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Cai D, Zhang H, Lei X, Chen O, Zeng K. The effect and mechanism of Debaryomyces nepalensis and six strains of winter jujube epiphytic bacteria in building a synthetic community to control post-harvest black spot disease of winter jujube. Int J Food Microbiol 2024; 424:110842. [PMID: 39098161 DOI: 10.1016/j.ijfoodmicro.2024.110842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/22/2024] [Accepted: 07/23/2024] [Indexed: 08/06/2024]
Abstract
The study aimed to develop a synthetic microbial community capable of managing postharvest black spot disease in winter jujube. The research revealed that treatment with Debaryomyces nepalensis altered the surface microbial community, reducing the presence of harmful fungi such as Alternaria, Penicillium, Fusarium, and Botrytis, while boosting beneficial bacteria like Pantoea, Bacillus, Staphylococcus, and Pseudomonas, leading to a decreased decay rate in date fruits. A synthetic community was crafted, integrating D. nepalensis with seven other bacterial strains selected for their abundance, compatibility, culturability, and interactions. This community was refined through homo-pore damage experiments and safety assessments to a final formulation consisting of D. nepalensis and six other bacteria: Bacillus subtilis, Bacillus velezensis, Staphylococcus arlettae, Staphylococcus gallinarum, Pseudomonas sp., and Pseudomonas psychrotolerans. Fruit inoculation tests demonstrated that this synthetic community (6 + 1) significantly lowered the incidence and size of black spot lesions compared to single-strain treatments. By the 10th day of storage, the incidence was 69.23 % lower than the control and 52.94 % lower than the group treated solely with D. nepalensis. Mechanistic studies of the synthetic community's antibacterial effects showed that it can produce volatile compounds, proteases, and β-1,3-glucanase to inhibit pathogen growth. Additionally, the community forms a biofilm to compete for nutrients and induce jujube resistance to disease.
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Affiliation(s)
- Die Cai
- College of Food Science, Southwest University, Chongqing 400715, PR China
| | - Hongyan Zhang
- College of Food Science, Southwest University, Chongqing 400715, PR China
| | - XingMeng Lei
- College of Food Science, Southwest University, Chongqing 400715, PR China
| | - Ou Chen
- College of Food Science, Southwest University, Chongqing 400715, PR China
| | - Kaifang Zeng
- College of Food Science, Southwest University, Chongqing 400715, PR China; Research Center for Fruits and Vegetables Logistics Preservation and Nutritional Quality Control, Southwest University, Chongqing 400715, PR China; National Citrus Engineering Research Center, Chongqing 400712, PR China.
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2
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Xiong X, Zeng J, Ning Q, Liu H, Bu Z, Zhang X, Zeng J, Zhuo R, Cui K, Qin Z, Gao Y, Liu X, Zhu Y. Ferroptosis induction in host rice by endophyte OsiSh-2 is necessary for mutualism and disease resistance in symbiosis. Nat Commun 2024; 15:5012. [PMID: 38866764 PMCID: PMC11169551 DOI: 10.1038/s41467-024-49099-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 05/21/2024] [Indexed: 06/14/2024] Open
Abstract
Ferroptosis is an iron-dependent cell death that was discovered recently. For beneficial microbes to establish mutualistic relationships with hosts, precisely controlled cell death in plant cells is necessary. However, whether ferroptosis is involved in the endophyte‒plant system is poorly understood. Here, we reported that endophytic Streptomyces hygroscopicus OsiSh-2, which established a sophisticated and beneficial interaction with host rice plants, caused ferroptotic cell death in rice characterized by ferroptosis- and immune-related markers. Treatments with ferroptosis inhibitors and inducers, different doses of OsiSh-2, and the siderophore synthesis-deficient mutant ΔcchH revealed that only moderate ferroptosis induced by endophytes is essential for the establishment of an optimal symbiont to enhance plant growth. Additionally, ferroptosis involved in a defence-primed state in rice, which contributed to improved resistance against rice blast disease. Overall, our study provides new insights into the mechanisms of endophyte‒plant interactions mediated by ferroptosis and suggests new directions for crop yield promotion.
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Affiliation(s)
- Xianqiu Xiong
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, Hunan, PR China
| | - Jing Zeng
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, Hunan, PR China
| | - Qing Ning
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, Hunan, PR China
| | - Heqin Liu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, Hunan, PR China
| | - Zhigang Bu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, Hunan, PR China
| | - Xuan Zhang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, Hunan, PR China
| | - Jiarui Zeng
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, Hunan, PR China
| | - Rui Zhuo
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, Hunan, PR China
| | - Kunpeng Cui
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, Hunan, PR China
| | - Ziwei Qin
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, Hunan, PR China
| | - Yan Gao
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, Hunan, PR China.
| | - Xuanming Liu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, Hunan, PR China.
| | - Yonghua Zhu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, Hunan, PR China.
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3
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Liu Y, LaBonte S, Brake C, LaFayette C, Rosebrock AP, Caudy AA, Straight PD. MOB rules: Antibiotic Exposure Reprograms Metabolism to Mobilize Bacillus subtilis in Competitive Interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585991. [PMID: 38562742 PMCID: PMC10983992 DOI: 10.1101/2024.03.20.585991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Antibiotics have dose-dependent effects on exposed bacteria. The medicinal use of antibiotics relies on their growth-inhibitory activities at sufficient concentrations. At subinhibitory concentrations, exposure effects vary widely among different antibiotics and bacteria. Bacillus subtilis responds to bacteriostatic translation inhibitors by mobilizing a population of cells (MOB-Mobilized Bacillus) to spread across a surface. How B. subtilis regulates the antibiotic-induced mobilization is not known. In this study, we used chloramphenicol to identify regulatory functions that B. subtilis requires to coordinate cell mobilization following subinhibitory exposure. We measured changes in gene expression and metabolism and mapped the results to a network of regulatory proteins that direct the mobile response. Our data reveal that several transcriptional regulators coordinately control the reprogramming of metabolism to support mobilization. The network regulates changes in glycolysis, nucleotide metabolism, and amino acid metabolism that are signature features of the mobilized population. Among the hundreds of genes with changing expression, we identified two, pdhA and pucA, where the magnitudes of their changes in expression, and in the abundance of associated metabolites, reveal hallmark metabolic features of the mobilized population. Using reporters of pdhA and pucA expression, we visualized the separation of major branches of metabolism in different regions of the mobilized population. Our results reveal a regulated response to chloramphenicol exposure that enables a population of bacteria in different metabolic states to mount a coordinated mobile response.
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Affiliation(s)
- Yongjin Liu
- Biochemistry and Biophysics Department, Texas A&M University, AgriLife Research, College Station, Texas, USA
| | - Sandra LaBonte
- Biochemistry and Biophysics Department, Texas A&M University, AgriLife Research, College Station, Texas, USA
- Interdisciplinary Program in Genetics and Genomics,Texas A&M University, College Station, Texas, USA
| | - Courtney Brake
- Department of Visualization, Institute for Applied Creativity, Texas A&M University, College Station, Texas, USA
| | - Carol LaFayette
- Department of Visualization, Institute for Applied Creativity, Texas A&M University, College Station, Texas, USA
| | | | - Amy A. Caudy
- Maple Flavored Solutions, LLC, Indianapolis, Indiana, USA
| | - Paul D. Straight
- Biochemistry and Biophysics Department, Texas A&M University, AgriLife Research, College Station, Texas, USA
- Interdisciplinary Program in Genetics and Genomics,Texas A&M University, College Station, Texas, USA
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4
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Su L, Souaibou Y, Hôtel L, Paris C, Weissman KJ, Aigle B. Biosynthesis of novel desferrioxamine derivatives requires unprecedented crosstalk between separate NRPS-independent siderophore pathways. Appl Environ Microbiol 2024; 90:e0211523. [PMID: 38323847 PMCID: PMC10952394 DOI: 10.1128/aem.02115-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 02/08/2024] Open
Abstract
Iron is essential to many biological processes but its poor solubility in aerobic environments restricts its bioavailability. To overcome this limitation, bacteria have evolved a variety of strategies, including the production and secretion of iron-chelating siderophores. Here, we describe the discovery of four series of siderophores from Streptomyces ambofaciens ATCC23877, three of which are unprecedented. MS/MS-based molecular networking revealed that one of these series corresponds to acylated desferrioxamines (acyl-DFOs) recently identified from S. coelicolor. The remaining sets include tetra- and penta-hydroxamate acyl-DFO derivatives, all of which incorporate a previously undescribed building block. Stable isotope labeling and gene deletion experiments provide evidence that biosynthesis of the acyl-DFO congeners requires unprecedented crosstalk between two separate non-ribosomal peptide synthetase (NRPS)-independent siderophore (NIS) pathways in the producing organism. Although the biological role(s) of these new derivatives remain to be elucidated, they may confer advantages in terms of metal chelation in the competitive soil environment due to the additional bidentate hydroxamic functional groups. The metabolites may also find application in various fields including biotechnology, bioremediation, and immuno-PET imaging.IMPORTANCEIron-chelating siderophores play important roles for their bacterial producers in the environment, but they have also found application in human medicine both in iron chelation therapy to prevent iron overload and in diagnostic imaging, as well as in biotechnology, including as agents for biocontrol of pathogens and bioremediation. In this study, we report the discovery of three novel series of related siderophores, whose biosynthesis depends on the interplay between two NRPS-independent (NIS) pathways in the producing organism S. ambofaciens-the first example to our knowledge of such functional cross-talk. We further reveal that two of these series correspond to acyl-desferrioxamines which incorporate four or five hydroxamate units. Although the biological importance of these novel derivatives is unknown, the increased chelating capacity of these metabolites may find utility in diagnostic imaging (for instance, 89Zr-based immuno-PET imaging) and other applications of metal chelators.
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Affiliation(s)
- Li Su
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Yaouba Souaibou
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- Université de Lorraine, CNRS, IMoPA, Nancy, France
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5
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Smith P, Schuster M. The fitness benefit of pyoverdine cross-feeding by Pseudomonas protegens Pf-5. Environ Microbiol 2024; 26:e16554. [PMID: 38097191 DOI: 10.1111/1462-2920.16554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/24/2023] [Indexed: 12/20/2023]
Abstract
Under iron-limiting conditions, fluorescent pseudomonads acquire iron from the environment by secreting strain-specific, iron-chelating siderophores termed pyoverdines (PVD). The rhizosphere bacterium Pseudomonas protegens Pf-5 produces its own PVD but also can cross-feed on PVDs produced by other species. Previous work has found that Pf-5 continues to produce its own PVD when allowed to cross-feed, raising questions about the benefit of heterologous PVD utilisation. Here, we investigate this question using a defined, unidirectional P. protegens Pf-5/Pseudomonas aeruginosa PAO1 cross-feeding model. Quantifying the production of PVD in the presence of heterologous PVD produced by PAO1, we show that cross-feeding Pf-5 strains reduce the production of their own PVD, while non-cross-feeding Pf-5 strains increase the production of PVD. Measuring the fitness of cross-feeding and non-cross-feeding Pf-5 strains in triple coculture with PAO1, we find that cross-feeding provides a fitness benefit to Pf-5 when the availability of heterologous PVD is high. We conclude that cross-feeding can reduce the costs of self-PVD production and may thus aid in the colonisation of iron-limited environments that contain compatible siderophores produced by other resident microbes. Taken together, these results expand our understanding of the mechanisms of interspecific competition for iron in microbial communities.
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Affiliation(s)
- Parker Smith
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Martin Schuster
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
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6
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O'Brien S, Culbert CT, Barraclough TG. Community composition drives siderophore dynamics in multispecies bacterial communities. BMC Ecol Evol 2023; 23:45. [PMID: 37658316 PMCID: PMC10472669 DOI: 10.1186/s12862-023-02152-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 08/17/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Intraspecific public goods are commonly shared within microbial populations, where the benefits of public goods are largely limited to closely related conspecifics. One example is the production of iron-scavenging siderophores that deliver iron to cells via specific cell envelope receptor and transport systems. Intraspecific social exploitation of siderophore producers is common, since non-producers avoid the costs of production but retain the cell envelope machinery for siderophore uptake. However, little is known about how interactions between species (i.e., interspecific interactions) can shape intraspecific public goods exploitation. Here, we predicted that strong competition for iron between species in diverse communities will increase costs of siderophore cooperation, and hence drive intraspecific exploitation. We examined how increasing microbial community species diversity shapes intraspecific social dynamics by monitoring the growth of siderophore producers and non-producers of the plant-growth promoting bacterium Pseudomonas fluorescens, embedded within tree-hole microbial communities ranging from 2 to 15 species. RESULTS We find, contrary to our prediction, that siderophore production is favoured at higher levels of community species richness, driven by increased likelihood of encountering key species that reduce the growth of siderophore non-producing (but not producing) strains of P. fluorescens. CONCLUSIONS Our results suggest that maintaining a diverse soil microbiota could partly contribute to the maintenance of siderophore production in natural communities.
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Affiliation(s)
- Siobhán O'Brien
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
| | - Christopher T Culbert
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK
| | - Timothy G Barraclough
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
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Wang P, Xiao Y, Gao D, Long Y, Xie Z. The Gene paaZ of the Phenylacetic Acid (PAA) Catabolic Pathway Branching Point and ech outside the PAA Catabolon Gene Cluster Are Synergistically Involved in the Biosynthesis of the Iron Scavenger 7-Hydroxytropolone in Pseudomonas donghuensis HYS. Int J Mol Sci 2023; 24:12632. [PMID: 37628812 PMCID: PMC10454607 DOI: 10.3390/ijms241612632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
The newly discovered iron scavenger 7-hydroxytropolone (7-HT) is secreted by Pseudomonas donghuensis HYS. In addition to possessing an iron-chelating ability, 7-HT has various other biological activities. However, 7-HT's biosynthetic pathway remains unclear. This study was the first to report that the phenylacetic acid (PAA) catabolon genes in cluster 2 are involved in the biosynthesis of 7-HT and that two genes, paaZ (orf13) and ech, are synergistically involved in the biosynthesis of 7-HT in P. donghuensis HYS. Firstly, gene knockout and a sole carbon experiment indicated that the genes orf17-21 (paaEDCBA) and orf26 (paaG) were involved in the biosynthesis of 7-HT and participated in the PAA catabolon pathway in P. donghuensis HYS; these genes were arranged in gene cluster 2 in P. donghuensis HYS. Interestingly, ORF13 was a homologous protein of PaaZ, but orf13 (paaZ) was not essential for the biosynthesis of 7-HT in P. donghuensis HYS. A genome-wide BLASTP search, including gene knockout, complemented assays, and site mutation, showed that the gene ech homologous to the ECH domain of orf13 (paaZ) is essential for the biosynthesis of 7-HT. Three key conserved residues of ech (Asp39, His44, and Gly62) were identified in P. donghuensis HYS. Furthermore, orf13 (paaZ) could not complement the role of ech in the production of 7-HT, and the single carbon experiment indicated that paaZ mainly participates in PAA catabolism. Overall, this study reveals a natural association between PAA catabolon and the biosynthesis of 7-HT in P. donghuensis HYS. These two genes have a synergistic effect and different functions: paaZ is mainly involved in the degradation of PAA, while ech is mainly related to the biosynthesis of 7-HT in P. donghuensis HYS. These findings complement our understanding of the mechanism of the biosynthesis of 7-HT in the genus Pseudomonas.
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Affiliation(s)
| | | | | | - Yan Long
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China; (P.W.); (Y.X.); (D.G.)
| | - Zhixiong Xie
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China; (P.W.); (Y.X.); (D.G.)
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8
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Nofiani R, Ardiningsih P, Zahra STA, Sukito A, Weisberg AJ, Chang JH, Mahmud T. Genome features and secondary metabolite potential of the marine symbiont Streptomyces sp. RS2. Arch Microbiol 2023; 205:244. [PMID: 37209150 DOI: 10.1007/s00203-023-03556-2] [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: 01/09/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 05/22/2023]
Abstract
Streptomyces sp. RS2 was isolated from an unidentified sponge collected around Randayan Island, Indonesia. The genome of Streptomyces sp. RS2 consists of a linear chromosome of 9,391,717 base pairs with 71.9% of G + C content, 8270 protein-coding genes, as well as 18 rRNA and 85 tRNA loci. Twenty-eight putative secondary metabolites biosynthetic gene clusters (BGCs) were identified in the genome sequence. Nine of them have 100% similarity to BGCs for albaflavenone, α-lipomycin, coelibactin, coelichelin, ectoine, geosmin, germicidin, hopene, and lanthionine (SapB). The remaining 19 BGCs have low (< 50%) or moderate (50-80%) similarity to other known secondary metabolite BGCs. Biological activity assays of extracts from 21 different cultures of the RS2 strain showed that SCB ASW was the best medium for the production of antimicrobial and cytotoxic compounds. Streptomyces sp. RS2 has great potential to be a producer of novel secondary metabolites, particularly those with antimicrobial and antitumor activities.
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Affiliation(s)
- Risa Nofiani
- Department of Chemistry, Universitas Tanjungpura, Pontianak, 78124, Indonesia.
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA.
| | - Puji Ardiningsih
- Department of Chemistry, Universitas Tanjungpura, Pontianak, 78124, Indonesia
| | | | - Agus Sukito
- Research Center for Applied Microbiology, National Research and Innovation Agency, Bogor, 16458, Indonesia
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA
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de Sousa LP, Filho OG, Mondego JMC. Age-Related Rhizosphere Analysis of Coffea arabica Plants. Curr Microbiol 2023; 80:130. [PMID: 36890285 DOI: 10.1007/s00284-023-03236-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/20/2023] [Indexed: 03/10/2023]
Abstract
The analysis of large-scale sequence data has revealed that plants over time recruit certain microbes that are efficient colonizers of the rhizosphere. This enrichment phenomenon is especially seen in annual crops, but we suggest that there could have been some type of enrichment in perennial crops such as coffee plants. To verify this hypothesis, we performed a metagenomic and chemical analysis in rhizosphere with three different plant ages (young, mature, and old) and cultivated on the same farm. We verified that from mature to old plants, there was a decrease in diversity, particularly Fusarium and Plenodomus, while there was an increase in Aspergillus, Cladosporium, Metarhizium, and Pseudomonas. We also detected that the abundance of anti-microbials and ACC-deaminase grows as plants age, although denitrification and carbon fixation had reduced abundances. In summary, we detected an enrichment in the microbial community, especially in the great increase in the participation of Pseudomonas, passing from 50% of the relative abundance as the plants get older. Such enrichment can occur through the dynamics of nutrients such as magnesium and boron.
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Affiliation(s)
- Leandro Pio de Sousa
- Centro de Pesquisa E Desenvolvimento de Recursos Genéticos Vegetais, Instituto Agronômico, Campinas, São Paulo, Brazil.
| | | | - Jorge Maurício Costa Mondego
- Centro de Pesquisa E Desenvolvimento de Recursos Genéticos Vegetais, Instituto Agronômico, Campinas, São Paulo, Brazil
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Stallforth P, Mittag M, Brakhage AA, Hertweck C, Hellmich UA. Functional modulation of chemical mediators in microbial communities. Trends Biochem Sci 2023; 48:71-81. [PMID: 35981931 DOI: 10.1016/j.tibs.2022.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/14/2022] [Accepted: 07/20/2022] [Indexed: 12/27/2022]
Abstract
Interactions between microorganisms are often mediated by specialized metabolites. Although the structures and biosynthesis of these compounds may have been elucidated, microbes exist within complex microbiomes and chemical signals can thus also be subject to community-dependent modifications. Increasingly powerful chemical and biological tools allow to shed light on this poorly understood aspect of chemical ecology. We provide an overview of loss-of-function and gain-of-function chemical mediator (CM) modifications within microbial multipartner relationships. Although loss-of-function modifications are abundant in the literature, few gain-of-function modifications have been described despite their important role in microbial interactions. Research in this field holds great potential for our understanding of microbial interactions and may also provide novel tools for targeted interference with microbial signaling.
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Affiliation(s)
- Pierre Stallforth
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll Institute, Beutenbergstrasse 11a, 07745 Jena, Germany; Friedrich Schiller University Jena, Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Humboldtstrasse 10, 07743 Jena, Germany.
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Axel A Brakhage
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll Institute, Beutenbergstrasse 11a, 07745 Jena, Germany; Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll Institute, Beutenbergstrasse 11a, 07745 Jena, Germany; Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Ute A Hellmich
- Friedrich Schiller University Jena, Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Humboldtstrasse 10, 07743 Jena, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany.
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11
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Iron acquisition strategies in pseudomonads: mechanisms, ecology, and evolution. Biometals 2022:10.1007/s10534-022-00480-8. [PMID: 36508064 PMCID: PMC10393863 DOI: 10.1007/s10534-022-00480-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
AbstractIron is important for bacterial growth and survival, as it is a common co-factor in essential enzymes. Although iron is very abundant in the earth crust, its bioavailability is low in most habitats because ferric iron is largely insoluble under aerobic conditions and at neutral pH. Consequently, bacteria have evolved a plethora of mechanisms to solubilize and acquire iron from environmental and host stocks. In this review, I focus on Pseudomonas spp. and first present the main iron uptake mechanisms of this taxa, which involve the direct uptake of ferrous iron via importers, the production of iron-chelating siderophores, the exploitation of siderophores produced by other microbial species, and the use of iron-chelating compounds produced by plants and animals. In the second part of this review, I elaborate on how these mechanisms affect interactions between bacteria in microbial communities, and between bacteria and their hosts. This is important because Pseudomonas spp. live in diverse communities and certain iron-uptake strategies might have evolved not only to acquire this essential nutrient, but also to gain relative advantages over competitors in the race for iron. Thus, an integrative understanding of the mechanisms of iron acquisition and the eco-evolutionary dynamics they drive at the community level might prove most useful to understand why Pseudomonas spp., in particular, and many other bacterial species, in general, have evolved such diverse iron uptake repertoires.
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12
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Santus W, Rana AP, Devlin JR, Kiernan KA, Jacob CC, Tjokrosurjo J, Underhill DM, Behnsen J. Mycobiota and diet-derived fungal xenosiderophores promote Salmonella gastrointestinal colonization. Nat Microbiol 2022; 7:2025-2038. [PMID: 36411353 DOI: 10.1038/s41564-022-01267-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 10/11/2022] [Indexed: 11/22/2022]
Abstract
The fungal gut microbiota (mycobiota) has been implicated in diseases that disturb gut homeostasis, such as inflammatory bowel disease. However, little is known about functional relationships between bacteria and fungi in the gut during infectious colitis. Here we investigated the role of fungal metabolites during infection with the intestinal pathogen Salmonella enterica serovar Typhimurium, a major cause of gastroenteritis worldwide. We found that, in the gut lumen, both the mycobiota and fungi present in the diet can be a source of siderophores, small molecules that scavenge iron from the host. The ability to use fungal siderophores, such as ferrichrome and coprogen, conferred a competitive growth advantage to Salmonella strains expressing the fungal siderophore receptors FhuA or FhuE in vitro and in a mouse model. Our study highlights the role of inter-kingdom cross-feeding between fungi and Salmonella and elucidates an additional function of the gut mycobiota, revealing the importance of these understudied members of the gut ecosystem during bacterial infection.
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Affiliation(s)
- William Santus
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Amisha P Rana
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Jason R Devlin
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Kaitlyn A Kiernan
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Carol C Jacob
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Joshua Tjokrosurjo
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, USA
| | - David M Underhill
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Judith Behnsen
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA.
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13
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Chávez-Moctezuma MP, Martínez-Cámara R, Hernández-Salmerón J, Moreno-Hagelsieb G, Santoyo G, Valencia-Cantero E. Comparative genomic and functional analysis of Arthrobacter sp. UMCV2 reveals the presence of luxR-related genes inducible by the biocompound N, N-dimethylhexadecilamine. Front Microbiol 2022; 13:1040932. [PMID: 36386619 PMCID: PMC9659744 DOI: 10.3389/fmicb.2022.1040932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/10/2022] [Indexed: 09/29/2023] Open
Abstract
Quorum sensing (QS) is a bacterial cell-cell communication system with genetically regulated mechanisms dependent on cell density. Canonical QS systems in gram-negative bacteria possess an autoinducer synthase (LuxI family) and a transcriptional regulator (LuxR family) that respond to an autoinducer molecule. In Gram-positive bacteria, the LuxR transcriptional regulators "solo" (not associated with a LuxI homolog) may play key roles in intracellular communication. Arthrobacter sp. UMCV2 is an actinobacterium that promotes plant growth by emitting the volatile organic compound N, N-dimethylhexadecylamine (DMHDA). This compound induces iron deficiency, defense responses in plants, and swarming motility in Arthrobacter sp. UMCV2. In this study, the draft genome of this bacterium was assembled and compared with the genomes of type strains of the Arthrobacter genus, finding that it does not belong to any previously described species. Genome explorations also revealed the presence of 16 luxR-related genes, but no luxI homologs were discovered. Eleven of these sequences possess the LuxR characteristic DNA-binding domain with a helix-turn-helix motif and were designated as auto-inducer-related regulators (AirR). Four sequences possessed LuxR analogous domains and were designated as auto-inducer analogous regulators (AiaR). When swarming motility was induced with DMHDA, eight airR genes and two aiaR genes were upregulated. These results indicate that the expression of multiple luxR-related genes is induced in actinobacteria, such as Arthrobacter sp. UMCV2, by the action of the bacterial biocompound DMHDA when QS behavior is produced.
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Affiliation(s)
| | - Ramiro Martínez-Cámara
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
- Tecnológico Nacional de México, Morelia, Michoacán, Mexico
| | | | | | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
| | - Eduardo Valencia-Cantero
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
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Cryptic specialized metabolites drive Streptomyces exploration and provide a competitive advantage during growth with other microbes. Proc Natl Acad Sci U S A 2022; 119:e2211052119. [PMID: 36161918 DOI: 10.1073/pnas.2211052119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptomyces bacteria have a complex life cycle that is intricately linked with their remarkable metabolic capabilities. Exploration is a recently discovered developmental innovation of these bacteria, that involves the rapid expansion of a structured colony on solid surfaces. Nutrient availability impacts exploration dynamics, and we have found that glycerol can dramatically increase exploration rates and alter the metabolic output of exploring colonies. We show here that glycerol-mediated growth acceleration is accompanied by distinct transcriptional signatures and by the activation of otherwise cryptic metabolites including the orange-pigmented coproporphyrin, the antibiotic chloramphenicol, and the uncommon, alternative siderophore foroxymithine. Exploring cultures are also known to produce the well-characterized desferrioxamine siderophore. Mutational studies of single and double siderophore mutants revealed functional redundancy when strains were cultured on their own; however, loss of the alternative foroxymithine siderophore imposed a more profound fitness penalty than loss of desferrioxamine during coculture with the yeast Saccharomyces cerevisiae. Notably, the two siderophores displayed distinct localization patterns, with desferrioxamine being confined within the colony area, and foroxymithine diffusing well beyond the colony boundary. The relative fitness advantage conferred by the alternative foroxymithine siderophore was abolished when the siderophore piracy capabilities of S. cerevisiae were eliminated (S. cerevisiae encodes a ferrioxamine-specific transporter). Our work suggests that exploring Streptomyces colonies can engage in nutrient-targeted metabolic arms races, deploying alternative siderophores that allow them to successfully outcompete other microbes for the limited bioavailable iron during coculture.
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15
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Saldaña-Ahuactzi Z, Knodler LA. FoxR is an AraC-like transcriptional regulator of ferrioxamine uptake in Salmonella enterica. Mol Microbiol 2022; 118:369-386. [PMID: 35970762 DOI: 10.1111/mmi.14970] [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: 03/23/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 01/07/2023]
Abstract
Salmonella enterica spp. produce siderophores to bind iron with high affinity and can also use three xenosiderophores secreted by other microorganisms, ferrichrome, coprogen, and ferrioxamine. Here we focused on FoxA, a TonB-dependent transporter of ferrioxamines. Adjacent to foxA is a gene annotated as a helix-turn-helix (HTH) domain-containing protein, SL0358 (foxR), in the Salmonella enterica serovar Typhimurium SL1344 genome. FoxR shares homology with transcriptional regulators belonging to the AraC/XylS family. foxR is syntenic with foxA in the Enterobacteriaceae family, suggesting their functional relatedness. Both foxA and foxR are repressed by the ferric uptake regulator (Fur) under iron-rich growth conditions. When iron is scarce, FoxR acts as a transcriptional activator of foxA by directly binding to its upstream regulatory region. A point mutation in the HTH domain of FoxR abolished this binding, as did mutation of a direct repeat motif in the foxA upstream regulatory region. Desferrioxamine (DFOE) enhanced FoxR protein stability and foxA transcription but did not affect the affinity of FoxR binding to the foxA regulatory region. In summary, we have identified FoxR as a new member of the AraC/XylS family that regulates xenosiderophore-mediated iron uptake by S. Typhimurium and likely other Enterobacteriaceae members.
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Affiliation(s)
- Zeus Saldaña-Ahuactzi
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Leigh A Knodler
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
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16
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Brault A, Mbuya B, Labbé S. Sib1, Sib2, and Sib3 proteins are required for ferrichrome-mediated cross-feeding interaction between Schizosaccharomyces pombe and Saccharomyces cerevisiae. Front Microbiol 2022; 13:962853. [PMID: 35928155 PMCID: PMC9344042 DOI: 10.3389/fmicb.2022.962853] [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: 06/06/2022] [Accepted: 07/01/2022] [Indexed: 11/15/2022] Open
Abstract
Although Saccharomyces cerevisiae is unable to produce siderophores, this fungal organism can assimilate iron bound to the hydroxamate-type siderophore ferrichrome (Fc) produced and secreted by other microbes. Fc can enter S. cerevisiae cells via Arn1. Unlike S. cerevisiae, Schizosaccharomyces pombe synthesizes and secretes Fc. The sib1+ and sib2+ genes encode, respectively, a Fc synthetase and an ornithine-N5-oxygenase, which are required for Fc production. When both genes were expressed in S. pombe, cross-feeding experiments revealed that S. cerevisiae fet3Δ arn1-4Δ cells expressing Arn1 could grow in the vicinity of S. pombe under low-iron conditions. In contrast, deletion of sib1+ and sib2+ produced a defect in the ability of S. pombe to keep S. cerevisiae cells alive when Fc is used as the sole source of iron. Further analysis identified a gene designated sib3+ that encodes an N5-transacetylase required for Fc production in S. pombe. The sib3Δ mutant strain exhibited a severe growth defect in iron-poor media, and it was unable to promote Fc-dependent growth of S. cerevisiae cells. Microscopic analyses of S. pombe cells expressing a functional Sib3-GFP protein revealed that Sib3 was localized throughout the cells, with a proportion of Sib3 being colocalized with Sib1 and Sib2 within the cytosol. Collectively, these results describe the first example of a one-way cross-feeding interaction, with S. pombe providing Fc that enables S. cerevisiae to grow when Fc is used as the sole source of iron.
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Fritsch S, Gasser V, Peukert C, Pinkert L, Kuhn L, Perraud Q, Normant V, Brönstrup M, Schalk IJ. Uptake Mechanisms and Regulatory Responses to MECAM- and DOTAM-Based Artificial Siderophores and Their Antibiotic Conjugates in Pseudomonas aeruginosa. ACS Infect Dis 2022; 8:1134-1146. [PMID: 35500104 DOI: 10.1021/acsinfecdis.2c00049] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The development of new antibiotics against Gram-negative bacteria has to deal with the low permeability of the outer membrane. This obstacle can be overcome by utilizing siderophore-dependent iron uptake pathways as entrance routes for antibiotic uptake. Iron-chelating siderophores are actively imported by bacteria, and their conjugation to antibiotics allows smuggling the latter into bacterial cells. Synthetic siderophore mimetics based on MECAM (1,3,5-N,N',N″-tris-(2,3-dihydroxybenzoyl)-triaminomethylbenzene) and DOTAM (1,4,7,10-tetrakis(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane) cores, both chelating iron via catechol groups, have been recently applied as versatile carriers of functional cargo. In the present study, we show that MECAM and the MECAM-ampicillin conjugate 3 transport iron into Pseudomonas aeruginosa cells via the catechol-type outer membrane transporters PfeA and PirA and DOTAM solely via PirA. Differential proteomics and quantitative real-time polymerase chain reaction (qRT-PCR) showed that MECAM import induced the expression of pfeA, whereas 3 led to an increase in the expression of pfeA and ampc, a gene conferring ampicillin resistance. The presence of DOTAM did not induce the expression of pirA but upregulated the expression of two zinc transporters (cntO and PA0781), pointing out that bacteria become zinc starved in the presence of this compound. Iron uptake experiments with radioactive 55Fe demonstrated that import of this nutrient by MECAM and DOTAM was as efficient as with the natural siderophore enterobactin. The study provides a functional validation for DOTAM- and MECAM-based artificial siderophore mimetics as vehicles for the delivery of cargo into Gram-negative bacteria.
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Affiliation(s)
- Sarah Fritsch
- CNRS, University of Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg 67070, France
| | - Véronique Gasser
- CNRS, University of Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg 67070, France
| | - Carsten Peukert
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig 38124, Germany
| | - Lukas Pinkert
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig 38124, Germany
| | - Lauriane Kuhn
- Plateforme Proteomique Strasbourg-Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS, FR1589, 15 rue Descartes, Strasbourg Cedex F-67084, France
| | - Quentin Perraud
- CNRS, University of Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg 67070, France
| | - Vincent Normant
- CNRS, University of Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg 67070, France
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig 38124, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig 38124, Germany
- Center of Biomolecular Drug Research (BMWZ), Leibniz Universität, Hannover 30159, Germany
| | - Isabelle J. Schalk
- CNRS, University of Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg 67070, France
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18
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Armin R, Zühlke S, Grunewaldt-Stöcker G, Mahnkopp-Dirks F, Kusari S. Production of Siderophores by an Apple Root-Associated Streptomyces ciscaucasicus Strain GS2 Using Chemical and Biological OSMAC Approaches. Molecules 2021; 26:molecules26123517. [PMID: 34207697 PMCID: PMC8228313 DOI: 10.3390/molecules26123517] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 11/29/2022] Open
Abstract
Apple Replant Disease (ARD) is a significant problem in apple orchards that causes root tissue damage, stunted plant growth, and decline in fruit quality, size, and overall yield. Dysbiosis of apple root-associated microbiome and selective richness of Streptomyces species in the rhizosphere typically concurs root impairment associated with ARD. However, possible roles of Streptomyces secondary metabolites within these observations remain unstudied. Therefore, we employed the One Strain Many Compounds (OSMAC) approach coupled to high-performance liquid chromatography-high-resolution tandem mass spectrometry (HPLC-HRMSn) to evaluate the chemical ecology of an apple root-associated Streptomycesciscaucasicus strain GS2, temporally over 14 days. The chemical OSMAC approach comprised cultivation media alterations using six different media compositions, which led to the biosynthesis of the iron-chelated siderophores, ferrioxamines. The biological OSMAC approach was concomitantly applied by dual-culture cultivation for microorganismal interactions with an endophytic Streptomyces pulveraceus strain ES16 and the pathogen Cylindrocarpon olidum. This led to the modulation of ferrioxamines produced and further triggered biosynthesis of the unchelated siderophores, desferrioxamines. The structures of the compounds were elucidated using HRMSn and by comparison with the literature. We evaluated the dynamics of siderophore production under the combined influence of chemical and biological OSMAC triggers, temporally over 3, 7, and 14 days, to discern the strain’s siderophore-mediated chemical ecology. We discuss our results based on the plausible chemical implications of S. ciscaucasicus strain GS2 in the rhizosphere.
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Affiliation(s)
- Reyhaneh Armin
- Center for Mass Spectrometry (CMS), Faculty of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany; (R.A.); (S.Z.)
| | - Sebastian Zühlke
- Center for Mass Spectrometry (CMS), Faculty of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany; (R.A.); (S.Z.)
| | - Gisela Grunewaldt-Stöcker
- Institute of Horticultural Production Systems, Section Phytomedicine, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany;
| | - Felix Mahnkopp-Dirks
- Institute of Horticultural Production Systems, Section Woody Plant and Propagation Physiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany;
| | - Souvik Kusari
- Center for Mass Spectrometry (CMS), Faculty of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany; (R.A.); (S.Z.)
- Correspondence: ; Tel.: +49-231-755-4086
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19
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Klebba PE, Newton SMC, Six DA, Kumar A, Yang T, Nairn BL, Munger C, Chakravorty S. Iron Acquisition Systems of Gram-negative Bacterial Pathogens Define TonB-Dependent Pathways to Novel Antibiotics. Chem Rev 2021; 121:5193-5239. [PMID: 33724814 PMCID: PMC8687107 DOI: 10.1021/acs.chemrev.0c01005] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Iron is an indispensable metabolic cofactor in both pro- and eukaryotes, which engenders a natural competition for the metal between bacterial pathogens and their human or animal hosts. Bacteria secrete siderophores that extract Fe3+ from tissues, fluids, cells, and proteins; the ligand gated porins of the Gram-negative bacterial outer membrane actively acquire the resulting ferric siderophores, as well as other iron-containing molecules like heme. Conversely, eukaryotic hosts combat bacterial iron scavenging by sequestering Fe3+ in binding proteins and ferritin. The variety of iron uptake systems in Gram-negative bacterial pathogens illustrates a range of chemical and biochemical mechanisms that facilitate microbial pathogenesis. This document attempts to summarize and understand these processes, to guide discovery of immunological or chemical interventions that may thwart infectious disease.
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Affiliation(s)
- Phillip E Klebba
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Salete M C Newton
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - David A Six
- Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States
| | - Ashish Kumar
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Taihao Yang
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Brittany L Nairn
- Department of Biological Sciences, Bethel University, 3900 Bethel Drive, St. Paul, Minnesota 55112, United States
| | - Colton Munger
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Somnath Chakravorty
- Jacobs School of Medicine and Biomedical Sciences, SUNY Buffalo, Buffalo, New York 14203, United States
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20
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Terra L, Ratcliffe N, Castro HC, Vicente ACP, Dyson P. Biotechnological Potential of Streptomyces Siderophores as New Antibiotics. Curr Med Chem 2021; 28:1407-1421. [PMID: 32389112 DOI: 10.2174/0929867327666200510235512] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 02/29/2020] [Accepted: 03/23/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Siderophores are small-molecule iron-chelators produced by microorganisms and plants growing mostly under low iron conditions. Siderophores allow iron capture and transport through cell membranes into the cytoplasm, where iron is released for use in biological processes. These bacterial iron uptake systems can be used for antibiotic conjugation or as targets for killing pathogenic bacteria. Siderophores have been explored recently because of their potential applications in environmental and therapeutic research. They are present in Streptomyces, Grampositive bacteria that are an important source for discovering new siderophores. OBJECTIVE This review summarizes siderophore molecules produced by the genus Streptomyces emphasizing their potential as biotechnological producers and also illustrating genomic tools for discovering siderophores useful for treating bacterial infections. METHODS The literature search was performed using PUBMED and MEDLINE databases with keywords siderophore, secondary metabolites, Trojan horse strategy, sideromycin and Streptomyces. The literature research focused on bibliographic databases including all siderophores identified in the genus Streptomyces. In addition, reference genomes of Streptomyces from GenBank were used to identify siderophore biosynthetic gene clusters by using the antiSMASH platform. RESULTS This review has highlighted some of the many siderophore molecules produced by Streptomyces, illustrating the diversity of their chemical structures and a wide spectrum of bioactivities against pathogenic bacteria. Furthermore, the possibility of using siderophores conjugated with antibiotics could be an alternative to overcome bacterial resistance to drugs and could improve their therapeutic efficacy. CONCLUSION This review confirms the importance of Streptomyces as a rich source of siderophores, and underlines their potential as antibacterial agents.
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Affiliation(s)
- Luciana Terra
- Programa de Pos-Graduacao em Ciencias e Biotecnologia, Instituto de Biologia, UFF, Brazil
| | - Norman Ratcliffe
- Programa de Pos-Graduacao em Ciencias e Biotecnologia, Instituto de Biologia, UFF, Brazil
| | - Helena Carla Castro
- Programa de Pos-Graduacao em Ciencias e Biotecnologia, Instituto de Biologia, UFF, Brazil
| | | | - Paul Dyson
- Institute of Life Science, Swansea University Medical School, Singleton Park, Swansea SA2 8PP, United Kingdom
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21
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Metabolic Interactions between Brachypodium and Pseudomonas fluorescens under Controlled Iron-Limited Conditions. mSystems 2021; 6:6/1/e00580-20. [PMID: 33402348 PMCID: PMC7786132 DOI: 10.1128/msystems.00580-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Rhizosphere bacteria influence the growth of their host plant by consuming and producing metabolites, nutrients, and antibiotic compounds within the root system that affect plant metabolism. Under Fe-limited growth conditions, different plant and microbial species have distinct Fe acquisition strategies, often involving the secretion of strong Fe-binding chelators that scavenge Fe and facilitate uptake. Iron (Fe) availability has well-known effects on plant and microbial metabolism, but its effects on interspecies interactions are poorly understood. The purpose of this study was to investigate metabolite exchange between the grass Brachypodium distachyon strain Bd21 and the soil bacterium Pseudomonas fluorescens SBW25::gfp/lux (SBW25) during Fe limitation under axenic conditions. We compared the transcriptional profiles and root exudate metabolites of B. distachyon plants grown semihydroponically with and without SBW25 inoculation and Fe amendment. Liquid chromatography-mass spectrometry analysis of the hydroponic solution revealed an increase in the abundance of the phytosiderophores mugineic acid and deoxymugineic acid under Fe-limited conditions compared to Fe-replete conditions, indicating greater secretion by roots presumably to facilitate Fe uptake. In SBW25-inoculated roots, expression of genes encoding phytosiderophore biosynthesis and uptake proteins increased compared to that in sterile roots, but external phytosiderophore abundances decreased. P. fluorescens siderophores were not detected in treatments without Fe. Rather, expression of SBW25 genes encoding a porin, a transporter, and a monooxygenase was significantly upregulated in response to Fe deprivation. Collectively, these results suggest that SBW25 consumed root-exuded phytosiderophores in response to Fe deficiency, and we propose target genes that may be involved. SBW25 also altered the expression of root genes encoding defense-related enzymes and regulators, including thionin and cyanogenic glycoside production, chitinase, and peroxidase activity, and transcription factors. Our findings provide insights into the molecular bases for the stress response and metabolite exchange of interacting plants and bacteria under Fe-deficient conditions. IMPORTANCE Rhizosphere bacteria influence the growth of their host plant by consuming and producing metabolites, nutrients, and antibiotic compounds within the root system that affect plant metabolism. Under Fe-limited growth conditions, different plant and microbial species have distinct Fe acquisition strategies, often involving the secretion of strong Fe-binding chelators that scavenge Fe and facilitate uptake. Here, we studied interactions between P. fluorescens SBW25, a plant-colonizing bacterium that produces siderophores with antifungal properties, and B. distachyon, a genetic model for cereal grain and biofuel grasses. Under controlled growth conditions, bacterial siderophore production was inhibited in the root system of Fe-deficient plants, bacterial inoculation altered transcription of genes involved in defense and stress response in the roots of B. distachyon, and SBW25 degraded phytosiderophores secreted by the host plant. These findings provide mechanistic insight into interactions that may play a role in rhizosphere dynamics and plant health in soils with low Fe solubility.
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Cunrath O, Graulier G, Carballido-Lopez A, Pérard J, Forster A, Geoffroy VA, Saint Auguste P, Bumann D, Mislin GLA, Michaud-Soret I, Schalk IJ, Fechter P. The pathogen Pseudomonas aeruginosa optimizes the production of the siderophore pyochelin upon environmental challenges. Metallomics 2020; 12:2108-2120. [PMID: 33355556 DOI: 10.1039/d0mt00029a] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Siderophores are iron chelators produced by bacteria to access iron, an essential nutrient. The pathogen Pseudomonas aeruginosa produces two siderophores, pyoverdine and pyochelin, the former with a high affinity for iron and the latter with a lower affinity. Furthermore, the production of both siderophores involves a positive auto-regulatory loop: the presence of the ferri-siderophore complex is essential for their large production. Since pyochelin has a lower affinity for iron it was hard to consider the role of pyochelin in drastic competitive environments where the host or the environmental microbiota produce strong iron chelators and may inhibit iron chelation by pyochelin. We showed here that the pyochelin pathway overcomes this difficulty through a more complex regulating mechanism for pyochelin production than previously described. Indeed, in the absence of pyoverdine, and thus higher difficulty to access iron, the bacteria are able to produce pyochelin independently of the presence of ferri-pyochelin. The regulation of the pyochelin pathway appeared to be more complex than expected with a more intricate tuning between repression and activation. Consequently, when the bacteria cannot produce pyoverdine they are able to produce pyochelin even in the presence of strong iron chelators. Such results support a more complex and varied role for this siderophore than previously described, and complexify the battle for iron during P. aeruginosa infection.
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Affiliation(s)
- Olivier Cunrath
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France.
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Perraud Q, Kuhn L, Fritsch S, Graulier G, Gasser V, Normant V, Hammann P, Schalk IJ. Opportunistic use of catecholamine neurotransmitters as siderophores to access iron by Pseudomonas aeruginosa. Environ Microbiol 2020; 24:878-893. [PMID: 33350053 DOI: 10.1111/1462-2920.15372] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 10/22/2022]
Abstract
Iron is an essential nutrient for bacterial growth and the cause of a fierce battle between the pathogen and host during infection. Bacteria have developed several strategies to access iron from the host, the most common being the production of siderophores, small iron-chelating molecules secreted into the bacterial environment. The opportunist pathogen Pseudomonas aeruginosa produces two siderophores, pyoverdine and pyochelin, and is also able to use a wide panoply of xenosiderophores, siderophores produced by other microorganisms. Here, we demonstrate that catecholamine neurotransmitters (dopamine, l-DOPA, epinephrine and norepinephrine) are able to chelate iron and efficiently bring iron into P. aeruginosa cells via TonB-dependent transporters (TBDTs). Bacterial growth assays under strong iron-restricted conditions and with numerous mutants showed that the TBDTs involved are PiuA and PirA. PiuA exhibited more pronounced specificity for dopamine uptake than for norepinephrine, epinephrine and l-DOPA, whereas PirA specificity appeared to be higher for l-DOPA and norepinephrine. Proteomic and qRT-PCR approaches showed pirA transcription and expression to be induced in the presence of all four catecholamines. Finally, the oxidative properties of catecholamines enable them to reduce iron, and we observed ferrous iron uptake via the FeoABC system in the presence of l-DOPA.
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Affiliation(s)
- Quentin Perraud
- Université de Strasbourg, InnoVec, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France.,CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
| | - Lauriane Kuhn
- Plateforme Proteomique Strasbourg - Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS, FR1589, 15 rue Descartes, Strasbourg Cedex, F-67084, France
| | - Sarah Fritsch
- Université de Strasbourg, InnoVec, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France.,CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
| | - Gwenaëlle Graulier
- Université de Strasbourg, InnoVec, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France.,CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
| | - Véronique Gasser
- Université de Strasbourg, InnoVec, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France.,CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
| | - Vincent Normant
- Université de Strasbourg, InnoVec, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France.,CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
| | - Philippe Hammann
- Plateforme Proteomique Strasbourg - Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS, FR1589, 15 rue Descartes, Strasbourg Cedex, F-67084, France
| | - Isabelle J Schalk
- Université de Strasbourg, InnoVec, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France.,CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
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24
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Hierarchical routing in carbon metabolism favors iron-scavenging strategy in iron-deficient soil Pseudomonas species. Proc Natl Acad Sci U S A 2020; 117:32358-32369. [PMID: 33273114 PMCID: PMC7768705 DOI: 10.1073/pnas.2016380117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Siderophore secretion confers competitive advantage to pathogenic and beneficial bacteria in various nutritional environments, including human infections and rhizosphere microbiome. The siderophore biosynthesis must be sustained during a compromised carbon metabolism in Fe-deficient cells. Here we demonstrate that Fe-deficient Pseudomonas species overcome this paradox by coupling selectivity in carbon utilization with a hierarchy in metabolic pathways to favor carbon and energy fluxes for siderophore biosynthesis. A reprogrammed metabolism is predicted from genomics-based data obtained with several marine and soil bacterial systems in response to Fe deficiency, but metabolomics evidence is lacking. The present study offers an important roadmap for investigating the underlying metabolic connections between Fe or other metal nutrient availability and carbon utilization. High-affinity iron (Fe) scavenging compounds, or siderophores, are widely employed by soil bacteria to survive scarcity in bioavailable Fe. Siderophore biosynthesis relies on cellular carbon metabolism, despite reported decrease in both carbon uptake and Fe-containing metabolic proteins in Fe-deficient cells. Given this paradox, the metabolic network required to sustain the Fe-scavenging strategy is poorly understood. Here, through multiple 13C-metabolomics experiments with Fe-replete and Fe-limited cells, we uncover how soil Pseudomonas species reprogram their metabolic pathways to prioritize siderophore biosynthesis. Across the three species investigated (Pseudomonas putida KT2440, Pseudomonas protegens Pf-5, and Pseudomonas putida S12), siderophore secretion is higher during growth on gluconeogenic substrates than during growth on glycolytic substrates. In response to Fe limitation, we capture decreased flux toward the tricarboxylic acid (TCA) cycle during the metabolism of glycolytic substrates but, due to carbon recycling to the TCA cycle via enhanced anaplerosis, the metabolism of gluconeogenic substrates results in an increase in both siderophore secretion (up to threefold) and Fe extraction (up to sixfold) from soil minerals. During simultaneous feeding on the different substrate types, Fe deficiency triggers a hierarchy in substrate utilization, which is facilitated by changes in protein abundances for substrate uptake and initial catabolism. Rerouted metabolism further promotes favorable fluxes in the TCA cycle and the gluconeogenesis–anaplerosis nodes, despite decrease in several proteins in these pathways, to meet carbon and energy demands for siderophore precursors in accordance with increased proteins for siderophore biosynthesis. Hierarchical carbon metabolism thus serves as a critical survival strategy during the metal nutrient deficiency.
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25
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Simora RMC, Li S, Abass NY, Terhune JS, Dunham RA. Cathelicidins enhance protection of channel catfish, Ictalurus punctatus, and channel catfish ♀ × blue catfish, Ictalurus furcatus ♂ hybrid catfish against Edwarsiella ictaluri infection. JOURNAL OF FISH DISEASES 2020; 43:1553-1562. [PMID: 32929767 DOI: 10.1111/jfd.13257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/13/2020] [Accepted: 08/15/2020] [Indexed: 06/11/2023]
Abstract
Cathelicidins are a class of antimicrobial peptides (AMPs) known to possess rapid and direct antimicrobial activities against a variety of microorganisms. Recently identified cathelicidins derived from alligator and sea snake were found to be more effective in inhibiting microbial growth than other AMPs previously characterized. The ability of these two cathelicidins along with the peptides, cecropin and pleurocidin, to protect channel catfish (Ictalurus punctatus, Rafinesque) and hybrid catfish (I. punctatus ♀ × blue catfish, Ictalurus furcatus, Valenciennes ♂) against Edwardsiella ictaluri, one of the most prevalent pathogens affecting commercial catfish industry, was investigated. Cathelicidin-injected fish (50 µg ml-1 fish-1 ) that were simultaneously challenged with E. ictaluri through bath immersion at a concentration of ~1 × 106 CFU/ml had increased survival rates compared with other peptide treatments and the infected control. Bacterial numbers were also reduced in the liver and kidney of channel catfish and hybrid catfish in the cathelicidin treatments 24 hr post-infection. After 8 days of challenge, serum was collected to determine immune-related parameters such as bactericidal activity, lysozyme, serum protein, albumin and globulin. These immune-related parameters were significantly elevated in fish injected with the two cathelicidins as compared to other peptide treatments. These results indicate that cathelicidins derived from alligator and sea snake can stimulate immunity and enhance the resistance to E. ictaluri infection in channel catfish and hybrid catfish.
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Affiliation(s)
- Rhoda Mae C Simora
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
- College of Fisheries and Ocean Sciences, University of the Philippines Visayas, Miagao, Philippines
| | - Shangjia Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Nermeen Y Abass
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
- Department of Agricultural Botany, Faculty of Agriculture Saba-Basha, Alexandria University, Alexandria City, Egypt
| | - Jeffery S Terhune
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Rex A Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
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26
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Kügler S, Cooper RE, Boessneck J, Küsel K, Wichard T. Rhizobactin B is the preferred siderophore by a novel Pseudomonas isolate to obtain iron from dissolved organic matter in peatlands. Biometals 2020; 33:415-433. [PMID: 33026607 PMCID: PMC7676072 DOI: 10.1007/s10534-020-00258-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 09/30/2020] [Indexed: 01/12/2023]
Abstract
Bacteria often release diverse iron-chelating compounds called siderophores to scavenge iron from the environment for many essential biological processes. In peatlands, where the biogeochemical cycle of iron and dissolved organic matter (DOM) are coupled, bacterial iron acquisition can be challenging even at high total iron concentrations. We found that the bacterium Pseudomonas sp. FEN, isolated from an Fe-rich peatland in the Northern Bavarian Fichtelgebirge (Germany), released an unprecedented siderophore for its genus. High-resolution mass spectrometry (HR-MS) using metal isotope-coded profiling (MICP), MS/MS experiments, and nuclear magnetic resonance spectroscopy (NMR) identified the amino polycarboxylic acid rhizobactin and a novel derivative at even higher amounts, which was named rhizobactin B. Interestingly, pyoverdine-like siderophores, typical for this genus, were not detected. With peat water extract (PWE), studies revealed that rhizobactin B could acquire Fe complexed by DOM, potentially through a TonB-dependent transporter, implying a higher Fe binding constant of rhizobactin B than DOM. The further uptake of Fe-rhizobactin B by Pseudomonas sp. FEN suggested its role as a siderophore. Rhizobactin B can complex several other metals, including Al, Cu, Mo, and Zn. The study demonstrates that the utilization of rhizobactin B can increase the Fe availability for Pseudomonas sp. FEN through ligand exchange with Fe-DOM, which has implications for the biogeochemical cycling of Fe in this peatland.
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Affiliation(s)
- Stefan Kügler
- Institute for Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, 07743, Jena, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Rebecca E Cooper
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Johanna Boessneck
- Institute for Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, 07743, Jena, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
- The German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, 07743, Jena, Germany.
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27
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Chevrette MG, Gutiérrez-García K, Selem-Mojica N, Aguilar-Martínez C, Yañez-Olvera A, Ramos-Aboites HE, Hoskisson PA, Barona-Gómez F. Evolutionary dynamics of natural product biosynthesis in bacteria. Nat Prod Rep 2019; 37:566-599. [PMID: 31822877 DOI: 10.1039/c9np00048h] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2008 up to 2019The forces of biochemical adaptive evolution operate at the level of genes, manifesting in complex phenotypes and the global biodiversity of proteins and metabolites. While evolutionary histories have been deciphered for some other complex traits, the origins of natural product biosynthesis largely remain a mystery. This fundamental knowledge gap is surprising given the many decades of research probing the genetic, chemical, and biophysical mechanisms of bacterial natural product biosynthesis. Recently, evolutionary thinking has begun to permeate this otherwise mechanistically dominated field. Natural products are now sometimes referred to as 'specialized' rather than 'secondary' metabolites, reinforcing the importance of their biological and ecological functions. Here, we review known evolutionary mechanisms underlying the overwhelming chemical diversity of bacterial secondary metabolism, focusing on enzyme promiscuity and the evolution of enzymatic domains that enable metabolic traits. We discuss the mechanisms that drive the assembly of natural product biosynthetic gene clusters and propose formal definitions for 'specialized' and 'secondary' metabolism. We further explore how biosynthetic gene clusters evolve to synthesize related molecular species, and in turn how the biological and ecological roles that emerge from metabolic diversity are acted on by selection. Finally, we reconcile chemical, functional, and genetic data into an evolutionary model, the dynamic chemical matrix evolutionary hypothesis, in which the relationships between chemical distance, biomolecular activity, and relative fitness shape adaptive landscapes.
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Affiliation(s)
- Marc G Chevrette
- Wisconsin Institute for Discovery, Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
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28
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Arginine Biosynthesis Modulates Pyoverdine Production and Release in Pseudomonas putida as Part of the Mechanism of Adaptation to Oxidative Stress. J Bacteriol 2019; 201:JB.00454-19. [PMID: 31451546 DOI: 10.1128/jb.00454-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 08/22/2019] [Indexed: 12/28/2022] Open
Abstract
Iron is essential for most life forms. Under iron-limiting conditions, many bacteria produce and release siderophores-molecules with high affinity for iron-which are then transported into the cell in their iron-bound form, allowing incorporation of the metal into a wide range of cellular processes. However, free iron can also be a source of reactive oxygen species that cause DNA, protein, and lipid damage. Not surprisingly, iron capture is finely regulated and linked to oxidative-stress responses. Here, we provide evidence indicating that in the plant-beneficial bacterium Pseudomonas putida KT2440, the amino acid l-arginine is a metabolic connector between iron capture and oxidative stress. Mutants defective in arginine biosynthesis show reduced production and release of the siderophore pyoverdine and altered expression of certain pyoverdine-related genes, resulting in higher sensitivity to iron limitation. Although the amino acid is not part of the siderophore side chain, addition of exogenous l-arginine restores pyoverdine release in the mutants, and increased pyoverdine production is observed in the presence of polyamines (agmatine and spermidine), of which arginine is a precursor. Spermidine also has a protective role against hydrogen peroxide in P. putida, whereas defects in arginine and pyoverdine synthesis result in increased production of reactive oxygen species.IMPORTANCE The results of this study show a previously unidentified connection between arginine metabolism, siderophore turnover, and oxidative stress in Pseudomonas putida Although the precise molecular mechanisms involved have yet to be characterized in full detail, our data are consistent with a model in which arginine biosynthesis and the derived pathway leading to polyamine production function as a homeostasis mechanism that helps maintain the balance between iron uptake and oxidative-stress response systems.
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29
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Zhang C, Straight PD. Antibiotic discovery through microbial interactions. Curr Opin Microbiol 2019; 51:64-71. [DOI: 10.1016/j.mib.2019.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/05/2019] [Accepted: 06/20/2019] [Indexed: 01/09/2023]
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30
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Josts I, Veith K, Tidow H. Ternary structure of the outer membrane transporter FoxA with resolved signalling domain provides insights into TonB-mediated siderophore uptake. eLife 2019; 8:48528. [PMID: 31385808 PMCID: PMC6699858 DOI: 10.7554/elife.48528] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/05/2019] [Indexed: 01/27/2023] Open
Abstract
Many microbes and fungi acquire the essential ion Fe3+ through the synthesis and secretion of high-affinity chelators termed siderophores. In Gram-negative bacteria, these ferric-siderophore complexes are actively taken up using highly specific TonB-dependent transporters (TBDTs) located in the outer bacterial membrane (OM). However, the detailed mechanism of how the inner-membrane protein TonB connects to the transporters in the OM as well as the interplay between siderophore- and TonB-binding to the transporter is still poorly understood. Here, we present three crystal structures of the TBDT FoxA from Pseudomonas aeruginosa (containing a signalling domain) in complex with the siderophore ferrioxamine B and TonB and combine them with a detailed analysis of binding constants. The structures show that both siderophore and TonB-binding is required to form a translocation-competent state of the FoxA transporter in a two-step TonB-binding mechanism. The complex structure also indicates how TonB-binding influences the orientation of the signalling domain.
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Affiliation(s)
- Inokentijs Josts
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Katharina Veith
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Henning Tidow
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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31
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Hesse E, Padfield D, Bayer F, van Veen EM, Bryan CG, Buckling A. Anthropogenic remediation of heavy metals selects against natural microbial remediation. Proc Biol Sci 2019; 286:20190804. [PMID: 31213187 PMCID: PMC6599979 DOI: 10.1098/rspb.2019.0804] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In an era of unprecedented environmental change, there have been increasing ecological and global public health concerns associated with exposure to anthropogenic pollutants. While there is a pressing need to remediate polluted ecosystems, human intervention might unwittingly oppose selection for natural detoxification, which is primarily carried out by microbes. We test this possibility in the context of a ubiquitous chemical remediation strategy aimed at targeting metal pollution: the addition of lime-containing materials. Here, we show that raising pH by liming decreased the availability of toxic metals in acidic mine-degraded soils, but as a consequence selected against microbial taxa that naturally remediate soil through the production of metal-binding siderophores. Our results therefore highlight the crucial need to consider the eco-evolutionary consequences of human environmental strategies on microbial ecosystem services and other traits.
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Affiliation(s)
- Elze Hesse
- 1 ESI and CEC, Biosciences, University of Exeter , Penryn Campus, Cornwall TR10 9FE , UK
| | - Daniel Padfield
- 1 ESI and CEC, Biosciences, University of Exeter , Penryn Campus, Cornwall TR10 9FE , UK
| | - Florian Bayer
- 1 ESI and CEC, Biosciences, University of Exeter , Penryn Campus, Cornwall TR10 9FE , UK
| | - Eleanor M van Veen
- 2 Camborne School of Mines, CEMPS, University of Exeter , Penryn Campus, Cornwall TR10 9FE , UK
| | - Christopher G Bryan
- 2 Camborne School of Mines, CEMPS, University of Exeter , Penryn Campus, Cornwall TR10 9FE , UK
| | - Angus Buckling
- 1 ESI and CEC, Biosciences, University of Exeter , Penryn Campus, Cornwall TR10 9FE , UK
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32
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Competition among Nasal Bacteria Suggests a Role for Siderophore-Mediated Interactions in Shaping the Human Nasal Microbiota. Appl Environ Microbiol 2019; 85:AEM.02406-18. [PMID: 30578265 DOI: 10.1128/aem.02406-18] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/14/2018] [Indexed: 12/26/2022] Open
Abstract
Resources available in the human nasal cavity are limited. Therefore, to successfully colonize the nasal cavity, bacteria must compete for scarce nutrients. Competition may occur directly through interference (e.g., antibiotics) or indirectly by nutrient sequestration. To investigate the nature of nasal bacterial competition, we performed coculture inhibition assays between nasal Actinobacteria and Staphylococcus spp. We found that isolates of coagulase-negative staphylococci (CoNS) were sensitive to growth inhibition by Actinobacteria but that Staphylococcus aureus isolates were resistant to inhibition. Among Actinobacteria, we observed that Corynebacterium spp. were variable in their ability to inhibit CoNS. We sequenced the genomes of 10 Corynebacterium species isolates, including 3 Corynebacterium propinquum isolates that strongly inhibited CoNS and 7 other Corynebacterium species isolates that only weakly inhibited CoNS. Using a comparative genomics approach, we found that the C. propinquum genomes were enriched in genes for iron acquisition and harbored a biosynthetic gene cluster (BGC) for siderophore production, absent in the noninhibitory Corynebacterium species genomes. Using a chrome azurol S assay, we confirmed that C. propinquum produced siderophores. We demonstrated that iron supplementation rescued CoNS from inhibition by C. propinquum, suggesting that inhibition was due to iron restriction through siderophore production. Through comparative metabolomics and molecular networking, we identified the siderophore produced by C. propinquum as dehydroxynocardamine. Finally, we confirmed that the dehydroxynocardamine BGC is expressed in vivo by analyzing human nasal metatranscriptomes from the NIH Human Microbiome Project. Together, our results suggest that bacteria produce siderophores to compete for limited available iron in the nasal cavity and improve their fitness.IMPORTANCE Within the nasal cavity, interference competition through antimicrobial production is prevalent. For instance, nasal Staphylococcus species strains can inhibit the growth of other bacteria through the production of nonribosomal peptides and ribosomally synthesized and posttranslationally modified peptides. In contrast, bacteria engaging in exploitation competition modify the external environment to prevent competitors from growing, usually by hindering access to or depleting essential nutrients. As the nasal cavity is a nutrient-limited environment, we hypothesized that exploitation competition occurs in this system. We determined that Corynebacterium propinquum produces an iron-chelating siderophore, and this iron-sequestering molecule correlates with the ability to inhibit the growth of coagulase-negative staphylococci. Furthermore, we found that the genes required for siderophore production are expressed in vivo Thus, although siderophore production by bacteria is often considered a virulence trait, our work indicates that bacteria may produce siderophores to compete for limited iron in the human nasal cavity.
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van der Heul HU, Bilyk BL, McDowall KJ, Seipke RF, van Wezel GP. Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era. Nat Prod Rep 2019; 35:575-604. [PMID: 29721572 DOI: 10.1039/c8np00012c] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2000 to 2018 The antimicrobial activity of many of their natural products has brought prominence to the Streptomycetaceae, a family of Gram-positive bacteria that inhabit both soil and aquatic sediments. In the natural environment, antimicrobial compounds are likely to limit the growth of competitors, thereby offering a selective advantage to the producer, in particular when nutrients become limited and the developmental programme leading to spores commences. The study of the control of this secondary metabolism continues to offer insights into its integration with a complex lifecycle that takes multiple cues from the environment and primary metabolism. Such information can then be harnessed to devise laboratory screening conditions to discover compounds with new or improved clinical value. Here we provide an update of the review we published in NPR in 2011. Besides providing the essential background, we focus on recent developments in our understanding of the underlying regulatory networks, ecological triggers of natural product biosynthesis, contributions from comparative genomics and approaches to awaken the biosynthesis of otherwise silent or cryptic natural products. In addition, we highlight recent discoveries on the control of antibiotic production in other Actinobacteria, which have gained considerable attention since the start of the genomics revolution. New technologies that have the potential to produce a step change in our understanding of the regulation of secondary metabolism are also described.
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34
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Williams JC, Sheldon JR, Imlay HD, Dutter BF, Draelos MM, Skaar EP, Sulikowski GA. Synthesis of the Siderophore Coelichelin and Its Utility as a Probe in the Study of Bacterial Metal Sensing and Response. Org Lett 2019; 21:679-682. [PMID: 30645132 PMCID: PMC6474248 DOI: 10.1021/acs.orglett.8b03857] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A convergent total synthesis of the siderophore coelichelin is described. The synthetic route also provided access to acetyl coelichelin and other congeners of the parent siderophore. The synthetic products were evaluated for their ability to bind ferric iron and promote growth of a siderophore-deficient strain of the Gram-negative bacterium Pseudomonas aeruginosa under iron restriction conditions. The results of these studies indicate coelichelin and several derivatives serve as ferric iron delivery vehicles for P. aeruginosa.
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Affiliation(s)
- Jade C. Williams
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jessica R. Sheldon
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Hunter D. Imlay
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Brendan F. Dutter
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Matthew M. Draelos
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Gary A. Sulikowski
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
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35
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McRose DL, Seyedsayamdost MR, Morel FMM. Multiple siderophores: bug or feature? J Biol Inorg Chem 2018; 23:983-993. [PMID: 30264174 DOI: 10.1007/s00775-018-1617-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/04/2018] [Indexed: 12/31/2022]
Abstract
It is common for bacteria to produce chemically diverse sets of small Fe-binding molecules called siderophores. Studies of siderophore bioinorganic chemistry have firmly established the role of these molecules in Fe uptake and provided great insight into Fe complexation. However, we still do not fully understand why microbes make so many siderophores. In many cases, the release of small structural variants or siderophore fragments has been ignored, or considered as an inefficiency of siderophore biosynthesis. Yet, in natural settings, microbes live in complex consortia and it has become increasingly clear that the secondary metabolite repertoires of microbes reflect this dynamic environment. Multiple siderophore production may, therefore, provide a window into microbial life in the wild. This minireview focuses on three biochemical routes by which multiple siderophores can be released by the same organism-multiple biosynthetic gene clusters, fragment release, and precursor-directed biosynthesis-and highlights emergent themes related to each. We also emphasize the plurality of reasons for multiple siderophore production, which include enhanced iron uptake via synergistic siderophore use, microbial warfare and cooperation, and non-classical functions such as the use of siderophores to take up metals other than Fe.
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Affiliation(s)
- Darcy L McRose
- Department of Geosciences, Princeton University, Princeton, USA.
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, USA.,Department of Molecular Biology, Princeton University, Princeton, USA
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Butaitė E, Kramer J, Wyder S, Kümmerli R. Environmental determinants of pyoverdine production, exploitation and competition in natural Pseudomonas communities. Environ Microbiol 2018; 20:3629-3642. [PMID: 30003663 DOI: 10.1111/1462-2920.14355] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/20/2018] [Accepted: 06/25/2018] [Indexed: 11/28/2022]
Abstract
Many bacteria rely on the secretion of siderophores to scavenge iron from the environment. Laboratory studies revealed that abiotic and biotic factors together determine how much siderophores bacteria make, and whether siderophores can be exploited by non-producing cheaters or be deployed by producers to inhibit competitors. Here, we explore whether these insights apply to natural communities, by comparing the production of the siderophore pyoverdine among 930 Pseudomonas strains from 48 soil and pond communities. We found that pH, iron content, carbon concentration and community diversity determine pyoverdine production levels, and the extent to which strains are either stimulated or inhibited by heterologous (non-self) pyoverdines. While pyoverdine non-producers occurred in both habitats, their prevalence was higher in soils. Environmental and genetic analyses suggest that non-producers can evolve as cheaters, exploiting heterologous pyoverdine, but also due to pyoverdine disuse in environments with increased iron availability. Overall, we found that environmental factors explained between-strain variation in pyoverdine production much better in soils than in ponds, presumably because high strain mixing in ponds impedes local adaption. Our study sheds light on the complexity of natural bacterial communities, and provides first insights into the multivariate nature of siderophore-based iron acquisition and competition among environmental pseudomonads.
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Affiliation(s)
- Elena Butaitė
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Jos Kramer
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Stefan Wyder
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Rolf Kümmerli
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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A Complex Mechanism Involving LysR and TetR/AcrR That Regulates Iron Scavenger Biosynthesis in Pseudomonas donghuensis HYS. J Bacteriol 2018; 200:JB.00087-18. [PMID: 29686142 DOI: 10.1128/jb.00087-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 04/18/2018] [Indexed: 11/20/2022] Open
Abstract
7-Hydroxytropolone (7-HT) is a symmetrical seven-membered heteroatomic ring with a carboxyl group and two hydroxyl groups and was recently reported to be an iron scavenger of Pseudomonas donghuensis HYS. Cluster 1 includes 12 genes related to the synthesis of 7-HT; among these genes, those for two regulators, Orf1 and Orf12, were predicted to regulate 7-HT biosynthesis and to be LysR-type transcriptional regulators (LTTRs) and TetR/AcrR family transcriptional regulators, respectively. Data from real-time quantitative PCR and β-galactosidase and classical siderophore assays indicated that the transcription levels of orf1 and orf12, as well as those of crucial genes orf6 to orf9, were repressed under high-iron conditions. The deletion of orf1 and orf12 led to an absence of 7-HT and a decrease in orf6-orf9 expression. Orf1 and Orf12 were essential for the production of 7-HT through orf6-orf9 These two regulators are regulated by the Gac/Rsm system; Orf1 facilitates the expression of Orf12, and Orf12 concomitantly stimulates the expression of orf6-orf9 to synthesize 7-HT. The overexpression of Orf12 decreased 7-HT yields, possibly through decreased orf6-orf9 expression. This work thus outlines a complex mechanism regulating the biosynthesis of the iron scavenger 7-HT in P. donghuensis HYS. The synergy between Orf1 and Orf12 ensures that 7-HT acts as an iron chelator despite being toxic to bacteria and provides new ideas for the novel regulation of dual-functional secondary metabolism and research on 7-HT and its derivates in other bacteria.IMPORTANCE A complex regulation mechanism including two regulators, LysR and TetR/AcrR, in the biosynthesis of the novel iron scavenger 7-hydroxytropolone (7-HT) was verified in Pseudomonas donghuensis HYS. The coaction of LysR Orf1 and TetR/AcrR Orf12 may balance the toxicity and iron chelation of 7-HT in P. donghuensis HYS to overcome iron deficiency, as well as improve the bacterial competitiveness under iron-scarce conditions because of the toxicity of 7-HT toward other bacteria, making the accurate regulation of 7-HT biosynthesis indispensable. This regulation mechanism may be ubiquitous in the Pseudomonas putida group but may better explain the group's strong adaptability.
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Gougoulias C, Meade A, Shaw LJ. Apportioning bacterial carbon source utilization in soil using 14 C isotope analysis of FISH-targeted bacterial populations sorted by fluorescence activated cell sorting (FACS): 14 C-FISH-FACS. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:245-254. [PMID: 29457691 DOI: 10.1111/1758-2229.12631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 02/13/2018] [Indexed: 05/25/2023]
Abstract
An unresolved need in microbial ecology is methodology to enable quantitative analysis of in situ microbial substrate carbon use at the population level. Here, we evaluated if a novel combination of radiocarbon-labelled substrate tracing, fluorescence in situ hybridisation (FISH) and fluorescence-activated cell sorting (FACS) to sort the FISH-targeted population for quantification of incorporated radioactivity (14 C-FISH-FACS) can address this need. Our test scenario used FISH probe PSE1284 targeting Pseudomonas spp. (and some Burkholderia spp.) and salicylic acid added to rhizosphere soil. We examined salicylic acid-14 C fate (mineralized, cell-incorporated, extractable and non-extractable) and mass balance (0-24 h) and show that the PSE1284 population captured ∼ 50% of the Nycodenz extracted biomass 14 C. Analysis of the taxonomic distribution of the salicylic acid biodegradation trait suggested that PSE1284 population success was not due to conservation of this trait but due to competitiveness for the added carbon. Adding 50KBq of 14 C sample-1 enabled detection of 14 C in the sorted population at ∼ 60-600 times background; a sensitivity which demonstrates potential extension to analysis of rarer/less active populations. Given its sensitivity and compatibility with obtaining a C mass balance, 14 C-FISH-FACS allows quantitative dissection of C flow within the microbial biomass that has hitherto not been achieved.
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Affiliation(s)
- Christos Gougoulias
- Soil Research Centre, Department of Geography and Environmental Science, School of Archaeology, Geography and Environmental Science, University of Reading, Whiteknights, Reading, RG6 6DW, UK
| | - Andrew Meade
- School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6BX, UK
| | - Liz J Shaw
- Soil Research Centre, Department of Geography and Environmental Science, School of Archaeology, Geography and Environmental Science, University of Reading, Whiteknights, Reading, RG6 6DW, UK
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39
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Thiem D, Złoch M, Gadzała-Kopciuch R, Szymańska S, Baum C, Hrynkiewicz K. Cadmium-induced changes in the production of siderophores by a plant growth promoting strain of Pseudomonas fulva. J Basic Microbiol 2018; 58:623-632. [PMID: 29775200 DOI: 10.1002/jobm.201800034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/23/2018] [Accepted: 04/28/2018] [Indexed: 11/07/2022]
Abstract
The impact of increasing Cd2+ exposure on the quality and quantity of siderophores produced by a plant growth promoting Pseudomonas fulva strain was tested to gain insight into the degree of change. P. fulva was cultured in the increasing concentrations of Cd2+ (0, 0.5, 1.0, 2.0 mM). The secreted siderophores were separated by HPLC and characterized by UHPLC-QTOF/MS. In the presence of 2 mM Cd2+ synthesis of siderophores (hydroxamates, catecholates, phenolates) was mitigated compared to the treatments with lower concentrations of Cd2+ (0.5 and 1 mM). Increased synthesis of catecholates in 0.5 and 1 mM Cd2+ and of phenolates in 0.5-2 mM Cd2+ was revealed compared to the variant without Cd2+ . Out of seven different hydroxamates, the secretion of ferrioxamine E was significantly decreased in the highest Cd2+ concentration. Two additional ferrioxamines, X2 and D2, were secreted independent of the presence or absence of Cd2+ . Exposure to Cd2+ change the composition of siderophores secreted by P. fulva with selective promotion of catecholates and phenolates at the expense of hydroxamates. Successful adaptation in a Cd-contaminated soil in the frame of practical applications to promote phytoremediation can be assumed.
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Affiliation(s)
- Dominika Thiem
- Faculty of Biology and Environment Protection, Department of Microbiology, Nicolaus Copernicus University, Torun, Poland.,Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - Michał Złoch
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland.,Faculty of Chemistry, Department of Environmental Chemistry and Bioanalytics, Nicolaus Copernicus University, Torun, Poland
| | - Renata Gadzała-Kopciuch
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland.,Faculty of Chemistry, Department of Environmental Chemistry and Bioanalytics, Nicolaus Copernicus University, Torun, Poland
| | - Sonia Szymańska
- Faculty of Biology and Environment Protection, Department of Microbiology, Nicolaus Copernicus University, Torun, Poland.,Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - Christel Baum
- Faculty of Agricultural and Environmental Sciences, Soil Science, University of Rostock, Rostock, Germany
| | - Katarzyna Hrynkiewicz
- Faculty of Biology and Environment Protection, Department of Microbiology, Nicolaus Copernicus University, Torun, Poland.,Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
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40
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Rivera GSM, Beamish CR, Wencewicz TA. Immobilized FhuD2 Siderophore-Binding Protein Enables Purification of Salmycin Sideromycins from Streptomyces violaceus DSM 8286. ACS Infect Dis 2018; 4:845-859. [PMID: 29460625 DOI: 10.1021/acsinfecdis.8b00015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Siderophores are a structurally diverse class of natural products common to most bacteria and fungi as iron(III)-chelating ligands. Siderophores, including trihydroxamate ferrioxamines, are used clinically to treat iron overload diseases and show promising activity against many other iron-related human diseases. Here, we present a new method for the isolation of ferrioxamine siderophores from complex mixtures using affinity chromatography based on resin-immobilized FhuD2, a siderophore-binding protein (SBP) from Staphylococcus aureus. The SBP-resin enabled purification of charge positive, charge negative, and neutral ferrioxamine siderophores. Treatment of culture supernatants from Streptomyces violaceus DSM 8286 with SBP-resin provided an analytically pure sample of the salmycins, a mixture of structurally complex glycosylated sideromycins (siderophore-antibiotic conjugates) with potent antibacterial activity toward human pathogenic Staphylococcus aureus (minimum inhibitory concentration (MIC) = 7 nM). Siderophore affinity chromatography could enable the rapid discovery of new siderophore and sideromycin natural products from complex mixtures to aid drug discovery and metabolite identification efforts in a broad range of therapeutic areas.
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Affiliation(s)
- Gerry Sann M. Rivera
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Catherine R. Beamish
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Timothy A. Wencewicz
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
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41
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Hesse E, O'Brien S, Tromas N, Bayer F, Luján AM, van Veen EM, Hodgson DJ, Buckling A. Ecological selection of siderophore-producing microbial taxa in response to heavy metal contamination. Ecol Lett 2017; 21:117-127. [PMID: 29161760 PMCID: PMC5765521 DOI: 10.1111/ele.12878] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/23/2017] [Accepted: 10/16/2017] [Indexed: 11/27/2022]
Abstract
Some microbial public goods can provide both individual and community-wide benefits, and are open to exploitation by non-producing species. One such example is the production of metal-detoxifying siderophores. Here, we investigate whether conflicting selection pressures on siderophore production by heavy metals - a detoxifying effect of siderophores, and exploitation of this detoxifying effect - result in a net increase or decrease. We show that the proportion of siderophore-producing taxa increases along a natural heavy metal gradient. A causal link between metal contamination and siderophore production was subsequently demonstrated in a microcosm experiment in compost, in which we observed changes in community composition towards taxa that produce relatively more siderophores following copper contamination. We confirmed the selective benefit of siderophores by showing that taxa producing large amounts of siderophore suffered less growth inhibition in toxic copper. Our results suggest that ecological selection will favour siderophore-mediated decontamination, with important consequences for potential remediation strategies.
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Affiliation(s)
- Elze Hesse
- ESI & CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
| | - Siobhán O'Brien
- ESI & CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK.,Institut für Integrative Biologie, ETH Zürich, Universitätstrasse 16, Zürich, 8092, Switzerland
| | - Nicolas Tromas
- Département de Sciences Biologiques, Université de Montréal, 90 Vincent-d'Indy, Montréal, QC, H2V 2S9, Canada
| | - Florian Bayer
- ESI & CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
| | - Adela M Luján
- ESI & CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK.,CIQUIBIC, Departamento de Química Biológica, Facultad de Ciencias Químicas, CONICET, Universidad Nacional de Córdoba, Córdoba, X5000HUA, Argentina
| | - Eleanor M van Veen
- Camborne School of Mines, CEMPS, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
| | - Dave J Hodgson
- CEC, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
| | - Angus Buckling
- ESI & CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
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42
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Siderophore cheating and cheating resistance shape competition for iron in soil and freshwater Pseudomonas communities. Nat Commun 2017; 8:414. [PMID: 28871205 PMCID: PMC5583256 DOI: 10.1038/s41467-017-00509-4] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 06/29/2017] [Indexed: 11/17/2022] Open
Abstract
All social organisms experience dilemmas between cooperators performing group-beneficial actions and cheats selfishly exploiting these actions. Although bacteria have become model organisms to study social dilemmas in laboratory systems, we know little about their relevance in natural communities. Here, we show that social interactions mediated by a single shareable compound necessary for growth (the iron-scavenging pyoverdine) have important consequences for competitive dynamics in soil and pond communities of Pseudomonas bacteria. We find that pyoverdine non- and low-producers co-occur in many natural communities. While non-producers have genes coding for multiple pyoverdine receptors and are able to exploit compatible heterologous pyoverdines from other community members, producers differ in the pyoverdine types they secrete, offering protection against exploitation from non-producers with incompatible receptors. Our findings indicate that there is both selection for cheating and cheating resistance, which could drive antagonistic co-evolution and diversification in natural bacterial communities. Lab strains of Pseudomonas are model systems for the evolution of cooperation over public goods (iron-scavenging siderophores). Here, Butaitė et al. add ecological and evolutionary insight into this system by showing that cheating and resistance to cheating both shape competition for iron in natural Pseudomonas communities.
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Cruz-Morales P, Ramos-Aboites HE, Licona-Cassani C, Selem-Mójica N, Mejía-Ponce PM, Souza-Saldívar V, Barona-Gómez F. Actinobacteria phylogenomics, selective isolation from an iron oligotrophic environment and siderophore functional characterization, unveil new desferrioxamine traits. FEMS Microbiol Ecol 2017; 93:3934648. [PMID: 28910965 PMCID: PMC5812494 DOI: 10.1093/femsec/fix086] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 07/04/2017] [Indexed: 01/29/2023] Open
Abstract
Desferrioxamines are hydroxamate siderophores widely conserved in both aquatic and soil-dwelling Actinobacteria. While the genetic and enzymatic bases of siderophore biosynthesis and their transport in model families of this phylum are well understood, evolutionary studies are lacking. Here, we perform a comprehensive desferrioxamine-centric (des genes) phylogenomic analysis, which includes the genomes of six novel strains isolated from an iron and phosphorous depleted oasis in the Chihuahuan desert of Mexico. Our analyses reveal previously unnoticed desferrioxamine evolutionary patterns, involving both biosynthetic and transport genes, likely to be related to desferrioxamines chemical diversity. The identified patterns were used to postulate experimentally testable hypotheses after phenotypic characterization, including profiling of siderophores production and growth stimulation of co-cultures under iron deficiency. Based in our results, we propose a novel des gene, which we term desG, as responsible for incorporation of phenylacetyl moieties during biosynthesis of previously reported arylated desferrioxamines. Moreover, a genomic-based classification of the siderophore-binding proteins responsible for specific and generalist siderophore assimilation is postulated. This report provides a much-needed evolutionary framework, with specific insights supported by experimental data, to direct the future ecological and functional analysis of desferrioxamines in the environment.
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Affiliation(s)
- Pablo Cruz-Morales
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, 36821 Irapuato, México
| | - Hilda E. Ramos-Aboites
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, 36821 Irapuato, México
| | - Cuauhtémoc Licona-Cassani
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, 36821 Irapuato, México
| | - Nelly Selem-Mójica
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, 36821 Irapuato, México
| | - Paulina M. Mejía-Ponce
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, 36821 Irapuato, México
| | - Valeria Souza-Saldívar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, 04510 Ciudad de México, México
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, 36821 Irapuato, México
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Rocha ER, Krykunivsky AS. Anaerobic utilization of Fe(III)-xenosiderophores among Bacteroides species and the distinct assimilation of Fe(III)-ferrichrome by Bacteroides fragilis within the genus. Microbiologyopen 2017; 6:e00479. [PMID: 28397401 PMCID: PMC5552952 DOI: 10.1002/mbo3.479] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/24/2017] [Accepted: 03/07/2017] [Indexed: 01/01/2023] Open
Abstract
In this study, we show that Bacteroides species utilize Fe(III)-xenosiderophores as the only source of exogenous iron to support growth under iron-limiting conditions in vitro anaerobically. Bacteroides fragilis was the only species able to utilize Fe(III)-ferrichrome while Bacteroides vulgatus ATCC 8482 and Bacteroides thetaiotaomicron VPI 5482 were able to utilize both Fe(III)-enterobactin and Fe(III)-salmochelin S4 as the only source of iron in a dose-dependent manner. We have investigated the way B. fragilis assimilates Fe(III)-ferrichrome as initial model to understand the utilization of xenosiderophores in anaerobes. B. fragilis contains two outer membrane TonB-dependent transporters (TBDTs), FchA1 and FchA2, which are homologues to Escherichia coli ferrichrome transporter FhuA. The disruption of fchA1 gene had only partial growth defect on Fe(III)-ferrichrome while the fchA2 mutant had no growth defect compared to the parent strain. The genetic complementation of fchA1 gene restored growth to parent strain levels indicating that it plays a role in Fe(III)-ferrichrome assimilation though we cannot rule out some functional overlap in transport systems as B. fragilis contains abundant TBDTs whose functions are yet not understood. However, the growth of B. fragilis on Fe(III)-ferrichrome was abolished in a feoAB mutant indicating that Fe(III)-ferrichrome transported into the periplasmic space was reduced in the periplasm releasing ferrous iron prior to transport through the FeoAB transport system. Moreover, the release of iron from the ferrichrome may be linked to the thiol redox system as the trxB deletion mutant was also unable to grow in the presence of Fe(III)-ferrichrome. The genetic complementation of feoAB and trxB mutants completely restored growth on Fe(III)-ferrichrome. Taken together, these findings show that Bacteroides species have developed mechanisms to utilize ferric iron bound to xenosiderophores under anaerobic growth conditions though the regulation and role in the biology of Bacteroides in the anaerobic intestinal environment remain to be understood.
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Affiliation(s)
- Edson R. Rocha
- Department of Microbiology and ImmunologyBrody School of MedicineEast Carolina UniversityGreenvilleNC
| | - Anna S. Krykunivsky
- Department of Microbiology and ImmunologyBrody School of MedicineEast Carolina UniversityGreenvilleNC
- Intern from the Undergraduate Research Internship Placement ProgramUniversity of the West of England (UWE)BristolUK
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Abstract
Microbes in nature often live in unfavorable conditions. To survive, they have to occupy niches close to food sources and efficiently utilize nutrients that are often present in very low concentrations. Moreover, they have to possess an arsenal of attack and defense mechanisms against competing bacteria. In this review, we will discuss strategies used by microbes to compete with each other in the rhizosphere and on fruits, with a focus on mechanisms of inter- and intra-species antagonism. Special attention will be paid to the recently discovered roles of volatile organic compounds. Several microbes with proven capabilities in the art of warfare are being applied in products used for the biological control of plant diseases, including post-harvest control of fruits and vegetables.
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Affiliation(s)
- Ben Lugtenberg
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Daniel E Rozen
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Faina Kamilova
- Koppert Biological Systems, Veilingweg 14, PO Box 155, 2650 AD Berkel en Rodenrijs, Netherlands
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46
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Hoff G, Bertrand C, Zhang L, Piotrowski E, Chipot L, Bontemps C, Confalonieri F, McGovern S, Lecointe F, Thibessard A, Leblond P. Multiple and Variable NHEJ-Like Genes Are Involved in Resistance to DNA Damage in Streptomyces ambofaciens. Front Microbiol 2016; 7:1901. [PMID: 27965636 PMCID: PMC5124664 DOI: 10.3389/fmicb.2016.01901] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/14/2016] [Indexed: 11/26/2022] Open
Abstract
Non-homologous end-joining (NHEJ) is a double strand break (DSB) repair pathway which does not require any homologous template and can ligate two DNA ends together. The basic bacterial NHEJ machinery involves two partners: the Ku protein, a DNA end binding protein for DSB recognition and the multifunctional LigD protein composed a ligase, a nuclease and a polymerase domain, for end processing and ligation of the broken ends. In silico analyses performed in the 38 sequenced genomes of Streptomyces species revealed the existence of a large panel of NHEJ-like genes. Indeed, ku genes or ligD domain homologues are scattered throughout the genome in multiple copies and can be distinguished in two categories: the “core” NHEJ gene set constituted of conserved loci and the “variable” NHEJ gene set constituted of NHEJ-like genes present in only a part of the species. In Streptomyces ambofaciens ATCC23877, not only the deletion of “core” genes but also that of “variable” genes led to an increased sensitivity to DNA damage induced by electron beam irradiation. Multiple mutants of ku, ligase or polymerase encoding genes showed an aggravated phenotype compared to single mutants. Biochemical assays revealed the ability of Ku-like proteins to protect and to stimulate ligation of DNA ends. RT-qPCR and GFP fusion experiments suggested that ku-like genes show a growth phase dependent expression profile consistent with their involvement in DNA repair during spores formation and/or germination.
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Affiliation(s)
- Grégory Hoff
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Claire Bertrand
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Lingli Zhang
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Emilie Piotrowski
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Ludovic Chipot
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Cyril Bontemps
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Fabrice Confalonieri
- Institute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud Orsay, France
| | - Stephen McGovern
- Institut Micalis, INRA, AgroParisTech, Université Paris-Saclay Jouy-en-Josas, France
| | - François Lecointe
- Institut Micalis, INRA, AgroParisTech, Université Paris-Saclay Jouy-en-Josas, France
| | - Annabelle Thibessard
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Pierre Leblond
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
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Deveau A, Gross H, Palin B, Mehnaz S, Schnepf M, Leblond P, Dorrestein PC, Aigle B. Role of secondary metabolites in the interaction between Pseudomonas fluorescens and soil microorganisms under iron-limited conditions. FEMS Microbiol Ecol 2016; 92:fiw107. [PMID: 27199346 PMCID: PMC5975829 DOI: 10.1093/femsec/fiw107] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/15/2016] [Accepted: 05/15/2016] [Indexed: 01/18/2023] Open
Abstract
Microorganisms can be versatile in their interactions with each other, being variously beneficial, neutral or antagonistic in their effect. Although this versatility has been observed among many microorganisms and in many environments, little is known regarding the mechanisms leading to these changes in behavior. In the present work, we analyzed the mechanism by which the soil bacterium Pseudomonas fluorescens BBc6R8 shifts from stimulating the growth of the ectomycorrhizal fungus Laccaria bicolor S238N to killing the fungus. We show that among the three secondary metabolites produced by the bacterial strain-the siderophores enantio-pyochelin and pyoverdine, and the biosurfactant viscosin-the siderophores are mainly responsible for the antagonistic activity of the bacterium under iron-limited conditions. While the bacterial strain continues to produce beneficial factors, their effects are overridden by the action of their siderophores. This antagonistic activity of the strain P. fluorescens BBC6R8 in iron-depleted environments is not restricted to its influence on L. bicolor, since it was also seen to inhibit the growth of the actinomycete Streptomyces ambofaciens ATCC23877. We show that the strain P. fluorescens BBc6R8 uses different strategies to acquire iron, depending on certain biotic and abiotic factors.
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Affiliation(s)
- Aurélie Deveau
- INRA, Interactions Arbres-Microorganismes, UMR1136, Université de Lorraine, F-54280 Champenoux, France
| | - Harald Gross
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Béatrice Palin
- INRA, Interactions Arbres-Microorganismes, UMR1136, Université de Lorraine, F-54280 Champenoux, France
| | - Samina Mehnaz
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany Department of Biological Sciences, Forman Christian College, Ferozepur Road, Lahore 54600, Pakistan
| | - Max Schnepf
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Pierre Leblond
- Dynamique des Génomes et Adaptation Microbienne, UMR1128, Université de Lorraine, Faculté des Sciences et Technologies-Campus Aiguillettes, Vandœuvre-lès-Nancy, F-54506, France
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA 92093, USA
| | - Bertrand Aigle
- Dynamique des Génomes et Adaptation Microbienne, UMR1128, Université de Lorraine, Faculté des Sciences et Technologies-Campus Aiguillettes, Vandœuvre-lès-Nancy, F-54506, France
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Abstract
Microbial communities span many orders of magnitude, ranging in scale from hundreds of cells on a single particle of soil to billions of cells within the lumen of the gastrointestinal tract. Bacterial cells in all habitats are members of densely populated local environments that facilitate competition between neighboring cells. Accordingly, bacteria require dynamic systems to respond to the competitive challenges and the fluctuations in environmental circumstances that tax their fitness. The assemblage of bacteria into communities provides an environment where competitive mechanisms are developed into new strategies for survival. In this minireview, we highlight a number of mechanisms used by bacteria to compete between species. We focus on recent discoveries that illustrate the dynamic and multifaceted functions used in bacterial competition and discuss how specific mechanisms provide a foundation for understanding bacterial community development and function.
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Pyoverdine and histicorrugatin-mediated iron acquisition in Pseudomonas thivervalensis. Biometals 2016; 29:467-85. [DOI: 10.1007/s10534-016-9929-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/19/2016] [Indexed: 12/17/2022]
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