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Wang M, Wu M, Han M, Niu X, Fan A, Zhu S, Tong Y. Mining the Biosynthetic Landscape of Lactic Acid Bacteria Unearths a New Family of RiPPs Assembled by a Novel Type of ThiF-like Adenylyltransferases. ACS OMEGA 2024; 9:30891-30903. [PMID: 39035879 PMCID: PMC11256085 DOI: 10.1021/acsomega.4c03760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are chemically diverse natural products of ribosomal origin. These peptides, which frequently act as signals or antimicrobials, are biosynthesized by conserved enzymatic machinery, making genome mining a powerful strategy for unearthing previously uncharacterized members of their class. Herein, we investigate the untapped biosynthetic potential of Lactobacillales (i.e., lactic acid bacteria), an order of Gram-positive bacteria closely associated with human life, including pathogenic species and industrially relevant fermenters of dairy products. Through genome mining methods, we systematically explored the distribution and diversity of ThiF-like adenylyltransferase-utilizing RiPP systems in lactic acid bacteria and identified a number of unprecedented biosynthetic gene clusters. In one of these clusters, we found a previously undescribed group of macrocyclic imide biosynthetic pathways containing multiple transporters that may be involved in a potential quorum sensing (QS) system. Through in vitro assays, we determined that one such adenylyltransferase specifically catalyzes the intracyclization of its precursor peptide through macrocyclic imide formation. Incubating the enzyme with various primary amines revealed that it could effectively amidate the C-terminus of the precursor peptide. This new transformation adds to the growing list of Nature's peptide macrocyclization strategies and expands the impressive catalytic repertoire of the adenylyltransferase family. The diverse RiPP systems identified herein represent a vast, unexploited landscape for the discovery of a novel class of natural products and QS systems.
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Affiliation(s)
- Mengjiao Wang
- College
of Life Science and Technology, Beijing
University of Chemical Technology, Beijing 100029, People’s Republic of China
| | - Mengyue Wu
- State
Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, People’s
Republic of China
| | - Meng Han
- MOE
Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Xiaogang Niu
- Beijing
Nuclear Magnetic Resonance Center, College of Chemistry and Molecular
Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Aili Fan
- State
Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, People’s
Republic of China
| | - Shaozhou Zhu
- National
Institutes for Food and Drug Control, Beijing 102629, People’s Republic of China
| | - Yigang Tong
- College
of Life Science and Technology, Beijing
University of Chemical Technology, Beijing 100029, People’s Republic of China
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2
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Ouchene R, Zaatout N, Suzuki MT. An Overview on Nocardiopsis Species Originating From North African Biotopes as a Promising Source of Bioactive Compounds and In Silico Genome Mining Analysis of Three Sequenced Genomes. J Basic Microbiol 2024:e2400046. [PMID: 38934516 DOI: 10.1002/jobm.202400046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/21/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024]
Abstract
Actinobacteria are renowned for their prolific production of diverse bioactive secondary metabolites. In recent years, there has been an increasing focus on exploring "rare" genera within this phylum for biodiscovery purposes, notably the Nocardiopsis genus, which will be the subject of the present study. Recognizing the absence of articles describing the research process of finding bioactive molecules from the genus Nocardiopsis in North African environments. We, therefore, present a historical overview of the discoveries of bioactive molecules of the genus Nocardiopsis originating from the region, highlighting their biological activities and associated reported molecules, providing a snapshot of the current state of the field, and offering insights into future opportunities and challenges for drug discovery. Additionally, we present a genome mining analysis of three genomes deposited in public databases that have been reported to be bioactive. A total of 36 biosynthetic gene clusters (BGCs) were identified, including those known to encode bioactive molecules. Notably, a substantial portion of the BGCs showed little to no similarity to those previously described, suggesting the possibility that the analyzed strains could be potential producers of new compounds. Further research on these genomes is essential to fully uncovering their biotechnological potential. Moving forward, we discuss the experimental designs adopted in the reported studies, as well as new avenues to guide the exploration of the Nocardiopsis genus in North Africa.
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Affiliation(s)
- Rima Ouchene
- Laboratoire de Microbiologie Appliquée (LMA), Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
- CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, Sorbonne Université, Paris, France
| | - Nawel Zaatout
- Faculty of Natural and Life Sciences, University of Batna, Batna, Algeria
| | - Marcelino T Suzuki
- CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, Sorbonne Université, Paris, France
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3
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da Hora GCA, Oh M, Nguyen JDM, Swanson JMJ. One Descriptor to Fold Them All: Harnessing Intuition and Machine Learning to Identify Transferable Lasso Peptide Reaction Coordinates. J Phys Chem B 2024; 128:4063-4075. [PMID: 38568862 DOI: 10.1021/acs.jpcb.3c08492] [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] [Indexed: 04/05/2024]
Abstract
Identifying optimal reaction coordinates for complex conformational changes and protein folding remains an outstanding challenge. This study combines collective variable (CV) discovery based on chemical intuition and machine learning with enhanced sampling to converge the folding free energy landscape of lasso peptides, a unique class of natural products with knot-like tertiary structures. This knotted scaffold imparts remarkable stability, making lasso peptides resistant to proteolytic degradation, thermal denaturation, and extreme pH conditions. Although their direct synthesis would enable therapeutic design, it has not yet been possible due to the improbable occurrence of spontaneous lasso folding. Thus, simulations characterizing the folding propensity are needed to identify strategies for increasing access to the lasso architecture by stabilizing the pre-lasso ensemble before isopeptide bond formation. Herein, harmonic linear discriminant analysis (HLDA) is combined with metadynamics-enhanced sampling to discover CVs capable of distinguishing the pre-lasso fold and converging the folding propensity. Intuitive CVs are compared to iterative rounds of HLDA to identify CVs that not only accomplish these goals for one lasso peptide but also seem to be transferable to others, establishing a protocol for the identification of folding reaction coordinates for lasso peptides.
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Affiliation(s)
- Gabriel C A da Hora
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Myongin Oh
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - John D M Nguyen
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jessica M J Swanson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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4
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Zhou X, Liang B, Lin W, Zha L. Identification of MACC1 as a potential biomarker for pulmonary arterial hypertension based on bioinformatics and machine learning. Comput Biol Med 2024; 173:108372. [PMID: 38552277 DOI: 10.1016/j.compbiomed.2024.108372] [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: 01/21/2024] [Revised: 03/13/2024] [Accepted: 03/24/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) is a life-threatening disease characterized by abnormal early activation of pulmonary arterial smooth muscle cells (PASMCs), yet the underlying mechanisms remain to be elucidated. METHODS Normal and PAH gene expression profiles were obtained from the Gene Expression Omnibus (GEO) database and analyzed using gene set enrichment analysis (GSEA) to uncover the underlying mechanisms. Weighted gene co-expression network analysis (WGCNA) and machine learning methods were deployed to further filter hub genes. A number of immune infiltration analysis methods were applied to explore the immune landscape of PAH. Enzyme-linked immunosorbent assay (ELISA) was employed to compare MACC1 levels between PAH and normal subjects. The important role of MACC1 in the progression of PAH was verified through Western blot and real-time qPCR, among others. RESULTS 39 up-regulated and 7 down-regulated genes were identified by 'limma' and 'RRA' packages. WGCNA and machine learning further narrowed down the list to 4 hub genes, with MACC1 showing strong diagnostic capacity. In vivo and in vitro experiments revealed that MACC1 was highsly associated with malignant features of PASMCs in PAH. CONCLUSIONS These findings suggest that targeting MACC1 may offer a promising therapeutic strategy for treating PAH, and further clinical studies are warranted to evaluate its efficacy.
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Affiliation(s)
- Xinyi Zhou
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Benhui Liang
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Wenchao Lin
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Lihuang Zha
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
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5
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Imai M, Colas K, Suga H. Protein Grafting Techniques: From Peptide Epitopes to Lasso-Grafted Neobiologics. Chempluschem 2024:e202400152. [PMID: 38693599 DOI: 10.1002/cplu.202400152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/03/2024]
Abstract
Protein engineering techniques have vastly expanded their domain of impact, notably following the success of antibodies. Likewise, smaller peptide therapeutics have carved an increasingly significant niche for themselves in the pharmaceutical landscape. The concept of grafting such peptides onto larger protein scaffolds, thus harvesting the advantages of both, has given rise to a variety of protein engineering strategies that are reviewed herein. We also describe our own "Lasso-Grafting" approach, which combines traditional grafting concepts with mRNA display to streamline the production of multiple grafted drug candidates for virtually any target.
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Affiliation(s)
- Mikio Imai
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kilian Colas
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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Baquero F, Beis K, Craik DJ, Li Y, Link AJ, Rebuffat S, Salomón R, Severinov K, Zirah S, Hegemann JD. The pearl jubilee of microcin J25: thirty years of research on an exceptional lasso peptide. Nat Prod Rep 2024; 41:469-511. [PMID: 38164764 DOI: 10.1039/d3np00046j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Covering: 1992 up to 2023Since their discovery, lasso peptides went from peculiarities to be recognized as a major family of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products that were shown to be spread throughout the bacterial kingdom. Microcin J25 was first described in 1992, making it one of the earliest known lasso peptides. No other lasso peptide has since then been studied to such an extent as microcin J25, yet, previous review articles merely skimmed over all the research done on this exceptional lasso peptide. Therefore, to commemorate the 30th anniversary of its first report, we give a comprehensive overview of all literature related to microcin J25. This review article spans the early work towards the discovery of microcin J25, its biosynthetic gene cluster, and the elucidation of its three-dimensional, threaded lasso structure. Furthermore, the current knowledge about the biosynthesis of microcin J25 and lasso peptides in general is summarized and a detailed overview is given on the biological activities associated with microcin J25, including means of self-immunity, uptake into target bacteria, inhibition of the Gram-negative RNA polymerase, and the effects of microcin J25 on mitochondria. The in vitro and in vivo models used to study the potential utility of microcin J25 in a (veterinary) medicine context are discussed and the efforts that went into employing the microcin J25 scaffold in bioengineering contexts are summed up.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- Network Center for Research in Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire OX11 0FA, UK
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, 4072 Brisbane, Queensland, Australia
| | - Yanyan Li
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - A James Link
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Raúl Salomón
- Instituto de Química Biológica "Dr Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, San Miguel de Tucumán, Argentina
| | - Konstantin Severinov
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany.
- Department of Pharmacy, Campus E8 1, Saarland University, 66123 Saarbrücken, Germany
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7
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He R, Guan C, Zhao X, Yu L, Cui Y. Expression of immune related genes and possible regulatory mechanisms in different stages of non-alcoholic fatty liver disease. Front Immunol 2024; 15:1364442. [PMID: 38524129 PMCID: PMC10957650 DOI: 10.3389/fimmu.2024.1364442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
Background Non-alcoholic fatty liver disease (NAFLD), which includes simple steatosis (SS) and non-alcoholic steatohepatitis (NASH), is a significant contributor to liver disease on a global scale. The change of immunity-related genes (IRGs) expression level leads to different immune infiltrations. However, the expression of IRGs and possible regulatory mechanisms involved in NAFLD remain unclear. The objective of our research is to investigate crucial genes linked to the development of NAFLD and the transition from SS to NASH. Methods Dataset GSE89632, which includes healthy controls, SS patients, and NASH patients, was obtained using the GEO database. To examine the correlation between sets of genes and clinical characteristics, we employed weighted gene co-expression network analysis (WGCNA) and differential expression analysis. Hub genes were extracted using a network of protein-protein interactions (PPI) and three different machine learning algorithms. To validate the findings, another dataset that is publicly accessible and mice that were subjected to a high-fat diet (HFD) or MCD diet were utilized. Furthermore, the ESTIMATE algorithm and ssGSEA were employed to investigate the immune landscape in the normal versus SS group and SS versus NASH group, additionally, the relationship between immune infiltration and the expression of hub genes was also examined. Results A total of 28 immune related key genes were selected. Most of these genes expressed reverse patterns in the initial and progressive stages of NAFLD. GO and KEGG analyses showed that they were focused on the cytokine related pathways and immune cell activation and chemotaxis. After screening by various algorithms, we obtained two hub genes, including JUN and CCL20. Validation of these findings was confirmed by analyzing gene expression patterns in both the validation dataset and the mouse model. Ultimately, two hub genes were discovered to have a significant correlation with the infiltration of immune cells. Conclusion We proposed that there were dynamic changes in the expression levels of IRGs in different stages of NAFLD disease, which led to different immune landscapes in SS and NASH. The findings of our research could serve as a guide for the accurate management of various phases of NAFLD.
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Affiliation(s)
| | | | | | - Liang Yu
- Department of Pancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yunfu Cui
- Department of Pancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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8
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He J, Ghosh P, Nitsche C. Biocompatible strategies for peptide macrocyclisation. Chem Sci 2024; 15:2300-2322. [PMID: 38362412 PMCID: PMC10866349 DOI: 10.1039/d3sc05738k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
Peptides are increasingly important drug candidates, offering numerous advantages over conventional small molecules. However, they face significant challenges related to stability, cellular uptake and overall bioavailability. While individual modifications may not address all these challenges, macrocyclisation stands out as a single modification capable of enhancing affinity, selectivity, proteolytic stability and membrane permeability. The recent successes of in situ peptide modifications during screening in combination with genetically encoded peptide libraries have increased the demand for peptide macrocyclisation reactions that can occur under biocompatible conditions. In this perspective, we aim to distinguish biocompatible conditions from those well-known examples that are fully bioorthogonal. We introduce key strategies for biocompatible peptide macrocyclisation and contextualise them within contemporary screening methods, providing an overview of available transformations.
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Affiliation(s)
- Junming He
- Research School of Chemistry, Australian National University Canberra ACT Australia
| | - Pritha Ghosh
- Research School of Chemistry, Australian National University Canberra ACT Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University Canberra ACT Australia
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9
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Chen S, Zhang K, Zou J, Yu Z, Gai C, Chai X, Zhao Q, Zou Y. Further structural optimization and SAR study of sungsanpin derivatives as cell-invasion inhibitors. Bioorg Med Chem Lett 2024; 99:129627. [PMID: 38272189 DOI: 10.1016/j.bmcl.2024.129627] [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: 12/12/2023] [Revised: 01/16/2024] [Accepted: 01/21/2024] [Indexed: 01/27/2024]
Abstract
Metastasis is one of the major causes of death in patients with cancer, and cell invasion plays a fundamental part in this process. Because of the absence of efficacious treatments, caring for these patients is challenging. Recently, we optimized the structure of the naturally occurring lasso peptide sungsanpin. We identified two peptides, octapeptide S3 and cyclic peptide S4, which inhibited invasion into A549 cells effectively. We undertook an alanine scan of S3 to explore the structure-activity relationship. The linear octapeptide S3-4 and cyclic peptide S4-1 exhibited improved inhibition of invasion into A549 cells. We modified S3-4 to obtain S3-4K, which displayed much higher inhibitory activity against invasion into A549 cells than S3-4. Of all peptides tested, S4-1 upregulated significantly mRNA of tissue inhibitor matrix metalloproteinase TIMP-1 and TIMP-2.
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Affiliation(s)
- Shuai Chen
- School of Pharmacy, Naval Medical University, Shanghai 200433, PR China
| | - Kai Zhang
- School of Pharmacy, Naval Medical University, Shanghai 200433, PR China
| | - Jihua Zou
- Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian Province 350122, PR China
| | - Zhou Yu
- School of Pharmacy, Naval Medical University, Shanghai 200433, PR China
| | - Conghao Gai
- School of Pharmacy, Naval Medical University, Shanghai 200433, PR China
| | - Xiaoyun Chai
- School of Pharmacy, Naval Medical University, Shanghai 200433, PR China
| | - Qingjie Zhao
- School of Pharmacy, Naval Medical University, Shanghai 200433, PR China.
| | - Yan Zou
- School of Pharmacy, Naval Medical University, Shanghai 200433, PR China.
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10
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Fernandez HN, Kretsch AM, Kunakom S, Kadjo AE, Mitchell DA, Eustáquio AS. High-Yield Lasso Peptide Production in a Burkholderia Bacterial Host by Plasmid Copy Number Engineering. ACS Synth Biol 2024; 13:337-350. [PMID: 38194362 PMCID: PMC10947786 DOI: 10.1021/acssynbio.3c00597] [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] [Indexed: 01/10/2024]
Abstract
The knotted configuration of lasso peptides confers thermal stability and proteolytic resistance, addressing two shortcomings of peptide-based drugs. However, low isolation yields hinder the discovery and development of lasso peptides. While testing Burkholderia sp. FERM BP-3421 as a bacterial host to produce the lasso peptide capistruin, an overproducer clone was previously identified. In this study, we show that an increase in the plasmid copy number partially contributed to the overproducer phenotype. Further, we modulated the plasmid copy number to recapitulate titers to an average of 160% relative to the overproducer, which is 1000-fold higher than previously reported with E. coli, reaching up to 240 mg/L. To probe the applicability of the developed tools for lasso peptide discovery, we targeted a new lasso peptide biosynthetic gene cluster from endosymbiont Mycetohabitans sp. B13, leading to the isolation of mycetolassin-15 and mycetolassin-18 in combined titers of 11 mg/L. These results validate Burkholderia sp. FERM BP-3421 as a production platform for lasso peptide discovery.
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Affiliation(s)
- Hannah N. Fernandez
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Ashley M. Kretsch
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sylvia Kunakom
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Adjo E. Kadjo
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Douglas A. Mitchell
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alessandra S. Eustáquio
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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11
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Carson DV, Zhang Y, So L, Cheung-Lee WL, Cartagena AJ, Darst SA, Link AJ. Discovery, Characterization, and Bioactivity of the Achromonodins: Lasso Peptides Encoded by Achromobacter. JOURNAL OF NATURAL PRODUCTS 2023; 86:2448-2456. [PMID: 37870195 PMCID: PMC10949989 DOI: 10.1021/acs.jnatprod.3c00536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Through genome mining efforts, two lasso peptide biosynthetic gene clusters (BGCs) within two different species of Achromobacter, a genus that contains pathogenic organisms that can infect patients with cystic fibrosis, were discovered. Using gene-refactored BGCs in E. coli, these lasso peptides, which were named achromonodin-1 and achromonodin-2, were heterologously expressed. Achromonodin-1 is naturally encoded by certain isolates from the sputum of patients with cystic fibrosis. The NMR structure of achromonodin-1 was determined, demonstrating that it is a threaded lasso peptide with a large loop and short tail structure, reminiscent of previously characterized lasso peptides that inhibit RNA polymerase (RNAP). Achromonodin-1 inhibits RNAP in vitro and has potent, focused activity toward Achromobacter pulmonis, another isolate from the sputum of a cystic fibrosis patient. These efforts expand the repertoire of antimicrobial lasso peptides and provide insights into how Achromobacter isolates from certain ecological niches interact with each other.
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Affiliation(s)
- Drew V. Carson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Yi Zhang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Larry So
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Wai Ling Cheung-Lee
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Alexis Jaramillo Cartagena
- Laboratory of Molecular Biophysics and Tri-Institutional Training Program in Chemical Biology, Rockefeller University, New York, NY 10065, United States
| | - Seth A. Darst
- Laboratory of Molecular Biophysics and Tri-Institutional Training Program in Chemical Biology, Rockefeller University, New York, NY 10065, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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12
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Saad H, Majer T, Bhattarai K, Lampe S, Nguyen DT, Kramer M, Straetener J, Brötz-Oesterhelt H, Mitchell DA, Gross H. Bioinformatics-guided discovery of biaryl-linked lasso peptides. Chem Sci 2023; 14:13176-13183. [PMID: 38023510 PMCID: PMC10664482 DOI: 10.1039/d3sc02380j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that feature an isopeptide bond and a distinct lariat fold. A growing number of secondary modifications have been described that further decorate lasso peptide scaffolds. Using genome mining, we have discovered a pair of lasso peptide biosynthetic gene clusters (BGCs) that include cytochrome P450 genes. Using mass spectrometry, stable isotope incorporation, and extensive 2D-NMR spectrometry, we report the structural characterization of two unique examples of (C-N) biaryl-linked lasso peptides. Nocapeptin A, from Nocardia terpenica, is tailored with a Trp-Tyr crosslink, while longipepetin A, from Longimycelium tulufanense, features a Trp-Trp linkage. Besides the unusual bicyclic frame, a Met of longipepetin A undergoes S-methylation to yield a trivalent sulfonium, a heretofore unprecedented RiPP modification. A bioinformatic survey revealed additional lasso peptide BGCs containing P450 enzymes which await future characterization. Lastly, nocapeptin A bioactivity was assessed against a panel of human and bacterial cell lines with modest growth-suppression activity detected towards Micrococcus luteus.
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Affiliation(s)
- Hamada Saad
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Thomas Majer
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Keshab Bhattarai
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Sarah Lampe
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Dinh T Nguyen
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Markus Kramer
- Institute of Organic Chemistry, University of Tübingen Auf der Morgenstelle 18 72076 Tübingen Germany
| | - Jan Straetener
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen Tübingen Germany
| | - Douglas A Mitchell
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Harald Gross
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen Tübingen Germany
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13
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Li JY, Liang JY, Liu ZY, Yi YZ, Zhao J, Huang ZY, Chen J. Multicopy Chromosome Integration and Deletion of Negative Global Regulators Significantly Increased the Heterologous Production of Aborycin in Streptomyces coelicolor. Mar Drugs 2023; 21:534. [PMID: 37888469 PMCID: PMC10608281 DOI: 10.3390/md21100534] [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: 09/13/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023] Open
Abstract
Aborycin is a type I lasso peptide with a stable interlocked structure, offering a favorable framework for drug development. The aborycin biosynthetic gene cluster gul from marine sponge-associated Streptomyces sp. HNS054 was cloned and integrated into the chromosome of S. coelicolor hosts with different copies. The three-copy gul-integration strain S. coelicolor M1346::3gul showed superior production compared to the one-copy or two-copy gul-integration strains, and the total titer reached approximately 10.4 mg/L, i.e., 2.1 times that of the native strain. Then, five regulatory genes, phoU (SCO4228), wblA (SCO3579), SCO1712, orrA (SCO3008) and gntR (SCO1678), which reportedly have negative effects on secondary metabolism, were further knocked out from the M1346::3gul genome by CRISPR/Cas9 technology. While the ΔSCO1712 mutant showed a significant decrease (4.6 mg/L) and the ΔphoU mutant showed no significant improvement (12.1 mg/L) in aborycin production, the ΔwblA, ΔorrA and ΔgntR mutations significantly improved the aborycin titers to approximately 23.6 mg/L, 56.3 mg/L and 48.2 mg/L, respectively, which were among the highest heterologous yields for lasso peptides in both Escherichia coli systems and Streptomyces systems. Thus, this study provides important clues for future studies on enhancing antibiotic production in Streptomyces systems.
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Affiliation(s)
- Jia-Yi Li
- Department of Marine Biological Science & Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (J.-Y.L.); (J.-Y.L.); (Z.-Y.L.); (Y.-Z.Y.); (J.Z.)
| | - Jun-Yu Liang
- Department of Marine Biological Science & Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (J.-Y.L.); (J.-Y.L.); (Z.-Y.L.); (Y.-Z.Y.); (J.Z.)
| | - Zhao-Yuan Liu
- Department of Marine Biological Science & Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (J.-Y.L.); (J.-Y.L.); (Z.-Y.L.); (Y.-Z.Y.); (J.Z.)
| | - Yue-Zhao Yi
- Department of Marine Biological Science & Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (J.-Y.L.); (J.-Y.L.); (Z.-Y.L.); (Y.-Z.Y.); (J.Z.)
| | - Jing Zhao
- Department of Marine Biological Science & Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (J.-Y.L.); (J.-Y.L.); (Z.-Y.L.); (Y.-Z.Y.); (J.Z.)
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen 361102, China
- Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen 361102, China
| | - Zhi-Yong Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Jun Chen
- Department of Marine Biological Science & Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (J.-Y.L.); (J.-Y.L.); (Z.-Y.L.); (Y.-Z.Y.); (J.Z.)
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen 361102, China
- Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen 361102, China
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14
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Qu Z, Fang J, Wang YX, Sun Y, Liu Y, Wu WH, Zhang WB. A single-domain green fluorescent protein catenane. Nat Commun 2023; 14:3480. [PMID: 37311944 DOI: 10.1038/s41467-023-39233-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 06/05/2023] [Indexed: 06/15/2023] Open
Abstract
Natural proteins exhibit rich structural diversity based on the folds of an invariably linear chain. Macromolecular catenanes that cooperatively fold into a single domain do not belong to the current protein universe, and their design and synthesis open new territories in chemistry. Here, we report the design, synthesis, and properties of a single-domain green fluorescent protein catenane via rewiring the connectivity of GFP's secondary motifs. The synthesis could be achieved in two steps via a pseudorotaxane intermediate or directly via expression in cellulo. Various proteins-of-interest may be inserted at the loop regions to give fusion protein catenanes where the two subunits exhibit enhanced thermal resilience, thermal stability, and mechanical stability due to strong conformational coupling. The strategy can be applied to other proteins with similar fold, giving rise to a family of single-domain fluorescent proteins. The results imply that there may be multiple protein topological variants with desirable functional traits beyond their corresponding linear protein counterparts, which are now made accessible and fully open for exploration.
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Affiliation(s)
- Zhiyu Qu
- Beijing National Laboratory for Molecular Sciences, Beijing, P. R. China
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing, P. R. China
- Center for Soft Matter Science and Engineering, Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences, Beijing, P. R. China
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing, P. R. China
- Center for Soft Matter Science and Engineering, Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Yu-Xiang Wang
- Beijing National Laboratory for Molecular Sciences, Beijing, P. R. China
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing, P. R. China
- Center for Soft Matter Science and Engineering, Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Yibin Sun
- Beijing National Laboratory for Molecular Sciences, Beijing, P. R. China
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing, P. R. China
- Center for Soft Matter Science and Engineering, Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Yajie Liu
- Beijing National Laboratory for Molecular Sciences, Beijing, P. R. China
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing, P. R. China
- Center for Soft Matter Science and Engineering, Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Wen-Hao Wu
- Beijing National Laboratory for Molecular Sciences, Beijing, P. R. China
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing, P. R. China
- Center for Soft Matter Science and Engineering, Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Beijing, P. R. China.
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing, P. R. China.
- Center for Soft Matter Science and Engineering, Peking University, Beijing, P. R. China.
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China.
- Beijing Academy of Artificial Intelligence, Beijing, P. R. China.
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15
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He J, Zhao Y, Zhou Z, Zhang M. Machine learning and integrative analysis identify the common pathogenesis of azoospermia complicated with COVID-19. Front Immunol 2023; 14:1114870. [PMID: 37283758 PMCID: PMC10239851 DOI: 10.3389/fimmu.2023.1114870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/05/2023] [Indexed: 06/08/2023] Open
Abstract
Background Although more recent evidence has indicated COVID-19 is prone to azoospermia, the common molecular mechanism of its occurrence remains to be elucidated. The aim of the present study is to further investigate the mechanism of this complication. Methods To discover the common differentially expressed genes (DEGs) and pathways of azoospermia and COVID-19, integrated weighted co-expression network (WGCNA), multiple machine learning analyses, and single-cell RNA-sequencing (scRNA-seq) were performed. Results Therefore, we screened two key network modules in the obstructive azoospermia (OA) and non-obstructive azoospermia (NOA) samples. The differentially expressed genes were mainly related to the immune system and infectious virus diseases. We then used multiple machine learning methods to detect biomarkers that differentiated OA from NOA. Enrichment analysis showed that azoospermia patients and COVID-19 patients shared a common IL-17 signaling pathway. In addition, GLO1, GPR135, DYNLL2, and EPB41L3 were identified as significant hub genes in these two diseases. Screening of two different molecular subtypes revealed that azoospermia-related genes were associated with clinicopathological characteristics of age, hospital-free-days, ventilator-free-days, charlson score, and d-dimer of patients with COVID-19 (P < 0.05). Finally, we used the Xsum method to predict potential drugs and single-cell sequencing data to further characterize whether azoospermia-related genes could validate the biological patterns of impaired spermatogenesis in cryptozoospermia patients. Conclusion Our study performs a comprehensive and integrated bioinformatics analysis of azoospermia and COVID-19. These hub genes and common pathways may provide new insights for further mechanism research.
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Affiliation(s)
- Jiarong He
- Department of Neurosurgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, PR, China
| | - Yuanqiao Zhao
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, PR, China
| | - Zhixian Zhou
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, PR, China
| | - Mingming Zhang
- Department of Neurosurgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, PR, China
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16
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Thokkadam A, Do T, Ran X, Brynildsen MP, Yang ZJ, Link AJ. High-Throughput Screen Reveals the Structure-Activity Relationship of the Antimicrobial Lasso Peptide Ubonodin. ACS CENTRAL SCIENCE 2023; 9:540-550. [PMID: 36968541 PMCID: PMC10037499 DOI: 10.1021/acscentsci.2c01487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Indexed: 06/16/2023]
Abstract
The Burkholderia cepacia complex (Bcc) is a group of bacteria including opportunistic human pathogens. Immunocompromised individuals and cystic fibrosis patients are especially vulnerable to serious infections by these bacteria, motivating the search for compounds with antimicrobial activity against the Bcc. Ubonodin is a lasso peptide with promising activity against Bcc species, working by inhibiting RNA polymerase in susceptible bacteria. We constructed a library of over 90 000 ubonodin variants with 2 amino acid substitutions and used a high-throughput screen and next-generation sequencing to examine the fitness of the entire library, generating the most comprehensive data set on lasso peptide activity so far. This screen revealed information regarding the structure-activity relationship of ubonodin over a large sequence space. Remarkably, the screen identified one variant with not only improved activity compared to wild-type ubonodin but also a submicromolar minimum inhibitory concentration (MIC) against a clinical isolate of the Bcc member Burkholderia cenocepacia. Ubonodin and several of the variants identified in this study had lower MICs against certain Bcc strains than those of many clinically approved antibiotics. Finally, the large library size enabled us to develop DeepLasso, a deep learning model that can predict the RNAP inhibitory activity of an ubonodin variant.
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Affiliation(s)
- Alina Thokkadam
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Truc Do
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Xinchun Ran
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Mark P. Brynildsen
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Zhongyue J. Yang
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data
Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - A. James Link
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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17
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Saad H, Majer T, Bhattarai K, Lampe S, Nguyen DT, Kramer M, Straetener J, Brötz-Oesterhelt H, Mitchell DA, Gross H. Bioinformatics-Guided Discovery of Biaryl-Tailored Lasso Peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531328. [PMID: 36945544 PMCID: PMC10028836 DOI: 10.1101/2023.03.06.531328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that feature an isopeptide bond and a distinct lariat fold. A growing number of secondary modifications have been described that further decorate lasso peptide scaffolds. Using genome mining, we have discovered a pair of lasso peptide biosynthetic gene clusters (BGCs) that include cytochrome P450 genes. Here, we report the structural characterization of two unique examples of (C-N) biaryl-containing lasso peptides. Nocapeptin A, from Nocardia terpenica, is tailored with Trp-Tyr crosslink while longipepetin A, from Longimycelium tulufanense, features Trp-Trp linkage. Besides the unusual bicyclic frame, longipepetin A receives an S-methylation by a new Met methyltransferase resulting in unprecedented sulfonium-bearing RiPP. Our bioinformatic survey revealed P450(s) and further maturating enzyme(s)-containing lasso BGCs awaiting future characterization.
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Affiliation(s)
- Hamada Saad
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen (Germany)
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (United States)
| | - Thomas Majer
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen (Germany)
| | - Keshab Bhattarai
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen (Germany)
| | - Sarah Lampe
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen (Germany)
| | - Dinh T. Nguyen
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (United States)
| | - Markus Kramer
- Institute of Organic Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076 Tübingen (Germany)
| | - Jan Straetener
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen (Germany)
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen (Germany)
| | - Douglas A. Mitchell
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (United States)
| | - Harald Gross
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen (Germany)
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18
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Zhong G, Wang ZJ, Yan F, Zhang Y, Huo L. Recent Advances in Discovery, Bioengineering, and Bioactivity-Evaluation of Ribosomally Synthesized and Post-translationally Modified Peptides. ACS BIO & MED CHEM AU 2023; 3:1-31. [PMID: 37101606 PMCID: PMC10125368 DOI: 10.1021/acsbiomedchemau.2c00062] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 04/28/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are of increasing interest in natural products as well as drug discovery. This empowers not only the unique chemical structures and topologies in natural products but also the excellent bioactivities such as antibacteria, antifungi, antiviruses, and so on. Advances in genomics, bioinformatics, and chemical analytics have promoted the exponential increase of RiPPs as well as the evaluation of biological activities thereof. Furthermore, benefiting from their relatively simple and conserved biosynthetic logic, RiPPs are prone to be engineered to obtain diverse analogues that exhibit distinct physiological activities and are difficult to synthesize. This Review aims to systematically address the variety of biological activities and/or the mode of mechanisms of novel RiPPs discovered in the past decade, albeit the characteristics of selective structures and biosynthetic mechanisms are briefly covered as well. Almost one-half of the cases are involved in anti-Gram-positive bacteria. Meanwhile, an increasing number of RiPPs related to anti-Gram-negative bacteria, antitumor, antivirus, etc., are also discussed in detail. Last but not least, we sum up some disciplines of the RiPPs' biological activities to guide genome mining as well as drug discovery and optimization in the future.
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Affiliation(s)
- Guannan Zhong
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou
Research Institute, Shandong University, Suzhou, Jiangsu 215123, P. R. China
| | - Zong-Jie Wang
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Fu Yan
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- CAS
Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Faculty
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Liujie Huo
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou
Research Institute, Shandong University, Suzhou, Jiangsu 215123, P. R. China
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19
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Cao L, Elashal HE, Link AJ. Kinetics of Aspartimide Formation and Hydrolysis in Lasso Peptide Lihuanodin. Biochemistry 2023; 62:695-699. [PMID: 36701287 PMCID: PMC10038108 DOI: 10.1021/acs.biochem.2c00707] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Aspartimides are notorious as undesired side products in solid-phase peptide synthesis and in pharmaceutical formulations. However, we have discovered several ribosomally synthesized and post-translationally modified peptides (RiPPs) in which aspartimide is installed intentionally via enzymatic activity of protein l-isoaspartyl methyltransferase (PIMT) homologues. In the case of the lasso peptide lihuanodin, the methyltransferase LihM recognizes the lassoed substrate pre-lihuanodin, specifically methylating the side chain of an l-Asp residue in the ring portion of the lasso peptide. The subsequent nucleophilic attack from the adjacent amide leads to the formation of an aspartimide. The resulting aspartimide hydrolyzes regioselectively to l-Asp in buffers above pH 7. Here we report the first Michaelis-Menten kinetic measurements of such a RiPP-associated PIMT homologue, LihM, acting on its cognate substrate pre-lihuanodin. Additionally, we measured the rate of aspartimide hydrolysis, which allowed us to deduce the kinetics of the entire reaction network. The relative magnitudes of these rates explain the accumulation and relative stability of aspartimide-containing lihuanodin. We also demonstrate that the residue C-terminal to the aspartimide controls the regioselectivity of hydrolysis and thus the threadedness of the peptide.
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Affiliation(s)
- Li Cao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - Hader E. Elashal
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
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20
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Li A, Zou J, Zhuo X, Chen S, Chai X, Gai C, Li X, Zhao Q, Zou Y. Rational Optimizations of the Marine-Derived Peptide Sungsanpin as Novel Inhibitors of Cell Invasion. Chem Biodivers 2023; 20:e202201221. [PMID: 36651671 DOI: 10.1002/cbdv.202201221] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/19/2023]
Abstract
Cancer metastasis, including cell invasion, is a major cause of poor clinical outcomes and death in numerous cancer patients. In recent years, many efforts have been made to develop potent therapeutic molecules from naturally derived peptides. Sungsanpin is a naturally derived lasso peptide that inhibits A549 cell invasion. We aimed to evaluate the potential of sungsanpin derivatives as candidates for anti-invasion drugs. We synthesized an analog of sungsanpin (Sun A) using a solid-phase peptide synthesis strategy (SPPS) and further modified its structure to improve its anti-invasion activity. All peptides were tested for their proliferative inhibition and anti-invasion activities in the A549 cell lines. Octapeptide S3 and cyclooctapeptide S4 upregulated the expression of TIMP-1 and TIMP-2 mRNA effectively and thus improved the inhibitory effect on the invasion of A549 cells. The two peptides can inhibit the invasion of A549 cells by up to 60 %, suggesting that they have potential as lead molecules for the development of peptide inhibitors.
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Affiliation(s)
- Anpeng Li
- School of Pharmacy, Naval Medical University, Shanghai, 200433, China
| | - Jihua Zou
- Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian Province 350122, China
| | - Xiaobin Zhuo
- School of Pharmacy, Naval Medical University, Shanghai, 200433, China
| | - Shuai Chen
- School of Pharmacy, Naval Medical University, Shanghai, 200433, China
| | - Xiaoyun Chai
- School of Pharmacy, Naval Medical University, Shanghai, 200433, China
| | - Conghao Gai
- School of Pharmacy, Naval Medical University, Shanghai, 200433, China
| | - Xiang Li
- School of Pharmacy, Naval Medical University, Shanghai, 200433, China
| | - Qingjie Zhao
- School of Pharmacy, Naval Medical University, Shanghai, 200433, China
| | - Yan Zou
- School of Pharmacy, Naval Medical University, Shanghai, 200433, China
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21
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Juarez RJ, Jiang Y, Tremblay M, Shao Q, Link AJ, Yang ZJ. LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling. J Chem Inf Model 2023; 63:522-530. [PMID: 36594886 PMCID: PMC10117200 DOI: 10.1021/acs.jcim.2c00945] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Lasso peptides are a subclass of ribosomally synthesized and post-translationally modified peptides with a slipknot conformation. With superior thermal stability, protease resistance, and antimicrobial activity, lasso peptides are promising candidates for bioengineering and pharmaceutical applications. To enable high-throughput computational prediction and design of lasso peptides, we developed a software, LassoHTP, for automatic lasso peptide structure construction and modeling. LassoHTP consists of three modules, including the scaffold constructor, mutant generator, and molecular dynamics (MD) simulator. With a user-provided sequence and conformational annotation, LassoHTP can either generate the structure and conformational ensemble as is or conduct random mutagenesis. We used LassoHTP to construct eight known lasso peptide structures de novo and to simulate their conformational ensembles for 100 ns MD simulations. For benchmarking, we calculated the root mean square deviation (RMSD) of these ensembles with reference to their experimental crystal or NMR PDB structures; we also compared these RMSD values against those of the MD ensembles that are initiated from the PDB structures. Dihedral principal component analysis was also conducted. The results show that the LassoHTP-initiated ensembles are similar to those of the PDB-initiated ensembles. LassoHTP offers a computational platform to develop strategies for lasso peptide prediction and design.
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Affiliation(s)
- Reecan J. Juarez
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Yaoyukun Jiang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Matthew Tremblay
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Qianzhen Shao
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Chemistry and Molecular Biology, Princeton University, 207 Hoyt Laboratory, Princeton, New Jersey 08544, United States
| | - Zhongyue J. Yang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
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22
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Do T, Link AJ. Protein Engineering in Ribosomally Synthesized and Post-translationally Modified Peptides (RiPPs). Biochemistry 2023; 62:201-209. [PMID: 35006671 PMCID: PMC9454058 DOI: 10.1021/acs.biochem.1c00714] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) make up a rapidly growing superfamily of natural products. RiPPs exhibit an extraordinary range of structures, but they all begin as gene-encoded precursor peptides that are linear chains of amino acids produced by ribosomes. Given the gene-encoded nature of RiPP precursor peptides, the toolbox of protein engineering can be directly applied to these precursors. This Perspective will discuss examples of site-directed mutagenesis, noncanonical amino acid mutagenesis, and the construction and screening of combinatorial libraries as applied to RiPPs. These studies have led to important insights into the biosynthesis and bioactivity of RiPPs and the reengineering of RiPPs for entirely new functions.
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Affiliation(s)
- Truc Do
- Department of Chemical and Biological Engineering, 207 Hoyt Laboratory Princeton University, Princeton, NJ 08544 USA
| | - A. James Link
- Department of Chemical and Biological Engineering, 207 Hoyt Laboratory Princeton University, Princeton, NJ 08544 USA
- Department of Chemistry, 207 Hoyt Laboratory Princeton University, Princeton, NJ 08544 USA
- Department of Molecular Biology, 207 Hoyt Laboratory Princeton University, Princeton, NJ 08544 USA
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23
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Mohri K, Nhat KPH, Zouda M, Warashina S, Wada Y, Watanabe Y, Tagami S, Mukai H. Lasso peptide microcin J25 variant containing RGD motif as a PET probe for integrin a v ß 3 in tumor imaging. Eur J Pharm Sci 2023; 180:106339. [PMID: 36414157 DOI: 10.1016/j.ejps.2022.106339] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/21/2022]
Abstract
Microcin J25 (MccJ25), a lasso peptide, has a unique 3-D interlocked structure that provides high stability under acidic conditions, at high temperatures, and in the presence of proteases. In this study, we generated a positron emission tomography (PET) probe based on MccJ25 analog with an RGD motif and investigated their pharmacokinetics and utility for integrin αvβ3 imaging in tumors. The MccJ25 variant with an RGD motif in the loop region and a lysine substitution at the C-terminus (MccJ25(RGDF)GtoK) was produced in E. coli transfected with plasmid DNA containing the MccJ25 biosynthetic gene cluster (mcjABCD). [64Cu]Cu-MccJ25(RGDF)GtoK was synthesized using the C-terminal lysine labeled with copper-64 (t1/2 = 12.7 h) via a bifunctional chelator; it showed stability in 90% mouse plasma for 45 min. Using PET imaging for integrin αvβ3 positive U87MG tumor bearing mice, [64Cu]Cu-MccJ25(RGDF)GtoK could clearly distinguish the tumor, and its accumulation was significantly higher than that of MccJ25(GIGT)GtoK without the binding motif for integrin αvβ3. Furthermore, MccJ25(RGDF)GtoK enabled visualization of only U87MG tumors but not MCF-7 tumors with low integrin αvβ3 expression in double tumor-bearing mice. In ex vivo biodistribution analysis, the integrin αvβ3 non-specific accumulation of [64Cu]Cu-MccJ25(RGDF)GtoK was significantly lower in various tissues, except for the kidneys, as compared to the control probe ([64Cu]Cu-cyclic RGD peptide). These results of the present study indicate that 64Cu-labeling methods are appropriate for the synthesis of MccJ25-based PET probes, and [64Cu]Cu-MccJ25 variants are useful tools for cancer molecular imaging.
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Affiliation(s)
- Kohta Mohri
- Laboratory for Molecular Delivery and Imaging Technology, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kim Phuong Huynh Nhat
- Laboratory for Advanced Biomolecular Engineering, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Maki Zouda
- Laboratory for Molecular Delivery and Imaging Technology, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Shota Warashina
- Laboratory for Molecular Delivery and Imaging Technology, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yasuhiro Wada
- Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yasuyoshi Watanabe
- Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Shunsuke Tagami
- Laboratory for Advanced Biomolecular Engineering, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Hidefumi Mukai
- Laboratory for Molecular Delivery and Imaging Technology, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Pharmaceutical Informatics, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki-shi, Nagasaki 852-8588, Japan.
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24
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Chowdhury A, Bandyopadhyay A. Compelling Cyclic Peptide Scaffolds for Antitubercular Action: An Account (2011-21) of the Natural Source. Curr Protein Pept Sci 2022; 23:823-836. [PMID: 36200246 DOI: 10.2174/1389203723666220930111259] [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: 07/01/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 01/20/2023]
Abstract
Natural cyclic peptide scaffolds are indispensable in medicinal chemistry, chemical biology, and drug discovery platforms due to their chemical diversity, structural integrity, proteolytic stability and biocompatibility. Historically, their isolation and profound understanding of target engagement have been identified as lead pharmacophore discovery. Natural cyclic peptides are the largest class of pharmacologically active scaffold, in which most show activity against drug-resistant Mycobacterium tuberculosis (Mtb). Nevertheless, eight recently discovered cyclic peptide scaffolds exhibit promising antitubercular activity among numerous naturally occurring antitubercular peptides, and they are amenable scaffolds to drug development. We examined their biological origin, scaffolds, isolations, chemical synthesis, and reasons for biological actions against Mtb. Understanding these peptide scaffold details will further allow synthetic and medicinal chemists to develop novel peptide therapeutics against tuberculosis-infected deadly diseases. This review emphasizes these cyclic peptides' in vitro and in vivo activity profiles, including their structural and chemical features.
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Affiliation(s)
- Arnab Chowdhury
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Punjab- 140001, India
| | - Anupam Bandyopadhyay
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Punjab- 140001, India
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25
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Elashal HE, Koos JD, Cheung-Lee WL, Choi B, Cao L, Richardson MA, White HL, Link AJ. Biosynthesis and characterization of fuscimiditide, an aspartimidylated graspetide. Nat Chem 2022; 14:1325-1334. [PMID: 35982233 PMCID: PMC10078976 DOI: 10.1038/s41557-022-01022-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 07/11/2022] [Indexed: 11/09/2022]
Abstract
Microviridins and other ω-ester-linked peptides, collectively known as graspetides, are characterized by side-chain-side-chain linkages installed by ATP-grasp enzymes. Here we report the discovery of a family of graspetides, the gene clusters of which also encode an O-methyltransferase with homology to the protein repair catalyst protein L-isoaspartyl methyltransferase. Using heterologous expression, we produced fuscimiditide, a ribosomally synthesized and post-translationally modified peptide (RiPP). NMR analysis of fuscimiditide revealed that the peptide contains two ester cross-links forming a stem-loop macrocycle. Furthermore, an unusually stable aspartimide moiety is found within the loop macrocycle. We fully reconstituted fuscimiditide biosynthesis in vitro including formation of the ester and aspartimide moieties. The aspartimide moiety embedded in fuscimiditide hydrolyses regioselectively to isoaspartate. Surprisingly, this isoaspartate-containing peptide is also a substrate for the L-isoaspartyl methyltransferase homologue, thus driving any hydrolysis products back to the aspartimide form. Whereas an aspartimide is often considered a nuisance product in protein formulations, our data suggest that some RiPPs have aspartimide residues intentionally installed via enzymatic activity.
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Affiliation(s)
- Hader E Elashal
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Joseph D Koos
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Wai Ling Cheung-Lee
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Brian Choi
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Li Cao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Michelle A Richardson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Heather L White
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - A James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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26
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Ongpipattanakul C, Desormeaux EK, DiCaprio A, van der Donk WA, Mitchell DA, Nair SK. Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides. Chem Rev 2022; 122:14722-14814. [PMID: 36049139 PMCID: PMC9897510 DOI: 10.1021/acs.chemrev.2c00210] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.
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Affiliation(s)
- Chayanid Ongpipattanakul
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Emily K. Desormeaux
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Adam DiCaprio
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
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27
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Do T, Thokkadam A, Leach R, Link AJ. Phenotype-Guided Comparative Genomics Identifies the Complete Transport Pathway of the Antimicrobial Lasso Peptide Ubonodin in Burkholderia. ACS Chem Biol 2022; 17:2332-2343. [PMID: 35802499 PMCID: PMC9454059 DOI: 10.1021/acschembio.2c00420] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New antibiotics are needed as bacterial infections continue to be a leading cause of death, but efforts to develop compounds with promising antibacterial activity are hindered by a poor understanding of─and limited strategies for elucidating─their modes of action. We recently discovered a novel lasso peptide, ubonodin, that is active against opportunistic human lung pathogens from the Burkholderia cepacia complex (Bcc). Ubonodin inhibits RNA polymerase, but only select strains were susceptible, indicating that having a conserved cellular target does not guarantee activity. Given the cytoplasmic target, we hypothesized that cellular uptake of ubonodin determines susceptibility. Although Bcc strains harbor numerous nutrient uptake systems, these organisms lack close homologues of the single known lasso peptide membrane receptor, FhuA. Thus, a straightforward homology-driven approach failed to uncover the identity of the ubonodin transporter(s). Here, we used phenotype-guided comparative genomics to identify genes uniquely associated with ubonodin-susceptible Bcc strains, leading to the identification of PupB as the ubonodin outer membrane (OM) receptor in Burkholderia. The loss of PupB renders B. cepacia resistant to ubonodin, whereas expressing PupB sensitizes a resistant strain. We also examine how a conserved iron-regulated transcriptional pathway controls PupB to further tune ubonodin susceptibility. PupB is only the second lasso peptide OM receptor to be uncovered and the first outside of enterobacteria. Finally, we elucidate the full transport pathway for ubonodin by identifying its inner membrane receptor YddA in Burkholderia. Our work provides a complete picture of the mode of action of ubonodin and establishes a general framework for deciphering the transport pathways of other natural products with cytoplasmic targets.
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Affiliation(s)
- Truc Do
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - Alina Thokkadam
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - Robert Leach
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
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28
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Jiang F, Zhou H, Shen H. Identification of Critical Biomarkers and Immune Infiltration in Rheumatoid Arthritis Based on WGCNA and LASSO Algorithm. Front Immunol 2022; 13:925695. [PMID: 35844557 PMCID: PMC9277141 DOI: 10.3389/fimmu.2022.925695] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/27/2022] [Indexed: 12/29/2022] Open
Abstract
Rheumatoid arthritis(RA) is the most common inflammatory arthritis, and a significant cause of morbidity and mortality. RA patients' synovial inflammation contains a variety of genes and signalling pathways that are poorly understood. It was the goal of this research to discover the major biomarkers related to the course of RA and how they connect to immune cell infiltration. The Gene Expression Omnibus was used to download gene microarray data. Differential expression analysis, weighted gene co-expression network analysis (WGCNA), and least absolute shrinkage and selection operator (LASSO) regression were used to identify hub markers for RA. Single-sample GSEA was used to examine the infiltration levels of 28 immune cells and their connection to hub gene markers. The hub genes' expression in RA-HFLS and HFLS cells was verified by RT-PCR. The CCK-8 assay was applied to determine the roles of hub genes in RA. In this study, we identified 21 differentially expressed genes (DEGs) in RA. WGCNA yielded two co-expression modules, one of which exhibited the strongest connection with RA. Using a combination of differential genes, a total of 6 intersecting genes was discovered. Six hub genes were identified as possible biomarkers for RA after a lasso analysis was performed on the data. Three hub genes, CKS2, CSTA, and LY96, were found to have high diagnostic value using ROC curve analysis. They were shown to be closely related to the concentrations of several immune cells. RT-PCR confirmed that the expressions of CKS2, CSTA and LY96 were distinctly upregulated in RA-HFLS cells compared with HFLS cells. More importantly, knockdown of CKS2 suppressed the proliferation of RA-HFLS cells. Overall, to help diagnose and treat RA, it's expected that CKS2, CSTA, and LY96 will be available, and the aforementioned infiltration of immune cells may have a significant impact on the onset and progression of the disease.
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Affiliation(s)
- Fan Jiang
- Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of General Medicine, Beijing Luhe Hospital, Capital Medical University, Beijing, China
| | - Hongyi Zhou
- Department of Anesthesiology, Tongzhou Maternal and Child Health Hospital of Beijing, Beijing, China
| | - Haili Shen
- Department of Rheumatology, Lanzhou University Second Hospital, Lanzhou, China
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29
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Wu WH, Guo J, Zhang L, Zhang WB, Gao W. Peptide/protein-based macrocycles: from biological synthesis to biomedical applications. RSC Chem Biol 2022; 3:815-829. [PMID: 35866174 PMCID: PMC9257627 DOI: 10.1039/d1cb00246e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/08/2022] [Indexed: 11/21/2022] Open
Abstract
Living organisms have evolved cyclic or multicyclic peptides and proteins with enhanced stability and high bioactivity superior to their linear counterparts for diverse purposes. Herein, we review recent progress in applying this concept to artificial peptides and proteins to exploit the functional benefits of these macrocycles. Not only have simple cyclic forms been prepared, numerous macrocycle variants, such as knots and links, have also been developed. The chemical tools and synthetic strategies are summarized for the biological synthesis of these macrocycles, demonstrating it as a powerful alternative to chemical synthesis. Its further application to therapeutic peptides/proteins has led to biomedicines with profoundly improved pharmaceutical performances. Finally, we present our perspectives on the field and its future developments.
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Affiliation(s)
- Wen-Hao Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Jianwen Guo
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology Beijing 100081 P. R. China
- Biomedical Engineering Department, Peking University Beijing 100191 P. R. China
| | - Longshuai Zhang
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology Beijing 100081 P. R. China
- Biomedical Engineering Department, Peking University Beijing 100191 P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Weiping Gao
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology Beijing 100081 P. R. China
- Biomedical Engineering Department, Peking University Beijing 100191 P. R. China
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30
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Unusual Post-Translational Modifications in the Biosynthesis of Lasso Peptides. Int J Mol Sci 2022; 23:ijms23137231. [PMID: 35806232 PMCID: PMC9266682 DOI: 10.3390/ijms23137231] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022] Open
Abstract
Lasso peptides are a subclass of ribosomally synthesized and post-translationally modified peptides (RiPPs) and feature the threaded, lariat knot-like topology. The basic post-translational modifications (PTMs) of lasso peptide contain two steps, including the leader peptide removal of the ribosome-derived linear precursor peptide by an ATP-dependent cysteine protease, and the macrolactam cyclization by an ATP-dependent macrolactam synthetase. Recently, advanced bioinformatic tools combined with genome mining have paved the way to uncover a rapidly growing number of lasso peptides as well as a series of PTMs other than the general class-defining processes. Despite abundant reviews focusing on lasso peptide discoveries, structures, properties, and physiological functionalities, few summaries concerned their unique PTMs. In this review, we summarized all the unique PTMs of lasso peptides uncovered to date, shedding light on the related investigations in the future.
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31
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Alfi A, Popov A, Kumar A, Zhang KYJ, Dubiley S, Severinov K, Tagami S. Cell-Free Mutant Analysis Combined with Structure Prediction of a Lasso Peptide Biosynthetic Protease B2. ACS Synth Biol 2022; 11:2022-2028. [PMID: 35674818 DOI: 10.1021/acssynbio.2c00176] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biochemical and structural analyses of purified proteins are essential for the understanding of their properties. However, many proteins are unstable and difficult to purify, hindering their characterization. The B2 proteins of the lasso peptide biosynthetic pathways are cysteine proteases that cleave precursor peptides during the maturation process. The B2 proteins are poorly soluble, and no experimentally solved structures are available. Here, we performed a rapid semicomprehensive mutational analysis of the B2 protein from the thermophilic actinobacterium, Thermobifida fusca (FusB2), using a cell-free transcription/translation system, and compared the results with the structure prediction by AlphaFold2. Analysis of 34 FusB2 mutants with substitutions of hydrophobic residues confirmed the accuracy of the predicted structure, and revealed a hydrophobic patch on the protein surface, which likely serves as the binding site of the partner protein, FusB1. Our results suggest that the combination of rapid cell-free mutant analyses with precise structure predictions can greatly accelerate structure-function research of proteins for which no structures are available.
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Affiliation(s)
- Almasul Alfi
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Aleksandr Popov
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
| | - Ashutosh Kumar
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kam Y J Zhang
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Svetlana Dubiley
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Konstantin Severinov
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia.,Waksman Institute for Microbiology, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
| | - Shunsuke Tagami
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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32
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Rosenthal E, Potnis N, Bull CT. Comparative Genomic Analysis of the Lettuce Bacterial Leaf Spot Pathogen, Xanthomonas hortorum pv. vitians, to Investigate Race Specificity. Front Microbiol 2022; 13:840311. [PMID: 35516433 PMCID: PMC9062649 DOI: 10.3389/fmicb.2022.840311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/09/2022] [Indexed: 01/01/2023] Open
Abstract
Bacterial leaf spot (BLS) of lettuce caused by Xanthomonas hortorum pv. vitians (Xhv) was first described over 100 years ago and remains a significant threat to lettuce cultivation today. This study investigated the genetic relatedness of the Xhv strains and the possible genetic sources of this race-specific pathogenicity. Whole genome sequences of eighteen Xhv strains representing the three races, along with eight related Xanthomonas strains, were included in the analysis. A maximum likelihood phylogeny based on concatenated whole genome SNPs confirmed previous results describing two major lineages of Xhv strains. Gene clusters encoding secretion systems, secondary metabolites, and bacteriocins were assessed to identify putative virulence factors that distinguish the Xhv races. Genome sequences were mined for effector genes, which have been shown to be involved in race specificity in other systems. Two effectors identified in this study, xopAQ and the novel variant xopAF2, were revealed as possible mediators of a gene-for-gene interaction between Xhv race 1 and 3 strains and wild lettuce Lactuca serriola ARM-09-161-10-1. Transposase sequence identified downstream of xopAF2 and prophage sequence found nearby within Xhv race 1 and 3 insertion sequences suggest that this gene may have been acquired through phage-mediated gene transfer. No other factors were identified from these analyses that distinguish the Xhv races.
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Affiliation(s)
- Emma Rosenthal
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United States
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United States
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33
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Hills E, Woodward TJ, Fields S, Brandsen BM. Comprehensive Mutational Analysis of the Lasso Peptide Klebsidin. ACS Chem Biol 2022; 17:998-1010. [PMID: 35315272 PMCID: PMC9976627 DOI: 10.1021/acschembio.2c00148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Antibiotic resistance is a growing threat to public health, making the development of antibiotics of critical importance. One promising class of potential new antibiotics are ribosomally synthesized and post-translationally modified peptides (RiPPs), which include klebsidin, a lasso peptide from Klebsiella pneumoniae that inhibits certain bacterial RNA polymerases. We develop a high-throughput assay based on growth inhibition of Escherichia coli to analyze the mutational tolerance of klebsidin. We transform a library of klebsidin variants into E. coli and use next-generation DNA sequencing to count the frequency of each variant before and after its expression, thereby generating functional scores for 320 of 361 single amino acid changes. We identify multiple positions in the macrocyclic ring and the C-terminal tail region of klebsidin that are intolerant to mutation, as well as positions in the loop region that are highly tolerant to mutation. Characterization of selected peptide variants scored as active reveals that each adopts a threaded lasso conformation; active loop variants applied extracellularly as peptides slow the growth of E. coli and K. pneumoniae. We generate an E. coli strain with a mutation in RNA polymerase that confers resistance to klebsidin and similarly carry out a selection with the klebsidin library. We identify a single variant, klebsidin F9Y, that maintains activity against the resistant E. coli when expressed intracellularly. This finding supports the utility of this method and suggests that comprehensive mutational analysis of lasso peptides can identify unique and potentially improved variants.
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Affiliation(s)
- Ethan Hills
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Tyler J. Woodward
- Department of Chemistry and Biochemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States,Department of Medicine, University of Washington, Seattle, Washington 98195, United States
| | - Benjamin M. Brandsen
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States,Department of Chemistry and Biochemistry, Creighton University, Omaha, Nebraska 68178, United States,Correspondence: Benjamin M. Brandsen, , ph. 402 280-2153
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Xiu H, Wang M, Fage CD, He Y, Niu X, Han M, Li F, An X, Fan H, Song L, Zheng G, Zhu S, Tong Y. Discovery and Characterization of Rubrinodin Provide Clues into the Evolution of Lasso Peptides. Biochemistry 2022; 61:595-607. [PMID: 35298141 DOI: 10.1021/acs.biochem.2c00029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lasso peptides are unique natural products that comprise a class of ribosomally synthesized and post-translationally modified peptides. Their defining three-dimensional structure is a lariat knot, in which the C-terminal tail is threaded through a macrolactam ring formed between the N-terminal amino group and an Asp or Glu side chain (i.e., an isopeptide bond). Recent genome mining strategies have revealed various types of lasso peptide biosynthetic gene clusters and have thus redefined the known chemical space of lasso peptides. To date, over 20 different types of these gene clusters have been discovered, including several different clades from Proteobacteria. Despite the diverse architectures of these gene clusters, which may or may not encode various tailoring enzymes, most currently known lasso peptides are synthesized by two discrete clades defined by the presence of an ATP-binding cassette transporter or its absence and (sometimes) concurrent appearance of an isopeptidase, raising questions about their evolutionary history. Herein, we discovered and characterized the lasso peptide rubrinodin, which is assembled by a gene cluster encoding both an ATP-binding cassette transporter and an isopeptidase. Our bioinformatics analyses of this and other representative cluster types provided new clues into the evolutionary history of lasso peptides. Furthermore, our structural and biochemical investigations of rubrinodin permitted the conversion of this thermolabile lasso peptide into a more thermostable scaffold.
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Affiliation(s)
- Huanhuan Xiu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Mengjiao Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | | | - Yile He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Xiaogang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meng Han
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| | - Fei Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Xiaoping An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Guojun Zheng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Shaozhou Zhu
- National Institutes for Food and Drug Control, Beijing 102629, People's Republic of China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
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Schröder HV, Stadlmeier M, Wühr M, Link AJ. The Shuttling Cascade in Lasso Peptide Benenodin-1 is Controlled by Non-Covalent Interactions. Chemistry 2022; 28:e202103615. [PMID: 34797593 PMCID: PMC8792204 DOI: 10.1002/chem.202103615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Indexed: 01/26/2023]
Abstract
The lasso peptide benenodin-1, a naturally occurring and bacterially produced [1]rotaxane, undergoes a reversible zip tie-like motion under heat activation, in which a peptidic wheel stepwise translates along a molecular thread in a cascade of "tail/loop pulling" equilibria. Conformational and structural analyses of four translational isomers, in solution and in the gas phase, reveal that the equilibrium distribution is controlled by mechanical and non-covalent forces within the lasso peptide. Furthermore, each dynamic pulling step is accompanied by a major restructuring of the intramolecular hydrogen bonding network between wheel and thread, which affects the peptide's physico-chemical properties.
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Affiliation(s)
- Hendrik V. Schröder
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
| | - Michael Stadlmeier
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Martin Wühr
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - A. James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544,Department of Chemistry and Department of Molecular Biology, Princeton University, Princeton, NJ 08544
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Paenibacillus piscarius sp. nov., a novel nitrogen-fixing species isolated from the gut of the armored catfish Parotocinclus maculicauda. Antonie van Leeuwenhoek 2022; 115:155-165. [PMID: 34993761 DOI: 10.1007/s10482-021-01694-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/22/2021] [Indexed: 10/19/2022]
Abstract
A Gram-positive, nitrogen-fixing and endospore-forming strain, designated P121T, was isolated from the gut of the armored catfish (Parotocinclus maculicauda) and identified as a member of the genus Paenibacillus based on the sequences of the 16S rRNA encoding gene, rpoB, gyrB and nifH genes and phenotypic analyses. The most closely related species to strain P121T were Paenibacillus rhizoplanae DSM 103993T, Paenibacillus silagei DSM 101953T and Paenibacillus borealis DSM 13188T, with similarity values of 98.9, 98.3 and 97.6%, respectively, based on 16S rRNA gene sequences. Genome sequencing revealed a genome size of 7,513,698 bp, DNA G + C content of 53.9 mol% and the presence of the structural nitrogenase encoding genes (nifK, nifD and nifH) and of other nif genes necessary for nitrogen fixation. Digital DNA-DNA hybridization (dDDH) experiments and average nucleotide identity (ANI) analyses between strain P121T and the type strains of the closest species demonstrated that the highest values were below the thresholds of 70% dDDH (42.3% with P. borealis) and 95% ANI (84.28% with P. silagei) for bacterial species delineation, indicating that strain P121T represents a distinct species. Its major cellular fatty acid was anteiso-C15:0 (42.4%), and the major isoprenoid quinone was MK-7. Based on physiological, genomic, biochemical and chemotaxonomic characteristics, we propose that strain P121T represents a novel species for which the name Paenibacillus piscarius sp. nov. is proposed (type strain = DSM 25072 = LFB-Fiocruz 1636).
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Negri T, Mantri S, Angelov A, Peter S, Muth G, Eustáquio AS, Ziemert N. A rapid and efficient strategy to identify and recover biosynthetic gene clusters from soil metagenomes. Appl Microbiol Biotechnol 2022; 106:3293-3306. [PMID: 35435454 PMCID: PMC9064862 DOI: 10.1007/s00253-022-11917-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 11/30/2022]
Abstract
Culture-independent metagenomic approaches offer a promising solution to the discovery of therapeutically relevant compounds such as antibiotics by enabling access to the hidden biosynthetic potential of microorganisms. These strategies, however, often entail laborious, multi-step, and time-consuming procedures to recover the biosynthetic gene clusters (BGCs) from soil metagenomes for subsequent heterologous expression. Here, we developed an efficient method we called single Nanopore read cluster mining (SNRCM), which enables the fast recovery of complete BGCs from a soil metagenome using long- and short-read sequencing. A metagenomic fosmid library of 83,700 clones was generated and sequenced using Nanopore as well as Illumina technologies. Hybrid assembled contigs of the sequenced fosmid library were subsequently analyzed to identify BGCs encoding secondary metabolites. Using SNRCM, we aligned the identified BGCs directly to Nanopore long-reads and were able to detect complete BGCs on single fosmids. This enabled us to select for and recover BGCs of interest for subsequent heterologous expression attempts. Additionally, the sequencing data of the fosmid library and its corresponding metagenomic DNA enabled us to assemble and recover a large nonribosomal peptide synthetase (NRPS) BGC from three different fosmids of our library and to directly amplify and recover a complete lasso peptide BGC from the high-quality metagenomic DNA. Overall, the strategies presented here provide a useful tool for accelerating and facilitating the identification and production of potentially interesting bioactive compounds from soil metagenomes. KEY POINTS: • An efficient approach for the recovery of BGCs from soil metagenomes was developed to facilitate natural product discovery. • A fosmid library was constructed from soil metagenomic HMW DNA and sequenced via Illumina and Nanopore. • Nanopore long-reads enabled the direct identification and recovery of complete BGCs on single fosmids.
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Affiliation(s)
- Timo Negri
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
| | - Shrikant Mantri
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany ,Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany ,Computational Biology Laboratory, National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab India
| | - Angel Angelov
- NGS Competence Center Tübingen (NCCT), Institut Für Medizinische Mikrobiologie Und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Silke Peter
- NGS Competence Center Tübingen (NCCT), Institut Für Medizinische Mikrobiologie Und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Günther Muth
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
| | | | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany. .,Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany. .,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
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Tochilina A, Belova I, Ilyicheva T, Marchenko V, Zhirnov V, Molodtsova S, Ikonnikov A, Muhkina I, Blagonravova A, Soloveva I. Genome Features of Probiotic Bifidobacteria Determining Their Strain-Specific Properties. Sovrem Tekhnologii Med 2022; 14:36-43. [PMID: 37181836 PMCID: PMC10171061 DOI: 10.17691/stm2022.14.5.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Indexed: 05/16/2023] Open
Abstract
The aim of the study was to analyze the genome features of the probiotic strains Bifidobacterium longum 379, Bifidobacterium bifidum 1, and Bifidobacterium bifidum 791 and study their antiviral activity. Materials and Methods Whole genome sequencing of three strains of bifidobacteria was performed on the MiSeq platform (Illumina Inc., USA). The genomes were annotated using the Prokka v. 1.11 utility and RAST genomic server. The individual genetic determinants were searched using the ResFinder 3.2, PathogenFinder, PlasmidFinder, RAST, and Bagel 4 software. The antiviral activity of the strains against influenza A viruses was studied using MDCK cells (Madin-Darby canine kidney cells), the epidemic strain of influenza A/Lipetsk/1V/2018 (H1N1 pdm09) (EPI_ISL_332798), the highly pathogenic avian influenza virus A/common gull/Saratov/1676/2018 (H5N6) strain (EPI_ISL_336925), and neutral red vital dye. Results The genomes of all studied strains contained determinants responsible for utilization of carbohydrates of plant origin; the genes of key enzymes for the synthesis of tryptophan and folic acid are present in the genomes of B. longum 379 and B. bifidum 791. A feature of the B. bifidum 791 genome is the presence of determinants responsible for the synthesis of thermostable type I bacteriocins - flavucin and lasso peptide. The B. bifidum 791 strain was found to show pronounced antiviral activity against both the strains of influenza A, the supernatant of which suppressed viral replication in vitro up to a dilution of 1:8, and the cells inhibited viral reproduction up to a concentration of 6·106 CFU/ml. Conclusion The analysis of complete genomes of B. longum 379, B. bifidum 1, and B. bifidum 791 showed features that determine their strain-specific properties, the findings on which were previously made empirically based on indirect signs. In the genomes of B. longum 379 and B. bifidum 791 strains, in contrast to B. bifidum 1 strain, key enzymes for the synthesis of tryptophan and folic acid were found. These substances have an impact on the human body in many ways, including having a thymoleptic effect (reducing emotional stress, irritability, anxiety, eliminating lethargy, apathy, melancholy, anxiety) and regulating cognitive activity. The presence of determinants responsible for the synthesis of thermostable type I bacteriocins in the genome of B. bifidum 791 strain determines its pronounced antiviral activity.
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Affiliation(s)
- A.G. Tochilina
- Senior Researcher, Laboratory of Human Microbiome and Means of Its Correction; Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology of Rospotrebnadzor (Russian Federal Consumer Rights Protection and Human Health Control Service), 71 Malaya Yamskaya St., Nizhny Novgorod, 603950, Russia; Associate Professor, Department of Epidemiology, Microbiology and Evidence-Based Medicine; Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
- Corresponding author: Anna G. Tochilina, e-mail:
| | - I.V. Belova
- Leading Researcher, Laboratory of Human Microbiome and Means of Its Correction; Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology of Rospotrebnadzor (Russian Federal Consumer Rights Protection and Human Health Control Service), 71 Malaya Yamskaya St., Nizhny Novgorod, 603950, Russia; Associate Professor, Department of Epidemiology, Microbiology and Evidence-Based Medicine; Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
| | - T.N. Ilyicheva
- Leading Researcher, Department of Zoonotic Infections and Influenza; State Research Center of Virology and Biotechnology “Vector” of Rospotrebnadzor, Koltsovo, Novosibirsk Region, 630559, Russia
| | - V.Yu. Marchenko
- Leading Researcher, Department of Zoonotic Infections and Influenza; State Research Center of Virology and Biotechnology “Vector” of Rospotrebnadzor, Koltsovo, Novosibirsk Region, 630559, Russia
| | - V.A. Zhirnov
- Researcher, Laboratory of Human Microbiome and Means of Its Correction; Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology of Rospotrebnadzor (Russian Federal Consumer Rights Protection and Human Health Control Service), 71 Malaya Yamskaya St., Nizhny Novgorod, 603950, Russia
| | - S.B. Molodtsova
- Researcher, Laboratory of Human Microbiome and Means of Its Correction; Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology of Rospotrebnadzor (Russian Federal Consumer Rights Protection and Human Health Control Service), 71 Malaya Yamskaya St., Nizhny Novgorod, 603950, Russia
| | - A.V. Ikonnikov
- Research Assistant; Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
| | - I.V. Muhkina
- Professor, Director of the Institute of Fundamental Medicine; Head of the Department of Normal Physiology named after N.Y. Belenkov; Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
| | - A.S. Blagonravova
- Head of the Department of Clinical Laboratory Diagnostics; Professor, Department of Epidemiology, Microbiology and Evidence-Based Medicine; Vice-Rector for Science; Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
| | - I.V. Soloveva
- Associate Professor, Leading Researcher, Head of the Laboratory of Human Microbiome and Means of its Correction; Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology of Rospotrebnadzor (Russian Federal Consumer Rights Protection and Human Health Control Service), 71 Malaya Yamskaya St., Nizhny Novgorod, 603950, Russia
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Pilon S, Jørgensen SI, van Maarseveen JH. Covalent [2]Catenane and [2]Rotaxane Synthesis via a δ-Amino Acid Template. ACS ORGANIC & INORGANIC AU 2021; 1:37-42. [PMID: 34870280 PMCID: PMC8640993 DOI: 10.1021/acsorginorgau.1c00017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Indexed: 11/29/2022]
Abstract
![]()
Despite the advances
in the synthesis of mechanically interlocked
molecules, a generally applicable approach to interlocked natural
products, such as lasso peptides, is yet to be formulated. While amino
acid sequences have been introduced into several rotaxanes, the key
structural components have always been dictated by the method used
for supramolecular preorganization. In this work, we report the use
of an ester-functionalized, aromatic δ-amino acid as the central
covalent templating unit in the synthesis of both a [2]catenane and
a [2]rotaxane from the same multimacrocyclic intermediate. This represents
a key step toward future synthetic peptide-based interlocked products.
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Affiliation(s)
- Simone Pilon
- Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Steen Ingemann Jørgensen
- Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Jan H. van Maarseveen
- Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
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Gauthier M, Waelès P, Coutrot F. Post-Synthetic Macrocyclization of Rotaxane Building Blocks. Chempluschem 2021; 87:e202100458. [PMID: 34811956 DOI: 10.1002/cplu.202100458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/11/2021] [Indexed: 11/06/2022]
Abstract
Although not often encountered, cyclic interlocked molecules are appealing molecular targets because of their restrained tridimensional structure which is related to both the cyclic and interlocked shapes. Interlocked molecules such as rotaxane building blocks may be good candidates for post-synthetic intramolecular cyclization if the preservation of the mechanical bond ensures the interlocked architecture throughout the reaction. This is obviously the case if the modification does not involve the cleavage of either the macrocycle's main chain or the encircled part of the axle. However, among the post-synthetic reactions, the chemical linkage between two reactive sites belonging to embedded elements of rotaxanes still consists of an underexploited route to interlocked cyclic molecules. This Review lists the rare examples of macrocyclization through chemical connection between reactive sites belonging to a surrounding macrocycle and/or an encircled axle of interlocked rotaxanes.
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Affiliation(s)
- Maxime Gauthier
- Supramolecular Machines and Architectures Team, IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Philip Waelès
- Supramolecular Machines and Architectures Team, IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Frédéric Coutrot
- Supramolecular Machines and Architectures Team, IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
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Wu WH, Bai X, Shao Y, Yang C, Wei J, Wei W, Zhang WB. Higher Order Protein Catenation Leads to an Artificial Antibody with Enhanced Affinity and In Vivo Stability. J Am Chem Soc 2021; 143:18029-18040. [PMID: 34664942 DOI: 10.1021/jacs.1c06169] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The chemical topology is a unique dimension for protein engineering, yet the topological diversity and architectural complexity of proteins remain largely untapped. Herein, we report the biosynthesis of complex topological proteins using a rationally engineered, cross-entwining peptide heterodimer motif derived from p53dim (an entangled homodimeric mutant of the tetramerization domain of the tumor suppressor protein p53). The incorporation of an electrostatic interaction at specific sites converts the p53dim homodimer motif into a pair of heterodimer motifs with high specificity for directing chain entanglement upon folding. Its combination with split-intein-mediated ligation and/or SpyTag/SpyCatcher chemistry facilitates the programmed synthesis of protein heterocatenane or [n]catenanes in cells, leading to a general and modular approach to complex protein catenanes containing various proteins of interest. Concatenation enhances not only the target protein's affinity but also the in vivo stability as shown by its prolonged circulation time in blood. As a proof of concept, artificial antibodies have been developed by embedding a human epidermal growth factor receptor 2-specific affibody onto the [n]catenane scaffolds and shown to exhibit a higher affinity and a better pharmacokinetic profile than the wild-type affibody. These results suggest that topology engineering holds great promise in the development of therapeutic proteins.
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Affiliation(s)
- Wen-Hao Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Xilin Bai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Yu Shao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Chao Yang
- College of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang, Henan 455000, P. R. China
| | - Jingjing Wei
- College of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang, Henan 455000, P. R. China
| | - Wei Wei
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
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Heilbronner S, Krismer B, Brötz-Oesterhelt H, Peschel A. The microbiome-shaping roles of bacteriocins. Nat Rev Microbiol 2021; 19:726-739. [PMID: 34075213 DOI: 10.1038/s41579-021-00569-w] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2021] [Indexed: 02/05/2023]
Abstract
The microbiomes on human body surfaces affect health in multiple ways. They include not only commensal or mutualistic bacteria but also potentially pathogenic bacteria, which can enter sterile tissues to cause invasive infection. Many commensal bacteria produce small antibacterial molecules termed bacteriocins that have the capacity to eliminate specific colonizing pathogens; as such, bacteriocins have attracted increased attention as potential microbiome-editing tools. Metagenome-based and activity-based screening approaches have strongly expanded our knowledge of the abundance and diversity of bacteriocin biosynthetic gene clusters and the properties of a continuously growing list of bacteriocin classes. The dynamic acquisition, diversification or loss of bacteriocin genes can shape the fitness of a bacterial strain that is in competition with bacteriocin-susceptible bacteria. However, a bacteriocin can only provide a competitive advantage if its fitness benefit exceeds the metabolic cost of production, if it spares crucial mutualistic partner strains and if major competitors cannot develop resistance. In contrast to most currently available antibiotics, many bacteriocins have only narrow activity ranges and could be attractive agents for precision therapy and prevention of infections. A common scientific strategy involving multiple disciplines is needed to uncover the immense potential of microbiome-shaping bacteriocins.
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Affiliation(s)
- Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany. .,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
| | - Bernhard Krismer
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, Department of Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany. .,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
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Wang M, Fage CD, He Y, Mi J, Yang Y, Li F, An X, Fan H, Song L, Zhu S, Tong Y. Recent Advances and Perspectives on Expanding the Chemical Diversity of Lasso Peptides. Front Bioeng Biotechnol 2021; 9:741364. [PMID: 34631682 PMCID: PMC8498205 DOI: 10.3389/fbioe.2021.741364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/13/2021] [Indexed: 12/16/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing family of natural products that exhibit a range of structures and bioactivities. Initially assembled from the twenty proteinogenic amino acids in a ribosome-dependent manner, RiPPs assume their peculiar bioactive structures through various post-translational modifications. The essential modifications representative of each subfamily of RiPP are performed on a precursor peptide by the so-called processing enzymes; however, various tailoring enzymes can also embellish the precursor peptide or processed peptide with additional functional groups. Lasso peptides are an interesting subfamily of RiPPs characterized by their unique lariat knot-like structure, wherein the C-terminal tail is inserted through a macrolactam ring fused by an isopeptide bond between the N-terminal amino group and an acidic side chain. Until recently, relatively few lasso peptides were found to be tailored with extra functional groups. Nevertheless, the development of new routes to diversify lasso peptides and thus introduce novel or enhanced biological, medicinally relevant, or catalytic properties is appealing. In this review, we highlight several strategies through which lasso peptides have been successfully modified and provide a brief overview of the latest findings on the tailoring of these peptides. We also propose future directions for lasso peptide tailoring as well as potential applications for these peptides in hybrid catalyst design.
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Affiliation(s)
- Mengjiao Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Christopher D Fage
- Department of Chemistry, University of Warwick, Coventry, United Kingdom
| | - Yile He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jinhui Mi
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yang Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Fei Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.,Clinical Laboratory Center, Taian City Central Hospital, Taian, China
| | - Xiaoping An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shaozhou Zhu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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44
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van Maarseveen JH, Cornelissen MD, Pilon S. Covalently Templated Syntheses of Mechanically Interlocked Molecules. SYNTHESIS-STUTTGART 2021. [DOI: 10.1055/a-1665-4650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractMechanically interlocked molecules (MiMs), such as catenanes and rotaxanes, exhibit unique properties due to the mechanical bond which unites their components. The translational and rotational freedom present in these compounds may be harnessed to create stimuli-responsive MiMs, which find potential application as artificial molecular machines. Mechanically interlocked structures such as lasso peptides have also been found in nature, making MiMs promising albeit elusive targets for drug discovery. Although the first syntheses of MiMs were based on covalent strategies, approaches based on non-covalent interactions rose to prominence thereafter and have remained dominant. Non-covalent strategies are generally short and efficient, but do require particular structural motifs which are difficult to alter. In a covalent approach, MiMs can be more easily modified while the components may have increased rotational and translational freedom. Both approaches have complementary merits and combining the unmatched efficiency of non-covalent approaches with the scope of covalent syntheses may open up vast opportunities. In this review, recent covalently templated syntheses of MiMs are discussed to show their complementarity and anticipate future developments in this field.1 Introduction2 Tetrahedral Templates2.1 A Carbonate Template for Non-Rusty Catenanes2.2 All-Benzene Catenanes on a Silicon Template2.3 Backfolding from Quaternary Carbon3 Planar Templates3.1 Rotaxanes Constructed in a Ring3.2 Hydrindacene as a Dynamic Covalent Template3.3 Templating on Tri- and Tetrasubstituted Benzenes4 Conclusion
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45
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Liu T, Ma X, Yu J, Yang W, Wang G, Wang Z, Ge Y, Song J, Han H, Zhang W, Yang D, Liu X, Ma M. Rational generation of lasso peptides based on biosynthetic gene mutations and site-selective chemical modifications. Chem Sci 2021; 12:12353-12364. [PMID: 34603665 PMCID: PMC8480316 DOI: 10.1039/d1sc02695j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/10/2021] [Indexed: 12/14/2022] Open
Abstract
Lasso peptides are a unique family of natural products whose structures feature a specific threaded fold, which confers these peptides the resistance to thermal and proteolytic degradation. This stability gives lasso peptides excellent pharmacokinetic properties, which together with their diverse reported bioactivities have garnered extensive attention because of their drug development potential. Notably, the threaded fold has proven quite inaccessible by chemical synthesis, which has hindered efficient generation of structurally diverse lasso peptides. We herein report the discovery of a new lasso peptide stlassin (1) by gene activation based on a Streptomyces heterologous expression system. Site-directed mutagenesis on the precursor peptide-encoding gene is carried out systematically, generating 17 stlassin derivatives (2–17 and 21) with residue-replacements at specific positions of 1. The solution NMR structures of 1, 3, 4, 14 and 16 are determined, supporting structural comparisons that ultimately enabled the rational production of disulfide bond-containing derivatives 18 and 19, whose structures do not belong to any of the four classes currently used to classify lasso peptides. Several site-selective chemical modifications are first applied on 16 and 21, efficiently generating new derivatives (20, 22–27) whose structures bear various decorations beyond the peptidyl monotonicity. The high production yields of these stlassin derivatives facilitate biological assays, which show that 1, 4, 16, 20, 21 and 24 possess antagonistic activities against the binding of lipopolysaccharides to toll-like receptor 4 (TLR4). These results demonstrate proof-of-concept for the combined mutational/chemical generation of lasso peptide libraries to support drug lead development. A new class II lasso peptide stlassin (1) was discovered and stlassin derivatives (2–27) were rationally generated by biosynthetic gene mutations and site-selective chemical modifications, expanding the structural diversity of lasso peptides.![]()
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Affiliation(s)
- Tan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xiaojie Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Jiahui Yu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Wensheng Yang
- School of Medicine, Tongji University 1239 Siping Road Shanghai 200092 China
| | - Guiyang Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Zhengdong Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Yuanjie Ge
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Juan Song
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Hua Han
- School of Medicine, Tongji University 1239 Siping Road Shanghai 200092 China
| | - Wen Zhang
- School of Medicine, Tongji University 1239 Siping Road Shanghai 200092 China
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xuehui Liu
- CAS Research Platform for Protein Sciences, Institute of Biophysics, Chinese Academy of Sciences 15 Datun Road, Chao-yang District Beijing 100101 China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
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46
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Fathizadeh H, Pakdel F, Saffari M, Esmaeili DD, Momen-Heravi M, Dao S, Ganbarov K, Kafil HS. Bacteriocins: Recent advances in application as an antimicrobial alternative. Curr Pharm Biotechnol 2021; 23:1028-1040. [PMID: 34493194 DOI: 10.2174/1389201022666210907121254] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 11/22/2022]
Abstract
Due to the emergence and development of antibiotic resistance in the treatment of bacterial infections, efforts to discover new antimicrobial agents have increased. One of these antimicrobial agents is a compound produced by a large number of bacteria called bacteriocin. Bacteriocins are small ribosomal polypeptides that can exert their antibacterial effects against bacteria close to their producer strain or even non-closely strains. Adequate knowledge of the structure and functional mechanisms of bacteriocins and their spectrum of activity, as well as knowledge of the mechanisms of possible resistance to these compounds will lead to further development of their use as an alternative to antibiotics. Furthermore, most bacteria that live in the gastrointestinal tract (GIT) have the ability to produce bacteriocins, which spread throughout the GIT. Despite antimicrobial studies in vitro, our knowledge of bacteriocins in the GIT and the migration of these bacteriocins from the epithelial barrier is low. Hence, in this study, we reviewed general information about bacteriocins, such as classification, mechanism of action and resistance, emphasizing their presence, stability, and spectrum of activity in the GIT.
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Affiliation(s)
- Hadis Fathizadeh
- Department of Microbiology and immunology, Kashan University of Medical Sciences, Kashan. Iran
| | - Farzaneh Pakdel
- Dental and Periodontal Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Mahmood Saffari
- Department of Microbiology and immunology, Kashan University of Medical Sciences, Kashan. Iran
| | - Davoud Davoud Esmaeili
- Department of Microbiology and Applied Microbiology Research Center, Systems biology and poisonings institute, Baqiyatallah University of Medical sciences, Tehran. Iran
| | - Mansooreh Momen-Heravi
- Infectious Diseases Research Center, Kashan University of Medical Sciences, Kashan. Iran
| | - Sounkalo Dao
- Faculté de Médecine, de Pharmacie et d'Odonto-Stomatologie (FMPOS), University of Bamako, Bamako. Mali
| | | | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, IR. Iran
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47
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Stariha LM, McCafferty DG. Discovery of the Class I Antimicrobial Lasso Peptide Arcumycin. Chembiochem 2021; 22:2632-2640. [PMID: 34133845 DOI: 10.1002/cbic.202100132] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/27/2021] [Indexed: 12/13/2022]
Abstract
Lasso peptides are a structurally diverse superfamily of conformationally constrained peptide natural products, of which a subset exhibits broad antimicrobial activity. Although advances in bioinformatics have increased our knowledge of strains harboring the biosynthetic machinery for lasso peptide production, relating peptide sequence to bioactivity remains a continuous challenge. To this end, genome mining investigation of Actinobacteria-produced antimicrobial lasso peptides was performed to correlate predicted structure with antibiotic activity. Bioinformatic evaluation revealed eight putative novel class I lasso peptide sequences. Fermentation of one of these hits, Streptomyces NRRL F-5639, resulted in the production of a novel class I lasso peptide, arcumycin. Arcumycin exhibited antibiotic activity against Gram-positive bacteria including Bacillus subtilis (4 μg/mL), Staphylococcus aureus (8 μg/mL), and Micrococcus luteus (8 μg/mL). Arcumycin treatment of B. subtilis liaI-β-gal promoter fusion reporter strain resulted in upregulation of the liaRS system by the promoter liaI, indicating arcumycin interferes with lipid II biosynthesis. Cumulatively, the results illustrate the relationship between phylogenetically related lasso peptides and their bioactivity as validated through the isolation, structural determination, and evaluation of bioactivity of the novel class I antimicrobial lasso peptide arcumycin.
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Affiliation(s)
- Lydia M Stariha
- Department of Chemistry, Duke University, Durham, NC, 27708-0346, USA
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48
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Cao L, Do T, Link AJ. Mechanisms of action of ribosomally synthesized and posttranslationally modified peptides (RiPPs). J Ind Microbiol Biotechnol 2021; 48:6121428. [PMID: 33928382 PMCID: PMC8183687 DOI: 10.1093/jimb/kuab005] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/22/2021] [Indexed: 12/19/2022]
Abstract
Natural products remain a critical source of medicines and drug leads. One of the most rapidly growing superclasses of natural products is RiPPs: ribosomally synthesized and posttranslationally modified peptides. RiPPs have rich and diverse bioactivities. This review highlights examples of the molecular mechanisms of action that underly those bioactivities. Particular emphasis is placed on RiPP/target interactions for which there is structural information. This detailed mechanism of action work is critical toward the development of RiPPs as therapeutics and can also be used to prioritize hits in RiPP genome mining studies.
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Affiliation(s)
- Li Cao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Truc Do
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - A James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.,Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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49
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Long T, Liu L, Tao Y, Zhang W, Quan J, Zheng J, Hegemann JD, Uesugi M, Yao W, Tian H, Wang H. Light‐Controlled Tyrosine Nitration of Proteins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Tengfang Long
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Lei Liu
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Youqi Tao
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Wanli Zhang
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals School of Life Science and Technology China Pharmaceutical University Nanjing 211198 China
| | - Jiale Quan
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals School of Life Science and Technology China Pharmaceutical University Nanjing 211198 China
| | - Jie Zheng
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Julian D. Hegemann
- Institute of Chemistry Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Motonari Uesugi
- Institute for Chemical Research and Institute for Integrated Cell-Material Sciences (WPI-iCeMS) Kyoto University Uji Kyoto 611-0011 Japan
- School of Pharmacy Fudan University Shanghai 201203 China
| | - Wenbing Yao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals School of Life Science and Technology China Pharmaceutical University Nanjing 211198 China
| | - Hong Tian
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals School of Life Science and Technology China Pharmaceutical University Nanjing 211198 China
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
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50
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Liu D, Rubin GM, Dhakal D, Chen M, Ding Y. Biocatalytic synthesis of peptidic natural products and related analogues. iScience 2021; 24:102512. [PMID: 34041453 PMCID: PMC8141463 DOI: 10.1016/j.isci.2021.102512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Peptidic natural products (PNPs) represent a rich source of lead compounds for the discovery and development of therapeutic agents for the treatment of a variety of diseases. However, the chemical synthesis of PNPs with diverse modifications for drug research is often faced with significant challenges, including the unavailability of constituent nonproteinogenic amino acids, inefficient cyclization protocols, and poor compatibility with other functional groups. Advances in the understanding of PNP biosynthesis and biocatalysis provide a promising, sustainable alternative for the synthesis of these compounds and their analogues. Here we discuss current progress in using native and engineered biosynthetic enzymes for the production of both ribosomally and nonribosomally synthesized peptides. In addition, we highlight new in vitro and in vivo approaches for the generation and screening of PNP libraries.
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Affiliation(s)
- Dake Liu
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Garret M. Rubin
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
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