- Bioorganic Chemistry and Bio-Crystallography laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Rosanna Caliandro
- Bioorganic Chemistry and Bio-Crystallography laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Luca Triboli
- Centre for Integrative Biology, University of Trento, via Sommarive n. 9, 38123, Povo, Trento, Italy
| | - Alfonso Esposito
- Centre for Integrative Biology, University of Trento, via Sommarive n. 9, 38123, Povo, Trento, Italy.
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy.
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