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Interconnected Set of Enzymes Provide Lysine Biosynthetic Intermediates and Ornithine Derivatives as Key Precursors for the Biosynthesis of Bioactive Secondary Metabolites. Antibiotics (Basel) 2023; 12:antibiotics12010159. [PMID: 36671360 PMCID: PMC9854754 DOI: 10.3390/antibiotics12010159] [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: 12/15/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Bacteria, filamentous fungi, and plants synthesize thousands of secondary metabolites with important biological and pharmacological activities. The biosynthesis of these metabolites is performed by networks of complex enzymes such as non-ribosomal peptide synthetases, polyketide synthases, and terpenoid biosynthetic enzymes. The efficient production of these metabolites is dependent upon the supply of precursors that arise from primary metabolism. In the last decades, an impressive array of biosynthetic enzymes that provide specific precursors and intermediates leading to secondary metabolites biosynthesis has been reported. Suitable knowledge of the elaborated pathways that synthesize these precursors or intermediates is essential for advancing chemical biology and the production of natural or semisynthetic biological products. Two of the more prolific routes that provide key precursors in the biosynthesis of antitumor, immunosuppressant, antifungal, or antibacterial compounds are the lysine and ornithine pathways, which are involved in the biosynthesis of β-lactams and other non-ribosomal peptides, and bacterial and fungal siderophores. Detailed analysis of the molecular genetics and biochemistry of the enzyme system shows that they are formed by closely related components. Particularly the focus of this study is on molecular genetics and the enzymatic steps that lead to the formation of intermediates of the lysine pathway, such as α-aminoadipic acid, saccharopine, pipecolic acid, and related compounds, and of ornithine-derived molecules, such as N5-Acetyl-N5-Hydroxyornithine and N5-anhydromevalonyl-N5-hydroxyornithine, which are precursors of siderophores. We provide evidence that shows interesting functional relationships between the genes encoding the enzymes that synthesize these products. This information will contribute to a better understanding of the possibilities of advancing the industrial applications of synthetic biology.
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Bacterial-Like Nonribosomal Peptide Synthetases Produce Cyclopeptides in the Zygomycetous Fungus Mortierella alpina. Appl Environ Microbiol 2021; 87:AEM.02051-20. [PMID: 33158886 DOI: 10.1128/aem.02051-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/30/2020] [Indexed: 12/20/2022] Open
Abstract
Fungi are traditionally considered a reservoir of biologically active natural products. However, an active secondary metabolism has long not been attributed to early-diverging fungi such as Mortierella Here, we report on the biosynthesis of two series of cyclic pentapeptides, the malpicyclins and malpibaldins, as products of Mortierella alpina ATCC 32222. The molecular structures of malpicyclins were elucidated by high-resolution tandem mass spectrometry (HR-MS/MS), Marfey's method, and one-dimensional (1D) and 2D nuclear magnetic resonance (NMR) spectroscopy. In addition, malpibaldin biosynthesis was confirmed by HR-MS. Genome mining and comparative quantitative real-time PCR (qRT-PCR) expression analysis pointed at two pentamodular nonribosomal peptide synthetases (NRPSs), malpicyclin synthetase MpcA and malpibaldin synthetase MpbA, as candidate biosynthetic enzymes. Heterologous production of the respective adenylation domains and substrate specificity assays proved promiscuous substrate selection and confirmed their respective biosynthetic roles. In stark contrast to known fungal NRPSs, MpbA and MpcA contain bacterial-like dual epimerase/condensation domains allowing the racemization of enzyme-tethered l-amino acids and the subsequent incorporation of d-amino acids into the metabolites. Phylogenetic analyses of both NRPS genes indicated a bacterial origin and a horizontal gene transfer into the fungal genome. We report on the as-yet-unexplored nonribosomal peptide biosynthesis in basal fungi which highlights this paraphylum as a novel and underrated resource of natural products.IMPORTANCE Fungal natural compounds are industrially produced, with application in antibiotic treatment, cancer medications, and crop plant protection. Traditionally, higher fungi have been intensively investigated concerning their metabolic potential, but reidentification of already known compounds is frequently observed. Hence, alternative strategies to acquire novel bioactive molecules are required. We present the genus Mortierella as representative of the early-diverging fungi as an underestimated resource of natural products. Mortierella alpina produces two families of cyclopeptides, designated malpicyclins and malpibaldins, respectively, via two pentamodular nonribosomal peptide synthetases (NRPSs). These enzymes are much more closely related to bacterial than to other fungal NRPSs, suggesting a bacterial origin of these NRPS genes in Mortierella Both enzymes were biochemically characterized and are involved in as-yet-unknown biosynthetic pathways of natural products in basal fungi. Hence, this report establishes early-diverging fungi as prolific natural compound producers and sheds light on the origin of their biosynthetic capacity.
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Indole-Induced Reversion of Intrinsic Multiantibiotic Resistance in Lysobacter enzymogenes. Appl Environ Microbiol 2017. [PMID: 28625984 DOI: 10.1128/aem.00995-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Lysobacter species are a group of environmental bacteria that are emerging as a new source of antibiotics. One characteristic of Lysobacter is intrinsic resistance to multiple antibiotics, which had not been studied. To understand the resistance mechanism, we tested the effect of blocking two-component regulatory systems (TCSs) on the antibiotic resistance of Lysobacter enzymogenes, a prolific producer of antibiotics. Upon treatment with LED209, an inhibitor of the widespread TCS QseC/QseB, L. enzymogenes produced a large amount of an unknown metabolite that was barely detectable in the untreated culture. Subsequent structural elucidation by nuclear magnetic resonance (NMR) unexpectedly revealed that the metabolite was indole. Indole production was also markedly induced by adrenaline, a known modulator of QseC/QseB. Next, we identified two TCS genes, L. enzymogenesqseC (Le-qseC) and Le-qseB, in L. enzymogenes and found that mutations of Le-qseC and Le-qseB also led to a dramatic increase in indole production. We then chemically synthesized a fluorescent indole probe that could label the cells. While the Le-qseB (cytoplasmic response regulator) mutant was clearly labeled by the probe, the Le-qseC (membrane sensor) mutant was not labeled. It was reported previously that indole can enhance antibiotic resistance in bacteria. Therefore, we tested if the dramatic increase in the level of indole production in L. enzymogenes upon blocking of Le-qseC and Le-qseB would lead to enhanced antibiotic resistance. Surprisingly, we found that indole caused the intrinsically multiantibiotic-resistant bacterium L. enzymogenes to become susceptible. Point mutations at conserved amino acids in Le-QseC also led to antibiotic susceptibility. Because indole is known as an interspecies signal, these findings may have implications.IMPORTANCE The environmental bacterium Lysobacter is a new source of antibiotic compounds and exhibits intrinsic antibiotic resistance. Here, we found that the inactivation of a two-component regulatory system (TCS) by an inhibitor or by gene deletion led to a remarkable increase in the level of production of a metabolite in L. enzymogenes, and this metabolite was identified to be indole. We chemically synthesized a fluorescent indole probe and found that it could label the wild type and a mutant of the TCS cytoplasmic response regulator but not a mutant of the TCS membrane sensor. Indole treatment caused the intrinsically multidrug-resistant bacterium L. enzymogenes to be susceptible to antibiotics. Mutations of the TCS sensor also led to antibiotic susceptibility. Because indole is known as an interspecies signal between gut microbiota and mammalian hosts, the observation that indole could render intrinsically resistant L. enzymogenes susceptible to common antibiotics may have implications.
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Zhang W, Huffman J, Li S, Shen Y, Du L. Unusual acylation of chloramphenicol in Lysobacter enzymogenes, a biocontrol agent with intrinsic resistance to multiple antibiotics. BMC Biotechnol 2017; 17:59. [PMID: 28676112 PMCID: PMC5496308 DOI: 10.1186/s12896-017-0377-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/20/2017] [Indexed: 02/07/2023] Open
Abstract
Background The environmental gliding bacteria Lysobacter are emerging as a new group of biocontrol agents due to their prolific production of lytic enzymes and potent antibiotic natural products. These bacteria are intrinsically resistant to many antibiotics, but the mechanisms behind the antibiotic resistance have not been investigated. Results Previously, we have used chloramphenicol acetyltransferase gene (cat) as a selection marker in genetic manipulation of natural product biosynthetic genes in Lysobacter, because chloramphenicol is one of the two common antibiotics that Lysobacter are susceptible to. Here, we found L. enzymogenes, the most studied species of this genus, could still grow in the presence of a low concentration of chloramphenicol. Three chloramphenicol derivatives (1–3) with an unusual acylation pattern were identified in a cat-containing mutant of L. enzymogenes and in the wild type. The compounds included chloramphenicol 3'-isobutyrate (1), a new compound chloramphenicol 1'-isobutyrate (2), and a rare chloramphenicol 3'-isovalerate (3). Furthermore, a mutation of a global regulator gene (clp) or a Gcn5-related N-acetyltransferase (GNAT) gene in L. enzymogenes led to nearly no growth in media containing chloramphenicol, whereas a complementation of clp restored the chloramphenicol acylation as well as antibiotic HSAF production in the clp mutant. Conclusions The results indicated that L. enzymogenes contains a pool of unusual acyl donors for enzymatic modification of chloramphenicol that confers the resistance, which may involve the Clp-GNAT regulatory system. Because Lysobacter are ubiquitous inhabitants of soil and water, the finding may have important implications in understanding microbial competitions and bioactive natural product regulation. Electronic supplementary material The online version of this article (doi:10.1186/s12896-017-0377-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuel, Chinese Academy of Sciences, Qingdao Institute of Bioenergy and Bioprocess Technology, 266101, Qingdao, China.,Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588-0304, USA
| | - Justin Huffman
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588-0304, USA
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuel, Chinese Academy of Sciences, Qingdao Institute of Bioenergy and Bioprocess Technology, 266101, Qingdao, China
| | - Yuemao Shen
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588-0304, USA. .,State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
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Odhiambo BO, Xu G, Qian G, Liu F. Evidence of an Unidentified Extracellular Heat-Stable Factor Produced by Lysobacter enzymogenes (OH11) that Degrade Fusarium graminearum PH1 Hyphae. Curr Microbiol 2017; 74:437-448. [PMID: 28213660 DOI: 10.1007/s00284-017-1206-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 01/25/2017] [Indexed: 11/26/2022]
Abstract
Lysobacter enzymogenes OH11 produces heat-stable antifungal factor (HSAF) and lytic enzymes possessing antifungal activity. This study bio-prospected for other potential antifungal factors besides those above. The cells and extracellular metabolites of L. enzymogenes OH11 and the mutants ΔchiA, ΔchiB, ΔchiC, Δclp, Δpks, and ΔpilA were examined for antifungal activity against Fusarium graminearum PH1, the causal agent of Fusarium head blight (FHB). Results evidenced that OH11 produces an unidentified extracellular heat-stable degrading metabolite (HSDM) that exhibit degrading activity on F. graminearum PH1 chitinous hyphae. Interestingly, both heat-treated and non-heat-treated extracellular metabolites of OH11 mutants exhibited hyphae-degrading activity against F. graminearum PH1. Enzyme activity detection of heat-treated metabolites ruled out the possibility of enzyme degradation activity. Remarkably, the PKS-NRPS-deficient mutant Δpks cannot produce HSAF or analogues, yet its metabolites exhibited hyphae-degrading activity. HPLC analysis confirmed no HSAF production by Δpks. Δclp lacks hyphae-degrading ability. Therefore, clp regulates HSDM and extracellular lytic enzymes production in L. enzymogenes OH11. ΔpilA had impaired surface cell motility and significantly reduced antagonistic properties. ΔchiA, ΔchiB, and ΔchiC retained hyphae-degrading ability, despite having reduced abilities to produce chitinase enzymes. Ultimately, L. enzymogenes OH11 can produce other unidentified HSDM independent of the PKS-NRPS genes. This suggests HSAF and lytic enzymes production are a fraction of the antifungal mechanisms in OH11. Characterization of HSDM, determination of its biosynthetic gene cluster and understanding its mode of action will provide new leads in the search for effective drugs for FHB management.
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Affiliation(s)
| | - Gaoge Xu
- College of Plant Protection Nanjing Agricultural University, Nanjing, 210095, China
| | - Guoliang Qian
- College of Plant Protection Nanjing Agricultural University, Nanjing, 210095, China
| | - Fengquan Liu
- College of Plant Protection Nanjing Agricultural University, Nanjing, 210095, China
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de Bruijn I, Cheng X, de Jager V, Expósito RG, Watrous J, Patel N, Postma J, Dorrestein PC, Kobayashi D, Raaijmakers JM. Comparative genomics and metabolic profiling of the genus Lysobacter. BMC Genomics 2015; 16:991. [PMID: 26597042 PMCID: PMC4657364 DOI: 10.1186/s12864-015-2191-z] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 11/03/2015] [Indexed: 11/10/2022] Open
Abstract
Background Lysobacter species are Gram-negative bacteria widely distributed in soil, plant and freshwater habitats. Lysobacter owes its name to the lytic effects on other microorganisms. To better understand their ecology and interactions with other (micro)organisms, five Lysobacter strains representing the four species L. enzymogenes, L. capsici, L. gummosus and L. antibioticus were subjected to genomics and metabolomics analyses. Results Comparative genomics revealed a diverse genome content among the Lysobacter species with a core genome of 2,891 and a pangenome of 10,028 coding sequences. Genes encoding type I, II, III, IV, V secretion systems and type IV pili were highly conserved in all five genomes, whereas type VI secretion systems were only found in L. enzymogenes and L. gummosus. Genes encoding components of the flagellar apparatus were absent in the two sequenced L. antibioticus strains. The genomes contained a large number of genes encoding extracellular enzymes including chitinases, glucanases and peptidases. Various nonribosomal peptide synthase (NRPS) and polyketide synthase (PKS) gene clusters encoding putative bioactive metabolites were identified but only few of these clusters were shared between the different species. Metabolic profiling by imaging mass spectrometry complemented, in part, the in silico genome analyses and allowed visualisation of the spatial distribution patterns of several secondary metabolites produced by or induced in Lysobacter species during interactions with the soil-borne fungus Rhizoctonia solani. Conclusions Our work shows that mining the genomes of Lysobacter species in combination with metabolic profiling provides novel insights into the genomic and metabolic potential of this widely distributed but understudied and versatile bacterial genus. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2191-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene de Bruijn
- Department of Microbial Ecology, Netherlands Institute of Ecology, P.O. Box 50, Wageningen, 6700 AB, The Netherlands. .,Wageningen University and Research Centre, Laboratory of Phytopathology, P.O. Box 8025, Wageningen, 6700 EE, The Netherlands.
| | - Xu Cheng
- Wageningen University and Research Centre, Laboratory of Phytopathology, P.O. Box 8025, Wageningen, 6700 EE, The Netherlands.
| | - Victor de Jager
- Department of Microbial Ecology, Netherlands Institute of Ecology, P.O. Box 50, Wageningen, 6700 AB, The Netherlands.
| | - Ruth Gómez Expósito
- Department of Microbial Ecology, Netherlands Institute of Ecology, P.O. Box 50, Wageningen, 6700 AB, The Netherlands. .,Wageningen University and Research Centre, Laboratory of Phytopathology, P.O. Box 8025, Wageningen, 6700 EE, The Netherlands.
| | - Jeramie Watrous
- Departments of Pharmacology, Chemistry and Biochemistry; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, San Diego, USA.
| | - Nrupali Patel
- Department of Plant Biology & Pathology, Cook College, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901-8520, USA.
| | - Joeke Postma
- Wageningen University and Research Centre, Plant Research International, PO Box 16, Wageningen, 6700 AA, The Netherlands.
| | - Pieter C Dorrestein
- Departments of Pharmacology, Chemistry and Biochemistry; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, San Diego, USA.
| | - Donald Kobayashi
- Department of Plant Biology & Pathology, Cook College, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901-8520, USA.
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, P.O. Box 50, Wageningen, 6700 AB, The Netherlands.
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Zhang J, Du L, Liu F, Xu F, Hu B, Venturi V, Qian G. Involvement of both PKS and NRPS in antibacterial activity in Lysobacter enzymogenes OH11. FEMS Microbiol Lett 2014; 355:170-6. [PMID: 24801439 DOI: 10.1111/1574-6968.12457] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 04/30/2014] [Accepted: 04/30/2014] [Indexed: 11/27/2022] Open
Abstract
Polyketides and nonribosomal peptides represent two large families of natural products (NPs) with diverse structures and important functions. They are synthesized by polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS), respectively. Lysobacter enzymogenes is emerging as a novel biocontrol agent against pathogens of crop plants and a new source of bioactive NPs, such as antibacterial antibiotic WAP-8294A2 and antifungal antibiotic HSAF. Genome survey of strain OH11, a Chinese L. enzymogenes isolate, detected four novel PKS, NRPS or hybrid gene clusters, designed as cluster A to D. We further individually mutated five genes (PKS or NRPS) located in these four gene clusters and showed that a PKS gene in cluster A and an NRPS gene in cluster D were involved in the antibacterial activity via a WAP-8294A2 dependent way. The data also showed that none of the five genes was associated with antifungal activity and the regulation of HSAF biosynthesis. Our results reveal the unusual regulatory role of these PKS and NRPS genes that were discovered from genome mining in L. enzymogenes.
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Affiliation(s)
- Juan Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Ministry of Education, Nanjing, China
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Wang Y, Qian G, Liu F, Li YZ, Shen Y, Du L. Facile method for site-specific gene integration in Lysobacter enzymogenes for yield improvement of the anti-MRSA antibiotics WAP-8294A and the antifungal antibiotic HSAF. ACS Synth Biol 2013; 2:670-8. [PMID: 23937053 DOI: 10.1021/sb4000806] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lysobacter is a genus of Gram-negative gliding bacteria that are emerged as novel biocontrol agents and new sources of bioactive natural products. The bacteria are naturally resistant to many antibiotics commonly used in transformant selection, which has hampered the genetic manipulations. Here, we described a facile method for quick-and-easy identification of the target transformants from a large population of the wild type and nontarget transformants. The method is based on a distinct yellow-to-black color change as a visual selection marker for site-specific integration of the gene of interest. Through transposon random mutagenesis, we identified a black-colored strain from the yellow-colored L. enzymogenes . The black strain was resulted from a disruption of hmgA, a gene required for tyrosine/phenylalanine metabolism. The disruption of hmgA led to accumulation of dark brown pigments. As proof of principle, we constructed a series of expression vectors for a regulator gene found within the WAP-8294A biosynthetic gene cluster. The yield of WAP-8294A in the black strains increased by 2 fold compared to the wild type. Interestingly, the yield of another antibiotic (HSAF) increased up to 7 fold in the black strains. WAP-8294A is a family of potent anti-MRSA antibiotics and is currently in clinical studies, and HSAF is an antifungal compound with distinct structural features and a novel mode of action. This work represents the first successful metabolic engineering in Lysobacter. The development of this facile method opens a way toward manipulating antibiotic production in the largely unexplored sources.
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Affiliation(s)
- Yan Wang
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Guoliang Qian
- Department
of Plant Pathology, Nanjing Agricultural University, Nanjing, China 210095
| | - Fengquan Liu
- Department
of Plant Pathology, Nanjing Agricultural University, Nanjing, China 210095
| | - Yue-Zhong Li
- State
Key Laboratory of Microbial Technology, College of Life Sciences, Shandong University, Jinan, China 250012
| | - Yuemao Shen
- State
Key Laboratory of Microbial Technology, College of Life Sciences, Shandong University, Jinan, China 250012
| | - Liangcheng Du
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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Wang Y, Qian G, Li Y, Wang Y, Wang Y, Wright S, Li Y, Shen Y, Liu F, Du L. Biosynthetic mechanism for sunscreens of the biocontrol agent Lysobacter enzymogenes. PLoS One 2013; 8:e66633. [PMID: 23826105 PMCID: PMC3691225 DOI: 10.1371/journal.pone.0066633] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 05/08/2013] [Indexed: 01/06/2023] Open
Abstract
Lysobacter are ubiquitous environmental bacteria emerging as novel biocontrol agents and new sources of anti-infectives. So far, very little effort has been invested in the study of the biology of these Gram-negative gliding bacteria. Many Lysobacter species are characterized by their yellow-orange appearance. Using transposon mutagenesis, we identified a stand-alone polyketide synthase (PKS) gene cluster required for the pigment production in L. enzymogenes OH11. The yellow pigments were abolished in the "white" mutants generated by target-specific deletions of ketosynthase (KS), acyl carrier protein, or ketoreductase. Spectroscopic data suggested that the pigments belong to xanthomonadin-like aryl polyenes. Polyene-type polyketides are known to be biosynthesized by modular PKS (Type I), not by stand-alone PKS (Type II) which always contain the heterodimer KS-CLF (chain-length factor) as the key catalytic component. Remarkably, this aryl polyene PKS complex only contains the KS (ORF17), but not the CLF. Instead, a hypothetical protein (ORF16) is located immediately next to ORF17. ORF16-17 homologs are widespread in numerous uncharacterized microbial genomes, in which an ORF17 homolog is always accompanied by an ORF16 homolog. The deletion of ORF16 eliminated pigment production, and homology modeling suggested that ORF16 shares a structural similarity to the N-terminal half of CLF. A point-mutation of glutamine (Q166A) that is the conserved active site of known CLF abolished pigment production. The "white" mutants are significantly more sensitive to UV/visible light radiation or H2O2 treatment than the wild type. These results unveil the first example of Type II PKS-synthesized polyene pigments and show that the metabolites serve as Lysobacter "sunscreens" that are important for the survival of these ubiquitous environmental organisms.
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Affiliation(s)
- Yan Wang
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- State Key Laboratory of Microbial Technology, College of Life Sciences, Shandong University, Jinan, China
| | - Guoliang Qian
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Yaoyao Li
- State Key Laboratory of Microbial Technology, College of Life Sciences, Shandong University, Jinan, China
| | - Yansheng Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Yulan Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Stephen Wright
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Yuezhong Li
- State Key Laboratory of Microbial Technology, College of Life Sciences, Shandong University, Jinan, China
| | - Yuemao Shen
- State Key Laboratory of Microbial Technology, College of Life Sciences, Shandong University, Jinan, China
| | - Fengquan Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
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Recent advances in the biosynthesis of penicillins, cephalosporins and clavams and its regulation. Biotechnol Adv 2013; 31:287-311. [DOI: 10.1016/j.biotechadv.2012.12.001] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 11/30/2012] [Accepted: 12/01/2012] [Indexed: 11/23/2022]
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Abstract
The gliding Gram-negative Lysobacter bacteria are emerging as a promising source of new bioactive natural products. These ubiquitous freshwater and soil microorganisms are fast growing, simple to use and maintain, and genetically amenable for biosynthetic engineering. This Highlight reviews a group of biologically active and structurally distinct natural products from the genus Lysobacter, with a focus on their biosyntheses. Although Lysobacter sp. are known as prolific producers of bioactive natural products, detailed molecular mechanistic studies of their enzymatic assembly have been surprisingly scarce. We hope to provide a snapshot of the important work done on the lysobacterial natural products and to provide useful information for future biosynthetic engineering of novel antibiotics in Lysobacter.
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Affiliation(s)
- Yunxuan Xie
- Department of Chemistry, University of Nebraska-Lincoln, NE 68588, USA
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Hamed RB, Gomez-Castellanos JR, Henry L, Ducho C, McDonough MA, Schofield CJ. The enzymes of β-lactam biosynthesis. Nat Prod Rep 2013; 30:21-107. [DOI: 10.1039/c2np20065a] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Identification and characterization of the anti-methicillin-resistant Staphylococcus aureus WAP-8294A2 biosynthetic gene cluster from Lysobacter enzymogenes OH11. Antimicrob Agents Chemother 2011; 55:5581-9. [PMID: 21930890 DOI: 10.1128/aac.05370-11] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lysobactor enzymogenes strain OH11 is an emerging biological control agent of fungal and bacterial diseases. We recently completed its genome sequence and found it contains a large number of gene clusters putatively responsible for the biosynthesis of nonribosomal peptides and polyketides, including the previously identified antifungal dihydromaltophilin (HSAF). One of the gene clusters contains two huge open reading frames, together encoding 12 modules of nonribosomal peptide synthetases (NRPS). Gene disruption of one of the NRPS led to the disappearance of a metabolite produced in the wild type and the elimination of its antibacterial activity. The metabolite and antibacterial activity were also affected by the disruption of some of the flanking genes. We subsequently isolated this metabolite and subjected it to spectroscopic analysis. The mass spectrometry and nuclear magnetic resonance data showed that its chemical structure is identical to WAP-8294A2, a cyclic lipodepsipeptide with potent anti-methicillin-resistant Staphylococcus aureus (MRSA) activity and currently in phase I/II clinical trials. The WAP-8294A2 biosynthetic genes had not been described previously. So far, the Gram-positive Streptomyces have been the primary source of anti-infectives. Lysobacter are Gram-negative soil/water bacteria that are genetically amendable and have not been well exploited. The WAP-8294A2 synthetase represents one of the largest NRPS complexes, consisting of 45 functional domains. The identification of these genes sets the foundation for the study of the WAP-8294A2 biosynthetic mechanism and opens the door for producing new anti-MRSA antibiotics through biosynthetic engineering in this new source of Lysobacter.
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Demirev AV, Lee CH, Jaishy BP, Nam DH, Ryu DDY. Substrate specificity of nonribosomal peptide synthetase modules responsible for the biosynthesis of the oligopeptide moiety of cephabacin in Lysobacter lactamgenus. FEMS Microbiol Lett 2006; 255:121-8. [PMID: 16436071 DOI: 10.1111/j.1574-6968.2005.00067.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Lysobacter lactamgenus produces cephabacins, a class of beta-lactam antibiotics which have an oligopeptide moiety attached to the cephem ring at the C-3 position. The nonribosomal peptide synthetase (NRPS) system, which comprises four distinct modules, is required for the biosynthesis of this short oligopeptide, when one takes the chemical structure of these antibiotics into consideration. The cpbI gene, which has been identified in a region upstream of the pcbAB gene, encodes the NRPS - polyketide synthase hybrid complex, where NRPS is composed of three modules, while the cpbK gene -- which has been reported as being upstream of cpbI-- comprises a single NRPS module. An in silico protein analysis was able to partially reveal the specificity of each module. The four recombinant adenylation (A) domains from each NRPS module were heterologously expressed in Escherichia coli and purified. Biochemical data from ATP-PPi exchange assays indicated that L-arginine was an effective substrate for the A1 domain, while the A2, A3 and A4 domains activated L-alanine. These findings are in an agreement with the known chemical structure of cephabacins, as well as with the anticipated substrate specificity of the NRPS modules in CpbI and CpbK, which are involved in the assembly of the tetrapeptide at the C-3 position.
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Guillemette T, Sellam A, Simoneau P. Analysis of a nonribosomal peptide synthetase gene from Alternaria brassicae and flanking genomic sequences. Curr Genet 2004; 45:214-24. [PMID: 14727058 DOI: 10.1007/s00294-003-0479-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2003] [Revised: 11/21/2003] [Accepted: 11/26/2003] [Indexed: 10/26/2022]
Abstract
Very little information is currently available concerning the pathogenic determinants produced by Alternaria brassicae, the causal agent of the blackspot disease of crucifers. We screened a genomic library of this fungus and identified a nonribosomal peptide synthetase (NRPS) gene named AbrePsy1. The complete coding sequence is 22 kbp long and encodes a large protein (792 kDa) showing typical NRPS modular organization. Structural analysis of AbrePsy1 revealed four complete elongation modules, two of which have epimerization domains. In the vicinity of AbrePsy1, a second gene (named AbreAtr1), which encodes an ATP-binding cassette transporter was identified. Increased expression of AbrePsy1 and AbreAtr1 was observed during host-plant infection. However, while physically linked, these two genes are probably not functionally clustered, as their expression patterns differed.
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Affiliation(s)
- Thomas Guillemette
- Faculté des Sciences, UMR PAVE 77, 2 Bd Lavoisier, 49045, Angers, France
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