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Canabal R, González-Bello C. Chemical sensors for the early diagnosis of bacterial resistance to β-lactam antibiotics. Bioorg Chem 2024; 150:107528. [PMID: 38852309 DOI: 10.1016/j.bioorg.2024.107528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
β-Lactamases are bacterial enzymes that inactivate β-lactam antibiotics and, as such, are the most prevalent cause of antibiotic resistance in Gram-negative bacteria. The ever-increasing production and worldwide dissemination of bacterial strains producing carbapenemases is currently a global health concern. These enzymes catalyze the hydrolysis of carbapenems - the β-lactam antibiotics with the broadest spectrum of activity that are often considered as drugs of last resort. The incidence of carbapenem-resistant pathogens such as Pseudomonas aeruginosa, Acinetobacter baumannii and carbapenemase or extended spectrum beta-lactamase (ESBL)-producing Enterobacterales, which are frequent in clinical settings, is worrisome since, in some cases, no therapies are available. These include all metallo-β-lactamases (VIM, IMP, NDM, SMP, and L1), and serine-carbapenemases of classes A (KPC, SME, IMI, and GES), and of classes D (OXA-23, OXA-24/40, OXA-48 and OXA-58). Consequently, the early diagnosis of bacterial strains harboring carbapenemases is a pivotal task in clinical microbiology in order to track antibiotic bacterial resistance and to improve the worldwide management of infectious diseases. Recent research efforts on the development of chromogenic and fluorescent chemical sensors for the specific and sensitive detection and quantification of β-lactamase production in multidrug-resistant pathogens are summarized herein. Studies to circumvent the main limitations of the phenotypic and molecular methods are discussed. Recently reported chromogenic and fluorogenic cephalosporin- and carbapenem-based β-lactamase substrates will be reviewed as alternative options to the currently available nitrocefin and related compounds, a chromogenic cephalosporin-based reagent widely used in clinical microbiology laboratories. The scope of these new chemical sensors, along with the synthetic approaches to synthesize them, is also summarized.
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Affiliation(s)
- Rafael Canabal
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
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Mena Navarro MP, Espinosa Bernal MA, Martinez-Avila AE, Aponte Pineda LS, Montes Flores LA, Chan Ku CD, Hernández Gómez YF, González Espinosa J, Pacheco Aguilar JR, Ramos López MÁ, Arvizu Gómez JL, Saldaña Gutierrez C, Rodríguez Morales JA, Amaro Reyes A, Hernández Flores JL, Campos Guillén J. Role of Volatile Organic Compounds Produced by Kosakonia cowanii Cp1 during Competitive Colonization Interaction against Pectobacterium aroidearum SM2. Microorganisms 2024; 12:930. [PMID: 38792761 PMCID: PMC11123878 DOI: 10.3390/microorganisms12050930] [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: 04/16/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
The competitive colonization of bacteria on similar ecological niches has a significant impact during their establishment. The synthesis speeds of different chemical classes of molecules during early competitive colonization can reduce the number of competitors through metabolic effects. In this work, we demonstrate for the first time that Kosakonia cowanii Cp1 previously isolated from the seeds of Capsicum pubescens R. P. produced volatile organic compounds (VOCs) during competitive colonization against Pectobacterium aroidearum SM2, affecting soft rot symptoms in serrano chili (Capsicum annuum L.). The pathogen P. aroidearum SM2 was isolated from the fruits of C. annuum var. Serrano with soft rot symptoms. The genome of the SM2 strain carries a 5,037,920 bp chromosome with 51.46% G + C content and 4925 predicted protein-coding genes. It presents 12 genes encoding plant-cell-wall-degrading enzymes (PCDEWs), 139 genes involved in five types of secretion systems, and 16 genes related to invasion motility. Pathogenic essays showed soft rot symptoms in the fruits of C. annuum L., Solanum lycopersicum, and Physalis philadelphica and the tubers of Solanum tuberosum. During the growth phases of K. cowanii Cp1, a mix of VOCs was identified by means of HS-SPME-GC-MS. Of these compounds, 2,5-dimethyl-pyrazine showed bactericidal effects and synergy with acetoin during the competitive colonization of K. cowanii Cp1 to completely reduce soft rot symptoms. This work provides novel evidence grounding a better understanding of bacterial interactions during competitive colonization on plant tissue, where VOC synthesis is essential and has a high potential capacity to control pathogenic microorganisms in agricultural systems.
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Affiliation(s)
- Mayra Paola Mena Navarro
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, Querétaro 76010, Qro, Mexico; (M.P.M.N.); (M.A.E.B.); (A.E.M.-A.); (L.S.A.P.); (L.A.M.F.); (C.D.C.K.); (Y.F.H.G.); (J.G.E.); (J.R.P.A.); (M.Á.R.L.); (A.A.R.)
| | - Merle Ariadna Espinosa Bernal
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, Querétaro 76010, Qro, Mexico; (M.P.M.N.); (M.A.E.B.); (A.E.M.-A.); (L.S.A.P.); (L.A.M.F.); (C.D.C.K.); (Y.F.H.G.); (J.G.E.); (J.R.P.A.); (M.Á.R.L.); (A.A.R.)
| | - Adriana Eunice Martinez-Avila
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, Querétaro 76010, Qro, Mexico; (M.P.M.N.); (M.A.E.B.); (A.E.M.-A.); (L.S.A.P.); (L.A.M.F.); (C.D.C.K.); (Y.F.H.G.); (J.G.E.); (J.R.P.A.); (M.Á.R.L.); (A.A.R.)
| | - Leonela Sofia Aponte Pineda
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, Querétaro 76010, Qro, Mexico; (M.P.M.N.); (M.A.E.B.); (A.E.M.-A.); (L.S.A.P.); (L.A.M.F.); (C.D.C.K.); (Y.F.H.G.); (J.G.E.); (J.R.P.A.); (M.Á.R.L.); (A.A.R.)
| | - Luis Alberto Montes Flores
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, Querétaro 76010, Qro, Mexico; (M.P.M.N.); (M.A.E.B.); (A.E.M.-A.); (L.S.A.P.); (L.A.M.F.); (C.D.C.K.); (Y.F.H.G.); (J.G.E.); (J.R.P.A.); (M.Á.R.L.); (A.A.R.)
| | - Carlos Daniel Chan Ku
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, Querétaro 76010, Qro, Mexico; (M.P.M.N.); (M.A.E.B.); (A.E.M.-A.); (L.S.A.P.); (L.A.M.F.); (C.D.C.K.); (Y.F.H.G.); (J.G.E.); (J.R.P.A.); (M.Á.R.L.); (A.A.R.)
| | - Yoali Fernanda Hernández Gómez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, Querétaro 76010, Qro, Mexico; (M.P.M.N.); (M.A.E.B.); (A.E.M.-A.); (L.S.A.P.); (L.A.M.F.); (C.D.C.K.); (Y.F.H.G.); (J.G.E.); (J.R.P.A.); (M.Á.R.L.); (A.A.R.)
| | - Jacqueline González Espinosa
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, Querétaro 76010, Qro, Mexico; (M.P.M.N.); (M.A.E.B.); (A.E.M.-A.); (L.S.A.P.); (L.A.M.F.); (C.D.C.K.); (Y.F.H.G.); (J.G.E.); (J.R.P.A.); (M.Á.R.L.); (A.A.R.)
| | - Juan Ramiro Pacheco Aguilar
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, Querétaro 76010, Qro, Mexico; (M.P.M.N.); (M.A.E.B.); (A.E.M.-A.); (L.S.A.P.); (L.A.M.F.); (C.D.C.K.); (Y.F.H.G.); (J.G.E.); (J.R.P.A.); (M.Á.R.L.); (A.A.R.)
| | - Miguel Ángel Ramos López
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, Querétaro 76010, Qro, Mexico; (M.P.M.N.); (M.A.E.B.); (A.E.M.-A.); (L.S.A.P.); (L.A.M.F.); (C.D.C.K.); (Y.F.H.G.); (J.G.E.); (J.R.P.A.); (M.Á.R.L.); (A.A.R.)
| | - Jackeline Lizzeta Arvizu Gómez
- Secretaría de Investigación y Posgrado, Centro Nayarita de Innovación y Transferencia de Tecnología (CENITT), Universidad Autónoma de Nayarit, Tepic 63173, Mexico;
| | - Carlos Saldaña Gutierrez
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. De las Ciencias s/n, Querétaro 76220, Mexico;
| | | | - Aldo Amaro Reyes
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, Querétaro 76010, Qro, Mexico; (M.P.M.N.); (M.A.E.B.); (A.E.M.-A.); (L.S.A.P.); (L.A.M.F.); (C.D.C.K.); (Y.F.H.G.); (J.G.E.); (J.R.P.A.); (M.Á.R.L.); (A.A.R.)
| | | | - Juan Campos Guillén
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, Querétaro 76010, Qro, Mexico; (M.P.M.N.); (M.A.E.B.); (A.E.M.-A.); (L.S.A.P.); (L.A.M.F.); (C.D.C.K.); (Y.F.H.G.); (J.G.E.); (J.R.P.A.); (M.Á.R.L.); (A.A.R.)
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Solanimycin: Biosynthesis and Distribution of a New Antifungal Antibiotic Regulated by Two Quorum-Sensing Systems. mBio 2022; 13:e0247222. [PMID: 36214559 PMCID: PMC9765074 DOI: 10.1128/mbio.02472-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The increasing emergence of drug-resistant fungal infections has necessitated a search for new compounds capable of combating fungal pathogens of plants, animals, and humans. Microorganisms represent the main source of antibiotics with applicability in agriculture and in the clinic, but many aspects of their metabolic potential remain to be explored. This report describes the discovery and characterization of a new antifungal compound, solanimycin, produced by a hybrid polyketide/nonribosomal peptide (PKS/NRPS) system in Dickeya solani, the enterobacterial pathogen of potato. Solanimycin was active against a broad range of plant-pathogenic fungi of global economic concern and the human pathogen Candida albicans. The genomic cluster responsible for solanimycin production was defined and analyzed to identify the corresponding biosynthetic proteins, which include four multimodular PKS/NRPS proteins and several tailoring enzymes. Antifungal production in D. solani was enhanced in response to experimental conditions found in infected potato tubers and high-density fungal cultures. Solanimycin biosynthesis was cell density dependent in D. solani and was controlled by both the ExpIR acyl-homoserine lactone and Vfm quorum-sensing systems of the bacterial phytopathogen. The expression of the solanimycin cluster was also regulated at the post-transcriptional level, with the regulator RsmA playing a major role. The solanimycin biosynthetic cluster was conserved across phylogenetically distant bacterial genera, and multiple pieces of evidence support that the corresponding gene clusters were acquired by horizontal gene transfer. Given its potent broad-range antifungal properties, this study suggests that solanimycin and related molecules may have potential utility for agricultural and clinical exploitation. IMPORTANCE Fungal infections represent a major clinical, agricultural, and food security threat worldwide, which is accentuated due to the difficult treatment of these infections. Microorganisms represent a prolific source of antibiotics, and current data support that this enormous biosynthetic potential has been scarcely explored. To improve the performance in the discovery of novel antimicrobials, there is a need to diversify the isolation niches for new antibiotic-producing microorganisms as well as to scrutinize novel phylogenetic positions. With the identification of the antifungal antibiotic solanimycin in a broad diversity of phytopathogenic Dickeya spp., we provide further support for the potential of plant-associated bacteria for the biosynthesis of novel antimicrobials. The complex regulatory networks involved in solanimycin production reflect the high metabolic cost of bacterial secondary metabolism. This metabolic regulatory control makes many antibiotics cryptic under standard laboratory conditions, and mimicking environmental conditions, as shown here, is a strategy to activate cryptic antibiotic clusters.
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Matilla MA, Evans TJ, Martín J, Udaondo Z, Lomas‐Martínez C, Rico‐Jiménez M, Reyes F, Salmond GPC. Herbicolin A production and its modulation by quorum sensing in a
Pantoea agglomerans
rhizobacterium bioactive against a broad spectrum of plant‐pathogenic fungi. Microb Biotechnol 2022. [PMID: 36528875 PMCID: PMC10364316 DOI: 10.1111/1751-7915.14193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/20/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022] Open
Abstract
Global population growth makes it necessary to increase agricultural production yields. However, climate change impacts and diseases caused by plant pathogens are challenging modern agriculture. Therefore, it is necessary to look for alternatives to the excessive use of chemical fertilizers and pesticides. The plant microbiota plays an essential role in plant nutrition and health, and offers enormous potential to meet future challenges of agriculture. In this context, here we characterized the antifungal properties of the rhizosphere bacterium Pantoea agglomerans 9Rz4, which is active against a broad spectrum of plant pathogenic fungi. Chemical analyses revealed that strain 9Rz4 produces the antifungal herbicolin A and its biosynthetic gene cluster was identified and characterized. We found that the only acyl-homoserine lactone-based quorum sensing system of 9Rz4 modulates herbicolin A gene cluster expression. No role of plasmid carriage in the production of herbicolin A was observed. Plant assays revealed that herbicolin A biosynthesis does not affect the root colonization ability of P. agglomerans 9Rz4. Current legislative restrictions are aimed at reducing the use of chemical pesticides in agriculture, and the results derived from this study may lay the foundations for the development of novel biopesticides from rhizosphere microorganisms.
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Affiliation(s)
- Miguel A. Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín Consejo Superior de Investigaciones Científicas Granada Spain
- Department of Biochemistry University of Cambridge Cambridge UK
| | - Terry J. Evans
- Department of Biochemistry University of Cambridge Cambridge UK
| | - Jesús Martín
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Granada Spain
| | - Zulema Udaondo
- Department of Biomedical Informatics University of Arkansas for Medical Sciences Little Rock Arkansas USA
| | - Cristina Lomas‐Martínez
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín Consejo Superior de Investigaciones Científicas Granada Spain
| | - Míriam Rico‐Jiménez
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín Consejo Superior de Investigaciones Científicas Granada Spain
| | - Fernando Reyes
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Granada Spain
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Knox HL, Booker SJ. Structural characterization of cobalamin-dependent radical S-adenosylmethionine methylases. Methods Enzymol 2022; 669:3-27. [PMID: 35644177 DOI: 10.1016/bs.mie.2021.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cobalamin-dependent radical S-adenosylmethionine (SAM) methylases catalyze key steps in the biosynthesis of numerous biomolecules, including protein cofactors, antibiotics, herbicides, and other natural products, but have remained a relatively understudied subclass of radical SAM enzymes due to their inherent insolubility upon overproduction in Escherichia coli. These enzymes contain two cofactors: a [4Fe-4S] cluster that is ligated by three cysteine residues, and a cobalamin cofactor typically bound by residues in the N-terminal portion of the enzyme. Recent advances in the expression and purification of these enzymes in their active states and with both cofactors present has allowed for more detailed biochemical studies as well as structure determination by X-ray crystallography. Herein, we use KsTsrM and TokK to highlight methods for the structural characterization of cobalamin-dependent radical SAM (RS) enzymes and describe recent advances in in the overproduction and purification of these enzymes.
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Affiliation(s)
- Hayley L Knox
- The Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Squire J Booker
- The Department of Chemistry, The Pennsylvania State University, University Park, PA, United States; The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States; The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, United States.
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6
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Wei H, Kong L, Wang Y, Huang Z, Yang X, Zhou C, Li C, Ma B, Li C, Lei C, Wang H. Characterization and Public Health Insights of the New Delhi Metallo-β-Lactamase-Producing Enterobacterales from Laying Hens in China. Microorganisms 2022; 10:microorganisms10040800. [PMID: 35456850 PMCID: PMC9029685 DOI: 10.3390/microorganisms10040800] [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: 02/24/2022] [Revised: 03/26/2022] [Accepted: 04/09/2022] [Indexed: 02/04/2023] Open
Abstract
The New Delhi metallo-β-lactamase (NDM) is a major element for the rapid expansion of the carbapenem-resistant Enterobacterales, which poses a great challenge to public health security. NDM-producing Enterobacterales strains (50 Escherichia coli, 40 Klebsiella pneumoniae, and 5 Enterobacter cloacae) were isolated from laying hens in China for the surveillance of antibiotic-resistant pathogens, and all were found to be multi-drug resistant bacteria. The genomic analysis of these NDM-positive bacteria revealed the ST167, ST617, and ST410 of the fifteen ST-type E. coli clones and ST37 of the four ST-type K. pneumoniae clones to be the same types as the human-derived strains. Among them, some new clone types were also found. Most of the blaNDM genes (blaNDM-1 or blaNDM-5) were on the IncX3 plasmids (n = 80) and were distributed in E. coli, K. pneumoniae, and E. cloacae, while the remaining blaNDM-5 genes were harbored in the E. coli ST167 with IncFII plasmids (n = 15). The typeⅠ1 of the eight IncX3 plasmid subtypes was consistent with the human-derived pNDM5_020001 plasmid (accession no. CP032424). In addition, these two plasmids did not affect the growth of the host bacteria and could be reproduced stably without antibiotics. Our study revealed the high genetic propensity of the NDM-positive Enterobacterales from the laying hens and human commensal Enterobacterales, suggesting the potentially enormous risk of its transmission to humans.
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Affiliation(s)
- Hongcheng Wei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Linghan Kong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Yulong Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Zheren Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Xue Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Changyu Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Chao Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Boheng Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Cui Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Changwei Lei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Hongning Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
- Correspondence: ; Tel.: +86-28-8547-1599
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Structure of a B 12-dependent radical SAM enzyme in carbapenem biosynthesis. Nature 2022; 602:343-348. [PMID: 35110734 DOI: 10.1038/s41586-021-04392-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 12/22/2021] [Indexed: 11/08/2022]
Abstract
Carbapenems are antibiotics of last resort in the clinic. Owing to their potency and broad-spectrum activity, they are an important part of the antibiotic arsenal. The vital role of carbapenems is exemplified by the approval acquired by Merck from the US Food and Drug Administration (FDA) for the use of an imipenem combination therapy to treat the increased levels of hospital-acquired and ventilator-associated bacterial pneumonia that have occurred during the COVID-19 pandemic1. The C6 hydroxyethyl side chain distinguishes the clinically used carbapenems from the other classes of β-lactam antibiotics and is responsible for their low susceptibility to inactivation by occluding water from the β-lactamase active site2. The construction of the C6 hydroxyethyl side chain is mediated by cobalamin- or B12-dependent radical S-adenosylmethionine (SAM) enzymes3. These radical SAM methylases (RSMTs) assemble the alkyl backbone by sequential methylation reactions, and thereby underlie the therapeutic usefulness of clinically used carbapenems. Here we present X-ray crystal structures of TokK, a B12-dependent RSMT that catalyses three-sequential methylations during the biosynthesis of asparenomycin A. These structures, which contain the two metallocofactors of the enzyme and were determined in the presence and absence of a carbapenam substrate, provide a visualization of a B12-dependent RSMT that uses the radical mechanism that is shared by most of these enzymes. The structures provide insight into the stereochemistry of initial C6 methylation and suggest that substrate positioning governs the rate of each methylation event.
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8
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Pacheco-Moreno A, Stefanato FL, Ford JJ, Trippel C, Uszkoreit S, Ferrafiat L, Grenga L, Dickens R, Kelly N, Kingdon AD, Ambrosetti L, Nepogodiev SA, Findlay KC, Cheema J, Trick M, Chandra G, Tomalin G, Malone JG, Truman AW. Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition. eLife 2021; 10:71900. [PMID: 34792466 PMCID: PMC8719888 DOI: 10.7554/elife.71900] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022] Open
Abstract
Agricultural soil harbors a diverse microbiome that can form beneficial relationships with plants, including the inhibition of plant pathogens. Pseudomonas spp. are one of the most abundant bacterial genera in the soil and rhizosphere and play important roles in promoting plant health. However, the genetic determinants of this beneficial activity are only partially understood. Here, we genetically and phenotypically characterize the Pseudomonas fluorescens population in a commercial potato field, where we identify strong correlations between specialized metabolite biosynthesis and antagonism of the potato pathogens Streptomyces scabies and Phytophthora infestans. Genetic and chemical analyses identified hydrogen cyanide and cyclic lipopeptides as key specialized metabolites associated with S. scabies inhibition, which was supported by in planta biocontrol experiments. We show that a single potato field contains a hugely diverse and dynamic population of Pseudomonas bacteria, whose capacity to produce specialized metabolites is shaped both by plant colonization and defined environmental inputs. Potato scab and blight are two major diseases which can cause heavy crop losses. They are caused, respectively, by the bacterium Streptomyces scabies and an oomycete (a fungus-like organism) known as Phytophthora infestans. Fighting these disease-causing microorganisms can involve crop management techniques – for example, ensuring that a field is well irrigated helps to keep S. scabies at bay. Harnessing biological control agents can also offer ways to control disease while respecting the environment. Biocontrol bacteria, such as Pseudomonas, can produce compounds that keep S. scabies and P. infestans in check. However, the identity of these molecules and how irrigation can influence Pseudomonas population remains unknown. To examine these questions, Pacheco-Moreno et al. sampled and isolated hundreds of Pseudomonas strains from a commercial potato field, closely examining the genomes of 69 of these. Comparing the genetic information of strains based on whether they could control the growth of S. scabies revealed that compounds known as cyclic lipopeptides are key to controlling the growth of S. scabies and P. infestans. Whether the field was irrigated also had a large impact on the strains forming the Pseudomonas population. Working out how Pseudomonas bacteria block disease could speed up the search for biological control agents. The approach developed by Pacheco-Moreno et al. could help to predict which strains might be most effective based on their genetic features. Similar experiments could also work for other combinations of plants and diseases.
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Affiliation(s)
- Alba Pacheco-Moreno
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Jonathan J Ford
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Christine Trippel
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Simon Uszkoreit
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Laura Ferrafiat
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Lucia Grenga
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Ruth Dickens
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Nathan Kelly
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Alexander Dh Kingdon
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Liana Ambrosetti
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Sergey A Nepogodiev
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Kim C Findlay
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Jitender Cheema
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Martin Trick
- Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Jacob G Malone
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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9
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Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal. Antimicrob Agents Chemother 2021; 65:e0255720. [PMID: 34152818 DOI: 10.1128/aac.02557-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antibiotic resistance genes exist naturally in various environments far from human usage. Here, we investigated multidrug-resistant Klebsiella pneumoniae, a common pathogen of chimpanzees and humans. We screened antibiotic-resistant K. pneumoniae from 48 chimpanzee stools and 38 termite mounds (n = 415 samples) collected in protected areas in Senegal. The microsatellite method was used to identify chimpanzee individuals (n = 13). Whole-genome sequencing was performed on K. pneumoniae complex isolates to identify antibiotic-resistant genes and characterize clones. We found a high prevalence of carbapenem-resistant K. pneumoniae among chimpanzee isolates (18/48 samples from 7/13 individuals) and ceftriaxone resistance among both chimpanzee individuals (19/48) and termite mounds (7/415 termites and 3/38 termite mounds). The blaOXA-48 and the blaKPC-2 genes were carried by international pOXA-48 and pKPC-2 plasmids, respectively. The ESBL plasmid carried blaCTX-M-15, blaTEM-1B, and blaOXA-1 genes. Genome sequencing of 56 isolates identified two major clones associated with hospital-acquired infections of K. pneumoniae (ST307 and ST147) in chimpanzees and termites, suggesting circulation of strains between the two species, as chimpanzees feed on termites. The source and selection pressure of these clones in this environment need to be explored.
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10
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Raoult D, Hadjadj L, Baron SA, Rolain JM. Role of glyphosate in the emergence of antimicrobial resistance in bacteria? J Antimicrob Chemother 2021; 76:1655-1657. [PMID: 33893490 DOI: 10.1093/jac/dkab102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/02/2021] [Indexed: 12/30/2022] Open
Abstract
There is a discrepancy between antibiotic use in medicine and agriculture in the intertropical zone and frequency of antibiotic resistance in clinical bacteria in these countries. We provide evidence that glyphosate (a herbicide but also an antibiotic drug) could be a possible driver of antibiotic resistance in countries where this herbicide is widely used because of modification of the microbial environment. Emergence of resistance in bacteria and fungi is correlated with glyphosate use in the world over the last 40 years.
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Affiliation(s)
- Didier Raoult
- Institut Hospitalo-universitaire Méditerranée Infection, Marseille, France
- Aix Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (APHM), Microbes Evolution Phylogénie et Infections (MEPHI), Marseille, France
| | - Linda Hadjadj
- Institut Hospitalo-universitaire Méditerranée Infection, Marseille, France
- Aix Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (APHM), Microbes Evolution Phylogénie et Infections (MEPHI), Marseille, France
| | - Sophie Alexandra Baron
- Institut Hospitalo-universitaire Méditerranée Infection, Marseille, France
- Aix Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (APHM), Microbes Evolution Phylogénie et Infections (MEPHI), Marseille, France
| | - Jean-Marc Rolain
- Institut Hospitalo-universitaire Méditerranée Infection, Marseille, France
- Aix Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (APHM), Microbes Evolution Phylogénie et Infections (MEPHI), Marseille, France
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11
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Diene SM, Pinault L, Baron SA, Azza S, Armstrong N, Hadjadj L, Chabrière E, Rolain JM, Pontarotti P, Raoult D. A metallo-β-lactamase enzyme for internal detoxification of the antibiotic thienamycin. Sci Rep 2021; 11:10062. [PMID: 33980996 PMCID: PMC8115136 DOI: 10.1038/s41598-021-89600-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/14/2021] [Indexed: 11/23/2022] Open
Abstract
Thienamycin, the first representative of carbapenem antibiotics was discovered in the mid-1970s from soil microorganism, Streptomyces cattleya, during the race to discover inhibitors of bacterial peptidoglycan synthesis. Chemically modified into imipenem (N-formimidoyl thienamycin), now one of the most clinically important antibiotics, thienamycin is encoded by a thienamycin gene cluster composed of 22 genes (thnA to thnV) from S. cattleya NRRL 8057 genome. Interestingly, the role of all thn-genes has been experimentally demonstrated in the thienamycin biosynthesis, except thnS, despite its annotation as putative β-lactamase. Here, we expressed thnS gene and investigated its activities against various substrates. Our analyses revealed that ThnS belonged to the superfamily of metallo-β-lactamase fold proteins. Compared to known β-lactamases such as OXA-48 and NDM-1, ThnS exhibited a lower affinity and less efficiency toward penicillin G and cefotaxime, while imipenem is more actively hydrolysed. Moreover, like most MBL fold enzymes, additional enzymatic activities of ThnS were detected such as hydrolysis of ascorbic acid, single strand DNA, and ribosomal RNA. ThnS appears as a MBL enzyme with multiple activities including a specialised β-lactamase activity toward imipenem. Thus, like toxin/antitoxin systems, the role of thnS gene within the thienamycin gene cluster appears as an antidote against the produced thienamycin.
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Affiliation(s)
- Seydina M Diene
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Lucile Pinault
- Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Sophie Alexandra Baron
- Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Saïd Azza
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Nicholas Armstrong
- Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Linda Hadjadj
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Eric Chabrière
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Jean-Marc Rolain
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Pierre Pontarotti
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,CNRS, Marseille, France
| | - Didier Raoult
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. .,IHU-Méditerranée Infection, Marseille, France.
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12
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Busi SB, de Nies L, Habier J, Wampach L, Fritz JV, Heintz-Buschart A, May P, Halder R, de Beaufort C, Wilmes P. Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life. ISME COMMUNICATIONS 2021; 1:8. [PMID: 36717704 PMCID: PMC9723731 DOI: 10.1038/s43705-021-00003-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/09/2020] [Accepted: 01/02/2021] [Indexed: 04/17/2023]
Abstract
Caesarean section delivery (CSD) disrupts mother-to-neonate transmission of specific microbial strains and functional repertoires as well as linked immune system priming. Here we investigate whether differences in microbiome composition and impacts on host physiology persist at 1 year of age. We perform high-resolution, quantitative metagenomic analyses of the gut microbiomes of infants born by vaginal delivery (VD) or by CSD, from immediately after birth through to 1 year of life. Several microbial populations show distinct enrichments in CSD-born infants at 1 year of age including strains of Bacteroides caccae, Bifidobacterium bifidum and Ruminococcus gnavus, whereas others are present at higher levels in the VD group including Faecalibacterium prausnitizii, Bifidobacterium breve and Bifidobacterium kashiwanohense. The stimulation of healthy donor-derived primary human immune cells with LPS isolated from neonatal stool samples results in higher levels of tumour necrosis factor alpha (TNF-α) in the case of CSD extracts over time, compared to extracts from VD infants for which no such changes were observed during the first year of life. Functional analyses of the VD metagenomes at 1 year of age demonstrate a significant increase in the biosynthesis of the natural antibiotics, carbapenem and phenazine. Concurrently, we find antimicrobial resistance (AMR) genes against several classes of antibiotics in both VD and CSD. The abundance of AMR genes against synthetic (including semi-synthetic) agents such as phenicol, pleuromutilin and diaminopyrimidine are increased in CSD children at day 5 after birth. In addition, we find that mobile genetic elements, including phages, encode AMR genes such as glycopeptide, diaminopyrimidine and multidrug resistance genes. Our results demonstrate persistent effects at 1 year of life resulting from birth mode-dependent differences in earliest gut microbiome colonisation.
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Affiliation(s)
- Susheel Bhanu Busi
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laura de Nies
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Janine Habier
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Linda Wampach
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Joëlle V Fritz
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Translational Neuroscience group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), 1445, Strassen, Luxembourg
| | - Anna Heintz-Buschart
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Metagenomics Support Unit, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Halle, Germany
- Department of Soil Ecology, Helmholtz-Centre for Environmental Research GmbH - UFZ, Halle, Germany
| | - Patrick May
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rashi Halder
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Carine de Beaufort
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Centre Hospitalier de Luxembourg, Department of Pediatric Endocrinology and Diabetes, Luxembourg, Luxembourg
- Department of Pediatric Endocrinology, UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Paul Wilmes
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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13
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Maglangit F, Yu Y, Deng H. Bacterial pathogens: threat or treat (a review on bioactive natural products from bacterial pathogens). Nat Prod Rep 2021; 38:782-821. [PMID: 33119013 DOI: 10.1039/d0np00061b] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to the second quarter of 2020 Threat or treat? While pathogenic bacteria pose significant threats, they also represent a huge reservoir of potential pharmaceuticals to treat various diseases. The alarming antimicrobial resistance crisis and the dwindling clinical pipeline urgently call for the discovery and development of new antibiotics. Pathogenic bacteria have an enormous potential for natural products drug discovery, yet they remained untapped and understudied. Herein, we review the specialised metabolites isolated from entomopathogenic, phytopathogenic, and human pathogenic bacteria with antibacterial and antifungal activities, highlighting those currently in pre-clinical trials or with potential for drug development. Selected unusual biosynthetic pathways, the key roles they play (where known) in various ecological niches are described. We also provide an overview of the mode of action (molecular target), activity, and minimum inhibitory concentration (MIC) towards bacteria and fungi. The exploitation of pathogenic bacteria as a rich source of antimicrobials, combined with the recent advances in genomics and natural products research methodology, could pave the way for a new golden age of antibiotic discovery. This review should serve as a compendium to communities of medicinal chemists, organic chemists, natural product chemists, biochemists, clinical researchers, and many others interested in the subject.
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Affiliation(s)
- Fleurdeliz Maglangit
- Department of Biology and Environmental Science, College of Science, University of the Philippines Cebu, Lahug, Cebu City, 6000, Philippines. and Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK.
| | - Yi Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Hubei Province Engineering and Technology Research Centre for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK.
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14
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Qin H, Liu Y, Cao X, Jiang J, Lian W, Qiao D, Xu H, Cao Y. RpoS is a pleiotropic regulator of motility, biofilm formation, exoenzymes, siderophore and prodigiosin production, and trade-off during prolonged stationary phase in Serratia marcescens. PLoS One 2020; 15:e0232549. [PMID: 32484808 PMCID: PMC7266296 DOI: 10.1371/journal.pone.0232549] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 04/16/2020] [Indexed: 02/07/2023] Open
Abstract
Prodigiosin is an important secondary metabolite produced by Serratia marcescens. It can help strains resist stresses from other microorganisms and environmental factors to achieve self-preservation. Prodigiosin is also a promising secondary metabolite due to its pharmacological characteristics. However, pigmentless S. marcescens mutants always emerge after prolonged starvation, which might be a way for the bacteria to adapt to starvation conditions, but it could be a major problem in the industrial application of S. marcescens. To identify the molecular mechanisms of loss of prodigiosin production, two mutants were isolated after 16 days of prolonged incubation of wild-type (WT) S. marcescens 1912768R; one mutant (named 1912768WR) exhibited reduced production of prodigiosin, and a second mutant (named 1912768W) was totally defective. Comparative genomic analysis revealed that the two mutants had either mutations or deletions in rpoS. Knockout of rpoS in S. marcescens 1912768R had pleiotropic effects. Complementation of rpoS in the ΔrpoS mutant further confirmed that RpoS was a positive regulator of prodigiosin production and that its regulatory role in prodigiosin biosynthesis was opposite that in Serratia sp. ATCC 39006, which had a different type of pig cluster; further, rpoS from Serratia sp. ATCC 39006 and other strains complemented the prodigiosin defect of the ΔrpoS mutant, suggesting that the pig promoters are more important than the genes in the regulation of prodigiosin production. Deletion of rpoS strongly impaired the resistance of S. marcescens to stresses but increased membrane permeability for nutritional competence; competition assays in rich and minimum media showed that the ΔrpoS mutant outcompeted its isogenic WT strain. All these data support the idea that RpoS is pleiotropic and that the loss of prodigiosin biosynthesis in S. marcescens 1912768R during prolonged incubation is due to a mutation in rpoS, which appears to be a self-preservation and nutritional competence (SPANC) trade-off.
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Affiliation(s)
- Han Qin
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, P.R. China
| | - Ying Liu
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, P.R. China
| | - Xiyue Cao
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, P.R. China
| | - Jia Jiang
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, P.R. China
| | - Weishao Lian
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, P.R. China
| | - Dairong Qiao
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, P.R. China
| | - Hui Xu
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, P.R. China
- * E-mail: (YC); (HX)
| | - Yi Cao
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, P.R. China
- * E-mail: (YC); (HX)
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15
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Quintero-Yanes A, Lee CM, Monson R, Salmond G. The FloR master regulator controls flotation, virulence and antibiotic production in Serratia sp. ATCC 39006. Environ Microbiol 2020; 22:2921-2938. [PMID: 32352190 DOI: 10.1111/1462-2920.15048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/23/2020] [Accepted: 04/25/2020] [Indexed: 11/26/2022]
Abstract
Serratia sp. ATCC 39006 produces intracellular gas vesicles to enable upward flotation in water columns. It also uses flagellar rotation to swim through liquid and swarm across semi-solid surfaces. Flotation and motility can be co-regulated with production of a β-lactam antibiotic (carbapenem carboxylate) and a linear tripyrrole red antibiotic, prodigiosin. Production of gas vesicles, carbapenem and prodigiosin antibiotics, and motility are controlled by master transcriptional and post-transcriptional regulators, including the SmaI/SmaR-based quorum sensing system and the mRNA binding protein, RsmA. Recently, the ribose operon repressor, RbsR, was also defined as a pleiotropic regulator of flotation and virulence factor elaboration in this strain. Here, we report the discovery of a new global regulator (FloR; a DeoR family transcription factor) that modulates flotation through control of gas vesicle morphogenesis. The floR mutation is highly pleiotropic, down-regulating production of gas vesicles, carbapenem and prodigiosin antibiotics, and infection in Caenorhabditis elegans, but up-regulating flagellar motility. Detailed proteomic analysis using TMT peptide labelling and LC-MS/MS revealed that FloR is a physiological master regulator that operates through subordinate pleiotropic regulators including Rap, RpoS, RsmA, PigU, PstS and PigT.
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Affiliation(s)
- Alex Quintero-Yanes
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Cambridge, CB2 1QW, UK.,Bacterial Cell cycle and Development (BCcD), University of Namur, 61 Rue de Bruxelles, Namur, 5000, Belgium
| | - Chin Mei Lee
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Cambridge, CB2 1QW, UK.,Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Gambang, 26300, Malaysia
| | - Rita Monson
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Cambridge, CB2 1QW, UK
| | - George Salmond
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Cambridge, CB2 1QW, UK
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16
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Nawaz H, Gul S, Shad M, Arshad R, Ali A, Altaf A, Gul T, Iqbal W. Response surface optimization of prodigiosin production by mutagen-treated Serratia marcescens in different growth media. Pharmacogn Mag 2020. [DOI: 10.4103/pm.pm_430_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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17
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Antimicrobial secondary metabolites from agriculturally important bacteria as next-generation pesticides. Appl Microbiol Biotechnol 2019; 104:1013-1034. [PMID: 31858191 DOI: 10.1007/s00253-019-10300-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/25/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
Abstract
The whole organisms can be packaged as biopesticides, but secondary metabolites secreted by microorganisms can also have a wide range of biological activities that either protect the plant against pests and pathogens or act as plant growth promotors which can be beneficial for the agricultural crops. In this review, we have compiled information about the most important secondary metabolites of three important bacterial genera currently used in agriculture pest and disease management.
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18
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Shyntum DY, Nkomo NP, Shingange NL, Gricia AR, Bellieny-Rabelo D, Moleleki LN. The Impact of Type VI Secretion System, Bacteriocins and Antibiotics on Bacterial Competition of Pectobacterium carotovorum subsp. brasiliense and the Regulation of Carbapenem Biosynthesis by Iron and the Ferric-Uptake Regulator. Front Microbiol 2019; 10:2379. [PMID: 31681235 PMCID: PMC6813493 DOI: 10.3389/fmicb.2019.02379] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/30/2019] [Indexed: 12/17/2022] Open
Abstract
The complexity of plant microbial communities provides a rich model for investigating biochemical and regulatory strategies involved in interbacterial competition. Within these niches, the soft rot Enterobacteriaceae (SRE) represents an emerging group of plant-pathogens causing soft rot/blackleg diseases resulting in economic losses worldwide in a variety of crops. A preliminary screening using next-generation sequencing of 16S rRNA comparatively analyzing healthy and diseased potato tubers, identified several taxa from Proteobacteria to Firmicutes as potential potato endophytes/plant pathogens. Subsequent to this, a range of molecular and computational techniques were used to determine the contribution of antimicrobial factors such as bacteriocins, carbapenem and type VI secretion system (T6SS), found in an aggressive SRE (Pectobacterium carotovorum subsp. brasiliense strain PBR1692 - Pcb1692) against these endophytes/plant pathogens. The results showed growth inhibition of several Proteobacteria by Pcb1692 depends either on carbapenem or pyocin production. Whereas for targeted Firmicutes, only the Pcb1692 pyocin seems to play a role in growth inhibition. Furthermore, production of carbapenem by Pcb1692 was observably dependent on the presence of environmental iron and oxygen. Additionally, upon deletion of fur, slyA and expI regulators, carbapenem production ceased, implying a complex regulatory mechanism involving these three genes. Finally, the results demonstrated that although T6SS confers no relevant advantage during in vitro competition, a significant attenuation in competition by the mutant strain lacking a functional T6SS was observed in planta. IMPORTANCE Soft rot Enterobacteriaceae (SRE) represents important phytopathogens causing soft rot/blackleg diseases in a variety of crops leading to huge economic losses worldwide. These pathogens have been isolated alongside other bacteria from different environments such as potato tubers, stems, roots and from the soil. In these environments, SREs coexist with other bacteria where they have to compete for scarce nutrients and other resources. In this report, we show that Pectobacterium carotovorum subsp. brasiliense strain PBR1692 - Pcb1692, which represents one of the SREs, inhibits growth of several different bacteria by producing different antimicrobial compounds. These antimicrobial compounds can be secreted inside or outside the plant host, allowing Pcb1692 to effectively colonize different types of ecological niches. By analyzing the genome sequences of several SREs, we show that other SREs likely deploy similar antimicrobials to target other bacteria.
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Affiliation(s)
- Divine Yufetar Shyntum
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Ntombikayise Precious Nkomo
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Ntwanano Luann Shingange
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Alessandro Rino Gricia
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Daniel Bellieny-Rabelo
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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19
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Matilla MA, Daddaoua A, Chini A, Morel B, Krell T. An auxin controls bacterial antibiotics production. Nucleic Acids Res 2019; 46:11229-11238. [PMID: 30500953 PMCID: PMC6265452 DOI: 10.1093/nar/gky766] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/21/2018] [Indexed: 01/02/2023] Open
Abstract
The majority of clinically used antibiotics originate from bacteria. As the need for new antibiotics grows, large-scale genome sequencing and mining approaches are being used to identify novel antibiotics. However, this task is hampered by the fact that many antibiotic biosynthetic clusters are not expressed under laboratory conditions. One strategy to overcome this limitation is the identification of signals that activate the expression of silent biosynthetic pathways. Here, we report the use of high-throughput screening to identify signals that control the biosynthesis of the acetyl-CoA carboxylase inhibitor antibiotic andrimid in the broad-range antibiotic-producing rhizobacterium Serratia plymuthica A153. We reveal that the pathway-specific transcriptional activator AdmX recognizes the auxin indole-3-acetic acid (IAA). IAA binding causes conformational changes in AdmX that result in the inhibition of the expression of the andrimid cluster and the suppression of antibiotic production. We also show that IAA synthesis by pathogenic and beneficial plant-associated bacteria inhibits andrimid production in A153. Because IAA is a signalling molecule that is present across all domains of life, this study highlights the importance of intra- and inter-kingdom signalling in the regulation of antibiotic synthesis. Our discovery unravels, for the first time, an IAA-dependent molecular mechanism for the regulation of antibiotic synthesis.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | | | - Andrea Chini
- Department of Plant Molecular Genetics, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Bertrand Morel
- Departament of Physical Chemistry and Institute for Biotechnology, Science Faculty, Granada University, 18071 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
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20
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Quintero-Yanes A, Monson RE, Salmond GPC. Environmental potassium regulates bacterial flotation, antibiotic production and turgor pressure in Serratia through the TrkH transporter. Environ Microbiol 2019; 21:2499-2510. [PMID: 31012245 PMCID: PMC6617781 DOI: 10.1111/1462-2920.14637] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/16/2019] [Accepted: 04/21/2019] [Indexed: 11/28/2022]
Abstract
Serratia sp. strain ATCC 39006 (S39006) can float in aqueous environments due to natural production of gas vesicles (GVs). Expression of genes for GV morphogenesis is stimulated in low oxygen conditions, thereby enabling migration to the air–liquid interface. Quorum sensing (via SmaI and SmaR) and transcriptional and post‐transcriptional regulators, including RbsR and RsmA, respectively, connect the control of cell buoyancy, motility and secondary metabolism. Here, we define a new pleiotropic regulator found in screens of GV mutants. A mutation in the gene trkH, encoding a potassium transporter, caused upregulation of GV formation, flotation, and the prodigiosin antibiotic, and downregulation of flagellar motility. Pressure nephelometry revealed that the mutation in trkH affected cell turgor pressure. Our results show that osmotic change is an important physiological parameter modulating cell buoyancy and antimicrobial production in S39006, in response to environmental potassium levels.
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Affiliation(s)
- Alex Quintero-Yanes
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site. Cambridge, CB2 1QW, UK
| | - Rita E Monson
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site. Cambridge, CB2 1QW, UK
| | - George P C Salmond
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site. Cambridge, CB2 1QW, UK
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21
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Duprey A, Taib N, Leonard S, Garin T, Flandrois JP, Nasser W, Brochier-Armanet C, Reverchon S. The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity. Environ Microbiol 2019; 21:2809-2835. [PMID: 30969462 DOI: 10.1111/1462-2920.14627] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 12/13/2022]
Abstract
Dickeya is a genus of phytopathogenic enterobacterales causing soft rot in a variety of plants (e.g. potato, chicory, maize). Among the species affiliated to this genus, Dickeya aquatica, described in 2014, remained particularly mysterious because it had no known host. Furthermore, while D. aquatica was proposed to represent a deep-branching species among Dickeya genus, its precise phylogenetic position remained elusive. Here, we report the complete genome sequence of the D. aquatica type strain 174/2. We demonstrate the affinity of D. aquatica strain 174/2 for acidic fruits such as tomato and cucumber and show that exposure of this bacterium to acidic pH induces twitching motility. An in-depth phylogenomic analysis of all available Dickeya proteomes pinpoints D. aquatica as the second deepest branching lineage within this genus and reclassifies two lineages that likely correspond to new genomospecies (gs.): Dickeya gs. poaceaephila (Dickeya sp NCPPB 569) and Dickeya gs. undicola (Dickeya sp 2B12), together with a new putative genus, tentatively named Prodigiosinella. Finally, from comparative analyses of Dickeya proteomes, we infer the complex evolutionary history of this genus, paving the way to study the adaptive patterns and processes of Dickeya to different environmental niches and hosts. In particular, we hypothesize that the lack of xylanases and xylose degradation pathways in D. aquatica could reflect adaptation to aquatic charophyte hosts which, in contrast to land plants, do not contain xyloglucans.
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Affiliation(s)
- Alexandre Duprey
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
| | - Najwa Taib
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Simon Leonard
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
| | - Tiffany Garin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Jean-Pierre Flandrois
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - William Nasser
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
| | - Céline Brochier-Armanet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Sylvie Reverchon
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
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22
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Wang C, Pu T, Lou W, Wang Y, Gao Z, Hu B, Fan J. Hfq, a RNA Chaperone, Contributes to Virulence by Regulating Plant Cell Wall-Degrading Enzyme Production, Type VI Secretion System Expression, Bacterial Competition, and Suppressing Host Defense Response in Pectobacterium carotovorum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1166-1178. [PMID: 30198820 DOI: 10.1094/mpmi-12-17-0303-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Hfq is a RNA chaperone and participates in a wide range of cellular processes and pathways. In this study, mutation of hfq gene from Pectobacterium carotovorum subsp. carotovorum PccS1 led to significantly reduced virulence and plant cell wall-degrading enzyme (PCWDE) activities. In addition, the mutant exhibited decreased biofilm formation and motility and greatly attenuated carbapenem production as well as secretion of hemolysin coregulated protein (Hcp) as compared with wild-type strain PccS1. Moreover, a higher level of callose deposition was induced in Nicotiana benthamiana leaves when infiltrated with the mutant. A total of 26 small (s)RNA deletion mutants were obtained among a predicted 27 sRNAs, and three mutants exhibited reduced virulence in the host plant. These results suggest that hfq plays a key role in Pectobacterium virulence by positively impacting PCWDE production, secretion of the type VI secretion system, bacterial competition, and suppression of host plant responses.
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Affiliation(s)
- Chunting Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianxin Pu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wangying Lou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yujie Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zishu Gao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Baishi Hu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiaqin Fan
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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23
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Viana Marques DDA, Machado SEF, Ebinuma VCS, Duarte CDAL, Converti A, Porto ALF. Production of β-Lactamase Inhibitors by Streptomyces Species. Antibiotics (Basel) 2018; 7:E61. [PMID: 30018235 PMCID: PMC6163296 DOI: 10.3390/antibiotics7030061] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/07/2018] [Accepted: 07/12/2018] [Indexed: 12/11/2022] Open
Abstract
β-Lactamase inhibitors have emerged as an effective alternative to reduce the effects of resistance against β-lactam antibiotics. The Streptomyces genus is known for being an exceptional natural source of antimicrobials and β-lactamase inhibitors such as clavulanic acid, which is largely applied in clinical practice. To protect against the increasing prevalence of multidrug-resistant bacterial strains, new antibiotics and β-lactamase inhibitors need to be discovered and developed. This review will cover an update about the main β-lactamase inhibitors producers belonging to the Streptomyces genus; advanced methods, such as genetic and metabolic engineering, to enhance inhibitor production compared with wild-type strains; and fermentation and purification processes. Moreover, clinical practice and commercial issues are discussed. The commitment of companies and governments to develop innovative strategies and methods to improve the access to new, efficient, and potentially cost-effective microbial products to combat the antimicrobial resistance is also highlighted.
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Affiliation(s)
- Daniela de Araújo Viana Marques
- Campus Serra Talhada, University of Pernambuco, Avenida Custódio Conrado, 600, AABB, Serra Talhada, Pernambuco 56912-550, Brazil.
| | - Suellen Emilliany Feitosa Machado
- Department of Antibiotics, Federal University of Pernambuco, Avenida da Engenharia, 2° andar, Cidade Universitária, Recife, Pernambuco 50740-600, Brazil.
| | - Valéria Carvalho Santos Ebinuma
- Department of Bioprocesses and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rodovia Araraquara-Jaú/Km 01, Araraquara 14800-903, Brazil.
| | | | - Attilio Converti
- Department of Civil, Chemical and Environmental Engineering, Chemical Pole, University of Genoa, Via Opera Pia 15, 16145 Genoa, Italy.
| | - Ana Lúcia Figueiredo Porto
- Department of Morphology and Animal Physiology, Federal Rural University of Pernambuco, Av. Dom Manoel de Medeiros, Recife, Pernambuco 52171-900, Brazil.
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24
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Metabolic engineering of a carbapenem antibiotic synthesis pathway in Escherichia coli. Nat Chem Biol 2018; 14:794-800. [DOI: 10.1038/s41589-018-0084-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/27/2018] [Indexed: 12/14/2022]
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25
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Oh J, Patel J, Park HB, Crawford JM. β-Lactam Biotransformations Activate Innate Immunity. J Org Chem 2018; 83:7173-7179. [PMID: 29616809 DOI: 10.1021/acs.joc.8b00241] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Antibiotics are widely prescribed to treat bacterial infections, but many of these drugs also affect patient immune responses. While the molecular mechanisms regulating these diverse immunomodulatory interactions are largely unknown, recent studies support two primary models: (1) antibiotics can alter immune function by directly interacting with human targets; and/or (2) antibiotics can indirectly affect immune responses via alteration of the human microbiota composition. Here, we describe results that could support a third model in which a nonimmunostimulatory antibiotic can be biotransformed by human microbiota members into an immunostimulatory product that lacks antibacterial activity. Specifically, we identified, characterized, and semisynthesized new biotransformation products derived from the β-lactams amoxicillin and ampicillin, antibiotics regularly prescribed in the clinic. The drug metabolism products were identified in bacterial cultures harboring β-lactamase, a common resistance determinant. One of the amoxicillin biotransformation products activated innate immunity, as assessed by NF-κB signaling in human leukemic monocytes, whereas amoxicillin itself exhibited no effect. Amoxicillin has previously been shown to have minimal long-term impact on human microbiota composition in clinical trial studies. Taken together, our results could support a broader immunomodulatory mechanism whereby antibiotics could indirectly regulate immune function in a stable, microbiome-dependent manner.
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Affiliation(s)
- Joonseok Oh
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Jaymin Patel
- Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States.,Department of Molecular, Cellular, and Developmental Biology , Yale University , New Haven , Connecticut 06520 , United States
| | - Hyun Bong Park
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Jason M Crawford
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States.,Department of Microbial Pathogenesis , Yale School of Medicine , New Haven , Connecticut 06536 , United States
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26
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An IgaA/UmoB Family Protein from Serratia marcescens Regulates Motility, Capsular Polysaccharide Biosynthesis, and Secondary Metabolite Production. Appl Environ Microbiol 2018; 84:AEM.02575-17. [PMID: 29305504 DOI: 10.1128/aem.02575-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 12/23/2017] [Indexed: 12/28/2022] Open
Abstract
Secondary metabolites are an important source of pharmaceuticals and key modulators of microbe-microbe interactions. The bacterium Serratia marcescens is part of the Enterobacteriaceae family of eubacteria and produces a number of biologically active secondary metabolites. In this study, we screened for novel regulators of secondary metabolites synthesized by a clinical isolate of S. marcescens and found mutations in a gene for an uncharacterized UmoB/IgaA family member here named gumB Mutation of gumB conferred a severe loss of the secondary metabolites prodigiosin and serratamolide. The gumB mutation conferred pleiotropic phenotypes, including altered biofilm formation, highly increased capsular polysaccharide production, and loss of swimming and swarming motility. These phenotypes corresponded to transcriptional changes in fimA, wecA, and flhD Unlike other UmoB/IgaA family members, gumB was found to be not essential for growth in S. marcescens, yet igaA from Salmonella enterica, yrfF from Escherichia coli, and an uncharacterized predicted ortholog from Klebsiella pneumoniae complemented the gumB mutant secondary metabolite defects, suggesting highly conserved function. These data support the idea that UmoB/IgaA family proteins are functionally conserved and extend the known regulatory influence of UmoB/IgaA family proteins to the control of competition-associated secondary metabolites and biofilm formation.IMPORTANCE IgaA/UmoB family proteins are found in members of the Enterobacteriaceae family of bacteria, which are of environmental and public health importance. IgaA/UmoB family proteins are thought to be inner membrane proteins that report extracellular stresses to intracellular signaling pathways that respond to environmental challenge. This study introduces a new member of the IgaA/UmoB family and demonstrates a high degree of functional similarity between IgaA/UmoB family proteins. Moreover, this study extends the phenomena controlled by IgaA/UmoB family proteins to include the biosynthesis of antimicrobial secondary metabolites.
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27
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STOCK SPATRICIA, KUSAKABE AYAKO, OROZCO ROUSELA. Secondary Metabolites Produced by Heterorhabditis Symbionts and Their Application in Agriculture: What We Know and What to Do Next. J Nematol 2018. [DOI: 10.21307/jofnem-2017-084] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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28
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Abstract
One of the greatest sources of metabolic and enzymatic diversity are microorganisms. In recent years, emerging recombinant DNA and genomic techniques have facilitated the development of new efficient expression systems, modification of biosynthetic pathways leading to new metabolites by metabolic engineering, and enhancement of catalytic properties of enzymes by directed evolution. Complete sequencing of industrially important microbial genomes is taking place very rapidly, and there are already hundreds of genomes sequenced. Functional genomics and proteomics are major tools used in the search for new molecules and development of higher-producing strains.
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Affiliation(s)
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, CDMX, México
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29
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Enomoto S, Chari A, Clayton AL, Dale C. Quorum Sensing Attenuates Virulence in Sodalis praecaptivus. Cell Host Microbe 2017; 21:629-636.e5. [PMID: 28494244 DOI: 10.1016/j.chom.2017.04.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 02/15/2017] [Accepted: 04/19/2017] [Indexed: 10/19/2022]
Abstract
Sodalis praecaptivus is a close relative and putative environmental progenitor of the widely distributed, insect-associated, Sodalis-allied symbionts. Here we show that mutant strains of S. praecaptivus that lack genetic components of a quorum-sensing (QS) apparatus have a rapid and potent killing phenotype following microinjection into an insect host. Transcriptomic and genetic analyses indicate that insect killing occurs as a consequence of virulence factors, including insecticidal toxins and enzymes that degrade the insect integument, which are normally repressed by QS at high infection densities. This method of regulation suggests that virulence factors are only utilized in early infection to initiate the insect-bacterial association. Once bacteria reach sufficient density in host tissues, the QS circuit represses expression of these harmful genes, facilitating a long-lasting and benign association. We discuss the implications of the functionality of this QS system in the context of establishment and evolution of mutualistic relationships involving these bacteria.
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Affiliation(s)
- Shinichiro Enomoto
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Abhishek Chari
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Adam Larsen Clayton
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Colin Dale
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA.
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30
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Lee CM, Monson RE, Adams RM, Salmond GPC. The LacI-Family Transcription Factor, RbsR, Is a Pleiotropic Regulator of Motility, Virulence, Siderophore and Antibiotic Production, Gas Vesicle Morphogenesis and Flotation in Serratia. Front Microbiol 2017; 8:1678. [PMID: 28955306 PMCID: PMC5601083 DOI: 10.3389/fmicb.2017.01678] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/21/2017] [Indexed: 11/21/2022] Open
Abstract
Gas vesicles (GVs) are proteinaceous, gas-filled organelles used by some bacteria to enable upward movement into favorable air/liquid interfaces in aquatic environments. Serratia sp. ATCC39006 (S39006) was the first enterobacterium discovered to produce GVs naturally. The regulation of GV assembly in this host is complex and part of a wider regulatory network affecting various phenotypes, including antibiotic biosynthesis. To identify new regulators of GVs, a comprehensive mutant library containing 71,000 insertion mutants was generated by random transposon mutagenesis and 311 putative GV-defective mutants identified. Three of these mutants were found to have a transposon inserted in a LacI family transcription regulator gene (rbsR) of the putative ribose operon. Each of these rbsR mutants was GV-defective; no GVs were visible by phase contrast microscopy (PCM) or transmission electron microscopy (TEM). GV deficiency was caused by the reduction of gvpA1 and gvrA transcription (the first genes of the two contiguous operons in the GV gene locus). Our results also showed that a mutation in rbsR was highly pleiotropic; the production of two secondary metabolites (carbapenem and prodigiosin antibiotics) was abolished. Interestingly, the intrinsic resistance to the carbapenem antibiotic was not affected by the rbsR mutation. In addition, the production of a siderophore, cellulase and plant virulence was reduced in the mutant, whereas it exhibited increased swimming and swarming motility. The RbsR protein was predicted to bind to regions upstream of at least 18 genes in S39006 including rbsD (the first gene of the ribose operon) and gvrA. Electrophoretic mobility shift assays (EMSA) confirmed that RbsR bound to DNA sequences upstream of rbsD, but not gvrA. The results of this study indicate that RbsR is a global regulator that affects the modulation of GV biogenesis, but also with complex pleiotropic physiological impacts in S39006.
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31
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Lohans CT, Wang DY, Wang J, Hamed RB, Schofield CJ. Crotonases: Nature’s Exceedingly Convertible Catalysts. ACS Catal 2017. [DOI: 10.1021/acscatal.7b01699] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Christopher T. Lohans
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - David Y. Wang
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Jimmy Wang
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Refaat B. Hamed
- Department
of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
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32
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Tichy EM, Hardwick SW, Luisi BF, Salmond GPC. 1.8 Å resolution crystal structure of the carbapenem intrinsic resistance protein CarF. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:549-556. [PMID: 28695855 DOI: 10.1107/s2059798317002236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 02/09/2017] [Indexed: 11/10/2022]
Abstract
The natural production of the β-lactam antibiotic carbapenem in bacteria involves a group of enzymes that form a synthetic pathway as well as proteins that protect the cell from self-intoxification by the products. Here, the crystal structure of CarF, one of the two proteins that confer resistance to synthesis of the antibiotic in the host organism, is reported. The CarF fold places it within a widely occurring structural family, indicating an ancient structural origin from which the resistance function has been derived.
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Affiliation(s)
- Evelyn M Tichy
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB2 1QW, England
| | - Steven W Hardwick
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB2 1QW, England
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB2 1QW, England
| | - George P C Salmond
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB2 1QW, England
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Shi D, An R, Zhang W, Zhang G, Yu Z. Stilbene Derivatives from Photorhabdus temperata SN259 and Their Antifungal Activities against Phytopathogenic Fungi. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:60-65. [PMID: 27960253 DOI: 10.1021/acs.jafc.6b04303] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Chemical investigation of an insect pathogenic enterobacterium, Photorhabdus temperata SN259, led to the isolation and identification of seven metabolites, which include three new compounds, 3-hydroxy-2-isopropyl-5-phenethylphenyl carbamate, 1, 2-(1-hydroxypropan-2-yl)-5-[2-phenylethyl]benzene-1,3-diol, 2, 2-(1-hydroxypropan-2-yl)-5-[(E)-2-phenylethenyl]benzene-1,3-diol, 3, and four known metabolites (4-7). Their structures were elucidated on the basis of MS and NMR data and by comparison with those reported previously. The activities of compounds 1-7 were evaluated against four phytopathogenic fungi (Pythium aphanidermatum, Rhizoctonia solani Kuhn, Exserohilum turcicum, and Fusarium oxysporum). In an agar medium assay, compounds 1 and 7 showed strong inhibition against P. aphanidermatum with EC50 values of 2.8 and 2.7 μg/mL, respectively. By comparing the structure of compounds 1-7, we deduced that the acylamino group in compound 1 and the isopropyl group in compound 7 contribute to the inhibitory activity.
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Affiliation(s)
- Danshu Shi
- College of Plant Protection, Shenyang Agricultural University , Shenyang 110866, People's Republic of China
| | - Ran An
- College of Plant Protection, Shenyang Agricultural University , Shenyang 110866, People's Republic of China
| | - Wenbo Zhang
- College of Plant Protection, Shenyang Agricultural University , Shenyang 110866, People's Republic of China
| | - Guilong Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture , Tianjin 300191, People's Republic of China
| | - Zhiguo Yu
- College of Plant Protection, Shenyang Agricultural University , Shenyang 110866, People's Republic of China
- Engineering & Technological Research Center of Biopesticide for Liaoning Province , Shenyang 110866, People's Republic of China
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Matilla MA, Nogellova V, Morel B, Krell T, Salmond GPC. Biosynthesis of the acetyl-CoA carboxylase-inhibiting antibiotic, andrimid in Serratia is regulated by Hfq and the LysR-type transcriptional regulator, AdmX. Environ Microbiol 2016; 18:3635-3650. [PMID: 26914969 PMCID: PMC5216899 DOI: 10.1111/1462-2920.13241] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/20/2016] [Indexed: 12/30/2022]
Abstract
Infections due to multidrug-resistant bacteria represent a major global health challenge. To combat this problem, new antibiotics are urgently needed and some plant-associated bacteria are a promising source. The rhizobacterium Serratia plymuthica A153 produces several bioactive secondary metabolites, including the anti-oomycete and antifungal haterumalide, oocydin A and the broad spectrum polyamine antibiotic, zeamine. In this study, we show that A153 produces a second broad spectrum antibiotic, andrimid. Using genome sequencing, comparative genomics and mutagenesis, we defined new genes involved in andrimid (adm) biosynthesis. Both the expression of the adm gene cluster and regulation of andrimid synthesis were investigated. The biosynthetic cluster is operonic and its expression is modulated by various environmental cues, including temperature and carbon source. Analysis of the genome context of the adm operon revealed a gene encoding a predicted LysR-type regulator, AdmX, apparently unique to Serratia strains. Mutagenesis and gene expression assays demonstrated that AdmX is a transcriptional activator of the adm gene cluster. At the post-transcriptional level, the expression of the adm cluster is positively regulated by the RNA chaperone, Hfq, in an RpoS-independent manner. Our results highlight the complexity of andrimid biosynthesis - an antibiotic with potential clinical and agricultural utility.
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Affiliation(s)
- Miguel A. Matilla
- Department of BiochemistryUniversity of CambridgeTennis Court RoadCambridgeCB2 1QWUK
- Department of Environmental ProtectionEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasProf. Albareda 1Granada18008Spain
| | - Veronika Nogellova
- Department of BiochemistryUniversity of CambridgeTennis Court RoadCambridgeCB2 1QWUK
| | - Bertrand Morel
- Department of Environmental ProtectionEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasProf. Albareda 1Granada18008Spain
| | - Tino Krell
- Department of Environmental ProtectionEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasProf. Albareda 1Granada18008Spain
| | - George P. C. Salmond
- Department of BiochemistryUniversity of CambridgeTennis Court RoadCambridgeCB2 1QWUK
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Rastegari B, Karbalaei-Heidari HR. Sulfate as a pivotal factor in regulation of Serratia sp. strain S2B pigment biosynthesis. Res Microbiol 2016; 167:638-646. [DOI: 10.1016/j.resmic.2016.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/17/2016] [Accepted: 05/19/2016] [Indexed: 11/26/2022]
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36
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Monson RE, Tashiro Y, Salmond GPC. Overproduction of individual gas vesicle proteins perturbs flotation, antibiotic production and cell division in the enterobacterium Serratia sp. ATCC 39006. Microbiology (Reading) 2016; 162:1595-1607. [DOI: 10.1099/mic.0.000347] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rita E. Monson
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Yosuke Tashiro
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu 432-8561, Japan
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Ding W, Li Q, Jia Y, Ji X, Qianzhu H, Zhang Q. Emerging Diversity of the Cobalamin-Dependent Methyltransferases Involving Radical-Based Mechanisms. Chembiochem 2016; 17:1191-7. [PMID: 27028019 DOI: 10.1002/cbic.201600107] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Indexed: 11/10/2022]
Abstract
Cobalamins comprise a group of cobalt-containing organometallic cofactors that play important roles in cellular metabolism. Although many cobalamin-dependent methyltransferases (e.g., methionine synthase MetH) have been extensively studied, a new group of methyltransferases that are cobalamin-dependent and utilize radical chemistry in catalysis is just beginning to be appreciated. In this Concept article, we summarize recent advances in the understanding of the radical-based and cobalamin-dependent methyltransferases and discuss the functional and mechanistic diversity of this emerging class of enzymes.
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Affiliation(s)
- Wei Ding
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Qien Li
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Youli Jia
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Haocheng Qianzhu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
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Joyce SA, Lango L, Clarke DJ. The Regulation of Secondary Metabolism and Mutualism in the Insect Pathogenic Bacterium Photorhabdus luminescens. ADVANCES IN APPLIED MICROBIOLOGY 2016; 76:1-25. [PMID: 21924970 DOI: 10.1016/b978-0-12-387048-3.00001-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Photorhabdus is a genus of insect-pathogenic Gram-negative bacteria that also maintain a mutualistic interaction with nematodes from the family Heterorhabditis. This complex life cycle, involving different interactions with different invertebrate hosts, coupled with the amenability of the system to laboratory culture has resulted in the development of Photorhabdus as a model system for studying bacterial-host interactions. Photorhabdus is predicted to have an extensive secondary metabolism with the genetic potential to produce >20 different small secondary metabolites. Therefore, this system also presents us with a unique opportunity to study the contribution of secondary metabolism to the environmental fitness of the producing organism in its natural habitat (i.e., the insect and/or the nematode). In vivo and in vitro studies have revealed that the vast majority of the genetic loci in Photorhabdus predicted to be involved in the production of secondary metabolites appear to be cryptic and, to date, although several have been characterized, only three compounds have been studied in any great detail: 3,5-dihydroxy-4-isopropylstilbene, the β-lactam antibiotic carbapenem, and an anthraquinone pigment. In this chapter, we describe how these compounds are made and the role (if any) that they have during the interactions between Photorhabdus and its invertebrate hosts. We will also outline recent work on the regulation of secondary metabolism in Photorhabdus and comment on how this has led to an increased understanding of mutualism in this bacterium.
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Affiliation(s)
- Susan A Joyce
- Department of Microbiology, University College Cork, Cork, Ireland
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Tashiro Y, Monson RE, Ramsay JP, Salmond GPC. Molecular genetic and physical analysis of gas vesicles in buoyant enterobacteria. Environ Microbiol 2016; 18:1264-76. [PMID: 26743231 PMCID: PMC4982088 DOI: 10.1111/1462-2920.13203] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/29/2015] [Indexed: 11/29/2022]
Abstract
Different modes of bacterial taxis play important roles in environmental adaptation, survival, colonization and dissemination of disease. One mode of taxis is flotation due to the production of gas vesicles. Gas vesicles are proteinaceous intracellular organelles, permeable only to gas, that enable flotation in aquatic niches. Gene clusters for gas vesicle biosynthesis are partially conserved in various archaea, cyanobacteria, and some proteobacteria, such as the enterobacterium, Serratia sp. ATCC 39006 (S39006). Here we present the first systematic analysis of the genes required to produce gas vesicles in S39006, identifying how this differs from the archaeon Halobacterium salinarum. We define 11 proteins essential for gas vesicle production. Mutation of gvpN or gvpV produced small bicone gas vesicles, suggesting that the cognate proteins are involved in the morphogenetic assembly pathway from bicones to mature cylindrical forms. Using volumetric compression, gas vesicles were shown to comprise 17% of S39006 cells, whereas in Escherichia coli heterologously expressing the gas vesicle cluster in a deregulated environment, gas vesicles can occupy around half of cellular volume. Gas vesicle production in S39006 and E. coli was exploited to calculate the instantaneous turgor pressure within cultured bacterial cells; the first time this has been performed in either strain.
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Affiliation(s)
- Yosuke Tashiro
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.,Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, 432-8561, Japan
| | - Rita E Monson
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Joshua P Ramsay
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.,Curtin Health Innovation Research Institute Biosciences Precinct, Faculty of Health Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - George P C Salmond
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
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40
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Bozhüyük KAJ, Zhou Q, Engel Y, Heinrich A, Pérez A, Bode HB. Natural Products from Photorhabdus and Other Entomopathogenic Bacteria. Curr Top Microbiol Immunol 2016; 402:55-79. [PMID: 28091935 DOI: 10.1007/82_2016_24] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Although the first natural products (NP) from Photorhabdus and Xenorhabdus bacteria have been known now for almost 30 years, a huge variety of new compounds have been identified in the last 5-10 years, mainly due to the application of modern mass spectrometry. Additionally, application of molecular methods that allow the activation of NP production in several different strains as well as efficient heterologous expression methods have led to the production and validation of many new compounds. In this chapter we discuss the benefit of using Photorhabdus as a model system for microbial chemical ecology. We also examine non-ribosomal peptide synthetases as the most important pathway for NP production. Finally, we discuss the origin and function of all currently known NPs and the development of the molecular and chemical tools used to identify these NPs faster.
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Affiliation(s)
- Kenan A J Bozhüyük
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Qiuqin Zhou
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Yvonne Engel
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Antje Heinrich
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Alexander Pérez
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Helge B Bode
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
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41
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Brameyer S, Heermann R. Quorum Sensing and LuxR Solos in Photorhabdus. Curr Top Microbiol Immunol 2016; 402:103-119. [PMID: 27848037 DOI: 10.1007/82_2016_28] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bacterial communication via small diffusible molecules to mediate group-coordinated behaviour is commonly referred to as 'quorum sensing'. The prototypical quorum sensing system of Gram-negative bacteria consists of a LuxI-type autoinducer synthase that produces acyl-homoserine lactones (AHLs) as signals and a LuxR-type receptor that detects the AHLs to control expression of specific genes. However, many bacteria possess LuxR homologs but lack a cognate LuxI-type AHL-synthase. Those LuxR-type receptors are designated as 'LuxR orphans' or 'solos'. Entomopathogenic bacteria of the genus Photorhabdus all harbour a large number of LuxR solos, more than any other bacteria examined so far. Two novel quorum sensing systems were found to regulate cell clumping in Photorhabdus and therefore affect pathogenicity. In Photorhabdus luminescens and Photorhabdus temperata the LuxR solo PluR senses α-pyrones named 'photopyrones' instead of AHLs, which are produced by the pyrone synthase PpyS. In contrast, Photorhabdus asymbiotica, a closely related insect and human pathogen, has the PluR homolog PauR, which senses dialkylresorcinols produced by the DarABC pathway to regulate pathogenicity. All three Photorhabdus species harbour at least one LuxR solo with an intact AHL-binding motif, which might also allow sensing of exogenous AHLs. However, the majority of the LuxR solos in all Photorhabdus species have a PAS4 signal-binding domain. These receptors are assumed to detect eukaryotic compounds and are proposed to be involved in host sensing. Overall, because of the large number of LuxR solos they encode, bacteria of the genus Photorhabdus are ideal candidates to study and to identify novel bacterial communication networks.
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Affiliation(s)
- Sophie Brameyer
- Biozentrum, Bereich Mikrobiologie, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152, Martinsried/München, Germany
| | - Ralf Heermann
- Biozentrum, Bereich Mikrobiologie, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152, Martinsried/München, Germany.
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42
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References. Antibiotics (Basel) 2015. [DOI: 10.1128/9781555819316.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Tan GY, Deng Z, Liu T. Recent advances in the elucidation of enzymatic function in natural product biosynthesis. F1000Res 2015; 4. [PMID: 26989472 PMCID: PMC4784017 DOI: 10.12688/f1000research.7187.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/24/2016] [Indexed: 01/20/2023] Open
Abstract
With the successful production of artemisinic acid in yeast, the promising potential of synthetic biology for natural product biosynthesis is now being realized. The recent total biosynthesis of opioids in microbes is considered to be another landmark in this field. The importance and significance of enzymes in natural product biosynthetic pathways have been re-emphasized by these advancements. Therefore, the characterization and elucidation of enzymatic function in natural product biosynthesis are undoubtedly fundamental for the development of new drugs and the heterologous biosynthesis of active natural products. Here, discoveries regarding enzymatic function in natural product biosynthesis over the past year are briefly reviewed.
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Affiliation(s)
- Gao-Yi Tan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, China
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LeRoux M, Peterson SB, Mougous JD. Bacterial danger sensing. J Mol Biol 2015; 427:3744-53. [PMID: 26434507 DOI: 10.1016/j.jmb.2015.09.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/03/2015] [Accepted: 09/21/2015] [Indexed: 11/30/2022]
Abstract
Here we propose that bacteria detect and respond to threats posed by other bacteria via an innate immune-like process that we term danger sensing. We find support for this contention by reexamining existing literature from the perspective that intermicrobial antagonism, not opportunistic pathogenesis, is the major evolutionary force shaping the defensive behaviors of most bacteria. We conclude that many bacteria possess danger sensing pathways composed of a danger signal receptor and corresponding signal transduction mechanism that regulate pathways important for survival in the presence of the perceived competitor.
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Affiliation(s)
- Michele LeRoux
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - S Brook Peterson
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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Ma G, Zhu W, Su H, Cheng N, Liu Y. Uncoupled Epimerization and Desaturation by Carbapenem Synthase: Mechanistic Insights from QM/MM Studies. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01275] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guangcai Ma
- Key Laboratory
of Colloid
and Interface Chemistry, Ministry of Education, School of Chemistry
and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Wenyou Zhu
- Key Laboratory
of Colloid
and Interface Chemistry, Ministry of Education, School of Chemistry
and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Hao Su
- Key Laboratory
of Colloid
and Interface Chemistry, Ministry of Education, School of Chemistry
and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Na Cheng
- Key Laboratory
of Colloid
and Interface Chemistry, Ministry of Education, School of Chemistry
and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- Key Laboratory
of Colloid
and Interface Chemistry, Ministry of Education, School of Chemistry
and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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Consecutive radical S-adenosylmethionine methylations form the ethyl side chain in thienamycin biosynthesis. Proc Natl Acad Sci U S A 2015; 112:10354-8. [PMID: 26240322 DOI: 10.1073/pnas.1508615112] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite their broad anti-infective utility, the biosynthesis of the paradigm carbapenem antibiotic, thienamycin, remains largely unknown. Apart from the first two steps shared with a simple carbapenem, the pathway sharply diverges to the more structurally complex members of this class of β-lactam antibiotics, such as thienamycin. Existing evidence points to three putative cobalamin-dependent radical S-adenosylmethionine (RS) enzymes, ThnK, ThnL, and ThnP, as potentially being responsible for assembly of the ethyl side chain at C6, bridgehead epimerization at C5, installation of the C2-thioether side chain, and C2/3 desaturation. The C2 substituent has been demonstrated to be derived by stepwise truncation of CoA, but the timing of these events with respect to C2-S bond formation is not known. We show that ThnK of the three apparent cobalamin-dependent RS enzymes performs sequential methylations to build out the C6-ethyl side chain in a stereocontrolled manner. This enzymatic reaction was found to produce expected RS methylase coproducts S-adenosylhomocysteine and 5'-deoxyadenosine, and to require cobalamin. For double methylation to occur, the carbapenam substrate must bear a CoA-derived C2-thioether side chain, implying the activity of a previous sulfur insertion by an as-yet unidentified enzyme. These insights allow refinement of the central steps in complex carbapenem biosynthesis.
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Matilla MA, Leeper FJ, Salmond GPC. Biosynthesis of the antifungal haterumalide, oocydin A, in Serratia, and its regulation by quorum sensing, RpoS and Hfq. Environ Microbiol 2015; 17:2993-3008. [PMID: 25753587 PMCID: PMC4552970 DOI: 10.1111/1462-2920.12839] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 02/02/2023]
Abstract
Polyketides represent an important class of bioactive natural products with a broad range of biological activities. We identified recently a large trans-acyltransferase (AT) polyketide synthase gene cluster responsible for the biosynthesis of the antifungal, anti-oomycete and antitumor haterumalide, oocydin A (ooc). Using genome sequencing and comparative genomics, we show that the ooc gene cluster is widespread within biocontrol and phytopathogenic strains of the enterobacteria, Serratia and Dickeya. The analysis of in frame deletion mutants confirmed the role of a hydroxymethylglutaryl-coenzyme A synthase cassette, three flavin-dependent tailoring enzymes, a free-standing acyl carrier protein and two hypothetical proteins in oocydin A biosynthesis. The requirement of the three trans-acting AT domains for the biosynthesis of the macrolide was also demonstrated. Expression of the ooc gene cluster was shown to be positively regulated by an N-acyl-L-homoserine lactone-based quorum sensing system, but operating in a strain-dependent manner. At a post-transcriptional level, the RNA chaperone, Hfq, plays a key role in oocydin A biosynthesis. The Hfq-dependent regulation is partially mediated by the stationary phase sigma factor, RpoS, which was also shown to positively regulate the synthesis of the macrolide. Our results reveal differential regulation of the divergently transcribed ooc transcriptional units, highlighting the complexity of oocydin A production.
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Affiliation(s)
- Miguel A Matilla
- Department of Biochemistry, University of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK
| | - Finian J Leeper
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW, UK
| | - George P C Salmond
- Department of Biochemistry, University of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK,*For correspondence. E-mail ; Tel. +44 (0)1223 333650; Fax +44 (0)1223 766108
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48
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Zaitseva YV, Popova AA, Khmel IA. Quorum sensing regulation in bacteria of the family enterobacteriaceae. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414030120] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Tichy EM, Luisi BF, Salmond GPC. Crystal structure of the carbapenem intrinsic resistance protein CarG. J Mol Biol 2014; 426:1958-70. [PMID: 24583229 PMCID: PMC4361734 DOI: 10.1016/j.jmb.2014.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/15/2014] [Accepted: 02/20/2014] [Indexed: 10/25/2022]
Abstract
In the Gram-negative enterobacterium Erwinia (Pectobacterium) and Serratia sp. ATCC 39006, intrinsic resistance to the carbapenem antibiotic 1-carbapen-2-em-3-carboxylic acid is mediated by the CarF and CarG proteins, by an unknown mechanism. Here, we report a high-resolution crystal structure for the Serratia sp. ATCC 39006 carbapenem resistance protein CarG. This structure of CarG is the first in the carbapenem intrinsic resistance (CIR) family of resistance proteins from carbapenem-producing bacteria. The crystal structure shows the protein to form a homodimer, in agreement with results from analytical gel filtration. The structure of CarG does not show homology with any known antibiotic resistance proteins nor does it belong to any well-characterised protein structural family. However, it is a close structural homologue of the bacterial inhibitor of invertebrate lysozyme, PliI-Ah, with some interesting structural variations, including the absence of the catalytic site responsible for lysozyme inhibition. Both proteins show a unique β-sandwich fold with short terminal α-helices. The core of the protein is formed by stacked anti-parallel sheets that are individually very similar in the two proteins but differ in their packing interface, causing the splaying of the two sheets in CarG. Furthermore, a conserved cation binding site identified in CarG is absent from the homologue.
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Affiliation(s)
- E M Tichy
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB21QW, UK
| | - B F Luisi
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB21QW, UK
| | - G P C Salmond
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB21QW, UK
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Chang WC, Guo Y, Wang C, Butch SE, Rosenzweig AC, Boal AK, Krebs C, Bollinger JM. Mechanism of the C5 stereoinversion reaction in the biosynthesis of carbapenem antibiotics. Science 2014; 343:1140-4. [PMID: 24604200 PMCID: PMC4160820 DOI: 10.1126/science.1248000] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The bicyclic β-lactam/2-pyrrolidine precursor to all carbapenem antibiotics is biosynthesized by attachment of a carboxymethylene unit to C5 of L-proline followed by β-lactam ring closure. Carbapenem synthase (CarC), an Fe(II) and 2-(oxo)glutarate (Fe/2OG)-dependent oxygenase, then inverts the C5 configuration. Here we report the structure of CarC in complex with its substrate and biophysical dissection of its reaction to reveal the stereoinversion mechanism. An Fe(IV)-oxo intermediate abstracts the hydrogen (H•) from C5, and tyrosine 165, a residue not visualized in the published structures of CarC lacking bound substrate, donates H• to the opposite face of the resultant radical. The reaction oxidizes the Fe(II) cofactor to Fe(III), limiting wild-type CarC to one turnover, but substitution of the H•-donating tyrosine disables stereoinversion and confers to CarC the capacity for catalytic substrate oxidation.
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Affiliation(s)
- Wei-chen Chang
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yisong Guo
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chen Wang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Susan E. Butch
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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