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Long Q, Zhou W, Zhou H, Tang Y, Chen W, Liu Q, Bian X. Polyamine-containing natural products: structure, bioactivity, and biosynthesis. Nat Prod Rep 2024; 41:525-564. [PMID: 37873660 DOI: 10.1039/d2np00087c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Covering: 2005 to August, 2023Polyamine-containing natural products (NPs) have been isolated from a wide range of terrestrial and marine organisms and most of them exhibit remarkable and diverse activities, including antimicrobial, antiprotozoal, antiangiogenic, antitumor, antiviral, iron-chelating, anti-depressive, anti-inflammatory, insecticidal, antiobesity, and antioxidant properties. Their extraordinary activities and potential applications in human health and agriculture attract increasing numbers of studies on polyamine-containing NPs. In this review, we summarized the source, structure, classification, bioactivities and biosynthesis of polyamine-containing NPs, focusing on the biosynthetic mechanism of polyamine itself and representative polyamine alkaloids, polyamine-containing siderophores with catechol/hydroxamate/hydroxycarboxylate groups, nonribosomal peptide-(polyketide)-polyamine (NRP-(PK)-PA), and NRP-PK-long chain poly-fatty amine (lcPFAN) hybrid molecules.
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Affiliation(s)
- Qingshan Long
- Hunan Provincial Engineering and Technology Research Center for Agricultural Microbiology Application, Hunan Institute of Microbiology, Changsha, 410009, China.
| | - Wen Zhou
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural, Affairs, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Ying Tang
- Hunan Provincial Engineering and Technology Research Center for Agricultural Microbiology Application, Hunan Institute of Microbiology, Changsha, 410009, China.
| | - Wu Chen
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China.
| | - Qingshu Liu
- Hunan Provincial Engineering and Technology Research Center for Agricultural Microbiology Application, Hunan Institute of Microbiology, Changsha, 410009, China.
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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Liang Z, Huang L, Liu H, Zheng Y, Feng J, Shi Z, Chen Y, Lv M, Zhou J, Zhang L, Chen S. Characterization of the Arn lipopolysaccharide modification system essential for zeamine resistance unveils its new roles in Dickeya oryzae physiology and virulence. MOLECULAR PLANT PATHOLOGY 2023; 24:1480-1494. [PMID: 37740253 PMCID: PMC10632790 DOI: 10.1111/mpp.13386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/14/2023] [Accepted: 08/22/2023] [Indexed: 09/24/2023]
Abstract
The zeamines produced by Dickeya oryzae are potent polyamine antibiotics and phytotoxins that are essential for bacterial virulence. We recently showed that the RND efflux pump DesABC in D. oryzae confers partial resistance to zeamines. To fully elucidate the bacterial self-protection mechanisms, in this study we used transposon mutagenesis to identify the genes encoding proteins involved in zeamine resistance in D. oryzae EC1. This led to the identification of a seven-gene operon, arnEC1 , that encodes enzyme homologues associated with lipopolysaccharide modification. Deletion of the arnEC1 genes in strain EC1 compromised its zeamine resistance 8- to 16-fold. Further deletion of the des gene in the arnEC1 mutant background reduced zeamine resistance to a level similar to that of the zeamine-sensitive Escherichia coli DH5α. Intriguingly, the arnEC1 mutants showed varied bacterial virulence on rice, potato, and Chinese cabbage. Further analyses demonstrated that ArnBCATEC1 are involved in maintenance of the bacterial nonmucoid morphotype by repressing the expression of capsular polysaccharide genes and that ArnBEC1 is a bacterial virulence determinant, influencing transcriptional expression of over 650 genes and playing a key role in modulating bacterial motility and virulence. Taken together, these findings decipher a novel zeamine resistance mechanism in D. oryzae and document new roles of the Arn enzymes in modulation of bacterial physiology and virulence.
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Affiliation(s)
- Zhibin Liang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Luhao Huang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Huidi Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Ying Zheng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Jiani Feng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Zurong Shi
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- School of Biological EngineeringHuainan Normal UniversityHuainanChina
| | - Yufan Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Research Center of Chinese Herbal Resource Science and EngineeringGuangzhou University of Chinese MedicineGuangzhouChina
| | - Mingfa Lv
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Lian‐Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Shaohua Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
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Liang Z, Lin Q, Wang Q, Huang L, Liu H, Shi Z, Cui Z, Zhou X, Gao YG, Zhou J, Zhang LH, Deng Y. Gram-negative bacteria resist antimicrobial agents by a DzrR-mediated envelope stress response. BMC Biol 2023; 21:62. [PMID: 36978084 PMCID: PMC10052836 DOI: 10.1186/s12915-023-01565-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Envelope stress responses (ESRs) are critical for adaptive resistance of Gram-negative bacteria to envelope-targeting antimicrobial agents. However, ESRs are poorly defined in a large number of well-known plant and human pathogens. Dickeya oryzae can withstand a high level of self-produced envelope-targeting antimicrobial agents zeamines through a zeamine-stimulated RND efflux pump DesABC. Here, we unraveled the mechanism of D. oryzae response to zeamines and determined the distribution and function of this novel ESR in a variety of important plant and human pathogens. RESULTS In this study, we documented that a two-component system regulator DzrR of D. oryzae EC1 mediates ESR in the presence of envelope-targeting antimicrobial agents. DzrR was found modulating bacterial response and resistance to zeamines through inducing the expression of RND efflux pump DesABC, which is likely independent on DzrR phosphorylation. In addition, DzrR could also mediate bacterial responses to structurally divergent envelope-targeting antimicrobial agents, including chlorhexidine and chlorpromazine. Significantly, the DzrR-mediated response was independent on the five canonical ESRs. We further presented evidence that the DzrR-mediated response is conserved in the bacterial species of Dickeya, Ralstonia, and Burkholderia, showing that a distantly located DzrR homolog is the previously undetermined regulator of RND-8 efflux pump for chlorhexidine resistance in B. cenocepacia. CONCLUSIONS Taken together, the findings from this study depict a new widely distributed Gram-negative ESR mechanism and present a valid target and useful clues to combat antimicrobial resistance.
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Affiliation(s)
- Zhibin Liang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Qiqi Lin
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Qingwei Wang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Luhao Huang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Huidi Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Zurong Shi
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
- School of Biological Engineering, HuaiNan Normal University, Huainan, 232038, China
| | - Zining Cui
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 639798, Singapore
| | - Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Lian-Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
| | - Yizhen Deng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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Lv M, Ye S, Hu M, Xue Y, Liang Z, Zhou X, Zhang L, Zhou J. Two-component system ArcBA modulates cell motility and biofilm formation in Dickeya oryzae. FRONTIERS IN PLANT SCIENCE 2022; 13:1033192. [PMID: 36340374 PMCID: PMC9634086 DOI: 10.3389/fpls.2022.1033192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Phytopathogen Dickeya oryzae is a causal agent of rice foot rot disease and the pathogen has an array of virulence factors, such as phytotoxin zeamines, plant cell wall degrading enzymes, cell motility, and biofilms, collectively contributing to the bacterial pathogenesis. In this study, through deletion analysis of predicted regulatory genes in D. oryzae EC1, we identified a two-component system associated with the regulation of bacterial virulence. The two-component system contains a histidine kinase ArcB and a response regulator ArcA, and deletion of their coding genes resulted in changed phenotypes in cell motility, biofilm formation, and bacterial virulence. Electrophoretic mobility shift assay revealed that ArcA bound to the promoters of the bcs operon and bssS, which respectively encode enzymes for the synthesis of celluloses and a biofilm formation regulatory protein. ArcA could also bind to the promoters of three virulence associated transcriptional regulatory genes, i.e., fis, slyA and ohrR. Surprisingly, although these three regulators were shown to modulate the production of cell wall degrading enzymes and zeamines, deletion of arcB and arcA did not seem to affect these phenotypes. Taken together, the findings from this study unveiled a new two-component system associated with the bacterial pathogenesis, which contributes to the virulence of D. oryzae mainly through its action on bacterial motility and biofilm formation.
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Affiliation(s)
- Mingfa Lv
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Sixuan Ye
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Ming Hu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Yang Xue
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Zhibin Liang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - Lianhui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
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Shi Z, Wang Q, Wang S, Wang C, Zhang LH, Liang Z. Hfq Is a Critical Modulator of Pathogenicity of Dickeya oryzae in Rice Seeds and Potato Tubers. Microorganisms 2022; 10:microorganisms10051031. [PMID: 35630473 PMCID: PMC9144144 DOI: 10.3390/microorganisms10051031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 02/05/2023] Open
Abstract
The frequent outbreaks of soft-rot diseases caused by Dickeya oryzae have emerged as severe problems in plant production in recent years and urgently require the elucidation of the virulence mechanisms of D. oryzae. Here, we report that Hfq, a conserved RNA chaperone protein in bacteria, is involved in modulating a series of virulence-related traits and bacterial virulence in D. oryzae EC1. The findings show that the null mutation of the hfqEC1 gene totally abolished the production of zeamine phytotoxins and protease, significantly attenuated the production of two other types of cell wall degrading enzymes, i.e., pectate lyase and cellulase, as well as attenuating swarming motility, biofilm formation, the development of hypersensitive response to Nicotiana benthamiana, and bacterial infections in rice seeds and potato tubers. QRT-PCR analysis and promoter reporter assay further indicated that HfqEC1 regulates zeamine production via modulating the expression of the key zeamine biosynthesis (zms) cluster genes. Taken together, these findings highlight that the Hfq of D. oryzae is one of the key regulators in modulating the production of virulence determinants and bacterial virulence in rice seeds and potato tubers.
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Affiliation(s)
- Zurong Shi
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; (Z.S.); (Q.W.)
- School of Biological Engineering, Huainan Normal University, Huainan 232038, China; (S.W.); (C.W.)
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Qingwei Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; (Z.S.); (Q.W.)
| | - Shunchang Wang
- School of Biological Engineering, Huainan Normal University, Huainan 232038, China; (S.W.); (C.W.)
| | - Chengrun Wang
- School of Biological Engineering, Huainan Normal University, Huainan 232038, China; (S.W.); (C.W.)
| | - Lian-Hui Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; (Z.S.); (Q.W.)
- Correspondence: (L.-H.Z.); (Z.L.)
| | - Zhibin Liang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; (Z.S.); (Q.W.)
- Correspondence: (L.-H.Z.); (Z.L.)
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6
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León-Buitimea A, Balderas-Cisneros FDJ, Garza-Cárdenas CR, Garza-Cervantes JA, Morones-Ramírez JR. Synthetic Biology Tools for Engineering Microbial Cells to Fight Superbugs. Front Bioeng Biotechnol 2022; 10:869206. [PMID: 35600895 PMCID: PMC9114757 DOI: 10.3389/fbioe.2022.869206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/18/2022] [Indexed: 11/23/2022] Open
Abstract
With the increase in clinical cases of bacterial infections with multiple antibiotic resistance, the world has entered a health crisis. Overuse, inappropriate prescribing, and lack of innovation of antibiotics have contributed to the surge of microorganisms that can overcome traditional antimicrobial treatments. In 2017, the World Health Organization published a list of pathogenic bacteria, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli (ESKAPE). These bacteria can adapt to multiple antibiotics and transfer their resistance to other organisms; therefore, studies to find new therapeutic strategies are needed. One of these strategies is synthetic biology geared toward developing new antimicrobial therapies. Synthetic biology is founded on a solid and well-established theoretical framework that provides tools for conceptualizing, designing, and constructing synthetic biological systems. Recent developments in synthetic biology provide tools for engineering synthetic control systems in microbial cells. Applying protein engineering, DNA synthesis, and in silico design allows building metabolic pathways and biological circuits to control cellular behavior. Thus, synthetic biology advances have permitted the construction of communication systems between microorganisms where exogenous molecules can control specific population behaviors, induce intracellular signaling, and establish co-dependent networks of microorganisms.
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Affiliation(s)
- Angel León-Buitimea
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - Francisco de Jesús Balderas-Cisneros
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - César Rodolfo Garza-Cárdenas
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - Javier Alberto Garza-Cervantes
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - José Rubén Morones-Ramírez
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
- *Correspondence: José Rubén Morones-Ramírez,
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Chen Y, Li Y, Zhu M, Lv M, Liu Z, Chen Z, Huang Y, Gu W, Liang Z, Chang C, Zhou J, Zhang LH, Liu Q. The GacA-GacS Type Two-Component System Modulates the Pathogenicity of Dickeya oryzae EC1 Mainly by Regulating the Production of Zeamines. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:369-379. [PMID: 35100009 DOI: 10.1094/mpmi-11-21-0292-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The GacS-GacA type two-component system (TCS) positively regulates pathogenicity-related phenotypes in many plant pathogens. In addition, Dickeya oryzae EC1, the causative agent of soft rot disease, produces antibiotic-like toxins called zeamines as one of the major virulence factors that inhibit the germination of rice seeds. The present study identified a GacS-GacA type TCS, named TzpS-TzpA, that positively controls the virulence of EC1, mainly by regulating production of the toxin zeamines. RNA-seq analysis of strain EC1 and its tzpA mutant showed that the TCS regulated a wide range of virulence genes, especially those encoding zeamines. Protein-protein interaction was detected between TzpS and TzpA through the bacterial two-hybrid system and pull-down assay. In trans expression of tzpA failed to rescue the defective phenotypes in both the ΔtzpS and ΔtzpSΔtzpA mutants. Furthermore, TzpA controls target gene expression by direct binding to DNA promoters that contain a Gac-box motif, including a regulatory RNA rsmB and the vfm quorum-sensing system regulator vfmE. These findings therefore suggested that the EC1 TzpS-TzpA TCS system mediates the pathogenicity of Dickeya oryzae EC1 mainly by regulating the production of zeamines.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Yufan Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Yanchang Li
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Minya Zhu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Mingfa Lv
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Zhiqing Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Zhongqiao Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Ying Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Weihan Gu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Zhibin Liang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Changqing Chang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Jianuan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Lian-Hui Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Qiongguang Liu
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
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8
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Zhang J, Arif M, Shen H, Sun D, Pu X, Hu J, Lin B, Yang Q. Genomic Comparisons and Phenotypic Diversity of Dickeya zeae Strains Causing Bacterial Soft Rot of Banana in China. FRONTIERS IN PLANT SCIENCE 2022; 13:822829. [PMID: 35222482 PMCID: PMC8864124 DOI: 10.3389/fpls.2022.822829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Bacterial soft rot of banana, caused by Dickeya zeae, is spreading rapidly in important banana growing areas in China and seriously threatens banana production. In this study, we sequenced the high-quality complete genomes of three typical banana strains, MS1 (size: 4,831,702-bp; genome coverages: 538x), MS_2014 (size: 4,740,000-bp; genome coverages: 586x) and MS_2018 (size: 4,787,201-bp; genome coverages: 583x), isolated in 2009, 2014, and 2018, respectively. To determine their genomic and phenotypic diversity with respect to their hosts of origin, they were compared with other D. zeae strains, including another representative banana strain MS2 from China. The sequenced strains were similar in utilization of carbon source and chemical substrates, and general genomic features of GC content, and tRNA and rRNA regions. They were also conserved in most virulence determinants, including gene-encoding secretion systems, plant cell wall degrading enzymes, and exopolysaccharides. We further explored their genomic diversity in the predicted genomic islands (GIs). These GIs were rich in integrases and transposases, where some genomic dissimilarity was observed in the flagellar gene cluster and several secondary metabolite gene clusters. Different constituents of core biosynthetic modules were found within the bacteriocin and aryl polyene (APE) pigment gene clusters, and the strains from banana showed different phenotypes with respect to antibiosis effects and colony pigmentation. Additionally, clustered regularly interspaced short palindromic repeat (CRISPR) and prophage elements, such as type I-F and III-A CRISPR arrays and an intact prophage of MS1-P5, contributed to bacterial diversity. Phylogenetic tree analysis and genome-genome nucleotide comparison confirmed the genomic divergence among the strains isolated from banana. Considering these characteristics, MS2 and MS_2014 probably diverged later than MS1, while MS_2018 was different and more similar to foreign strains isolated from other hosts in several characteristics. Strain MS_2018 caused severe symptoms on banana varieties previously considered moderately resistant or moderately susceptible, including varieties of Cavendish (Musa AAA) and Plantain (Musa ABB). Our study of genomic and phenotypic diversity raises public attention to the risk of spreading new pathogenic variants within banana growing regions and supports development of predictive strategies for disease control.
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Affiliation(s)
- Jingxin Zhang
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Huifang Shen
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Dayuan Sun
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoming Pu
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - John Hu
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Birun Lin
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qiyun Yang
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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9
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Abebew D, Sayedain FS, Bode E, Bode HB. Uncovering Nematicidal Natural Products from Xenorhabdus Bacteria. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:498-506. [PMID: 34981939 PMCID: PMC8778618 DOI: 10.1021/acs.jafc.1c05454] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Parasitic nematodes infect different species of animals and plants. Root-knot nematodes are members of the genus Meloidogyne, which is distributed worldwide and parasitizes numerous plants, including vegetables, fruits, and crops. To reduce the global burden of nematode infections, only a few chemical therapeutic classes are currently available. The majority of nematicides are prohibited due to their harmful effects on the environment and public health. This study was intended to identify new nematicidal natural products (NPs) from the bacterial genus Xenorhabdus, which exists in symbiosis with Steinernema nematodes. Cell-free culture supernatants of Xenorhabdus bacteria were used for nematicidal bioassay, and high mortality rates for Caenorhabditis elegans and Meloidogyne javanica were observed. Promoter exchange mutants of biosynthetic gene clusters encoding nonribosomal peptide synthetases (NRPS) or NRPS-polyketide synthase hybrids in Xenorhabdus bacteria carrying additionally a hfq deletion produce a single NP class, which have been tested for their bioactivity. Among the NPs tested, fabclavines, rhabdopeptides, and xenocoumacins were highly toxic to nematodes and resulted in mortalities of 95.3, 74.6, and 72.6% to C. elegans and 82.0, 90.0, and 85.3% to M. javanica, respectively. The findings of such nematicidal NPs can provide templates for uncovering effective and environmentally safe alternatives to commercially available nematicides.
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Affiliation(s)
- Desalegne Abebew
- Molekulare
Biotechnologie, Goethe Universität
Frankfurt, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - Fatemeh S. Sayedain
- Department
of Natural Products in Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Edna Bode
- Department
of Natural Products in Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Helge B. Bode
- Molekulare
Biotechnologie, Goethe Universität
Frankfurt, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Department
of Natural Products in Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg 35043, Germany
- Senckenberg
Gesellschaft für Naturforschung, Frankfurt am Main 60325, Germany
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10
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Lv M, Chen Y, Hu M, Yu Q, Duan C, Ye S, Ling J, Zhou J, Zhou X, Zhang L. OhrR is a central transcriptional regulator of virulence in Dickeya zeae. MOLECULAR PLANT PATHOLOGY 2022; 23:45-59. [PMID: 34693617 PMCID: PMC8659590 DOI: 10.1111/mpp.13141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/20/2021] [Accepted: 09/01/2021] [Indexed: 06/12/2023]
Abstract
Dickeya zeae is the causal agent of rice foot rot disease. The pathogen is known to rely on a range of virulence factors, including phytotoxin zeamines, extracellular enzymes, cell motility, and biofilm, which collectively contribute to the establishment of infections. Phytotoxin zeamines play a critical role in bacterial virulence; signalling pathways and regulatory mechanisms that govern bacterial virulence remain unclear. In this study, we identified a transcriptional regulator OhrR (organic hydroperoxide reductase regulator) that is involved in the regulation of zeamine production in D. zeae EC1. The OhrR null mutant was significantly attenuated in its virulence against rice seed, potato tubers and radish roots. Phenotype analysis showed that OhrR was also involved in the regulation of other virulence traits, including the production of extracellular cellulase, biofilm formation, and swimming/swarming motility. DNA electrophoretic mobility shift assay showed that OhrR directly regulates the transcription of key virulence genes and genes encoding bis-(3'-5')-cyclic dimeric guanosine monophosphate synthetases. Furthermore, OhrR positively regulates the transcription of regulatory genes slyA and fis through binding to their promoter regions. Our findings identify a key regulator of the virulence of D. zeae and add new insights into the complex regulatory network that modulates the physiology and virulence of D. zeae.
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Affiliation(s)
- Mingfa Lv
- Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Yufan Chen
- Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Ming Hu
- Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Qinglin Yu
- Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Cheng Duan
- Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Sixuan Ye
- Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jinfeng Ling
- Guangdong Provincial Key Laboratory of High Technology for Plant ProtectionResearch Institute of Plant ProtectionGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Jianuan Zhou
- Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Xiaofan Zhou
- Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lianhui Zhang
- Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
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11
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Zhang W, Fan X, Li J, Ye T, Mishra S, Zhang L, Chen S. Exploration of the Quorum-Quenching Mechanism in Pseudomonas nitroreducens W-7 and Its Potential to Attenuate the Virulence of Dickeya zeae EC1. Front Microbiol 2021; 12:694161. [PMID: 34413838 PMCID: PMC8369503 DOI: 10.3389/fmicb.2021.694161] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022] Open
Abstract
Quorum quenching (QQ) is a novel, promising strategy that opens up a new perspective for controlling quorum-sensing (QS)-mediated bacterial pathogens. QQ is performed by interfering with population-sensing systems, such as by the inhibition of signal synthesis, catalysis of degrading enzymes, and modification of signals. In many Gram-negative pathogenic bacteria, a class of chemically conserved signaling molecules named N-acyl homoserine lactones (AHLs) have been widely studied. AHLs are involved in the modulation of virulence factors in various bacterial pathogens including Dickeya zeae. Dickeya zeae is the causal agent of plant-rot disease of bananas, rice, maize, potatoes, etc., causing enormous economic losses of crops. In this study, a highly efficient AHL-degrading bacterial strain W-7 was isolated from activated-sludge samples and identified as Pseudomonas nitroreducens. Strain W-7 revealed a superior ability to degrade N-(3-oxododecanoyl)-l-homoserine lactone (OdDHL) and completely degraded 0.2 mmol/L of OdDHL within 48 h. Gas chromatography-mass spectrometry (GC-MS) identified N-cyclohexyl-propanamide as the main intermediate metabolite during AHL biodegradation. A metabolic pathway for AHL in strain W-7 was proposed based on the chemical structure of AHL and intermediate products. In addition to the degradation of OdDHL, this strain was also found to be capable of degrading a wide range of AHLs including N-(3-oxohexanoyl)-l-homoserine lactone (OHHL), N-(3-oxooctanoyl)-l-homoserine lactone (OOHL), and N-hexanoyl-l-homoserine lactone (HHL). Moreover, the application of strain W-7 as a biocontrol agent could substantially attenuate the soft rot caused by D. zeae EC1 to suppress tissue maceration in various host plants. Similarly, the application of crude enzymes of strain W-7 significantly reduced the disease incidence and severity in host plants. These original findings unveil the biochemical aspects of a highly efficient AHL-degrading bacterial isolate and provide useful agents that exhibit great potential for the control of infectious diseases caused by AHL-dependent bacterial pathogens.
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Affiliation(s)
- Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xinghui Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jiayi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Tian Ye
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Lianhui Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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12
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Wenski SL, Berghaus N, Keller N, Bode HB. Structure and biosynthesis of deoxy-polyamine in Xenorhabdus bovienii. J Ind Microbiol Biotechnol 2021; 48:6119917. [PMID: 33693901 PMCID: PMC9113149 DOI: 10.1093/jimb/kuab006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022]
Abstract
Polyamine moieties have been described as part of the fabclavine and zeamine family of natural products. While the corresponding biosynthetic gene clusters have been found in many different proteobacteria, a unique BGC was identified in the entomopathogenic bacterium Xenorhabdus bovienii. Mass spectrometric analysis of a X. bovienii mutant strain revealed a new deoxy-polyamine. The corresponding biosynthesis includes two additional reductive steps, initiated by an additional dehydratase (DH) domain, which was not found in any other Xenorhabdus strain. Moreover, this DH domain could be successfully integrated into homologous biosynthesis pathways, leading to the formation of other deoxy-polyamines. Additional heterologous production experiments revealed that the DH domain could act in cis as well as in trans.
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Affiliation(s)
- Sebastian L Wenski
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, 60438 Frankfurt, Germany
| | - Natalie Berghaus
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, 60438 Frankfurt, Germany
| | - Nadine Keller
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, 60438 Frankfurt, Germany
| | - Helge B Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, 60438 Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, 60438 Frankfurt, Germany
- Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt, Germany
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
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13
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Genomic divergence between Dickeya zeae strain EC2 isolated from rice and previously identified strains, suggests a different rice foot rot strain. PLoS One 2020; 15:e0240908. [PMID: 33079956 PMCID: PMC7575072 DOI: 10.1371/journal.pone.0240908] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 10/06/2020] [Indexed: 11/19/2022] Open
Abstract
Rice foot rot caused by Dickeya zeae is an important bacterial disease of rice worldwide. In this study, we identified a new strain EC2 from rice in Guangdong province, China. This strain differed from the previously identified strain from rice in its biochemical characteristics, pathogenicity, and genomic constituents. To explore genomic discrepancies between EC2 and previously identified strains from rice, a complete genome sequence of EC2 was obtained and used for comparative genomic analyses. The complete genome sequence of EC2 is 4,575,125 bp in length. EC2 was phylogenetically closest to previously identified Dickeya strains from rice, but not within their subgroup. In terms of secretion systems, genomic comparisons revealed that EC2 harbored only type I (T1SS), typeⅡ (T2SS), and type VI (T6SS) secretion systems. The flagella cluster of this strain possessed specific genomic characteristics like other D. zeae strains from Guangdong and from rice; within this locus, the genetic diversity among strains from rice was much lower than that of within strains from non-rice hosts. Unlike other strains from rice, EC2 lost the zeamine cluster, but retained the clustered regularly interspaced short palindromic repeats-1 (CRISPR-1) array. Compared to the other D. zeae strains containing both exopolysaccharide (EPS) and capsular polysaccharide (CPS) clusters, EC2 harbored only the CPS cluster, while the other strains from rice carried only the EPS cluster. Furthermore, we found strain MS1 from banana, carrying both EPS and CPS clusters, produced significantly more EPS than the strains from rice, and exhibited different biofilm-associated phenotypes. Comparative genomics analyses suggest EC2 likely evolved through a pathway different from the other D. zeae strains from rice, producing a new type of rice foot rot pathogen. These findings emphasize the emergence of a new type of D. zeae strain causing rice foot rot, an essential step in the early prevention of this rice bacterial disease.
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14
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Shi Z, Wang Q, Li Y, Liang Z, Xu L, Zhou J, Cui Z, Zhang LH. Putrescine Is an Intraspecies and Interkingdom Cell-Cell Communication Signal Modulating the Virulence of Dickeya zeae. Front Microbiol 2019; 10:1950. [PMID: 31497009 PMCID: PMC6712546 DOI: 10.3389/fmicb.2019.01950] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 08/08/2019] [Indexed: 11/13/2022] Open
Abstract
The infections caused by Dickeya zeae become a severe problem in recent years, but the regulatory mechanisms that govern the bacterial virulence remain to be fragmental. Here we report the investigation of potential involvement of polyamines in regulation of D. zeae virulence. We showed that null mutation of speA encoding arginine decarboxylase dramatically decreased the bacterial swimming motility, swarming motility and biofilm formation, and exogenous addition of putrescine effectively rescues the defective phenotypes of D. zeae. HPLC and mass spectrometry analysis validated that speA was essential for production of putrescine in D. zeae. In addition, we demonstrated that D. zeae EC1 could detect and response to putrescine molecules produced by itself or from host plant through specific transporters. Among the two transporters identified, the one represented by PotF played a dominated role over the other represented by PlaP in modulation of putrescine-dependent biological functions. Furthermore, we provided evidence that putrescine signal is critical for D. zeae EC1 bacterial invasion and virulence against rice seeds. Our data depict a novel function of putrescine signal in pathogen-host communication and in modulation of the virulence of an important plant bacterial pathogen.
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Affiliation(s)
- Zurong Shi
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,College of Agriculture and Biology, Zhongkai University of Agricluture and Engineering, Guangzhou, China
| | - Qingwei Wang
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Yasheng Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Zhibing Liang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Linghui Xu
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Zining Cui
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Lian-Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
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15
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Shi YM, Bode HB. Chemical language and warfare of bacterial natural products in bacteria-nematode-insect interactions. Nat Prod Rep 2019; 35:309-335. [PMID: 29359226 DOI: 10.1039/c7np00054e] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: up to November 2017 Organismic interaction is one of the fundamental principles for survival in any ecosystem. Today, numerous examples show the interaction between microorganisms like bacteria and higher eukaryotes that can be anything between mutualistic to parasitic/pathogenic symbioses. There is also increasing evidence that microorganisms are used by higher eukaryotes not only for the supply of essential factors like vitamins but also as biological weapons to protect themselves or to kill other organisms. Excellent examples for such systems are entomopathogenic nematodes of the genera Heterorhabditis and Steinernema that live in mutualistic symbiosis with bacteria of the genera Photorhabdus and Xenorhabdus, respectively. Although these systems have been used successfully in organic farming on an industrial scale, it was only shown during the last 15 years that several different natural products (NPs) produced by the bacteria play key roles in the complex life cycle of the bacterial symbionts, the nematode host and the insect prey that is killed by and provides nutrients for the nematode-bacteria pair. Since the bacteria can switch from mutualistic to pathogenic lifestyle, interacting with two different types of higher eukaryotes, and since the full system with all players can be established in the lab, they are promising model systems to elucidate the natural function of microbial NPs. This review summarizes the current knowledge as well as open questions for NPs from Photorhabdus and Xenorhabdus and tries to assign their roles in the tritrophic relationship.
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Affiliation(s)
- Yi-Ming Shi
- Merck-Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main 60438, Germany
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16
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Abstract
Zeamines are a family of newly identified phytotoxins and potent antibiotics produced by D. zeae EC1. Unlike most bacterial organisms, which are highly sensitive, D. zeae EC1 is tolerant to zeamines, but the mechanisms involved are unknown. Our study showed, for the first time, that a new RND efflux pump, DesABC, is indispensable for D. zeae EC1 against zeamines. We found that the DesABC efflux pump was zeamine specific and appeared to be conserved only in the Dickeya species, which may explain the high potency of zeamines against a wide range of bacterial pathogens. We also showed that expression of DesABC efflux system genes was induced by zeamines. These findings not only provide an answer to why D. zeae EC1 is much more tolerant to zeamines than other bacterial pathogens but also document a signaling role of zeamines in modulation of gene expression. Zeamines are a family of polyamino phytotoxins produced by Dickeya zeae EC1. These phytotoxins are also potent antibiotics against a range of microorganisms. To understand how D. zeae EC1 can protect itself from the antimicrobial activity of zeamines, we tested whether the ABC transporter genes within the zms (zeamine synthesis) gene cluster were related to zeamine resistance. Our results ruled out the possible involvement of these ABC transporters in zeamine resistance and instead unveiled an RND (resistance-nodulation-cell division) efflux pump, DesABC, which plays an important role in zeamine resistance in D. zeae EC1. The desAB genes are located next to the zms gene cluster, but desC is at a distant location in the bacterial genome. Null mutation of the desABC genes in a zeamine-minus derivative of strain EC1 led to about an 8- to 32-fold decrease in zeamine tolerance level. This efflux pump was zeamine specific and appeared to be conserved only in Dickeya species, which may explain the high potency of zeamines against a wide range of bacterial pathogens. Significantly, expression of the desAB genes was abolished by deletion of zmsA, which encodes zeamine biosynthesis but could be induced by exogenous addition of zeamines. The results suggest that sophisticated and coordinated regulatory mechanisms have evolved to govern zeamine production and tolerance. Taken together, these findings documented a novel signaling role of zeamines and the first resistance mechanism against zeamines, which is a family of potent and promising antibiotics against both Gram-positive and Gram-negative bacterial pathogens.
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17
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Lv M, Hu M, Li P, Jiang Z, Zhang LH, Zhou J. A two-component regulatory system VfmIH modulates multiple virulence traits in Dickeya zeae. Mol Microbiol 2019; 111:1493-1509. [PMID: 30825339 DOI: 10.1111/mmi.14233] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2019] [Indexed: 12/27/2022]
Abstract
Bacterial pathogen Dickeya zeae strain EC1 produces antibiotics-like phytotoxins called zeamines, which are major virulence determinants encoded by the zms gene cluster. In this study, we identified a zeamine-deficient mutant with a Tn5 insertion in a gene designated as vfmI encoding a two-component system (TCS) sensor histidine kinase (HK), which is accompanied by vfmH encoding a response regulator (RR) at the same genetic locus. Domain analysis shows this TCS is analogous to the VfmIH of D. dadantii, with typical characteristics of sensor HK and RR, respectively, and sharing the same operon. Deletion of either vfmI or vfmH resulted in decreased production of zeamines and cell wall degrading enzymes (CWDEs), and alleviated virulence on rice seeds and potato tubers. In D. dadantii 3937, VfmH was shown to bind to the promoters of vfmA and vfmE, while in D. zeae EC1, VfmH could bind to the promoters of vfmA, vfmE and vfmF. RNA-seq analysis of strain EC1 and its vfmH mutant also showed that the TCS positively regulated a range of virulence genes, including zms, T1SS, T2SS, T3SS, T6SS, flagellar and CWDE genes.
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Affiliation(s)
- Mingfa Lv
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Ming Hu
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Peng Li
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Zide Jiang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Lian-Hui Zhang
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Jianuan Zhou
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
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18
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Chen X, Yu C, Li S, Li X, Liu Q. Integration Host Factor Is Essential for Biofilm Formation, Extracellular Enzyme, Zeamine Production, and Virulence in Dickeya zeae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:325-335. [PMID: 30226395 DOI: 10.1094/mpmi-04-18-0096-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Dickeya zeae is a globally important pathogenic bacterium that infects many crops, including rice, maize, potato, and banana. Bacterial foot rot of rice caused by D. zeae is one of the most important bacterial diseases of rice in China and some Southeast Asian countries. To investigate the functions of integration host factor (IHF) in D. zeae, we generated knockout mutants of ihfA and ihfB. Phenotypic assays showed that both the ΔihfA and ΔihfB strains had greatly reduced mobility, biofilm formation, extracellular protease, and pectinase activities, and toxin production compared with the wild-type strain. In addition, the mutants did not inhibit the germination of rice seeds, failed to cause soft rot in potatoes and a hypersensitive response in tobacco, and were avirulent in rice. Quantitative reverse-transcription polymerase chain reaction analysis demonstrated that IHF positively regulates the expression of zmsA, hrpN/Y, pelA/B/C, pehX, celZ, prtG, fliC, and DGC (diguanylate cyclase). Electrophoretic mobility shift assays further confirmed that IhfA binds to the promoter region of the DGC gene and may alter the levels of a second bacterial messenger, c-di-GMP, to regulate the pathogenicity or other physiological functions of D. zeae. In summary, IHF is an important integrated regulator of pathogenicity in D. zeae.
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Affiliation(s)
- Xuefeng Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Chengpeng Yu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Shuangchun Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xinwei Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Qiongguang Liu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
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19
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Baldeweg F, Hoffmeister D, Nett M. A genomics perspective on natural product biosynthesis in plant pathogenic bacteria. Nat Prod Rep 2019; 36:307-325. [DOI: 10.1039/c8np00025e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This review summarizes findings from genomics-inspired natural product research in plant pathogenic bacteria and discusses emerging trends in this field.
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Affiliation(s)
- Florian Baldeweg
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute
- Friedrich-Schiller-University Jena
- 07745 Jena
- Germany
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute
- Friedrich-Schiller-University Jena
- 07745 Jena
- Germany
| | - Markus Nett
- Department of Biochemical and Chemical Engineering
- TU Dortmund University
- 44227 Dortmund
- Germany
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20
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Mullowney MW, McClure RA, Robey MT, Kelleher NL, Thomson RJ. Natural products from thioester reductase containing biosynthetic pathways. Nat Prod Rep 2018; 35:847-878. [PMID: 29916519 PMCID: PMC6146020 DOI: 10.1039/c8np00013a] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Covering: up to 2018 Thioester reductase domains catalyze two- and four-electron reductions to release natural products following assembly on nonribosomal peptide synthetases, polyketide synthases, and their hybrid biosynthetic complexes. This reductive off-loading of a natural product yields an aldehyde or alcohol, can initiate the formation of a macrocyclic imine, and contributes to important intermediates in a variety of biosyntheses, including those for polyketide alkaloids and pyrrolobenzodiazepines. Compounds that arise from reductase-terminated biosynthetic gene clusters are often reactive and exhibit biological activity. Biomedically important examples include the cancer therapeutic Yondelis (ecteinascidin 743), peptide aldehydes that inspired the first therapeutic proteasome inhibitor bortezomib, and numerous synthetic derivatives and antibody drug conjugates of the pyrrolobenzodiazepines. Recent advances in microbial genomics, metabolomics, bioinformatics, and reactivity-based labeling have facilitated the detection of these compounds for targeted isolation. Herein, we summarize known natural products arising from this important category, highlighting their occurrence in Nature, biosyntheses, biological activities, and the technologies used for their detection and identification. Additionally, we review publicly available genomic data to highlight the remaining potential for novel reductively tailored compounds and drug leads from microorganisms. This thorough retrospective highlights various molecular families with especially privileged bioactivity while illuminating challenges and prospects toward accelerating the discovery of new, high value natural products.
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Affiliation(s)
- Michael W Mullowney
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - Ryan A McClure
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - Matthew T Robey
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA. and Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Regan J Thomson
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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Fis is a global regulator critical for modulation of virulence factor production and pathogenicity of Dickeya zeae. Sci Rep 2018; 8:341. [PMID: 29321600 PMCID: PMC5762655 DOI: 10.1038/s41598-017-18578-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 12/11/2017] [Indexed: 12/25/2022] Open
Abstract
Dickeya zeae is the causal agent of rice foot rot disease, which has recently become a great threat to rice planting countries and regions. The pathogen produces a family of phytotoxins named zeamines that is critical for bacterial virulence, but little is known about the signaling pathways and regulatory mechanisms that govern zeamine production. In this study, we showed that a conserved transcriptional regulator Fis is involved in the regulation of zeamine production in D. zeae strain EC1. Deletion mutants were markedly attenuated in the virulence against rice seed germination. Transcriptome and phenotype analyses showed that Fis is a potent global transcriptional regulator modulating various virulence traits, including production of extracellular enzymes and exopolysaccharides, swimming and swarming motility, biofilm formation and cell aggregation. DNA gel retardation analysis showed that Fis directly regulates the transcription of key virulence genes and the genes encoding Vfm quorum sensing system through DNA/protein interaction. Our findings unveil a key regulator associated with the virulence of D. zeae EC1, and present useful clues for further elucidation of the regulatory complex and signaling pathways which govern the virulence of this important pathogen.
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22
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Masschelein J, Jenner M, Challis GL. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Nat Prod Rep 2017. [PMID: 28650032 DOI: 10.1039/c7np00010c] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
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Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
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23
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Zhou J, Zhang H, Lv M, Chen Y, Liao L, Cheng Y, Liu S, Chen S, He F, Cui Z, Jiang Z, Chang C, Zhang L. SlyA regulates phytotoxin production and virulence in Dickeya zeae EC1. MOLECULAR PLANT PATHOLOGY 2016; 17:1398-1408. [PMID: 26814706 PMCID: PMC6638372 DOI: 10.1111/mpp.12376] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 01/23/2016] [Accepted: 01/24/2016] [Indexed: 06/05/2023]
Abstract
Dickeya zeae is a causal agent of rice root rot disease. The pathogen is known to produce a range of virulence factors, including phytotoxic zeamines and extracellular enzymes, but the mechanisms of virulence regulation remain vague. In this study, we identified a SlyA/MarR family transcription factor SlyA in D. zeae strain EC1. Disruption of slyA significantly decreased zeamine production, enhanced swimming and swarming motility, reduced biofilm formation and significantly decreased pathogenicity on rice. Quantitative polymerase chain reaction (qPCR) analysis confirmed the role of SlyA in transcriptional modulation of a range of genes associated with bacterial virulence. In trans expression of slyA in expI mutants recovered the phenotypes of motility and biofilm formation, suggesting that SlyA is downstream of the acylhomoserine lactone-mediated quorum sensing pathway. Taken together, the findings from this study unveil a key transcriptional regulatory factor involved in the modulation of virulence factor production and overall pathogenicity of D. zeae EC1.
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Affiliation(s)
- Jia‐Nuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Hai‐Bao Zhang
- Institute of Molecular and Cell Biology 61 Biopolis DriveSingapore138673
| | - Ming‐Fa Lv
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Yu‐Fan Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Li‐Sheng Liao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Ying‐Ying Cheng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Shi‐Yin Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Shao‐Hua Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Fei He
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Zi‐Ning Cui
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Zi‐De Jiang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Chang‐Qing Chang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Lian‐Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
- Institute of Molecular and Cell Biology 61 Biopolis DriveSingapore138673
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Genetic Modulation of c-di-GMP Turnover Affects Multiple Virulence Traits and Bacterial Virulence in Rice Pathogen Dickeya zeae. PLoS One 2016; 11:e0165979. [PMID: 27855163 PMCID: PMC5113947 DOI: 10.1371/journal.pone.0165979] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 10/20/2016] [Indexed: 11/19/2022] Open
Abstract
The frequent outbreaks of rice foot rot disease caused by Dickeya zeae have become a significant concern in rice planting regions and countries, but the regulatory mechanisms that govern the virulence of this important pathogen remain vague. Given that the second messenger cyclic di-GMP (c-di-GMP) is associated with modulation of various virulence-related traits in various microorganisms, here we set to investigate the role of the genes encoding c-di-GMP metabolism in the regulation of the bacterial physiology and virulence by construction all in-frame deletion mutants targeting the annotated c-di-GMP turnover genes in D. zeae strain EC1. Phenotype analyses identified individual mutants showing altered production of exoenzymes and phytotoxins, biofilm formation and bacterial motilities. The results provide useful clues and a valuable toolkit for further characterization and dissection of the regulatory complex that modulates the pathogenesis and persistence of this important bacterial pathogen.
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25
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Polyamine derivatives: a revival of an old neglected scaffold to fight resistant Gram-negative bacteria? Future Med Chem 2016; 8:963-73. [DOI: 10.4155/fmc-2016-0011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Emergence of multidrug-resistant pathogens was responsible for microbial infections and inefficacy of numerous antimicrobial therapies has induced a need for the research of new classes of antibiotics. In this review, we will focus our interest toward the biological properties of polyamino antimicrobial agents.
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Paioti PHS, Abboud KA, Aponick A. Catalytic Enantioselective Synthesis of Amino Skipped Diynes. J Am Chem Soc 2016; 138:2150-3. [PMID: 26855017 DOI: 10.1021/jacs.5b13387] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The Cu-catalyzed synthesis of nonracemic 3-amino skipped diynes via an enantiodetermining C-C bond formation is described using StackPhos as ligand. Despite challenging issues of reactivity and stereoselectivity inherent to these chiral skipped diynes, the reaction tolerates an extremely broad substrate scope with respect to all components and provides the title compounds in excellent enantiomeric excess. The alkyne moieties are demonstrated here to be useful synthetic handles, and 3-amino skipped diynes are convenient building blocks for enantioselective synthesis.
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Affiliation(s)
- Paulo H S Paioti
- Center for Heterocyclic Compounds, Department of Chemistry and ‡Center for X-ray Crystallography, Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States
| | - Khalil A Abboud
- Center for Heterocyclic Compounds, Department of Chemistry and ‡Center for X-ray Crystallography, Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States
| | - Aaron Aponick
- Center for Heterocyclic Compounds, Department of Chemistry and ‡Center for X-ray Crystallography, Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States
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27
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Control of litchi downy blight by zeamines produced by Dickeya zeae. Sci Rep 2015; 5:15719. [PMID: 26499339 PMCID: PMC4620559 DOI: 10.1038/srep15719] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/02/2015] [Indexed: 11/25/2022] Open
Abstract
Zeamines (ZMS), a class of polyamine-polyketide-nonribosomal peptide produced by bacterial isolate Dickeya zeae, were shown recently to be potent antibiotics against some bacterial pathogens. In this study, the results indicated that ZMS showed antifungal activity against Peronophythora litchii and other fungal pathogens. The activity of ZMS against the oomycete pathogen P. litchi, which causes the devastating litchi downy blight, was further investigated under in vitro and in vivo conditions. ZMS displayed potent inhibitory activity against the mycelial growth and sporangia germination of P. litchii. At a concentration of 2 μg/mL, about 99% of the sporangia germination was inhibited. Scanning electron microscopy and transmission electron microscopy analyses showed that treatment with ZMS could cause substantial damages to the oomycete endomembrane system. Furthermore, treatment of litchi fruits with ZMS solution significantly (P < 0.05) reduced the fruits decay and peel browning caused by P. litchii infection during storage at 28 °C. Taken together, our results provide useful clues on the antifungal mechanisms of ZMS, and highlight the promising potentials of ZMS as a fungicide, which in particular, may be useful for prevention and control of litchi fruits decay and browning caused by P. litchii infection during storage and transportation.
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28
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Zhou J, Cheng Y, Lv M, Liao L, Chen Y, Gu Y, Liu S, Jiang Z, Xiong Y, Zhang L. The complete genome sequence of Dickeya zeae EC1 reveals substantial divergence from other Dickeya strains and species. BMC Genomics 2015; 16:571. [PMID: 26239726 PMCID: PMC4522980 DOI: 10.1186/s12864-015-1545-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 04/17/2015] [Indexed: 12/26/2022] Open
Abstract
Background Dickeya zeae is a bacterial species that infects monocotyledons and dicotyledons. Two antibiotic-like phytotoxins named zeamine and zeamine II were reported to play an important role in rice seed germination, and two genes associated with zeamines production, i.e., zmsA and zmsK, have been thoroughly characterized. However, other virulence factors and its molecular mechanisms of host specificity and pathogenesis are hardly known. Results The complete genome of D. zeae strain EC1 isolated from diseased rice plants was sequenced, annotated, and compared with the genomes of other Dickeya spp.. The pathogen contains a chromosome of 4,532,364 bp with 4,154 predicted protein-coding genes. Comparative genomics analysis indicates that D. zeae EC1 is most co-linear with D. chrysanthemi Ech1591, most conserved with D. zeae Ech586 and least similar to D. paradisiaca Ech703. Substantial genomic rearrangement was revealed by comparing EC1 with Ech586 and Ech703. Most virulence genes were well-conserved in Dickeya strains except Ech703. Significantly, the zms gene cluster involved in biosynthesis of zeamines, which were shown previously as key virulence determinants, is present in D. zeae strains isolated from rice, and some D. solani strains, but absent in other Dickeya species and the D. zeae strains isolated from other plants or sources. In addition, a DNA fragment containing 9 genes associated with fatty acid biosynthesis was found inserted in the fli gene cluster encoding flagellar biosynthesis of strain EC1 and other two rice isolates but not in other strains. This gene cluster shares a high protein similarity to the fatty acid genes from Pantoea ananatis. Conlusion Our findings delineate the genetic background of D. zeae EC1, which infects both dicotyledons and monocotyledons, and suggest that D. zeae strains isolated from rice could be grouped into a distinct pathovar, i.e., D. zeae subsp. oryzae. In addition, the results of this study also unveiled that the zms gene cluster presented in the genomes of D. zeae rice isolates and D. solani strains, and the fatty acid genes inserted in the fli gene cluster of strain EC1 were likely derived from horizontal gene transfer during later stage of bacterial evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1545-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Yingying Cheng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Mingfa Lv
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Lisheng Liao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Yufan Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Yanfang Gu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Shiyin Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Zide Jiang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Yuanyan Xiong
- State Key laboratory for Biocontrol, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Lianhui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China. .,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Republic of Singapore.
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29
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Hellberg JEEU, Matilla MA, Salmond GPC. The broad-spectrum antibiotic, zeamine, kills the nematode worm Caenorhabditis elegans. Front Microbiol 2015; 6:137. [PMID: 25767467 PMCID: PMC4341552 DOI: 10.3389/fmicb.2015.00137] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 02/05/2015] [Indexed: 12/02/2022] Open
Abstract
Soil bacteria can be prolific producers of secondary metabolites and other biologically active compounds of economic and clinical importance. These natural products are often synthesized by large multi-enzyme complexes such as polyketide synthases (PKSs) or non-ribosomal peptide synthases (NRPSs). The plant-associated Gram-negative bacterium, Serratia plymuthica A153, produces several secondary metabolites and is capable of killing the nematode worm Caenorhabditis elegans; a commonly used model for the study of bacterial virulence. In this study, we show that disruption of the hybrid PKS/NRPS zeamine (zmn) gene cluster results in the attenuation of “fast-killing” of C. elegans, indicating that zeamine has nematicidal activity. C. elegans also exhibits age-dependent susceptibility to zeamine, with younger worms being most sensitive to the bioactive molecule. The zmn gene cluster is widely distributed within Serratia and phytopathogenic Dickeya species and investigation of strains harboring the zmn gene cluster showed that several of them are highly virulent in C. elegans. Zeamine was described previously as a phytotoxin and broad-spectrum antibacterial compound. In addition to its nematicidal properties, we show here that zeamine can also kill Saccharomyces cerevisiae and Schizosaccharomyces pombe. The expression of the zmn gene cluster and regulation of zeamine production were also investigated. Transcription of the cluster was growth phase-dependent, and was modulated by the post-transcriptional RNA chaperone, Hfq. The results of this study show that zeamine is a highly toxic molecule with little, or no, apparent host specificity in very diverse biological systems. In its current form, zeamine(s) may be useful as a lead compound suitable for chemical modification and structure-activity assays. However, because of widespread non-selective toxicity in multiple bioassays, unmodified zeamine(s) is unlikely to be suitable as a therapeutic antibiotic.
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Affiliation(s)
| | - Miguel A Matilla
- Department of Biochemistry, University of Cambridge Cambridge, UK ; Department of Environmental Protection, Estación Experimental del Zaidín - Consejo Superior de Investigaciones Científicas Granada, Spain
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Liao L, Cheng Y, Liu S, Zhou J, An S, Lv M, Chen Y, Gu Y, Chen S, Zhang LH. Production of novel antibiotics zeamines through optimizing Dickeya zeae fermentation conditions. PLoS One 2014; 9:e116047. [PMID: 25541733 PMCID: PMC4277462 DOI: 10.1371/journal.pone.0116047] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/30/2014] [Indexed: 01/20/2023] Open
Abstract
Dickeya zeae strain EC1 was recently shown to produce a new type of phytotoxins designated as zeamine and zeamine II, which are potent wide-spectrum antibiotics against Gram-positive and Gram-negative bacterial pathogens, suggesting their promising potential as clinical medicines. In this study, the optimized medium composition and culture conditions for biosynthesis of novel antibiotics zeamines have been established by using response surface methodology, largely increasing the yield of zeamines from original about 7.35 µg · mL(-1) in minimal medium to about 150 µg · mL(-1) in LS5 medium. The study identified the major factors contributing to zeamines production, which include nitrate, sucrose, asparaginate, mineral elements Mg2+ and K+, and optimized amount of phosphate. In addition, the results showed that overexpression of zmsK in D. zeae strain EC1 could further increase zeamines yield to about 180 µg · mL(-1) in LS5 medium. The findings from this study could facilitate further characterization and utilization of these two novel antibiotics, and also provide useful clues for understanding the regulatory mechanisms that govern D. zeae virulence.
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Affiliation(s)
- Lisheng Liao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Peoples' Republic of China
| | - Yingying Cheng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Peoples' Republic of China
| | - Shiyin Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Peoples' Republic of China
| | - Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Peoples' Republic of China
| | - Shuwen An
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Mingfa Lv
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Peoples' Republic of China
| | - Yufan Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Peoples' Republic of China
| | - Yanfang Gu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Peoples' Republic of China
| | - Shaohua Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Peoples' Republic of China
- * E-mail: (SC); (LHZ)
| | - Lian-Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Peoples' Republic of China
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Republic of Singapore
- * E-mail: (SC); (LHZ)
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31
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Masschelein J, Clauwers C, Awodi UR, Stalmans K, Vermaelen W, Lescrinier E, Aertsen A, Michiels C, Challis GL, Lavigne R. A combination of polyunsaturated fatty acid, nonribosomal peptide and polyketide biosynthetic machinery is used to assemble the zeamine antibiotics. Chem Sci 2014; 6:923-929. [PMID: 29560178 PMCID: PMC5811116 DOI: 10.1039/c4sc01927j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 10/15/2014] [Indexed: 11/21/2022] Open
Abstract
The zeamines are a unique group of antibiotics produced by Serratia plymuthica RVH1 that contain variable hybrid peptide-polyketide moieties connected to a common pentaamino-hydroxyalkyl chain. They exhibit potent activity against a broad spectrum of Gram-positive and Gram-negative bacteria. Here we report a combination of targeted gene deletions, high resolution LC-MS(/MS) analyses, in vitro biochemical assays and feeding studies that define the functions of several key zeamine biosynthetic enzymes. The pentaamino-hydroxyalkyl chain is assembled by an iterative multienzyme complex (Zmn10-13) that bears a close resemblance to polyunsaturated fatty acid synthases. Zmn14 was shown to function as an NADH-dependent thioester reductase and is proposed to release a tetraamino-hydroxyalkyl thioester from the acyl carrier protein domain of Zmn10 as an aldehyde. Despite the intrinsic ability of Zmn14 to catalyze further reduction of aldehydes to alcohols, the initially-formed aldehyde intermediate is proposed to undergo preferential transamination to produce zeamine II. In a parallel pathway, hexapeptide-monoketide and hexapeptide-diketide thioesters are generated by a hybrid nonribosomal peptide synthetase-polyketide synthase multienzyme complex (Zmn16-18) and subsequently conjugated to zeamine II by a stand-alone condensing enzyme (Zmn19). Structures for the resulting prezeamines were elucidated using a combination of high resolution LC-MS/MS and 1- and 2-D NMR spectroscopic analyses. The prezeamines are hypothesized to be precursors of the previously-identified zeamines, which are generated by the action of Zmn22, an acylpeptide hydrolase that specifically cleaves the N-terminal pentapeptide of the prezeamines in a post-assembly processing step. Thus, the zeamine antibiotics are assembled by a unique combination of nonribosomal peptide synthetase, type I modular polyketide synthase and polyunsaturated fatty acid synthase-like biosynthetic machinery.
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Affiliation(s)
- Joleen Masschelein
- Laboratory of Gene Technology , KU Leuven , Kasteelpark Arenberg 21-box 2462 , B-3001 Heverlee , Belgium . ; ; Tel: +32 (0) 16 37 95 24.,Laboratory of Food Microbiology , KU Leuven , Kasteelpark Arenberg 22 , B-3001 Heverlee , Belgium
| | - Charlien Clauwers
- Laboratory of Gene Technology , KU Leuven , Kasteelpark Arenberg 21-box 2462 , B-3001 Heverlee , Belgium . ; ; Tel: +32 (0) 16 37 95 24.,Laboratory of Food Microbiology , KU Leuven , Kasteelpark Arenberg 22 , B-3001 Heverlee , Belgium
| | - Ufedo R Awodi
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , UK . ; ; Tel: +44 (0) 2476 574024
| | - Karen Stalmans
- Laboratory of Gene Technology , KU Leuven , Kasteelpark Arenberg 21-box 2462 , B-3001 Heverlee , Belgium . ; ; Tel: +32 (0) 16 37 95 24
| | - Wesley Vermaelen
- Laboratory of Gene Technology , KU Leuven , Kasteelpark Arenberg 21-box 2462 , B-3001 Heverlee , Belgium . ; ; Tel: +32 (0) 16 37 95 24
| | - Eveline Lescrinier
- Laboratory of Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , B-3000 Leuven , Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology , KU Leuven , Kasteelpark Arenberg 22 , B-3001 Heverlee , Belgium
| | - Chris Michiels
- Laboratory of Food Microbiology , KU Leuven , Kasteelpark Arenberg 22 , B-3001 Heverlee , Belgium
| | - Gregory L Challis
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , UK . ; ; Tel: +44 (0) 2476 574024
| | - Rob Lavigne
- Laboratory of Gene Technology , KU Leuven , Kasteelpark Arenberg 21-box 2462 , B-3001 Heverlee , Belgium . ; ; Tel: +32 (0) 16 37 95 24
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32
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Fuchs SW, Grundmann F, Kurz M, Kaiser M, Bode HB. Fabclavines: bioactive peptide-polyketide-polyamino hybrids from Xenorhabdus. Chembiochem 2014; 15:512-6. [PMID: 24532262 DOI: 10.1002/cbic.201300802] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Indexed: 11/12/2022]
Abstract
The structure of the fabclavines-unique mixtures of nonribosomally derived peptide-polyketide hybrids connected to an unusual polyamino moiety-has been solved by detailed NMR and MS methods. These compounds have been identified in two different entomopathogenic Xenorhabdus strains, thereby leading also to the identification of the fabclavine biosynthesis gene cluster. Detailed analysis of these clusters and initial mutagenesis experiments allowed the prediction of a biosynthesis pathway in which the polyamino moiety is derived from an unusual type of fatty acid synthase that is normally involved in formation of polyunsaturated fatty acids. As fabclavines show broad-spectrum activity against bacteria, fungi, and other eukaryotic cells, they might act as "protection factors" against all kinds of food competitors during the complex life cycle of Xenorhabdus, its nematode host, and their insect prey.
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Affiliation(s)
- Sebastian W Fuchs
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany)
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Genome Sequence of Dickeya solani, a New soft Rot Pathogen of Potato, Suggests its Emergence May Be Related to a Novel Combination of Non-Ribosomal Peptide/Polyketide Synthetase Clusters. DIVERSITY-BASEL 2013. [DOI: 10.3390/d5040824] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Cheng Y, Liu X, An S, Chang C, Zou Y, Huang L, Zhong J, Liu Q, Jiang Z, Zhou J, Zhang LH. A nonribosomal peptide synthase containing a stand-alone condensation domain is essential for phytotoxin zeamine biosynthesis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:1294-1301. [PMID: 23883359 DOI: 10.1094/mpmi-04-13-0098-r] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Dickeya zeae is the causal agent of rice foot rot and maize stalk rot diseases, which could cause severe economic losses. The pathogen is known to produce two phytotoxins known as zeamine and zeamine II which are also potent antibiotics against both gram-positive and gram-negative bacteria pathogens. Zeamine II is a long-chain aminated polyketide and zeamine shares the same polyketide structure as zeamine II, with an extra valine derivative moiety conjugated to the primary amino group of zeamine II. In this study, we have identified a gene designated as zmsK encoding a putative nonribosomal peptide synthase (NRPS) by screening of the transposon mutants defective in zeamine production. Different from most known NRPS enzymes, which are commonly multidomain proteins, ZmsK contains only a condensation domain. High-performance liquid chromatography and mass spectrometry analyses showed that the ZmsK deletion mutant produced only zeamine II but not zeamine, suggesting that ZmsK catalyzes the amide bond formation by using zeamine II as a substrate to generate zeamine. We also present evidence that a partially conserved catalytic motif within the condensation domain is critical for zeamine production. Furthermore, we show that deletion of zmsK substantially decreased the total antimicrobial activity and virulence of D. zeae. Our findings provide a new insight into the biosynthesis pathway of zeamines and the virulence mechanisms of the bacterial pathogen D. zeae.
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Zhang JX, Lin BR, Shen HF, Pu XM. Genome Sequence of the Banana Pathogen Dickeya zeae Strain MS1, Which Causes Bacterial Soft Rot. GENOME ANNOUNCEMENTS 2013; 1:e00317-13. [PMID: 23766402 PMCID: PMC3707573 DOI: 10.1128/genomea.00317-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 05/01/2013] [Indexed: 11/20/2022]
Abstract
We report a draft genome sequence of Dickeya zeae strain MS1, which is the causative agent of banana soft rot in China, and we show several of its specific properties compared with those of other D. zeae strains. Genome sequencing provides a tool for understanding the genomic determination of the pathogenicity and phylogeny placement of this pathogen.
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Affiliation(s)
- Jing-Xin Zhang
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangdong, China
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Masschelein J, Mattheus W, Gao LJ, Moons P, Van Houdt R, Uytterhoeven B, Lamberigts C, Lescrinier E, Rozenski J, Herdewijn P, Aertsen A, Michiels C, Lavigne R. A PKS/NRPS/FAS hybrid gene cluster from Serratia plymuthica RVH1 encoding the biosynthesis of three broad spectrum, zeamine-related antibiotics. PLoS One 2013; 8:e54143. [PMID: 23349809 PMCID: PMC3547906 DOI: 10.1371/journal.pone.0054143] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 12/06/2012] [Indexed: 11/21/2022] Open
Abstract
Serratia plymuthica strain RVH1, initially isolated from an industrial food processing environment, displays potent antimicrobial activity towards a broad spectrum of Gram-positive and Gram-negative bacterial pathogens. Isolation and subsequent structure determination of bioactive molecules led to the identification of two polyamino antibiotics with the same molecular structure as zeamine and zeamine II as well as a third, closely related analogue, designated zeamine I. The gene cluster encoding the biosynthesis of the zeamine antibiotics was cloned and sequenced and shown to encode FAS, PKS as well as NRPS related enzymes in addition to putative tailoring and export enzymes. Interestingly, several genes show strong homology to the pfa cluster of genes involved in the biosynthesis of long chain polyunsaturated fatty acids in marine bacteria. We postulate that a mixed FAS/PKS and a hybrid NRPS/PKS assembly line each synthesize parts of the backbone that are linked together post-assembly in the case of zeamine and zeamine I. This interaction reflects a unique interplay between secondary lipid and secondary metabolite biosynthesis. Most likely, the zeamine antibiotics are produced as prodrugs that undergo activation in which a nonribosomal peptide sequence is cleaved off.
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Affiliation(s)
- Joleen Masschelein
- Division of Gene Technology, KU Leuven, Heverlee, Belgium
- Laboratory of Food Microbiology, KU Leuven, Heverlee, Belgium
| | | | - Ling-Jie Gao
- Interface Valorisation Platform, KU Leuven, Leuven, Belgium
| | - Pieter Moons
- Laboratory of Food Microbiology, KU Leuven, Heverlee, Belgium
| | - Rob Van Houdt
- Laboratory of Food Microbiology, KU Leuven, Heverlee, Belgium
| | | | | | - Eveline Lescrinier
- Laboratory for Medicinal Chemistry, Rega Institute for Medicinal Research, Leuven, Belgium
| | - Jef Rozenski
- Laboratory for Medicinal Chemistry, Rega Institute for Medicinal Research, Leuven, Belgium
| | - Piet Herdewijn
- Interface Valorisation Platform, KU Leuven, Leuven, Belgium
- Laboratory for Medicinal Chemistry, Rega Institute for Medicinal Research, Leuven, Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology, KU Leuven, Heverlee, Belgium
| | - Chris Michiels
- Laboratory of Food Microbiology, KU Leuven, Heverlee, Belgium
| | - Rob Lavigne
- Division of Gene Technology, KU Leuven, Heverlee, Belgium
- * E-mail:
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Charkowski A, Blanco C, Condemine G, Expert D, Franza T, Hayes C, Hugouvieux-Cotte-Pattat N, López Solanilla E, Low D, Moleleki L, Pirhonen M, Pitman A, Perna N, Reverchon S, Rodríguez Palenzuela P, San Francisco M, Toth I, Tsuyumu S, van der Waals J, van der Wolf J, Van Gijsegem F, Yang CH, Yedidia I. The role of secretion systems and small molecules in soft-rot Enterobacteriaceae pathogenicity. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:425-49. [PMID: 22702350 DOI: 10.1146/annurev-phyto-081211-173013] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Soft-rot Enterobacteriaceae (SRE), which belong to the genera Pectobacterium and Dickeya, consist mainly of broad host-range pathogens that cause wilt, rot, and blackleg diseases on a wide range of plants. They are found in plants, insects, soil, and water in agricultural regions worldwide. SRE encode all six known protein secretion systems present in gram-negative bacteria, and these systems are involved in attacking host plants and competing bacteria. They also produce and detect multiple types of small molecules to coordinate pathogenesis, modify the plant environment, attack competing microbes, and perhaps to attract insect vectors. This review integrates new information about the role protein secretion and detection and production of ions and small molecules play in soft-rot pathogenicity.
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Affiliation(s)
- Amy Charkowski
- Department of Plant Pathology, University of Wisconsin, Madison, Wisconsin 53706, USA.
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Zhou J, Zhang H, Wu J, Liu Q, Xi P, Lee J, Liao J, Jiang Z, Zhang LH. A novel multidomain polyketide synthase is essential for zeamine production and the virulence of Dickeya zeae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:1156-64. [PMID: 21899437 DOI: 10.1094/mpmi-04-11-0087] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Dickeya zeae is the causal agent of the rice foot rot disease, but its mechanism of infection remains largely unknown. In this study, we identified and characterized a novel gene designated as zmsA. The gene encodes a large protein of 2,346 amino acids in length, which consists of multidomains arranged in the order of N-terminus, β-ketoacyl synthase, acyl transferase, acyl carrier protein, β-ketoacyl reductase, dehydratase. This multidomain structure and sequence alignment analysis suggest that ZmsA is a member of the polyketide synthase family. Mutation of zmsA abolished antimicrobial activity and attenuated the virulence of D. zeae. To determine the relationship between antimicrobial activity and virulence, active compounds were purified from D. zeae EC1 and were structurally characterized. This led to identification of two polyamino compounds, i.e., zeamine and zeamine II, that were phytotoxins and potent antibiotics. These results have established the essential role of ZmsA in zeamine biosynthesis and presented a new insight on the molecular mechanisms of D. zeae pathogenicity.
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Affiliation(s)
- Jianuan Zhou
- Department of plant Pathology, South China Agricultural University, Guangzhou 51642, People's Republich of China
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Gulder TAM, Freeman MF, Piel J. The Catalytic Diversity of Multimodular Polyketide Synthases: Natural Product Biosynthesis Beyond Textbook Assembly Rules. Top Curr Chem (Cham) 2011. [PMID: 21360321 DOI: 10.1007/128_2010_113] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Bacterial multimodular polyketide synthases (PKSs) are responsible for the biosynthesis of a wide range of pharmacologically active natural products. These megaenzymes contain numerous catalytic and structural domains and act as biochemical templates to generate complex polyketides in an assembly line-like fashion. While the prototypical PKS is composed of only a few different domain types that are fused together in a combinatorial fashion, an increasing number of enzymes is being found that contain additional components. These domains can introduce remarkably diverse modifications into polyketides. This review discusses our current understanding of such noncanonical domains and their role in expanding the biosynthetic versatility of bacterial PKSs.
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