1
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Patel KP, Chen WT, Delbecq L, Bruner SD. Alternative Linkage Chemistries in the Chemoenzymatic Synthesis of Microviridin-Based Cyclic Peptides. Org Lett 2024; 26:1138-1142. [PMID: 38306609 DOI: 10.1021/acs.orglett.3c04045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
Engineering biosynthetic pathways to ribosomally synthesized and post-translationally modified peptides (RiPPs) offers several advantages for both in vivo and in vitro applications. Here we probe the ability of peptide cyclases to generate trimacrocycle microviridin analogs with non-native cross-links. The results demonstrate that diverse chemistries are tolerated by macrocyclases in the ATP-grasp family and allow for the construction of unique cyclic peptide architectures that retain protease inhibition activity. In addition, cocomplex structures of analogs bound to a model protease were determined, illustrating how changes in functional groups maintain peptide conformation and target binding.
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Affiliation(s)
- Krishna P Patel
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Wen-Ting Chen
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Léa Delbecq
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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2
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Choi B, Link AJ. Discovery, Function, and Engineering of Graspetides. TRENDS IN CHEMISTRY 2023; 5:620-633. [PMID: 37614740 PMCID: PMC10443899 DOI: 10.1016/j.trechm.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Graspetides are a class of RiPPs (ribosomally synthesized and post-translationally modified peptides) defined by the presence of ester or amide side chain-side chain linkages resulting in peptide macrocycles. The graspetide name comes from the ATP-grasp enzymes that install the side chain-side chain linkages. This review covers the early, activity-based isolation of the first graspetides, marinostatins and microviridins, as well as the key genomics-driven experiments that established graspetide as RiPPs. The mechanism and structure of graspetide-associated ATP-grasp enzymes is discussed. Genome mining methods to discover new graspetides as well as the analytical techniques used to determine the linkages in graspetides are described. Extant knowledge on the bioactivity of graspetides as protease inhibitors is reviewed. Further chemical modifications to graspetides as well graspetide engineering studies are also described. We conclude with several suggestions about future directions of graspetide research.
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Affiliation(s)
- Brian Choi
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
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3
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Dreher TW, Matthews R, Davis EW, Mueller RS. Woronichinia naegeliana: A common nontoxigenic component of temperate freshwater cyanobacterial blooms with 30% of its genome in transposons. HARMFUL ALGAE 2023; 125:102433. [PMID: 37220973 DOI: 10.1016/j.hal.2023.102433] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/13/2023] [Accepted: 03/28/2023] [Indexed: 05/25/2023]
Abstract
Monitoring in the U.S. state of Washington across the period 2007-2019 showed that Woronichinia has been present in many lakes state-wide. This cyanobacterium was commonly dominant or sub-dominant in cyanobacterial blooms in the wet temperate region west of the Cascade Mountains. In these lakes, Woronichinia often co-existed with Microcystis, Dolichospermum and Aphanizomenon flos-aquae and the cyanotoxin microcystin has often been present in those blooms, although it has not been known whether Woronichinia is a toxin producer. We report the first complete genome of Woronichinia naegeliana WA131, assembled from the metagenome of a sample collected from Wiser Lake, Washington, in 2018. The genome contains no genes for cyanotoxin biosynthesis or taste-and-odor compounds, but there are biosynthetic gene clusters for other bioactive peptides, including anabaenopeptins, cyanopeptolins, microginins and ribosomally produced, post-translationally modified peptides. Genes for photosynthesis, nutrient acquisition, vitamin synthesis and buoyancy that are typical of bloom-forming cyanobacteria are present, although nitrate and nitrite reductase genes are conspicuously absent. However, the 7.9 Mbp genome is 3-4 Mbp larger than those of the above-mentioned frequently co-existing cyanobacteria. The increased genome size is largely due to an extraordinary number of insertion sequence elements (transposons), which account for 30.3% of the genome and many of which are present in multiple copies. The genome contains a relatively large number of pseudogenes, 97% of which are transposase genes. W. naegeliana WA131 thus seems to be able to limit the potentially deleterious effects of high rates of recombination and transposition to the mobilome fraction of its genome.
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Affiliation(s)
- Theo W Dreher
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331 USA.
| | - Robin Matthews
- Department of Environmental Sciences, Western Washington University, Bellingham, WA 98225, USA.
| | - Edward W Davis
- Center for Quantitative Life Sciences, Oregon State University, Corvallis, Oregon 97331 USA
| | - Ryan S Mueller
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331 USA
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4
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Zdarta J, Kołodziejczak-Radzimska A, Bachosz K, Rybarczyk A, Bilal M, Iqbal HMN, Buszewski B, Jesionowski T. Nanostructured supports for multienzyme co-immobilization for biotechnological applications: Achievements, challenges and prospects. Adv Colloid Interface Sci 2023; 315:102889. [PMID: 37030261 DOI: 10.1016/j.cis.2023.102889] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 03/14/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023]
Abstract
The synergistic combination of current biotechnological and nanotechnological research has turned to multienzyme co-immobilization as a promising concept to design biocatalysis engineering. It has also intensified the development and deployment of multipurpose biocatalysts, for instance, multienzyme co-immobilized constructs, via biocatalysis/protein engineering to scale-up and fulfil the ever-increasing industrial demands. Considering the characteristic features of both the loaded multienzymes and nanostructure carriers, i.e., selectivity, specificity, stability, resistivity, induce activity, reaction efficacy, multi-usability, high catalytic turnover, optimal yield, ease in recovery, and cost-effectiveness, multienzyme-based green biocatalysts have become a powerful norm in biocatalysis/protein engineering sectors. In this context, the current state-of-the-art in enzyme engineering with a synergistic combination of nanotechnology, at large, and nanomaterials, in particular, are significantly contributing and providing robust tools to engineer and/or tailor enzymes to fulfil the growing catalytic and contemporary industrial needs. Considering the above critics and unique structural, physicochemical, and functional attributes, herein, we spotlight important aspects spanning across prospective nano-carriers for multienzyme co-immobilization. Further, this work comprehensively discuss the current advances in deploying multienzyme-based cascade reactions in numerous sectors, including environmental remediation and protection, drug delivery systems (DDS), biofuel cells development and energy production, bio-electroanalytical devices (biosensors), therapeutical, nutraceutical, cosmeceutical, and pharmaceutical oriented applications. In conclusion, the continuous developments in nano-assembling the multienzyme loaded co-immobilized nanostructure carriers would be a unique way that could act as a core of modern biotechnological research.
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Affiliation(s)
- Jakub Zdarta
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland.
| | - Agnieszka Kołodziejczak-Radzimska
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland
| | - Karolina Bachosz
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland
| | - Agnieszka Rybarczyk
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland
| | - Muhammad Bilal
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Torun, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland.
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5
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Wang T, Wang X, Zhao H, Huo L, Fu C. Uncovering a Subtype of Microviridins via the Biosynthesis Study of FR901451. ACS Chem Biol 2022; 17:3489-3498. [PMID: 36373602 DOI: 10.1021/acschembio.2c00688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microviridins are a class of ribosomally synthesized and post-translationally modified peptides originally discovered from cyanobacteria, featured by intramolecular ω-ester and ω-amide bonds catalyzed by two ATP-grasp ligases. In this study, 104 biosynthetic gene clusters of microviridins from Bacteroidetes were bioinformatically analyzed, which unveiled unique features of precursor peptides. The analysis of core peptides revealed a microviridin-like biosynthetic gene cluster from Chitinophagia japonensis DSM13484 consisting of two potential precursors ChiA1 and ChiA2. Unexpectedly, the core peptide sequence of ChiA1 is consistent with the backbone of the elastase-inhibiting peptide FR901451, while ChiA2 is likely to be a precursor of an unknown product. However, an unusual C-terminal follower cleavage compared to the previously known microviridin pathways was observed and found to be dispensable for other modifications. To confirm the biosynthetic origin of FR901451, ATP-grasp ligases ChiC and ChiB were biochemically characterized to be responsible for the intramolecular ester and amide bond formation, respectively. In vitro reconstitution of the pathway showed the three-fold dehydrations of ChiA1 while unusual four-fold dehydrations were observed for ChiA2. Furthermore, in vivo gene coexpression facilitated the production of chitinoviridin A1 (FR901451) and two novel microviridin-class compounds chitinoviridin A2A and chitinoviridin A2B, with an extra macrolactone ring. All of these peptides showed potent inhibitory effects against elastase and chymotrypsin independently.
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Affiliation(s)
- Tingting Wang
- Workgroup Genome Mining for Secondary Metabolites, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.,Helmholtz International Lab for Anti-Infectives, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
| | - Xiaotong Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China.,Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Haowen Zhao
- Workgroup Genome Mining for Secondary Metabolites, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.,Helmholtz International Lab for Anti-Infectives, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
| | - Liujie Huo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China.,Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Chengzhang Fu
- Workgroup Genome Mining for Secondary Metabolites, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.,Helmholtz International Lab for Anti-Infectives, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
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6
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Elashal HE, Koos JD, Cheung-Lee WL, Choi B, Cao L, Richardson MA, White HL, Link AJ. Biosynthesis and characterization of fuscimiditide, an aspartimidylated graspetide. Nat Chem 2022; 14:1325-1334. [PMID: 35982233 PMCID: PMC10078976 DOI: 10.1038/s41557-022-01022-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 07/11/2022] [Indexed: 11/09/2022]
Abstract
Microviridins and other ω-ester-linked peptides, collectively known as graspetides, are characterized by side-chain-side-chain linkages installed by ATP-grasp enzymes. Here we report the discovery of a family of graspetides, the gene clusters of which also encode an O-methyltransferase with homology to the protein repair catalyst protein L-isoaspartyl methyltransferase. Using heterologous expression, we produced fuscimiditide, a ribosomally synthesized and post-translationally modified peptide (RiPP). NMR analysis of fuscimiditide revealed that the peptide contains two ester cross-links forming a stem-loop macrocycle. Furthermore, an unusually stable aspartimide moiety is found within the loop macrocycle. We fully reconstituted fuscimiditide biosynthesis in vitro including formation of the ester and aspartimide moieties. The aspartimide moiety embedded in fuscimiditide hydrolyses regioselectively to isoaspartate. Surprisingly, this isoaspartate-containing peptide is also a substrate for the L-isoaspartyl methyltransferase homologue, thus driving any hydrolysis products back to the aspartimide form. Whereas an aspartimide is often considered a nuisance product in protein formulations, our data suggest that some RiPPs have aspartimide residues intentionally installed via enzymatic activity.
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Affiliation(s)
- Hader E Elashal
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Joseph D Koos
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Wai Ling Cheung-Lee
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Brian Choi
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Li Cao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Michelle A Richardson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Heather L White
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - A James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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7
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Scholz S, Kerestetzopoulou S, Wiebach V, Schnegotzki R, Schmid B, Reyna‐González E, Ding L, Süssmuth RD, Dittmann E, Baunach M. One-Pot Chemoenzymatic Synthesis of Microviridin Analogs Containing Functional Tags. Chembiochem 2022; 23:e202200345. [PMID: 35995730 PMCID: PMC9826346 DOI: 10.1002/cbic.202200345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/31/2022] [Indexed: 01/11/2023]
Abstract
Microviridins are a prominent family of ribosomally synthesized and posttranslationally modified peptides (RiPPs) featuring characteristic lactone and lactam rings. Their unusual cage-like architecture renders them highly potent serine protease inhibitors of which individual variants specifically inhibit different types of proteases of pharmacological interest. While posttranslational modifications are key for the stability and bioactivity of RiPPs, additional attractive properties can be introduced by functional tags. To date - although highly desirable - no method has been reported to incorporate functional tags in microviridin scaffolds or the overarching class of graspetides. In this study, a chemoenzymatic in vitro platform is used to introduce functional tags in various microviridin variants yielding biotinylated, dansylated or propargylated congeners. This straightforward approach paves the way for customized protease inhibitors with built-in functionalities that can help to unravel the still elusive ecological roles and targets of this remarkable class of compounds and to foster applications based on protease inhibition.
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Affiliation(s)
- Stella Scholz
- Department of MicrobiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Sofia Kerestetzopoulou
- Department of MicrobiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Vincent Wiebach
- Department of Biotechnology and BiomedicineTechnical University of DenmarkSøltofts Plads, Building 221DK-2800 Kgs.LyngbyDenmark
| | - Romina Schnegotzki
- Institute of ChemistryTechnical University BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Bianca Schmid
- Institute of ChemistryTechnical University BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Emmanuel Reyna‐González
- Department of MicrobiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Ling Ding
- Department of Biotechnology and BiomedicineTechnical University of DenmarkSøltofts Plads, Building 221DK-2800 Kgs.LyngbyDenmark
| | - Roderich D. Süssmuth
- Institute of ChemistryTechnical University BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Elke Dittmann
- Department of MicrobiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Martin Baunach
- Department of MicrobiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany,Institute of Pharmaceutical BiologyUniversity of BonnNussallee 653115BonnGermany
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8
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Phan CS, Mehjabin JJ, Anas ARJ, Hayasaka M, Onoki R, Wang J, Umezawa T, Washio K, Morikawa M, Okino T. Nostosin G and Spiroidesin B from the Cyanobacterium Dolichospermum sp. NIES-1697. JOURNAL OF NATURAL PRODUCTS 2022; 85:2000-2005. [PMID: 35948062 DOI: 10.1021/acs.jnatprod.2c00382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Chemical investigation of the cyanobacterium Dolichospermum sp. NIES-1697 afforded nostosin G (1), a linear tripeptide, spiroidesin B (2), and two known compounds, anabaenopeptins I (3) and J (4). Planar structures and absolute configurations for 1 and 2 were determined by 2D NMR, HRMS, Marfey's methodology, chiral-phase HPLC, and enzymatic degradation. Nostosin G (1) is a unique example of a linear peptide containing three subunits, 4-hydroxyphenyllactic acid (Hpla), homotyrosine (Hty), and argininal, with potent trypsin inhibitory properties. The biosynthetic gene clusters for nostosin G (1) and spiroidesin B (2) were investigated based on the genome sequence of Dolichospermum sp. NIES-1697.
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9
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Entfellner E, Li R, Jiang Y, Ru J, Blom J, Deng L, Kurmayer R. Toxic/Bioactive Peptide Synthesis Genes Rearranged by Insertion Sequence Elements Among the Bloom-Forming Cyanobacteria Planktothrix. Front Microbiol 2022; 13:901762. [PMID: 35966708 PMCID: PMC9366434 DOI: 10.3389/fmicb.2022.901762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/23/2022] [Indexed: 11/28/2022] Open
Abstract
It has been generally hypothesized that mobile elements can induce genomic rearrangements and influence the distribution and functionality of toxic/bioactive peptide synthesis pathways in microbes. In this study, we performed in depth genomic analysis by completing the genomes of 13 phylogenetically diverse strains of the bloom-forming freshwater cyanobacteria Planktothrix spp. to investigate the role of insertion sequence (IS) elements in seven pathways. Chromosome size varied from 4.7–4.8 Mbp (phylogenetic Lineage 1 of P. agardhii/P. rubescens thriving in shallow waterbodies) to 5.4–5.6 Mbp (Lineage 2 of P. agardhii/P. rubescens thriving in deeper physically stratified lakes and reservoirs) and 6.3–6.6 Mbp (Lineage 3, P. pseudagardhii/P. tepida including planktic and benthic ecotypes). Although the variation in chromosome size was positively related to the proportion of IS elements (1.1–3.7% on chromosome), quantitatively, IS elements and other paralogs only had a minor share in chromosome size variation. Thus, the major part of genomic variation must have resulted from gene loss processes (ancestor of Lineages 1 and 2) and horizontal gene transfer (HGT). Six of seven peptide synthesis gene clusters were found located on the chromosome and occurred already in the ancestor of P. agardhii/P. rubescens, and became partly lost during evolution of Lineage 1. In general, no increased IS element frequency in the vicinity of peptide synthesis gene clusters was observed. We found a higher proportion of IS elements in ten breaking regions related to chromosomal rearrangements and a tendency for colocalization of toxic/bioactive peptide synthesis gene clusters on the chromosome.
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Affiliation(s)
| | - Ruibao Li
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Yiming Jiang
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Jinlong Ru
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University, Giessen, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Rainer Kurmayer
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
- *Correspondence: Rainer Kurmayer,
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10
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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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11
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Ramesh S, Guo X, DiCaprio AJ, De Lio AM, Harris LA, Kille BL, Pogorelov TV, Mitchell DA. Bioinformatics-Guided Expansion and Discovery of Graspetides. ACS Chem Biol 2021; 16:2787-2797. [PMID: 34766760 DOI: 10.1021/acschembio.1c00672] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Graspetides are a class of ribosomally synthesized and post-translationally modified peptide natural products featuring ATP-grasp ligase-dependent formation of macrolactones/macrolactams. These modifications arise from serine, threonine, or lysine donor residues linked to aspartate or glutamate acceptor residues. Characterized graspetides include serine protease inhibitors such as the microviridins and plesiocin. Here, we report an update to Rapid ORF Description and Evaluation Online (RODEO) for the automated detection of graspetides, which identified 3,923 high-confidence graspetide biosynthetic gene clusters. Sequence and co-occurrence analyses doubled the number of graspetide groups from 12 to 24, defined based on core consensus sequence and putative secondary modification. Bioinformatic analyses of the ATP-grasp ligase superfamily suggest that extant graspetide synthetases diverged once from an ancestral ATP-grasp ligase and later evolved to introduce a variety of ring connectivities. Furthermore, we characterized thatisin and iso-thatisin, two graspetides related by conformational stereoisomerism from Lysobacter antibioticus. Derived from a newly identified graspetide group, thatisin and iso-thatisin feature two interlocking macrolactones with identical ring connectivity, as determined by a combination of tandem mass spectrometry (MS/MS), methanolytic, and mutational analyses. NMR spectroscopy of thatisin revealed a cis conformation for a key proline residue, while molecular dynamics simulations, solvent-accessible surface area calculations, and partial methanolytic analysis coupled with MS/MS support a trans conformation for iso-thatisin at the same position. Overall, this work provides a comprehensive overview of the graspetide landscape, and the improved RODEO algorithm will accelerate future graspetide discoveries by enabling open-access analysis of existing and emerging genomes.
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Affiliation(s)
- Sangeetha Ramesh
- Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Xiaorui Guo
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Adam J. DiCaprio
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ashley M. De Lio
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 West Clark Street, Urbana, Illinois 61801, United States
| | - Lonnie A. Harris
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Bryce L. Kille
- Department of Computer Science, University of Illinois at Urbana-Champaign, 201 North Goodwin Avenue, Urbana, Illinois 61801, United States
| | - Taras V. Pogorelov
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 West Clark Street, Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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12
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Song I, Kim Y, Yu J, Go SY, Lee HG, Song WJ, Kim S. Molecular mechanism underlying substrate recognition of the peptide macrocyclase PsnB. Nat Chem Biol 2021; 17:1123-1131. [PMID: 34475564 DOI: 10.1038/s41589-021-00855-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 07/08/2021] [Indexed: 01/02/2023]
Abstract
Graspetides, also known as ω-ester-containing peptides (OEPs), are a family of ribosomally synthesized and post-translationally modified peptides (RiPPs) bearing side chain-to-side chain macrolactone or macrolactam linkages. Here, we present the molecular details of precursor peptide recognition by the macrocyclase enzyme PsnB in the biosynthesis of plesiocin, a group 2 graspetide. Biochemical analysis revealed that, in contrast to other RiPPs, the core region of the plesiocin precursor peptide noticeably enhanced the enzyme-precursor interaction via the conserved glutamate residues. We obtained four crystal structures of symmetric or asymmetric PsnB dimers, including those with a bound core peptide and a nucleotide, and suggest that the highly conserved Arg213 at the enzyme active site specifically recognizes a ring-forming acidic residue before phosphorylation. Collectively, this study provides insights into the mechanism underlying substrate recognition in graspetide biosynthesis and lays a foundation for engineering new variants.
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Affiliation(s)
- Inseok Song
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Younghyeon Kim
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Jaeseung Yu
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Su Yong Go
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Hong Geun Lee
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Woon Ju Song
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, Seoul, South Korea.
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13
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Kaweewan I, Nakagawa H, Kodani S. Heterologous expression of a cryptic gene cluster from Marinomonas fungiae affords a novel tricyclic peptide marinomonasin. Appl Microbiol Biotechnol 2021; 105:7241-7250. [PMID: 34480236 DOI: 10.1007/s00253-021-11545-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/01/2021] [Accepted: 08/24/2021] [Indexed: 10/20/2022]
Abstract
The ω-ester-containing peptides (OEPs) are a group of ribosomally synthesized and post-translationally modified peptides (RiPPs). The biosynthetic gene clusters of ω-ester-containing peptides commonly include ATP-grasp ligase coding genes and are distributed over the genomes of a wide variety of bacteria. A new biosynthetic gene cluster of ω-ester-containing peptides was found in the genome sequence of the marine proteobacterium Marinomonas fungiae. Heterologous production of a new tricyclic peptide named marinomonasin was accomplished using the biosynthetic gene cluster in Escherichia coli expression host strain BL21(DE3). By ESI-MS and NMR experiments, the structure of marinomonasin was determined to be a tricyclic peptide 18 amino acids in length with one ester and two isopeptide bonds in the molecule. The bridging patterns of the three intramolecular bonds were determined by the interpretation of HMBC and NOESY data. The bridging pattern of marinomonasin was unprecedented in the ω-ester-containing peptide group. The results indicated that the ATP-grasp ligase for the production of marinomonasin was a novel enzyme possessing bifunctional activity to form one ester and two isopeptide bonds. KEY POINTS: • New tricyclic peptide marinomonasin was heterologously produced in Escherichia coli. • Marinomonasin contained one ester and two isopeptide bonds in the molecule. • The bridging pattern of intramolecular bonds was novel.
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Affiliation(s)
- Issara Kaweewan
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
| | - Hiroyuki Nakagawa
- Institute of Food Research, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan.,Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Shinya Kodani
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan. .,Shizuoka Institute for the Study of Marine Biology and Chemistry, Shizuoka University, Shizuoka, Japan. .,College of Agriculture, Academic Institute, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
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14
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Patel KP, Silsby LM, Li G, Bruner SD. Structure-Based Engineering of Peptide Macrocyclases for the Chemoenzymatic Synthesis of Microviridins. J Org Chem 2021; 86:11212-11219. [PMID: 34263606 DOI: 10.1021/acs.joc.1c00785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microviridins are cyanobacterial tricyclic depsipeptides with unique ring architectures and function as serine protease inhibitors. In this study, we explore two strategies to probe the structure and mechanism of macrocyclases involved in microviridin biosynthesis. The results both provide approaches for in vitro chemoenzymatic synthesis and insight into the molecular interactions and function of the biosynthetic enzymes. The first strategy involves generating constitutively activated macrocyclases whereby the leader portion of the substrate peptide is covalently attached to the ATP-grasp ligases to examine leader peptide/enzyme interactions. The second strategy uses a structure-based design to create disulfide cross-linked peptide/enzyme complexes. Together, the strategies provide constitutively active enzymes and tools to study the catalysis of the macrocyclizations on synthetic core peptides.
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Affiliation(s)
- Krishna P Patel
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Lily M Silsby
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Gengnan Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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15
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Morón-Asensio R, Schuler D, Wiedlroither A, Offterdinger M, Kurmayer R. Differential Labeling of Chemically Modified Peptides and Lipids among Cyanobacteria Planktothrix and Microcystis. Microorganisms 2021; 9:1578. [PMID: 34442657 PMCID: PMC8398151 DOI: 10.3390/microorganisms9081578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/18/2021] [Accepted: 07/19/2021] [Indexed: 11/20/2022] Open
Abstract
The cyanoHAB forming cyanobacteria Microcystis and Planktothrix frequently produce high intracellular amounts of microcystins (MCs) or anabaenopeptins (APs). In this study, chemically modified MCs and APs have been localized on a subcellular level in Microcystis and Planktothrix applying copper-catalyzed alkyne-azide cycloaddition (CuACC). For this purpose, three different non-natural amino acids carrying alkyne or azide moieties were fed to individual P. agardhii strains No371/1 and CYA126/8 as well as to M. aeruginosa strain Hofbauer showing promiscuous incorporation of various amino acid substrates during non-ribosomal peptide synthesis (NRPS). Moreover, CYA126/8 peptide knock-out mutants and non-toxic strain Synechocystis PCC6803 were processed under identical conditions. Simultaneous labeling of modified peptides with ALEXA405 and ALEXA488 and lipid staining with BODIPY 505/515 were performed to investigate the intracellular location of the modified peptides. Pearson correlation coefficients (PCC) obtained from confocal images were calculated between the different fluorophores and the natural autofluorescence (AF), and between labeled modified peptides and dyed lipids to investigate the spatial overlap between peptides and the photosynthetic complex, and between peptides and lipids. Overall, labeling of modified MCs (M. aeruginosa) and APs (P. agardhii) using both fluorophores revealed increased intensity in MC/AP producing strains. For Synechocystis lacking NRPS, no labeling using either ALEXA405 or ALEXA488 was observed. Lipid staining in M. aeruginosa and Synechocystis was intense while in Planktothrix it was more variable. When compared with AF, both modified peptides and lipids showed a heterologous distribution. In comparison, the correlation between stained lipids and labeled peptides was not increased suggesting a reduced spatial overlap.
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Affiliation(s)
- Rubén Morón-Asensio
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, 5310 Mondsee, Austria; (D.S.); (A.W.)
| | - David Schuler
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, 5310 Mondsee, Austria; (D.S.); (A.W.)
| | - Anneliese Wiedlroither
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, 5310 Mondsee, Austria; (D.S.); (A.W.)
| | - Martin Offterdinger
- Core Facility Biooptics (CCB), Medical University Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria;
| | - Rainer Kurmayer
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, 5310 Mondsee, Austria; (D.S.); (A.W.)
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16
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Uzunov B, Stefanova K, Radkova M, Descy JP, Gärtner G, Stoyneva-Gärtner M. First Report on Microcystis as a Potential Microviridin Producer in Bulgarian Waterbodies. Toxins (Basel) 2021; 13:toxins13070448. [PMID: 34203459 PMCID: PMC8310014 DOI: 10.3390/toxins13070448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/30/2022] Open
Abstract
Bulgaria, situated on the Balkan Peninsula, is rich in small and shallow, natural and man-made non-lotic waterbodies, which are threatened by blooms of Cyanoprokaryota/Cyanobacteria. Although cyanotoxins in Bulgarian surface waters are receiving increased attention, there is no information on microviridins and their producers. This paper presents results from a phytoplankton study, conducted in August 2019 in three lakes (Durankulak, Vaya, Uzungeren) and five reservoirs (Duvanli, Mandra, Poroy, Sinyata Reka, Zhrebchevo) in which a molecular-genetic analysis (PCR based on the precursor mdnA gene and subsequent translation to amino acid alignments), combined with conventional light microscopy and an HPLC analysis of marker pigments, were applied for the identification of potential microviridin producers. The results provide evidence that ten strains of the genus Microcystis, and of its most widespread species M. aeruginosa in particular, are potentially toxigenic in respect to microviridins. The mdnA sequences were obtained from all studied waterbodies and their translation to amino-acid alignments revealed the presence of five microviridin variants (types B/C, Izancya, CBJ55500.1 (Microcystis 199), and MC19, as well as a variant, which was very close to type A). This study adds to the general understanding of the microviridin occurrence, producers, and sequence diversity.
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Affiliation(s)
- Blagoy Uzunov
- Department of Botany, Faculty of Biology, Sofia University, 8 blvd. Dragan Zankov, 1164 Sofia, Bulgaria
- Correspondence: (B.U.); (M.S.-G.)
| | - Katerina Stefanova
- AgroBioInstitute, Bulgarian Agricultural Academy, 8 blvd. Dragan Zankov, 1164 Sofia, Bulgaria; (K.S.); (M.R.)
| | - Mariana Radkova
- AgroBioInstitute, Bulgarian Agricultural Academy, 8 blvd. Dragan Zankov, 1164 Sofia, Bulgaria; (K.S.); (M.R.)
| | - Jean-Pierre Descy
- Unité d’Océanographie Chimique, Université de Liège, Sart Tilman, 4000 Liège, Belgium;
| | - Georg Gärtner
- Institut für Botanik der Universität Innsbruck, Sternwartestrasse 15, 6020 Innsbruck, Austria;
| | - Maya Stoyneva-Gärtner
- Department of Botany, Faculty of Biology, Sofia University, 8 blvd. Dragan Zankov, 1164 Sofia, Bulgaria
- Correspondence: (B.U.); (M.S.-G.)
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17
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Zhao G, Kosek D, Liu HB, Ohlemacher SI, Blackburne B, Nikolskaya A, Makarova KS, Sun J, Barry Iii CE, Koonin EV, Dyda F, Bewley CA. Structural Basis for a Dual Function ATP Grasp Ligase That Installs Single and Bicyclic ω-Ester Macrocycles in a New Multicore RiPP Natural Product. J Am Chem Soc 2021; 143:8056-8068. [PMID: 34028251 DOI: 10.1021/jacs.1c02316] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Among the ribosomally synthesized and post-translationally modified peptide (RiPP) natural products, "graspetides" (formerly known as microviridins) contain macrocyclic esters and amides that are formed by ATP-grasp ligase tailoring enzymes using the side chains of Asp/Glu as acceptors and Thr/Ser/Lys as donors. Graspetides exhibit diverse patterns of macrocylization and connectivities exemplified by microviridins, that have a caged tricyclic core, and thuringin and plesiocin that feature a "hairpin topology" with cross-strand ω-ester bonds. Here, we characterize chryseoviridin, a new type of multicore RiPP encoded by Chryseobacterium gregarium DS19109 (Phylum Bacteroidetes) and solve a 2.44 Å resolution crystal structure of a quaternary complex consisting of the ATP-grasp ligase CdnC bound to ADP, a conserved leader peptide and a peptide substrate. HRMS/MS analyses show that chryseoviridin contains four consecutive five- or six-residue macrocycles ending with a microviridin-like core. The crystal structure captures respective subunits of the CdnC homodimer in the apo or substrate-bound state revealing a large conformational change in the B-domain upon substrate binding. A docked model of ATP places the γ-phosphate group within 2.8 Å of the Asp acceptor residue. The orientation of the bound substrate is consistent with a model in which macrocyclization occurs in the N- to C-terminal direction for core peptides containing multiple Thr/Ser-to-Asp macrocycles. Using systematically varied sequences, we validate this model and identify two- or three-amino acid templating elements that flank the macrolactone and are required for enzyme activity in vitro. This work reveals the structural basis for ω-ester bond formation in RiPP biosynthesis.
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Affiliation(s)
- Gengxiang Zhao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Dalibor Kosek
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Hong-Bing Liu
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Shannon I Ohlemacher
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Brittney Blackburne
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Anastasia Nikolskaya
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Jiadong Sun
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Clifton E Barry Iii
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Carole A Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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18
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Liu D, Rubin GM, Dhakal D, Chen M, Ding Y. Biocatalytic synthesis of peptidic natural products and related analogues. iScience 2021; 24:102512. [PMID: 34041453 PMCID: PMC8141463 DOI: 10.1016/j.isci.2021.102512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Peptidic natural products (PNPs) represent a rich source of lead compounds for the discovery and development of therapeutic agents for the treatment of a variety of diseases. However, the chemical synthesis of PNPs with diverse modifications for drug research is often faced with significant challenges, including the unavailability of constituent nonproteinogenic amino acids, inefficient cyclization protocols, and poor compatibility with other functional groups. Advances in the understanding of PNP biosynthesis and biocatalysis provide a promising, sustainable alternative for the synthesis of these compounds and their analogues. Here we discuss current progress in using native and engineered biosynthetic enzymes for the production of both ribosomally and nonribosomally synthesized peptides. In addition, we highlight new in vitro and in vivo approaches for the generation and screening of PNP libraries.
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Affiliation(s)
- Dake Liu
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Garret M. Rubin
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
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19
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Kang D, Shoaie S, Jacquiod S, Sørensen SJ, Ledesma-Amaro R. Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production. Microorganisms 2021; 9:microorganisms9051042. [PMID: 34066089 PMCID: PMC8151938 DOI: 10.3390/microorganisms9051042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/25/2021] [Accepted: 05/06/2021] [Indexed: 01/07/2023] Open
Abstract
A promising keratin-degrading strain from the genus Chryseobacterium (Chryseobacterium sp. KMC2) was investigated using comparative genomic tools against three publicly available reference genomes to reveal the keratinolytic potential for biosynthesis of valuable secondary metabolites. Genomic features and metabolic potential of four species were compared, showing genomic differences but similar functional categories. Eleven different secondary metabolite gene clusters of interest were mined from the four genomes successfully, including five common ones shared across all genomes. Among the common metabolites, we identified gene clusters involved in biosynthesis of flexirubin-type pigment, microviridin, and siderophore, showing remarkable conservation across the four genomes. Unique secondary metabolite gene clusters were also discovered, for example, ladderane from Chryseobacterium sp. KMC2. Additionally, this study provides a more comprehensive understanding of the potential metabolic pathways of keratin utilization in Chryseobacterium sp. KMC2, with the involvement of amino acid metabolism, TCA cycle, glycolysis/gluconeogenesis, propanoate metabolism, and sulfate reduction. This work uncovers the biosynthesis of secondary metabolite gene clusters from four keratinolytic Chryseobacterium species and shades lights on the keratinolytic potential of Chryseobacterium sp. KMC2 from a genome-mining perspective, can provide alternatives to valorize keratinous materials into high-value bioactive natural products.
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Affiliation(s)
- Dingrong Kang
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark;
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, Lodon SE1 9RT, UK;
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
- Correspondence: (D.K.); (R.L-A.)
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, Lodon SE1 9RT, UK;
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, 114 17 Stockholm, Sweden
| | - Samuel Jacquiod
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne Franche-Comté, F-21000 Dijon, France;
| | - Søren J. Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark;
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Correspondence: (D.K.); (R.L-A.)
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20
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Algal Toxic Compounds and Their Aeroterrestrial, Airborne and other Extremophilic Producers with Attention to Soil and Plant Contamination: A Review. Toxins (Basel) 2021; 13:toxins13050322. [PMID: 33946968 PMCID: PMC8145420 DOI: 10.3390/toxins13050322] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022] Open
Abstract
The review summarizes the available knowledge on toxins and their producers from rather disparate algal assemblages of aeroterrestrial, airborne and other versatile extreme environments (hot springs, deserts, ice, snow, caves, etc.) and on phycotoxins as contaminants of emergent concern in soil and plants. There is a growing body of evidence that algal toxins and their producers occur in all general types of extreme habitats, and cyanobacteria/cyanoprokaryotes dominate in most of them. Altogether, 55 toxigenic algal genera (47 cyanoprokaryotes) were enlisted, and our analysis showed that besides the “standard” toxins, routinely known from different waterbodies (microcystins, nodularins, anatoxins, saxitoxins, cylindrospermopsins, BMAA, etc.), they can produce some specific toxic compounds. Whether the toxic biomolecules are related with the harsh conditions on which algae have to thrive and what is their functional role may be answered by future studies. Therefore, we outline the gaps in knowledge and provide ideas for further research, considering, from one side, the health risk from phycotoxins on the background of the global warming and eutrophication and, from the other side, the current surge of interest which phycotoxins provoke due to their potential as novel compounds in medicine, pharmacy, cosmetics, bioremediation, agriculture and all aspects of biotechnological implications in human life.
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21
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Unno K, Nakagawa H, Kodani S. Heterologous production of new protease inhibitory peptide marinostatin E. Biosci Biotechnol Biochem 2021; 85:97-102. [DOI: 10.1093/bbb/zbaa011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/09/2020] [Indexed: 01/30/2023]
Abstract
Abstract
Bicyclic peptides, marinostatins, are protease inhibitors derived from the marine bacterium Algicola sagamiensis. The biosynthetic gene cluster of marinostatin was previously identified, although no heterologous production was reported. In this report, the biosynthetic gene cluster of marinostatin (mstA and mstB) was cloned into the expression vector pET-41a(+). As a result of the coexpression experiment, a new analogous peptide named marinostatin E was successfully produced using Escherichia coli BL21(DE3). The structure of marinostatin E was determined by a combination of chemical treatments and tandem mass spectrometry experiments. Marinostatin E exhibited inhibitory activities against chymotrypsin and subtilisin with an IC50 of 4.0 and 39.6 μm, respectively.
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Affiliation(s)
- Kohta Unno
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hiroyuki Nakagawa
- Food Research Institute, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
- Advanced Analysis Center, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, Japan
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22
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Current Knowledge on Microviridin from Cyanobacteria. Mar Drugs 2021; 19:md19010017. [PMID: 33406599 PMCID: PMC7823629 DOI: 10.3390/md19010017] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 12/18/2022] Open
Abstract
Cyanobacteria are a rich source of secondary metabolites with a vast biotechnological potential. These compounds have intrigued the scientific community due their uniqueness and diversity, which is guaranteed by a rich enzymatic apparatus. The ribosomally synthesized and post-translationally modified peptides (RiPPs) are among the most promising metabolite groups derived from cyanobacteria. They are interested in numerous biological and ecological processes, many of which are entirely unknown. Microviridins are among the most recognized class of ribosomal peptides formed by cyanobacteria. These oligopeptides are potent inhibitors of protease; thus, they can be used for drug development and the control of mosquitoes. They also play a key ecological role in the defense of cyanobacteria against microcrustaceans. The purpose of this review is to systematically identify the key characteristics of microviridins, including its chemical structure and biosynthesis, as well as its biotechnological and ecological significance.
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23
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Shimura Y, Fujisawa T, Hirose Y, Misawa N, Kanesaki Y, Nakamura Y, Kawachi M. Complete sequence and structure of the genome of the harmful algal bloom-forming cyanobacterium Planktothrix agardhii NIES-204 T and detailed analysis of secondary metabolite gene clusters. HARMFUL ALGAE 2021; 101:101942. [PMID: 33526179 DOI: 10.1016/j.hal.2020.101942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
Planktothrix species are distributed worldwide, and these prevalent cyanobacteria occasionally form potentially devastating toxic blooms. Given the ecological and taxonomic importance of Planktothrix agardhii as a bloom species, we set out to determine the complete genome sequence of the type strain Planktothrix agardhii NIES-204. Remarkably, we found that the 5S ribosomal RNA genes are not adjacent to the 16S and 23S ribosomal RNA genes. The genomic structure of P. agardhii NIES-204 is highly similar to that of another P. agardhii strain isolated from a geographically distant site, although they differ distinctly by a large inversion. We identified numerous gene clusters that encode the components of the metabolic pathways that generate secondary metabolites. We found that the aeruginosin biosynthetic gene cluster was more similar to that of another toxic bloom-forming cyanobacterium Microcystis aeruginosa than to that of other strains of Planktothrix, suggesting horizontal gene transfer. Prenyltransferases encoded in the prenylagaramide gene cluster of Planktothrix strains were classified into two phylogenetically distinct types, suggesting a functional difference. In addition to the secondary metabolite gene clusters, we identified genes for inorganic nitrogen and phosphate uptake components and gas vesicles. Our findings contribute to further understanding of the ecologically important genus Planktothrix.
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Affiliation(s)
- Yohei Shimura
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan.
| | - Takatomo Fujisawa
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Hibarigaoka 1-1, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Naomi Misawa
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Hibarigaoka 1-1, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
| | - Yasukazu Nakamura
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
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24
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Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep 2021; 38:130-239. [PMID: 32935693 PMCID: PMC7864896 DOI: 10.1039/d0np00027b] [Citation(s) in RCA: 375] [Impact Index Per Article: 125.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
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25
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Unno K, Kodani S. Heterologous expression of cryptic biosynthetic gene cluster from Streptomyces prunicolor yields novel bicyclic peptide prunipeptin. Microbiol Res 2020; 244:126669. [PMID: 33360751 DOI: 10.1016/j.micres.2020.126669] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/02/2020] [Accepted: 12/06/2020] [Indexed: 11/18/2022]
Abstract
Recently, ω-ester-containing peptides (OEPs) were indicated to be a class of ribosomally synthesized and post-translationally modified peptides. Based on genome mining, new biosynthetic gene cluster of OEPs was found in the genome sequence of actinobacterium Streptomyces prunicolor. The biosynthetic gene cluster contained just two genes including precursor peptide (pruA) and ATP-grasp ligase (pruB) coding genes. Heterologous co-expression of the two genes was accomplished using expression vector pET-41a(+) in Escherichia coli. As a result, new OEP named prunipeptin was produced by this system. By site-directed mutagenesis experiment, a variant peptide prunipeptin 15HW was obtained. The bridging pattern of prunipeptin 15HW was determined by combination of chemical cleavage and MS experiments. Prunipeptin 15HW possessed bicyclic structure with an ester bond and an isopeptide bond. The ATP-grasp ligase PruB was indicated to catalyze the two different intramolecular bonds.
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Affiliation(s)
- Kohta Unno
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan; College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, Japan.
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26
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Jeong Y, Cho SH, Lee H, Choi HK, Kim DM, Lee CG, Cho S, Cho BK. Current Status and Future Strategies to Increase Secondary Metabolite Production from Cyanobacteria. Microorganisms 2020; 8:E1849. [PMID: 33255283 PMCID: PMC7761380 DOI: 10.3390/microorganisms8121849] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/15/2020] [Accepted: 11/23/2020] [Indexed: 12/16/2022] Open
Abstract
Cyanobacteria, given their ability to produce various secondary metabolites utilizing solar energy and carbon dioxide, are a potential platform for sustainable production of biochemicals. Until now, conventional metabolic engineering approaches have been applied to various cyanobacterial species for enhanced production of industrially valued compounds, including secondary metabolites and non-natural biochemicals. However, the shortage of understanding of cyanobacterial metabolic and regulatory networks for atmospheric carbon fixation to biochemical production and the lack of available engineering tools limit the potential of cyanobacteria for industrial applications. Recently, to overcome the limitations, synthetic biology tools and systems biology approaches such as genome-scale modeling based on diverse omics data have been applied to cyanobacteria. This review covers the synthetic and systems biology approaches for advanced metabolic engineering of cyanobacteria.
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Affiliation(s)
- Yujin Jeong
- Department of Biological Sciences and KAIST Institutes for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (Y.J.); (S.-H.C.)
| | - Sang-Hyeok Cho
- Department of Biological Sciences and KAIST Institutes for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (Y.J.); (S.-H.C.)
| | - Hookeun Lee
- Institute of Pharmaceutical Research, College of Pharmacy, Gachon University, Incheon 21999, Korea;
| | | | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 34134, Korea;
| | - Choul-Gyun Lee
- Department of Biological Engineering, Inha University, Incheon 22212, Korea;
| | - Suhyung Cho
- Department of Biological Sciences and KAIST Institutes for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (Y.J.); (S.-H.C.)
| | - Byung-Kwan Cho
- Department of Biological Sciences and KAIST Institutes for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (Y.J.); (S.-H.C.)
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Ya’u Sabo Ajingi, Nujarin Jongruja. Antimicrobial Peptide Engineering: Rational Design, Synthesis, and Synergistic Effect. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020040044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Zhong Z, He B, Li J, Li YX. Challenges and advances in genome mining of ribosomally synthesized and post-translationally modified peptides (RiPPs). Synth Syst Biotechnol 2020; 5:155-172. [PMID: 32637669 PMCID: PMC7327761 DOI: 10.1016/j.synbio.2020.06.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 01/05/2023] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a class of cyclic or linear peptidic natural products with remarkable structural and functional diversity. Recent advances in genomics and synthetic biology, are facilitating us to discover a large number of new ribosomal natural products, including lanthipeptides, lasso peptides, sactipeptides, thiopeptides, microviridins, cyanobactins, linear thiazole/oxazole-containing peptides and so on. In this review, we summarize bioinformatic strategies that have been developed to identify and prioritize biosynthetic gene clusters (BGCs) encoding RiPPs, and the genome mining-guided discovery of novel RiPPs. We also prospectively provide a vision of what genomics-guided discovery of RiPPs may look like in the future, especially the discovery of RiPPs from dominant but uncultivated microbes, which will be promoted by the combinational use of synthetic biology and metagenome mining strategies.
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Affiliation(s)
- Zheng Zhong
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong SAR, China
| | - Beibei He
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong SAR, China
| | - Jie Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, USA
| | - Yong-Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong SAR, China
- The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China
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29
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Al-Awadhi FH, Luesch H. Targeting eukaryotic proteases for natural products-based drug development. Nat Prod Rep 2020; 37:827-860. [PMID: 32519686 PMCID: PMC7406119 DOI: 10.1039/c9np00060g] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to April 2020 Proteases are involved in the regulation of many physiological processes. Their overexpression and dysregulated activity are linked to diseases such as hypertension, diabetes, viral infections, blood clotting disorders, respiratory diseases, and cancer. Therefore, they represent an important class of therapeutic targets. Several protease inhibitors have reached the market and >60% of them are directly related to natural products, even when excluding synthetic natural product mimics. Historically, natural products have been a valuable and validated source of therapeutic agents, as over half of the marketed drugs across targets and diseases are inspired by natural product structures. In the past two decades the number of new protease inhibitors discovered from nature has sharply increased. Additionally, the availability of 3D structural information for proteases has permitted structure-based design and accelerated the synthesis of optimized lead structures with improved potency and selectivity profiles, resulting in some of the most-potent-in-class inhibitors. These discoveries were oftentimes maximized by in-depth biological assessments of lead inhibitors, linking them to a relevant disease state. This review will discuss some of the current and emerging drug targets and their involvement in various disease processes, highlighting selected success stories behind several FDA-approved protease inhibitors that have natural products scaffolds as well as recent selected pharmacologically well-characterized inhibitors derived from marine or terrestrial sources.
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Affiliation(s)
- Fatma H Al-Awadhi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kuwait University, P.O. Box 24923, Safat 13110, Kuwait.
| | - Hendrik Luesch
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, USA.
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30
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Unno K, Kaweewan I, Nakagawa H, Kodani S. Heterologous expression of a cryptic gene cluster from Grimontia marina affords a novel tricyclic peptide grimoviridin. Appl Microbiol Biotechnol 2020; 104:5293-5302. [DOI: 10.1007/s00253-020-10605-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/01/2020] [Accepted: 04/01/2020] [Indexed: 10/24/2022]
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31
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Sieber S, Grendelmeier SM, Harris LA, Mitchell DA, Gademann K. Microviridin 1777: A Toxic Chymotrypsin Inhibitor Discovered by a Metabologenomic Approach. JOURNAL OF NATURAL PRODUCTS 2020; 83:438-446. [PMID: 31989826 PMCID: PMC7050427 DOI: 10.1021/acs.jnatprod.9b00986] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The toxicity of the cyanobacterium Microcystis aeruginosa EAWAG 127a was evaluated against the sensitive grazer Thamnocephalus platyurus, and the extract possessed strong activity. To investigate the compounds responsible for cytotoxicity, a series of peptides from this cyanobacterium were studied using a combined genomic and molecular networking approach. The results led to the isolation, structure elucidation, and biological evaluation of microviridin 1777, which represents the most potent chymotrypsin inhibitor characterized from this family of peptides to date. Furthermore, the biosynthetic gene clusters of microviridin, anabaenopeptin, aeruginosin, and piricyclamide were located in the producing organism, and six additional natural products were identified by tandem mass spectrometry analyses. These results highlight the potential of modern techniques for the identification of natural products, demonstrate the ecological role of protease inhibitors produced by cyanobacteria, and raise ramifications concerning the presence of novel, yet uncharacterized, toxin families in cyanobacteria beyond microcystin.
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Affiliation(s)
- Simon Sieber
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH 8057, Switzerland
| | - Simone M. Grendelmeier
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH 8057, Switzerland
| | - Lonnie A. Harris
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Karl Gademann
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH 8057, Switzerland
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32
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Lee H, Choi M, Park JU, Roh H, Kim S. Genome Mining Reveals High Topological Diversity of ω-Ester-Containing Peptides and Divergent Evolution of ATP-Grasp Macrocyclases. J Am Chem Soc 2020; 142:3013-3023. [PMID: 31961152 DOI: 10.1021/jacs.9b12076] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
ω-Ester-containing peptides (OEPs) are a family of ribosomally synthesized and post-translationally modified peptides (RiPPs) containing intramolecular ω-ester or ω-amide bonds. Although their distinct side-to-side connections may create considerable topological diversity of multicyclic peptides, it is largely unknown how diverse ring patterns have been developed in nature. Here, using genome mining of biosynthetic enzymes of OEPs, we identified genes encoding nine new groups of putative OEPs with novel core consensus sequences, disclosing a total of ∼1500 candidate OEPs in 12 groups. Connectivity analysis revealed that OEPs from three different groups contain novel tricyclic structures, one of which has a distinct biosynthetic pathway where a single ATP-grasp enzyme produces both ω-ester and ω-amide linkages. Analysis of the enzyme cross-reactivity showed that, while enzymes are promiscuous to nonconserved regions of the core peptide, they have high specificity to the cognate core consensus sequence, suggesting that the enzyme-core pair has coevolved to create a unique ring topology within the same group and has sufficiently diversified across different groups. Collectively, our results demonstrate that the diverse ring topologies, in addition to diverse sequences, have been developed in nature with multiple ω-ester or ω-amide linkages in the OEP family of RiPPs.
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Affiliation(s)
- Hyunbin Lee
- Department of Chemistry , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , South Korea
| | - Mingyu Choi
- Department of Chemistry , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , South Korea
| | - Jung-Un Park
- Department of Chemistry , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , South Korea
| | - Heejin Roh
- Department of Chemistry , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , South Korea
| | - Seokhee Kim
- Department of Chemistry , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , South Korea
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33
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Lee C, Lee H, Park JU, Kim S. Introduction of Bifunctionality into the Multidomain Architecture of the ω-Ester-Containing Peptide Plesiocin. Biochemistry 2019; 59:285-289. [DOI: 10.1021/acs.biochem.9b00803] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chanwoo Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Hyunbin Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Jung-Un Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
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34
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Kim Tiam S, Gugger M, Demay J, Le Manach S, Duval C, Bernard C, Marie B. Insights into the Diversity of Secondary Metabolites of Planktothrix Using a Biphasic Approach Combining Global Genomics and Metabolomics. Toxins (Basel) 2019; 11:E498. [PMID: 31461939 PMCID: PMC6784222 DOI: 10.3390/toxins11090498] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/14/2019] [Accepted: 08/22/2019] [Indexed: 12/19/2022] Open
Abstract
Cyanobacteria are an ancient lineage of slow-growing photosynthetic bacteria and a prolific source of natural products with diverse chemical structures and potent biological activities and toxicities. The chemical identification of these compounds remains a major bottleneck. Strategies that can prioritize the most prolific strains and novel compounds are of great interest. Here, we combine chemical analysis and genomics to investigate the chemodiversity of secondary metabolites based on their pattern of distribution within some cyanobacteria. Planktothrix being a cyanobacterial genus known to form blooms worldwide and to produce a broad spectrum of toxins and other bioactive compounds, we applied this combined approach on four closely related strains of Planktothrix. The chemical diversity of the metabolites produced by the four strains was evaluated using an untargeted metabolomics strategy with high-resolution LC-MS. Metabolite profiles were correlated with the potential of metabolite production identified by genomics for the different strains. Although, the Planktothrix strains present a global similarity in terms of a biosynthetic cluster gene for microcystin, aeruginosin, and prenylagaramide for example, we found remarkable strain-specific chemodiversity. Only few of the chemical features were common to the four studied strains. Additionally, the MS/MS data were analyzed using Global Natural Products Social Molecular Networking (GNPS) to identify molecular families of the same biosynthetic origin. In conclusion, we depict an efficient, integrative strategy for elucidating the chemical diversity of a given genus and link the data obtained from analytical chemistry to biosynthetic genes of cyanobacteria.
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Affiliation(s)
- Sandra Kim Tiam
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries, 28 rue du Dr Roux, 75724 Paris Cedex 05, France
| | - Justine Demay
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Séverine Le Manach
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Charlotte Duval
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Cécile Bernard
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Benjamin Marie
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France.
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35
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Huang IS, Zimba PV. Cyanobacterial bioactive metabolites-A review of their chemistry and biology. HARMFUL ALGAE 2019; 86:139-209. [PMID: 31358273 DOI: 10.1016/j.hal.2019.05.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/14/2018] [Accepted: 11/16/2018] [Indexed: 06/10/2023]
Abstract
Cyanobacterial blooms occur when algal densities exceed baseline population concentrations. Cyanobacteria can produce a large number of secondary metabolites. Odorous metabolites affect the smell and flavor of aquatic animals, whereas bioactive metabolites cause a range of lethal and sub-lethal effects in plants, invertebrates, and vertebrates, including humans. Herein, the bioactivity, chemistry, origin, and biosynthesis of these cyanobacterial secondary metabolites were reviewed. With recent revision of cyanobacterial taxonomy by Anagnostidis and Komárek as part of the Süβwasserflora von Mitteleuropa volumes 19(1-3), names of many cyanobacteria that produce bioactive compounds have changed, thereby confusing readers. The original and new nomenclature are included in this review to clarify the origins of cyanobacterial bioactive compounds. Due to structural similarity, the 157 known bioactive classes produced by cyanobacteria have been condensed to 55 classes. This review will provide a basis for more formal procedures to adopt a logical naming system. This review is needed for efficient management of water resources to understand, identify, and manage cyanobacterial harmful algal bloom impacts.
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Affiliation(s)
- I-Shuo Huang
- Center for Coastal Studies, Texas A&M University-Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA.
| | - Paul V Zimba
- Center for Coastal Studies, Texas A&M University-Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
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36
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Roh H, Han Y, Lee H, Kim S. A Topologically Distinct Modified Peptide with Multiple Bicyclic Core Motifs Expands the Diversity of Microviridin‐Like Peptides. Chembiochem 2019; 20:1051-1059. [DOI: 10.1002/cbic.201800678] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Heejin Roh
- Department of ChemistrySeoul National University 1 Gwanak-ro Gwanak-gu Seoul 08826 South Korea
| | - Yeji Han
- Department of ChemistrySeoul National University 1 Gwanak-ro Gwanak-gu Seoul 08826 South Korea
| | - Hyunbin Lee
- Department of ChemistrySeoul National University 1 Gwanak-ro Gwanak-gu Seoul 08826 South Korea
| | - Seokhee Kim
- Department of ChemistrySeoul National University 1 Gwanak-ro Gwanak-gu Seoul 08826 South Korea
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37
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Huang IS, Zimba PV. Cyanobacterial bioactive metabolites-A review of their chemistry and biology. HARMFUL ALGAE 2019; 83:42-94. [PMID: 31097255 DOI: 10.1016/j.hal.2018.11.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/14/2018] [Accepted: 11/16/2018] [Indexed: 06/09/2023]
Abstract
Cyanobacterial blooms occur when algal densities exceed baseline population concentrations. Cyanobacteria can produce a large number of secondary metabolites. Odorous metabolites affect the smell and flavor of aquatic animals, whereas bioactive metabolites cause a range of lethal and sub-lethal effects in plants, invertebrates, and vertebrates, including humans. Herein, the bioactivity, chemistry, origin, and biosynthesis of these cyanobacterial secondary metabolites were reviewed. With recent revision of cyanobacterial taxonomy by Anagnostidis and Komárek as part of the Süβwasserflora von Mitteleuropa volumes 19(1-3), names of many cyanobacteria that produce bioactive compounds have changed, thereby confusing readers. The original and new nomenclature are included in this review to clarify the origins of cyanobacterial bioactive compounds. Due to structural similarity, the 157 known bioactive classes produced by cyanobacteria have been condensed to 55 classes. This review will provide a basis for more formal procedures to adopt a logical naming system. This review is needed for efficient management of water resources to understand, identify, and manage cyanobacterial harmful algal bloom impacts.
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Affiliation(s)
- I-Shuo Huang
- Center for Coastal Studies, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA.
| | - Paul V Zimba
- Center for Coastal Studies, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
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38
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Kaysser L. Built to bind: biosynthetic strategies for the formation of small-molecule protease inhibitors. Nat Prod Rep 2019; 36:1654-1686. [DOI: 10.1039/c8np00095f] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The discovery and characterization of natural product protease inhibitors has inspired the development of numerous pharmaceutical agents.
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Affiliation(s)
- Leonard Kaysser
- Department of Pharmaceutical Biology
- University of Tübingen
- 72076 Tübingen
- Germany
- German Centre for Infection Research (DZIF)
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39
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A distributive peptide cyclase processes multiple microviridin core peptides within a single polypeptide substrate. Nat Commun 2018; 9:1780. [PMID: 29725007 PMCID: PMC5934393 DOI: 10.1038/s41467-018-04154-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 02/23/2018] [Indexed: 11/16/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important family of natural products. Their biosynthesis follows a common scheme in which the leader peptide of a precursor peptide guides the modifications of a single core peptide. Here we describe biochemical studies of the processing of multiple core peptides within a precursor peptide, rare in RiPP biosynthesis. In a cyanobacterial microviridin pathway, an ATP-grasp ligase, AMdnC, installs up to two macrolactones on each of the three core peptides within AMdnA. The enzyme catalysis occurs in a distributive fashion and follows an unstrict N-to-C overall directionality, but a strict order in macrolactonizing each core peptide. Furthermore, AMdnC is catalytically versatile to process unnatural substrates carrying one to four core peptides, and kinetic studies provide insights into its catalytic properties. Collectively, our results reveal a distinct biosynthetic logic of RiPPs, opening up the possibility of modular production via synthetic biology approaches. Microviridins belong to the family of ribosomally synthesized and post-translationally modified peptides (RiPPs). Here, the authors discover a microviridin-synthesizing enzyme in a cyanobacterium that modifies multiple core peptides from a single substrate in a distributive and unstrictly directional manner, an unusual biosynthetic logic for RiPPs.
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Lee H, Park Y, Kim S. Enzymatic Cross-Linking of Side Chains Generates a Modified Peptide with Four Hairpin-like Bicyclic Repeats. Biochemistry 2017; 56:4927-4930. [DOI: 10.1021/acs.biochem.7b00808] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Hyunbin Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Youngseon Park
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
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Bartholomae M, Buivydas A, Viel JH, Montalbán-López M, Kuipers OP. Major gene-regulatory mechanisms operating in ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthesis. Mol Microbiol 2017; 106:186-206. [DOI: 10.1111/mmi.13764] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Maike Bartholomae
- Department of Molecular Genetics; University of Groningen, Nijenborgh 7; 9747AG Groningen The Netherlands
| | - Andrius Buivydas
- Department of Molecular Genetics; University of Groningen, Nijenborgh 7; 9747AG Groningen The Netherlands
| | - Jakob H. Viel
- Department of Molecular Genetics; University of Groningen, Nijenborgh 7; 9747AG Groningen The Netherlands
| | - Manuel Montalbán-López
- Department of Microbiology; University of Granada, C. Fuentenueva s/n; 18071 Granada Spain
| | - Oscar P. Kuipers
- Department of Molecular Genetics; University of Groningen, Nijenborgh 7; 9747AG Groningen The Netherlands
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Ogasawara Y, Dairi T. Biosynthesis of Oligopeptides Using ATP-Grasp Enzymes. Chemistry 2017; 23:10714-10724. [PMID: 28488371 DOI: 10.1002/chem.201700674] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 11/08/2022]
Abstract
Peptides are biologically occurring oligomers of amino acids linked by amide bonds and are indispensable for all living organisms. Many bioactive peptides are used as antibiotics, antivirus agents, insecticides, pheromones, and food preservatives. Nature employs several different strategies to form amide bonds. ATP-grasp enzymes that catalyze amide bond formation (ATP-dependent carboxylate-amine ligases) utilize a strategy of activating carboxylic acid as an acylphosphate intermediate to form amide bonds and are involved in many different biological processes in both primary and secondary metabolisms. The recent discovery of several new ATP-dependent carboxylate-amine ligases has expanded the diversity of this group of enzymes and showed their usefulness for generating oligopeptides. In this review, an overview of findings on amide bond formation catalyzed by ATP-grasp enzymes in the past decade is presented.
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Affiliation(s)
- Yasushi Ogasawara
- Division of Applied Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan
| | - Tohru Dairi
- Division of Applied Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan
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Ahmed MN, Reyna-González E, Schmid B, Wiebach V, Süssmuth RD, Dittmann E, Fewer DP. Phylogenomic Analysis of the Microviridin Biosynthetic Pathway Coupled with Targeted Chemo-Enzymatic Synthesis Yields Potent Protease Inhibitors. ACS Chem Biol 2017; 12:1538-1546. [PMID: 28406289 DOI: 10.1021/acschembio.7b00124] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Natural products and their semisynthetic derivatives are an important source of drugs for the pharmaceutical industry. Bacteria are prolific producers of natural products and encode a vast diversity of natural product biosynthetic gene clusters. However, much of this diversity is inaccessible to natural product discovery. Here, we use a combination of phylogenomic analysis of the microviridin biosynthetic pathway and chemo-enzymatic synthesis of bioinformatically predicted microviridins to yield new protease inhibitors. Phylogenomic analysis demonstrated that microviridin biosynthetic gene clusters occur across the bacterial domain and encode three distinct subtypes of precursor peptides. Our analysis shed light on the evolution of microviridin biosynthesis and enabled prioritization of their chemo-enzymatic production. Targeted one-pot synthesis of four microviridins encoded by the cyanobacterium Cyanothece sp. PCC 7822 identified a set of novel and potent serine protease inhibitors, the most active of which had an IC50 value of 21.5 nM. This study advances the genome mining techniques available for natural product discovery and obviates the need to culture bacteria.
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Affiliation(s)
- Muhammad N. Ahmed
- Microbiology
and Biotechnology Division, Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 56, Viikki Biocenter, Viikinkaari 9, Helsinki FIN-00014, Finland
| | - Emmanuel Reyna-González
- Institute
of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam-Golm, Germany
| | - Bianca Schmid
- Institute
of Chemistry, Technical University Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Vincent Wiebach
- Institute
of Chemistry, Technical University Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Roderich D. Süssmuth
- Institute
of Chemistry, Technical University Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Elke Dittmann
- Institute
of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam-Golm, Germany
| | - David P. Fewer
- Microbiology
and Biotechnology Division, Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 56, Viikki Biocenter, Viikinkaari 9, Helsinki FIN-00014, Finland
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Entfellner E, Frei M, Christiansen G, Deng L, Blom J, Kurmayer R. Evolution of Anabaenopeptin Peptide Structural Variability in the Cyanobacterium Planktothrix. Front Microbiol 2017; 8:219. [PMID: 28261178 PMCID: PMC5311044 DOI: 10.3389/fmicb.2017.00219] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 01/31/2017] [Indexed: 11/22/2022] Open
Abstract
Cyanobacteria are frequently involved in the formation of harmful algal blooms wherein, apart from the toxic microcystins, other groups of bioactive peptides are abundant as well, such as anabaenopeptins (APs). The APs are synthesized nonribosomally as cyclic hexapeptides with various amino acids at the exocyclic position. We investigated the presence and recombination of the AP synthesis gene cluster (apnA-E) through comparing 125 strains of the bloom-forming cyanobacterium Planktothrix spp., which were isolated from numerous shallow and deep water habitats in the temperate and tropical climatic zone. Ten ecologically divergent strains were purified and genome sequenced to compare their entire apnA-E gene cluster. In order to quantify apn gene distribution patterns, all the strains were investigated by PCR amplification of 2 kbp portions of the entire apn gene cluster without interruption. Within the 11 strains assigned to P. pseudagardhii, P. mougeotii, or P. tepida (Lineage 3), neither apnA-E genes nor remnants were observed. Within the P. agardhii/P. rubescens strains from shallow waters (Lineage 1, 52 strains), strains both carrying and lacking apn genes occurred, while among the strains lacking the apnA-E genes, the presence of the 5'end flanking region indicated a gene cluster deletion. Among the strains of the more derived deep water ecotype (Lineage 2, 62 strains), apnA-E genes were always present. A high similarity of apn genes of the genus Planktothrix when compared with strains of the genus Microcystis suggested its horizontal gene transfer during the speciation of P. agardhii/P. rubescens. Genetic analysis of the first (A1-) domain of the apnA gene, encoding synthesis of the exocyclic position of the AP molecule, revealed four genotype groups that corresponded with substrate activation. Groups of genotypes were either related to Arginine only, the coproduction of Arginine and Tyrosine or Arginine and Lysine, or even the coproduction of Arginine, Tyrosine, and Lysine in the exocyclic position of the AP-molecule. The increased structural diversity resulted from the evolution of apnA A1 genotypes through a small number of positively selected point mutations that occurred repeatedly and independently from phylogenetic association.
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Affiliation(s)
| | - Mark Frei
- Research Institute for Limnology, University of InnsbruckMondsee, Austria
| | - Guntram Christiansen
- Research Institute for Limnology, University of InnsbruckMondsee, Austria
- Miti Biosystems GmbH, Max F Perutz LaboratoriesWien, Austria
| | - Li Deng
- Institute of Virology, Helmholtz Zentrum MünchenMünchen, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-UniversityGiessen, Germany
| | - Rainer Kurmayer
- Research Institute for Limnology, University of InnsbruckMondsee, Austria
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Structural basis for precursor protein-directed ribosomal peptide macrocyclization. Nat Chem Biol 2016; 12:973-979. [PMID: 27669417 PMCID: PMC5117808 DOI: 10.1038/nchembio.2200] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 08/03/2016] [Indexed: 11/08/2022]
Abstract
Macrocyclization is a common feature of natural product biosynthetic pathways including the diverse family of ribosomal peptides. Microviridins are architecturally complex cyanobacterial ribosomal peptides whose members target proteases with potent reversible inhibition. The product structure is constructed by three macrocyclizations catalyzed sequentially by two members of the ATP-grasp family, a unique strategy for ribosomal peptide macrocyclization. Here, we describe the detailed structural basis for the enzyme-catalyzed macrocyclizations in the microviridin J pathway of Microcystis aeruginosa. The macrocyclases, MdnC and MdnB, interact with a conserved α-helix of the precursor peptide using a novel precursor peptide recognition mechanism. The results provide insight into the unique protein/protein interactions key to the chemistry, suggest an origin of the natural combinatorial synthesis of microviridin peptides and provide a framework for future engineering efforts to generate designed compounds.
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Reyna‐González E, Schmid B, Petras D, Süssmuth RD, Dittmann E. Leader Peptide‐Free In Vitro Reconstitution of Microviridin Biosynthesis Enables Design of Synthetic Protease‐Targeted Libraries. Angew Chem Int Ed Engl 2016; 55:9398-401. [DOI: 10.1002/anie.201604345] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 05/23/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Emmanuel Reyna‐González
- Institute of Biochemistry and BiologyUniversity of Potsdam Karl-Liebknecht-Straße 24-25 14476 Potsdam-Golm Germany
| | - Bianca Schmid
- Institute of ChemistryTechnical University Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Daniel Petras
- Institute of ChemistryTechnical University Berlin Straße des 17. Juni 124 10623 Berlin Germany
- Skaggs School of Pharmacy & Pharmaceutical SciencesUniversity of California—San Diego 9500 Gilman Drive La Jolla CA 92093-0751 USA
| | - Roderich D. Süssmuth
- Institute of ChemistryTechnical University Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Elke Dittmann
- Institute of Biochemistry and BiologyUniversity of Potsdam Karl-Liebknecht-Straße 24-25 14476 Potsdam-Golm Germany
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Reyna‐González E, Schmid B, Petras D, Süssmuth RD, Dittmann E. Leader Peptide‐Free In Vitro Reconstitution of Microviridin Biosynthesis Enables Design of Synthetic Protease‐Targeted Libraries. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Emmanuel Reyna‐González
- Institute of Biochemistry and BiologyUniversity of Potsdam Karl-Liebknecht-Straße 24-25 14476 Potsdam-Golm Germany
| | - Bianca Schmid
- Institute of ChemistryTechnical University Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Daniel Petras
- Institute of ChemistryTechnical University Berlin Straße des 17. Juni 124 10623 Berlin Germany
- Skaggs School of Pharmacy & Pharmaceutical SciencesUniversity of California—San Diego 9500 Gilman Drive La Jolla CA 92093-0751 USA
| | - Roderich D. Süssmuth
- Institute of ChemistryTechnical University Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Elke Dittmann
- Institute of Biochemistry and BiologyUniversity of Potsdam Karl-Liebknecht-Straße 24-25 14476 Potsdam-Golm Germany
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Truman AW. Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides. Beilstein J Org Chem 2016; 12:1250-68. [PMID: 27559376 PMCID: PMC4979651 DOI: 10.3762/bjoc.12.120] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/02/2016] [Indexed: 12/15/2022] Open
Abstract
Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a large class of natural products that are remarkably chemically diverse given an intrinsic requirement to be assembled from proteinogenic amino acids. The vast chemical space occupied by RiPPs means that they possess a wide variety of biological activities, and the class includes antibiotics, co-factors, signalling molecules, anticancer and anti-HIV compounds, and toxins. A considerable amount of RiPP chemical diversity is generated from cyclisation reactions, and the current mechanistic understanding of these reactions will be discussed here. These cyclisations involve a diverse array of chemical reactions, including 1,4-nucleophilic additions, [4 + 2] cycloadditions, ATP-dependent heterocyclisation to form thiazolines or oxazolines, and radical-mediated reactions between unactivated carbons. Future prospects for RiPP pathway discovery and characterisation will also be highlighted.
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Affiliation(s)
- Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
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49
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Ziemert N, Alanjary M, Weber T. The evolution of genome mining in microbes - a review. Nat Prod Rep 2016; 33:988-1005. [PMID: 27272205 DOI: 10.1039/c6np00025h] [Citation(s) in RCA: 404] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering: 2006 to 2016The computational mining of genomes has become an important part in the discovery of novel natural products as drug leads. Thousands of bacterial genome sequences are publically available these days containing an even larger number and diversity of secondary metabolite gene clusters that await linkage to their encoded natural products. With the development of high-throughput sequencing methods and the wealth of DNA data available, a variety of genome mining methods and tools have been developed to guide discovery and characterisation of these compounds. This article reviews the development of these computational approaches during the last decade and shows how the revolution of next generation sequencing methods has led to an evolution of various genome mining approaches, techniques and tools. After a short introduction and brief overview of important milestones, this article will focus on the different approaches of mining genomes for secondary metabolites, from detecting biosynthetic genes to resistance based methods and "evo-mining" strategies including a short evaluation of the impact of the development of genome mining methods and tools on the field of natural products and microbial ecology.
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Affiliation(s)
- Nadine Ziemert
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tuebingen, Germany.
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50
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Kurmayer R, Deng L, Entfellner E. Role of toxic and bioactive secondary metabolites in colonization and bloom formation by filamentous cyanobacteria Planktothrix. HARMFUL ALGAE 2016; 54:69-86. [PMID: 27307781 PMCID: PMC4892429 DOI: 10.1016/j.hal.2016.01.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 01/15/2016] [Accepted: 01/15/2016] [Indexed: 05/22/2023]
Abstract
Bloom-forming cyanobacteria Planktothrix agardhii and P. rubescens are regularly involved in the occurrence of cyanotoxin in lakes and reservoirs. Besides microcystins (MCs), which inhibit eukaryotic protein phosphatase 1 and 2A, several families of bioactive peptides are produced, thereby resulting in impressive secondary metabolite structural diversity. This review will focus on the current knowledge of the phylogeny, morphology, and ecophysiological adaptations of Planktothrix as well as the toxins and bioactive peptides produced. The relatively well studied ecophysiological adaptations (buoyancy, shade tolerance, nutrient storage capacity) can partly explain the invasiveness of this group of cyanobacteria that bloom within short periods (weeks to months). The more recent elucidation of the genetic basis of toxin and bioactive peptide synthesis paved the way for investigating its regulation both in the laboratory using cell cultures as well as under field conditions. The high frequency of several toxin and bioactive peptide synthesis genes observed within P. agardhii and P. rubescens, but not for other Planktothrix species (e.g. P. pseudagardhii), suggests a potential functional linkage between bioactive peptide production and the colonization potential and possible dominance in habitats. It is hypothesized that, through toxin and bioactive peptide production, Planktothrix act as a niche constructor at the ecosystem scale, possibly resulting in an even higher ability to monopolize resources, positive feedback loops, and resilience under stable environmental conditions. Thus, refocusing harmful algal bloom management by integrating ecological and phylogenetic factors acting on toxin and bioactive peptide synthesis gene distribution and concentrations could increase the predictability of the risks originating from Planktothrix blooms.
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Affiliation(s)
- Rainer Kurmayer
- University of Innsbruck, Research Institute for Limnology, Mondseestrasse 9, 5310 Mondsee, Austria.
| | - Li Deng
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Elisabeth Entfellner
- University of Innsbruck, Research Institute for Limnology, Mondseestrasse 9, 5310 Mondsee, Austria
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