1
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Morandini L, Caulier S, Bragard C, Mahillon J. Bacillus cereus sensu lato antimicrobial arsenal: An overview. Microbiol Res 2024; 283:127697. [PMID: 38522411 DOI: 10.1016/j.micres.2024.127697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/25/2024] [Accepted: 03/16/2024] [Indexed: 03/26/2024]
Abstract
The Bacillus cereus group contains genetically closed bacteria displaying a variety of phenotypic features and lifestyles. The group is mainly known through the properties of three major species: the entomopathogen Bacillus thuringiensis, the animal and human pathogen Bacillus anthracis and the foodborne opportunistic strains of B. cereus sensu stricto. Yet, the actual diversity of the group is far broader and includes multiple lifestyles. Another less-appreciated aspect of B. cereus members lies within their antimicrobial potential which deserves consideration in the context of growing emergence of resistance to antibiotics and pesticides, and makes it crucial to find new sources of antimicrobial molecules. This review presents the state of knowledge on the known antimicrobial compounds of the B. cereus group members, which are grouped according to their chemical features and biosynthetic pathways. The objective is to provide a comprehensive review of the antimicrobial range exhibited by this group of bacteria, underscoring the interest in its potent biocontrol arsenal and encouraging further research in this regard.
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Affiliation(s)
| | - Simon Caulier
- Laboratory of Plant Health, Earth and Life Institute, UCLouvain, Louvain-la-Neuve B-1348, Belgium
| | - Claude Bragard
- Laboratory of Plant Health, Earth and Life Institute, UCLouvain, Louvain-la-Neuve B-1348, Belgium
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2
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Montoya-Giraldo M, Piper KR, Ikhimiukor OO, Park CJ, Caimi NA, Buecher DC, Valdez EW, Northup DE, Andam CP. Ecology shapes the genomic and biosynthetic diversification of Streptomyces bacteria from insectivorous bats. Microb Genom 2024; 10. [PMID: 38625724 DOI: 10.1099/mgen.0.001238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024] Open
Abstract
Streptomyces are prolific producers of secondary metabolites from which many clinically useful compounds have been derived. They inhabit diverse habitats but have rarely been reported in vertebrates. Here, we aim to determine to what extent the ecological source (bat host species and cave sites) influence the genomic and biosynthetic diversity of Streptomyces bacteria. We analysed draft genomes of 132 Streptomyces isolates sampled from 11 species of insectivorous bats from six cave sites in Arizona and New Mexico, USA. We delineated 55 species based on the genome-wide average nucleotide identity and core genome phylogenetic tree. Streptomyces isolates that colonize the same bat species or inhabit the same site exhibit greater overall genomic similarity than they do with Streptomyces from other bat species or sites. However, when considering biosynthetic gene clusters (BGCs) alone, BGC distribution is not structured by the ecological or geographical source of the Streptomyces that carry them. Each genome carried between 19-65 BGCs (median=42.5) and varied even among members of the same Streptomyces species. Nine major classes of BGCs were detected in ten of the 11 bat species and in all sites: terpene, non-ribosomal peptide synthetase, polyketide synthase, siderophore, RiPP-like, butyrolactone, lanthipeptide, ectoine, melanin. Finally, Streptomyces genomes carry multiple hybrid BGCs consisting of signature domains from two to seven distinct BGC classes. Taken together, our results bring critical insights to understanding Streptomyces-bat ecology and BGC diversity that may contribute to bat health and in augmenting current efforts in natural product discovery, especially from underexplored or overlooked environments.
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Affiliation(s)
- Manuela Montoya-Giraldo
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Kathryn R Piper
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Odion O Ikhimiukor
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Cooper J Park
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Nicole A Caimi
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | | | - Ernest W Valdez
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Diana E Northup
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
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3
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Wang J, Ping Y, Liu W, He X, Du C. Improvement of lipopeptide production in Bacillus subtilis HNDF2-3 by overexpression of the sfp and comA genes. Prep Biochem Biotechnol 2024; 54:184-192. [PMID: 37158496 DOI: 10.1080/10826068.2023.2209890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Bacillus subtilis HNDF2-3 can produce a variety of lipopeptide antibiotics with lower production. To improve its lipopeptide production, three genetically engineered strains were constructed. The results of real-time PCR showed that the highest transcriptional levels of the sfp gene in F2-3sfp, F2-3comA and F2-3sfp-comA were 29.01, 6.65 and 17.50 times of the original strain, respectively, while the highest transcriptional levels of the comA gene in F2-3comA and F2-3sfp-comA were 10.44 and 4.13 times of the original strain, respectively. The results of ELISA showed that the malonyl-CoA transacylase activity of F2-3comA was the highest, reaching 18.53 IU/L at 24 h, the data was 32.74% higher than that of the original strain. The highest total lipopeptide production of F2-3sfp, F2-3comA and F2-3sfp-comA induced by IPTG at optimal concentration were 33.51, 46.05 and 38.96% higher than that of the original strain, respectively. The results of HPLC showed that iturin A production of F2-3sfp-comA was the highest, which was 63.16% higher than that of the original strain. This study laid the foundation for further construction of genetically engineered strains with high lipopeptide production.
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Affiliation(s)
- Jiawen Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Yuan Ping
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Wei Liu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Xin He
- Hebei Key Laboratory of Agroecological Safety, Hebei University of Environmental Engineering, Qinhuangdao, China
| | - Chunmei Du
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
- Hebei Key Laboratory of Agroecological Safety, Hebei University of Environmental Engineering, Qinhuangdao, China
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4
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Villalobos-Escobedo JM, Mercado-Esquivias MB, Adams C, Kauffman WB, Malmstrom RR, Deutschbauer AM, Glass NL. Genome-wide fitness profiling reveals molecular mechanisms that bacteria use to interact with Trichoderma atroviride exometabolites. PLoS Genet 2023; 19:e1010909. [PMID: 37651474 PMCID: PMC10516422 DOI: 10.1371/journal.pgen.1010909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 09/22/2023] [Accepted: 08/07/2023] [Indexed: 09/02/2023] Open
Abstract
Trichoderma spp. are ubiquitous rhizosphere fungi capable of producing several classes of secondary metabolites that can modify the dynamics of the plant-associated microbiome. However, the bacterial-fungal mechanisms that mediate these interactions have not been fully characterized. Here, a random barcode transposon-site sequencing (RB-TnSeq) approach was employed to identify bacterial genes important for fitness in the presence of Trichoderma atroviride exudates. We selected three rhizosphere bacteria with RB-TnSeq mutant libraries that can promote plant growth: the nitrogen fixers Klebsiella michiganensis M5aI and Herbaspirillum seropedicae SmR1, and Pseudomonas simiae WCS417. As a non-rhizosphere species, Pseudomonas putida KT2440 was also included. From the RB-TnSeq data, nitrogen-fixing bacteria competed mainly for iron and required the siderophore transport system TonB/ExbB for optimal fitness in the presence of T. atroviride exudates. In contrast, P. simiae and P. putida were highly dependent on mechanisms associated with membrane lipid modification that are required for resistance to cationic antimicrobial peptides (CAMPs). A mutant in the Hog1-MAP kinase (Δtmk3) gene of T. atroviride showed altered expression patterns of many nonribosomal peptide synthetase (NRPS) biosynthetic gene clusters with potential antibiotic activity. In contrast to exudates from wild-type T. atroviride, bacterial mutants containing lesions in genes associated with resistance to antibiotics did not show fitness defects when RB-TnSeq libraries were exposed to exudates from the Δtmk3 mutant. Unexpectedly, exudates from wild-type T. atroviride and the Δtmk3 mutant rescued purine auxotrophic mutants of H. seropedicae, K. michiganensis and P. simiae. Metabolomic analysis on exudates from wild-type T. atroviride and the Δtmk3 mutant showed that both strains excrete purines and complex metabolites; functional Tmk3 is required to produce some of these metabolites. This study highlights the complex interplay between Trichoderma-metabolites and soil bacteria, revealing both beneficial and antagonistic effects, and underscoring the intricate and multifaceted nature of this relationship.
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Affiliation(s)
- José Manuel Villalobos-Escobedo
- Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Maria Belen Mercado-Esquivias
- Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Catharine Adams
- Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - W. Berkeley Kauffman
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Rex R. Malmstrom
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Adam M. Deutschbauer
- Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - N. Louise Glass
- Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
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Zhgun AA. Fungal BGCs for Production of Secondary Metabolites: Main Types, Central Roles in Strain Improvement, and Regulation According to the Piano Principle. Int J Mol Sci 2023; 24:11184. [PMID: 37446362 PMCID: PMC10342363 DOI: 10.3390/ijms241311184] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Filamentous fungi are one of the most important producers of secondary metabolites. Some of them can have a toxic effect on the human body, leading to diseases. On the other hand, they are widely used as pharmaceutically significant drugs, such as antibiotics, statins, and immunosuppressants. A single fungus species in response to various signals can produce 100 or more secondary metabolites. Such signaling is possible due to the coordinated regulation of several dozen biosynthetic gene clusters (BGCs), which are mosaically localized in different regions of fungal chromosomes. Their regulation includes several levels, from pathway-specific regulators, whose genes are localized inside BGCs, to global regulators of the cell (taking into account changes in pH, carbon consumption, etc.) and global regulators of secondary metabolism (affecting epigenetic changes driven by velvet family proteins, LaeA, etc.). In addition, various low-molecular-weight substances can have a mediating effect on such regulatory processes. This review is devoted to a critical analysis of the available data on the "turning on" and "off" of the biosynthesis of secondary metabolites in response to signals in filamentous fungi. To describe the ongoing processes, the model of "piano regulation" is proposed, whereby pressing a certain key (signal) leads to the extraction of a certain sound from the "musical instrument of the fungus cell", which is expressed in the production of a specific secondary metabolite.
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Affiliation(s)
- Alexander A Zhgun
- Group of Fungal Genetic Engineering, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky Prosp. 33-2, 119071 Moscow, Russia
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6
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Puja H, Mislin GLA, Rigouin C. Engineering Siderophore Biosynthesis and Regulation Pathways to Increase Diversity and Availability. Biomolecules 2023; 13:959. [PMID: 37371539 DOI: 10.3390/biom13060959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/23/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Siderophores are small metal chelators synthesized by numerous organisms to access iron. These secondary metabolites are ubiquitously present on Earth, and because their production represents the main strategy to assimilate iron, they play an important role in both positive and negative interactions between organisms. In addition, siderophores are used in biotechnology for diverse applications in medicine, agriculture and the environment. The generation of non-natural siderophore analogs provides a new opportunity to create new-to-nature chelating biomolecules that can offer new properties to expand applications. This review summarizes the main strategies of combinatorial biosynthesis that have been used to generate siderophore analogs. We first provide a brief overview of siderophore biosynthesis, followed by a description of the strategies, namely, precursor-directed biosynthesis, the design of synthetic or heterologous pathways and enzyme engineering, used in siderophore biosynthetic pathways to create diversity. In addition, this review highlights the engineering strategies that have been used to improve the production of siderophores by cells to facilitate their downstream utilization.
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Affiliation(s)
- Hélène Puja
- CNRS-UMR7242, Biotechnologie et Signalisation Cellulaire, 300 Bld Sébastien Brant, 67412 Illkirch, France
- Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), Université de Strasbourg, 300 Bld Sébastien Brant, 67412 Illkirch, France
| | - Gaëtan L A Mislin
- CNRS-UMR7242, Biotechnologie et Signalisation Cellulaire, 300 Bld Sébastien Brant, 67412 Illkirch, France
- Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), Université de Strasbourg, 300 Bld Sébastien Brant, 67412 Illkirch, France
| | - Coraline Rigouin
- CNRS-UMR7242, Biotechnologie et Signalisation Cellulaire, 300 Bld Sébastien Brant, 67412 Illkirch, France
- Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), Université de Strasbourg, 300 Bld Sébastien Brant, 67412 Illkirch, France
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7
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Murphy A, Corney M, Monson RE, Matilla MA, Salmond GPC, Leeper FJ. Biosynthesis of Antifungal Solanimycin May Involve an Iterative Nonribosomal Peptide Synthetase Module. ACS Chem Biol 2023; 18:1148-1157. [PMID: 37068480 PMCID: PMC10204066 DOI: 10.1021/acschembio.2c00947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 04/05/2023] [Indexed: 04/19/2023]
Abstract
Dickeya solani, a plant-pathogenic bacterium, produces solanimycin, a potent hybrid polyketide/nonribosomal peptide (PKS/NRPS) anti-fungal compound. The biosynthetic gene cluster responsible for synthesis of this compound has been identified. Because of instability, the complete structure of the compound has not yet been elucidated, but LC-MS2 identified that the cluster produces two main compounds, solanimycin A and B, differing by a single hydroxyl group. The fragmentation pattern revealed that the central part of solanimycin A is a hexapeptide, Gly-Dha-Dha-Dha-Dha-Dha (where Dha is dehydroalanine). This is supported by isotopic labeling studies using labeled serine and glycine. The N-terminal group is a polyketide-derived C16 acyl group containing a conjugated hexaene, a hydroxyl, and an amino group. The additional hydroxyl group in solanimycin B is on the α-carbon of the glycine residue. The incorporation of five sequential Dha residues is unprecedented because there is only one NRPS module in the cluster that is predicted to activate and attach serine (which is subsequently dehydrated to Dha), meaning that this NRPS module must act iteratively. While a few other iterative NRPS modules are known, they all involve iteration of two or three modules. We believe that the repetitive use of a single module makes the solanimycin biosynthetic pathway unique among NRPSs so far reported.
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Affiliation(s)
- Annabel
C. Murphy
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Matthew Corney
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Rita E. Monson
- Department
of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K.
| | - Miguel A. Matilla
- Department
of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K.
| | - George P. C. Salmond
- Department
of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K.
| | - Finian J. Leeper
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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Yamaguchi S, Fujioka T, Yoshimi A, Kumagai T, Umemura M, Abe K, Machida M, Kawai K. Discovery of a gene cluster for the biosynthesis of novel cyclic peptide compound, KK-1, in Curvularia clavata. FRONTIERS IN FUNGAL BIOLOGY 2023; 3:1081179. [PMID: 37746209 PMCID: PMC10512319 DOI: 10.3389/ffunb.2022.1081179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/15/2022] [Indexed: 09/26/2023]
Abstract
KK-1, a cyclic depsipeptide with 10 residues produced by a filamentous fungus Curvularia clavata BAUA-2787, is a promising pesticide active compound with high activity against many plant pathogens, especially Botrytis cinerea. As a first step toward the future mass production of KK-1 through synthetic biological approaches, we aimed to identify the genes responsible for the KK-1 biosynthesis. To achieve this, we conducted whole genome sequencing and transcriptome analysis of C. clavata BAUA-2787 to predict the KK-1 biosynthetic gene cluster. We then generated the overexpression and deletion mutants for each cluster gene using our originally developed transformation system for this fungus, and analyzed the KK-1 production and the cluster gene expression levels to confirm their involvement in KK-1 biosynthesis. As a result of these, a region of approximately 71 kb was found, containing 10 open reading frames, which were co-induced during KK-1 production, as a biosynthetic gene cluster. These include kk1B, which encodes nonribosomal peptide synthetase with a domain structure that is consistent with the structural features of KK-1, and kk1F, which encodes a transcription factor. The overexpression of kk1F increased the expression of the entire cluster genes and, consequently, improved KK-1 production, whereas its deletion decreased the expression of the entire cluster genes and almost eliminated KK-1 production, demonstrating that the protein encoded by kk1F regulates the expressions of the other nine cluster genes cooperatively as the pathway-specific transcription factor. Furthermore, the deletion of each cluster gene caused a reduction in KK-1 productivity, indicating that each gene is involved in KK-1 production. The genes kk1A, kk1D, kk1H, and kk1I, which showed a significant decrease in KK-1 productivity due to deletion, were presumed to be directly involved in KK-1 structure formation, including the biosynthesis of the constituent residues. kk1C, kk1E, kk1G, and kk1J, which maintained a certain level of KK-1 productivity despite deletion, were possibly involved in promoting or assisting KK-1 production, such as extracellular transportation and the removal of aberrant units incorporated into the peptide chain.
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Affiliation(s)
- Shigenari Yamaguchi
- Biotechnology Laboratory, Life & Environment Research Center, Life Science Research Institute, Research & Development Division, Kumiai Chemical Industry Co., Ltd., Shizuoka, Japan
| | - Tomonori Fujioka
- Biotechnology Laboratory, Life & Environment Research Center, Life Science Research Institute, Research & Development Division, Kumiai Chemical Industry Co., Ltd., Shizuoka, Japan
| | - Akira Yoshimi
- ABE-Project, New Industry Creation Hatchery Center, Tohoku University, Sendai, Japan
- Laboratory of Terrestrial Microbial Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | - Maiko Umemura
- Bio-system Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Keietsu Abe
- ABE-Project, New Industry Creation Hatchery Center, Tohoku University, Sendai, Japan
- Laboratory of Applied Microbiology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Masayuki Machida
- Bio-system Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Graduate School of Engineering, Genome Biotechnology Laboratory, Kanazawa Institute of Technology, Ishikawa, Japan
| | - Kiyoshi Kawai
- Biotechnology Laboratory, Life & Environment Research Center, Life Science Research Institute, Research & Development Division, Kumiai Chemical Industry Co., Ltd., Shizuoka, Japan
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9
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Miyanaga A, Kudo F, Eguchi T. Recent advances in the structural analysis of adenylation domains in natural product biosynthesis. Curr Opin Chem Biol 2022; 71:102212. [PMID: 36116190 DOI: 10.1016/j.cbpa.2022.102212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 01/27/2023]
Abstract
Adenylation (A) domains catalyze the biosynthetic incorporation of acyl building blocks into nonribosomal peptides and related natural products by selectively transferring acyl substrates onto cognate carrier proteins (CP). The use of noncanonical acyl units, such as nonproteinogenic amino acids and keto acids, by A domains expands the structural diversity of natural products. Furthermore, interrupted A domains, which have embedded auxiliary domains, are able to modify the incorporated acyl units. Structural information on A domains is important for rational protein engineering to generate unnatural compounds. In this review, we summarize recent advances in the structural analysis of A domains. First, we discuss the mechanisms by which A domains recognize noncanonical acyl units. We then focus on the interactions of A domains with CP domains and embedded auxiliary domains.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, 152-8551, Japan.
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, 152-8551, Japan
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10
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Wang Y, Chen Y, Zhang J, Zhang C. Overexpression of llm1 Affects the Synthesis of Secondary Metabolites of Aspergillus cristatus. Microorganisms 2022; 10:microorganisms10091707. [PMID: 36144309 PMCID: PMC9502445 DOI: 10.3390/microorganisms10091707] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 12/04/2022] Open
Abstract
Putative methyltransferases are thought to be involved in the regulation of secondary metabolites in filamentous fungi. Here, we report the effects of overexpression of a predicted LaeA-like methyltransferase gene llm1 on the synthesis of secondary metabolites in Aspergillus cristatus. Our results revealed that overexpression of the gene llm1 in A. cristatus significantly hindered the production of conidia and enhanced sexual development, and reduced oxidative tolerance to hydrogen peroxide. Compared with the wild-type, the metabolic profile of the overexpression transformant was distinct, and the contents of multiple secondary metabolites were markedly increased, mainly including terpenoids and flavonoids, such as (S)-olEuropeic acid, gibberellin A62, gibberellin A95, ovalitenone, PD 98059, and 1-isomangostin. A total of 600 significantly differentially expressed genes (DEGs) were identified utilizing transcriptome sequencing, and the DEGs were predominantly enriched in transmembrane transport and secondary metabolism-related biological processes. In summary, the strategy of overexpressing global secondary metabolite regulators successfully activated the expression of secondary metabolite gene clusters, and the numerous secondary metabolites were greatly strengthened in A. cristatus. This study provides new insights into the in-depth exploitation and utilization of novel secondary metabolites of A. cristatus.
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11
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Cociancich S, Leclère V. Editorial for the Special Issue “Microbial Nonribosomal Synthesis of Secondary Metabolites”. Microorganisms 2022; 10:microorganisms10051064. [PMID: 35630506 PMCID: PMC9146935 DOI: 10.3390/microorganisms10051064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 12/04/2022] Open
Affiliation(s)
- Stéphane Cociancich
- CIRAD, UMR PHIM, F-34398 Montpellier, France
- PHIM, Université Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
- Correspondence:
| | - Valérie Leclère
- Université de Lille, Université de Liège, UMRT 1158 BioEcoAgro, Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, F-59000 Lille, France;
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