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Puja H, Bianchetti L, Revol-Tissot J, Simon N, Shatalova A, Nommé J, Fritsch S, Stote RH, Mislin GLA, Potier N, Dejaegere A, Rigouin C. Biosynthesis of a clickable pyoverdine via in vivo enzyme engineering of an adenylation domain. Microb Cell Fact 2024; 23:207. [PMID: 39044227 DOI: 10.1186/s12934-024-02472-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 07/07/2024] [Indexed: 07/25/2024] Open
Abstract
The engineering of non ribosomal peptide synthetases (NRPS) for new substrate specificity is a potent strategy to incorporate non-canonical amino acids into peptide sequences, thereby creating peptide diversity and broadening applications. The non-ribosomal peptide pyoverdine is the primary siderophore produced by Pseudomonas aeruginosa and holds biomedical promise in diagnosis, bio-imaging and antibiotic vectorization. We engineered the adenylation domain of PvdD, the terminal NRPS in pyoverdine biosynthesis, to accept a functionalized amino acid. Guided by molecular modeling, we rationally designed mutants of P. aeruginosa with mutations at two positions in the active site. A single amino acid change results in the successful incorporation of an azido-L-homoalanine leading to the synthesis of a new pyoverdine analog, functionalized with an azide function. We further demonstrated that copper free click chemistry is efficient on the functionalized pyoverdine and that the conjugated siderophore retains the iron chelation properties and its capacity to be recognized and transported by P. aeruginosa. The production of clickable pyoverdine holds substantial biotechnological significance, paving the way for numerous downstream applications.
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Affiliation(s)
- Hélène Puja
- CNRS, UMR7242 Biotechnologie et Signalisation Cellulaire, 300 Boulevard Sébastien Brant, 67412, Illkirch-Graffenstaden, France
- Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), 300 Boulevard Sébastien Brant, 67412, Illkirch-Graffenstaden, France
| | - Laurent Bianchetti
- Département de Biologie structurale intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de La Santé et de La Recherche Médicale (INSERM), U1258/Centre National de Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Johan Revol-Tissot
- CNRS, UMR7242 Biotechnologie et Signalisation Cellulaire, 300 Boulevard Sébastien Brant, 67412, Illkirch-Graffenstaden, France
- Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), 300 Boulevard Sébastien Brant, 67412, Illkirch-Graffenstaden, France
| | - Nicolas Simon
- Département de Biologie structurale intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de La Santé et de La Recherche Médicale (INSERM), U1258/Centre National de Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Anastasiia Shatalova
- Département de Biologie structurale intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de La Santé et de La Recherche Médicale (INSERM), U1258/Centre National de Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Julian Nommé
- Département de Biologie structurale intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de La Santé et de La Recherche Médicale (INSERM), U1258/Centre National de Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Sarah Fritsch
- CNRS, UMR7242 Biotechnologie et Signalisation Cellulaire, 300 Boulevard Sébastien Brant, 67412, Illkirch-Graffenstaden, France
- Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), 300 Boulevard Sébastien Brant, 67412, Illkirch-Graffenstaden, France
| | - Roland H Stote
- Département de Biologie structurale intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de La Santé et de La Recherche Médicale (INSERM), U1258/Centre National de Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Gaëtan L A Mislin
- CNRS, UMR7242 Biotechnologie et Signalisation Cellulaire, 300 Boulevard Sébastien Brant, 67412, Illkirch-Graffenstaden, France
- Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), 300 Boulevard Sébastien Brant, 67412, Illkirch-Graffenstaden, France
| | - Noëlle Potier
- CNRS, UMR7140 Chimie de la Matière Complexe, Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes, Université de Strasbourg, 4 Rue Blaise Pascal, 67082, Strasbourg, France
| | - Annick Dejaegere
- Département de Biologie structurale intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de La Santé et de La Recherche Médicale (INSERM), U1258/Centre National de Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Coraline Rigouin
- CNRS, UMR7242 Biotechnologie et Signalisation Cellulaire, 300 Boulevard Sébastien Brant, 67412, Illkirch-Graffenstaden, France.
- Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), 300 Boulevard Sébastien Brant, 67412, Illkirch-Graffenstaden, France.
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Tarafder E, Nizamani MM, Karunarathna SC, Das D, Zeng X, Rind RA, Wang Y, Tian F. Advancements in genetic studies of mushrooms: a comprehensive review. World J Microbiol Biotechnol 2024; 40:275. [PMID: 39034336 DOI: 10.1007/s11274-024-04079-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 07/10/2024] [Indexed: 07/23/2024]
Abstract
Genetic studies in mushrooms, driven by innovations such as CRISPR-Cas9 genome editing and RNA interference, transform our understanding of these enigmatic fungi and their multifaceted roles in agriculture, medicine, and conservation. This comprehensive review explores the rationale and significance of genetic research in mushrooms, delving into the ethical, regulatory, and ecological dimensions of this field. CRISPR-Cas9 emerges as a game-changing technology, enabling precise genome editing, targeted gene knockouts, and pathway manipulation. RNA interference complements these efforts by downregulating genes for improved crop yield and enhanced pest and disease resistance. Genetic studies also contribute to the conservation of rare species and developing more robust mushroom strains, fostering sustainable cultivation practices. Moreover, they unlock the potential for discovering novel medicinal compounds, offering new horizons in pharmaceuticals and nutraceuticals. As emerging technologies and ethical considerations shape the future of mushroom research, these studies promise to revolutionize our relationship with these fungi, paving the way for a more sustainable and innovative world.
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Affiliation(s)
- Entaj Tarafder
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, 550025, People's Republic of China
| | - Mir Muhammad Nizamani
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, 550025, People's Republic of China
| | - Samantha C Karunarathna
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, 655011, People's Republic of China
- National Institute of Fundamental Studies, Kandy, Sri Lanka
| | - Diptosh Das
- Molecular and Applied Mycology and Plant Pathology Laboratory, Centre of Advanced Study, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Xiangyu Zeng
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, 550025, People's Republic of China
| | - Raza Ali Rind
- Department of Plant Breeding and Genetics, Sindh Agriculture University Tandojam, Hyderabad, Pakistan
| | - Yong Wang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, 550025, People's Republic of China.
| | - Fenghua Tian
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, 550025, People's Republic of China.
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Ji S, An F, Zhang T, Lou M, Guo J, Liu K, Zhu Y, Wu J, Wu R. Antimicrobial peptides: An alternative to traditional antibiotics. Eur J Med Chem 2024; 265:116072. [PMID: 38147812 DOI: 10.1016/j.ejmech.2023.116072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/04/2023] [Accepted: 12/17/2023] [Indexed: 12/28/2023]
Abstract
As antibiotic-resistant bacteria and genes continue to emerge, the identification of effective alternatives to traditional antibiotics has become a pressing issue. Antimicrobial peptides are favored for their safety, low residue, and low resistance properties, and their unique antimicrobial mechanisms show significant potential in combating antibiotic resistance. However, the high production cost and weak activity of antimicrobial peptides limit their application. Moreover, traditional laboratory methods for identifying and designing new antimicrobial peptides are time-consuming and labor-intensive, hindering their development. Currently, novel technologies, such as artificial intelligence (AI) are being employed to develop and design new antimicrobial peptide resources, offering new opportunities for the advancement of antimicrobial peptides. This article summarizes the basic characteristics and antimicrobial mechanisms of antimicrobial peptides, as well as their advantages and limitations, and explores the application of AI in antimicrobial peptides prediction amd design. This highlights the crucial role of AI in enhancing the efficiency of antimicrobial peptide research and provides a reference for antimicrobial drug development.
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Affiliation(s)
- Shuaiqi Ji
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, 110866, PR China
| | - Feiyu An
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang, 110866, PR China
| | - Taowei Zhang
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, 110866, PR China
| | - Mengxue Lou
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang, 110866, PR China
| | - Jiawei Guo
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, 110866, PR China
| | - Kexin Liu
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, 110866, PR China
| | - Yi Zhu
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang, 110866, PR China
| | - Junrui Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang, 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, 110866, PR China.
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang, 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, 110866, PR China.
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Liu Y, Lu X, Chen M, Wei Z, Peng G, Yang J, Tang C, Yu P. Advances in screening, synthesis, modification, and biomedical applications of peptides and peptide aptamers. Biofactors 2024; 50:33-57. [PMID: 37646383 DOI: 10.1002/biof.2001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
Peptides and peptide aptamers have emerged as promising molecules for a wide range of biomedical applications due to their unique properties and versatile functionalities. The screening strategies for identifying peptides and peptide aptamers with desired properties are discussed, including high-throughput screening, display screening technology, and in silico design approaches. The synthesis methods for the efficient production of peptides and peptide aptamers, such as solid-phase peptide synthesis and biosynthesis technology, are described, along with their advantages and limitations. Moreover, various modification techniques are explored to enhance the stability, specificity, and pharmacokinetic properties of peptides and peptide aptamers. This includes chemical modifications, enzymatic modifications, biomodifications, genetic engineering modifications, and physical modifications. Furthermore, the review highlights the diverse biomedical applications of peptides and peptide aptamers, including targeted drug delivery, diagnostics, and therapeutic. This review provides valuable insights into the advancements in screening, synthesis, modification, and biomedical applications of peptides and peptide aptamers. A comprehensive understanding of these aspects will aid researchers in the development of novel peptide-based therapeutics and diagnostic tools for various biomedical challenges.
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Affiliation(s)
- Yijie Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Xiaoling Lu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Meilun Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Zheng Wei
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Guangnan Peng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Jie Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Chunhua Tang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Peng Yu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
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Hellinger R, Sigurdsson A, Wu W, Romanova EV, Li L, Sweedler JV, Süssmuth RD, Gruber CW. Peptidomics. NATURE REVIEWS. METHODS PRIMERS 2023; 3:25. [PMID: 37250919 PMCID: PMC7614574 DOI: 10.1038/s43586-023-00205-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 05/31/2023]
Abstract
Peptides are biopolymers, typically consisting of 2-50 amino acids. They are biologically produced by the cellular ribosomal machinery or by non-ribosomal enzymes and, sometimes, other dedicated ligases. Peptides are arranged as linear chains or cycles, and include post-translational modifications, unusual amino acids and stabilizing motifs. Their structure and molecular size render them a unique chemical space, between small molecules and larger proteins. Peptides have important physiological functions as intrinsic signalling molecules, such as neuropeptides and peptide hormones, for cellular or interspecies communication, as toxins to catch prey or as defence molecules to fend off enemies and microorganisms. Clinically, they are gaining popularity as biomarkers or innovative therapeutics; to date there are more than 60 peptide drugs approved and more than 150 in clinical development. The emerging field of peptidomics comprises the comprehensive qualitative and quantitative analysis of the suite of peptides in a biological sample (endogenously produced, or exogenously administered as drugs). Peptidomics employs techniques of genomics, modern proteomics, state-of-the-art analytical chemistry and innovative computational biology, with a specialized set of tools. The complex biological matrices and often low abundance of analytes typically examined in peptidomics experiments require optimized sample preparation and isolation, including in silico analysis. This Primer covers the combination of techniques and workflows needed for peptide discovery and characterization and provides an overview of various biological and clinical applications of peptidomics.
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Affiliation(s)
- Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Arnar Sigurdsson
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Wenxin Wu
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Elena V Romanova
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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