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Huang X, Sun Y, Liu S, Li Y, Li C, Sun Y, Ding X, Xia L, Hu Y, Hu S. Recombineering using RecET-like recombinases from Xenorhabdus and its application in mining of natural products. Appl Microbiol Biotechnol 2022; 106:7857-7866. [DOI: 10.1007/s00253-022-12258-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/14/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
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Wang Y, Zhang F, Wang C, Guo P, Han Y, Zhang Y, Sun B, Shan S, Ruan W, Pan J. Antifungal Substances Produced by Xenorhabdus bovienii and Its Inhibition Mechanism against Fusarium solani. Int J Mol Sci 2022; 23:ijms23169040. [PMID: 36012310 PMCID: PMC9409070 DOI: 10.3390/ijms23169040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/03/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
Fungal colonization can severely damage artifacts. Nematode endosymbiotic bacteria exhibit good prospects in protecting artifacts from fungal damage. We previously found that supernatant from the fermentation of nematode endosymbiotic bacterium, Xenorhabdus bovienii, is effective in inhibiting the growth of Fusarium solani NK-NH1, the major disease fungus in the Nanhai No.1 Shipwreck. Further experiments proved that X. bovienii produces volatile organic compounds (VOCs) that inhibit NK-NH1. Here, using metabolomic analysis, GC–MS, and transcriptomic analysis, we explored the antifungal substances and VOCs produced by X. bovienii and investigated the mechanism underlying its inhibitory effect against NK-NH1. We show that X. bovienii produces several metabolites, mainly lipids and lipid-like molecules, organic acids and derivatives, and organoheterocyclic compounds. The VOCs produced by X. bovienii showed two specific absorption peaks, and based on the library ratio results, these were predicted to be of 2-pentanone, 3-(phenylmethylene) and 1-hexen-3-one, 5-methyl-1-phenyl. The inhibition of F. solani by VOCs resulted in upregulation of genes related to ribosome, ribosome biogenesis, and the oxidative phosphorylation and downregulation of many genes associated with cell cycle, meiosis, DNA replication, and autophagy. These results are significant for understanding the inhibitory mechanisms employed by nematode endosymbiotic bacteria and should serve as reference in the protection of artifacts.
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Affiliation(s)
- Yu Wang
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Fengyu Zhang
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Cen Wang
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Peifeng Guo
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yeqing Han
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yingting Zhang
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Bingjiao Sun
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shaojie Shan
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Weibin Ruan
- College of Life Sciences, Nankai University, Tianjin 300071, China
- Correspondence: (W.R.); (J.P.); Tel.: +86-139-2093-5913 (W.R.); +86-138-2006-8355 (J.P.)
| | - Jiao Pan
- College of Life Sciences, Nankai University, Tianjin 300071, China
- Institute for Cultural Heritage and History of Science & Technology, University of Science and Technology Beijing, Beijing 100083, China
- Correspondence: (W.R.); (J.P.); Tel.: +86-139-2093-5913 (W.R.); +86-138-2006-8355 (J.P.)
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Abstract
With the overmining of actinomycetes for compounds acting against Gram-negative pathogens, recent efforts to discover novel antibiotics have been focused on other groups of bacteria. Teixobactin, the first antibiotic without detectable resistance that binds lipid II, comes from an uncultured Eleftheria terra, a betaproteobacterium; odilorhabdins, from Xenorhabdus, are broad-spectrum inhibitors of protein synthesis, and darobactins from Photorhabdus target BamA, the essential chaperone of the outer membrane of Gram-negative bacteria. Xenorhabdus and Photorhabdus are symbionts of the nematode gut microbiome and attractive producers of secondary metabolites. Only small portions of their biosynthetic gene clusters (BGC) are expressed in vitro. To access their silent operons, we first separated extracts from a small library of isolates into fractions, resulting in 200-fold concentrated material, and then screened them for antimicrobial activity. This resulted in a hit with selective activity against Escherichia coli, which we identified as a novel natural product antibiotic, 3′-amino 3′-deoxyguanosine (ADG). Mutants resistant to ADG mapped to gsk and gmk, kinases of guanosine. Biochemical analysis shows that ADG is a prodrug that is converted into an active ADG triphosphate (ADG-TP), a mimic of GTP. ADG incorporates into a growing RNA chain, interrupting transcription, and inhibits cell division, apparently by interfering with the GTPase activity of FtsZ. Gsk of the purine salvage pathway, which is the first kinase in the sequential phosphorylation of ADG, is restricted to E. coli and closely related species, explaining the selectivity of the compound. There are probably numerous targets of ADG-TP among GTP-dependent proteins. The discovery of ADG expands our knowledge of prodrugs, which are rare among natural compounds.
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Lulamba TE, Green E, Serepa-Dlamini MH. Genome assembly and annotation of Photorhabdus heterorhabditis strain ETL reveals genetic features involved in pathogenicity with its associated entomopathogenic nematode and anti-host effectors with biocontrol potential applications. Gene 2021; 795:145780. [PMID: 34147570 DOI: 10.1016/j.gene.2021.145780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/24/2021] [Accepted: 06/14/2021] [Indexed: 11/28/2022]
Abstract
The genome sequences of entomopathogenic nematode (EPN) bacteria and their functional analyses can lead to the genetic engineering of the bacteria for use as biocontrol agents. The bacterial symbiont Photorhabdus heterorhabditis strain ETL isolated from an insect pathogenic nematode, Heterorhabditis zealandica strain ETL, collected in the northernmost region of South Africa was studied to reveal information that can be useful in the design of improvement strategies for both effective and liquid production method of EPN-based pesticides. The strain ETL genome was found closely related to the type strain genome of P. australis DSM 17,609 (~60 to 99.9% CDSs similarity), but closely related to the not yet genome-sequenced type strain, P. heterorhabditis. It has a genome size of 4,866,148 bp and G + C content of 42.4% similar to other Photorhabdus. It contains 4,351 protein coding genes (CDSs) of which, at least 84% are shared with the de facto type strain P. luminescens subsp. laumondii TTO1, and has 318 unknown CDSs and the genome has a higher degree of plasticity allowing it to adapt to different environmental conditions, and to be virulent against various insects; observed through genes acquired through horizontal gene transfer mechanisms, clustered regularly interspaced short palindromic repeats, non-determined polyketide- and non-ribosomal peptide- synthase gene clusters, and many genes associated with uncharacterized proteins; which also justify the strain ETL's genes differences (quantity and quality) compared to P. luminescens subsp. laumondii TTO1. The protein coding sequences contained genes with both bio-engineering and EPNs mass production importance, of which numerous are uncharacterized.
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Affiliation(s)
- Tshikala Eddie Lulamba
- Department of Biotechnology and Food Technology, University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa
| | - Ezekiel Green
- Department of Biotechnology and Food Technology, University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa
| | - Mahloro Hope Serepa-Dlamini
- Department of Biotechnology and Food Technology, University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa.
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Dong Y, Li X, Duan J, Qin Y, Yang X, Ren J, Li G. Improving the Yield of Xenocoumacin 1 Enabled by In Situ Product Removal. ACS OMEGA 2020; 5:20391-20398. [PMID: 32832792 PMCID: PMC7439382 DOI: 10.1021/acsomega.0c02357] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Xenocoumacin 1 (Xcn1), a major antimicrobial compound produced by Xenorhabdus nematophila CB6, has great potential to be developed into a novel biofungicide. However, its low yield in the producing cells has limited its possible commercial applications. In this study, we explored the effect of in situ product removal (ISPR), a well-established recovery technique, with the use of macroporous resin X-5 on the production of Xcn1 in a fermentation setting. Relative to the routine fermentation process, the yield of Xcn1 was improved from 42.5 to 73.8 μg/mL (1.7-fold) and 12.9 to 60.3 μg/mL (4.7-fold) in three and ten days, respectively. By agar diffusion plate and growth inhibition assays, the antibiotic activity against Bacillus subtilis and Alternaria solani was also found to be improved. Further study revealed that protection of Xcn1 against degradation and decrease in cell self-toxicity as well as upregulation of biosynthesis-related genes of Xcn1 at the transcription level contributed to yield improvement of Xcn1. In addition, resin X-5 significantly altered the metabolite profile of X. nematophila CB6, which could promote the discovery of new antibiotics.
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Affiliation(s)
- Yijie Dong
- State
Key Laboratory for Biology of Plant Diseases and Insect Pests/Key
Laboratory of Control of Biological Hazard Factors (Plant Origin)
for Agri-product Quality and Safety, Ministry of Agriculture, Institute
of Plant Protection, Chinese Academy of
Agricultural Sciences, Beijing 100081, People’s Republic
of China
- Guangdong
Provincial Key Laboratory of Microbial Culture Collection and Application,
State Key Laboratory of Applied Microbiology Southern China, Guangdong
Institute of Microbiology, Guangdong Academy
of Sciences, Guangzhou 510070, People’s Republic of China
| | - Xiaohui Li
- State
Key Laboratory for Biology of Plant Diseases and Insect Pests/Key
Laboratory of Control of Biological Hazard Factors (Plant Origin)
for Agri-product Quality and Safety, Ministry of Agriculture, Institute
of Plant Protection, Chinese Academy of
Agricultural Sciences, Beijing 100081, People’s Republic
of China
| | - Jiaqi Duan
- State
Key Laboratory for Biology of Plant Diseases and Insect Pests/Key
Laboratory of Control of Biological Hazard Factors (Plant Origin)
for Agri-product Quality and Safety, Ministry of Agriculture, Institute
of Plant Protection, Chinese Academy of
Agricultural Sciences, Beijing 100081, People’s Republic
of China
| | - Youcai Qin
- State
Key Laboratory for Biology of Plant Diseases and Insect Pests/Key
Laboratory of Control of Biological Hazard Factors (Plant Origin)
for Agri-product Quality and Safety, Ministry of Agriculture, Institute
of Plant Protection, Chinese Academy of
Agricultural Sciences, Beijing 100081, People’s Republic
of China
| | - Xiufen Yang
- State
Key Laboratory for Biology of Plant Diseases and Insect Pests/Key
Laboratory of Control of Biological Hazard Factors (Plant Origin)
for Agri-product Quality and Safety, Ministry of Agriculture, Institute
of Plant Protection, Chinese Academy of
Agricultural Sciences, Beijing 100081, People’s Republic
of China
| | - Jie Ren
- State
Key Laboratory for Biology of Plant Diseases and Insect Pests/Key
Laboratory of Control of Biological Hazard Factors (Plant Origin)
for Agri-product Quality and Safety, Ministry of Agriculture, Institute
of Plant Protection, Chinese Academy of
Agricultural Sciences, Beijing 100081, People’s Republic
of China
| | - Guangyue Li
- State
Key Laboratory for Biology of Plant Diseases and Insect Pests/Key
Laboratory of Control of Biological Hazard Factors (Plant Origin)
for Agri-product Quality and Safety, Ministry of Agriculture, Institute
of Plant Protection, Chinese Academy of
Agricultural Sciences, Beijing 100081, People’s Republic
of China
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Vlisidou I, Hapeshi A, Healey JR, Smart K, Yang G, Waterfield NR. The Photorhabdus asymbiotica virulence cassettes deliver protein effectors directly into target eukaryotic cells. eLife 2019; 8:46259. [PMID: 31526474 PMCID: PMC6748792 DOI: 10.7554/elife.46259] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/12/2019] [Indexed: 01/19/2023] Open
Abstract
Photorhabdus is a highly effective insect pathogen and symbiont of insecticidal nematodes. To exert its potent insecticidal effects, it elaborates a myriad of toxins and small molecule effectors. Among these, the Photorhabdus Virulence Cassettes (PVCs) represent an elegant self-contained delivery mechanism for diverse protein toxins. Importantly, these self-contained nanosyringes overcome host cell membrane barriers, and act independently, at a distance from the bacteria itself. In this study, we demonstrate that Pnf, a PVC needle complex associated toxin, is a Rho-GTPase, which acts via deamidation and transglutamination to disrupt the cytoskeleton. TEM and Western blots have shown a physical association between Pnf and its cognate PVC delivery mechanism. We demonstrate that for Pnf to exert its effect, translocation across the cell membrane is absolutely essential.
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Affiliation(s)
- Isabella Vlisidou
- All Wales Genetics Laboratory, Institute of Medical Genetics, University Hospital of Wales, Cardiff, United Kingdom
| | - Alexia Hapeshi
- Warwick Medical School, Warwick University, Coventry, United Kingdom
| | - Joseph Rj Healey
- Warwick Medical School, Warwick University, Coventry, United Kingdom
| | - Katie Smart
- Warwick Medical School, Warwick University, Coventry, United Kingdom
| | - Guowei Yang
- Beijing Friendship Hospital, Capital Medical University, Beijing, China
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Wolff H, Bode HB. The benzodiazepine-like natural product tilivalline is produced by the entomopathogenic bacterium Xenorhabdus eapokensis. PLoS One 2018; 13:e0194297. [PMID: 29596433 PMCID: PMC5875774 DOI: 10.1371/journal.pone.0194297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/28/2018] [Indexed: 01/05/2023] Open
Abstract
The pyrrolobenzodiazepine tilivalline (1) was originally identified in the human gut pathobiont Klebsiella oxytoca, the causative agent of antibiotic-associated hemorrhagic colitis. Here we show the identification of tilivalline and analogs thereof in the entomopathogenic bacterium Xenorhabdus eapokensis as well as the identification of its biosynthesis gene cluster encoding a bimodular non-ribosomal peptide synthetase. Heterologous expression of both genes in E. coli resulted in the production of 1 and from mutasynthesis and precursor directed biosynthesis 11 new tilivalline analogs were identified in X. eapokensis. These results allowed the prediction of the tilivalline biosynthesis being similar to that in K. oxytoca.
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Affiliation(s)
- Hendrik Wolff
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B. Bode
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Frankfurt am Main, Germany
- * E-mail:
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