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Pfeiffer IPM, Schröder MP, Mordhorst S. Opportunities and challenges of RiPP-based therapeutics. Nat Prod Rep 2024. [PMID: 38411278 DOI: 10.1039/d3np00057e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Covering: up to 2024Ribosomally synthesised and post-translationally modified peptides (RiPPs) comprise a substantial group of peptide natural products exhibiting noteworthy bioactivities ranging from antiinfective to anticancer and analgesic effects. Furthermore, RiPP biosynthetic pathways represent promising production routes for complex peptide drugs, and the RiPP technology is well-suited for peptide engineering to produce derivatives with specific functions. Thus, RiPP natural products possess features that render them potentially ideal candidates for drug discovery and development. Nonetheless, only a small number of RiPP-derived compounds have successfully reached the market thus far. This review initially outlines the therapeutic opportunities that RiPP-based compounds can offer, whilst subsequently discussing the limitations that require resolution in order to fully exploit the potential of RiPPs towards the development of innovative drugs.
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Affiliation(s)
- Isabel P-M Pfeiffer
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
| | - Maria-Paula Schröder
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
| | - Silja Mordhorst
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
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2
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Kumari S, Raj S, Babu MA, Bhatti GK, Bhatti JS. Antibody-drug conjugates in cancer therapy: innovations, challenges, and future directions. Arch Pharm Res 2024; 47:40-65. [PMID: 38153656 DOI: 10.1007/s12272-023-01479-6] [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: 06/27/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
The emergence of antibody-drug conjugates (ADCs) as a potential therapeutic avenue in cancer treatment has garnered significant attention. By combining the selective specificity of monoclonal antibodies with the cytotoxicity of drug molecules, ADCs aim to increase the therapeutic index, selectively targeting cancer cells while minimizing systemic toxicity. Various ADCs have been licensed for clinical usage, with ongoing research paving the way for additional options. However, the manufacture of ADCs faces several challenges. These include identifying suitable target antigens, enhancing antibodies, linkers, and payloads, and managing resistance mechanisms and side effects. This review focuses on the strategies to overcome these hurdles, such as site-specific conjugation techniques, novel antibody formats, and combination therapy. Our focus lies on current advancements in antibody engineering, linker technology, and cytotoxic payloads while addressing the challenges associated with ADC development. Furthermore, we explore the future potential of personalized medicine, leveraging individual patients' molecular profiles, to propel ADC treatments forward. As our understanding of the molecular mechanisms driving cancer progression continues to expand, we anticipate the development of new ADCs that offer more effective and personalized therapeutic options for cancer patients.
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Affiliation(s)
- Shivangi Kumari
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Sonam Raj
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - M Arockia Babu
- Institute of Pharmaceutical Research, GLA University, Mathura, U.P., India
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, India
| | - Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India.
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3
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Skellam E. Subcellular localization of fungal specialized metabolites. Fungal Biol Biotechnol 2022; 9:11. [PMID: 35614515 PMCID: PMC9134587 DOI: 10.1186/s40694-022-00140-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/10/2022] [Indexed: 01/07/2023] Open
Abstract
Fungal specialized metabolites play an important role in the environment and have impacted human health and survival significantly. These specialized metabolites are often the end product of a series of sequential and collaborating biosynthetic enzymes that reside within different subcellular compartments. A wide variety of methods have been developed to understand fungal specialized metabolite biosynthesis in terms of the chemical conversions and the biosynthetic enzymes required, however there are far fewer studies elucidating the compartmentalization of the same enzymes. This review illustrates the biosynthesis of specialized metabolites where the localization of all, or some, of the biosynthetic enzymes have been determined and describes the methods used to identify the sub-cellular localization.
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Affiliation(s)
- Elizabeth Skellam
- Department of Chemistry and BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX, 76201, USA.
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4
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Lamer T, van Belkum MJ, Wijewardane A, Chiorean S, Martin-Visscher LA, Vederas JC. SPI "sandwich": Combined SUMO-Peptide-Intein expression system and isolation procedure for improved stability and yield of peptides. Protein Sci 2022; 31:e4316. [PMID: 35481634 PMCID: PMC9045064 DOI: 10.1002/pro.4316] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/28/2022] [Accepted: 04/05/2022] [Indexed: 11/11/2022]
Abstract
Recombinant peptide production in Escherichia coli is often accomplished through cloning and expression of a fusion protein. The fusion protein partner generally has two requirements: (a) it contains an affinity tag to assist with purification and (b) it can be cleaved off to leave only the desired peptide sequence behind. Common soluble fusion partners include small ubiquitin-like modifier protein (SUMO), maltose-binding protein (MBP), glutathione S-transferase (GST), or intein proteins. However, heterologously expressed peptides can suffer from proteolytic degradation or instability. This degradation can pose a major issue for applications requiring a large amount of purified peptide, such as NMR structural assignments or biochemical assays. Improving peptide yield by testing various expression and isolation conditions requires a significant amount of effort and may not lead to improved results. Here, we cloned and expressed four different peptides as SUMO fusion proteins. These peptides (lactococcin A, leucocin A, faerocin MK, neopetrosiamide A) were truncated during expression and isolation as SUMO fusions, resulting in low yields of purified peptide. To prevent this degradation and improve yield, we designed a new expression system to create a "sandwiched" fusion protein of the form: His6 -SUMO-peptide-intein (SPI). These sandwiched peptides were more stable and protected against degradation, resulting in improved yields (up to 17-fold) under a set of standard expression and isolation procedures. This SPI expression system uses only two commercially available vectors and standard protein purification techniques, and therefore may offer an economical and facile route to improve yields for peptides that undergo degradation.
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Affiliation(s)
- Tess Lamer
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Marco J van Belkum
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Anjalee Wijewardane
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.,Department of Chemistry, The King's University, Edmonton, Alberta, Canada
| | - Sorina Chiorean
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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5
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Kessler SC, Chooi YH. Out for a RiPP: challenges and advances in genome mining of ribosomal peptides from fungi. Nat Prod Rep 2022; 39:222-230. [PMID: 34581394 DOI: 10.1039/d1np00048a] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Covering up to June 2021Ribosomally synthesized and post-translationally modified peptides (RiPPs) from fungi are an underexplored class of natural products, despite their propensity for diverse bioactivities and unique structural features. Surveys of fungal genomes for biosynthetic gene clusters encoding RiPPs have been limited in their scope due to our incomplete understanding of fungal RiPP biosynthesis. Through recent discoveries, along with earlier research, a clearer picture has been emerging of the biosynthetic principles that underpin fungal RiPP pathways. In this Highlight, we trace the approaches that have been used for discovering currently known fungal RiPPs and show that all of them can be assigned to one of three distinct families based on hallmarks of their biosynthesis, which are in turn imprinted on their corresponding gene clusters. We hope that our systematic exposition of fungal RiPP structural and gene cluster features will facilitate more comprehensive approaches to genome mining efforts in the future.
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Affiliation(s)
- Simon C Kessler
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
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6
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Rodríguez V. Insights into post-translational modification enzymes from RiPPs: A toolkit for applications in peptide synthesis. Biotechnol Adv 2022; 56:107908. [PMID: 35032597 DOI: 10.1016/j.biotechadv.2022.107908] [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: 03/05/2021] [Revised: 12/30/2021] [Accepted: 01/09/2022] [Indexed: 11/02/2022]
Abstract
The increasing length and complexity of peptide drug candidates foster the development of novel strategies for their manufacture, which should include sustainable and efficient technologies. In this context, including enzymatic catalysis in the production of peptide molecules has gained interest. Here, several enzymes from ribosomally synthesized and post-translationally modified peptides biosynthesis pathways are reviewed, with attention to their capacity to introduce stability-promoting structural features on peptides, providing an initial framework towards their use in therapeutic peptide production processes.
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Affiliation(s)
- Vida Rodríguez
- Faculty of Engineering, Science and Technology, Bernardo O'Higgins University, Viel 1497, Santiago, Chile.
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7
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Li H, Tian Y, Menolli N, Ye L, Karunarathna SC, Perez-Moreno J, Rahman MM, Rashid MH, Phengsintham P, Rizal L, Kasuya T, Lim YW, Dutta AK, Khalid AN, Huyen LT, Balolong MP, Baruah G, Madawala S, Thongklang N, Hyde KD, Kirk PM, Xu J, Sheng J, Boa E, Mortimer PE. Reviewing the world's edible mushroom species: A new evidence-based classification system. Compr Rev Food Sci Food Saf 2021; 20:1982-2014. [PMID: 33599116 DOI: 10.1111/1541-4337.12708] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 12/04/2020] [Accepted: 12/21/2020] [Indexed: 12/16/2022]
Abstract
Wild mushrooms are a vital source of income and nutrition for many poor communities and of value to recreational foragers. Literature relating to the edibility of mushroom species continues to expand, driven by an increasing demand for wild mushrooms, a wider interest in foraging, and the study of traditional foods. Although numerous case reports have been published on edible mushrooms, doubt and confusion persist regarding which species are safe and suitable to consume. Case reports often differ, and the evidence supporting the stated properties of mushrooms can be incomplete or ambiguous. The need for greater clarity on edible species is further underlined by increases in mushroom-related poisonings. We propose a system for categorizing mushroom species and assigning a final edibility status. Using this system, we reviewed 2,786 mushroom species from 99 countries, accessing 9,783 case reports, from over 1,100 sources. We identified 2,189 edible species, of which 2,006 can be consumed safely, and a further 183 species which required some form of pretreatment prior to safe consumption or were associated with allergic reactions by some. We identified 471 species of uncertain edibility because of missing or incomplete evidence of consumption, and 76 unconfirmed species because of unresolved, differing opinions on edibility and toxicity. This is the most comprehensive list of edible mushrooms available to date, demonstrating the huge number of mushrooms species consumed. Our review highlights the need for further information on uncertain and clash species, and the need to present evidence in a clear, unambiguous, and consistent manner.
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Affiliation(s)
- Huili Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,East and Central Asia Regional Office, World Agroforestry Centre (ICRAF), Kunming, Yunnan, China.,Centre for Mountain Futures, Kunming Institute of Botany, Kunming, Yunnan, China
| | - Yang Tian
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Nelson Menolli
- Núcleo de Pesquisa em Micologia, Instituto de Botânica, São Paulo, Brazil.,Departamento de Ciências da Natureza e Matemática (DCM), Subárea de Biologia (SAB), Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), São Paulo, Brazil
| | - Lei Ye
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,East and Central Asia Regional Office, World Agroforestry Centre (ICRAF), Kunming, Yunnan, China.,Centre for Mountain Futures, Kunming Institute of Botany, Kunming, Yunnan, China
| | - Samantha C Karunarathna
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,East and Central Asia Regional Office, World Agroforestry Centre (ICRAF), Kunming, Yunnan, China.,Centre for Mountain Futures, Kunming Institute of Botany, Kunming, Yunnan, China
| | | | - Mohammad Mahmudur Rahman
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Md Harunur Rashid
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | | | - Leela Rizal
- The University of Queensland, School of Biological Sciences, Brisbane, Queensland, Australia
| | - Taiga Kasuya
- Department of Biology, Keio University, Yokohama, Kanagawa, Japan
| | - Young Woon Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Korea
| | - Arun Kumar Dutta
- Department of Botany, West Bengal State University, Barasat, West Bengal, India
| | | | - Le Thanh Huyen
- Department of Toxicology and Environmental Monitoring, Faculty of Environment, Hanoi University of Natural Resources and Environment, Tu Liem North District, Hanoi, Vietnam
| | - Marilen Parungao Balolong
- Department of Biology, College of Arts and Sciences, University of the Philippines, Manila, the Philippines
| | - Gautam Baruah
- Balipara Tract and Frontier Foundation, Guwahati, Assam, India
| | - Sumedha Madawala
- Department of Botany, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Naritsada Thongklang
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand.,School of Science, Mae Fah Luang University, Chiang Rai, Thailand
| | - Kevin D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand.,School of Science, Mae Fah Luang University, Chiang Rai, Thailand.,Mushroom Research Foundation, Chiang Mai, Thailand
| | - Paul M Kirk
- Biodiversity Informatics and Spatial Analysis, Jodrell Laboratory, Royal Botanic Gardens Kew, Surrey, UK
| | - Jianchu Xu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,East and Central Asia Regional Office, World Agroforestry Centre (ICRAF), Kunming, Yunnan, China.,Centre for Mountain Futures, Kunming Institute of Botany, Kunming, Yunnan, China
| | - Jun Sheng
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Eric Boa
- Institute of Biology, University of Aberdeen, Aberdeen, UK
| | - Peter E Mortimer
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Centre for Mountain Futures, Kunming Institute of Botany, Kunming, Yunnan, China
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8
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Feng S, Bao L, Qiu G, Liao Z, Deng Z, Chen N, Chu Y, Luo Z, Jin Y, Li X, Yang Y, Zhao L. [Observation of dendrite osteocytes of mice at different developmental stages using Ploton silver staining and phalloidin staining]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2020; 40:1656-1661. [PMID: 33243734 DOI: 10.12122/j.issn.1673-4254.2020.11.19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To assess the value of Ploton silver staining and phalloidin-iFlour 488 staining in observation of the morphology of osteocyte dendrites of mice at different developmental stages. METHODS The humerus and femurs were harvested from mice at 0 (P0), 5 (P5), 15 (P15), 21 (P21), 28 (P28), and 35 days (P35) after birth to prepare cryo-sections and paraffin sections. HE staining of P35 mouse femur sections served as a reference for observing osteocytes in the trabecular bone and cortical bone. The humeral sections at different developmental stages were stained with Ploton silver staining to observe the morphology of osteocytes and canaliculi, and the canalicular lengths in the cortical and trabecular bones of the humerus of the mice in each developmental stage were recorded. The cryo-sections of the humerus from P10 and P15 mice were stained with phalloidin iFlour-488 to observe the morphology of osteocytes and measurement of the length of osteocyte dendrites in the cortical bone. RESULTS In the trabecular bone of the humerus of P0-P15 mice, Ploton silver staining only visualized the outline of the osteocytes, and the morphology of the canaliculi was poorly defined. In P21 or older mice, Ploton silver staining revealed the morphology of the trabecular bone osteocytes and the canaliculi, which were neatly arranged and whose lengths increased significantly with age (P21 vs P28, P < 0.05; P21 vs P35, P < 0.05). In the humeral cortical bone of P15 mice, the morphology of the osteocytes and canalicular could be observed with Ploton silver staining, and the length of the regularly arranged canaliculi of the osteocytes increased significantly with age (P15 vs P21, P < 0.005; P15 vs P28, P < 0.0001; P15 vs P35, P < 0.0001). Phalloidin iFlour-488 staining was capable of visualizing the complete morphology of the osteocytes at P10 and P15; the osteocyte dendrites elongated progressively with age (P10 vs P15, P < 0.01) to form connections with the surrounding osteocytes. CONCLUSIONS Mouse osteocyte dendrites elongate progressively and their arrangement gradually becomes regular with age. Ploton silver staining can clearly visualize the morphology of the osteocytes and the canaliculi in adult mice but not in mice in early stages of development. Phalloidin iFlour-488 staining for labeling the cytoskeleton can be applied for mouse osteocytes at all developmental stages and allows morphological observation of mouse osteocytes in early developmental stages.
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Affiliation(s)
- Shuhao Feng
- Department of Joint and Orthopedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Developmental Biology, Harvard School of Dental Medicine, Harvard University, Boston 02115, USA
| | - Liangxiao Bao
- Department of Joint and Orthopedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Gengtao Qiu
- Department of Joint and Orthopedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Zheting Liao
- Department of Joint and Orthopedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Zhonghao Deng
- Department of Joint and Orthopedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Nachun Chen
- Department of Joint and Orthopedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yuhao Chu
- Department of Joint and Orthopedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Ziheng Luo
- Department of Joint and Orthopedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yu Jin
- Department of Joint and Orthopedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xiaoyu Li
- Department of Joint and Orthopedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yingzi Yang
- Department of Developmental Biology, Harvard School of Dental Medicine, Harvard University, Boston 02115, USA
| | - Liang Zhao
- Department of Joint and Orthopedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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9
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Kotynia A, Marciniak A, Brasuń J. The formation of di-copper (II) complexes with a hetero-site cyclopeptide–spectroscopic and potentiometric studies. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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10
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He Z, Long P, Fang F, Li S, Zhang P, Chen Z. Diversity of MSDIN family members in amanitin-producing mushrooms and the phylogeny of the MSDIN and prolyl oligopeptidase genes. BMC Genomics 2020; 21:440. [PMID: 32590929 PMCID: PMC7318481 DOI: 10.1186/s12864-020-06857-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/22/2020] [Indexed: 11/14/2022] Open
Abstract
Background Amanitin-producing mushrooms, mainly distributed in the genera Amanita, Galerina and Lepiota, possess MSDIN gene family for the biosynthesis of many cyclopeptides catalysed by prolyl oligopeptidase (POP). Recently, transcriptome sequencing has proven to be an efficient way to mine MSDIN and POP genes in these lethal mushrooms. Thus far, only A. palloides and A. bisporigera from North America and A. exitialis and A. rimosa from Asia have been studied based on transcriptome analysis. However, the MSDIN and POP genes of many amanitin-producing mushrooms in China remain unstudied; hence, the transcriptomes of these speices deserve to be analysed. Results In this study, the MSDIN and POP genes from ten Amanita species, two Galerina species and Lepiota venenata were studied and the phylogenetic relationships of their MSDIN and POP genes were analysed. Through transcriptome sequencing and PCR cloning, 19 POP genes and 151 MSDIN genes predicted to encode 98 non-duplicated cyclopeptides, including α-amanitin, β-amanitin, phallacidin, phalloidin and 94 unknown peptides, were found in these species. Phylogenetic analysis showed that (1) MSDIN genes generally clustered depending on the taxonomy of the genus, while Amanita MSDIN genes clustered depending on the chemical substance; and (2) the POPA genes of Amanita, Galerina and Lepiota clustered and were separated into three different groups, but the POPB genes of the three distinct genera were clustered in a highly supported monophyletic group. Conclusions These results indicate that lethal Amanita species have the genetic capacity to produce numerous cyclopeptides, most of which are unknown, while lethal Galerina and Lepiota species seem to only have the genetic capacity to produce α-amanitin. Additionally, the POPB phylogeny of Amanita, Galerina and Lepiota conflicts with the taxonomic status of the three genera, suggesting that underlying horizontal gene transfer has occurred among these three genera.
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Affiliation(s)
- Zhengmi He
- College of Life Science, Hunan Normal University, Lushan Road, Changsha, 410081, China
| | - Pan Long
- College of Life Science, Hunan Normal University, Lushan Road, Changsha, 410081, China
| | - Fang Fang
- College of Life Science, Hunan Normal University, Lushan Road, Changsha, 410081, China
| | - Sainan Li
- College of Life Science, Hunan Normal University, Lushan Road, Changsha, 410081, China
| | - Ping Zhang
- College of Life Science, Hunan Normal University, Lushan Road, Changsha, 410081, China
| | - Zuohong Chen
- College of Life Science, Hunan Normal University, Lushan Road, Changsha, 410081, China.
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11
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Minimal lactazole scaffold for in vitro thiopeptide bioengineering. Nat Commun 2020; 11:2272. [PMID: 32385237 PMCID: PMC7210931 DOI: 10.1038/s41467-020-16145-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/06/2020] [Indexed: 12/16/2022] Open
Abstract
Lactazole A is a cryptic thiopeptide from Streptomyces lactacystinaeus, encoded by a compact 9.8 kb biosynthetic gene cluster. Here, we establish a platform for in vitro biosynthesis of lactazole A, referred to as the FIT-Laz system, via a combination of the flexible in vitro translation (FIT) system with recombinantly produced lactazole biosynthetic enzymes. Systematic dissection of lactazole biosynthesis reveals remarkable substrate tolerance of the biosynthetic enzymes and leads to the development of the minimal lactazole scaffold, a construct requiring only 6 post-translational modifications for macrocyclization. Efficient assembly of such minimal thiopeptides with FIT-Laz opens access to diverse lactazole analogs with 10 consecutive mutations, 14- to 62-membered macrocycles, and 18 amino acid-long tail regions, as well as to hybrid thiopeptides containing non-proteinogenic amino acids. This work suggests that the minimal lactazole scaffold is amenable to extensive bioengineering and opens possibilities to explore untapped chemical space of thiopeptides. Lactazole A is a thiopeptide from Streptomyces lactacystinaeus, encoded by a compact 9.8 kb biosynthetic gene cluster. Here, the authors show a platform for in vitro biosynthesis of lactazole A via a combination of a flexible in vitro translation system with recombinantly produced lactazole biosynthetic enzymes.
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12
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Siegert MJ, Knittel CH, Süssmuth RD. A Convergent Total Synthesis of the Death Cap Toxin α-Amanitin. Angew Chem Int Ed Engl 2020; 59:5500-5504. [PMID: 31846557 PMCID: PMC7154671 DOI: 10.1002/anie.201914620] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Indexed: 11/07/2022]
Abstract
The toxic bicyclic octapeptide α-amanitin is mostly found in different species of the mushroom genus Amanita, with the death cap (Amanita phalloides) as one of the most prominent members. Due to its high selective inhibition of RNA polymerase II, which is directly linked to its high toxicity, particularly to hepatocytes, α-amanitin received an increased attention as a toxin-component of antibody-drug conjugates (ADC) in cancer research. Furthermore, the isolation of α-amanitin from mushrooms as the sole source severely restricts compound supply as well as further investigations, as structure-activity relationship (SAR) studies. Based on a straightforward access to the non-proteinogenic amino acid dihydroxyisoleucine, we herein present a robust total synthesis of α-amanitin providing options for production at larger scale as well as future structural diversifications.
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Affiliation(s)
- Mary‐Ann J. Siegert
- Institute of ChemistryTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Caroline H. Knittel
- Institute of ChemistryTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Roderich D. Süssmuth
- Institute of ChemistryTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
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13
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Siegert MJ, Knittel CH, Süssmuth RD. Eine konvergente Totalsynthese des Pilztoxins α‐Amanitin. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mary‐Ann J. Siegert
- Institut für Chemie Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Caroline H. Knittel
- Institut für Chemie Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Roderich D. Süssmuth
- Institut für Chemie Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Deutschland
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14
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Zheng W, Zhou T, Li J, Jiang W, Zhang J, Xiao C, Wei D, Yang C, Xu R, Gong A, Zhang C, Bi Y. The Biosynthesis of Heterophyllin B in Pseudostellaria heterophylla From prePhHB-Encoded Precursor. FRONTIERS IN PLANT SCIENCE 2019; 10:1259. [PMID: 31749814 PMCID: PMC6842982 DOI: 10.3389/fpls.2019.01259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
Plant cyclic peptides (CPs) are a large group of small molecule metabolites found in a wide variety of plants, including traditional Chinese medicinal plants. However, the majority of plant CPs have not been studied for their biosynthetic mechanisms, including heterophyllin B (HB), which is one of the characteristic chemical components of Pseudostellaria heterophylla. Here, we screened the precursor gene (prePhHB) of HB in P. heterophylla and functionally identified its correctness in vivo and in vitro. First, we developed a new method to screen the precursors of HB from 16 candidate linear peptides. According to transcriptome sequencing data, we cloned the genes that encoded the HB precursor peptides and confirmed that the prePhHB-encoded precursor peptide could enzymatically synthesize HB. Next, we generated the transgenic tobacco that expressed prePhHB, and the results showed that HB was detected in transgenic tobacco. Moreover, we revealed that prePhHB gene expression is positively correlated with HB accumulation in P. heterophylla. Mutations in the prePhHB gene may influence the accumulation of HB in P. heterophylla. These results suggest that HB is ribosomally synthesized and posttranslationally modified peptide (RiPP) derived from the precursor gene prePhHB-encoded precursor peptide, and the core peptide sequence of HB is IFGGLPPP in P. heterophylla. This study developed a new idea for the rapid identification of Caryophyllaceae-type CP precursor peptides via RNA-sequencing data mining.
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Affiliation(s)
- Wei Zheng
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Tao Zhou
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Jun Li
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Weike Jiang
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Jinqiang Zhang
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Chenghong Xiao
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Dequn Wei
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Changgui Yang
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Rong Xu
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Anhui Gong
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Chen Zhang
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Yan Bi
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
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15
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Pahl A, Lutz C, Hechler T. Amatoxins as RNA Polymerase II Inhibiting Antibody–Drug Conjugate (ADC) Payloads. CYTOTOXIC PAYLOADS FOR ANTIBODY – DRUG CONJUGATES 2019. [DOI: 10.1039/9781788012898-00398] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Amatoxins are a group of natural toxins which occur in the death cap mushroom (Amanita phalloides). They work by inhibiting RNA polymerase II, which results in apoptosis. RNA-polymerase II inhibition is a novel mechanism of action in cancer therapy and offers the possibility of breaking through drug resistance or destroying dormant tumour cells, which could produce major clinical advances. Amanitin, as the most potent member of this toxin family, has been made accessible for cancer therapy by developing it as a payload for antibody–drug conjugates (ADCs). This chapter describes the discovery and chemistry of the amatoxins, and the development of the amanitin-ADC technology.
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Affiliation(s)
- Andreas Pahl
- Heidelberg Pharma Schriesheimer Str. 101 68526 Ladenburg Germany
| | - Christian Lutz
- Heidelberg Pharma Schriesheimer Str. 101 68526 Ladenburg Germany
| | - Torsten Hechler
- Heidelberg Pharma Schriesheimer Str. 101 68526 Ladenburg Germany
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16
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Vogt E, Künzler M. Discovery of novel fungal RiPP biosynthetic pathways and their application for the development of peptide therapeutics. Appl Microbiol Biotechnol 2019; 103:5567-5581. [PMID: 31147756 DOI: 10.1007/s00253-019-09893-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/06/2019] [Accepted: 05/06/2019] [Indexed: 12/18/2022]
Abstract
Bioactive peptide natural products are an important source of therapeutics. Prominent examples are the antibiotic penicillin and the immunosuppressant cyclosporine which are both produced by fungi and have revolutionized modern medicine. Peptide biosynthesis can occur either non-ribosomally via large enzymes referred to as non-ribosomal peptide synthetases (NRPS) or ribosomally. Ribosomal peptides are synthesized as part of a larger precursor peptide where they are posttranslationally modified and subsequently proteolytically released. Such peptide natural products are referred to as ribosomally synthesized and posttranslationally modified peptides (RiPPs). Their biosynthetic pathways have recently received a lot of attention, both from a basic and applied research point of view, due to the discoveries of several novel posttranslational modifications of the peptide backbone. Some of these modifications were so far only known from NRPSs and significantly increase the chemical space covered by this class of peptide natural products. Latter feature, in combination with the promiscuity of the modifying enzymes and the genetic encoding of the peptide sequence, makes RiPP biosynthetic pathways attractive for synthetic biology approaches to identify novel peptide therapeutics via screening of de novo generated peptide libraries and, thus, exploit bioactive peptide natural products beyond their direct use as therapeutics. This review focuses on the recent discovery and characterization of novel RiPP biosynthetic pathways in fungi and their possible application for the development of novel peptide therapeutics.
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Affiliation(s)
- Eva Vogt
- ETH Zürich, Department of Biology, Institute of Microbiology, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Markus Künzler
- ETH Zürich, Department of Biology, Institute of Microbiology, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland.
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17
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Yin X, Yang AA, Gao JM. Mushroom Toxins: Chemistry and Toxicology. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5053-5071. [PMID: 30986058 DOI: 10.1021/acs.jafc.9b00414] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Mushroom consumption is a global tradition that is still gaining popularity. However, foraging for wild mushrooms and accidental ingestion of toxic mushrooms can result in serious illness and even death. The early diagnosis and treatment of mushroom poisoning are quite difficult, as the symptoms are similar to those caused by common diseases. Chemically, mushroom poisoning is related to very powerful toxins, suggesting that the isolation and identification of toxins have great research value, especially in determining the lethal components of toxic mushrooms. In contrast, most of these toxins have remarkable physiological properties that could promote advances in chemistry, biochemistry, physiology, and pharmacology. Although more than 100 toxins have been elucidated, there are a number of lethal mushrooms that have not been fully investigated. This review provides information on the chemistry (including chemical structures, total synthesis, and biosynthesis) and the toxicology of these toxins, hoping to inspire further research in this area.
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Affiliation(s)
- Xia Yin
- Shaanxi Key Laboratory of Natural Products & Chemistry Biology, College of Chemistry & Pharmacy , Northwest A & F University , Yangling 712100 , People's Republic of China
| | - An-An Yang
- Department of Pathology , The 969th Hospital of PLA , Hohhot , Inner Mongolia 010000 , People's Republic of China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemistry Biology, College of Chemistry & Pharmacy , Northwest A & F University , Yangling 712100 , People's Republic of China
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18
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Luo S, Dong SH. Recent Advances in the Discovery and Biosynthetic Study of Eukaryotic RiPP Natural Products. Molecules 2019; 24:molecules24081541. [PMID: 31003555 PMCID: PMC6514808 DOI: 10.3390/molecules24081541] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 12/22/2022] Open
Abstract
Natural products have played indispensable roles in drug development and biomedical research. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a group of fast-expanding natural products attribute to genome mining efforts in recent years. Most RiPP natural products were discovered from bacteria, yet many eukaryotic cyclic peptides turned out to be of RiPP origin. This review article presents recent advances in the discovery of eukaryotic RiPP natural products, the elucidation of their biosynthetic pathways, and the molecular basis for their biosynthetic enzyme catalysis.
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Affiliation(s)
- Shangwen Luo
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China.
| | - Shi-Hui Dong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China.
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19
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Tayyrov A, Stanley CE, Azevedo S, Künzler M. Combining microfluidics and RNA-sequencing to assess the inducible defensome of a mushroom against nematodes. BMC Genomics 2019; 20:243. [PMID: 30909884 PMCID: PMC6434838 DOI: 10.1186/s12864-019-5607-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 03/14/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Fungi are an attractive source of nutrients for predators. As part of their defense, some fungi are able to induce the production of anti-predator protein toxins in response to predation. A previous study on the interaction of the model mushroom Coprinopsis cinerea by the fungivorous nematode Aphelenchus avenae on agar plates has shown that the this fungal defense response is most pronounced in the part of the mycelium that is in direct contact with the nematode. Hence, we hypothesized that, for a comprehensive characterization of this defense response, an experimental setup that maximizes the zone of direct interaction between the fungal mycelium and the nematode, was needed. RESULTS In this study, we conducted a transcriptome analysis of C. cinerea vegetative mycelium upon challenge with A. avenae using a tailor-made microfluidic device. The device was designed such that the interaction between the fungus and the nematode was confined to a specific area and that the mycelium could be retrieved from this area for analysis. We took samples from the confrontation area after different time periods and extracted and sequenced the poly(A)+ RNA thereof. The identification of 1229 differentially expressed genes (DEGs) shows that this setup profoundly improved sensitivity over co-cultivation on agar plates where only 37 DEGs had been identified. The product of one of the most highly upregulated genes shows structural homology to bacterial pore-forming toxins, and revealed strong toxicity to various bacterivorous nematodes. In addition, bacteria associated with the fungivorous nematode A. avenae were profiled with 16S rRNA deep sequencing. Similar to the bacterivorous and plant-feeding nematodes, Proteobacteria and Bacteroidetes were the most dominant phyla in A. avenae. CONCLUSIONS The use of a novel experimental setup for the investigation of the defense response of a fungal mycelium to predation by fungivorous nematodes resulted in the identification of a comprehensive set of DEGs and the discovery of a novel type of fungal defense protein against nematodes. The bacteria found to be associated with the fungivorous nematode are a possible explanation for the induction of some antibacterial defense proteins upon nematode challenge.
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Affiliation(s)
- Annageldi Tayyrov
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
| | - Claire E. Stanley
- Agroecology and Environment Research Division, Agroscope, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Sophie Azevedo
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
| | - Markus Künzler
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
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20
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Molecular cloning and the expression pattern of AePOPB involved in the α-amanitin biosynthesis in Amanita exitialis fruiting bodies. Gene 2018; 662:123-130. [PMID: 29627524 DOI: 10.1016/j.gene.2018.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 04/02/2018] [Accepted: 04/04/2018] [Indexed: 12/31/2022]
Abstract
Amanita exitialis Zhu L. Yang & T. H. Li is the species responsible for the largest number of mushroom-associated human poisonings and fatalities in South China due to its lethal cyclic peptide toxins. Prolyl oligopeptidase B (POPB) is considered a key enzyme in the production of the highly toxic cyclic peptide α-amanitin. However, the POPB gene of A. exitialis has not been studied. In the present study we cloned and sequenced the full-length A. exitialis POPB (AePOPB) gene. The aim was to verify the gene structure and functions of AePOPB. The full-length sequence of AePOPB is 3144 bp, including 18 exons encoding 730 aa, and the advanced structure is very similar to that of the previously reported POPB in Galerina marginata (GmPOPB). The amino acid sequence of AePOPB is highly homologous with those from other amanitin-producing lethal mushrooms, implying that AePOPB may have a similar role in the biosynthesis of cyclic peptide toxins. Expression levels of AePOPB were detectable in all parts and developmental stages of the fruiting bodies, and AePOPB was expressed more strongly at early development stages (early and late elongation stages). At early and late elongation stages, the expression peaks occurred in the stipe, whereas at early and late mature stages, the expression peaks occurred in the pileus. The expression patterns of AePOPB in different stages and different parts of the fruiting bodies were highly consistent with those of Aeα-AMA, which is required for α-amanitin accumulation. These results indicate that AePOPB should be involved in the α-amanitin biosynthesis in A. exitialis.
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21
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Ongpipattanakul C, Nair SK. Biosynthetic Proteases That Catalyze the Macrocyclization of Ribosomally Synthesized Linear Peptides. Biochemistry 2018; 57:3201-3209. [PMID: 29553721 DOI: 10.1021/acs.biochem.8b00114] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Circular peptides have long been sought after as scaffolds for drug design as they demonstrate protein-like properties in the context of small, constrained peptides. Traditional routes toward the production of cyclic peptides rely on synthesis or semisynthetic methods, which restrict their use as platforms for the production of large, structurally diverse chemical libraries. Here, we discuss the biosynthetic routes toward the N-C macrocyclization of linear peptide precursors, specifically, those transformations that are catalyzed by peptidases. While canonical peptidases catalyze the proteolysis of linear peptides, the biosynthetic macrocyclases couple proteolytic cleavage with cyclization to produce macrocyclic compounds. In this Perspective, we explore the different structural features that impart on each of these biosynthetic proteases the distinct ability to perform macrocyclization and focus on their potential use in biotechnology.
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22
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Wang X, Lin M, Xu D, Lai D, Zhou L. Structural Diversity and Biological Activities of Fungal Cyclic Peptides, Excluding Cyclodipeptides. Molecules 2017; 22:E2069. [PMID: 29186926 PMCID: PMC6150023 DOI: 10.3390/molecules22122069] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 11/20/2017] [Accepted: 11/23/2017] [Indexed: 11/23/2022] Open
Abstract
Cyclic peptides are cyclic compounds formed mainly by the amide bonds between either proteinogenic or non-proteinogenic amino acids. This review highlights the occurrence, structures and biological activities of fungal cyclic peptides (excluding cyclodipeptides, and peptides containing ester bonds in the core ring) reported until August 2017. About 293 cyclic peptides belonging to the groups of cyclic tri-, tetra-, penta-, hexa-, hepta-, octa-, nona-, deca-, undeca-, dodeca-, tetradeca-, and octadecapeptides as well as cyclic peptides containing ether bonds in the core ring have been isolated from fungi. They were mainly isolated from the genera Aspergillus, Penicillium, Fusarium, Acremonium and Amanita. Some of them were screened to have antimicrobial, antiviral, cytotoxic, phytotoxic, insecticidal, nematicidal, immunosuppressive and enzyme-inhibitory activities to show their potential applications. Some fungal cyclic peptides such as the echinocandins, pneumocandins and cyclosporin A have been developed as pharmaceuticals.
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Affiliation(s)
- Xiaohan Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Minyi Lin
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Dan Xu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Daowan Lai
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Ligang Zhou
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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23
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Patel S. A critical review on serine protease: Key immune manipulator and pathology mediator. Allergol Immunopathol (Madr) 2017; 45:579-591. [PMID: 28236540 PMCID: PMC7126602 DOI: 10.1016/j.aller.2016.10.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/31/2016] [Indexed: 11/29/2022]
Abstract
Proteolytic activity is fundamental to survival, so it is not surprising that all living organisms have proteases, especially seine protease. This enzyme in its numerous isoforms and homologues, constitutes the quintessential offence and defence factors, in the form of surface proteins, secreted molecules, gut digestive enzymes, venom in specialised glands or plant latex, among other manifestations. Occurring as trypsin, chymotrypsin, elastase, collagenase, thrombin, subtilisin etc., it mediates a diverse array of functions, including pathological roles as inflammatory, coagulatory to haemorrhagic. This review emphasizes that despite the superficial differences in mechanisms, most health issues, be they infectious, allergic, metabolic, or neural have a common conduit. This enzyme, in its various glycosylated forms leads to signal misinterpretations, wreaking havoc. However, organisms are endowed with serine protease inhibitors which might restrain this ubiquitous yet deleterious enzyme. Hence, serine proteases-driven pathogenesis and antagonising role of inhibitors is the focal point of this critical review.
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24
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Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates. Nat Commun 2017; 8:1045. [PMID: 29051530 PMCID: PMC5648786 DOI: 10.1038/s41467-017-00862-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/02/2017] [Indexed: 01/30/2023] Open
Abstract
Peptide macrocycles are promising therapeutic molecules because they are protease resistant, structurally rigid, membrane permeable, and capable of modulating protein-protein interactions. Here, we report the characterization of the dual function macrocyclase-peptidase enzyme involved in the biosynthesis of the highly toxic amanitin toxin family of macrocycles. The enzyme first removes 10 residues from the N-terminus of a 35-residue substrate. Conformational trapping of the 25 amino-acid peptide forces the enzyme to release this intermediate rather than proceed to macrocyclization. The enzyme rebinds the 25 amino-acid peptide in a different conformation and catalyzes macrocyclization of the N-terminal eight residues. Structures of the enzyme bound to both substrates and biophysical analysis characterize the different binding modes rationalizing the mechanism. Using these insights simpler substrates with only five C-terminal residues were designed, allowing the enzyme to be more effectively exploited in biotechnology.
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25
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Abstract
ABSTRACT
The fungal lineage is one of the three large eukaryotic lineages that dominate terrestrial ecosystems. They share a common ancestor with animals in the eukaryotic supergroup Opisthokonta and have a deeper common ancestry with plants, yet several phenotypes, such as morphological, physiological, or nutritional traits, make them unique among all living organisms. This article provides an overview of some of the most important fungal traits, how they evolve, and what major genes and gene families contribute to their development. The traits highlighted here represent just a sample of the characteristics that have evolved in fungi, including polarized multicellular growth, fruiting body development, dimorphism, secondary metabolism, wood decay, and mycorrhizae. However, a great number of other important traits also underlie the evolution of the taxonomically and phenotypically hyperdiverse fungal kingdom, which could fill up a volume on its own. After reviewing the evolution of these six well-studied traits in fungi, we discuss how the recurrent evolution of phenotypic similarity, that is, convergent evolution in the broad sense, has shaped their phylogenetic distribution in extant species.
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26
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Nielsen DS, Shepherd NE, Xu W, Lucke AJ, Stoermer MJ, Fairlie DP. Orally Absorbed Cyclic Peptides. Chem Rev 2017; 117:8094-8128. [PMID: 28541045 DOI: 10.1021/acs.chemrev.6b00838] [Citation(s) in RCA: 247] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Peptides and proteins are not orally bioavailable in mammals, although a few peptides are intestinally absorbed in small amounts. Polypeptides are generally too large and polar to passively diffuse through lipid membranes, while most known active transport mechanisms facilitate cell uptake of only very small peptides. Systematic evaluations of peptides with molecular weights above 500 Da are needed to identify parameters that influence oral bioavailability. Here we describe 125 cyclic peptides containing four to thirty-seven amino acids that are orally absorbed by mammals. Cyclization minimizes degradation in the gut, blood, and tissues by removing cleavable N- and C-termini and by shielding components from metabolic enzymes. Cyclization also folds peptides into bioactive conformations that determine exposure of polar atoms to solvation by water and lipids and therefore can influence oral bioavailability. Key chemical properties thought to influence oral absorption and bioavailability are analyzed, including molecular weight, octanol-water partitioning, hydrogen bond donors/acceptors, rotatable bonds, and polar surface area. The cyclic peptides violated to different degrees all of the limits traditionally considered to be important for oral bioavailability of drug-like small molecules, although fewer hydrogen bond donors and reduced flexibility generally favored oral absorption.
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Affiliation(s)
- Daniel S Nielsen
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Nicholas E Shepherd
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Weijun Xu
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Andrew J Lucke
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Martin J Stoermer
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
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27
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Dunbar KL, Scharf DH, Litomska A, Hertweck C. Enzymatic Carbon-Sulfur Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5521-5577. [PMID: 28418240 DOI: 10.1021/acs.chemrev.6b00697] [Citation(s) in RCA: 345] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sulfur plays a critical role for the development and maintenance of life on earth, which is reflected by the wealth of primary metabolites, macromolecules, and cofactors bearing this element. Whereas a large body of knowledge has existed for sulfur trafficking in primary metabolism, the secondary metabolism involving sulfur has long been neglected. Yet, diverse sulfur functionalities have a major impact on the biological activities of natural products. Recent research at the genetic, biochemical, and chemical levels has unearthed a broad range of enzymes, sulfur shuttles, and chemical mechanisms for generating carbon-sulfur bonds. This Review will give the first systematic overview on enzymes catalyzing the formation of organosulfur natural products.
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Affiliation(s)
- Kyle L Dunbar
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Daniel H Scharf
- Life Sciences Institute, University of Michigan , 210 Washtenaw Avenue, Ann Arbor, Michigan 48109-2216, United States
| | - Agnieszka Litomska
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany.,Friedrich Schiller University , 07743 Jena, Germany
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28
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Mamo G. Anaerobes as Sources of Bioactive Compounds and Health Promoting Tools. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 156:433-464. [PMID: 27432247 DOI: 10.1007/10_2016_6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Aerobic microorganisms have been sources of medicinal agents for several decades and an impressive variety of drugs have been isolated from their cultures, studied and formulated to treat or prevent diseases. On the other hand, anaerobes, which are believed to be the oldest life forms on earth and evolved remarkably diverse physiological functions, have largely been neglected as sources of bioactive compounds. However, results obtained from the limited research done so far show that anaerobes are capable of producing a range of interesting bioactive compounds that can promote human health. In fact, some of these bioactive compounds are found to be novel in their structure and/or mode of action.Anaerobes play health-promoting roles through their bioactive products as well as application of whole cells. The bioactive compounds produced by these microorganisms include antimicrobial agents and substances such as immunomodulators and vitamins. Bacteriocins produced by anaerobes have been in use as preservatives for about 40 years. Because these substances are effective at low concentrations, encounter relatively less resistance from bacteria and are safe to use, there is a growing interest in these antimicrobial agents. Moreover, several antibiotics have been reported from the cultures of anaerobes. Closthioamide and andrimid produced by Clostridium cellulolyticum and Pantoea agglomerans, respectively, are examples of novel antibiotics of anaerobe origin. The discovery of such novel bioactive compounds is expected to encourage further studies which can potentially lead to tapping of the antibiotic production potential of this fascinating group of microorganisms.Anaerobes are widely used in preparation of fermented foods and beverages. During the fermentation processes, these organisms produce a number of bioactive compounds including anticancer, antihypertensive and antioxidant substances. The well-known health promoting effect of fermented food is mostly due to these bioactive compounds. In addition to their products, whole cell anaerobes have very interesting applications for enhancing the quality of life. Probiotic anaerobes have been on the market for many years and are receiving growing acceptance as health promoters. Gut anaerobes have been used to treat patients suffering from severe Clostridium difficile infection syndromes including diarrhoea and colitis which cannot be treated by other means. Whole cell anaerobes are also studied to detect and cure cancer. In recent years, evidence is emerging that anaerobes constituting the microbiome are linked to our overall health. A dysfunctional microbiome is believed to be the cause of many diseases including cancer, allergy, infection, obesity, diabetes and several other disorders. Maintaining normal microflora is believed to alleviate some of these serious health problems. Indeed, the use of probiotics and prebiotics which favourably change the number and composition of the gut microflora is known to render a health promoting effect. Our interaction with the microbiome anaerobes is complex. In fact, not only our lives but also our identities are more closely linked to the anaerobic microbial world than we may possibly imagine. We are just at the beginning of unravelling the secret of association between the microbiome and human body, and a clear understanding of the association may bring a paradigm shift in the way we diagnose and treat diseases and disorders. This chapter highlights some of the work done on bioactive compounds and whole cell applications of the anaerobes that foster human health and improve the quality of life.
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Affiliation(s)
- Gashaw Mamo
- Biotechnology, Center for Chemistry & Chemical Engineering, Lund University, 221 00, Lund, Sweden.
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Fichtner M, Voigt K, Schuster S. The tip and hidden part of the iceberg: Proteinogenic and non-proteinogenic aliphatic amino acids. Biochim Biophys Acta Gen Subj 2017; 1861:3258-3269. [DOI: 10.1016/j.bbagen.2016.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 07/14/2016] [Accepted: 08/15/2016] [Indexed: 12/26/2022]
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de Mattos-Shipley K, Ford K, Alberti F, Banks A, Bailey A, Foster G. The good, the bad and the tasty: The many roles of mushrooms. Stud Mycol 2016; 85:125-157. [PMID: 28082758 PMCID: PMC5220184 DOI: 10.1016/j.simyco.2016.11.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Fungi are often inconspicuous in nature and this means it is all too easy to overlook their importance. Often referred to as the "Forgotten Kingdom", fungi are key components of life on this planet. The phylum Basidiomycota, considered to contain the most complex and evolutionarily advanced members of this Kingdom, includes some of the most iconic fungal species such as the gilled mushrooms, puffballs and bracket fungi. Basidiomycetes inhabit a wide range of ecological niches, carrying out vital ecosystem roles, particularly in carbon cycling and as symbiotic partners with a range of other organisms. Specifically in the context of human use, the basidiomycetes are a highly valuable food source and are increasingly medicinally important. In this review, seven main categories, or 'roles', for basidiomycetes have been suggested by the authors: as model species, edible species, toxic species, medicinal basidiomycetes, symbionts, decomposers and pathogens, and two species have been chosen as representatives of each category. Although this is in no way an exhaustive discussion of the importance of basidiomycetes, this review aims to give a broad overview of the importance of these organisms, exploring the various ways they can be exploited to the benefit of human society.
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Affiliation(s)
- K.M.J. de Mattos-Shipley
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - K.L. Ford
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - F. Alberti
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
- School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - A.M. Banks
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
- School of Biology, Devonshire Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - A.M. Bailey
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - G.D. Foster
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
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Biosynthetic investigation of phomopsins reveals a widespread pathway for ribosomal natural products in Ascomycetes. Proc Natl Acad Sci U S A 2016; 113:3521-6. [PMID: 26979951 DOI: 10.1073/pnas.1522907113] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Production of ribosomally synthesized and posttranslationally modified peptides (RiPPs) has rarely been reported in fungi, even though organisms of this kingdom have a long history as a prolific source of natural products. Here we report an investigation of the phomopsins, antimitotic mycotoxins. We show that phomopsin is a fungal RiPP and demonstrate the widespread presence of a pathway for the biosynthesis of a family of fungal cyclic RiPPs, which we term dikaritins. We characterize PhomM as an S-adenosylmethionine-dependent α-N-methyltransferase that converts phomopsin A to an N,N-dimethylated congener (phomopsin E), and show that the methyltransferases involved in dikaritin biosynthesis have evolved differently and likely have broad substrate specificities. Genome mining studies identified eight previously unknown dikaritins in different strains, highlighting the untapped capacity of RiPP biosynthesis in fungi and setting the stage for investigating the biological activities and unknown biosynthetic transformations of this family of fungal natural products.
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A novel family of cyclic oligopeptides derived from ribosomal peptide synthesis of an in planta-induced gene, gigA, in Epichloë endophytes of grasses. Fungal Genet Biol 2015; 85:14-24. [DOI: 10.1016/j.fgb.2015.10.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 10/16/2015] [Accepted: 10/26/2015] [Indexed: 11/19/2022]
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Plaza DF, Schmieder SS, Lipzen A, Lindquist E, Künzler M. Identification of a Novel Nematotoxic Protein by Challenging the Model Mushroom Coprinopsis cinerea with a Fungivorous Nematode. G3 (BETHESDA, MD.) 2015; 6:87-98. [PMID: 26585824 PMCID: PMC4704728 DOI: 10.1534/g3.115.023069] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/29/2015] [Indexed: 01/06/2023]
Abstract
The dung of herbivores, the natural habitat of the model mushroom Coprinopsis cinerea, is a nutrient-rich but also very competitive environment for a saprophytic fungus. We showed previously that C. cinerea expresses constitutive, tissue-specific armories against antagonists such as animal predators and bacterial competitors. In order to dissect the inducible armories against such antagonists, we sequenced the poly(A)-positive transcriptome of C. cinerea vegetative mycelium upon challenge with fungivorous and bacterivorous nematodes, Gram-negative and Gram-positive bacteria and mechanical damage. As a response to the fungivorous nematode Aphelenchus avenae, C. cinerea was found to specifically induce the transcription of several genes encoding previously characterized nematotoxic lectins. In addition, a previously not characterized gene encoding a cytoplasmic protein with several predicted Ricin B-fold domains, was found to be strongly upregulated under this condition. Functional analysis of the recombinant protein revealed a high toxicity toward the bacterivorous nematode Caenorhabditis elegans. Challenge of the mycelium with A. avenae also lead to the induction of several genes encoding putative antibacterial proteins. Some of these genes were also induced upon challenge of the mycelium with the bacteria Escherichia coli and Bacillus subtilis. These results suggest that fungi have the ability to induce specific innate defense responses similar to plants and animals.
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Affiliation(s)
- David Fernando Plaza
- Institute of Microbiology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Anna Lipzen
- Genomic Technologies, Joint Genome Institute, Walnut Creek, California 94598
| | - Erika Lindquist
- Genomic Technologies, Joint Genome Institute, Walnut Creek, California 94598
| | - Markus Künzler
- Institute of Microbiology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
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34
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Mitchell CL, Yeager RD, Johnson ZJ, D’Annunzio SE, Vogel KR, Werner T. Long-Term Resistance of Drosophila melanogaster to the Mushroom Toxin Alpha-Amanitin. PLoS One 2015; 10:e0127569. [PMID: 25978397 PMCID: PMC4433104 DOI: 10.1371/journal.pone.0127569] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/16/2015] [Indexed: 11/19/2022] Open
Abstract
Insect resistance to toxins exerts not only a great impact on our economy, but also on the ecology of many species. Resistance to one toxin is often associated with cross-resistance to other, sometimes unrelated, chemicals. In this study, we investigated mushroom toxin resistance in the fruit fly Drosophila melanogaster (Meigen). This fruit fly species does not feed on mushrooms in nature and may thus have evolved cross-resistance to α-amanitin, the principal toxin of deadly poisonous mushrooms, due to previous pesticide exposure. The three Asian D. melanogaster stocks used in this study, Ama-KTT, Ama-MI, and Ama-KLM, acquired α-amanitin resistance at least five decades ago in their natural habitats in Taiwan, India, and Malaysia, respectively. Here we show that all three stocks have not lost the resistance phenotype despite the absence of selective pressure over the past half century. In response to α-amanitin in the larval food, several signs of developmental retardation become apparent in a concentration-dependent manner: higher pre-adult mortality, prolonged larva-to-adult developmental time, decreased adult body size, and reduced adult longevity. In contrast, female fecundity nearly doubles in response to higher α-amanitin concentrations. Our results suggest that α-amanitin resistance has no fitness cost, which could explain why the resistance has persisted in all three stocks over the past five decades. If pesticides caused α-amanitin resistance in D. melanogaster, their use may go far beyond their intended effects and have long-lasting effects on ecosystems.
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Affiliation(s)
- Chelsea L. Mitchell
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Roger D. Yeager
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Zachary J. Johnson
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Stephanie E. D’Annunzio
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Kara R. Vogel
- Department of Experimental and Systems Pharmacology, Washington State University, Spokane, Washington, United States of America
| | - Thomas Werner
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, United States of America
- * E-mail:
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35
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Molecular cloning of α-amanitin and characterization of its expression pattern in different parts and development stages of Amanita exitialis fruitbody. Mycol Prog 2014. [DOI: 10.1007/s11557-014-0988-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Li P, Deng W, Li T. The molecular diversity of toxin gene families in lethal Amanita mushrooms. Toxicon 2014; 83:59-68. [PMID: 24613547 DOI: 10.1016/j.toxicon.2014.02.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/16/2013] [Accepted: 02/25/2014] [Indexed: 11/16/2022]
Abstract
Mushrooms in lethal Amanita species are responsible for a large number of food poisoning cases and deaths. However, the diversity of the toxins in these mushrooms remains largely unknown. This study analyzed the gene families of toxins found in 6 lethal Amanitae from Asia and Europe. Fifty-four gene sequences were obtained, accounting for 70.1% of the known MSDIN family members. Of the 54 gene sequences, 20 encode α-amanitin, 5 encode β-amanitin, 16 encode phallacidin, and 13 encode peptides of unknown functions. Bayesian analysis of MSDIN family members identified differences in the number of toxin genes in different toxin families among the Amanita species. Ten of the 13 peptides of unknown functions were closely related to known phallotoxins, while the remaining 3 were similar to amatoxins. The α-AMA tree indicated that there were significant differences between the Amanita and Galerina species. However, both the α-AMA and PHA trees showed that these toxin genes have similar upstream and downstream motif sequences among the Amanita species. This study greatly enriches the available diversity information regarding toxin gene families in lethal Amanita mushrooms, and could lay a strong foundation for further research about the evolution of Amanita toxin genes.
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Affiliation(s)
- Peng Li
- School of Bioscience & Bioengineering, South China University of Technology, Guangzhou 510006, China; State Key Laboratory of Applied Microbiology, South China (The Ministry-Province Joint Development), Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Wangqiu Deng
- State Key Laboratory of Applied Microbiology, South China (The Ministry-Province Joint Development), Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Taihui Li
- School of Bioscience & Bioengineering, South China University of Technology, Guangzhou 510006, China; State Key Laboratory of Applied Microbiology, South China (The Ministry-Province Joint Development), Guangdong Institute of Microbiology, Guangzhou 510070, China.
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37
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Craik DJ, Malik U. Cyclotide biosynthesis. Curr Opin Chem Biol 2013; 17:546-54. [PMID: 23809361 DOI: 10.1016/j.cbpa.2013.05.033] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
Abstract
Cyclotides are bioactive macrocyclic peptides from plants that are characterized by their exceptional stability and potential applications as protein engineering or drug design frameworks. Their stability arises from their unique cyclic cystine knot structure, which combines a head-to-tail cyclic peptide backbone with three conserved disulfide bonds having a knotted topology. Cyclotides are ribosomally synthesized by plants and expressed in a wide range of tissues, including leaves, flowers, stems and roots. Here we describe recent studies that have examined the biosynthesis of cyclotides and in particular the mechanism associated with post-translational backbone cyclization.
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Affiliation(s)
- David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
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38
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Flygare JA, Pillow TH, Aristoff P. Antibody-drug conjugates for the treatment of cancer. Chem Biol Drug Des 2013; 81:113-21. [PMID: 23253133 DOI: 10.1111/cbdd.12085] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
With over 20 antibody-drug conjugates in clinical trials as well as a recently FDA-approved drug, it is clear that this is becoming an important and viable approach for selectively delivering highly cytotoxic agents to tumor cells while sparing normal tissue. This review discusses the critical aspects for this approach with an emphasis on the properties of the linker between the antibody and the cytotoxic payload that are required for an effective antibody-drug conjugate. Different linkers are illustrated with attention focused on (i) the specifics of attachment to the antibody, (ii) the polarity of the linker, (iii) the trigger on the linker that initiates cleavage from the drug, and (iv) the self-immolative spacer that liberates the active payload. Future directions in the field are proposed.
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Affiliation(s)
- John A Flygare
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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Barber CJS, Pujara PT, Reed DW, Chiwocha S, Zhang H, Covello PS. The two-step biosynthesis of cyclic peptides from linear precursors in a member of the plant family Caryophyllaceae involves cyclization by a serine protease-like enzyme. J Biol Chem 2013; 288:12500-10. [PMID: 23486480 DOI: 10.1074/jbc.m112.437947] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Caryophyllaceae-type cyclic peptides (CPs) of 5-12 proteinogenic amino acids occur in 10 plant families. In Saponaria vaccaria (Caryophyllaceae), they have been shown to be formed from linear peptide precursors derived from ribosomal translation. There is also evidence for such precursors in other members of the Caryophyllaceae, Rutaceae, and Linaceae families. The biosynthesis of CP in the developing seeds of S. vaccaria was investigated with respect to the enzymes involved in precursor processing. Through biochemical assays with seed extracts and synthetic peptides, an enzyme named oligopeptidase 1 (OLP1) was found that catalyzes the cleavage of intermediates at the N terminus of the incipient CP. A second enzyme, peptide cyclase 1 (PCY1), which was separated chromatographically from OLP1, was found to act on the product of OLP1, giving rise to a cyclic peptide and concomitant removal of a C-terminal flanking sequence. PCY1 was partially purified, and using the methods of proteomics, a full-length cDNA clone encoding an enzyme matching the properties of PCY1 was obtained. The substrate specificity of purified recombinant PCY1, believed to be the first cloned plant enzyme whose function is peptide cyclization, was tested with synthetic peptides. The results are discussed in the light of CP biosynthetic systems of other organisms.
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Affiliation(s)
- Carla J S Barber
- National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
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40
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Evaluation of micronuclei in mice bone marrow and antioxidant systems in erythrocytes exposed to α-amanitin. Toxicon 2013; 63:147-53. [DOI: 10.1016/j.toxicon.2012.11.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 08/13/2012] [Accepted: 11/29/2012] [Indexed: 01/26/2023]
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41
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Vaagt F, Haase I, Fischer M. Loop-mediated isothermal amplification (LAMP)-based method for rapid mushroom species identification. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:1833-1840. [PMID: 23350919 DOI: 10.1021/jf304824b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Toxic mushroom species, such as the death cap ( Amanita phalloides ), are responsible for most mushroom poisonings. In the present work, novel loop-mediated isothermal amplification (LAMP) assays were used for the differentiation of even closely related edible and toxic mushroom species. The applicability of these methods was tested by cross-reaction studies and analysis of spiked mushroom samples (raw and fried material). Contaminations at the level of 2% (w/w) could be detected in different mushroom blends. Three detection methods were used: agarose gel analysis, fluorimetric real-time detection, and visual detection by lateral flow dipsticks (LFD). The LAMP assay combined with LFD detection allows the identification of A. phalloides in about 2 h (including DNA extraction) at a very low level of technical equipment (micropestle, water bath, and mobile centrifuge), which makes this technique perfectly suited for on-site applications.
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Affiliation(s)
- Franziska Vaagt
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Hamburg, Germany
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42
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Moshnikova A, Moshnikova V, Andreev OA, Reshetnyak YK. Antiproliferative effect of pHLIP-amanitin. Biochemistry 2013; 52:1171-8. [PMID: 23360641 DOI: 10.1021/bi301647y] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Toxins could be effective anticancer drugs, if their selective delivery into cancer cells could be achieved. We have shown that the energy of membrane-associated folding of water-soluble membrane peptides of the pHLIP (pH low insertion peptide) family could be used to move cell-impermeable cargo across the lipid bilayer into the cytoplasm of cancer cells. Here we present the results of a study of pHLIP-mediated cellular delivery of a polar cell-impermeable toxin, α-amanitin, an inhibitor of RNA polymerase II. We show that pHLIP can deliver α-amanitin into cells in a pH-dependent fashion and induce cell death within 48 h. Translocation capability could be tuned by conjugating amanitin to the C-terminus of pHLIP via linkers of different hydrophobicities that could be cleaved in the cytoplasm. pHLIP-SPDP-amanitin, which exhibits 4-5 times higher antiproliferative ability at pH 6 than at pH 7.4, was selected as the best construct. The major mechanism of amanitin delivery is direct translocation (flip) across a membrane by pHLIP and cleavage of the S-S bond in the cytoplasm. The antiproliferative effect was monitored on four different human cancer cell lines. pHLIP-mediated cytoplasmic delivery of amanitin could create great opportunities to use the toxin as a potent pH-selective anticancer agent, which predominantly targets highly proliferative cancer cells at low extracellular pH values.
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Affiliation(s)
- Anna Moshnikova
- Physics Department, University of Rhode Island, 2 Lippitt Road, Kingston, RI 02881, USA
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Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, Camarero JA, Campopiano DJ, Challis GL, Clardy J, Cotter PD, Craik DJ, Dawson M, Dittmann E, Donadio S, Dorrestein PC, Entian KD, Fischbach MA, Garavelli JS, Göransson U, Gruber CW, Haft DH, Hemscheidt TK, Hertweck C, Hill C, Horswill AR, Jaspars M, Kelly WL, Klinman JP, Kuipers OP, Link AJ, Liu W, Marahiel MA, Mitchell DA, Moll GN, Moore BS, Müller R, Nair SK, Nes IF, Norris GE, Olivera BM, Onaka H, Patchett ML, Piel J, Reaney MJT, Rebuffat S, Ross RP, Sahl HG, Schmidt EW, Selsted ME, Severinov K, Shen B, Sivonen K, Smith L, Stein T, Süssmuth RD, Tagg JR, Tang GL, Truman AW, Vederas JC, Walsh CT, Walton JD, Wenzel SC, Willey JM, van der Donk WA. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep 2013; 30:108-60. [PMID: 23165928 DOI: 10.1039/c2np20085f] [Citation(s) in RCA: 1441] [Impact Index Per Article: 131.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. The current knowledge regarding the biosynthesis of the >20 distinct compound classes is also reviewed, and commonalities are discussed.
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Affiliation(s)
- Paul G Arnison
- Prairie Plant Systems Inc, Botanical Alternatives Inc, Suite 176, 8B-3110 8th Street E, Saskatoon, SK, S7H 0W2, Canada
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Göransson U, Burman R, Gunasekera S, Strömstedt AA, Rosengren KJ. Circular proteins from plants and fungi. J Biol Chem 2012; 287:27001-6. [PMID: 22700984 DOI: 10.1074/jbc.r111.300129] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Circular proteins, defined as head-to-tail cyclized polypeptides originating from ribosomal synthesis, represent a novel class of natural products attracting increasing interest. From a scientific point of view, these compounds raise questions of where and why they occur in nature and how they are formed. From a rational point of view, these proteins and their structural concept may be exploited for crop protection and novel pharmaceuticals. Here, we review the current knowledge of three protein families: cyclotides and circular sunflower trypsin inhibitors from the kingdom of plants and the Amanita toxins from fungi. A particular emphasis is placed on their biological origin, structure, and activity. In addition, the opportunity for discovery of novel circular proteins and recent insights into their mechanism of action are discussed.
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Affiliation(s)
- Ulf Göransson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden.
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Moldenhauer G, Salnikov AV, Lüttgau S, Herr I, Anderl J, Faulstich H. Therapeutic potential of amanitin-conjugated anti-epithelial cell adhesion molecule monoclonal antibody against pancreatic carcinoma. J Natl Cancer Inst 2012; 104:622-34. [PMID: 22457476 DOI: 10.1093/jnci/djs140] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human epithelial cell adhesion molecule (EpCAM) is overexpressed in many cancers. Anti-EpCAM antibodies have shown promise in preclinical studies, but showed no tumor regression in a recent phase II clinical trial. Therefore, we generated a novel anti-EpCAM antibody-drug conjugate and assessed whether it showed enhanced antitumor effects. METHODS Chemical cross-linking was conducted to covalently conjugate α-amanitin, a toxin known to inhibit DNA transcription, with chiHEA125, a chimerized anti-EpCAM monoclonal antibody, to generate the antibody-drug conjugate α-amanitin-glutarate-chiHEA125 (chiHEA125-Ama). Antiproliferative activity of chiHEA125-Ama was tested in human pancreatic (BxPc-3 and Capan-1), colorectal (Colo205), breast (MCF-7), and bile duct (OZ) cancer cell lines in vitro using [(3)H]-thymidine incorporation assay. Antitumor activity of chiHEA125-Ama was assessed in vivo in immunocompromised mice bearing subcutaneous human BxPc-3 pancreatic carcinoma xenograft tumors (n = 66 mice). Cell proliferation and apoptosis were evaluated in xenograft tumors by immunohistochemistry. All statistical tests were two-sided. RESULTS In all cell lines, chiHEA125-Ama reduced cell proliferation (mean half maximal inhibitory concentration [IC(50)] = 2.5 × 10(-10) to 5.4 × 10(-12) M). A single dose of chiHEA125-Ama inhibited BxPc-3 xenograft tumor growth (chiHEA125 [control, n = 4 mice] vs. chiHEA125-Ama [n = 6 mice], dose of 15 mg/kg with respect to IgG and 50 μg/kg with respect to α-amanitin, mean relative increase in tumor volume on day 16 = 884% vs. -79%, difference = 963%, 95% CI = 582% to 1344%, P = .019). Two higher doses of chiHEA125-Ama (100 μg/kg with respect to α-amanitin), administered 1 week apart (n = 10 mice per group), led to complete tumor regression in nine of 10 (90%) mice compared with chiHEA125, during the observation period of 16 days; increased apoptosis and reduced cell proliferation were observed in mice treated with chiHEA125-Ama. CONCLUSION This preclinical study suggests that anti-EpCAM antibody conjugates with α-amanitin have the potential to be highly effective therapeutic agents for pancreatic carcinomas and various EpCAM-expressing malignancies.
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Affiliation(s)
- Gerhard Moldenhauer
- Department of Translational Immunology (D015), German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
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He W, Chan LY, Zeng G, Daly NL, Craik DJ, Tan N. Isolation and characterization of cytotoxic cyclotides from Viola philippica. Peptides 2011; 32:1719-23. [PMID: 21723349 DOI: 10.1016/j.peptides.2011.06.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Revised: 06/16/2011] [Accepted: 06/16/2011] [Indexed: 11/24/2022]
Abstract
Cyclotides are a large family of plant peptides characterized by a macrocyclic backbone and knotted arrangement of three disulfide bonds. This unique structure renders cyclotides exceptionally stable to thermal, chemical and enzymatic treatments. They exhibit a variety of bioactivities, including uterotonic, anti-HIV, cytotoxic and hemolytic activity and it is these properties that make cyclotides an interesting peptide scaffold for drug design. In this study, eight new cyclotides (Viphi A-H), along with eight known cyclotides, were isolated from Viola philippica, a plant from the Violaceae family. In addition, Viba 17 and Mram 8 were isolated for the first time as peptides. The sequences of these cyclotides were elucidated primarily by using a strategy involving reduction, enzymatic digestion and tandem mass spectroscopy sequencing. Several of the cyclotides showed cytotoxic activities against the cancer cell lines MM96L, HeLa and BGC-823. The novel cyclotides reported here: (1) enhance the known sequence variation observed for cyclotides; (2) extend the number of species known to contain cyclotides; (3) provide interesting structure-activity relationships that delineate residues important for cytotoxic activity. In addition, this study provides insights into the potential active ingredients of traditional Chinese medicines.
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Affiliation(s)
- Wenjun He
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132# Lanhei Road, Heilongtan, Kunming 650204, Yunnan, PR China
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Condie JA, Nowak G, Reed DW, Balsevich JJ, Reaney MJT, Arnison PG, Covello PS. The biosynthesis of Caryophyllaceae-like cyclic peptides in Saponaria vaccaria L. from DNA-encoded precursors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 67:682-90. [PMID: 21554452 DOI: 10.1111/j.1365-313x.2011.04626.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Cyclic peptides (CPs) are produced in a very wide range of taxa. Their biosynthesis generally involves either non-ribosomal peptide synthases or ribosome-dependent production of precursor peptides. Plants within the Caryophyllaceae and certain other families produce CPs which generally consist of 5-9 proteinogenic amino acids. The biological roles for these CPs in the plant are not very clear, but many of them have activity in mammalian systems. There is currently very little known about the biosynthesis of CPs in the Caryophyllaceae. A collection of expressed sequence tags from developing seeds of Saponaria vaccaria was investigated for information about CP biosynthesis. This revealed genes that appeared to encode CP precursors which are subsequently cyclized to mature CPs. This was tested and confirmed by the expression of a cDNA encoding a putative precursor of the CP segetalin A in transformed S. vaccaria roots. Similarly, extracts of developing S. vaccaria seeds were shown to catalyze the production of segetalin A from the same putative (synthetic) precursor. Moreover, the presence in S. vaccaria seeds of two segetalins, J [cyclo(FGTHGLPAP)] and K [cyclo(GRVKA)], which was predicted by sequence analysis, was confirmed by liquid chromatography/mass spectrometry. Sequence analysis also predicts the presence of similar CP precursor genes in Dianthus caryophyllus and Citrus spp. The data support the ribosome-dependent biosynthesis of Caryophyllaceae-like CPs in the Caryophyllaceae and Rutaceae.
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Affiliation(s)
- Janet A Condie
- Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7NOW9, Canada
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Colgrave ML, Korsinczky MJL, Clark RJ, Foley F, Craik DJ. Sunflower trypsin inhibitor-1, proteolytic studies on a trypsin inhibitor peptide and its analogs. Biopolymers 2010; 94:665-72. [DOI: 10.1002/bip.21415] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Conlan BF, Gillon AD, Craik DJ, Anderson MA. Circular proteins and mechanisms of cyclization. Biopolymers 2010; 94:573-83. [DOI: 10.1002/bip.21422] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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