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Patil RS, Sharma S, Bhaskarwar AV, Nambiar S, Bhat NA, Koppolu MK, Bhukya H. TetR and OmpR family regulators in natural product biosynthesis and resistance. Proteins 2023. [PMID: 37874037 DOI: 10.1002/prot.26621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/30/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023]
Abstract
This article provides a comprehensive review and sequence-structure analysis of transcription regulator (TR) families, TetR and OmpR/PhoB, involved in specialized secondary metabolite (SSM) biosynthesis and resistance. Transcription regulation is a fundamental process, playing a crucial role in orchestrating gene expression to confer a survival advantage in response to frequent environmental stress conditions. This process, coupled with signal sensing, enables bacteria to respond to a diverse range of intra and extracellular signals. Thus, major bacterial signaling systems use a receptor domain to sense chemical stimuli along with an output domain responsible for transcription regulation through DNA-binding. Sensory and output domains on a single polypeptide chain (one component system, OCS) allow response to stimuli by allostery, that is, DNA-binding affinity modulation upon signal presence/absence. On the other hand, two component systems (TCSs) allow cross-talk between the sensory and output domains as they are disjoint and transmit information by phosphorelay to mount a response. In both cases, however, TRs play a central role. Biosynthesis of SSMs, which includes antibiotics, is heavily regulated by TRs as it diverts the cell's resources towards the production of these expendable compounds, which also have clinical applications. These TRs have evolved to relay information across specific signals and target genes, thus providing a rich source of unique mechanisms to explore towards addressing the rapid escalation in antimicrobial resistance (AMR). Here, we focus on the TetR and OmpR family TRs, which belong to OCS and TCS, respectively. These TR families are well-known examples of regulators in secondary metabolism and are ubiquitous across different bacteria, as they also participate in a myriad of cellular processes apart from SSM biosynthesis and resistance. As a result, these families exhibit higher sequence divergence, which is also evident from our bioinformatic analysis of 158 389 and 77 437 sequences from TetR and OmpR family TRs, respectively. The analysis of both sequence and structure allowed us to identify novel motifs in addition to the known motifs responsible for TR function and its structural integrity. Understanding the diverse mechanisms employed by these TRs is essential for unraveling the biosynthesis of SSMs. This can also help exploit their regulatory role in biosynthesis for significant pharmaceutical, agricultural, and industrial applications.
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Affiliation(s)
- Rachit S Patil
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Siddhant Sharma
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Aditya V Bhaskarwar
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Souparnika Nambiar
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Niharika A Bhat
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Mani Kanta Koppolu
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Hussain Bhukya
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
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Zhan C, Lee N, Lan G, Dan Q, Cowan A, Wang Z, Baidoo EEK, Kakumanu R, Luckie B, Kuo RC, McCauley J, Liu Y, Valencia L, Haushalter RW, Keasling JD. Improved polyketide production in C. glutamicum by preventing propionate-induced growth inhibition. Nat Metab 2023; 5:1127-1140. [PMID: 37443355 DOI: 10.1038/s42255-023-00830-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/25/2023] [Indexed: 07/15/2023]
Abstract
Corynebacterium glutamicum is a promising host for production of valuable polyketides. Propionate addition, a strategy known to increase polyketide production by increasing intracellular methylmalonyl-CoA availability, causes growth inhibition in C. glutamicum. The mechanism of this inhibition was unclear before our work. Here we provide evidence that accumulation of propionyl-CoA and methylmalonyl-CoA induces growth inhibition in C. glutamicum. We then show that growth inhibition can be relieved by introducing methylmalonyl-CoA-dependent polyketide synthases. With germicidin as an example, we used adaptive laboratory evolution to leverage the fitness advantage of polyketide production in the presence of propionate to evolve improved germicidin production. Whole-genome sequencing revealed mutations in germicidin synthase, which improved germicidin titer, as well as mutations in citrate synthase, which effectively evolved the native glyoxylate pathway to a new methylcitrate pathway. Together, our results show that C. glutamicum is a capable host for polyketide production and we can take advantage of propionate growth inhibition to drive titers higher using laboratory evolution or to screen for production of polyketides.
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Affiliation(s)
- Chunjun Zhan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA
| | - Namil Lee
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA
| | - Guangxu Lan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Qingyun Dan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Aidan Cowan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Zilong Wang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ramu Kakumanu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bridget Luckie
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Rita C Kuo
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Joshua McCauley
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Luis Valencia
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Robert W Haushalter
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA.
- Center for Biosustainability, Danish Technical University, Lyngby, Denmark.
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
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Diversity of Bacterial Secondary Metabolite Biosynthetic Gene Clusters in Three Vietnamese Sponges. Mar Drugs 2022; 21:md21010029. [PMID: 36662202 PMCID: PMC9864124 DOI: 10.3390/md21010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
Recent reviews have reinforced sponge-associated bacteria as a valuable source of structurally diverse secondary metabolites with potent biological properties, which makes these microbial communities promising sources of new drug candidates. However, the overall diversity of secondary metabolite biosynthetic potential present in bacteria is difficult to access due to the fact that the majority of bacteria are not readily cultured in the laboratory. Thus, use of cultivation-independent approaches may allow accessing "silent" and "cryptic" secondary metabolite biosynthetic gene clusters present in bacteria that cannot yet be cultured. In the present study, we investigated the diversity of secondary metabolite biosynthetic gene clusters (BGCs) in metagenomes of bacterial communities associated with three sponge species: Clathria reinwardti, Rhabdastrella globostellata, and Spheciospongia sp. The results reveal that the three metagenomes contain a high number of predicted BGCs, ranging from 282 to 463 BGCs per metagenome. The types of BGCs were diverse and represented 12 different cluster types. Clusters predicted to encode fatty acid synthases and polyketide synthases (PKS) were the most dominant BGC types, followed by clusters encoding synthesis of terpenes and bacteriocins. Based on BGC sequence similarity analysis, 363 gene cluster families (GCFs) were identified. Interestingly, no GCFs were assigned to pathways responsible for the production of known compounds, implying that the clusters detected might be responsible for production of several novel compounds. The KS gene sequences from PKS clusters were used to predict the taxonomic origin of the clusters involved. The KS sequences were related to 12 bacterial phyla with Actinobacteria, Proteobacteria, and Firmicutes as the most predominant. At the genus level, the KSs were most related to those found in the genera Mycolicibacterium, Mycobacterium, Burkholderia, and Streptomyces. Phylogenetic analysis of KS sequences resulted in detection of two known 'sponge-specific' BGCs, i.e., SupA and SwfA, as well as a new 'sponge-specific' cluster related to fatty acid synthesis in the phylum Candidatus Poribacteria and composed only by KS sequences of the three sponge-associated bacterial communities assessed here.
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Delineating biosynthesis of Huperzine A, A plant-derived medicine for the treatment of Alzheimer's disease. Biotechnol Adv 2022; 60:108026. [DOI: 10.1016/j.biotechadv.2022.108026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/01/2022] [Accepted: 07/26/2022] [Indexed: 11/22/2022]
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The thick waxy coat of mycobacteria, a protective layer against antibiotics and the host's immune system. Biochem J 2020; 477:1983-2006. [PMID: 32470138 PMCID: PMC7261415 DOI: 10.1042/bcj20200194] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 12/22/2022]
Abstract
Tuberculosis, caused by the pathogenic bacterium Mycobacterium tuberculosis (Mtb), is the leading cause of death from an infectious disease, with a mortality rate of over a million people per year. This pathogen's remarkable resilience and infectivity is largely due to its unique waxy cell envelope, 40% of which comprises complex lipids. Therefore, an understanding of the structure and function of the cell wall lipids is of huge indirect clinical significance. This review provides a synopsis of the cell envelope and the major lipids contained within, including structure, biosynthesis and roles in pathogenesis.
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Xu X, Qu R, Wu W, Jiang C, Shao D, Shi J. Applications of microbial co-cultures in polyketides production. J Appl Microbiol 2020; 130:1023-1034. [PMID: 32897644 DOI: 10.1111/jam.14845] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/28/2020] [Accepted: 08/31/2020] [Indexed: 12/21/2022]
Abstract
Polyketides are a large group of natural biomolecules that are normally produced by bacteria, fungi and plants. These molecules have clinical importance due to their anti-cancer, anti-microbial, anti-oxidant and anti-inflammatory properties. Polyketides are biosynthesized from units of acyl-CoA by different polyketide synthases (PKSs), which display wide diversity of functional domains and mechanisms of action between fungi and bacteria. Co-culture of different micro-organisms can produce novel products distinctive from those produced during single cultures. This study compared the new polyketides produced in such co-culture systems and discusses aspects of the cultivation systems, product structures and identification techniques. Current results indicate that the formation of new polyketides may be the result of activation of previously silent PKSs genes induced during co-culture. This review indicated a potential way to produce pure therapeutic polyketides by microbial fermentation and a potential way to develop functional foods and agricultural products using co-co-culture of different micro-organisms. It also pointed out a new perspective for studies on the process of functional foods, especially those involving multiple micro-organisms.
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Affiliation(s)
- X Xu
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - R Qu
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - W Wu
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - C Jiang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - D Shao
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - J Shi
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
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Pandith SA, Ramazan S, Khan MI, Reshi ZA, Shah MA. Chalcone synthases (CHSs): the symbolic type III polyketide synthases. PLANTA 2019; 251:15. [PMID: 31776718 DOI: 10.1007/s00425-019-03307-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/02/2019] [Indexed: 05/08/2023]
Abstract
Present review provides a thorough insight on some significant aspects of CHSs over a period of about past three decades with a better outlook for future studies toward comprehending the structural and mechanistic intricacy of this symbolic enzyme. Polyketide synthases (PKSs) form a large family of iteratively acting multifunctional proteins that are involved in the biosynthesis of spectrum of natural products. They exhibit remarkable versatility in the structural configuration and functional organization with an incredible ability to generate different classes of compounds other than the characteristic secondary metabolite constituents. Architecturally, chalcone synthase (CHS) is considered to be the simplest representative of Type III PKSs. The enzyme is pivotal for phenylpropanoid biosynthesis and is also well known for catalyzing the initial step of the flavonoid/isoflavonoid pathway. Being the first Type III enzyme to be discovered, CHS has been subjected to ample investigations which, to a greater extent, have tried to understand its structural complexity and promiscuous functional behavior. In this context, we vehemently tried to collect the fragmented information entirely focussed on this symbolic enzyme from about past three-four decades. The aim of this review is to selectively summarize data on some of the fundamental aspects of CHSs viz, its history and distribution, localization, structure and analogs in non-plant hosts, promoter analyses, and role in defense, with an emphasis on mechanistic studies in different species and vis-à-vis mutation-led changes, and evolutionary significance which has been discussed in detail. The present review gives an insight with a better perspective for the scientific community for future studies devoted towards delimiting the mechanistic and structural basis of polyketide biosynthetic machinery vis-à-vis CHS.
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Affiliation(s)
- Shahzad A Pandith
- Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India.
| | - Salika Ramazan
- Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India
| | - Mohd Ishfaq Khan
- Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India
| | - Manzoor A Shah
- Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India.
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Reiter S, Cahn JKB, Wiebach V, Ueoka R, Piel J. Characterization of an Orphan Type III Polyketide Synthase Conserved in Uncultivated "Entotheonella" Sponge Symbionts. Chembiochem 2019; 21:564-571. [PMID: 31430416 PMCID: PMC7064976 DOI: 10.1002/cbic.201900352] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/19/2019] [Indexed: 02/06/2023]
Abstract
Uncultivated bacterial symbionts from the candidate genus "Entotheonella" have been shown to produce diverse natural products previously attributed to their sponge hosts. In addition to these known compounds, "Entotheonella" genomes contain rich sets of biosynthetic gene clusters that lack identified natural products. Among these is a small type III polyketide synthase (PKS) cluster, one of only three clusters present in all known "Entotheonella" genomes. This conserved "Entotheonella" PKS (cep) cluster encodes the type III PKS CepA and the putative methyltransferase CepB. Herein, the characterization of CepA as an enzyme involved in phenolic lipid biosynthesis is reported. In vitro analysis showed a specificity for alkyl starter substrates and the production of tri- and tetraketide pyrones and tetraketide resorcinols. The conserved distribution of the cep cluster suggests an important role for the phenolic lipid polyketides produced in "Entotheonella" variants.
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Affiliation(s)
- Silke Reiter
- Department of Microbiology, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland.,Institute for Insect Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Jackson K B Cahn
- Department of Microbiology, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Vincent Wiebach
- Department of Microbiology, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Reiko Ueoka
- Department of Microbiology, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Jörn Piel
- Department of Microbiology, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
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Biosynthesis of Polyketides in Streptomyces. Microorganisms 2019; 7:microorganisms7050124. [PMID: 31064143 PMCID: PMC6560455 DOI: 10.3390/microorganisms7050124] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/24/2019] [Accepted: 04/27/2019] [Indexed: 12/12/2022] Open
Abstract
Polyketides are a large group of secondary metabolites that have notable variety in their structure and function. Polyketides exhibit a wide range of bioactivities such as antibacterial, antifungal, anticancer, antiviral, immune-suppressing, anti-cholesterol, and anti-inflammatory activity. Naturally, they are found in bacteria, fungi, plants, protists, insects, mollusks, and sponges. Streptomyces is a genus of Gram-positive bacteria that has a filamentous form like fungi. This genus is best known as one of the polyketides producers. Some examples of polyketides produced by Streptomyces are rapamycin, oleandomycin, actinorhodin, daunorubicin, and caprazamycin. Biosynthesis of polyketides involves a group of enzyme activities called polyketide synthases (PKSs). There are three types of PKSs (type I, type II, and type III) in Streptomyces responsible for producing polyketides. This paper focuses on the biosynthesis of polyketides in Streptomyces with three structurally-different types of PKSs.
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Hovde BT, Hanschen ER, Steadman Tyler CR, Lo CC, Kunde Y, Davenport K, Daligault H, Msanne J, Canny S, Eyun SI, Riethoven JJM, Polle J, Starkenburg SR. Genomic characterization reveals significant divergence within Chlorella sorokiniana (Chlorellales, Trebouxiophyceae). ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Thanapipatsiri A, Gomez‐Escribano JP, Song L, Bibb MJ, Al‐Bassam M, Chandra G, Thamchaipenet A, Challis GL, Bibb MJ. Discovery of Unusual Biaryl Polyketides by Activation of a Silent Streptomyces venezuelae Biosynthetic Gene Cluster. Chembiochem 2016; 17:2189-2198. [PMID: 27605017 PMCID: PMC5132015 DOI: 10.1002/cbic.201600396] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Indexed: 11/22/2022]
Abstract
Comparative transcriptional profiling of a ΔbldM mutant of Streptomyces venezuelae with its unmodified progenitor revealed that the expression of a cryptic biosynthetic gene cluster containing both type I and type III polyketide synthase genes is activated in the mutant. The 29.5 kb gene cluster, which was predicted to encode an unusual biaryl metabolite, which we named venemycin, and potentially halogenated derivatives, contains 16 genes including one-vemR-that encodes a transcriptional activator of the large ATP-binding LuxR-like (LAL) family. Constitutive expression of vemR in the ΔbldM mutant led to the production of sufficient venemycin for structural characterisation, confirming its unusual biaryl structure. Co-expression of the venemycin biosynthetic gene cluster and vemR in the heterologous host Streptomyces coelicolor also resulted in venemycin production. Although the gene cluster encodes two halogenases and a flavin reductase, constitutive expression of all three genes led to the accumulation only of a monohalogenated venemycin derivative, both in the native producer and the heterologous host. A competition experiment in which equimolar quantities of sodium chloride and sodium bromide were fed to the venemycin-producing strains resulted in the preferential incorporation of bromine, thus suggesting that bromide is the preferred substrate for one or both halogenases.
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Affiliation(s)
- Anyarat Thanapipatsiri
- Department of GeneticsFaculty of ScienceKasetsart University, 50 Ngamwongwan Road, Ladyao, ChatuchakBangkok10900Thailand
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | | | - Lijiang Song
- Department of ChemistryUniversity of WarwickGibbet Hill RoadCoventryCV4 7ALUK
| | - Maureen J. Bibb
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Mahmoud Al‐Bassam
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Department of BioengineeringUniversity of California San Diego9500 Gilman Drive, MC 0412La JollaCA92093-0412USA
| | - Govind Chandra
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Arinthip Thamchaipenet
- Department of GeneticsFaculty of ScienceKasetsart University, 50 Ngamwongwan Road, Ladyao, ChatuchakBangkok10900Thailand
- Center for Advanced Studies in Tropical Natural ResourcesNRU–KUKasetsart University50 Ngamwongwan Road, Ladyao, ChatuchakBangkok10900Thailand
| | - Gregory L. Challis
- Department of ChemistryUniversity of WarwickGibbet Hill RoadCoventryCV4 7ALUK
| | - Mervyn J. Bibb
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
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Iterative polyketide biosynthesis by modular polyketide synthases in bacteria. Appl Microbiol Biotechnol 2015; 100:541-57. [PMID: 26549236 DOI: 10.1007/s00253-015-7093-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/10/2015] [Accepted: 10/13/2015] [Indexed: 10/22/2022]
Abstract
Modular polyketide synthases (type I PKSs) in bacteria are responsible for synthesizing a significant percentage of bioactive natural products. This group of synthases has a characteristic modular organization, and each module within a PKS carries out one cycle of polyketide chain elongation; thus each module is non-iterative in function. It was possible to predict the basic structure of a polyketide product from the module organization of the PKSs, since there generally existed a co-linearity between the number of modules and the number of chain elongations. However, more and more bacterial modular PKSs fail to conform to the canonical rules, and a particularly noteworthy group of non-canonical PKSs is the bacterial iterative type I PKSs. This review covers recent examples of iteratively used modular PKSs in bacteria. These non-canonical PKSs give rise to a large array of natural products with impressive structural diversity. The molecular mechanism behind the iterations is often unclear, presenting a new challenge to the rational engineering of these PKSs with the goal of generating new natural products. Structural elucidation of these synthase complexes and better understanding of potential PKS-PKS interactions as well as PKS-substrate recognition may provide new prospects and inspirations for the discovery and engineering of new bioactive polyketides.
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A Streptomyces coelicolor host for the heterologous expression of Type III polyketide synthase genes. Microb Cell Fact 2015; 14:145. [PMID: 26376792 PMCID: PMC4573997 DOI: 10.1186/s12934-015-0335-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/03/2015] [Indexed: 11/30/2022] Open
Abstract
Background Recent advances in genome sequencing, combined with bioinformatic analysis, has led to the identification of numerous novel natural product gene clusters, particularly in actinomycetes of terrestrial and marine origin. Many of these gene clusters encode uncharacterised Type III polyketide synthases. To facilitate the study of these genes and their potentially novel products, we set out to construct an actinomycete expression host specifically designed for the heterologous expression of Type III PKS genes and their gene clusters. Results A derivative of Streptomyces coelicolor A3(2) designed for the expression of Type III polyketide synthase (PKS) genes was constructed from the previously engineered expression strain S. coelicolor M1152 [Δact Δred Δcpk Δcda rpoB(C1298T)] by removal of all three of the endogenous Type III PKS genes (gcs,srsA,rppA) by PCR targeting. The resulting septuple deletion mutant, M1317, proved to be an effective surrogate host for the expression of actinobacterial Type III PKS genes: expression of the reintroduced gcs gene from S. coelicolor and of the heterologous rppA gene from Streptomyces venezuelae under the control of the constitutive ermE* promoter resulted in copious production of germicidin and flaviolin, respectively. Conclusions The newly constructed expression host S. coelicolor M1317 should be particularly useful for the discovery and analysis of new Type III polyketide metabolites.
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Ma XK, Li L, Peterson EC, Ruan T, Duan X. The influence of naphthaleneacetic acid (NAA) and coumarin on flavonoid production by fungus Phellinus sp.: modeling of production kinetic profiles. Appl Microbiol Biotechnol 2015; 99:9417-26. [DOI: 10.1007/s00253-015-6824-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/25/2015] [Accepted: 07/05/2015] [Indexed: 10/25/2022]
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Müller CA, Oberauner-Wappis L, Peyman A, Amos GCA, Wellington EMH, Berg G. Mining for Nonribosomal Peptide Synthetase and Polyketide Synthase Genes Revealed a High Level of Diversity in the Sphagnum Bog Metagenome. Appl Environ Microbiol 2015; 81:5064-72. [PMID: 26002894 PMCID: PMC4495229 DOI: 10.1128/aem.00631-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/12/2015] [Indexed: 01/01/2023] Open
Abstract
Sphagnum bog ecosystems are among the oldest vegetation forms harboring a specific microbial community and are known to produce an exceptionally wide variety of bioactive substances. Although the Sphagnum metagenome shows a rich secondary metabolism, the genes have not yet been explored. To analyze nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), the diversity of NRPS and PKS genes in Sphagnum-associated metagenomes was investigated by in silico data mining and sequence-based screening (PCR amplification of 9,500 fosmid clones). The in silico Illumina-based metagenomic approach resulted in the identification of 279 NRPSs and 346 PKSs, as well as 40 PKS-NRPS hybrid gene sequences. The occurrence of NRPS sequences was strongly dominated by the members of the Protebacteria phylum, especially by species of the Burkholderia genus, while PKS sequences were mainly affiliated with Actinobacteria. Thirteen novel NRPS-related sequences were identified by PCR amplification screening, displaying amino acid identities of 48% to 91% to annotated sequences of members of the phyla Proteobacteria, Actinobacteria, and Cyanobacteria. Some of the identified metagenomic clones showed the closest similarity to peptide synthases from Burkholderia or Lysobacter, which are emerging bacterial sources of as-yet-undescribed bioactive metabolites. This report highlights the role of the extreme natural ecosystems as a promising source for detection of secondary compounds and enzymes, serving as a source for biotechnological applications.
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Affiliation(s)
- Christina A Müller
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Graz, Austria Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Lisa Oberauner-Wappis
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Graz, Austria Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Armin Peyman
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Graz, Austria Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Gregory C A Amos
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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Al Toma RS, Brieke C, Cryle MJ, Süssmuth RD. Structural aspects of phenylglycines, their biosynthesis and occurrence in peptide natural products. Nat Prod Rep 2015; 32:1207-35. [DOI: 10.1039/c5np00025d] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Phenylglycine-type amino acids occur in a wide variety of peptide natural products. Herein structures and properties of these peptides as well as the biosynthetic origin and incorporation of phenylglycines are discussed.
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Affiliation(s)
| | - Clara Brieke
- Max Planck Institute for Medical Research
- Department of Biomolecular Mechanisms
- 69120 Heidelberg
- Germany
| | - Max J. Cryle
- Max Planck Institute for Medical Research
- Department of Biomolecular Mechanisms
- 69120 Heidelberg
- Germany
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17
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Melanins: Skin Pigments and Much More—Types, Structural Models, Biological Functions, and Formation Routes. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/498276] [Citation(s) in RCA: 277] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This review presents a general view of all types of melanin in all types of organisms. Melanin is frequently considered just an animal cutaneous pigment and is treated separately from similar fungal or bacterial pigments. Similarities concerning the phenol precursors and common patterns in the formation routes are discussed. All melanins are formed in a first enzymatically-controlled phase, generally a phenolase, and a second phase characterized by an uncontrolled polymerization of the oxidized intermediates. In that second phase, quinones derived from phenol oxidation play a crucial role. Concerning functions, all melanins show a common feature, a protective role, but they are not merely photoprotective pigments against UV sunlight. In pathogenic microorganisms, melanization becomes a virulence factor since melanin protects microbial cells from defense mechanisms in the infected host. In turn, some melanins are formed in tissues where sunlight radiation is not a potential threat. Then, their redox, metal chelating, or free radical scavenging properties are more important than light absorption capacity. These pigments sometimes behave as a double-edged sword, and inhibition of melanogenesis is desirable in different cells. Melanin biochemistry is an active field of research from dermatological, biomedical, cosmetical, and microbiological points of view, as well as fruit technology.
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18
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Putignani L, Massa O, Alisi A. Engineered Escherichia coli as new source of flavonoids and terpenoids. Food Res Int 2013. [DOI: 10.1016/j.foodres.2013.01.062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Jeya M, Kim TS, Tiwari MK, Li J, Zhao H, Lee JK. The Botrytis cinerea type III polyketide synthase shows unprecedented high catalytic efficiency toward long chain acyl-CoAs. MOLECULAR BIOSYSTEMS 2012; 8:2864-7. [PMID: 22945364 DOI: 10.1039/c2mb25282a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
BPKS from Botrytis cinerea is a novel type III polyketide synthase that accepts C(4)-C(18) aliphatic acyl-CoAs and benzoyl-CoA as the starters to form pyrones, resorcylic acids and resorcinols through sequential condensation with malonyl-CoA. The catalytic efficiency (k(cat)/K(m)) of BPKS was 2.8 × 10(5) s(-1) M(-1) for palmitoyl-CoA, the highest ever reported. Substrate docking analyses addressed the unique features of BPKS such as its high activity and high specificity toward long chain acyl-CoAs.
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Affiliation(s)
- Marimuthu Jeya
- Department of Chemical Engineering, Konkuk University, Seoul 143-701, Korea
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20
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The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity. PLoS One 2012; 7:e34064. [PMID: 22479523 PMCID: PMC3315503 DOI: 10.1371/journal.pone.0034064] [Citation(s) in RCA: 304] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Accepted: 02/26/2012] [Indexed: 11/19/2022] Open
Abstract
New bioinformatic tools are needed to analyze the growing volume of DNA sequence data. This is especially true in the case of secondary metabolite biosynthesis, where the highly repetitive nature of the associated genes creates major challenges for accurate sequence assembly and analysis. Here we introduce the web tool Natural Product Domain Seeker (NaPDoS), which provides an automated method to assess the secondary metabolite biosynthetic gene diversity and novelty of strains or environments. NaPDoS analyses are based on the phylogenetic relationships of sequence tags derived from polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes, respectively. The sequence tags correspond to PKS-derived ketosynthase domains and NRPS-derived condensation domains and are compared to an internal database of experimentally characterized biosynthetic genes. NaPDoS provides a rapid mechanism to extract and classify ketosynthase and condensation domains from PCR products, genomes, and metagenomic datasets. Close database matches provide a mechanism to infer the generalized structures of secondary metabolites while new phylogenetic lineages provide targets for the discovery of new enzyme architectures or mechanisms of secondary metabolite assembly. Here we outline the main features of NaPDoS and test it on four draft genome sequences and two metagenomic datasets. The results provide a rapid method to assess secondary metabolite biosynthetic gene diversity and richness in organisms or environments and a mechanism to identify genes that may be associated with uncharacterized biochemistry.
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Abstract
Phylogenetics is the study of the evolutionary relatedness among groups of organisms. Molecular phylogenetics uses sequence data to infer these relationships for both organisms and the genes they maintain. With the large amount of publicly available sequence data, phylogenetic inference has become increasingly important in all fields of biology. In the case of natural product research, phylogenetic relationships are proving to be highly informative in terms of delineating the architecture and function of the genes involved in secondary metabolite biosynthesis. Polyketide synthases and nonribosomal peptide synthetases provide model examples in which individual domain phylogenies display different predictive capacities, resolving features ranging from substrate specificity to structural motifs associated with the final metabolic product. This chapter provides examples in which phylogeny has proven effective in terms of predicting functional or structural aspects of secondary metabolism. The basics of how to build a reliable phylogenetic tree are explained along with information about programs and tools that can be used for this purpose. Furthermore, it introduces the Natural Product Domain Seeker, a recently developed Web tool that employs phylogenetic logic to classify ketosynthase and condensation domains based on established enzyme architecture and biochemical function.
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Affiliation(s)
- Nadine Ziemert
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
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Mohanty D, Sankaranarayanan R, Gokhale RS. Fatty acyl-AMP ligases and polyketide synthases are unique enzymes of lipid biosynthetic machinery in Mycobacterium tuberculosis. Tuberculosis (Edinb) 2011; 91:448-55. [PMID: 21601529 DOI: 10.1016/j.tube.2011.04.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 04/21/2011] [Indexed: 12/24/2022]
Abstract
The cell envelope of Mycobacterium tuberculosis (Mtb) possesses a repertoire of unusual lipids that are believed to play an important role in pathogenesis. In this review, we specifically focus on computational, biochemical and structural studies in lipid biosynthesis that have established functional role of polyketide synthases (PKSs) and fatty acyl-AMP ligases (FAALs). Mechanistic and structural studies with FAALs suggest that this group of proteins may have evolved from omnipresent fatty acyl-CoA ligases (FACLs). FAALs activate fatty acids as acyl-adenylates and transfer them on to the PKSs which then produce unusual acyl chains that are the components of mycobacterial lipids. FAALs are a newly discovered family of enzymes; whereas involvement of PKSs in lipid metabolism was not known prior to their discovery in Mtb. Since Mtb genome contains multiple homologs of FAALs and PKSs and owing to the conserved reaction mechanism and overlapping substrate specificity; there is tempting opportunity to develop 'systemic drugs' against these enzymes as anti-tuberculosis agents.
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Affiliation(s)
- Debasisa Mohanty
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India.
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23
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Type III polyketide synthases in lichen mycobionts. Fungal Biol 2010; 114:379-85. [DOI: 10.1016/j.funbio.2010.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 03/03/2010] [Accepted: 03/03/2010] [Indexed: 11/19/2022]
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Nett M, Ikeda H, Moore BS. Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep 2009; 26:1362-84. [PMID: 19844637 PMCID: PMC3063060 DOI: 10.1039/b817069j] [Citation(s) in RCA: 543] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The phylum Actinobacteria hosts diverse high G + C, Gram-positive bacteria that have evolved a complex chemical language of natural product chemistry to help navigate their fascinatingly varied lifestyles. To date, 71 Actinobacteria genomes have been completed and annotated, with the vast majority representing the Actinomycetales, which are the source of numerous antibiotics and other drugs from genera such as Streptomyces, Saccharopolyspora and Salinispora . These genomic analyses have illuminated the secondary metabolic proficiency of these microbes – underappreciated for years based on conventional isolation programs – and have helped set the foundation for a new natural product discovery paradigm based on genome mining. Trends in the secondary metabolomes of natural product-rich actinomycetes are highlighted in this review article, which contains 199 references.
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Affiliation(s)
- Markus Nett
- Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany.
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, Sagamihara, Kanagawa, 228-8555, Japan.
| | - Bradley S. Moore
- Scripps Institution of Oceanography and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, 92093, USA
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25
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Li Y, Müller R. Non-modular polyketide synthases in myxobacteria. PHYTOCHEMISTRY 2009; 70:1850-1857. [PMID: 19586645 DOI: 10.1016/j.phytochem.2009.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2009] [Revised: 04/14/2009] [Accepted: 05/12/2009] [Indexed: 05/28/2023]
Abstract
Myxobacteria are prolific producers of a wide variety of secondary metabolites. The vast majority of these compounds are complex polyketides which are biosynthesised by multimodular polyketide synthases (PKSs). In contrast, few myxobacterial metabolites isolated to date are derived from non-modular PKSs, in particular type III PKSs. This review reports our progress on the characterisation of type III PKSs in myxobacteria. We also summarize current knowledge on bacterial type III PKSs, with a special focus on the evolutionary relationship between plant and bacterial enzymes. The biosynthesis of a quinoline alkaloid in Stigmatella aurantiaca by a non-modular PKS is also discussed.
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Affiliation(s)
- Yanyan Li
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
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26
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Bringmann G, Irmer A, Feineis D, Gulder TAM, Fiedler HP. Convergence in the biosynthesis of acetogenic natural products from plants, fungi, and bacteria. PHYTOCHEMISTRY 2009; 70:1776-1786. [PMID: 19786287 DOI: 10.1016/j.phytochem.2009.08.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 08/05/2009] [Accepted: 08/21/2009] [Indexed: 05/28/2023]
Abstract
This review deals with polyketides to which nature has developed different biosynthetic pathways in the course of evolution. The anthraquinone chrysophanol is the first example of an acetogenic natural product that is, in an organism-specific manner, formed via more than one polyketide folding mode: In eukaryotes, like e.g., in fungi, in higher plants, and in insects, it is synthesized via folding mode F, while in prokaryotes it originates through mode S. It has, more recently, even been found to be synthesized by a third pathway, named mode S'. Thus, chrysophanol is the first polyketide synthase product that originates through a divergent-convergent biosynthesis (depending on the respective producing organisms). A second example of a striking biosynthetic convergence is the isoquinoline alkaloids. While all as yet investigated representatives of this large family of plant-derived metabolites (more than 2500 known representatives!) are formed from aromatic amino acids, the biosynthetic origin of naphthylisoquinoline alkaloids like dioncophylline A is unprecedented in following a route to isoquinolines in plants: we have shown that such naphthylisoquinolines represent the as yet only known polyketidic di- and tetrahydroisoquinolines, originating from acetate and malonate units, exclusively. Both molecular halves, the isoquinoline part and the naphthalene portion, are even synthesized from a joint polyketide precursor, the first proven case of the F-type folding mode in higher plants. The biosynthetic origins of the natural products presented in this paper were elucidated by feeding (13)C(2)-labeled acetate (or advanced precursors) to the respective producing organisms, with subsequent NMR analysis of their (13)C(2) incorporation patterns using the potent cryoprobe methodology, thus making the full polyketide folding pattern visible.
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Affiliation(s)
- Gerhard Bringmann
- Institute of Organic Chemistry, University of Würzburg, Würzburg, Germany.
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28
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Fowler ZL, Koffas MAG. Biosynthesis and biotechnological production of flavanones: current state and perspectives. Appl Microbiol Biotechnol 2009; 83:799-808. [PMID: 19475406 DOI: 10.1007/s00253-009-2039-z] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 05/07/2009] [Accepted: 05/07/2009] [Indexed: 01/18/2023]
Abstract
Polyphenols produced in a wide variety of flowering and fruit-bearing plants have the potential to be valuable fine chemicals for the treatment of an assortment of human maladies. One of the major constituents within this chemical class are flavonoids, among which flavanones, as the precursor to all flavonoid structures, are the most prevalent. We review the current status of flavanone production technology using microorganisms, with focus on heterologous protein expression. Such processes appear as attractive production alternatives for commercial synthesis of these high-value chemicals as traditional chemical, and plant cell cultures have significant drawbacks. Other issues of importance, including fermentation configurations and economics, are also considered.
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Affiliation(s)
- Zachary L Fowler
- Department of Chemical and Biological Engineering, University at Buffalo, NY 14260, USA
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30
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Tae H, Sohng JK, Park K. MapsiDB: an integrated web database for type I polyketide synthases. Bioprocess Biosyst Eng 2009; 32:723-7. [PMID: 19205748 DOI: 10.1007/s00449-008-0296-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Accepted: 12/30/2008] [Indexed: 11/25/2022]
Abstract
Polyketides have diverse biological activities, including pharmacological functions such as antibiotic, antitumor and agrochemical properties. They are biosynthesized from short carboxylic acid precursors by polyketide synthases (PKSs). As natural polyketide products include many clinically important drugs and the volume of data on polyketides is rapidly increasing, the development of a database system to manage polyketide data is essential. MapsiDB is an integrated web database formulated to contain data on type I polyketides and their PKSs, including domain and module composition and related genome information. Data on polyketides were collected from journals and online resources and processed with analysis programs. Web interfaces were utilized to construct and to access this database, allowing polyketide researchers to add their data to this database and to use it easily.
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Affiliation(s)
- Hongseok Tae
- SmallSoft Co, Ltd, Jang-Dong 59-5, Yusung-Gu, Daejeon 305-343, South Korea.
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31
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A computational screen for type I polyketide synthases in metagenomics shotgun data. PLoS One 2008; 3:e3515. [PMID: 18953415 PMCID: PMC2568958 DOI: 10.1371/journal.pone.0003515] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Accepted: 09/22/2008] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Polyketides are a diverse group of biotechnologically important secondary metabolites that are produced by multi domain enzymes called polyketide synthases (PKS). METHODOLOGY/PRINCIPAL FINDINGS We have estimated frequencies of type I PKS (PKS I) - a PKS subgroup - in natural environments by using Hidden-Markov-Models of eight domains to screen predicted proteins from six metagenomic shotgun data sets. As the complex PKS I have similarities to other multi-domain enzymes (like those for the fatty acid biosynthesis) we increased the reliability and resolution of the dataset by maximum-likelihood trees. The combined information of these trees was then used to discriminate true PKS I domains from evolutionary related but functionally different ones. We were able to identify numerous novel PKS I proteins, the highest density of which was found in Minnesota farm soil with 136 proteins out of 183,536 predicted genes. We also applied the protocol to UniRef database to improve the annotation of proteins with so far unknown function and identified some new instances of horizontal gene transfer. CONCLUSIONS/SIGNIFICANCE The screening approach proved powerful in identifying PKS I sequences in large sequence data sets and is applicable to many other protein families.
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Pankewitz F, Hilker M. Polyketides in insects: ecological role of these widespread chemicals and evolutionary aspects of their biogenesis. Biol Rev Camb Philos Soc 2008; 83:209-26. [PMID: 18410406 DOI: 10.1111/j.1469-185x.2008.00040.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polyketides are known to be used by insects for pheromone communication and defence against enemies. Although in microorganisms (fungi, bacteria) and plants polyketide biogenesis is known to be catalysed by polyketide synthases (PKS), no insect PKS involved in biosynthesis of pheromones or defensive compounds have yet been found. Polyketides detected in insects may also be biosynthesized by endosymbionts. From a chemical perspective, polyketide biogenesis involves the formation of a polyketide chain using carboxylic acids as precursors. Fatty acid biosynthesis also requires carboxylic acids as precursors, but utilizes fatty acid synthases (FAS) to catalyse this process. In the present review, studies of the biosynthesis of insect polyketides applying labelled carboxylic acids as precursors are outlined to exemplify chemical approaches used to elucidate insect polyketide formation. However, since compounds biosynthesised by FAS may use the same precursors, it still remains unclear whether the structures that are formed from e.g. acetate chains (acetogenins) or propanoate chains (propanogenins) are PKS or FAS products. A critical comparison of PKS and FAS architectures and activities supports the hypothesis of a common evolutionary origin of these enzyme complexes and highlights why PKS can catalyse the biosynthesis of much more complex products than can FAS. Finally, we summarise knowledge which might assist researchers in designing approaches for the detection of insect PKS genes.
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Affiliation(s)
- Florian Pankewitz
- Freie Universität Berlin, Institute of Biology, Haderslebener Str. 9, D-12163 Berlin, Germany
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Zha W, Rubin-Pitel SB, Zhao H. Exploiting genetic diversity by directed evolution: molecular breeding of type III polyketide synthases improves productivity. MOLECULAR BIOSYSTEMS 2008; 4:246-8. [PMID: 18437267 DOI: 10.1039/b717705d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Applying directed evolution to the phloroglucinol synthase PhlD from Pseudomonas fluorescens Pf-5 has provided the first example of engineering enhanced productivity in a type III polyketide synthase, and a rare instance of improving the activity of a biosynthetic enzyme from secondary metabolism.
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Affiliation(s)
- Wenjuan Zha
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
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John U, Beszteri B, Derelle E, Van de Peer Y, Read B, Moreau H, Cembella A. Novel Insights into Evolution of Protistan Polyketide Synthases through Phylogenomic Analysis. Protist 2008; 159:21-30. [DOI: 10.1016/j.protis.2007.08.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Accepted: 07/31/2007] [Indexed: 11/28/2022]
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Castoe TA, Stephens T, Noonan BP, Calestani C. A novel group of type I polyketide synthases (PKS) in animals and the complex phylogenomics of PKSs. Gene 2007; 392:47-58. [PMID: 17207587 DOI: 10.1016/j.gene.2006.11.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 11/03/2006] [Accepted: 11/10/2006] [Indexed: 11/18/2022]
Abstract
Type I polyketide synthases (PKSs), and related fatty acid synthases (FASs), represent a large group of proteins encoded by a diverse gene family that occurs in eubacteria and eukaryotes (mainly in fungi). Collectively, enzymes encoded by this gene family produce a wide array of polyketide compounds that encompass a broad spectrum of biological activity including antibiotic, antitumor, antifungal, immunosuppressive, and predator defense functional roles. We employed a phylogenomics approach to estimate relationships among members of this gene family from eubacterial and eukaryotic genomes. Our results suggest that some animal genomes (sea urchins, birds, and fish) possess a previously unidentified group of pks genes, in addition to possessing fas genes used in fatty acid metabolism. These pks genes in the chicken, fish, and sea urchin genomes do not appear to be closely related to any other animal or fungal genes, and instead are closely related to pks genes from the slime mold Dictyostelium and eubacteria. Continued accumulation of genome sequence data from diverse animal lineages is required to clarify whether the presence of these (non-fas) pks genes in animal genomes owes their origins to horizontal gene transfer (from eubacterial or Dictostelium genomes) or to more conventional patterns of vertical inheritance coupled with massive gene loss in several animal lineages. Additionally, results of our broad-scale phylogenetic analyses bolster the support for previous hypotheses of horizontal gene transfer of pks genes from bacterial to fungal and protozoan lineages.
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Affiliation(s)
- Todd A Castoe
- Department of Biology, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816-2368, USA
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Gross H. Strategies to unravel the function of orphan biosynthesis pathways: recent examples and future prospects. Appl Microbiol Biotechnol 2007; 75:267-77. [PMID: 17340107 DOI: 10.1007/s00253-007-0900-5] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 02/19/2007] [Accepted: 02/19/2007] [Indexed: 10/23/2022]
Abstract
The recent increase and availability of whole genome sequences have revised our view of the metabolic capabilities of microorganisms. From these data, a large number of orphan biosynthesis pathways have been identified by bio-informatics. Orphan biosynthetic pathways are gene clusters for which the encoded natural product is unknown. It is worthy to note that the number of orphan pathways coding for putative natural products outnumbers by far the number of currently known metabolites for a given organism. Whilst Streptomyces coelicolor was known to produce only 4 secondary metabolites, the genome analysis revealed 18 additional orphan biosynthetic pathways. It is intriguing to note that this is not a particular case because analysis of other microbial genomes originating from myxobacteria, cyanobacteria and filamentous fungi showed the presence of a comparable or even larger number of orphan pathways. The discovery of these numerous pathways represents a treasure trove, which is likely to grow exponentially in the future, uncovering many novel and possibly bio-active compounds. The few natural products that have been correlated with their orphan pathway are merely the tip of the iceberg, whilst plenty of metabolites await discovery. The recent strategies and methods to access these promising hidden natural products are discussed in this review.
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Affiliation(s)
- Harald Gross
- Institute for Pharmaceutical Biology, Nussallee 6, 53115, Bonn, Germany.
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Li S, Grüschow S, Dordick JS, Sherman DH. Molecular analysis of the role of tyrosine 224 in the active site of Streptomyces coelicolor RppA, a bacterial type III polyketide synthase. J Biol Chem 2007; 282:12765-72. [PMID: 17331946 DOI: 10.1074/jbc.m700393200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Streptomyces coelicolor RppA (Sc-RppA), a bacterial type III polyketide synthase, utilizes malonyl-CoA as both starter and extender unit substrate to form 1,3,6,8-tetrahydroxynaphthalene (THN) (therefore RppA is also known as THN synthase (THNS)). The significance of the active site Tyr(224) for substrate specificity has been established previously, and its aromatic ring is believed to be essential for RppA to select malonyl-CoA as starter unit. Herein, we describe a series of Tyr(224) mutants of Sc-RppA including Y224F, Y224L, Y224C, Y224M, and Y224A that were able to catalyze a physiological assembly of THN, albeit with lower efficiency, challenging the necessity for the Tyr(224) aromatic ring. Steady-state kinetics and radioactive substrate binding analysis of the mutant enzymes corroborated these unexpected results. Functional examination of the Tyr(224) series of RppA mutants using diverse unnatural acyl-CoA substrates revealed the unique role of malonyl-CoA as starter unit substrate for RppA, leading to the development of a novel stericelectronic constraint model.
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Affiliation(s)
- Shengying Li
- Life Sciences Institute and Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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Lai JR, Koglin A, Walsh CT. Carrier protein structure and recognition in polyketide and nonribosomal peptide biosynthesis. Biochemistry 2007; 45:14869-79. [PMID: 17154525 DOI: 10.1021/bi061979p] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carrier proteins, 80-100 residues in length, serve as information-rich platforms to present growing acyl and peptidyl chains as covalently tethered phosphopantetheinyl-thioester intermediates during the biosynthesis of fatty acid, polyketide, and nonribosomal natural products. Carrier proteins are recognized both in cis and in trans by partner catalytic domains that effect chain-elongating condensations, redox adjustments, other tailoring steps, and finally kinetically controlled disconnection and release of the mature natural product. Dissection of regions of carrier proteins that are specifically recognized by upstream and downstream catalytic partner proteins is deciphering the logic for multiprotein assembly line construction of these large classes of natural products.
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Affiliation(s)
- Jonathan R Lai
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
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Van Wagoner RM, Drummond AK, Wright JLC. Biogenetic Diversity of Cyanobacterial Metabolites. ADVANCES IN APPLIED MICROBIOLOGY 2007; 61:89-217. [PMID: 17448789 DOI: 10.1016/s0065-2164(06)61004-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Ryan M Van Wagoner
- Center for Marine Science, University of North Carolina at Wilmington, Wilmington, NC 28409, USA
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40
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Characterization of the Substrate Specificity of PhlD, a Type III Polyketide Synthase from Pseudomonas fluorescens. J Biol Chem 2006. [DOI: 10.1016/s0021-9258(19)84117-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] Open
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41
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Zha W, Rubin-Pitel SB, Zhao H. Characterization of the substrate specificity of PhlD, a type III polyketide synthase from Pseudomonas fluorescens. J Biol Chem 2006; 281:32036-47. [PMID: 16931521 DOI: 10.1074/jbc.m606500200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PhlD, a type III polyketide synthase from Pseudomonas fluorescens, catalyzes the synthesis of phloroglucinol from three molecules of malonyl-CoA. Kinetic analysis by direct measurement of the appearance of the CoASH product (k(cat) = 24 +/- 4 min(-1) and Km = 13 +/- 1 microM) gave a k(cat) value more than an order of magnitude higher than that of any other known type III polyketide synthase. PhlD exhibits broad substrate specificity, accepting C4-C12 aliphatic acyl-CoAs and phenylacetyl-CoA as the starters to form C6-polyoxoalkylated alpha-pyrones from sequential condensation with malonyl-CoA. Interestingly, when primed with long chain acyl-CoAs, PhlD catalyzed extra polyketide elongation to form up to heptaketide products. A homology structural model of PhlD showed the presence of a buried tunnel extending out from the active site to assist the binding of long chain acyl-CoAs. To probe the structural basis for the unusual ability of PhlD to accept long chain acyl-CoAs, both site-directed mutagenesis and saturation mutagenesis were carried out on key residues lining the tunnel. Three mutations, M21I, H24V, and L59M, were found to significantly reduce the reactivity of PhlD with lauroyl-CoA while still retaining its physiological activity to synthesize phloroglucinol. Our homology modeling and mutational studies indicated that even subtle changes in the tunnel volume could affect the ability of PhlD to accept long chain acyl-CoAs. This suggested novel strategies for combinatorial biosynthesis of unnatural pharmaceutically important polyketides.
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Affiliation(s)
- Wenjuan Zha
- Department of Chemical and Biomolecular Engineering, Center for Biophysics and Computational Biology, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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O'Callaghan J, Dobson ADW. Phylogenetic analysis of polyketide synthase genes fromAspergillus ochraceus. Mycotoxin Res 2006; 22:125-33. [DOI: 10.1007/bf02956776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Gross F, Luniak N, Perlova O, Gaitatzis N, Jenke-Kodama H, Gerth K, Gottschalk D, Dittmann E, Müller R. Bacterial type III polyketide synthases: phylogenetic analysis and potential for the production of novel secondary metabolites by heterologous expression in pseudomonads. Arch Microbiol 2006; 185:28-38. [PMID: 16395556 DOI: 10.1007/s00203-005-0059-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2005] [Revised: 10/07/2005] [Accepted: 11/10/2005] [Indexed: 11/29/2022]
Abstract
Type III polyketide synthases (PKS) were regarded as typical for plant secondary metabolism before they were found in microorganisms recently. Due to microbial genome sequencing efforts, more and more type III PKS are found, most of which of unknown function. In this manuscript, we report a comprehensive analysis of the phylogeny of bacterial type III PKS and report the expression of a type III PKS from the myxobacterium Sorangium cellulosum in pseudomonads. There is no precedent of a secondary metabolite that might be biosynthetically correlated to a type III PKS from any myxobacterium. Additionally, an inactivation mutant of the S. cellulosum gene shows no physiological difference compared to the wild-type strain which is why these type III PKS are assumed to be "silent" under the laboratory conditions administered. One type III PKS (SoceCHS1) was expressed in different Pseudomonas sp. after the heterologous expression in Escherichia coli failed. Cultures of recombinant Pseudomonas sp. harbouring SoceCHS1 turned red upon incubation and the diffusible pigment formed was identified as 2,5,7-trihydroxy-1,4-naphthoquinone, the autooxidation product of 1,3,6,8-tetrahydroxynaphthalene. The successful heterologous production of a secondary metabolite using a gene not expressed under administered laboratory conditions provides evidence for the usefulness of our approach to activate such secondary metabolite genes for the production of novel metabolites.
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Affiliation(s)
- Frank Gross
- Institut für Pharmazeutische Biotechnologie, Universität des Saarlandes, Postfach 151150, 66041, Saarbrücken, Germany
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Hill AM. The biosynthesis, molecular genetics and enzymology of the polyketide-derived metabolites. Nat Prod Rep 2005; 23:256-320. [PMID: 16572230 DOI: 10.1039/b301028g] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This review covers the biosynthesis of aliphatic and aromatic polyketides as well as mixed polyketide/NRPS metabolites, and discusses the molecular genetics and enzymology of the proteins responsible for their formation.
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Gutierrez-Lugo MT, Woldemichael GM, Singh MP, Suarez PA, Maiese WM, Montenegro G, Timmermann BN. Isolation of three new naturally occurring compounds from the culture of Micromonospora sp. P1068. Nat Prod Res 2005; 19:645-52. [PMID: 16076633 DOI: 10.1080/14786410412331272040] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Bioassay guided isolation of an antibacterial extract prepared from the fermentation broth of a Micromonospora sp. P1068 led to the isolation of eight compounds identified as (3R) 3,4',7-trihydroxy-isoflavanone (1), 3-hydroxydehydrodaidzein, daidzein (2), 3-methyl-1H-indole-2-carboxylic acid (3), 1H-indole-3-carboxaldehyde (4), 3-(p-hydroxyphenyl)-N-methylpropionamide, N-methylphloretamide (5), phenyl acetic acid (6), 2-hydroxy phenyl acetic acid (7) and 4-hydroxy-5-methoxy-benzoic acid (8). Compounds 1 and 5 were found to be novel chemical entities while 3 was isolated from a natural source for the first time. All compounds were evaluated for their antimicrobial activities against a panel of clinically significant microorganisms. Compound 4 was active against Staphylococcus aureus (MIC, 32 microg/ml), Enterococcus faecium (MIC, 32 microg/ml) and Escherichia coli (MIC, 64 microg/ml).
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Affiliation(s)
- Maria-Teresa Gutierrez-Lugo
- Department of Pharmacology and Toxicology, Division of Medicinal and Natural Products Chemistry, College of Pharmacy, University of Arizona, 1703 E, Mabel Street, Tucson, Arizona 85721-0207, USA
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46
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Dembitsky VM. Astonishing diversity of natural surfactants: 2. Polyether glycosidic ionophores and macrocyclic glycosides. Lipids 2005; 40:219-48. [PMID: 15957249 DOI: 10.1007/s11745-005-1378-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Polyether glycosidic ionophores and macrocyclic glycosides are of great interest, especially for the medicinal and pharmaceutical industries. These biologically active natural surfactants are good prospects for the future chemical preparation of compounds useful as antibiotics, anticancer agents, or in industry. More than 300 interesting and unusual natural surfactants are described in this review article, including their chemical structures and biological activities.
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Affiliation(s)
- Valery M Dembitsky
- Department of Organic Chemistry and School of Pharmacy, Hebrew University, Jerusalem, Israel.
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Bode HB, Müller R. Der Einfluss bakterieller Genomik auf die Naturstoff-Forschung. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501080] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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48
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Abstract
"There's life in the old dog yet!" This adage also holds true for natural product research. After the era of natural products was declared to be over, because of the introduction of combinatorial synthesis techniques, natural product research has taken a surprising turn back towards a major field of pharmaceutical research. Current challenges, such as emerging multidrug-resistant bacteria, might be overcome by developments which combine genomic knowledge with applied biology and chemistry to identify, produce, and alter the structure of new lead compounds. Significant biological activity is reported much less frequently for synthetic compounds, a fact reflected in the large proportion of natural products and their derivatives in clinical use. This Review describes the impact of microbial genomics on natural products research, in particularly the search for new lead structures and their optimization. The limitations of this research are also discussed, thus allowing a look into future developments.
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Affiliation(s)
- Helge B Bode
- Institut für Pharmazeutische Biotechnologie, Universität des Saarlandes, Postfach 151150, 66041 Saarbrücken, Germany
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Seshime Y, Juvvadi PR, Fujii I, Kitamoto K. Discovery of a novel superfamily of type III polyketide synthases in Aspergillus oryzae. Biochem Biophys Res Commun 2005; 331:253-60. [PMID: 15845386 DOI: 10.1016/j.bbrc.2005.03.160] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2005] [Indexed: 11/28/2022]
Abstract
Identification of genes encoding type III polyketide synthase (PKS) superfamily members in the industrially useful filamentous fungus, Aspergillus oryzae, revealed that their distribution is not specific to plants or bacteria. Among other Aspergilli (Aspergillus nidulans and Aspergillus fumigatus), A. oryzae was unique in possessing four chalcone synthase (CHS)-like genes (csyA, csyB, csyC, and csyD). Expression of csyA, csyB, and csyD genes was confirmed by RT-PCR. Comparative genome analyses revealed single putative type III PKS in Neurospora crassa and Fusarium graminearum, two each in Magnaporthe grisea and Podospora anserina, and three in Phenarocheate chrysosporium, with a phylogenic distinction from bacteria and plants. Conservation of catalytic residues in the CHSs across species implicated enzymatically active nature of these newly discovered homologs.
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Affiliation(s)
- Yasuyo Seshime
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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50
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Wilkinson B, Kendrew SG, Sheridan RM, Leadlay PF. Biosynthetic engineering of polyketide synthases. Expert Opin Ther Pat 2005. [DOI: 10.1517/13543776.13.10.1579] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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