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Jiko C, Morimoto Y, Tsukihara T, Gerle C. Large-scale column-free purification of bovine F-ATP synthase. J Biol Chem 2024; 300:105603. [PMID: 38159856 PMCID: PMC10851226 DOI: 10.1016/j.jbc.2023.105603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024] Open
Abstract
Mammalian F-ATP synthase is central to mitochondrial bioenergetics and is present in the inner mitochondrial membrane in a dynamic oligomeric state of higher oligomers, tetramers, dimers, and monomers. In vitro investigations of mammalian F-ATP synthase are often limited by the ability to purify the oligomeric forms present in vivo at a quantity, stability, and purity that meets the demand of the planned experiment. We developed a purification approach for the isolation of bovine F-ATP synthase from heart muscle mitochondria that uses a combination of buffer conditions favoring inhibitor factor 1 binding and sucrose density gradient ultracentrifugation to yield stable complexes at high purity in the milligram range. By tuning the glyco-diosgenin to lauryl maltose neopentyl glycol ratio in a final gradient, fractions that are either enriched in tetrameric or monomeric F-ATP synthase can be obtained. It is expected that this large-scale column-free purification strategy broadens the spectrum of in vitro investigation on mammalian F-ATP synthase.
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Affiliation(s)
- Chimari Jiko
- Division of Radiation Life Science, Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, Japan.
| | - Yukio Morimoto
- Division of Radiation Life Science, Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, Japan
| | - Tomitake Tsukihara
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto, Kamigori, Hyogo, Japan; Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Christoph Gerle
- Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Osaka, Japan; Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Kouto, Hyogo, Japan.
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2
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Liu S, Tian L, Cong Y, Shi Q, Wang L, Lu Y, Wang L, Yang G. Recent advances in polygalacturonase: Industrial applications and challenges. Carbohydr Res 2023; 528:108816. [PMID: 37094533 DOI: 10.1016/j.carres.2023.108816] [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: 08/27/2022] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
This review focuses on the applications of polygalacturonase (PG), one of the most commercially produced enzymes on the biocatalyst market, in the food, beverage, feed, textile, and paper industries. Most PGs are acidic mesophilic enzymes, as shown by a summary of their biochemical properties. However, the acidic PGs discovered to date are insufficiently effective for industrial applications. The sequence and structural characteristics of thermophilic PGs are analyzed based on the results of extensive discussions regarding the catalytic mechanism and structural characteristics of PGs with shared right-handed parallel β-helical structures. In addition, the molecular modification methods for obtaining thermostable PGs are systematically presented. Notably, the demand for alkaline heat-resistant PGs has increased significantly concurrent with the biomanufacturing industry development. Therefore, this review also provides a theoretical guideline for mining heat-resistant PG gene resources and modifying PG thermostability.
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Affiliation(s)
- Siyi Liu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Linfang Tian
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Yuting Cong
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Qianqian Shi
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Lianshun Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Yanan Lu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Li Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Guojun Yang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China.
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3
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Bonhomme S, Contreras-Martel C, Dessen A, Macheboeuf P. Architecture of a PKS-NRPS hybrid megaenzyme involved in the biosynthesis of the genotoxin colibactin. Structure 2023:S0969-2126(23)00095-3. [PMID: 37059096 DOI: 10.1016/j.str.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/21/2022] [Accepted: 03/20/2023] [Indexed: 04/16/2023]
Abstract
The genotoxin colibactin produced by Escherichia coli is involved in the development of colorectal cancers. This secondary metabolite is synthesized by a multi-protein machinery, mainly composed of non-ribosomal peptide synthetase (NRPS)/polyketide synthase (PKS) enzymes. In order to decipher the function of a PKS-NRPS hybrid enzyme implicated in a key step of colibactin biosynthesis, we conducted an extensive structural characterization of the ClbK megaenzyme. Here we present the crystal structure of the complete trans-AT PKS module of ClbK showing structural specificities of hybrid enzymes. In addition, we report the SAXS solution structure of the full-length ClbK hybrid that reveals a dimeric organization as well as several catalytic chambers. These results provide a structural framework for the transfer of a colibactin precursor through a PKS-NRPS hybrid enzyme and can pave the way for re-engineering PKS-NRPS hybrid megaenzymes to generate diverse metabolites with many applications.
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Affiliation(s)
- Sarah Bonhomme
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Bacterial Pathogenesis Group, 38000 Grenoble, France
| | - Carlos Contreras-Martel
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Bacterial Pathogenesis Group, 38000 Grenoble, France
| | - Andréa Dessen
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Bacterial Pathogenesis Group, 38000 Grenoble, France
| | - Pauline Macheboeuf
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Bacterial Pathogenesis Group, 38000 Grenoble, France.
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4
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Motoyama T, Nogawa T, Shimizu T, Kawatani M, Kashiwa T, Yun CS, Hashizume D, Osada H. Fungal NRPS-PKS Hybrid Enzymes Biosynthesize New γ-Lactam Compounds, Taslactams A-D, Analogous to Actinomycete Proteasome Inhibitors. ACS Chem Biol 2023; 18:396-403. [PMID: 36692171 DOI: 10.1021/acschembio.2c00830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Proteasome inhibitors with γ-lactam structure, such as lactacystin and salinosporamide A, have been isolated from actinomycetes and have attracted attention as lead compounds for anticancer drugs. Previously, we identified a unique enzyme TAS1, which is the first reported fungal NRPS-PKS hybrid enzyme, from the filamentous fungus Pyricularia oryzae for the biosynthesis of a mycotoxin tenuazonic acid, a tetramic acid compound without γ-lactam structure. Homologues of TAS1 have been identified in several fungal genomes and classified into four groups (A-D). Here, we show that the group D TAS1 homologues from two filamentous fungi can biosynthesize γ-lactam compounds, taslactams A-D, with high similarity to actinomycete proteasome inhibitors. One of the γ-lactam compounds, taslactam C, showed potent proteasome inhibitory activity. In contrast to actinomycete γ-lactam compounds which require multiple enzymes for biosynthesis, the TAS1 homologue alone was sufficient for the biosynthesis of the fungal γ-lactam compounds.
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Affiliation(s)
- Takayuki Motoyama
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Toshihiko Nogawa
- Molecular Structure Characterization Unit, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Takeshi Shimizu
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Makoto Kawatani
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan.,Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan.,Chemical Resource Development Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Takeshi Kashiwa
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Choong-Soo Yun
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Daisuke Hashizume
- Materials Characterization Support Team, RIKEN Center for Emergent Matter Science (CEMS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan.,Chemical Resource Development Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan.,Department of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yata, Suruga-ku, Shizuoka 422-8526, Japan
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5
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Recent advances in the structural biology of modular polyketide synthases and nonribosomal peptide synthetases. Curr Opin Chem Biol 2022; 71:102223. [PMID: 36265331 DOI: 10.1016/j.cbpa.2022.102223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 01/27/2023]
Abstract
Polyketides and nonribosomal peptides are an important class of natural products with useful bioactivities. These compounds are similarly biosynthesized using enzymes with modular structures despite having different physicochemical properties. These enzymes are attractive targets for bioengineering to produce "unnatural" natural products owing to their modular structures. Therefore, their structures have been studied for a long time; however, the main focus was on truncated-single domains. Surprisingly, there is an increasing number of the structures of whole modules reported, most of which have been enabled through the recent advances in cryogenic electron microscopy technology. In this review, we have summarized the recent advances in the structural elucidation of whole modules.
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6
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Gakuubi MM, Ching KC, Munusamy M, Wibowo M, Lim CT, Ma GL, Liang ZX, Kanagasundaram Y, Ng SB. CRISPR/Cas9 RNP-assisted validation of palmarumycin biosynthetic gene cluster in Lophiotrema sp. F6932. Front Microbiol 2022; 13:1012115. [PMID: 36246293 PMCID: PMC9556985 DOI: 10.3389/fmicb.2022.1012115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Lophiotrema is a genus of ascomycetous fungi within the family Lophiotremataceae. Members of this genus have been isolated as endophytes from a wide range of host plants and also from plant debris within terrestrial and marine habitats, where they are thought to function as saprobes. Lophiotrema sp. F6932 was isolated from white mangrove (Avicennia officinalis) in Pulau Ubin Island, Singapore. Crude extracts from the fungus exhibited strong antibacterial activity, and bioassay-guided isolation and structure elucidation of bioactive constituents led to the isolation of palmarumycin C8 and a new analog palmarumycin CP30. Whole-genome sequencing analysis resulted in the identification of a putative type 1 iterative PKS (iPKS) predicated to be involved in the biosynthesis of palmarumycins. To verify the involvement of palmarumycin (PAL) gene cluster in the biosynthesis of these compounds, we employed ribonucleoprotein (RNP)-mediated CRISPR-Cas9 to induce targeted deletion of the ketosynthase (KS) domain in PAL. Double-strand breaks (DSBs) upstream and downstream of the KS domain was followed by homology-directed repair (HDR) with a hygromycin resistance cassette flanked by a 50 bp of homology on both sides of the DSBs. The resultant deletion mutants displayed completely different phenotypes compared to the wild-type strain, as they had different colony morphology and were no longer able to produce palmarumycins or melanin. This study, therefore, confirms the involvement of PAL in the biosynthesis of palmarumycins, and paves the way for implementing a similar approach in the characterization of other gene clusters of interest in this largely understudied fungal strain.
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Affiliation(s)
- Martin Muthee Gakuubi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kuan Chieh Ching
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Madhaiyan Munusamy
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mario Wibowo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chun Teck Lim
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- *Correspondence: Siew Bee Ng,
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7
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Bon C, Cabantous S, Julien S, Guillet V, Chalut C, Rima J, Brison Y, Malaga W, Sanchez-Dafun A, Gavalda S, Quémard A, Marcoux J, Waldo GS, Guilhot C, Mourey L. Solution structure of the type I polyketide synthase Pks13 from Mycobacterium tuberculosis. BMC Biol 2022; 20:147. [PMID: 35729566 PMCID: PMC9210659 DOI: 10.1186/s12915-022-01337-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Type I polyketide synthases (PKSs) are multifunctional enzymes responsible for the biosynthesis of a group of diverse natural compounds with biotechnological and pharmaceutical interest called polyketides. The diversity of polyketides is impressive despite the limited set of catalytic domains used by PKSs for biosynthesis, leading to considerable interest in deciphering their structure-function relationships, which is challenging due to high intrinsic flexibility. Among nineteen polyketide synthases encoded by the genome of Mycobacterium tuberculosis, Pks13 is the condensase required for the final condensation step of two long acyl chains in the biosynthetic pathway of mycolic acids, essential components of the cell envelope of Corynebacterineae species. It has been validated as a promising druggable target and knowledge of its structure is essential to speed up drug discovery to fight against tuberculosis. RESULTS We report here a quasi-atomic model of Pks13 obtained using small-angle X-ray scattering of the entire protein and various molecular subspecies combined with known high-resolution structures of Pks13 domains or structural homologues. As a comparison, the low-resolution structures of two other mycobacterial polyketide synthases, Mas and PpsA from Mycobacterium bovis BCG, are also presented. This study highlights a monomeric and elongated state of the enzyme with the apo- and holo-forms being identical at the resolution probed. Catalytic domains are segregated into two parts, which correspond to the condensation reaction per se and to the release of the product, a pivot for the enzyme flexibility being at the interface. The two acyl carrier protein domains are found at opposite sides of the ketosynthase domain and display distinct characteristics in terms of flexibility. CONCLUSIONS The Pks13 model reported here provides the first structural information on the molecular mechanism of this complex enzyme and opens up new perspectives to develop inhibitors that target the interactions with its enzymatic partners or between catalytic domains within Pks13 itself.
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Affiliation(s)
- Cécile Bon
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.
| | - Stéphanie Cabantous
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Los Alamos National Laboratory, Bioscience Division B-N2, Los Alamos, NM, 87545, USA.,Present address: Centre de Recherche en Cancérologie de Toulouse (CRCT), Inserm, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sylviane Julien
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Valérie Guillet
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Christian Chalut
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julie Rima
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yoann Brison
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Present address: Toulouse White Biotechnology, 31400, Toulouse, France
| | - Wladimir Malaga
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Angelique Sanchez-Dafun
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sabine Gavalda
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Present address: Carbios, Biopole Clermont Limagne, 63360, Saint-Beauzire, France
| | - Annaïk Quémard
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Geoffrey S Waldo
- Los Alamos National Laboratory, Bioscience Division B-N2, Los Alamos, NM, 87545, USA
| | - Christophe Guilhot
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.
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Metabolic Profile, Biotransformation, Docking Studies and Molecular Dynamics Simulations of Bioactive Compounds Secreted by CG3 Strain. Antibiotics (Basel) 2022; 11:antibiotics11050657. [PMID: 35625301 PMCID: PMC9137728 DOI: 10.3390/antibiotics11050657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 02/01/2023] Open
Abstract
Actinobacteria isolated from untapped environments and exposed to extreme conditions such as saltpans are a promising source of novel bioactive compounds. These microorganisms can provide new molecules through either the biosynthetic pathway or the biotransformation of organic molecules. In the present study, we performed a chemical metabolic screening of secondary metabolites secreted by the new strain CG3, which was isolated from a saltpan located in the Sahara of Algeria, via high-performance liquid chromatography coupled with high-resolution mass spectrometry (HPLC-ESI-HRMS). The results indicated that this strain produced five new polyene macrolactams, kenalactams A–E, along with two known compounds, mitomycin C and 6″-hydroxy-4,2′,3′,4″ tetramethoxy-p-terphenyl. Furthermore, the CG3 isolate could have excellent properties for converting the aglycone isoflavone glycitein to the compounds 6,7-dimethoxy-3-(4-methoxyphenyl)chromen-4-one (50) and 6,7-dimethoxy-3-phenylchromen-4-one (54), and the isoflavone genistein can be converted to 5,7-dimethoxy-3-(4-methoxyphenyl)chromen-4-one (52). Docking studies and molecular dynamics simulations indicated that these three isoflavones, generated via biotransformation, are potent inhibitors of the target protein aromatase (CYP19A1); consequently, they can be used to prevent breast cancer risk in postmenopausal women.
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Enzymatic assembly of the salinosporamide γ-lactam-β-lactone anticancer warhead. Nat Chem Biol 2022; 18:538-546. [PMID: 35314816 PMCID: PMC9058210 DOI: 10.1038/s41589-022-00993-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 02/04/2022] [Indexed: 12/25/2022]
Abstract
The marine microbial natural product salinosporamide A (Marizomib) is a potent proteasome inhibitor currently in clinical trials for the treatment of brain cancer. Salinosporamide A is characterized by a complex and densely functionalized γ-lactam-β-lactone bicyclic warhead, the assembly of which has long remained a biosynthetic mystery. Here, we report an enzymatic route to the salinosporamide core catalyzed by a standalone ketosynthase, SalC. Chemoenzymatic synthesis of carrier protein-tethered substrates, as well as intact proteomics, allowed us to probe the reactivity of SalC and understand its role as an intramolecular aldolase/β-lactone synthase with roles in both transacylation and bond forming reactions. Additionally, we present the 2.85 Å SalC crystal structure that, combined with site-directed mutagenesis, allowed us to propose a bicyclization reaction mechanism. This work challenges our current understanding of the role of ketosynthase enzymes and establishes a basis for future efforts towards streamlined production of a clinically relevant chemotherapeutic.
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Wang H, Guo Y, Luo Z, Gao L, Li R, Zhang Y, Kalaji HM, Qiang S, Chen S. Recent Advances in Alternaria Phytotoxins: A Review of Their Occurrence, Structure, Bioactivity and Biosynthesis. J Fungi (Basel) 2022; 8:jof8020168. [PMID: 35205922 PMCID: PMC8878860 DOI: 10.3390/jof8020168] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 12/04/2022] Open
Abstract
Alternaria is a ubiquitous fungal genus in many ecosystems, consisting of species and strains that can be saprophytic, endophytic, or pathogenic to plants or animals, including humans. Alternaria species can produce a variety of secondary metabolites (SMs), especially low molecular weight toxins. Based on the characteristics of host plant susceptibility or resistance to the toxin, Alternaria phytotoxins are classified into host-selective toxins (HSTs) and non-host-selective toxins (NHSTs). These Alternaria toxins exhibit a variety of biological activities such as phytotoxic, cytotoxic, and antimicrobial properties. Generally, HSTs are toxic to host plants and can cause severe economic losses. Some NHSTs such as alternariol, altenariol methyl-ether, and altertoxins also show high cytotoxic and mutagenic activities in the exposed human or other vertebrate species. Thus, Alternaria toxins are meaningful for drug and pesticide development. For example, AAL-toxin, maculosin, tentoxin, and tenuazonic acid have potential to be developed as bioherbicides due to their excellent herbicidal activity. Like altersolanol A, bostrycin, and brefeldin A, they exhibit anticancer activity, and ATX V shows high activity to inhibit the HIV-1 virus. This review focuses on the classification, chemical structure, occurrence, bioactivity, and biosynthesis of the major Alternaria phytotoxins, including 30 HSTs and 50 NHSTs discovered to date.
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Affiliation(s)
- He Wang
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (Y.G.); (Z.L.); (L.G.); (Y.Z.); (S.Q.)
| | - Yanjing Guo
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (Y.G.); (Z.L.); (L.G.); (Y.Z.); (S.Q.)
| | - Zhi Luo
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (Y.G.); (Z.L.); (L.G.); (Y.Z.); (S.Q.)
| | - Liwen Gao
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (Y.G.); (Z.L.); (L.G.); (Y.Z.); (S.Q.)
| | - Rui Li
- Agricultural and Animal Husbandry Ecology and Resource Protection Center, Ordos Agriculture and Animal Husbandry Bureau, Ordos 017010, China;
| | - Yaxin Zhang
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (Y.G.); (Z.L.); (L.G.); (Y.Z.); (S.Q.)
| | - Hazem M. Kalaji
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences SGGW, 159 Nowoursynowska 159, 02-776 Warsaw, Poland;
- Institute of Technology and Life Sciences—National Research Institute, Falenty, Al. Hrabska 3, 05-090 Raszyn, Poland
| | - Sheng Qiang
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (Y.G.); (Z.L.); (L.G.); (Y.Z.); (S.Q.)
| | - Shiguo Chen
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (Y.G.); (Z.L.); (L.G.); (Y.Z.); (S.Q.)
- Correspondence: ; Tel.: +86-25-84395117
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Motoyama T, Yun CS, Osada H. Biosynthesis and biological function of secondary metabolites of the rice blast fungus Pyricularia oryzae. J Ind Microbiol Biotechnol 2021; 48:kuab058. [PMID: 34379774 PMCID: PMC8788799 DOI: 10.1093/jimb/kuab058] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/05/2021] [Indexed: 11/18/2022]
Abstract
Filamentous fungi have many secondary metabolism genes and produce a wide variety of secondary metabolites with complex and unique structures. However, the role of most secondary metabolites remains unclear. Moreover, most fungal secondary metabolism genes are silent or poorly expressed under laboratory conditions and are difficult to utilize. Pyricularia oryzae, the causal pathogen of rice blast disease, is a well-characterized plant pathogenic fungus. P. oryzae also has a large number of secondary metabolism genes and appears to be a suitable organism for analyzing secondary metabolites. However, in case of this fungus, biosynthetic genes for only four groups of secondary metabolites have been well characterized. Among two of the four groups of secondary metabolites, biosynthetic genes were identified by activating secondary metabolism. These secondary metabolites include melanin, a polyketide compound required for rice infection; tenuazonic acid, a well-known mycotoxin produced by various plant pathogenic fungi and biosynthesized by a unique nonribosomal peptide synthetase-polyketide synthase hybrid enzyme; nectriapyrones, antibacterial polyketide compounds produced mainly by symbiotic fungi, including plant pathogens and endophytes, and pyriculols, phytotoxic polyketide compounds. This review mainly focuses on the biosynthesis and biological functions of the four groups of P. oryzae secondary metabolites.
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Affiliation(s)
- Takayuki Motoyama
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Choong-Soo Yun
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
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Little RF, Hertweck C. Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis. Nat Prod Rep 2021; 39:163-205. [PMID: 34622896 DOI: 10.1039/d1np00035g] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Review covering up to mid-2021The structure of polyketide and non-ribosomal peptide natural products is strongly influenced by how they are released from their biosynthetic enzymes. As such, Nature has evolved a diverse range of release mechanisms, leading to the formation of bioactive chemical scaffolds such as lactones, lactams, diketopiperazines, and tetronates. Here, we review the enzymes and mechanisms used for chain release in polyketide and non-ribosomal peptide biosynthesis, how these mechanisms affect natural product structure, and how they could be utilised to introduce structural diversity into the products of engineered biosynthetic pathways.
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Affiliation(s)
- Rory F Little
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
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Motoyama T, Ishii T, Kamakura T, Osada H. Screening of tenuazonic acid production-inducing compounds and identification of NPD938 as a regulator of fungal secondary metabolism. Biosci Biotechnol Biochem 2021; 85:2200-2208. [PMID: 34379730 DOI: 10.1093/bbb/zbab143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/05/2021] [Indexed: 11/12/2022]
Abstract
The control of secondary metabolism in fungi is essential for the regulation of various cellular functions. In this study, we searched the RIKEN Natural Products Depository (NPDepo) chemical library for inducers of tenuazonic acid (TeA) production in the rice blast fungus Pyricularia oryzae and identified NPD938. NPD938 transcriptionally induced TeA production. We explored the mode of action of NPD938 and observed that this compound enhanced TeA production via LAE1, a global regulator of fungal secondary metabolism. NPD938 could also induce production of terpendoles and pyridoxatins in Tolypocladium album RK99-F33. Terpendole production was induced transcriptionally. We identified the pyridoxatin biosynthetic gene cluster among transcriptionally induced secondary metabolite biosynthetic gene clusters. Therefore, NPD938 is useful for the control of fungal secondary metabolism.
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Affiliation(s)
| | - Tomoaki Ishii
- Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama, Japan.,Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Takashi Kamakura
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama, Japan
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Li C, Ju J, Xie Y, Yu H, Guo Y, Yao W, Qian H. Effects of interactions between polygalacturonase and pesticide residues during enzymatic hydrolysis on the yield of apple juice. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Mo X, Gulder TAM. Biosynthetic strategies for tetramic acid formation. Nat Prod Rep 2021; 38:1555-1566. [PMID: 33710214 DOI: 10.1039/d0np00099j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Covering: up to the end of 2020Natural products bearing tetramic acid units as part of complex molecular architectures exhibit a broad range of potent biological activities. These compounds thus attract significant interest from both the biosynthetic and synthetic communities. Biosynthetically, most of the tetramic acids are derived from hybrid polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) machineries. To date, over 30 biosynthetic gene clusters (BGCs) involved in tetramate formation have been identified, from which different biosynthetic strategies evolved in Nature to assemble this intriguing structural unit were characterized. In this Highlight we focus on the biosynthetic concepts of tetramic acid formation and discuss the molecular mechanism towards selected representatives in detail, providing a systematic overview for the development of strategies for targeted tetramate genome mining and future applications of tetramate-forming biocatalysts for chemo-enzymatic synthesis.
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Affiliation(s)
- Xuhua Mo
- Shandong Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 266109 Qingdao, China. and Chair of Technical Biochemistry, Technische Universität Dresden, Bergstraße 66, 01069 Dresden, Germany.
| | - Tobias A M Gulder
- Chair of Technical Biochemistry, Technische Universität Dresden, Bergstraße 66, 01069 Dresden, Germany.
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Research progress and the biotechnological applications of multienzyme complex. Appl Microbiol Biotechnol 2021; 105:1759-1777. [PMID: 33564922 DOI: 10.1007/s00253-021-11121-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/07/2021] [Accepted: 01/16/2021] [Indexed: 11/26/2022]
Abstract
The multienzyme complex system has become a research focus in synthetic biology due to its highly efficient overall catalytic ability and has been applied to various fields. Multienzyme complexes are formed by cascading complexes, which are multiple functionally related enzymes that continuously and efficiently catalyze the production of substrates. Compared with current mainstream microbial cell catalytic systems, in vitro multienzyme molecular machines have many advantages, such as fewer side reactions, a high product yield, a fast reaction speed, easy product separation, a tolerable toxic environment, and robust system operability, showing increasing competitiveness in the field of biomanufacturing. In this review, the research progress of multienzyme complexes in nature and multienzyme cascades in vivo or in vitro will be introduced, and the discovered enzyme cascades concerning scaffolding proteins will also be discussed. This review is expected to provide a more theoretical basis for the modification of multienzyme complexes and broaden their application in the field of synthetic biology. KEY POINTS: • The cascade reactions of some natural multienzyme complexes are reviewed. • The main approaches of constructing artificial multienzyme complexes are summarized. • The structure and application of cellulosomes are discussed and prospected.
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Secondary Metabolites of the Rice Blast Fungus Pyricularia oryzae: Biosynthesis and Biological Function. Int J Mol Sci 2020; 21:ijms21228698. [PMID: 33218033 PMCID: PMC7698770 DOI: 10.3390/ijms21228698] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
Plant pathogenic fungi produce a wide variety of secondary metabolites with unique and complex structures. However, most fungal secondary metabolism genes are poorly expressed under laboratory conditions. Moreover, the relationship between pathogenicity and secondary metabolites remains unclear. To activate silent gene clusters in fungi, successful approaches such as epigenetic control, promoter exchange, and heterologous expression have been reported. Pyricularia oryzae, a well-characterized plant pathogenic fungus, is the causal pathogen of rice blast disease. P. oryzae is also rich in secondary metabolism genes. However, biosynthetic genes for only four groups of secondary metabolites have been well characterized in this fungus. Biosynthetic genes for two of the four groups of secondary metabolites have been identified by activating secondary metabolism. This review focuses on the biosynthesis and roles of the four groups of secondary metabolites produced by P. oryzae. These secondary metabolites include melanin, a polyketide compound required for rice infection; pyriculols, phytotoxic polyketide compounds; nectriapyrones, antibacterial polyketide compounds produced mainly by symbiotic fungi including endophytes and plant pathogens; and tenuazonic acid, a well-known mycotoxin produced by various plant pathogenic fungi and biosynthesized by a unique NRPS-PKS enzyme.
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