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Cortés-Albayay C, Delgado-Torres M, Larama G, Paredes-Negron C, de la Luz Mora M, Durán P, Barra PJ. Comparative genomics of plant growth promoting phosphobacteria isolated from acidic soils. Antonie Van Leeuwenhoek 2024; 117:76. [PMID: 38705910 DOI: 10.1007/s10482-024-01961-1] [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: 01/25/2024] [Accepted: 03/26/2024] [Indexed: 05/07/2024]
Abstract
Despite being one of the most abundant elements in soil, phosphorus (P) often becomes a limiting macronutrient for plants due to its low bioavailability, primarily locked away in insoluble organic and inorganic forms. Phosphate solubilizing and mineralizing bacteria, also called phosphobacteria, isolated from P-deficient soils have emerged as a promising biofertilizer alternative, capable of converting these recalcitrant P forms into plant-available phosphates. Three such phosphobacteria strains-Serratia sp. RJAL6, Klebsiella sp. RCJ4, and Enterobacter sp. 198-previously demonstrated their particular strength as plant growth promoters for wheat, ryegrass, or avocado under abiotic stresses and P deficiency. Comparative genomic analysis of their draft genomes revealed several genes encoding key functionalities, including alkaline phosphatases, isonitrile secondary metabolites, enterobactin biosynthesis and genes associated to the production of indole-3-acetic acid (IAA) and gluconic acid. Moreover, overall genome relatedness indexes (OGRIs) revealed substantial divergence between Serratia sp. RJAL6 and its closest phylogenetic neighbours, Serratia nematodiphila and Serratia bockelmanii. This compelling evidence suggests that RJAL6 merits classification as a novel species. This in silico genomic analysis provides vital insights into the plant growth-promoting capabilities and provenance of these promising PSRB strains. Notably, it paves the way for further characterization and potential application of the newly identified Serratia species as a powerful bioinoculant in future agricultural settings.
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Affiliation(s)
- Carlos Cortés-Albayay
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, 4811230, Temuco, Chile
| | - Mabel Delgado-Torres
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile
| | - Giovanni Larama
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, 4811230, Temuco, Chile
| | - Cecilia Paredes-Negron
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile
| | - María de la Luz Mora
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile
| | - Paola Durán
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile.
- Biocontrol Research Laboratory, Universidad de La Frontera, 4811230, Temuco, Chile.
- Facultad de Ciencias Agropecuarias y Medioambiente, Departamento de Producción Agropecuaria, Universidad de La Frontera, 4811230, Temuco, Chile.
| | - Patricio Javier Barra
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile.
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2
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Khazaal MT, Faraag AHI, Hamada MA, El-Hendawy HH. Characterization and Statistical Optimization of Enterobatin Synthesized by Escherichia coli OQ866153. Biochem Genet 2024:10.1007/s10528-023-10626-z. [PMID: 38245887 DOI: 10.1007/s10528-023-10626-z] [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: 08/10/2023] [Accepted: 12/07/2023] [Indexed: 01/23/2024]
Abstract
Microorganisms produce siderophores, which are secondary metabolites with a high affinity for iron. Siderophores have received significant attention due to their diverse applications in ecological and clinical research. In this study, siderophores production by Escherichia coli OQ866153 was optimized using two-stage statistical approach involving Plackett-Burman design (PBD) and response surface methodology (RSM) using central composite design (CCD). Out of 23 variables, succinate, tryptophan, Na2HPO4, CaCl2, agitation, and KH2PO4 were found to have the most significant effect on siderophores production in the first optimization stage with the highest SU% of 43.67%. In the second stage, RSM using CCD was utilized, and the optimal conditions were determined to be 0.3 g/l succinate, 0 g/l tryptophan, 6 g/l Na2HPO4, 0.1 g/l CaCl2, 150 RPM agitation, and 0.6 g/l KH2PO4, resulting in a maximum siderophore units (SU%) of 89.13%. The model was significant, as indicated by the model f-value of 314.14 (p-value = 0.0004) and coefficient of determination R2 of 0.9950. During validation experiments, the obtained maximum SU% was increased up to 87.1472%, which was two times as the value obtained under ordinary conditions (46.62%). The produced siderophores were purified and characterized using 1H, 13C NMR, IR spectroscopy. The obtained results indicated that the compound was enterobactin and entABCDEF genes were further detected in Escherichia coli OQ866153 extracted DNA. To our knowledge, this is the first report of statistical optimization for enterobactin synthesis by an E. coli strain isolated from a clinical source in Egypt.
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Affiliation(s)
- Mohamed T Khazaal
- Botany and Microbiology Department, Faculty of Science, Helwan University, Helwan, Cairo, 11795, Egypt
| | - Ahmed H I Faraag
- Botany and Microbiology Department, Faculty of Science, Helwan University, Helwan, Cairo, 11795, Egypt
| | - Marwa A Hamada
- Botany and Microbiology Department, Faculty of Science, Helwan University, Helwan, Cairo, 11795, Egypt
| | - Hoda H El-Hendawy
- Botany and Microbiology Department, Faculty of Science, Helwan University, Helwan, Cairo, 11795, Egypt.
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3
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Zou Z, Robinson JI, Steinberg LK, Henderson JP. Uropathogenic Escherichia coli wield enterobactin-derived catabolites as siderophores. J Biol Chem 2024; 300:105554. [PMID: 38072063 PMCID: PMC10788543 DOI: 10.1016/j.jbc.2023.105554] [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: 07/28/2023] [Revised: 11/20/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) secrete multiple siderophore types to scavenge extracellular iron(III) ions during clinical urinary tract infections, despite the metabolic costs of biosynthesis. Here, we find the siderophore enterobactin (Ent) and its related products to be prominent components of the iron-responsive extracellular metabolome of a model UPEC strain. Using defined Ent biosynthesis and import mutants, we identify lower molecular weight dimeric exometabolites as products of incomplete siderophore catabolism, rather than prematurely released biosynthetic intermediates. In E. coli, iron acquisition from iron(III)-Ent complexes requires intracellular esterases that hydrolyze the siderophore. Although UPEC are equipped to consume the products of completely hydrolyzed Ent, we find that Ent and its derivatives may be incompletely hydrolyzed to yield products with retained siderophore activity. These results are consistent with catabolic inefficiency as means to obtain more than one iron ion per siderophore molecule. This is compatible with an evolved UPEC strategy to maximize the nutritional returns from metabolic investments in siderophore biosynthesis.
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Affiliation(s)
- Zongsen Zou
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, St Louis, Missouri, USA; Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - John I Robinson
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, St Louis, Missouri, USA; Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Lindsey K Steinberg
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, St Louis, Missouri, USA; Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Jeffrey P Henderson
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, St Louis, Missouri, USA; Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, USA.
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4
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Gutiérrez-García K, Whitaker MRL, Bustos-Díaz ED, Salzman S, Ramos-Aboites HE, Reitz ZL, Pierce NE, Cibrián-Jaramillo A, Barona-Gómez F. Gut microbiomes of cycad-feeding insects tolerant to β-methylamino-L-alanine (BMAA) are rich in siderophore biosynthesis. ISME COMMUNICATIONS 2023; 3:122. [PMID: 37993724 PMCID: PMC10665472 DOI: 10.1038/s43705-023-00323-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/17/2023] [Accepted: 10/25/2023] [Indexed: 11/24/2023]
Abstract
Ingestion of the cycad toxins β-methylamino-L-alanine (BMAA) and azoxyglycosides is harmful to diverse organisms. However, some insects are specialized to feed on toxin-rich cycads with apparent immunity. Some cycad-feeding insects possess a common set of gut bacteria, which might play a role in detoxifying cycad toxins. Here, we investigated the composition of gut microbiota from a worldwide sample of cycadivorous insects and characterized the biosynthetic potential of selected bacteria. Cycadivorous insects shared a core gut microbiome consisting of six bacterial taxa, mainly belonging to the Proteobacteria, which we were able to isolate. To further investigate selected taxa from diverging lineages, we performed shotgun metagenomic sequencing of co-cultured bacterial sub-communities. We characterized the biosynthetic potential of four bacteria from Serratia, Pantoea, and two different Stenotrophomonas lineages, and discovered a suite of biosynthetic gene clusters notably rich in siderophores. Siderophore semi-untargeted metabolomics revealed a broad range of chemically related yet diverse iron-chelating metabolites, including desferrioxamine B, suggesting the occurrence of an unprecedented desferrioxamine-like biosynthetic pathway that remains to be identified. These results provide a foundation for future investigations into how cycadivorous insects tolerate diets rich in azoxyglycosides, BMAA, and other cycad toxins, including a possible role for bacterial siderophores.
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Affiliation(s)
- Karina Gutiérrez-García
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Irapuato - León, Irapuato, Guanajuato, 36824, México
- Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD, 21218, USA
| | - Melissa R L Whitaker
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA.
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37614, USA.
| | - Edder D Bustos-Díaz
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Irapuato - León, Irapuato, Guanajuato, 36824, México
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE, The Netherlands
| | - Shayla Salzman
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- University of Georgia, Entomology Department, Athens, GA, 30602, USA
| | - Hilda E Ramos-Aboites
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Irapuato - León, Irapuato, Guanajuato, 36824, México
| | - Zachary L Reitz
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Naomi E Pierce
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Angélica Cibrián-Jaramillo
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Irapuato - León, Irapuato, Guanajuato, 36824, México
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Irapuato - León, Irapuato, Guanajuato, 36824, México.
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE, The Netherlands.
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5
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Zou Z, Robinson JI, Steinberg LK, Henderson JP. Uropathogenic Escherichia coli wield enterobactin-derived catabolites as siderophores. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550588. [PMID: 37546885 PMCID: PMC10402112 DOI: 10.1101/2023.07.25.550588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Uropathogenic E. coli (UPEC) secrete multiple siderophore types to scavenge extracellular iron(III) ions during clinical urinary tract infections, despite the metabolic costs of biosynthesis. Here we find the siderophore enterobactin and its related products to be prominent components of the iron-responsive extracellular metabolome of a model UPEC strain. Using defined enterobactin biosynthesis and import mutants, we identify lower molecular weight, dimeric exometabolites as products of incomplete siderophore catabolism, rather than prematurely released biosynthetic intermediates. In E. coli, iron acquisition from iron(III)-enterobactin complexes requires intracellular esterases that hydrolyze the siderophore. Although UPEC are equipped to consume the products of completely hydrolyzed enterobactin, we find that enterobactin and its derivatives may be incompletely hydrolyzed to yield products with retained siderophore activity. These results are consistent with catabolic inefficiency as means to obtain more than one iron ion per siderophore molecule. This is compatible with an evolved UPEC strategy to maximize the nutritional returns from metabolic investments in siderophore biosynthesis.
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Affiliation(s)
- Zongsen Zou
- Center for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - John I. Robinson
- Center for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lindsey K. Steinberg
- Center for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jeffrey P. Henderson
- Center for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
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6
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Jiang L, Zhao Y, Yao Y, Lou J, Zhao Y, Hu B. Adding siderophores: A new strategy to reduce greenhouse gas emissions in composting. BIORESOURCE TECHNOLOGY 2023:129319. [PMID: 37315620 DOI: 10.1016/j.biortech.2023.129319] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/10/2023] [Accepted: 06/10/2023] [Indexed: 06/16/2023]
Abstract
Microbial community is the primary driver causing the greenhouse gas emissions in composting. Thus, regulating the microbial communities is a strategy to reduce them. Here, two different siderophores (enterobactin and putrebactin) were added, which could bind and translocate iron by specific microbes, to regulate the composting communities. The results showed that adding enterobactin enriched Acinetobacter and Bacillus with specific receptors by 6.84-fold and 6.78-fold. It promoted carbohydrate degradation and amino acid metabolism. This resulted in a 1.28-fold increase in humic acid content, as well as a 14.02% and 18.27% decrease in CO2 and CH4 emissions, respectively. Meanwhile, adding putrebactin boosted the microbial diversity by 1.21-fold and enhanced potential microbial interactions by 1.76-fold. The attenuated denitrification process led to a 1.51-fold increase in the total nitrogen content and a 27.47% reduction in N2O emissions. Overall, adding siderophores is an efficient strategy to reduce greenhouse gas emissions and promote the compost quality.
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Affiliation(s)
- Liyan Jiang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuting Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuqing Yao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jingxuan Lou
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuxiang Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Baolan Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou310058, China.
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7
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Liu Z, Huang T, Shi Q, Deng Z, Lin S. Catechol siderophores framed on 2,3-dihydroxybenzoyl-L-serine from Streptomyces varsoviensis. Front Microbiol 2023; 14:1182449. [PMID: 37206338 PMCID: PMC10188961 DOI: 10.3389/fmicb.2023.1182449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/10/2023] [Indexed: 05/21/2023] Open
Abstract
Enterobactin is an archetypical catecholate siderophore that plays a key role in the acquisition of ferric iron by microorganisms. Catechol moieties have been shown to be promising siderophore cores. Variants of the conserved 2,3-dihydroxybenzoate (DHB) moiety with structural modifications expand the bioactivity. Streptomyces are characterized by metabolites with diverse structures. The genomic sequence of Streptomyces varsoviensis indicated that it possessed a biosynthetic gene cluster for DHB containing siderophores and metabolic profiling revealed metabolites correlated with catechol-type natural products. Here, we report the discovery of a series of catecholate siderophores produced by S. varsoviensis and a scale-up fermentation was performed to purify these compounds for structural elucidation. A biosynthetic route for the catecholate siderophores is also proposed. These new structural features enrich the structural diversity of the enterobactin family compounds. One of the new linear enterobactin congeners shows moderate activity against a food-borne pathogen Listeria monocytogenes. This work demonstrated that changing culture conditions is still a promising approach to explore unexplored chemical diversity. The availability of the biosynthetic machinery will enrich the genetic toolbox of catechol siderophores and facilitate such engineering efforts.
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Affiliation(s)
- Zhixiang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tingting Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Haihe Laboratory of Synthetic Biology, Tianjin, China
| | - Qing Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Haihe Laboratory of Synthetic Biology, Tianjin, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Haihe Laboratory of Synthetic Biology, Tianjin, China
- Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Shuangjun Lin,
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8
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Asamizu S, Pramana AAC, Kawai SJ, Arakawa Y, Onaka H. Comparative Metabolomics Reveals a Bifunctional Antibacterial Conjugate from Combined-Culture of Streptomyces hygroscopicus HOK021 and Tsukamurella pulmonis TP-B0596. ACS Chem Biol 2022; 17:2664-2672. [PMID: 36074093 DOI: 10.1021/acschembio.2c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
To investigate the potential for secondary metabolite biosynthesis by Streptomyces species, we employed a coculture method to discover natural bioactive products and identified specific antibacterial activity from a combined-culture of Streptomyces hygroscopicus HOK021 and Tsukamurella pulmonis TP-B0596. Molecular networking using ultrahigh performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (UPLC-QTOF-MS/MS) data revealed a specific clade of metabolites in this combined-culture that were not detected in both monocultures. Using the chemical profiles, a previously unidentified conjugate between FabF inhibitor and catechol-type siderophore was successfully identified and named harundomycin A. Harundomycin A was a conjugate between the 2,4-dihydroxy-3-aminobenzoate moiety of platensimycin and N,N'-bis(2,3-dihydroxybenzoyl)-O-seryl-cysteine (bisDHBA-Ser-Cys) with a thioester linkage. Along with the production of harundomycin A, platensimycin, its thiocarboxylic acid form thioplatensimycin, enterobactin, and its degradation product N,N'-bis(2,3-dihydroxybenzoyl)-O-l-seryl-dehydroalanine (bisDHBA-Ser-Dha) were also induced in the combined-culture. Genomic data of S. hygroscopicus HOK021 and T. pulmonis TP-B0596 indicated that strain HOK021 possessed biosynthetic gene clusters for both platensimycin and enterobactin, and thereby revealed that T. pulmonis stimulates HOK021 and acts as an inducer of both of these metabolites. Although the harundomycin A was modified by bulky bisDHBA-Ser-Cys, responsible for the binding to the target molecule FabF, it showed a similar antibacterial spectrum to platensimycin, including against methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci, suggesting that the pharmacophore is platensimycin. Additionally, Chrome Azurol S assay showed that harundomycin A possesses ferric iron-chelating activity comparable to that of enterobactin. Our study demonstrated the transformation of existing natural products to bifunctional molecules driven by bacterial interaction.
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Affiliation(s)
- Shumpei Asamizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Abrory Agus Cahya Pramana
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Sung-Jin Kawai
- New Field Pioneering Division, Toyota Boshoku Corporation, 1-1 Toyoda, Kariya, Aichi 448-8651, Japan
| | - Yoshichika Arakawa
- Graduate School of Medicine, Nagoya University, 65 Tsurumai, Showa, Nagoya 466-8550, Japan
| | - Hiroyasu Onaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
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9
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Lee YJ, Park S, Kim Y, Kim SH, Seo J. Facile synthetic method for peptoids bearing multiple azoles on side chains. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yen Jea Lee
- Department of Chemistry Gwangju Institute of Science and Technology Gwangju Republic of Korea
| | - Soyeon Park
- Department of Chemistry Gwangju Institute of Science and Technology Gwangju Republic of Korea
| | - Yujeong Kim
- Western Seoul Center Korea Basic Science Institute Seoul Republic of Korea
| | - Sun Hee Kim
- Western Seoul Center Korea Basic Science Institute Seoul Republic of Korea
- Department of Chemistry and Nano Science Ewha Womans University Seoul Republic of Korea
| | - Jiwon Seo
- Department of Chemistry Gwangju Institute of Science and Technology Gwangju Republic of Korea
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10
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Wellawa DH, Lam PKS, White AP, Gomis S, Allan B, Köster W. High Affinity Iron Acquisition Systems Facilitate but Are Not Essential for Colonization of Chickens by Salmonella Enteritidis. Front Microbiol 2022; 13:824052. [PMID: 35308377 PMCID: PMC8928163 DOI: 10.3389/fmicb.2022.824052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/24/2022] [Indexed: 01/02/2023] Open
Abstract
The roles of TonB mediated Fe3+ (ferric iron) uptake via enterobactin (involving biosynthesis genes entABCDEF) and Fe2+ (ferrous iron) uptake through the FeoABC transporter are poorly defined in the context of chicken-Salmonella interactions. Both uptake systems are believed to be the major contributors of iron supply in the Salmonella life cycle. Current evidence suggests that these iron uptake systems play a major role in pathogenesis in mammals and as such, they represent promising antibacterial targets with therapeutic potential. We investigated the role of these iron uptake mechanisms regarding the ability of Salmonella Enteritidis (SEn) strains to colonize in a chicken infection model. Further we constructed a bioluminescent reporter to sense iron limitation during gastrointestinal colonization of Salmonella in chicken via ex vivo imaging. Our data indicated that there is some redundancy between the ferric and ferrous iron uptake mechanisms regarding iron acquisition during SEn pathogenesis in chicken. We believe that this redundancy of iron acquisition in the host reservoir may be the consequence of adaptation to unique avian environments, and thus warrants further investigation. To our knowledge, this the first report providing direct evidence that both enterobactin synthesis and FeoABC mediated iron uptake contribute to the virulence of SEn in chickens.
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Affiliation(s)
- Dinesh H Wellawa
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Po-King S Lam
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Aaron P White
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Susantha Gomis
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Brenda Allan
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Wolfgang Köster
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
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11
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Nonribosomal Peptide Synthesis Definitely Working Out of the Rules. Microorganisms 2022; 10:microorganisms10030577. [PMID: 35336152 PMCID: PMC8949500 DOI: 10.3390/microorganisms10030577] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 12/04/2022] Open
Abstract
Nonribosomal peptides are microbial secondary metabolites exhibiting a tremendous structural diversity and a broad range of biological activities useful in the medical and agro-ecological fields. They are built up by huge multimodular enzymes called nonribosomal peptide synthetases. These synthetases are organized in modules constituted of adenylation, thiolation, and condensation core domains. As such, each module governs, according to the collinearity rule, the incorporation of a monomer within the growing peptide. The release of the peptide from the assembly chain is finally performed by a terminal core thioesterase domain. Secondary domains with modifying catalytic activities such as epimerization or methylation are sometimes included in the assembly lines as supplementary domains. This assembly line structure is analyzed by bioinformatics tools to predict the sequence and structure of the final peptides according to the sequence of the corresponding synthetases. However, a constantly expanding literature unravels new examples of nonribosomal synthetases exhibiting very rare domains and noncanonical organizations of domains and modules, leading to several amazing strategies developed by microorganisms to synthesize nonribosomal peptides. In this review, through several examples, we aim at highlighting these noncanonical pathways in order for the readers to perceive their complexity.
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12
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Klahn P, Zscherp R, Jimidar CC. Advances in the Synthesis of Enterobactin, Artificial Analogues, and Enterobactin-Derived Antimicrobial Drug Conjugates and Imaging Tools for Infection Diagnosis. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/a-1783-0751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
AbstractIron is an essential growth factor for bacteria, but although highly abundant in nature, its bioavailability during infection in the human host or the environment is limited. Therefore, bacteria produce and secrete siderophores to ensure their supply of iron. The triscatecholate siderophore enterobactin and its glycosylated derivatives, the salmochelins, play a crucial role for iron acquisition in several bacteria. As these compounds can serve as carrier molecules for the design of antimicrobial siderophore drug conjugates as well as siderophore-derived tool compounds for the detection of infections with bacteria, their synthesis and the design of artificial analogues is of interest. In this review, we give an overview on the synthesis of enterobactin, biomimetic as well as totally artificial analogues, and related drug-conjugates covering up to 12/2021.1 Introduction2 Antibiotic Crisis and Sideromycins as Natural Templates for New Antimicrobial Drugs3 Biosynthesis of Enterobactin, Salmochelins, and Microcins4 Total Synthesis of Enterobactin and Salmochelins5 Chemoenzymatic Semi-synthesis of Salmochelins and Microcin E492m Derivatives6 Synthesis of Biomimetic Enterobactin Derivatives with Natural Tris-lactone Backbone7 Synthesis of Artificial Enterobactin Derivatives without Tris-lactone Backbone8 Conclusions
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Affiliation(s)
- Philipp Klahn
- Institute of Organic Chemistry, Technische Universität Braunschweig
- Department for Chemistry and Molecular Biology, University of Gothenburg
| | - Robert Zscherp
- Institute of Organic Chemistry, Technische Universität Braunschweig
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13
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Pandey A, Śmiłowicz D, Boros E. Galbofloxacin: a xenometal-antibiotic with potent in vitro and in vivo efficacy against S. aureus. Chem Sci 2021; 12:14546-14556. [PMID: 34881006 PMCID: PMC8580130 DOI: 10.1039/d1sc04283a] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/14/2021] [Indexed: 11/21/2022] Open
Abstract
Siderophore-antibiotic drug conjugates are considered potent tools to deliver and potentiate the antibacterial activity of antibiotics, but only few have seen preclinical and clinical success. Here, we introduce the gallium(iii) complex of a ciprofloxacin-functionalized linear desferrichrome, Galbofloxacin, with a cleavable serine linker as a potent therapeutic for S. aureus bacterial infections. We employed characterization using in vitro inhibitory assays, radiochemical, tracer-based uptake and pharmacokinetic assessment of our lead compound, culminating in in vivo efficacy studies in a soft tissue model of infection. Galbofloxacin exhibits a minimum inhibitory concentration of (MIC98) 93 nM in wt S. aureus, exceeding the potency of the parent antibiotic ciprofloxacin (0.9 μM). Galbofloxacin is a protease substrate that can release the antibiotic payload in the bacterial cytoplasm. Radiochemical experiments with wt bacterial strains reveal that 67Galbofloxacin is taken up efficiently using siderophore mediated, active uptake. Biodistribution of 67Galbofloxacin in a mouse model of intramuscular S. aureus infection revealed renal clearance and enhanced uptake in infected muscle when compared to 67Ga-citrate, which showed no selectivity. A subsequent in vivo drug therapy study reveals efficient reduction in S. aureus infection burden and sustained survival with Galbofloxacin for 7 days. Ciprofloxacin had no treatment efficacy at identical molecular dose (9.3 μmol kg−1) and resulted in death of all study animals in <24 hours. Taken together, the favorable bacterial growth inhibitory, pharmacokinetic and in vivo efficacy properties qualify Galbofloxacin as the first rationally designed Ga-coordination complex for the management of S. aureus bacterial infections. Galbofloxacin, a novel theranostic xenosiderophore antibiotic, exhibits unparalleled potency in combating S. aureus infections in vivo.![]()
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Affiliation(s)
- Apurva Pandey
- Department of Chemistry, Stony Brook University 100 Nicolls Road, Stony Brook New York 11790 USA
| | - Dariusz Śmiłowicz
- Department of Chemistry, Stony Brook University 100 Nicolls Road, Stony Brook New York 11790 USA
| | - Eszter Boros
- Department of Chemistry, Stony Brook University 100 Nicolls Road, Stony Brook New York 11790 USA
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14
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Stow PR, Reitz ZL, Johnstone TC, Butler A. Genomics-driven discovery of chiral triscatechol siderophores with enantiomeric Fe(iii) coordination. Chem Sci 2021; 12:12485-12493. [PMID: 34603680 PMCID: PMC8480324 DOI: 10.1039/d1sc03541j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/18/2021] [Indexed: 11/21/2022] Open
Abstract
Ferric complexes of triscatechol siderophores may assume one of two enantiomeric configurations at the iron site. Chirality is known to be important in the iron uptake process, however an understanding of the molecular features directing stereospecific coordination remains ambiguous. Synthesis of the full suite of (DHBL/DLysL/DSer)3 macrolactone diastereomers, which includes the siderophore cyclic trichrysobactin (CTC), enables the effects that the chirality of Lys and Ser residues exert on the configuration of the Fe(iii) complex to be defined. Computationally optimized geometries indicate that the Λ/Δ configurational preferences are set by steric interactions between the Lys sidechains and the peptide backbone. The ability of each (DHBL/DLysL/DSer)3 diastereomer to form a stable Fe(iii) complex prompted a genomic search for biosynthetic gene clusters (BGCs) encoding the synthesis of these diastereomers in microbes. The genome of the plant pathogen Dickeya chrysanthemi EC16 was sequenced and the genes responsible for the biosynthesis of CTC were identified. A related but distinct BGC was identified in the genome of the opportunistic pathogen Yersinia frederiksenii ATCC 33641; isolation of the siderophore from Y. frederiksenii ATCC 33641, named frederiksenibactin (FSB), revealed the triscatechol oligoester, linear-(DHBLLysLSer)3. Circular dichroism (CD) spectroscopy establishes that Fe(iii)-CTC and Fe(iii)-FSB are formed in opposite enantiomeric configuration, consistent with the results of the ferric complexes of the cyclic (DHBL/DLysL/DSer)3 diastereomers.
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Affiliation(s)
- Parker R Stow
- Department of Chemistry and Biochemistry, University of California Santa Barbara CA 93106-9510 USA
| | - Zachary L Reitz
- Department of Chemistry and Biochemistry, University of California Santa Barbara CA 93106-9510 USA
| | - Timothy C Johnstone
- Department of Chemistry and Biochemistry, University of California Santa Cruz CA 95064 USA
| | - Alison Butler
- Department of Chemistry and Biochemistry, University of California Santa Barbara CA 93106-9510 USA
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15
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Wu Q, Throckmorton K, Maity M, Chevrette MG, Braun DR, Rajski SR, Currie CR, Thomas MG, Bugni TS. Bacillibactins E and F from a Marine Sponge-Associated Bacillus sp. JOURNAL OF NATURAL PRODUCTS 2021; 84:136-141. [PMID: 33337146 PMCID: PMC7856188 DOI: 10.1021/acs.jnatprod.0c01170] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chemical investigation of a marine sponge-associated Bacillus sp. led to the discovery of bacillibactins E and F (1 and 2). Despite containing the well-established cyclic triester core of iron-binding natural products such as enterobactin, bacillibactins E and F (1 and 2) are the first bacterial siderophores that contain nicotinic and benzoic acid moieties. The structures of the new compounds, including their absolute configurations, were determined by extensive spectroscopic analyses and Marfey's method. A plausible biosynthetic pathway to 1 and 2 is proposed; this route bears great similarity to other previously established bacillibactin-like pathways but appears to differentiate itself by a promiscuous DhbE, which likely installs the nicotinic moiety of 1 and the benzoic acid group of 2.
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Affiliation(s)
- Qihao Wu
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Kurt Throckmorton
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Mitasree Maity
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Marc G Chevrette
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Plant Pathology, Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
| | - Doug R Braun
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Scott R Rajski
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Michael G Thomas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Tim S Bugni
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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16
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Dekimpe S, Masschelein J. Beyond peptide bond formation: the versatile role of condensation domains in natural product biosynthesis. Nat Prod Rep 2021; 38:1910-1937. [DOI: 10.1039/d0np00098a] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Condensation domains perform highly diverse functions during natural product biosynthesis and are capable of generating remarkable chemical diversity.
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Affiliation(s)
- Sofie Dekimpe
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
| | - Joleen Masschelein
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
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17
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The Serratia marcescens Siderophore Serratiochelin Is Necessary for Full Virulence during Bloodstream Infection. Infect Immun 2020; 88:IAI.00117-20. [PMID: 32393508 DOI: 10.1128/iai.00117-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/06/2020] [Indexed: 12/31/2022] Open
Abstract
Serratia marcescens is a bacterium frequently found in the environment, but over the last several decades it has evolved into a concerning clinical pathogen, causing fatal bacteremia. To establish such infections, pathogens require specific nutrients; one very limited but essential nutrient is iron. We sought to characterize the iron acquisition systems in S. marcescens isolate UMH9, which was recovered from a clinical bloodstream infection. Using RNA sequencing (RNA-seq), we identified two predicted siderophore gene clusters (cbs and sch) that were regulated by iron. Mutants were constructed to delete each iron acquisition locus individually and in conjunction, generating both single and double mutants for the putative siderophore systems. Mutants lacking the sch gene cluster lost their iron-chelating ability as quantified by the chrome azurol S (CAS) assay, whereas the cbs mutant retained wild-type activity. Mass spectrometry-based analysis identified the chelating siderophore to be serratiochelin, a siderophore previously identified in Serratia plymuthica Serratiochelin-producing mutants also displayed a decreased growth rate under iron-limited conditions created by dipyridyl added to LB medium. Additionally, mutants lacking serratiochelin were significantly outcompeted during cochallenge with wild-type UMH9 in the kidneys and spleen after inoculation via the tail vein in a bacteremia mouse model. This result was further confirmed by an independent challenge, suggesting that serratiochelin is required for full S. marcescens pathogenesis in the bloodstream. Nine other clinical isolates have at least 90% protein identity to the UMH9 serratiochelin system; therefore, our results are broadly applicable to emerging clinical isolates of S. marcescens causing bacteremia.
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18
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Liu D, Yan R, Fu Y, Wang X, Zhang J, Xiang W. Antifungal, Plant Growth-Promoting, and Genomic Properties of an Endophytic Actinobacterium Streptomyces sp. NEAU-S7GS2. Front Microbiol 2019; 10:2077. [PMID: 31551997 PMCID: PMC6746918 DOI: 10.3389/fmicb.2019.02077] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 08/22/2019] [Indexed: 11/23/2022] Open
Abstract
Diseases caused by Sclerotinia sclerotiorum have caused severe losses of many economically important crops worldwide. Due to the long-term persistence of sclerotia in soil and the production of air-borne ascospores, synthetic fungicides play limited roles in controlling the diseases. The application of antagonistic microorganisms can effectively reduce the number of sclerotia and eventually eradicate S. sclerotiorum from soil, and therefore considerable interest has been focused on biological control. Streptomyces sp. NEAU-S7GS2 was isolated from the root of Glycine max and its rhizosphere soil. It showed significant inhibitory activity against the mycelial growth of S. sclerotiorum (99.1%) and completely inhibited sclerotia germination. Compared to the control, in the pot experiment the application of NEAU-S7GS2 not only demonstrated excellent potential to control sclerotinia stem rot of soybean with 77 and 38% decrease in disease incidence and disease index, respectively, but could promote the growth of soybean. The light microscopy and scanning electron microscopy showed that co-culture of NEAU-S7GS2 with S. sclerotiorum on potato dextrose agar could lead to contorted and fragmented mycelia of S. sclerotiorum, which was associated with the secretion of hydrolytic glucanase and cellulase and the production of active secondary metabolites by NEAU-S7GS2. The plant growth promoting activity of NEAU-S7GS2 was related to the solubilization of inorganic phosphate, and production of 1-aminocyclopropane-1-carboxylate (ACC) deaminase and indole acetic acid (IAA). To further explore the plant growth promoting and antifungal mechanisms, the complete genome of strain NEAU-S7GS2 was sequenced. Several genes associated with ammonia assimilation, phosphate solubilization and IAA synthesis, together with genes encoding ACC deaminase, glucanase and α-amylase, were identified. AntiSMASH analysis led to the identification of four gene clusters responsible for the biosynthesis of siderophores including desferrioxamine B and enterobactin. Moreover, the biosynthetic gene clusters of lydicamycins, phenazines, and a glycosylated polyol macrolide showing 88% gene similarity to PM100117/PM100118 were identified. These results suggested that strain NEAU-S7GS2 may be a potential biocontrol agent and biofertilizer used in agriculture.
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Affiliation(s)
- Dongli Liu
- Heilongjiang Provinical Key Laboratory of Agricultural Microbiology, Northeast Agricultural University, Harbin, China
| | - Rui Yan
- Heilongjiang Provinical Key Laboratory of Agricultural Microbiology, Northeast Agricultural University, Harbin, China
| | - Yansong Fu
- Heilongjiang Provinical Key Laboratory of Agricultural Microbiology, Northeast Agricultural University, Harbin, China
| | - Xiangjing Wang
- Heilongjiang Provinical Key Laboratory of Agricultural Microbiology, Northeast Agricultural University, Harbin, China
| | - Ji Zhang
- Heilongjiang Provinical Key Laboratory of Agricultural Microbiology, Northeast Agricultural University, Harbin, China
| | - Wensheng Xiang
- Heilongjiang Provinical Key Laboratory of Agricultural Microbiology, Northeast Agricultural University, Harbin, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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19
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Qin Y, He Y, She Q, Larese-Casanova P, Li P, Chai Y. Heterogeneity in respiratory electron transfer and adaptive iron utilization in a bacterial biofilm. Nat Commun 2019; 10:3702. [PMID: 31420537 PMCID: PMC6697725 DOI: 10.1038/s41467-019-11681-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 07/26/2019] [Indexed: 11/16/2022] Open
Abstract
In Bacillus subtilis, robust biofilm formation requires large quantities of ferric iron. Here we show that this process requires preferential production of a siderophore precursor, 2,3-dihydroxybenzoate, instead of the siderophore bacillibactin. A large proportion of iron is associated extracellularly with the biofilm matrix. The biofilms are conductive, with extracellular iron potentially acting as electron acceptor. A relatively small proportion of ferric iron is internalized and boosts production of iron-containing enzymes involved in respiratory electron transfer and establishing strong membrane potential, which is key to biofilm matrix production. Our study highlights metabolic diversity and versatile energy generation strategies within B. subtilis biofilms. Biofilm formation in Bacillus subtilis requires high levels of ferric iron. Here, Qin et al. show that iron accumulation requires production of dihydroxybenzoate (a precursor in siderophore biosynthesis), and matrix-associated iron may be acting as extracellular electron acceptor during respiratory electron transfer.
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Affiliation(s)
- Yuxuan Qin
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.,Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Yinghao He
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Qianxuan She
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Philip Larese-Casanova
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, 02115, USA
| | - Pinglan Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
| | - Yunrong Chai
- Department of Biology, Northeastern University, Boston, MA, 02115, USA.
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20
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Que L. Alison Butler: papers in celebration of her 2018 ACS Alfred Bader Award in Bioorganic or Bioinorganic Chemistry. J Biol Inorg Chem 2018; 26:375-377. [PMID: 30288609 DOI: 10.1007/s00775-018-1618-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lawrence Que
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN, 55455-0431, USA.
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21
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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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22
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Amphi-enterobactin commonly produced among Vibrio campbellii and Vibrio harveyi strains can be taken up by a novel outer membrane protein FapA that also can transport canonical Fe(III)-enterobactin. J Biol Inorg Chem 2018; 23:1009-1022. [PMID: 30135989 DOI: 10.1007/s00775-018-1601-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/08/2018] [Indexed: 10/28/2022]
Abstract
Vibrio campbellii BAA-1116 (formerly Vibrio harveyi) is a model organism for quorum sensing study and produces the siderophores anguibactin and amphi-enterobactin. This study examined the mechanisms and specificity of siderophore uptake in V. campbellii and V. harveyi, and surveyed the diversity of siderophore production in V. campbellii and V. harveyi strains. The amphi-enterobactin gene cluster of BAA-1116 harbors a gene, named fapA, that is a homologue of genes encoding Fe(III)-siderophore-specific outer membrane receptors. Another strain, V. campbellii HY01, a strain pathogenic to shrimp, also carries this cluster including fapA. Our siderophore bioassay results using HY01-derived indicator strains show that the FapA protein localized in the outer membrane fraction of V. campbellii HY01 is essential for the uptake of Fe(III)-amphi-enterobactin as well as exogenous siderophores, including enterobactin from E. coli, but not vanchrobactin from V. anguillarum RV22 while Fe(III)-amphi-enterobactin can be utilized by V. anguillarum. Electrospray ionization mass spectrometry as well as bioassay revealed that various V. campbellii and V. harveyi strains produce a suite of amphi-enterobactins with various fatty acid appendages, including several novel amphi-enterobactins, and these amphi-enterobactins can be taken up by V. campbellii HY01 via FapA, indicating that amphi-enterobactin production is a common phenotype among V. campbellii and V. harveyi, whereas our previous work, confirmed herein, showed that anguibactin is only produced by V. campbellii strains. These results along with the additional finding that a 2,3-dihydroxybenzoic acid biosynthesis gene, aebA, located in the amphi-enterobactin gene cluster, is essential for both anguibactin and amphi-enterobactin biosynthesis, suggest the possibility that amphi-enterobactin is a native siderophore of V. campbellii and V. harveyi, while the anguibactin system has been acquired by V. campbellii during evolution.
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23
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Quorum sensing and iron regulate a two-for-one siderophore gene cluster in Vibrio harveyi. Proc Natl Acad Sci U S A 2018; 115:7581-7586. [PMID: 29954861 DOI: 10.1073/pnas.1805791115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The secretion of small Fe-binding molecules called siderophores is an important microbial strategy for survival in Fe-limited environments. Siderophore production is often regulated by quorum sensing (QS), a microbial counting technique that allows organisms to alter gene expression based on cell density. However, the identity and quantities of siderophores produced under QS regulation are rarely studied in the context of their roles in Fe uptake. We investigated the link between QS, siderophores, and Fe uptake in the model marine organism Vibrio harveyi where QS is thought to repress siderophore production. We find that V. harveyi uses a single QS- and Fe-repressed gene cluster to produce both cell-associated siderophores (amphiphilic enterobactins) as well as several related soluble siderophores, which we identify and quantify using liquid chromatography-coupled (LC)-MS as well as tandem high-resolution MS (LC-HR-MS/MS). Measurements of siderophore production show that soluble siderophores are present at ∼100× higher concentrations than amphi-enterobactin and that over the course of growth V. harveyi decreases amphi-enterobactin concentrations but accumulates soluble siderophores. 55Fe radio-tracer uptake experiments demonstrate that these soluble siderophores play a significant role in Fe uptake and that the QS-dictated concentrations of soluble siderophores in stationary phase are near the limit of cellular uptake capacities. We propose that cell-associated and soluble siderophores are beneficial to V. harveyi in different environmental and growth contexts and that QS allows V. harveyi to exploit "knowledge" of its population size to avoid unnecessary siderophore production.
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24
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Thode SK, Rojek E, Kozlowski M, Ahmad R, Haugen P. Distribution of siderophore gene systems on a Vibrionaceae phylogeny: Database searches, phylogenetic analyses and evolutionary perspectives. PLoS One 2018; 13:e0191860. [PMID: 29444108 PMCID: PMC5812596 DOI: 10.1371/journal.pone.0191860] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 01/13/2018] [Indexed: 11/19/2022] Open
Abstract
Siderophores are small molecules synthesized and secreted by bacteria and fungi to scavenge iron. Extracellular ferri-siderohores are recognized by cognate receptors on the cell surface for transport over membranes. Several siderophore systems from Vibrionaceae representatives are known and well understood, e.g., the molecular structure of the siderophore, the biosynthesis gene cluster and pathway, and the gene expression pattern. Less is known about how these systems are distributed among the ~140 Vibrionaceae species, and which evolutionary processes contributed to the present-day distribution. In this work, we compiled existing knowledge on siderophore biosynthesis systems and siderophore receptors from Vibrionaceae and used phylogenetic analyses to investigate their organization, distribution, origin and evolution. Through literature searches, we identified nine different siderophore biosynthesis systems and thirteen siderophore receptors in Vibrionaceae. Homologs were identified by BLAST searches, and the results were mapped onto a Vibrionaceae phylogeny. We identified 81 biosynthetic systems distributed in 45 Vibrionaceae species and 16 unclassified Vibrionaceae strains, and 409 receptors in 89 Vibrionaceae species and 49 unclassified Vibrionaceae strains. The majority of taxa are associated with at least one type of siderophore biosynthesis system, some (e.g., aerobactin and vibrioferrin) of which are widely distributed in the family, whereas others (i.e., bisucaberin and vibriobactin) are found in one lineage. Cognate receptors are found more widespread. Phylogenetic analysis of three siderophore systems (piscibactin, vibrioferrin and aerobactin) show that their present-day distribution can be explained by an old insertion into Vibrionaceae, followed mainly by stable vertical evolution and extensive loss, and some cases of horizontal gene transfers. The present work provides an up to date overview of the distribution of siderophore-based iron acquisition systems in Vibrionaceae, and presents phylogenetic analysis of these systems. Our results suggest that the present-day distribution is a result of several evolutionary processes, such as old and new gene acquisitions, gene loss, and both vertical and horizontal gene transfers.
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Affiliation(s)
- Sunniva Katharina Thode
- Department of Chemistry and Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT − The Arctic University of Norway, Tromsø, Norway
| | - Ewelina Rojek
- Department of Natural Sciences and Technology, Faculty of Education and Natural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Mikolaj Kozlowski
- Department of Natural Sciences and Technology, Faculty of Education and Natural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Rafi Ahmad
- Department of Natural Sciences and Technology, Faculty of Education and Natural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway
- * E-mail: (PH); (RA)
| | - Peik Haugen
- Department of Chemistry and Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT − The Arctic University of Norway, Tromsø, Norway
- * E-mail: (PH); (RA)
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