101
|
Wiemann P, Soukup AA, Folz JS, Wang PM, Noack A, Keller NP. CoIN: co-inducible nitrate expression system for secondary metabolites in Aspergillus nidulans. Fungal Biol Biotechnol 2018; 5:6. [PMID: 29564145 PMCID: PMC5851313 DOI: 10.1186/s40694-018-0049-2] [Citation(s) in RCA: 18] [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: 12/21/2017] [Accepted: 03/05/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sequencing of fungal species has demonstrated the existence of thousands of putative secondary metabolite gene clusters, the majority of them harboring a unique set of genes thought to participate in production of distinct small molecules. Despite the ready identification of key enzymes and potential cluster genes by bioinformatics techniques in sequenced genomes, the expression and identification of fungal secondary metabolites in the native host is often hampered as the genes might not be expressed under laboratory conditions and the species might not be amenable to genetic manipulation. To overcome these restrictions, we developed an inducible expression system in the genetic model Aspergillus nidulans. RESULTS We genetically engineered a strain of A. nidulans devoid of producing eight of the most abundant endogenous secondary metabolites to express the sterigmatocystin Zn(II)2Cys6 transcription factor-encoding gene aflR and its cofactor aflS under control of the nitrate inducible niiA/niaD promoter. Furthermore, we identified a subset of promoters from the sterigmatocystin gene cluster that are under nitrate-inducible AflR/S control in our production strain in order to yield coordinated expression without the risks from reusing a single inducible promoter. As proof of concept, we used this system to produce β-carotene from the carotenoid gene cluster of Fusarium fujikuroi. CONCLUSION Utilizing one-step yeast recombinational cloning, we developed an inducible expression system in the genetic model A. nidulans and show that it can be successfully used to produce commercially valuable metabolites.
Collapse
Affiliation(s)
- Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
- Present Address: Hexagon Bio, Menlo Park, CA 94025 USA
| | - Alexandra A. Soukup
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
- Present Address: Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53705 USA
| | - Jacob S. Folz
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
- Present Address: Davis Genome Center – Metabolomics, University of California, 451 Health Science Drive, Davis, CA 95616 USA
| | - Pin-Mei Wang
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
- Present Address: Ocean College, Zhejiang University, Hangzhou, 310058 Zhejiang Province People’s Republic of China
| | - Andreas Noack
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706 USA
| |
Collapse
|
102
|
Loureiro C, Medema MH, van der Oost J, Sipkema D. Exploration and exploitation of the environment for novel specialized metabolites. Curr Opin Biotechnol 2018; 50:206-213. [PMID: 29454184 DOI: 10.1016/j.copbio.2018.01.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 01/22/2018] [Accepted: 01/22/2018] [Indexed: 11/26/2022]
Abstract
Microorganisms are Nature's little engineers of a remarkable array of bioactive small molecules that represent most of our new drugs. The wealth of genomic and metagenomic sequence data generated in the last decade has shown that the majority of novel biosynthetic gene clusters (BGCs) is identified from cultivation-independent studies, which has led to a strong expansion of the number of microbial taxa known to harbour BGCs. The large size and repeat sequences of BGCs remain a bioinformatic challenge, but newly developed software tools have been created to overcome these issues and are paramount to identify and select the most promising BGCs for further research and exploitation. Although heterologous expression of BGCs has been the greatest challenge until now, a growing number of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS)-encoding gene clusters have been cloned and expressed in bacteria and fungi based on techniques that mostly rely on homologous recombination. Finally, combining ecological insights with state-of-the-art computation and molecular methodologies will allow for further comprehension and exploitation of microbial specialized metabolites.
Collapse
Affiliation(s)
- Catarina Loureiro
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Marnix H Medema
- Wageningen University & Research, Bioinformatics Group, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - John van der Oost
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Detmer Sipkema
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| |
Collapse
|
103
|
Hamal KB, Chalifoux WA. One-Pot Synthesis of α-Carbonyl Bicyclic Furans via a Sequential Diels–Alder/5-Exo-Dig Cyclization/Oxidation Reaction. J Org Chem 2017; 82:12920-12927. [DOI: 10.1021/acs.joc.7b02479] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Khagendra B. Hamal
- Department of Chemistry, University of Nevada, Reno, Nevada 89557-0216, United States
| | - Wesley A. Chalifoux
- Department of Chemistry, University of Nevada, Reno, Nevada 89557-0216, United States
| |
Collapse
|
104
|
Li G, Lou HX. Strategies to diversify natural products for drug discovery. Med Res Rev 2017; 38:1255-1294. [PMID: 29064108 DOI: 10.1002/med.21474] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/18/2017] [Accepted: 09/28/2017] [Indexed: 12/11/2022]
Abstract
Natural product libraries contain specialized metabolites derived from plants, animals, and microorganisms that play a pivotal role in drug discovery due to their immense structural diversity and wide variety of biological activities. The strategies to greatly extend natural product scaffolds through available biological and chemical approaches offer unique opportunities to access a new series of natural product analogues, enabling the construction of diverse natural product-like libraries. The affordability of these structurally diverse molecules has been a crucial step in accelerating drug discovery. This review provides an overview of various approaches to exploit the diversity of compounds for natural product-based drug development, drawing upon a series of examples to illustrate each strategy.
Collapse
Affiliation(s)
- Gang Li
- Department of Natural Medicine and Pharmacognosy, School of Pharmacy, Qingdao University, Qingdao, China
| | - Hong-Xiang Lou
- Department of Natural Medicine and Pharmacognosy, School of Pharmacy, Qingdao University, Qingdao, China.,Department of Natural Products Chemistry, Key Lab of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| |
Collapse
|
105
|
Hillman ET, Readnour LR, Solomon KV. Exploiting the natural product potential of fungi with integrated -omics and synthetic biology approaches. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.07.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
106
|
Clevenger KD, Bok JW, Ye R, Miley GP, Verdan MH, Velk T, Chen C, Yang K, Robey MT, Gao P, Lamprecht M, Thomas PM, Islam MN, Palmer JM, Wu CC, Keller NP, Kelleher NL. A scalable platform to identify fungal secondary metabolites and their gene clusters. Nat Chem Biol 2017; 13:895-901. [PMID: 28604695 PMCID: PMC5577364 DOI: 10.1038/nchembio.2408] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/13/2017] [Indexed: 12/02/2022]
Abstract
The genomes of filamentous fungi contain up to 90 biosynthetic gene clusters (BGCs) encoding diverse secondary metabolites-an enormous reservoir of untapped chemical potential. However, the recalcitrant genetics, cryptic expression, and unculturability of these fungi prevent scientists from systematically exploiting these gene clusters and harvesting their products. As heterologous expression of fungal BGCs is largely limited to the expression of single or partial clusters, we established a scalable process for the expression of large numbers of full-length gene clusters, called FAC-MS. Using fungal artificial chromosomes (FACs) and metabolomic scoring (MS), we screened 56 secondary metabolite BGCs from diverse fungal species for expression in Aspergillus nidulans. We discovered 15 new metabolites and assigned them with confidence to their BGCs. Using the FAC-MS platform, we extensively characterized a new macrolactone, valactamide A, and its hybrid nonribosomal peptide synthetase-polyketide synthase (NRPS-PKS). The ability to regularize access to fungal secondary metabolites at an unprecedented scale stands to revitalize drug discovery platforms with renewable sources of natural products.
Collapse
Affiliation(s)
- Kenneth D Clevenger
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Jin Woo Bok
- Department of Medical Microbiology and Immunology and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Rosa Ye
- Intact Genomics, Inc., St. Louis, Missouri, USA
| | - Galen P Miley
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Maria H Verdan
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Thomas Velk
- Department of Medical Microbiology and Immunology and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - KaHoua Yang
- Department of Medical Microbiology and Immunology and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Matthew T Robey
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Peng Gao
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | | | - Paul M Thomas
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | | | - Jonathan M Palmer
- Center for Forest Mycology Research, Northern Research Station, US Forest Service, Madison, Wisconsin, USA
| | | | - Nancy P Keller
- Department of Medical Microbiology and Immunology and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| |
Collapse
|
107
|
Romano G, Costantini M, Sansone C, Lauritano C, Ruocco N, Ianora A. Marine microorganisms as a promising and sustainable source of bioactive molecules. MARINE ENVIRONMENTAL RESEARCH 2017; 128:58-69. [PMID: 27160988 DOI: 10.1016/j.marenvres.2016.05.002] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/29/2016] [Accepted: 05/01/2016] [Indexed: 06/05/2023]
Abstract
There is an urgent need to discover new drug entities due to the increased incidence of severe diseases as cancer and neurodegenerative pathologies, and reducing efficacy of existing antibiotics. Recently, there is a renewed interest in exploring the marine habitat for new pharmaceuticals also thanks to the advancement in cultivation technologies and in molecular biology techniques. Microorganisms represent a still poorly explored resource for drug discovery. The possibility of obtaining a continuous source of bioactives from marine microorganisms, more amenable to culturing compared to macro-organisms, may be able to meet the challenging demands of pharmaceutical industries. This would enable a more environmentally-friendly approach to drug discovery and overcome the over-utilization of marine resources and the use of destructive collection practices. The importance of the topic is underlined by the number of EU projects funded aimed at improving the exploitation of marine organisms for drug discovery.
Collapse
Affiliation(s)
- G Romano
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
| | - M Costantini
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - C Sansone
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - C Lauritano
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - N Ruocco
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy; Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, Pozzuoli, Naples 80078, Italy
| | - A Ianora
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| |
Collapse
|
108
|
Abstract
As eukaryotes, filamentous fungi share many features with humans, and they produce numerous active metabolites, some of which are toxic. Traditional genetic approaches are generally inefficient, but the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system that has been widely used for basic research on bacteria, mammals and plants offers a simple, fast, versatile technology for systemic research on filamentous fungi. In this review, we summarized the current knowledge on Cas9 and its variants, various selective markers used to screen positive clones, different ways used to detect off-target mutations, and different approaches used to express and transform the CRISPR complex. We also highlight several methods that improve the nuclease specificity and efficiency, and discuss current and potential applications of CRISPR/Cas9 system in filamentous fungi for pathogenesis decoding, confirmation of the gene and pathway, bioenergy process, drug discovery, and chromatin dynamics. We also describe how the synthetic gene circuit of CRISPR/Cas9 systems has been used in the response to various complex environmental signals to redirect metabolite flux and ensure continuous metabolite biosynthesis.
Collapse
Affiliation(s)
- Huaxiang Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China
| | - Ruijie Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China
| | - Xiangru Liao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China.
| |
Collapse
|
109
|
Zhang P, Wang X, Fan A, Zheng Y, Liu X, Wang S, Zou H, Oakley BR, Keller NP, Yin WB. A cryptic pigment biosynthetic pathway uncovered by heterologous expression is essential for conidial development inPestalotiopsis fici. Mol Microbiol 2017; 105:469-483. [DOI: 10.1111/mmi.13711] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Peng Zhang
- State Key Laboratory of Mycology; Institute of Microbiology, Chinese Academy of Sciences; Beijing People's Republic of China
- College of Life Science, University of Chinese Academy of Sciences; Beijing People's Republic of China
| | - Xiuna Wang
- State Key Laboratory of Mycology; Institute of Microbiology, Chinese Academy of Sciences; Beijing People's Republic of China
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences; Fujian Agriculture and Forestry University; Fuzhou People's Republic of China
| | - Aili Fan
- State Key Laboratory of Mycology; Institute of Microbiology, Chinese Academy of Sciences; Beijing People's Republic of China
| | - Yanjing Zheng
- Zhejiang Provincial (Wenzhou) Key Lab for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science; Wenzhou University; Wenzhou People's Republic of China
| | - Xingzhong Liu
- State Key Laboratory of Mycology; Institute of Microbiology, Chinese Academy of Sciences; Beijing People's Republic of China
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences; Fujian Agriculture and Forestry University; Fuzhou People's Republic of China
| | - Huixi Zou
- Zhejiang Provincial (Wenzhou) Key Lab for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science; Wenzhou University; Wenzhou People's Republic of China
| | - Berl R. Oakley
- Department of Molecular Biosciences; University of Kansas; Lawrence KS USA
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology; University of Wisconsin-Madison; Madison Wisconsin, WI USA
| | - Wen-Bing Yin
- State Key Laboratory of Mycology; Institute of Microbiology, Chinese Academy of Sciences; Beijing People's Republic of China
- College of Life Science, University of Chinese Academy of Sciences; Beijing People's Republic of China
| |
Collapse
|
110
|
Dinesh R, Srinivasan V, T E S, Anandaraj M, Srambikkal H. Endophytic actinobacteria: Diversity, secondary metabolism and mechanisms to unsilence biosynthetic gene clusters. Crit Rev Microbiol 2017; 43:546-566. [PMID: 28358596 DOI: 10.1080/1040841x.2016.1270895] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Endophytic actinobacteria, which reside in the inner tissues of host plants, are gaining serious attention due to their capacity to produce a plethora of secondary metabolites (e.g. antibiotics) possessing a wide variety of biological activity with diverse functions. This review encompasses the recent reports on endophytic actinobacterial species diversity, in planta habitats and mechanisms underlying their mode of entry into plants. Besides, their metabolic potential, novel bioactive compounds they produce and mechanisms to unravel their hidden metabolic repertoire by activation of cryptic or silent biosynthetic gene clusters (BGCs) for eliciting novel secondary metabolite production are discussed. The study also reviews the classical conservative techniques (chemical/biological/physical elicitation, co-culturing) as well as modern microbiology tools (e.g. next generation sequencing) that are being gainfully employed to uncover the vast hidden scaffolds for novel secondary metabolites produced by these endophytes, which would subsequently herald a revolution in drug engineering. The potential role of these endophytes in the agro-environment as promising biological candidates for inhibition of phytopathogens and the way forward to thoroughly exploit this unique microbial community by inducing expression of cryptic BGCs for encoding unseen products with novel therapeutic properties are also discussed.
Collapse
Affiliation(s)
- Raghavan Dinesh
- a ICAR-Indian Institute of Spices Research , Kozhikode, Kerala , India
| | | | - Sheeja T E
- a ICAR-Indian Institute of Spices Research , Kozhikode, Kerala , India
| | | | - Hamza Srambikkal
- a ICAR-Indian Institute of Spices Research , Kozhikode, Kerala , India
| |
Collapse
|
111
|
Nielsen JC, Nielsen J. Development of fungal cell factories for the production of secondary metabolites: Linking genomics and metabolism. Synth Syst Biotechnol 2017; 2:5-12. [PMID: 29062956 PMCID: PMC5625732 DOI: 10.1016/j.synbio.2017.02.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 12/01/2022] Open
Abstract
The genomic era has revolutionized research on secondary metabolites and bioinformatics methods have in recent years revived the antibiotic discovery process after decades with only few new active molecules being identified. New computational tools are driven by genomics and metabolomics analysis, and enables rapid identification of novel secondary metabolites. To translate this increased discovery rate into industrial exploitation, it is necessary to integrate secondary metabolite pathways in the metabolic engineering process. In this review, we will describe the novel advances in discovery of secondary metabolites produced by filamentous fungi, highlight the utilization of genome-scale metabolic models (GEMs) in the design of fungal cell factories for the production of secondary metabolites and review strategies for optimizing secondary metabolite production through the construction of high yielding platform cell factories.
Collapse
Affiliation(s)
| | - Jens Nielsen
- Chalmers University of Technology, Kemivägen 10, Sweden
| |
Collapse
|
112
|
Sung CT, Chang SL, Entwistle R, Ahn G, Lin TS, Petrova V, Yeh HH, Praseuth MB, Chiang YM, Oakley BR, Wang CCC. Overexpression of a three-gene conidial pigment biosynthetic pathway in Aspergillus nidulans reveals the first NRPS known to acetylate tryptophan. Fungal Genet Biol 2017; 101:1-6. [PMID: 28108400 DOI: 10.1016/j.fgb.2017.01.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 01/05/2017] [Accepted: 01/14/2017] [Indexed: 01/11/2023]
Abstract
Fungal nonribosomal peptide synthetases (NRPSs) are megasynthetases that produce cyclic and acyclic peptides. In Aspergillus nidulans, the NRPS ivoA (AN10576) has been associated with the biosynthesis of grey-brown conidiophore pigments. Another gene, ivoB (AN0231), has been demonstrated to be an N-acetyl-6-hydroxytryptophan oxidase that putatively acts downstream of IvoA. A third gene, ivoC, has also been predicted to be involved in pigment biosynthesis based on publicly available genomic and transcriptomic information. In this paper, we report the replacement of the promoters of the ivoA, ivoB, and ivoC genes with the inducible promoter alcA in a single cotransformation. Co-overexpression of the three genes resulted in the production of a dark-brown pigment in hyphae. In addition, overexpression of each of the Ivo genes, ivoA-C, individually or in combination, allowed us to isolate intermediates and confirm the function of each gene. IvoA was found to be the first known NRPS to carry out the acetylation of the amino acid, tryptophan.
Collapse
Affiliation(s)
- Calvin T Sung
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Shu-Lin Chang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA; Drug Discovery and Development Center, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan, ROC.
| | - Ruth Entwistle
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.
| | - Green Ahn
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Tzu-Shyang Lin
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Vessela Petrova
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Hsu-Hua Yeh
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA; Drug Discovery and Development Center, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan, ROC.
| | - Mike B Praseuth
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA; Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan, ROC.
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| |
Collapse
|
113
|
van Dijk JWA, Guo CJ, Wang CCC. Engineering Fungal Nonribosomal Peptide Synthetase-like Enzymes by Heterologous Expression and Domain Swapping. Org Lett 2016; 18:6236-6239. [DOI: 10.1021/acs.orglett.6b02821] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Johannes W. A. van Dijk
- Department
of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, Los Angeles, California 90089, United States
| | - Chun-Jun Guo
- Department
of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, Los Angeles, California 90089, United States
| | - Clay C. C. Wang
- Department
of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, Los Angeles, California 90089, United States
- Department
of Chemistry, College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California 90089, United States
| |
Collapse
|
114
|
Oakley CE, Ahuja M, Sun WW, Entwistle R, Akashi T, Yaegashi J, Guo CJ, Cerqueira GC, Russo Wortman J, Wang CCC, Chiang YM, Oakley BR. Discovery of McrA, a master regulator of Aspergillus secondary metabolism. Mol Microbiol 2016; 103:347-365. [PMID: 27775185 DOI: 10.1111/mmi.13562] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2016] [Indexed: 01/17/2023]
Abstract
Fungal secondary metabolites (SMs) are extremely important in medicine and agriculture, but regulation of their biosynthesis is incompletely understood. We have developed a genetic screen in Aspergillus nidulans for negative regulators of fungal SM gene clusters and we have used this screen to isolate mutations that upregulate transcription of the non-ribosomal peptide synthetase gene required for nidulanin A biosynthesis. Several of these mutations are allelic and we have identified the mutant gene by genome sequencing. The gene, which we designate mcrA, is conserved but uncharacterized, and it encodes a putative transcription factor. Metabolite profiles of mcrA deletant, mcrA overexpressing, and parental strains reveal that mcrA regulates at least ten SM gene clusters. Deletion of mcrA stimulates SM production even in strains carrying a deletion of the SM regulator laeA, and deletion of mcrA homologs in Aspergillus terreus and Penicillum canescens alters the secondary metabolite profile of these organisms. Deleting mcrA in a genetic dereplication strain has allowed us to discover two novel compounds as well as an antibiotic not known to be produced by A. nidulans. Deletion of mcrA upregulates transcription of hundreds of genes including many that are involved in secondary metabolism, while downregulating a smaller number of genes.
Collapse
Affiliation(s)
- C Elizabeth Oakley
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
| | - Manmeet Ahuja
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
| | - Wei-Wen Sun
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California, 90089, USA
| | - Ruth Entwistle
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
| | - Tomohiro Akashi
- Division of OMICS analysis, Nagoya University Graduate School of Medicine, 65 Tsurumai, Nagoya, Aichi, 466-8550, Japan
| | - Junko Yaegashi
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California, 90089, USA
| | - Chun-Jun Guo
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California, 90089, USA
| | - Gustavo C Cerqueira
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Jennifer Russo Wortman
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California, 90089, USA.,Department of Chemistry, Dornsife Colleges of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California, 90089, USA.,Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan City, Taiwan, 71710, Republic of China
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
| |
Collapse
|
115
|
Henke MT, Kelleher NL. Modern mass spectrometry for synthetic biology and structure-based discovery of natural products. Nat Prod Rep 2016; 33:942-50. [PMID: 27376415 PMCID: PMC4981503 DOI: 10.1039/c6np00024j] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: up to 2016In this highlight, we describe the current landscape for dereplication and discovery of natural products based on the measurement of the intact mass by LC-MS. Often it is assumed that because better mass accuracy (provided by higher resolution mass spectrometers) is necessary for absolute chemical formula determination (≤1 part-per-million), that it is also necessary for dereplication of natural products. However, the average ability to dereplicate tapers off at ∼10 ppm, with modest improvement gained from better mass accuracy when querying focused databases of natural products. We also highlight some recent examples of how these platforms are applied to synthetic biology, and recent methods for dereplication and correlation of substructures using tandem MS data. We also offer this highlight to serve as a brief primer for those entering the field of mass spectrometry-based natural products discovery.
Collapse
Affiliation(s)
- Matthew T Henke
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| | | |
Collapse
|
116
|
Yeh HH, Ahuja M, Chiang YM, Oakley CE, Moore S, Yoon O, Hajovsky H, Bok JW, Keller NP, Wang CCC, Oakley BR. Resistance Gene-Guided Genome Mining: Serial Promoter Exchanges in Aspergillus nidulans Reveal the Biosynthetic Pathway for Fellutamide B, a Proteasome Inhibitor. ACS Chem Biol 2016; 11:2275-84. [PMID: 27294372 DOI: 10.1021/acschembio.6b00213] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fungal genome projects are revealing thousands of cryptic secondary metabolism (SM) biosynthetic gene clusters that encode pathways that potentially produce valuable compounds. Heterologous expression systems should allow these clusters to be expressed and their products obtained, but approaches are needed to identify the most valuable target clusters. The inp cluster of Aspergillus nidulans contains a gene, inpE, that encodes a proteasome subunit, leading us to hypothesize that the inp cluster produces a proteasome inhibitor and inpE confers resistance to this compound. Previous efforts to express this cluster have failed, but by sequentially replacing the promoters of the genes of the cluster with a regulatable promotor, we have expressed them successfully. Expression reveals that the product of the inp cluster is the proteasome inhibitor fellutamide B, and our data allow us to propose a biosynthetic pathway for the compound. By deleting inpE and activating expression of the inp cluster, we demonstrate that inpE is required for resistance to internally produced fellutamide B. These data provide experimental validation for the hypothesis that some fungal SM clusters contain genes that encode resistant forms of the enzymes targeted by the compound produced by the cluster.
Collapse
Affiliation(s)
- Hsu-Hua Yeh
- Department
of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
| | - Manmeet Ahuja
- Department
of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Yi-Ming Chiang
- Department
of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
- Department
of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan City 71710, Taiwan
| | - C. Elizabeth Oakley
- Department
of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Shauna Moore
- Department
of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Olivia Yoon
- Department
of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Heather Hajovsky
- Department
of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Jin-Woo Bok
- Department
of Bacteriology and Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Nancy P. Keller
- Department
of Bacteriology and Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Clay C. C. Wang
- Department
of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
- Department
of Chemistry, University of Southern California, Dornsife College of Letters, Arts, and Sciences, Los Angeles, California 90089, United States
| | - Berl R. Oakley
- Department
of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| |
Collapse
|
117
|
Yin Y, Cai M, Zhou X, Li Z, Zhang Y. Polyketides in Aspergillus terreus: biosynthesis pathway discovery and application. Appl Microbiol Biotechnol 2016; 100:7787-98. [PMID: 27455860 DOI: 10.1007/s00253-016-7733-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 07/03/2016] [Accepted: 07/07/2016] [Indexed: 01/01/2023]
Abstract
The knowledge of biosynthesis gene clusters, production improving methods, and bioactivity mechanisms is very important for the development of filamentous fungi metabolites. Metabolic engineering and heterologous expression methods can be applied to improve desired metabolite production, when their biosynthesis pathways have been revealed. And, stable supplement is a necessary basis of bioactivity mechanism discovery and following clinical trial. Aspergillus terreus is an outstanding producer of many bioactive agents, and a large part of them are polyketides. In this review, we took polyketides from A. terreus as examples, focusing on 13 polyketide synthase (PKS) genes in A. terreus NIH 2624 genome. The biosynthesis pathways of nine PKS genes have been reported, and their downstream metabolites are lovastatin, terreic acid, terrein, geodin, terretonin, citreoviridin, and asperfuranone, respectively. Among them, lovastatin is a well-known hypolipidemic agent. Terreic acid, terrein, citreoviridin, and asperfuranone show good bioactivities, especially anticancer activities. On the other hand, geodin and terretonin are mycotoxins. So, biosynthesis gene cluster information is important for the production or elimination of them. We also predicted three possible gene clusters that contain four PKS genes by homologous gene alignment with other Aspergillus strains. We think that this is an effective way to mine secondary metabolic gene clusters.
Collapse
Affiliation(s)
- Ying Yin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China. .,Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai, 200237, China.
| |
Collapse
|
118
|
Hemmerling F, Hahn F. Biosynthesis of oxygen and nitrogen-containing heterocycles in polyketides. Beilstein J Org Chem 2016; 12:1512-50. [PMID: 27559404 PMCID: PMC4979870 DOI: 10.3762/bjoc.12.148] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/22/2016] [Indexed: 01/01/2023] Open
Abstract
This review highlights the biosynthesis of heterocycles in polyketide natural products with a focus on oxygen and nitrogen-containing heterocycles with ring sizes between 3 and 6 atoms. Heterocycles are abundant structural elements of natural products from all classes and they often contribute significantly to their biological activity. Progress in recent years has led to a much better understanding of their biosynthesis. In this context, plenty of novel enzymology has been discovered, suggesting that these pathways are an attractive target for future studies.
Collapse
Affiliation(s)
- Franziska Hemmerling
- Institut für Organische Chemie and Zentrum für Biomolekulare Wirkstoffe, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany; Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
| | - Frank Hahn
- Institut für Organische Chemie and Zentrum für Biomolekulare Wirkstoffe, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany; Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
| |
Collapse
|
119
|
Characterization of the product of a nonribosomal peptide synthetase-like (NRPS-like) gene using the doxycycline dependent Tet-on system in Aspergillus terreus. Fungal Genet Biol 2016; 89:84-88. [DOI: 10.1016/j.fgb.2016.01.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 01/07/2016] [Accepted: 01/26/2016] [Indexed: 11/18/2022]
|
120
|
Lin TS, Chiang YM, Wang CCC. Biosynthetic Pathway of the Reduced Polyketide Product Citreoviridin in Aspergillus terreus var. aureus Revealed by Heterologous Expression in Aspergillus nidulans. Org Lett 2016; 18:1366-9. [DOI: 10.1021/acs.orglett.6b00299] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tzu-Shyang Lin
- Department
of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, 1985 Zonal Avenue, Los Angeles, California 90089, United States
| | - Yi-Ming Chiang
- Department
of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, 1985 Zonal Avenue, Los Angeles, California 90089, United States
- Department
of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan
| | - Clay C. C. Wang
- Department
of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, 1985 Zonal Avenue, Los Angeles, California 90089, United States
- Department
of Chemistry, University of Southern California, College of Letters, Arts, and Sciences, Los Angeles, California 90089, United States
| |
Collapse
|
121
|
Bai J, Lu Y, Xu YM, Zhang W, Chen M, Lin M, Gunatilaka AAL, Xu Y, Molnár I. Diversity-Oriented Combinatorial Biosynthesis of Hybrid Polyketide Scaffolds from Azaphilone and Benzenediol Lactone Biosynthons. Org Lett 2016; 18:1262-5. [PMID: 26934205 DOI: 10.1021/acs.orglett.6b00110] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two disparate polyketide families, the benzenediol lactones and the azaphilones, are produced by fungi using iterative polyketide synthase (iPKS) enzymes consisting of collaborating partner subunits. Exploitation of this common biosynthetic logic using iPKS subunit shuffling allowed the diversity-oriented combinatorial biosynthesis of unprecedented polyketide scaffolds new to nature, bearing structural motifs from both of these orthogonal natural product families. Starter unit acyltransferase domain replacements proved necessary but not sufficient to guarantee communication between iPKS subunits.
Collapse
Affiliation(s)
- Jing Bai
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences , 12 Zhongguancun South Street, Beijing 100081, P. R. China.,Natural Products Center, School of Natural Resources and the Environment, The University of Arizona , 250 East Valencia Road, Tucson, Arizona 85706, United States
| | - Yuanyuan Lu
- Natural Products Center, School of Natural Resources and the Environment, The University of Arizona , 250 East Valencia Road, Tucson, Arizona 85706, United States.,State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University , 24 Tong Jia Xiang, Nanjing 210009, P. R. China
| | - Ya-ming Xu
- Natural Products Center, School of Natural Resources and the Environment, The University of Arizona , 250 East Valencia Road, Tucson, Arizona 85706, United States
| | - Wei Zhang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences , 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Ming Chen
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences , 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Min Lin
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences , 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - A A Leslie Gunatilaka
- Natural Products Center, School of Natural Resources and the Environment, The University of Arizona , 250 East Valencia Road, Tucson, Arizona 85706, United States
| | - Yuquan Xu
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences , 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - István Molnár
- Natural Products Center, School of Natural Resources and the Environment, The University of Arizona , 250 East Valencia Road, Tucson, Arizona 85706, United States
| |
Collapse
|
122
|
Luo Y, Enghiad B, Zhao H. New tools for reconstruction and heterologous expression of natural product biosynthetic gene clusters. Nat Prod Rep 2016; 33:174-82. [PMID: 26647833 PMCID: PMC4742407 DOI: 10.1039/c5np00085h] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Natural product scaffolds remain a major source and inspiration for human therapeutics. However, generation of a natural product in the post-genomic era often requires reconstruction of the corresponding biosynthetic gene cluster in a heterologous host. In the burgeoning fields of synthetic biology and metabolic engineering, a significant amount of efforts has been devoted to develop DNA assembly techniques with higher efficiency, fidelity, and modularity, and heterologous expression systems with higher productivity and yield. Here we describe recent advances in DNA assembly and host engineering and highlight their applications in natural product discovery and engineering.
Collapse
Affiliation(s)
- Yunzi Luo
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P. R. China and Department of Chemical and Biomolecular Engineering and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Behnam Enghiad
- Department of Chemical and Biomolecular Engineering and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. and Departments of Chemistry, Biochemistry and Bioengineering, Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
123
|
Chiang YM, Ahuja M, Oakley CE, Entwistle R, Asokan A, Zutz C, Wang CCC, Oakley BR. Development of Genetic Dereplication Strains in Aspergillus nidulans Results in the Discovery of Aspercryptin. Angew Chem Int Ed Engl 2016; 55:1662-5. [PMID: 26563584 PMCID: PMC4724294 DOI: 10.1002/anie.201507097] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/04/2015] [Indexed: 11/07/2022]
Abstract
To reduce the secondary metabolite background in Aspergillus nidulans and minimize the rediscovery of compounds and pathway intermediates, we created a "genetic dereplication" strain in which we deleted eight of the most highly expressed secondary metabolite gene clusters (more than 244,000 base pairs deleted in total). This strain allowed us to discover a novel compound that we designate aspercryptin and to propose a biosynthetic pathway for the compound. Interestingly, aspercryptin is formed from compounds produced by two separate gene clusters, one of which makes the well-known product cichorine. This raises the exciting possibility that fungi use differential regulation of expression of secondary metabolite gene clusters to increase the diversity of metabolites they produce.
Collapse
Affiliation(s)
- Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan, 71710, Taiwan
| | - Manmeet Ahuja
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
- Industrial Biotechnology Division, Reliance Technology Group, Reliance Industries Limited, Reliance Corporate Park, Thane Belapur Road, Ghansoli, Navi, Mumbai, 400701, India
| | - C Elizabeth Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Ruth Entwistle
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Anabanadam Asokan
- Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, 66045, USA
| | - Christoph Zutz
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA.
| |
Collapse
|
124
|
van der Lee TAJ, Medema MH. Computational strategies for genome-based natural product discovery and engineering in fungi. Fungal Genet Biol 2016; 89:29-36. [PMID: 26775250 DOI: 10.1016/j.fgb.2016.01.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 01/08/2016] [Accepted: 01/11/2016] [Indexed: 12/20/2022]
Abstract
Fungal natural products possess biological activities that are of great value to medicine, agriculture and manufacturing. Recent metagenomic studies accentuate the vastness of fungal taxonomic diversity, and the accompanying specialized metabolic diversity offers a great and still largely untapped resource for natural product discovery. Although fungal natural products show an impressive variation in chemical structures and biological activities, their biosynthetic pathways share a number of key characteristics. First, genes encoding successive steps of a biosynthetic pathway tend to be located adjacently on the chromosome in biosynthetic gene clusters (BGCs). Second, these BGCs are often are located on specific regions of the genome and show a discontinuous distribution among evolutionarily related species and isolates. Third, the same enzyme (super)families are often involved in the production of widely different compounds. Fourth, genes that function in the same pathway are often co-regulated, and therefore co-expressed across various growth conditions. In this mini-review, we describe how these partly interlinked characteristics can be exploited to computationally identify BGCs in fungal genomes and to connect them to their products. Particular attention will be given to novel algorithms to identify unusual classes of BGCs, as well as integrative pan-genomic approaches that use a combination of genomic and metabolomic data for parallelized natural product discovery across multiple strains. Such novel technologies will not only expedite the natural product discovery process, but will also allow the assembly of a high-quality toolbox for the re-design or even de novo design of biosynthetic pathways using synthetic biology approaches.
Collapse
Affiliation(s)
- Theo A J van der Lee
- Biointeractions & Plant Health, Plant Research International, Wageningen UR, Wageningen, The Netherlands.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
| |
Collapse
|
125
|
van Dijk J, Wang C. Heterologous Expression of Fungal Secondary Metabolite Pathways in the Aspergillus nidulans Host System. Methods Enzymol 2016; 575:127-42. [DOI: 10.1016/bs.mie.2016.02.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
126
|
Abe H, Itaya S, Sasaki K, Kobayashi T, Ito H. Enantioselective Total Synthesis of the Proposed Structure of Furan-Containing Polyketide. Chem Pharm Bull (Tokyo) 2016; 64:772-7. [DOI: 10.1248/cpb.c16-00147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Hideki Abe
- Tokyo University of Pharmacy and Life Sciences
| | | | - Kei Sasaki
- Tokyo University of Pharmacy and Life Sciences
| | | | | |
Collapse
|
127
|
Chiang YM, Ahuja M, Oakley CE, Entwistle R, Asokan A, Zutz C, Wang CCC, Oakley BR. Development of Genetic Dereplication Strains in Aspergillus nidulans
Results in the Discovery of Aspercryptin. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507097] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy; University of Southern California; Los Angeles CA 90089 USA
- Department of Pharmacy; Chia Nan University of Pharmacy and Science; Tainan 71710 Taiwan
| | - Manmeet Ahuja
- Department of Molecular Biosciences; University of Kansas; Lawrence KS 66045 USA
- Industrial Biotechnology Division, Reliance Technology Group; Reliance Industries Limited, Reliance Corporate Park; Thane Belapur Road, Ghansoli, Navi Mumbai 400701 India
| | - C. Elizabeth Oakley
- Department of Molecular Biosciences; University of Kansas; Lawrence KS 66045 USA
| | - Ruth Entwistle
- Department of Molecular Biosciences; University of Kansas; Lawrence KS 66045 USA
| | - Anabanadam Asokan
- Del Shankel Structural Biology Center; University of Kansas; Lawrence KS 66045 USA
| | - Christoph Zutz
- Institute for Milk Hygiene; University of Veterinary Medicine Vienna; Vienna 1210 Austria
| | - Clay C. C. Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy; University of Southern California; Los Angeles CA 90089 USA
- Department of Chemistry; University of Southern California; Los Angeles CA 90089 USA
| | - Berl R. Oakley
- Department of Molecular Biosciences; University of Kansas; Lawrence KS 66045 USA
| |
Collapse
|
128
|
Reinvigorating natural product combinatorial biosynthesis with synthetic biology. Nat Chem Biol 2015; 11:649-59. [PMID: 26284672 DOI: 10.1038/nchembio.1893] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/22/2015] [Indexed: 12/24/2022]
Abstract
Natural products continue to play a pivotal role in drug-discovery efforts and in the understanding if human health. The ability to extend nature's chemistry through combinatorial biosynthesis--altering functional groups, regiochemistry and scaffold backbones through the manipulation of biosynthetic enzymes--offers unique opportunities to create natural product analogs. Incorporating emerging synthetic biology techniques has the potential to further accelerate the refinement of combinatorial biosynthesis as a robust platform for the diversification of natural chemical drug leads. Two decades after the field originated, we discuss the current limitations, the realities and the state of the art of combinatorial biosynthesis, including the engineering of substrate specificity of biosynthetic enzymes and the development of heterologous expression systems for biosynthetic pathways. We also propose a new perspective for the combinatorial biosynthesis of natural products that could reinvigorate drug discovery by using synthetic biology in combination with synthetic chemistry.
Collapse
|
129
|
Chávez R, Fierro F, García-Rico RO, Vaca I. Filamentous fungi from extreme environments as a promising source of novel bioactive secondary metabolites. Front Microbiol 2015; 6:903. [PMID: 26441853 PMCID: PMC4563253 DOI: 10.3389/fmicb.2015.00903] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/17/2015] [Indexed: 12/12/2022] Open
Abstract
Natural product search is undergoing resurgence upon the discovery of a huge previously unknown potential for secondary metabolite (SM) production hidden in microbial genomes. This is also the case for filamentous fungi, since their genomes contain a high number of "orphan" SM gene clusters. Recent estimates indicate that only 5% of existing fungal species have been described, thus the potential for the discovery of novel metabolites in fungi is huge. In this context, fungi thriving in harsh environments are of particular interest since they are outstanding producers of unusual chemical structures. At present, there are around 16 genomes from extreme environment-isolated fungi in databases. In a preliminary analysis of three of these genomes we found that several of the predicted SM gene clusters are probably involved in the biosynthesis of compounds not yet described. Genome mining strategies allow the exploitation of the information in genome sequences for the discovery of new natural compounds. The synergy between genome mining strategies and the expected abundance of SMs in fungi from extreme environments is a promising path to discover new natural compounds as a source of medically useful drugs.
Collapse
Affiliation(s)
- Renato Chávez
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile Santiago, Chile
| | - Francisco Fierro
- División de Ciencias Biológicas y de la Salud, Departamento de Biotecnología, Universidad Autónoma Metropolitana-Unidad Iztapalapa México D.F., Mexico
| | - Ramón O García-Rico
- Grupo GIMBIO, Facultad de Ciencias Básicas, Departamento de Microbiología, Universidad de Pamplona Pamplona, Colombia
| | - Inmaculada Vaca
- Facultad de Ciencias, Departamento de Química, Universidad de Chile Santiago, Chile
| |
Collapse
|
130
|
Luo Y, Li BZ, Liu D, Zhang L, Chen Y, Jia B, Zeng BX, Zhao H, Yuan YJ. Engineered biosynthesis of natural products in heterologous hosts. Chem Soc Rev 2015; 44:5265-90. [PMID: 25960127 PMCID: PMC4510016 DOI: 10.1039/c5cs00025d] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Natural products produced by microorganisms and plants are a major resource of antibacterial and anticancer drugs as well as industrially useful compounds. However, the native producers often suffer from low productivity and titers. Here we summarize the recent applications of heterologous biosynthesis for the production of several important classes of natural products such as terpenoids, flavonoids, alkaloids, and polyketides. In addition, we will discuss the new tools and strategies at multi-scale levels including gene, pathway, genome and community levels for highly efficient heterologous biosynthesis of natural products.
Collapse
Affiliation(s)
- Yunzi Luo
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China.
| | | | | | | | | | | | | | | | | |
Collapse
|
131
|
Use of a biosynthetic intermediate to explore the chemical diversity of pseudo-natural fungal polyketides. Nat Chem 2015; 7:737-43. [DOI: 10.1038/nchem.2308] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 06/23/2015] [Indexed: 01/20/2023]
|
132
|
Mattern DJ, Valiante V, Unkles SE, Brakhage AA. Synthetic biology of fungal natural products. Front Microbiol 2015; 6:775. [PMID: 26284053 PMCID: PMC4519758 DOI: 10.3389/fmicb.2015.00775] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/14/2015] [Indexed: 01/08/2023] Open
Abstract
Synthetic biology is an ever-expanding field in science, also encompassing the research area of fungal natural product (NP) discovery and production. Until now, different aspects of synthetic biology have been covered in fungal NP studies from the manipulation of different regulatory elements and heterologous expression of biosynthetic pathways to the engineering of different multidomain biosynthetic enzymes such as polyketide synthases or non-ribosomal peptide synthetases. The following review will cover some of the exemplary studies of synthetic biology in filamentous fungi showing the capacity of these eukaryotes to be used as model organisms in the field. From the vast array of different NPs produced to the ease for genetic manipulation, filamentous fungi have proven to be an invaluable source for the further development of synthetic biology tools.
Collapse
Affiliation(s)
- Derek J Mattern
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Institute for Microbiology, Friedrich Schiller University , Jena, Germany
| | - Vito Valiante
- Leibniz Junior Research Group "Biobricks of Microbial Natural Product Syntheses" , Jena, Germany
| | - Shiela E Unkles
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews , St Andrews, UK
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Institute for Microbiology, Friedrich Schiller University , Jena, Germany
| |
Collapse
|
133
|
Metabolic Impacts of Using Nitrogen and Copper-Regulated Promoters to Regulate Gene Expression in Neurospora crassa. G3-GENES GENOMES GENETICS 2015; 5:1899-908. [PMID: 26194204 PMCID: PMC4555226 DOI: 10.1534/g3.115.020073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The filamentous fungus Neurospora crassa is a long-studied eukaryotic microbial system amenable to heterologous expression of native and foreign proteins. However, relatively few highly tunable promoters have been developed for this species. In this study, we compare the tcu-1 and nit-6 promoters for controlled expression of a GFP reporter gene in N. crassa. Although the copper-regulated tcu-1 has been previously characterized, this is the first investigation exploring nitrogen-controlled nit-6 for expression of heterologous genes in N. crassa. We determined that fragments corresponding to 1.5-kb fragments upstream of the tcu-1 and nit-6 open reading frames are needed for optimal repression and expression of GFP mRNA and protein. nit-6 was repressed using concentrations of glutamine from 2 to 20 mM and induced in medium containing 0.5–20 mM nitrate as the nitrogen source. Highest levels of expression were achieved within 3 hr of induction for each promoter and GFP mRNA could not be detected within 1 hr after transfer to repressing conditions using the nit-6 promoter. We also performed metabolic profiling experiments using proton NMR to identify changes in metabolite levels under inducing and repressing conditions for each promoter. The results demonstrate that conditions used to regulate tcu-1 do not significantly change the primary metabolome and that the differences between inducing and repressing conditions for nit-6 can be accounted for by growth under nitrate or glutamine as a nitrogen source. Our findings demonstrate that nit-6 is a tunable promoter that joins tcu-1 as a choice for regulation of gene expression in N. crassa.
Collapse
|
134
|
Guo CJ, Sun WW, Bruno KS, Oakley BR, Keller NP, Wang CCC. Spatial regulation of a common precursor from two distinct genes generates metabolite diversity. Chem Sci 2015; 6:5913-5921. [PMID: 28791090 PMCID: PMC5523082 DOI: 10.1039/c5sc01058f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/12/2015] [Indexed: 12/04/2022] Open
Abstract
We have demonstrated that spatial regulation of the same product from two distinct genes generates metabolite diversity.
In secondary metabolite biosynthesis, core synthetic genes such as polyketide synthase genes usually encode proteins that generate various backbone precursors. These precursors are modified by other tailoring enzymes to yield a large variety of different secondary metabolites. The number of core synthesis genes in a given species correlates, therefore, with the number of types of secondary metabolites the organism can produce. In our study, heterologous expression of all the A. terreus NRPS-like genes showed that two NRPS-like proteins, encoded by atmelA and apvA, release the same natural product, aspulvinone E. In hyphae this compound is converted to aspulvinones whereas in conidia it is converted to melanin. The genes are expressed in different tissues and this spatial control is probably regulated by their own specific promoters. Comparative genomics indicates that atmelA and apvA might share a same ancestral gene and the gene apvA is located in a highly conserved region in Aspergillus species that contains genes coding for life-essential proteins. Our data reveal the first case in secondary metabolite biosynthesis in which the tissue specific production of a single compound directs it into two separate pathways, producing distinct compounds with different functions. Our data also reveal that a single trans-prenyltransferase, AbpB, prenylates two substrates, aspulvinones and butyrolactones, revealing that genes outside of contiguous secondary metabolism gene clusters can modify more than one compound thereby expanding metabolite diversity. Our study raises the possibility of incorporation of spatial, cell-type specificity in expression of secondary metabolites of biological interest and provides new insight into designing and reconstituting their biosynthetic pathways.
Collapse
Affiliation(s)
- Chun-Jun Guo
- Department of Pharmacology and Pharmaceutical Sciences , School of Pharmacy , University of Southern California , Los Angeles , CA 90089 , USA .
| | - Wei-Wen Sun
- Department of Pharmacology and Pharmaceutical Sciences , School of Pharmacy , University of Southern California , Los Angeles , CA 90089 , USA .
| | - Kenneth S Bruno
- Chemical and Biological Process Development Group , Energy and Environment Directorate , Pacific Northwest National Laboratory , Richland , WA 99352 , USA
| | - Berl R Oakley
- Department of Molecular Biosciences , University of Kansas , Lawrence , KS 66045 , USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology , University of Wisconsin-Madison , Madison , WI 53706 , USA
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences , School of Pharmacy , University of Southern California , Los Angeles , CA 90089 , USA . .,Department of Chemistry , College of Letters, Arts, and Sciences , University of Southern California , Los Angeles , CA 90089 , USA
| |
Collapse
|
135
|
Emri T, Szarvas V, Orosz E, Antal K, Park H, Han KH, Yu JH, Pócsi I. Core oxidative stress response in Aspergillus nidulans. BMC Genomics 2015; 16:478. [PMID: 26115917 PMCID: PMC4482186 DOI: 10.1186/s12864-015-1705-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 06/15/2015] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The b-Zip transcription factor AtfA plays a key role in regulating stress responses in the filamentous fungus Aspergillus nidulans. To identify the core regulons of AtfA, we examined genome-wide expression changes caused by various stresses in the presence/absence of AtfA using A. nidulans microarrays. We also intended to address the intriguing question regarding the existence of core environmental stress response in this important model eukaryote. RESULTS Examination of the genome wide expression changes caused by five different oxidative stress conditions in wild type and the atfA null mutant has identified a significant number of stereotypically regulated genes (Core Oxidative Stress Response genes). The deletion of atfA increased the oxidative stress sensitivity of A. nidulans and affected mRNA accumulation of several genes under both unstressed and stressed conditions. The numbers of genes under the AtfA control appear to be specific to a stress-type. We also found that both oxidative and salt stresses induced expression of some secondary metabolite gene clusters and the deletion of atfA enhanced the stress responsiveness of additional clusters. Moreover, certain clusters were down-regulated by the stresses tested. CONCLUSION Our data suggest that the observed co-regulations were most likely consequences of the overlapping physiological effects of the stressors and not of the existence of a general environmental stress response. The function of AtfA in governing various stress responses is much smaller than anticipated and/or other regulators may play a redundant or overlapping role with AtfA. Both stress inducible and stress repressive regulations of secondary metabolism seem to be frequent features in A. nidulans.
Collapse
Affiliation(s)
- Tamás Emri
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, P.O. Box 63, H-4032, Debrecen, Hungary.
| | - Vera Szarvas
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, P.O. Box 63, H-4032, Debrecen, Hungary.
| | - Erzsébet Orosz
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, P.O. Box 63, H-4032, Debrecen, Hungary.
| | - Károly Antal
- Department of Zoology, Faculty of Sciences, Eszterházy Károly College, Eszterházy út 1, H-3300, Eger, Hungary.
| | - HeeSoo Park
- Department of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI, 53706, USA.
| | - Kap-Hoon Han
- Department of Pharmaceutical Engineering, Woosuk University, 565-701, Wanju, Republic of Korea.
| | - Jae-Hyuk Yu
- Department of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI, 53706, USA.
| | - István Pócsi
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, P.O. Box 63, H-4032, Debrecen, Hungary.
| |
Collapse
|
136
|
Li J, Jaitzig J, Lu P, Süssmuth RD, Neubauer P. Scale-up bioprocess development for production of the antibiotic valinomycin in Escherichia coli based on consistent fed-batch cultivations. Microb Cell Fact 2015; 14:83. [PMID: 26063334 PMCID: PMC4464625 DOI: 10.1186/s12934-015-0272-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/08/2015] [Indexed: 02/05/2023] Open
Abstract
Background Heterologous production of natural products in Escherichia coli has emerged as an attractive strategy to obtain molecules of interest. Although technically feasible most of them are still constrained to laboratory scale production. Therefore, it is necessary to develop reasonable scale-up strategies for bioprocesses aiming at the overproduction of targeted natural products under industrial scale conditions. To this end, we used the production of the antibiotic valinomycin in E. coli as a model system for scalable bioprocess development based on consistent fed-batch cultivations. Results In this work, the glucose limited fed-batch strategy based on pure mineral salt medium was used throughout all scales for valinomycin production. The optimal glucose feed rate was initially detected by the use of a biocatalytically controlled glucose release (EnBase® technology) in parallel cultivations in 24-well plates with continuous monitoring of pH and dissolved oxygen. These results were confirmed in shake flasks, where the accumulation of valinomycin was highest when the specific growth rate decreased below 0.1 h−1. This correlation was also observed for high cell density fed-batch cultivations in a lab-scale bioreactor. The bioreactor fermentation produced valinomycin with titers of more than 2 mg L−1 based on the feeding of a concentrated glucose solution. Valinomycin production was not affected by oscillating conditions (i.e. glucose and oxygen) in a scale-down two-compartment reactor, which could mimic similar situations in industrial bioreactors, suggesting that the process is very robust and a scaling of the process to a larger industrial scale appears a realistic scenario. Conclusions Valinomycin production was scaled up from mL volumes to 10 L with consistent use of the fed-batch technology. This work presents a robust and reliable approach for scalable bioprocess development and represents an example for the consistent development of a process for a heterologously expressed natural product towards the industrial scale.
Collapse
Affiliation(s)
- Jian Li
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, 13355, Berlin, Germany. .,Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA.
| | - Jennifer Jaitzig
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, 13355, Berlin, Germany.
| | - Ping Lu
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, 13355, Berlin, Germany.
| | - Roderich D Süssmuth
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany.
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, 13355, Berlin, Germany.
| |
Collapse
|
137
|
Xiang X, Qiu R, Yao X, Arst HN, Peñalva MA, Zhang J. Cytoplasmic dynein and early endosome transport. Cell Mol Life Sci 2015; 72:3267-80. [PMID: 26001903 DOI: 10.1007/s00018-015-1926-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/04/2015] [Accepted: 05/05/2015] [Indexed: 11/25/2022]
Abstract
Microtubule-based distribution of organelles/vesicles is crucial for the function of many types of eukaryotic cells and the molecular motor cytoplasmic dynein is required for transporting a variety of cellular cargos toward the microtubule minus ends. Early endosomes represent a major cargo of dynein in filamentous fungi, and dynein regulators such as LIS1 and the dynactin complex are both required for early endosome movement. In fungal hyphae, kinesin-3 and dynein drive bi-directional movements of early endosomes. Dynein accumulates at microtubule plus ends; this accumulation depends on kinesin-1 and dynactin, and it is important for early endosome movements towards the microtubule minus ends. The physical interaction between dynein and early endosome requires the dynactin complex, and in particular, its p25 component. The FTS-Hook-FHIP (FHF) complex links dynein-dynactin to early endosomes, and within the FHF complex, Hook interacts with dynein-dynactin, and Hook-early endosome interaction depends on FHIP and FTS.
Collapse
Affiliation(s)
- Xin Xiang
- Department of Biochemistry and Molecular Biology, F. Edward Hébert School of Medicine, The Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD, 20814, USA,
| | | | | | | | | | | |
Collapse
|
138
|
Kakule TB, Jadulco RC, Koch M, Janso JE, Barrows LR, Schmidt EW. Native promoter strategy for high-yielding synthesis and engineering of fungal secondary metabolites. ACS Synth Biol 2015; 4:625-33. [PMID: 25226362 PMCID: PMC4487227 DOI: 10.1021/sb500296p] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Strategies
are needed for the robust production of cryptic, silenced,
or engineered secondary metabolites in fungi. The filamentous fungus Fusarium heterosporum natively synthesizes the polyketide
equisetin at >2 g L–1 in a controllable manner.
We hypothesized that this production level was achieved by regulatory
elements in the equisetin pathway, leading to the prediction that
the same regulatory elements would be useful in producing other secondary
metabolites. This was tested by using the native eqxS promoter and eqxR regulator in F. heterosporum, synthesizing heterologous natural products in yields of ∼1
g L–1. As proof of concept for the practical application,
we resurrected an extinct pathway from an endophytic fungus with an
initial yield of >800 mg L–1, leading to the
practical
synthesis of a selective antituberculosis agent. Finally, the method
enabled new insights into the function of polyketide synthases in
filamentous fungi. These results demonstrate a strategy for optimally
employing native regulators for the robust synthesis of secondary
metabolites.
Collapse
Affiliation(s)
| | | | | | - Jeffrey E. Janso
- Natural Products,
Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, Groton, Connecticut 06355, United States
| | | | | |
Collapse
|
139
|
Bok JW, Ye R, Clevenger KD, Mead D, Wagner M, Krerowicz A, Albright JC, Goering AW, Thomas PM, Kelleher NL, Keller NP, Wu CC. Fungal artificial chromosomes for mining of the fungal secondary metabolome. BMC Genomics 2015; 16:343. [PMID: 25925221 PMCID: PMC4413528 DOI: 10.1186/s12864-015-1561-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 04/20/2015] [Indexed: 01/08/2023] Open
Abstract
Background With thousands of fungal genomes being sequenced, each genome containing up to 70 secondary metabolite (SM) clusters 30–80 kb in size, breakthrough techniques are needed to characterize this SM wealth. Results Here we describe a novel system-level methodology for unbiased cloning of intact large SM clusters from a single fungal genome for one-step transformation and expression in a model host. All 56 intact SM clusters from Aspergillus terreus were individually captured in self-replicating fungal artificial chromosomes (FACs) containing both the E. coli F replicon and an Aspergillus autonomously replicating sequence (AMA1). Candidate FACs were successfully shuttled between E. coli and the heterologous expression host A. nidulans. As proof-of-concept, an A. nidulans FAC strain was characterized in a novel liquid chromatography-high resolution mass spectrometry (LC-HRMS) and data analysis pipeline, leading to the discovery of the A. terreus astechrome biosynthetic machinery. Conclusion The method we present can be used to capture the entire set of intact SM gene clusters and/or pathways from fungal species for heterologous expression in A. nidulans and natural product discovery. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1561-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jin Woo Bok
- Department of Medical Microbiology and Immunology and Bacteriology, University of Wisconsin at Madison, Madison, WI, USA.
| | - Rosa Ye
- Intact Genomics, Inc., St Louis, MO, USA. .,Lucigen Corporation, Middleton, WI, USA.
| | - Kenneth D Clevenger
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.
| | - David Mead
- Lucigen Corporation, Middleton, WI, USA.
| | | | | | | | - Anthony W Goering
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
| | - Paul M Thomas
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA. .,Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
| | - Neil L Kelleher
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA. .,Department of Chemistry, Northwestern University, Evanston, IL, USA. .,Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology and Bacteriology, University of Wisconsin at Madison, Madison, WI, USA.
| | - Chengcang C Wu
- Intact Genomics, Inc., St Louis, MO, USA. .,Lucigen Corporation, Middleton, WI, USA.
| |
Collapse
|
140
|
Kuthning A, Mösker E, Süssmuth RD. Engineering the heterologous expression of lanthipeptides in Escherichia coli by multigene assembly. Appl Microbiol Biotechnol 2015; 99:6351-61. [PMID: 25846334 DOI: 10.1007/s00253-015-6557-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/13/2015] [Accepted: 03/19/2015] [Indexed: 10/23/2022]
Abstract
Lantibiotics are an important class of ribosomally synthesised peptide antibiotics with a remarkable pharmacological potential. Structural variants of lantibiotics generated by peptide engineering in vivo are an important aspect for improving the peptide's efficacy, stability and bioavailability as well as production titre, which severely impacts the potential exploitation in pharmaceutical applications. Therefore, expression systems are needed which allow for a robust genetic access for ample mutagenesis experiments. Based on previous heterologous expression of the two-component lanthipeptide lichenicidin (Bliα and Bliβ) in Escherichia coli BLic5, we now employ a multigene assembly strategy for recombinant lantibiotic peptide production in the Gram-negative host. Two E. coli high copy plasmids for separate and increased expression of a two-component lantibiotic were cloned and tested for expression. From these E. coli HP expression strains, an up to 100 times increased expression was found compared with Bacillus licheniformis I89 and E. coli BLic5. Total expression yields reach 4 mg L(-1) for Bliα and 6 mg L(-1) for Bliβ. The expression system developed in this study constitutes an important cornerstone for future in vivo peptide engineering studies and is of significance for potential applications aiming at higher production titres of ribosomally synthesised, post translationally modified peptides.
Collapse
Affiliation(s)
- Anja Kuthning
- Institut für Chemie, Technische Universität Berlin, Straße des 17 Juni 124, 10623, Berlin, Germany
| | | | | |
Collapse
|
141
|
Fischer R. Promiscuity breeds diversity: the role of polyketide synthase in natural product biosynthesis. ACTA ACUST UNITED AC 2015; 21:701-2. [PMID: 24950100 DOI: 10.1016/j.chembiol.2014.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Secondary metabolites are often highly biologically active molecules and are widely used from antibacterial to anticancer drugs. In this issue of Chemistry and Biology, Zaehle and coworkers describe the gene cluster and biosynthesis of the polyketide terrein, a secondary metabolite produced by the soil-borne fungus Aspergillus terreus.
Collapse
Affiliation(s)
- Reinhard Fischer
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT)-South Campus, Hertzstrasse 16, 76187 Karlsruhe, Germany.
| |
Collapse
|
142
|
Hashimoto M, Wakana D, Ueda M, Kobayashi D, Goda Y, Fujii I. Product identification of non-reducing polyketide synthases with C-terminus methyltransferase domain from Talaromyces stipitatus using Aspergillus oryzae heterologous expression. Bioorg Med Chem Lett 2015; 25:1381-4. [PMID: 25770780 DOI: 10.1016/j.bmcl.2015.02.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 02/20/2015] [Accepted: 02/23/2015] [Indexed: 01/26/2023]
Abstract
Talaromyces stipitatus ATCC 10500 possesses 17 non-reducing polyketide synthase (NR-PKS) genes. During the course of our functional analysis of PKS genes with a C-terminus methyltransferase domain from T. stipitatus, we expressed tspks2, tspks3 and tspks4 genes in the heterologous host Aspergillus oryzae, respectively. Although the tspks4 transformant gave no apparent product in HPLC analysis, a novel azaphilone pentaketide (3) was identified along with two known related products from the tspks2 transformant. Of four hexaketide products from the tspks3 transformant, two new compounds were identified to be 2-acetyl-7-methyl-3,6,8-trihydroxynaphthalene (4) and its derivative fused with α-methyl-α,β-unsaturated γ-lactone (7).
Collapse
Affiliation(s)
- Makoto Hashimoto
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Daigo Wakana
- National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Miki Ueda
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Daisuke Kobayashi
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Yukihiro Goda
- National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Isao Fujii
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan.
| |
Collapse
|
143
|
Abe H, Itaya S, Sasaki K, Kobayashi T, Ito H. Total synthesis of the proposed structure of a polyketide from Phialomyces macrosporus. Chem Commun (Camb) 2015; 51:3586-9. [PMID: 25634478 DOI: 10.1039/c5cc00129c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Total synthesis of the proposed structure of a polyketide isolated from Phialomyces macrosporus is described. The synthesis involved chemoselective epoxidation, regioselective epoxide ring opening, chemo- and diastereoselective dihydroxylation, and vinylation of lactone accompanied by the formation of a furan ring.
Collapse
Affiliation(s)
- Hideki Abe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
| | | | | | | | | |
Collapse
|
144
|
Ramamoorthy V, Govindaraj L, Dhanasekaran M, Vetrivel S, Kumar KK, Ebenezar E. Combination of driselase and lysing enzyme in one molar potassium chloride is effective for the production of protoplasts from germinated conidia of Fusarium verticillioides. J Microbiol Methods 2015; 111:127-34. [PMID: 25724844 DOI: 10.1016/j.mimet.2015.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 02/23/2015] [Accepted: 02/23/2015] [Indexed: 11/30/2022]
Abstract
Various cell wall degrading enzymes and the protoplasting media were evaluated for the production of protoplast in Fusarium verticillioides. Among the various enzymes tested, driselase at 12.5 mg/ml in 1 M KCl protoplasting medium produced the maximum number of protoplast. Next to driselase, lysing enzyme at 10 mg/ml in 1.2 M MgSO4 protoplasting medium was found to be the second best enzyme for the production of protoplast. More interestingly, the combined use of driselase @ 12.5 mg/ml and lysing enzyme @ 10 mg/ml in 1 M KCl exhibited the additive effect on protoplast formation. Germinated conidia of F. verticillioides are the most susceptible fungal material for protoplast production. The use of sucrose at 1.2 M in the regeneration medium supported the maximum regeneration of protoplast. From the present study, we recommend driselase (12.5 mg/ml) and lysing enzyme (10 mg/ml) in 1 M KCl protoplasting medium and germinated conidia of F. verticillioides for the maximum production of protoplasts and 1.2 M sucrose is the best osmoticum for the regeneration of protoplasts.
Collapse
Affiliation(s)
- Vellaisamy Ramamoorthy
- Department of Plant Pathology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Killikulam, Vallanadu, Tamil Nadu 628 252, India.
| | - Lavanya Govindaraj
- Department of Plant Pathology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Killikulam, Vallanadu, Tamil Nadu 628 252, India
| | - Madhumitha Dhanasekaran
- Department of Plant Pathology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Killikulam, Vallanadu, Tamil Nadu 628 252, India
| | - Sharmilee Vetrivel
- Department of Plant Pathology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Killikulam, Vallanadu, Tamil Nadu 628 252, India
| | - Krish K Kumar
- Department of Plant Pathology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Killikulam, Vallanadu, Tamil Nadu 628 252, India
| | - Edward Ebenezar
- Department of Plant Pathology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Killikulam, Vallanadu, Tamil Nadu 628 252, India
| |
Collapse
|
145
|
Anyaogu DC, Mortensen UH. Heterologous production of fungal secondary metabolites in Aspergilli. Front Microbiol 2015; 6:77. [PMID: 25713568 PMCID: PMC4322707 DOI: 10.3389/fmicb.2015.00077] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 01/21/2015] [Indexed: 12/24/2022] Open
Abstract
Fungal natural products comprise a wide range of compounds. Some are medically attractive as drugs and drug leads, some are used as food additives, while others are harmful mycotoxins. In recent years the genome sequence of several fungi has become available providing genetic information of a large number of putative biosynthetic pathways. However, compound discovery is difficult as the genes required for the production of the compounds often are silent or barely expressed under laboratory conditions. Furthermore, the lack of available tools for genetic manipulation of most fungal species hinders pathway discovery. Heterologous expression of the biosynthetic pathway in model systems or cell factories facilitates product discovery, elucidation, and production. This review summarizes the recent strategies for heterologous expression of fungal biosynthetic pathways in Aspergilli.
Collapse
Affiliation(s)
- Diana Chinyere Anyaogu
- Section for Eukaryotic Biotechnology, Department of Systems Biology, Technical University of Denmark Kongens Lyngby, Denmark
| | - Uffe Hasbro Mortensen
- Section for Eukaryotic Biotechnology, Department of Systems Biology, Technical University of Denmark Kongens Lyngby, Denmark
| |
Collapse
|
146
|
Muria-Gonzalez MJ, Chooi YH, Breen S, Solomon PS. The past, present and future of secondary metabolite research in the Dothideomycetes. MOLECULAR PLANT PATHOLOGY 2015; 16:92-107. [PMID: 24889519 PMCID: PMC6638331 DOI: 10.1111/mpp.12162] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The Dothideomycetes represents a large and diverse array of fungi in which prominent plant pathogens are over-represented. Species within the Cochliobolus, Alternaria, Pyrenophora and Mycosphaerella (amongst others) all cause diseases that threaten food security in many parts of the world. Significant progress has been made over the past decade in understanding how some of these pathogens cause disease at a molecular level. It is reasonable to suggest that much of this progress can be attributed to the increased availability of genome sequences. However, together with revealing mechanisms of pathogenicity, these genome sequences have also highlighted the capacity of the Dothideomycetes to produce an extensive array of secondary metabolites, far greater than originally thought. Indeed, it is now clear that we appear to have only scratched the surface to date in terms of the identification of secondary metabolites produced by these fungi. In the first half of this review, we examine the current status of secondary metabolite research in the Dothideomycetes and highlight the diversity of the molecules discovered thus far, in terms of both structure and biological activity. In the second part of this review, we survey the emerging techniques and technologies that will be required to shed light on the vast array of secondary metabolite potential that is encoded within these genomes. Experimental design, analytical chemistry and synthetic biology are all discussed in the context of how they will contribute to this field.
Collapse
Affiliation(s)
- Mariano Jordi Muria-Gonzalez
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, 0200, Australia
| | | | | | | |
Collapse
|
147
|
Guo CJ, Wang CCC. Recent advances in genome mining of secondary metabolites in Aspergillus terreus. Front Microbiol 2014; 5:717. [PMID: 25566227 PMCID: PMC4274970 DOI: 10.3389/fmicb.2014.00717] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/01/2014] [Indexed: 11/23/2022] Open
Abstract
Filamentous fungi are rich resources of secondary metabolites (SMs) with a variety of interesting biological activities. Recent advances in genome sequencing and techniques in genetic manipulation have enabled researchers to study the biosynthetic genes of these SMs. Aspergillus terreus is the well-known producer of lovastatin, a cholesterol-lowering drug. This fungus also produces other SMs, including acetylaranotin, butyrolactones, and territram, with interesting bioactivities. This review will cover recent progress in genome mining of SMs identified in this fungus. The identification and characterization of the gene cluster for these SMs, as well as the proposed biosynthetic pathways, will be discussed in depth.
Collapse
Affiliation(s)
- Chun-Jun Guo
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California Los Angeles, CA, USA
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California Los Angeles, CA, USA ; Department of Chemistry, College of Letters, Arts, and Sciences, University of Southern California Los Angeles, CA, USA
| |
Collapse
|
148
|
A modified recombineering protocol for the genetic manipulation of gene clusters in Aspergillus fumigatus. PLoS One 2014; 9:e111875. [PMID: 25372385 PMCID: PMC4221250 DOI: 10.1371/journal.pone.0111875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/02/2014] [Indexed: 01/07/2023] Open
Abstract
Genomic analyses of fungal genome structure have revealed the presence of physically-linked groups of genes, termed gene clusters, where collective functionality of encoded gene products serves a common biosynthetic purpose. In multiple fungal pathogens of humans and plants gene clusters have been shown to encode pathways for biosynthesis of secondary metabolites including metabolites required for pathogenicity. In the major mould pathogen of humans Aspergillus fumigatus, multiple clusters of co-ordinately upregulated genes were identified as having heightened transcript abundances, relative to laboratory cultured equivalents, during the early stages of murine infection. The aim of this study was to develop and optimise a methodology for manipulation of gene cluster architecture, thereby providing the means to assess their relevance to fungal pathogenicity. To this end we adapted a recombineering methodology which exploits lambda phage-mediated recombination of DNA in bacteria, for the generation of gene cluster deletion cassettes. By exploiting a pre-existing bacterial artificial chromosome (BAC) library of A. fumigatus genomic clones we were able to implement single or multiple intra-cluster gene replacement events at both subtelomeric and telomere distal chromosomal locations, in both wild type and highly recombinogenic A. fumigatus isolates. We then applied the methodology to address the boundaries of a gene cluster producing a nematocidal secondary metabolite, pseurotin A, and to address the role of this secondary metabolite in insect and mammalian responses to A. fumigatus challenge.
Collapse
|
149
|
Yadav JS, Ganganna B, Dutta P, Singarapu KK. Synthesis and determination of absolute configuration of α-pyrones isolated from Penicillium corylophilum. J Org Chem 2014; 79:10762-71. [PMID: 25337961 DOI: 10.1021/jo5015382] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The first total synthesis of (S)-6-(2,9-dihydroxynonyl)-4-hydroxy-3-methyl-2H-pyran-2-one, 4-hydroxy-3-methyl-6-((2S,4R)-2,4,11-trihydroxyundecyl)-2H-pyran-2-one, and its unnatural 2R,4R-isomer starting from commercially available 1,8-octanediol is described. The synthesis led to the revision of the proposed structural assignment of the natural product as (R)-6-(2,9-dihydroxynonyl)-4-hydroxy-3-methyl-2H-pyran-2-one. The key steps include chiral auxiliary mediated asymmetric acetate aldol reaction, dianion addition, and base mediated cyclization to form an α-pyrone ring.
Collapse
Affiliation(s)
- J S Yadav
- Academy of Scientific and Innovative Research, ‡Division of Natural Products Chemistry, CSIR-Indian Institute of Chemical Technology , Hyderabad-500007, India
| | | | | | | |
Collapse
|
150
|
Engineering of Aspergillus niger for the production of secondary metabolites. Fungal Biol Biotechnol 2014; 1:4. [PMID: 28955446 PMCID: PMC5598268 DOI: 10.1186/s40694-014-0004-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/13/2014] [Indexed: 01/17/2023] Open
Abstract
Background Filamentous fungi can each produce dozens of secondary metabolites which are attractive as therapeutics, drugs, antimicrobials, flavour compounds and other high-value chemicals. Furthermore, they can be used as an expression system for eukaryotic proteins. Application of most fungal secondary metabolites is, however, so far hampered by the lack of suitable fermentation protocols for the producing strain and/or by low product titers. To overcome these limitations, we report here the engineering of the industrial fungus Aspergillus niger to produce high titers (up to 4,500 mg • l−1) of secondary metabolites belonging to the class of nonribosomal peptides. Results For a proof-of-concept study, we heterologously expressed the 351 kDa nonribosomal peptide synthetase ESYN from Fusarium oxysporum in A. niger. ESYN catalyzes the formation of cyclic depsipeptides of the enniatin family, which exhibit antimicrobial, antiviral and anticancer activities. The encoding gene esyn1 was put under control of a tunable bacterial-fungal hybrid promoter (Tet-on) which was switched on during early-exponential growth phase of A. niger cultures. The enniatins were isolated and purified by means of reverse phase chromatography and their identity and purity proven by tandem MS, NMR spectroscopy and X-ray crystallography. The initial yields of 1 mg • l−1 of enniatin were increased about 950 fold by optimizing feeding conditions and the morphology of A. niger in liquid shake flask cultures. Further yield optimization (about 4.5 fold) was accomplished by cultivating A. niger in 5 l fed batch fermentations. Finally, an autonomous A. niger expression host was established, which was independent from feeding with the enniatin precursor d-2-hydroxyvaleric acid d-Hiv. This was achieved by constitutively expressing a fungal d-Hiv dehydrogenase in the esyn1-expressing A. niger strain, which used the intracellular α-ketovaleric acid pool to generate d-Hiv. Conclusions This is the first report demonstrating that A. niger is a potent and promising expression host for nonribosomal peptides with titers high enough to become industrially attractive. Application of the Tet-on system in A. niger allows precise control on the timing of product formation, thereby ensuring high yields and purity of the peptides produced. Electronic supplementary material The online version of this article (doi:10.1186/s40694-014-0004-9) contains supplementary material, which is available to authorized users.
Collapse
|