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Begum K, Hasan N, Shammi M. Selective Biotic Stressors' Action on Seed Germination: A Review. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024:112156. [PMID: 38866107 DOI: 10.1016/j.plantsci.2024.112156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/05/2024] [Accepted: 06/08/2024] [Indexed: 06/14/2024]
Abstract
In the realm of plant biology and agriculture, seed germination serves as a fundamental process with far-reaching implications for crop production and environmental health. This comprehensive review seeks to unravel the intricate web of interactions between some biotic stressors and seed germination, addressing the pertinent issue of how these stressors influence seed germination. Different chemicals produced by interacting plants (different parts), fungi, bacteria, or insects can either promote or inhibit seed germination. Releasing chemicals that modulate signaling pathways and cellular processes significantly disrupt essential cellular functions. This disruption leads to diverse germination outcomes, introducing additional layers of complexity to this regulatory landscape. The chemicals perturb enzyme activity and membrane integrity, imposing unique challenges on the germination process. Understanding the mechanisms- how allelochemicals, mycotoxins, or bacterial toxins affect seed germination or the modes of action holds promise for more sustainable agricultural practices, enhanced pest control, and improved environmental outcomes. In sum, this review contributes to a fundamental exposition of the pivotal role of biotic stressors in shaping the germination of seeds.
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Affiliation(s)
- Kohinoor Begum
- Tropical Crop Improvement Laboratory, Saga University, Saga 840-8503, Japan; United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan.
| | - Nazmul Hasan
- Tropical Crop Improvement Laboratory, Saga University, Saga 840-8503, Japan; United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Fruit Science Laboratory, Saga University, Saga 840-8502, Japan.
| | - Mashura Shammi
- Hydrobiogeochemistry and Pollution Control Laboratory, Department of Environmental Sciences, Jahangirnagar University, Dhaka 1342, Bangladesh.
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Sun L, David KT, Wolters JF, Karlen SD, Gonçalves C, Opulente DA, LaBella AL, Groenewald M, Zhou X, Shen XX, Rokas A, Hittinger CT. Functional and Evolutionary Integration of a Fungal Gene With a Bacterial Operon. Mol Biol Evol 2024; 41:msae045. [PMID: 38415839 PMCID: PMC11043216 DOI: 10.1093/molbev/msae045] [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: 11/21/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 02/29/2024] Open
Abstract
Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin synthesis. Yet, how these yeasts absorb the iron bound by enterobactin remains unresolved. Here, we demonstrate that Enb1 is the key enterobactin importer in the W/S-clade species Starmerella bombicola. Through phylogenomic analyses, we show that ENB1 is present in all W/S clade yeast species that retained the enterobactin biosynthetic genes. Conversely, it is absent in species that lost the ent genes, except for Starmerella stellata, making this species the only cheater in the W/S clade that can utilize enterobactin without producing it. Through phylogenetic analyses, we infer that ENB1 is a fungal gene that likely existed in the W/S clade prior to the acquisition of the ent genes and subsequently experienced multiple gene losses and duplications. Through phylogenetic topology tests, we show that ENB1 likely underwent horizontal gene transfer from an ancient W/S clade yeast to the order Saccharomycetales, which includes the model yeast Saccharomyces cerevisiae, followed by extensive secondary losses. Taken together, these results suggest that the fungal ENB1 and bacterial ent genes were cooperatively integrated into a functional unit within the W/S clade that enabled adaptation to iron-limited environments. This integrated fungal-bacterial circuit and its dynamic evolution determine the extant distribution of yeast enterobactin producers and cheaters.
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Affiliation(s)
- Liang Sun
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Kyle T David
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - John F Wolters
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Steven D Karlen
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Carla Gonçalves
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Dana A Opulente
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Biology Department, Villanova University, Villanova, PA 19085, USA
| | - Abigail Leavitt LaBella
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | | | - Xiaofan Zhou
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xing-Xing Shen
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | - Antonis Rokas
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
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3
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Sun L, David KT, Wolters JF, Karlen SD, Gonçalves C, Opulente DA, Leavitt LaBella A, Groenewald M, Zhou X, Shen XX, Rokas A, Todd Hittinger C. Functional and evolutionary integration of a fungal gene with a bacterial operon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568075. [PMID: 38045280 PMCID: PMC10690196 DOI: 10.1101/2023.11.21.568075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin synthesis. Yet, how these yeasts absorb the iron bound by enterobactin remains unresolved. Here, we demonstrate that Enb1 is the key enterobactin importer in the W/S-clade species Starmerella bombicola. Through phylogenomic analyses, we show that ENB1 is present in all W/S clade yeast species that retained the enterobactin biosynthetic genes. Conversely, it is absent in species that lost the ent genes, except for Starmerella stellata, making this species the only cheater in the W/S clade that can utilize enterobactin without producing it. Through phylogenetic analyses, we infer that ENB1 is a fungal gene that likely existed in the W/S clade prior to the acquisition of the ent genes and subsequently experienced multiple gene losses and duplications. Through phylogenetic topology tests, we show that ENB1 likely underwent horizontal gene transfer from an ancient W/S clade yeast to the order Saccharomycetales, which includes the model yeast Saccharomyces cerevisiae, followed by extensive secondary losses. Taken together, these results suggest that the fungal ENB1 and bacterial ent genes were cooperatively integrated into a functional unit within the W/S clade that enabled adaptation to iron-limited environments. This integrated fungal-bacterial circuit and its dynamic evolution determines the extant distribution of yeast enterobactin producers and cheaters.
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Affiliation(s)
- Liang Sun
- DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Kyle T. David
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - John F. Wolters
- DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Steven D. Karlen
- DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Carla Gonçalves
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Dana A. Opulente
- DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Biology Department, Villanova University, Villanova, PA 19085, USA
| | - Abigail Leavitt LaBella
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223
| | | | - Xiaofan Zhou
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | - Xing-Xing Shen
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Antonis Rokas
- Evolutionary Studies Initiative and Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
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Yamada K, Tazaki A, Ushio-Watanabe N, Usui Y, Takeda A, Matsunaga M, Suzumura A, Shimizu H, Zheng H, Ariefta NR, Yamamoto M, Hara H, Goto H, Sonoda KH, Nishiguchi KM, Kato M, Nishikawa Y, Toyokuni S, Kaneko H. Retinal ferroptosis as a critical mechanism for the induction of retinochoroiditis during ocular toxoplasmosis. Redox Biol 2023; 67:102890. [PMID: 37738924 PMCID: PMC10519826 DOI: 10.1016/j.redox.2023.102890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 09/13/2023] [Indexed: 09/24/2023] Open
Abstract
Toxoplasmosis is a major infectious disease, affecting approximately one-third of the world's population; its main clinical manifestation, ocular toxoplasmosis (OT), is a severe sight-threatening disease. Nevertheless, the diagnosis of OT is based on clinical findings, which needs improvement, even with biochemical tests, such as polymerase chain reaction and antibody detections. Furthermore, the efficacy of OT-targeted treatment is limited; thus, additional measures for diagnosis and treatments are needed. Here, we for the first time report a significantly reduced iron concentration in the vitreous humor (VH) of human patients infected with OT. To obtain further insights into molecular mechanisms, we established a mouse model of T. gondii infection, in which intravitreally injected tracer 57Fe, was accumulated in the neurosensory retina. T. gondii-infected eyes showed increased lipid peroxidation, reduction of glutathione peroxidase-4 expression and mitochondrial deformity in the photoreceptor as cristae loss. These findings strongly suggest the involvement of ferroptotic process in the photoreceptor of OT. In addition, deferiprone, an FDA-approved iron chelator, reduced the iron uptake but also ameliorated toxoplasma-induced retinochoroiditis by reducing retinal inflammation. In conclusion, the iron levels in the VH could serve as diagnostic markers and iron chelators as potential treatments for OT.
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Affiliation(s)
- Kazuhisa Yamada
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.
| | - Akira Tazaki
- Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.
| | - Nanako Ushio-Watanabe
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, 080-8555, Japan.
| | - Yoshihiko Usui
- Department of Ophthalmology, Tokyo Medical University, Tokyo, 160-8402, Japan.
| | - Atsunobu Takeda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Masaaki Matsunaga
- Department of Public Health, Fujita Health University School of Medicine, Toyoake, 470-1192, Japan.
| | - Ayana Suzumura
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.
| | - Hideyuki Shimizu
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.
| | - Hao Zheng
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.
| | - Nanang R Ariefta
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, 080-8555, Japan.
| | - Masahiro Yamamoto
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan.
| | - Hideaki Hara
- Department of Biofunctional Evaluation, Molecular Pharmacology, Gifu Pharmaceutical University, Gifu, 501-1196, Japan.
| | - Hiroshi Goto
- Department of Ophthalmology, Tokyo Medical University, Tokyo, 160-8402, Japan.
| | - Koh-Hei Sonoda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Koji M Nishiguchi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.
| | - Masashi Kato
- Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.
| | - Yoshifumi Nishikawa
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, 080-8555, Japan.
| | - Shinya Toyokuni
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan; Center for Low-Temperature Plasma Sciences, Nagoya University, Furo-Cho, Chikusa-ku, Nagoya, 464-8603, Japan.
| | - Hiroki Kaneko
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.
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Kahl LJ, Stremmel N, Esparza-Mora MA, Wheatley RM, MacLean RC, Ralser M. Interkingdom interactions between Pseudomonas aeruginosa and Candida albicans affect clinical outcomes and antimicrobial responses. Curr Opin Microbiol 2023; 75:102368. [PMID: 37677865 DOI: 10.1016/j.mib.2023.102368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 09/09/2023]
Abstract
Infections that involve interkingdom microbial communities, such as those between bacteria and yeast pathogens, are difficult to treat, associated with worse patient outcomes, and may be a source of antimicrobial resistance. In this review, we address co-occurrence and co-infections of Candida albicans and Pseudomonas aeruginosa, two pathogens that occupy multiple infection niches in the human body, especially in immunocompromised patients. The interaction between the pathogen species influences microbe-host interactions, the effectiveness of antimicrobials and even infection outcomes, and may thus require adapted treatment strategies. However, the molecular details of bacteria-fungal interactions both inside and outside the infection sites, are insufficiently characterised. We argue that comprehensively understanding the P. aeruginosa-C. albicans interaction network through integrated systems biology approaches will capture the highly dynamic and complex nature of these polymicrobial infections and lead to a more comprehensive understanding of clinical observations such as reshaped immune defences and low antimicrobial treatment efficacy.
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Affiliation(s)
- Lisa J Kahl
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Nina Stremmel
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | | | - Rachel M Wheatley
- University of Oxford, Department of Biology, Oxford OX1 3SZ, United Kingdom
| | - R Craig MacLean
- University of Oxford, Department of Biology, Oxford OX1 3SZ, United Kingdom
| | - Markus Ralser
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; University of Oxford, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, Oxford OX3 7BN, United Kingdom; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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Gómez-Garzón C, Payne SM. Divide and conquer: genetics, mechanism, and evolution of the ferrous iron transporter Feo in Helicobacter pylori. Front Microbiol 2023; 14:1219359. [PMID: 37469426 PMCID: PMC10353542 DOI: 10.3389/fmicb.2023.1219359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/14/2023] [Indexed: 07/21/2023] Open
Abstract
Introduction Feo is the most widespread and conserved system for ferrous iron uptake in bacteria, and it is important for virulence in several gastrointestinal pathogens. However, its mechanism remains poorly understood. Hitherto, most studies regarding the Feo system were focused on Gammaproteobacterial models, which possess three feo genes (feoA, B, and C) clustered in an operon. We found that the human pathogen Helicobacter pylori possesses a unique arrangement of the feo genes, in which only feoA and feoB are present and encoded in distant loci. In this study, we examined the functional significance of this arrangement. Methods Requirement and regulation of the individual H. pylori feo genes were assessed through in vivo assays and gene expression profiling. The evolutionary history of feo was inferred via phylogenetic reconstruction, and AlphaFold was used for predicting the FeoA-FeoB interaction. Results and Discussion Both feoA and feoB are required for Feo function, and feoB is likely subjected to tight regulation in response to iron and nickel by Fur and NikR, respectively. Also, we established that feoA is encoded in an operon that emerged in the common ancestor of most, but not all, helicobacters, and this resulted in feoA transcription being controlled by two independent promoters. The H. pylori Feo system offers a new model to understand ferrous iron transport in bacterial pathogens.
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Affiliation(s)
- Camilo Gómez-Garzón
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States
| | - Shelley M. Payne
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States
- John Ring LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX, United States
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Comitini F, Canonico L, Agarbati A, Ciani M. Biocontrol and Probiotic Function of Non- Saccharomyces Yeasts: New Insights in Agri-Food Industry. Microorganisms 2023; 11:1450. [PMID: 37374952 DOI: 10.3390/microorganisms11061450] [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: 04/29/2023] [Revised: 05/27/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
Fermented food matrices, including beverages, can be defined as the result of the activity of complex microbial ecosystems where different microorganisms interact according to different biotic and abiotic factors. Certainly, in industrial production, the technological processes aim to control the fermentation to place safe foods on the market. Therefore, if food safety is the essential prerogative, consumers are increasingly oriented towards a healthy and conscious diet driving the production and consequently the applied research towards natural processes. In this regard, the aim to guarantee the safety, quality and diversity of products should be reached limiting or avoiding the addition of antimicrobials or synthetic additives using the biological approach. In this paper, the recent re-evaluation of non-Saccharomyces yeasts (NSYs) has been reviewed in terms of bio-protectant and biocontrol activity with a particular focus on their antimicrobial power using different application modalities including biopackaging, probiotic features and promoting functional aspects. In this review, the authors underline the contribution of NSYs in the food production chain and their role in the technological and fermentative features for their practical and useful use as a biocontrol agent in food preparations.
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Affiliation(s)
- Francesca Comitini
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Laura Canonico
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Alice Agarbati
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Maurizio Ciani
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
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Stelitano G, Cocorullo M, Mori M, Villa S, Meneghetti F, Chiarelli LR. Iron Acquisition and Metabolism as a Promising Target for Antimicrobials (Bottlenecks and Opportunities): Where Do We Stand? Int J Mol Sci 2023; 24:ijms24076181. [PMID: 37047161 PMCID: PMC10094389 DOI: 10.3390/ijms24076181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) infections is one of the most crucial challenges currently faced by the scientific community. Developments in the fundamental understanding of their underlying mechanisms may open new perspectives in drug discovery. In this review, we conducted a systematic literature search in PubMed, Web of Science, and Scopus, to collect information on innovative strategies to hinder iron acquisition in bacteria. In detail, we discussed the most interesting targets from iron uptake and metabolism pathways, and examined the main chemical entities that exhibit anti-infective activities by interfering with their function. The mechanism of action of each drug candidate was also reviewed, together with its pharmacodynamic, pharmacokinetic, and toxicological properties. The comprehensive knowledge of such an impactful area of research will hopefully reflect in the discovery of newer antibiotics able to effectively tackle the antimicrobial resistance issue.
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9
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Gaiatto ACM, Bibo TA, de Godoy Moreira N, Raimundo JRS, da Costa Aguiar Alves B, Gascón T, Carvalho SS, Pereira EC, Fonseca FLA, da Veiga GL. COVID-19 compromises iron homeostasis: Transferrin as a target of investigation. J Trace Elem Med Biol 2023; 76:127109. [PMID: 36509021 PMCID: PMC9694355 DOI: 10.1016/j.jtemb.2022.127109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/26/2022] [Accepted: 11/18/2022] [Indexed: 11/26/2022]
Abstract
IMPORTANCE Since the beginning of the COVID-19 pandemic, numerous metabolic alterations have been observed in individuals with this disease. It is known that SARS-CoV-2 can mimic the action of hepcidin, altering intracellular iron metabolism, but gaps remain in the understanding of possible outcomes in other pathways involved in the iron cycle. OBJECTIVE To profile iron, ferritin and hepcidin levels and transferrin receptor gene expression in patients diagnosed with COVID-19 between June 2020 and September 2020. DESIGN, SETTING AND PARTICIPANTS Cross-sectional study that evaluated iron metabolism markers in 427 participants, 218 with COVID-19 and 209 without the disease. EXPOSURES The primary exposure was positive diagnose to COVID-19 in general population of Santo André and São Bernardo cities. The positive and negative diagnose were determinate through RT-qPCR. MAIN OUTCOMES AND MEASURES Devido a evidências de alterações do ciclo do ferro em pacientes diagnosticados com COVID-19 e devido a corregulação entre hepcidina e receptor de transferrina, uma análise da expressão gênica deste último, poderia trazer insights sobre o estado de ferro celular. A hipótese foi confirmada, mostrando aumento da expressão de receptor de transferrina concomitante com redução do nível de hepcidina circulante. RESULTS Serum iron presented lower values in individuals diagnosed with COVID-19, whereas serum ferritin presented much higher values in infected patients. Elderly subjects had lower serum iron levels and higher ferritin levels, and men with COVID-19 had higher ferritin values than women. Serum hepcidin was lower in the COVID-19 patient group and transferrin receptor gene expression was higher in the infected patient group compared to controls. CONCLUSIONS AND RELEVANCE COVID-19 causes changes in several iron cycle pathways, with iron and ferritin levels being markers that reflect the state and evolution of infection, as well as the prognosis of the disease. The increased expression of the transferrin receptor gene suggests increased iron internalization and the mimicry of hepcidin action by SARS-CoV-2, reduces iron export via ferroportin, which would explain the low circulating levels of iron by intracellular trapping.
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Affiliation(s)
| | - Thaciane Alkmim Bibo
- Laboratório de Análises Clínicas, Centro Universitário FMABC, Santo André, Brazil
| | | | | | | | - Thaís Gascón
- Laboratório de Análises Clínicas, Centro Universitário FMABC, Santo André, Brazil
| | | | | | - Fernando Luiz Affonso Fonseca
- Laboratório de Análises Clínicas, Centro Universitário FMABC, Santo André, Brazil; Departamento de Ciências Farmacêuticas, UNIFESP, Campus Diadema, Diadema, Brazil
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10
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Chang X, Wei D, Zeng Y, Zhao X, Hu Y, Wu X, Song C, Gong G, Chen H, Yang C, Zhang M, Liu T, Chen W, Yang W. Maize-soybean relay strip intercropping reshapes the rhizosphere bacterial community and recruits beneficial bacteria to suppress Fusarium root rot of soybean. Front Microbiol 2022; 13:1009689. [PMID: 36386647 PMCID: PMC9643879 DOI: 10.3389/fmicb.2022.1009689] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/29/2022] [Indexed: 11/29/2022] Open
Abstract
Rhizosphere microbes play a vital role in plant health and defense against soil-borne diseases. Previous studies showed that maize-soybean relay strip intercropping altered the diversity and composition of pathogenic Fusarium species and biocontrol fungal communities in the soybean rhizosphere, and significantly suppressed soybean root rot. However, whether the rhizosphere bacterial community participates in the regulation of this intercropping on soybean root rot is not clear. In this study, the rhizosphere soil of soybean healthy plants was collected in the continuous cropping of maize-soybean relay strip intercropping and soybean monoculture in the fields, and the integrated methods of microbial profiling, dual culture assays in vitro, and pot experiments were employed to systematically investigate the diversity, composition, and function of rhizosphere bacteria related to soybean root rot in two cropping patterns. We found that intercropping reshaped the rhizosphere bacterial community and increased microbial community diversity, and meanwhile, it also recruited much richer and more diverse species of Pseudomonas sp., Bacillus sp., Streptomyces sp., and Microbacterium sp. in soybean rhizosphere when compared with monoculture. From the intercropping, nine species of rhizosphere bacteria displayed good antagonism against the pathogen Fusarium oxysporum B3S1 of soybean root rot, and among them, IRHB3 (Pseudomonas chlororaphis), IRHB6 (Streptomyces), and IRHB9 (Bacillus) were the dominant bacteria and extraordinarily rich. In contrast, MRHB108 (Streptomyces virginiae) and MRHB205 (Bacillus subtilis) were the only antagonistic bacteria from monoculture, which were relatively poor in abundance. Interestingly, introducing IRHB3 into the cultured substrates not only significantly promoted the growth and development of soybean roots but also improved the survival rate of seedlings that suffered from F. oxysporum infection. Thus, this study proves that maize-soybean relay strip intercropping could help the host resist soil-borne Fusarium root rot by reshaping the rhizosphere bacterial community and driving more beneficial microorganisms to accumulate in the soybean rhizosphere.
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Affiliation(s)
- Xiaoli Chang
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengqin Wei
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Yuhan Zeng
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Xinyu Zhao
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Yu Hu
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Xiaoling Wu
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Chun Song
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Guoshu Gong
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Huabao Chen
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Chunping Yang
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Min Zhang
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Taiguo Liu
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Wanquan Chen
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Wenyu Yang
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
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Whole genome sequencing of Moraxella bovis strains from North America reveals two genotypes with different genetic determinants. BMC Microbiol 2022; 22:258. [PMID: 36271336 DOI: 10.1186/s12866-022-02670-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Moraxella bovis and Moraxella bovoculi both associate with infectious bovine keratoconjunctivitis (IBK), an economically significant and painful ocular disease that affects cattle worldwide. There are two genotypes of M. bovoculi (genotypes 1 and 2) that differ in their gene content and potential virulence factors, although neither have been experimentally shown to cause IBK. M. bovis is a causative IBK agent, however, not all strains carry a complete assortment of known virulence factors. The goals of this study were to determine the population structure and depth of M. bovis genomic diversity, and to compare core and accessory genes and predicted outer membrane protein profiles both within and between M. bovis and M. bovoculi. RESULTS Phylogenetic trees and bioinformatic analyses of 36 M. bovis chromosomes sequenced in this study and additional available chromosomes of M. bovis and both genotype 1 and 2 M. bovoculi, showed there are two genotypes (1 and 2) of M. bovis. The two M. bovis genotypes share a core of 2015 genes, with 121 and 186 genes specific to genotype 1 and 2, respectively. The two genotypes differ by their chromosome size and prophage content, encoded protein variants of the virulence factor hemolysin, and by their affiliation with different plasmids. Eight plasmid types were identified in this study, with types 1 and 6 observed in 88 and 56% of genotype 2 strains, respectively, and absent from genotype 1 strains. Only type 1 plasmids contained one or two gene copies encoding filamentous haemagglutinin-like proteins potentially involved with adhesion. A core of 1403 genes was shared between the genotype 1 and 2 strains of both M. bovis and M. bovoculi, which encoded a total of nine predicted outer membrane proteins. CONCLUSIONS There are two genotypes of M. bovis that differ in both chromosome content and plasmid profiles and thus may not equally associate with IBK. Immunological reagents specifically targeting select genotypes of M. bovis, or all genotypes of M. bovis and M. bovoculi together could be designed from the outer membrane proteins identified in this study.
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12
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Host–Pathogen Interactions of Marine Gram-Positive Bacteria. BIOLOGY 2022; 11:biology11091316. [PMID: 36138795 PMCID: PMC9495620 DOI: 10.3390/biology11091316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Complex interactions between marine Gram-positive pathogens and fish hosts in the marine environment can result in diseases of economically important finfish, which cause economic losses in the aquaculture industry. Understanding how these pathogens interact with the fish host and generate disease will contribute to efficient prophylactic measures and treatments. To our knowledge, there are no systematic reviews on marine Gram-positive pathogens. Therefore, here we reviewed the host–pathogen interactions of marine Gram-positive pathogens from the pathogen-centric and host-centric points of view. Abstract Marine Gram-positive bacterial pathogens, including Renibacterium salmoninarum, Mycobacterium marinum, Nocardia seriolae, Lactococcus garvieae, and Streptococcus spp. cause economic losses in marine fish aquaculture worldwide. Comprehensive information on these pathogens and their dynamic interactions with their respective fish–host systems are critical to developing effective prophylactic measures and treatments. While much is known about bacterial virulence and fish immune response, it is necessary to synthesize the knowledge in terms of host–pathogen interactions as a centerpiece to establish a crucial connection between the intricate details of marine Gram-positive pathogens and their fish hosts. Therefore, this review provides a holistic view and discusses the different stages of the host–pathogen interactions of marine Gram-positive pathogens. Gram-positive pathogens can invade fish tissues, evade the fish defenses, proliferate in the host system, and modulate the fish immune response. Marine Gram-positive pathogens have a unique set of virulence factors that facilitate adhesion (e.g., adhesins, hemagglutination activity, sortase, and capsules), invasion (e.g., toxins, hemolysins/cytolysins, the type VII secretion system, and immune-suppressive proteins), evasion (e.g., free radical quenching, actin-based motility, and the inhibition of phagolysosomal fusion), and proliferation and survival (e.g., heme utilization and siderophore-mediated iron acquisition systems) in the fish host. After infection, the fish host initiates specific innate and adaptive immune responses according to the extracellular or intracellular mechanism of infection. Although efforts have continued to be made in understanding the complex interplay at the host–pathogen interface, integrated omics-based investigations targeting host–pathogen–marine environment interactions hold promise for future research.
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Jagdish T, Nguyen Ba AN. Microbial experimental evolution in a massively multiplexed and high-throughput era. Curr Opin Genet Dev 2022; 75:101943. [PMID: 35752001 DOI: 10.1016/j.gde.2022.101943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022]
Abstract
Experimental evolution with microbial model systems has transformed our understanding of the basic rules underlying ecology and evolution. Experiments leveraging evolution as a central feature put evolutionary theories to the test, and modern sequencing and engineering tools then characterized the molecular basis of adaptation. As theory and experimentations refined our understanding of evolution, a need to increase throughput and experimental complexity has emerged. Here, we summarize recent technologies that have made high-throughput experiments practical and highlight studies that have capitalized on these tools, defining an exciting new era in microbial experimental evolution. Multiple research directions previously limited by experimental scale are now accessible for study and we believe applying evolutionary lessons from in vitro studies onto these applied settings has the potential for major innovations and discoveries across ecology and medicine.
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Affiliation(s)
- Tanush Jagdish
- Department of Molecular and Cellular Biology and The Program for Systems Synthetic and Quantitative Biology, Harvard University, Cambridge, United States.
| | - Alex N Nguyen Ba
- Department of Biology, University of Toronto at Mississauga, Mississauga, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.
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14
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Zarrella TM, Khare A. Systematic identification of molecular mediators of interspecies sensing in a community of two frequently coinfecting bacterial pathogens. PLoS Biol 2022; 20:e3001679. [PMID: 35727825 PMCID: PMC9249247 DOI: 10.1371/journal.pbio.3001679] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 07/01/2022] [Accepted: 05/17/2022] [Indexed: 11/18/2022] Open
Abstract
Bacteria typically exist in dynamic, multispecies communities where polymicrobial interactions influence fitness. Elucidating the molecular mechanisms underlying these interactions is critical for understanding and modulating bacterial behavior in natural environments. While bacterial responses to foreign species are frequently characterized at the molecular and phenotypic level, the exogenous molecules that elicit these responses are understudied. Here, we outline a systematic strategy based on transcriptomics combined with genetic and biochemical screens of promoter-reporters to identify the molecules from one species that are sensed by another. We utilized this method to study interactions between the pathogens Pseudomonas aeruginosa and Staphylococcus aureus that are frequently found in coinfections. We discovered that P. aeruginosa senses diverse staphylococcal exoproducts including the metallophore staphylopine (StP), intermediate metabolites citrate and acetoin, and multiple molecules that modulate its iron starvation response. We observed that StP inhibits biofilm formation and that P. aeruginosa can utilize citrate and acetoin for growth, revealing that these interactions have both antagonistic and beneficial effects. Due to the unbiased nature of our approach, we also identified on a genome scale the genes in S. aureus that affect production of each sensed exoproduct, providing possible targets to modify multispecies community dynamics. Further, a combination of these identified S. aureus products recapitulated a majority of the transcriptional response of P. aeruginosa to S. aureus supernatant, validating our screening strategy. Cystic fibrosis (CF) clinical isolates of both S. aureus and P. aeruginosa also showed varying degrees of induction or responses, respectively, which suggests that these interactions are widespread among pathogenic strains. Our screening approach thus identified multiple S. aureus secreted molecules that are sensed by P. aeruginosa and affect its physiology, demonstrating the efficacy of this approach, and yielding new insight into the molecular basis of interactions between these two species.
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Affiliation(s)
- Tiffany M. Zarrella
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Anupama Khare
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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15
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Shalev O, Ashkenazy H, Neumann M, Weigel D. Commensal Pseudomonas protect Arabidopsis thaliana from a coexisting pathogen via multiple lineage-dependent mechanisms. THE ISME JOURNAL 2022; 16:1235-1244. [PMID: 34897280 PMCID: PMC9038753 DOI: 10.1038/s41396-021-01168-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/19/2021] [Accepted: 11/26/2021] [Indexed: 11/09/2022]
Abstract
AbstractPlants are protected from pathogens not only by their own immunity but often also by colonizing commensal microbes. In Arabidopsis thaliana, a group of cryptically pathogenic Pseudomonas strains often dominates local populations. This group coexists in nature with commensal Pseudomonas strains that can blunt the deleterious effects of the pathogens in the laboratory. We have investigated the interaction between one of the Pseudomonas pathogens and 99 naturally co-occurring commensals, finding plant protection to be common among non-pathogenic Pseudomonas. While protective ability is enriched in one specific lineage, there is also a substantial variation for this trait among isolates of this lineage. These functional differences do not align with core-genome phylogenies, suggesting repeated gene inactivation or loss as causal. Using genome-wide association, we discovered that different bacterial genes are linked to plant protection in each lineage. We validated a protective role of several lineage-specific genes by gene inactivation, highlighting iron acquisition and biofilm formation as prominent mechanisms of plant protection in this Pseudomonas lineage. Collectively, our work illustrates the importance of functional redundancy in plant protective traits across an important group of commensal bacteria.
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16
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Long M, Sanchez-Martinez A, Longo M, Suomi F, Stenlund H, Johansson AI, Ehsan H, Salo VT, Montava-Garriga L, Naddafi S, Ikonen E, Ganley IG, Whitworth AJ, McWilliams TG. DGAT1 activity synchronises with mitophagy to protect cells from metabolic rewiring by iron depletion. EMBO J 2022; 41:e109390. [PMID: 35411952 PMCID: PMC9108618 DOI: 10.15252/embj.2021109390] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 12/28/2022] Open
Abstract
Mitophagy removes defective mitochondria via lysosomal elimination. Increased mitophagy coincides with metabolic reprogramming, yet it remains unknown whether mitophagy is a cause or consequence of such state changes. The signalling pathways that integrate with mitophagy to sustain cell and tissue integrity also remain poorly defined. We performed temporal metabolomics on mammalian cells treated with deferiprone, a therapeutic iron chelator that stimulates PINK1/PARKIN-independent mitophagy. Iron depletion profoundly rewired the metabolome, hallmarked by remodelling of lipid metabolism within minutes of treatment. DGAT1-dependent lipid droplet biosynthesis occurred several hours before mitochondrial clearance, with lipid droplets bordering mitochondria upon iron chelation. We demonstrate that DGAT1 inhibition restricts mitophagy in vitro, with impaired lysosomal homeostasis and cell viability. Importantly, genetic depletion of DGAT1 in vivo significantly impaired neuronal mitophagy and locomotor function in Drosophila. Our data define iron depletion as a potent signal that rapidly reshapes metabolism and establishes an unexpected synergy between lipid homeostasis and mitophagy that safeguards cell and tissue integrity.
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Affiliation(s)
- Maeve Long
- Translational Stem Cell Biology & Metabolism Program, Research Programs Unit, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | | | - Marianna Longo
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, The Sir James Black Centre, University of Dundee, Dundee, UK
| | - Fumi Suomi
- Translational Stem Cell Biology & Metabolism Program, Research Programs Unit, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Hans Stenlund
- Swedish Metabolomics Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Annika I Johansson
- Swedish Metabolomics Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Homa Ehsan
- Translational Stem Cell Biology & Metabolism Program, Research Programs Unit, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Veijo T Salo
- Translational Stem Cell Biology & Metabolism Program, Research Programs Unit, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.,Department of Anatomy, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.,Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Lambert Montava-Garriga
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, The Sir James Black Centre, University of Dundee, Dundee, UK
| | - Seyedehshima Naddafi
- Translational Stem Cell Biology & Metabolism Program, Research Programs Unit, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Elina Ikonen
- Translational Stem Cell Biology & Metabolism Program, Research Programs Unit, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.,Department of Anatomy, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.,Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Ian G Ganley
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, The Sir James Black Centre, University of Dundee, Dundee, UK
| | | | - Thomas G McWilliams
- Translational Stem Cell Biology & Metabolism Program, Research Programs Unit, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.,Department of Anatomy, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
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Habitat Adaptation Drives Speciation of a Streptomyces Species with Distinct Habitats and Disparate Geographic Origins. mBio 2022; 13:e0278121. [PMID: 35012331 PMCID: PMC8749437 DOI: 10.1128/mbio.02781-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Microbial diversification is driven by geographic and ecological factors, but how the relative importance of these factors varies among species, geographic scales, and habitats remains unclear. Streptomyces, a genus of antibiotic-producing, spore-forming, and widespread bacteria, offers a robust model for identifying the processes underlying population differentiation. We examined the population structure of 37 Streptomyces olivaceus strains isolated from various sources, showing that they diverged into two habitat-associated (free-living and insect-associated) and geographically disparate lineages. More frequent gene flow within than between the lineages confirmed genetic isolation in S. olivaceus. Geographic isolation could not explain the genetic isolation; instead, habitat type was a strong predictor of genetic distance when controlling for geographic distance. The identification of habitat-specific genetic variations, including genes involved in regulation, resource use, and secondary metabolism, suggested a significant role of habitat adaptation in the diversification process. Physiological assays revealed fitness trade-offs under different environmental conditions in the two lineages. Notably, insect-associated isolates could outcompete free-living isolates in a free-iron-deficient environment. Furthermore, substrate (e.g., sialic acid and glycogen) utilization but not thermal traits differentiated the two lineages. Overall, our results argue that adaptive processes drove ecological divergence among closely related streptomycetes, eventually leading to dispersal limitation and gene flow barriers between the lineages. S. olivaceus may best be considered a species complex consisting of two cryptic species. IMPORTANCE Both isolation by distance and isolation by environment occur in bacteria, and different diversification patterns may apply to different species. Streptomyces species, typified by producing useful natural products, are widespread in nature and possess high genetic diversity. However, the ecological processes and evolutionary mechanisms that shape their distribution are not well understood. Here, we show that the population structure of a ubiquitous Streptomyces species complex matches its habitat distribution and can be defined by gene flow discontinuities. Using comparative genomics and physiological assays, we reveal that gains and losses of specific genomic traits play a significant role in the transition between free-living and host-associated lifestyles, driving speciation of the species. These results provide new insights into the evolutionary trajectory of Streptomyces and the notion of species.
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18
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Normant V, Kuhn L, Munier M, Hammann P, Mislin GLA, Schalk IJ. How the Presence of Hemin Affects the Expression of the Different Iron Uptake Pathways in Pseudomonas aeruginosa Cells. ACS Infect Dis 2022; 8:183-196. [PMID: 34878758 DOI: 10.1021/acsinfecdis.1c00525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iron is an essential nutriment for almost all organisms, but this metal is poorly bioavailable. During infection, bacteria access iron from the host by importing either iron or heme. Pseudomonas aeruginosa, a gram-negative pathogen, secretes two siderophores, pyoverdine (PVD) and pyochelin (PCH), to access iron and is also able to use many siderophores produced by other microorganisms (called xenosiderophores). To access heme, P. aeruginosa uses three distinct uptake pathways, named Has, Phu, and Hxu. We previously showed that P. aeruginosa expresses the Has and Phu heme uptake systems and the PVD- and PCH-dependent iron uptake pathways in iron-restricted growth conditions, using proteomic and RT-qPCR approaches. Here, using the same approaches, we show that physiological concentrations of hemin in the bacterial growth medium result in the repression of the expression of the proteins of the PVD- and PCH-dependent iron uptake pathways, leading to less production of these two siderophores. This indicates that the pathogen adapts its phenotype to use hemin as an iron source rather than produce PVD and PCH to access iron. Moreover, the presence of both hemin and a xenosiderophore resulted in (i) the strong induction of the expression of the proteins of the added xenosiderophore uptake pathway, (ii) repression of the PVD- and PCH-dependent iron uptake pathways, and (iii) no effect on the expression levels of the Has, Phu, or Hxu systems, indicating that bacteria use both xenosiderophores and heme to access iron.
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Affiliation(s)
- Vincent Normant
- CNRS/Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412 Strasbourg, France
| | - Lauriane Kuhn
- Plateforme Proteomique Strasbourg - Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS, FR1589, 15 rue Descartes, F-67084 Strasbourg Cedex, France
| | - Mathilde Munier
- CNRS/Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412 Strasbourg, France
| | - Philippe Hammann
- Plateforme Proteomique Strasbourg - Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS, FR1589, 15 rue Descartes, F-67084 Strasbourg Cedex, France
| | - Gaëtan L. A. Mislin
- CNRS/Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412 Strasbourg, France
| | - Isabelle J. Schalk
- CNRS/Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412 Strasbourg, France
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Charbonnier M, González-Espinoza G, Kehl-Fie TE, Lalaouna D. Battle for Metals: Regulatory RNAs at the Front Line. Front Cell Infect Microbiol 2022; 12:952948. [PMID: 35865816 PMCID: PMC9294342 DOI: 10.3389/fcimb.2022.952948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Metal such as iron, zinc, manganese, and nickel are essential elements for bacteria. These nutrients are required in crucial structural and catalytic roles in biological processes, including precursor biosynthesis, DNA replication, transcription, respiration, and oxidative stress responses. While essential, in excess these nutrients can also be toxic. The immune system leverages both of these facets, to limit bacterial proliferation and combat invaders. Metal binding immune proteins reduce the bioavailability of metals at the infection sites starving intruders, while immune cells intoxicate pathogens by providing metals in excess leading to enzyme mismetallation and/or reactive oxygen species generation. In this dynamic metal environment, maintaining metal homeostasis is a critical process that must be precisely coordinated. To achieve this, bacteria utilize diverse metal uptake and efflux systems controlled by metalloregulatory proteins. Recently, small regulatory RNAs (sRNAs) have been revealed to be critical post-transcriptional regulators, working in conjunction with transcription factors to promote rapid adaptation and to fine-tune bacterial adaptation to metal abundance. In this mini review, we discuss the expanding role for sRNAs in iron homeostasis, but also in orchestrating adaptation to the availability of other metals like manganese and nickel. Furthermore, we describe the sRNA-mediated interdependency between metal homeostasis and oxidative stress responses, and how regulatory networks controlled by sRNAs contribute to survival and virulence.
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Affiliation(s)
- Mathilde Charbonnier
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | | | - Thomas E Kehl-Fie
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana IL, United States.,Carl R. Woese Institute for Genomic Biology University of Illinois Urbana-Champaign, Urbana IL, United States
| | - David Lalaouna
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
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Low Transferrin Levels Predict Heightened Inflammation in COVID-19 Patients: New Insights. Int J Infect Dis 2021; 116:74-79. [PMID: 34952211 PMCID: PMC8688186 DOI: 10.1016/j.ijid.2021.12.340] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/22/2022] Open
Abstract
Objectives Mounting evidence links hyperinflammation in gravely ill patients to low serum iron levels and hyperferritinemia. However, little attention has been paid to other iron-associated markers such as transferrin. The aim of this study was to investigate the association of different iron parameters in severe COVID-19 and their relation to disease severity. Subjects and methods This study involved 73 hospitalized patients with positive test results for SARS-CoV-2. Patients were classified into two groups according to symptom severity: mild and severe. Blood levels of anti–SARS-CoV-2 antibodies, interleukin 6 (IL-6), C-reactive protein (CRP), and iron-related biomarkers were measured. Results The results revealed a significant increase in IL-6, CRP, and ferritin levels and decreased transferrin and iron levels in severe COVID-19. Transferrin negatively predicted variations in IgM and IgG levels (P < 0.001), as well as 34.4% and 36.6% increase in IL-6 and CRP levels, respectively (P < 0.005). Importantly, transferrin was the main negative predictor of ferritin levels, determining 22.7% of serum variations (P < 0.001). Conclusion Reduced serum transferrin and iron levels, along with the increased CRP and high ferritin, were strongly associated with the heightened inflammatory and immune state in COVID-19. Transferrin can be used as a valuable predictor of increased severity and progression of the disease.
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Tanabe T, Miyamoto K, Nagaoka K, Tsujibo H, Funahashi T. Binding of AraC-Type Activator DesR to the Promoter Region of Vibrio vulnificus Ferrioxamine B Receptor Gene. Biol Pharm Bull 2021; 44:1790-1795. [PMID: 34719655 DOI: 10.1248/bpb.b21-00372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Vibrio vulnificus can utilize the xenosiderophore desferrioxamine B (DFOB) as an iron source under iron-restricted conditions. We previously identified in V. vulnificus that transcription of the desA gene encoding the outer membrane receptor for ferrioxamine B (FOXB) is activated by the AraC-type transcriptional regulator encoded by desR together with DFOB. In this study, we overexpressed and purified DesR as a glutathione S-transferase-fused protein and examined interaction between the promoter region of desA and DesR. Electrophoretic mobility shift assay (EMSA) revealed that DesR directly binds to the regulatory region of desA, and this binding was enhanced by the presence of DFOB in a concentration-dependent manner, while the presence of FOXB did not affect the potentiation of their binding. Moreover, EMSA identified that DNA fragments lacking a probable DesR binding sequence were unable to form complexes with DesR. Finally, deoxyribonuclease I footprinting assay demonstrated that the DNA binding sequence of DesR is located between -27 and -50 nucleotides upstream of the desA transcription start site. These results strongly indicate that DesR can directly activate the transcription of desA in cooperation with DFOB, which acts as a coactivator for DesR.
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Affiliation(s)
- Tomotaka Tanabe
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University
| | - Katsushiro Miyamoto
- Department of Microbiology and Infection Control, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University
| | - Kenjiro Nagaoka
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University
| | - Hiroshi Tsujibo
- Department of Microbiology and Infection Control, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University
| | - Tatsuya Funahashi
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University
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22
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Wang S, Zhang H, Ruan C, Yi L, Deng L, Zeng K. Metschnikowia citriensis FL01 antagonize Geotrichum citri-aurantii in citrus fruit through key action of iron depletion. Int J Food Microbiol 2021; 357:109384. [PMID: 34517294 DOI: 10.1016/j.ijfoodmicro.2021.109384] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 08/23/2021] [Accepted: 09/03/2021] [Indexed: 12/29/2022]
Abstract
Metschnikowia citriensis FL01 has great potential for biocontrol applications for its excellent biocontrol efficacy on postharvest diseases of citrus fruit, and the iron depletion by pulcherriminic acid (PA) and then formation of insoluble pigment pulcherrimin had been speculated as an important action mechanism. To identify the genes involved in pulcherrimin synthesis and reutilization in M. citriensis FL01, we de novo assembled the genome of M. citriensis FL01 based on long-read PacBio sequencing. The final assembled genome consisted of 12 contigs with a genome size of 25.74 Mb, G + C content of 49.16% and 9310 protein-coding genes. The genome-wide BLAST of the PUL genes of M. pulcherrima APC 1.2 showed that the four PUL genes were clustered and located on Contig 4 of M. citriensis FL01. In order to further clarify the role of pulcherrimin pigment on biocontrol of M. citriensis FL01, CRISPR/cas9 technology was used to knock out PUL2 gene that was responsible for PA synthesis and the pigmentless mutants with stable phenotype were obtained. The mutant strains of M. citriensis FL01 lost the ability to produce pulcherrimin pigment, and simultaneously lost the ability to inhibit the growth of Geotrichum citri-aurantii in vitro. Moreover, the biocontrol efficacy of pigmentless mutant strains against sour rot was about 80% lower than that of wild-type M. citriensis FL01. These results directly proved that the iron depletion was an important mechanism of M. citriensis FL01.
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Affiliation(s)
- Shupei Wang
- College of Food Science, Southwest University, Chongqing 400715, PR China; College of Environmental and Life Sciences, Nanning Normal university, Nanning 530001, PR China
| | - Hongyan Zhang
- College of Food Science, Southwest University, Chongqing 400715, PR China
| | - Changqing Ruan
- College of Food Science, Southwest University, Chongqing 400715, PR China; Food Storage and Logistics Research Center, Southwest University, Chongqing 400715, PR China
| | - Lanhua Yi
- College of Food Science, Southwest University, Chongqing 400715, PR China; Food Storage and Logistics Research Center, Southwest University, Chongqing 400715, PR China
| | - Lili Deng
- College of Food Science, Southwest University, Chongqing 400715, PR China; Key Laboratory of Plant Hormones and Development Regulation of Chongqing, 401331 Chongqing, PR China
| | - Kaifang Zeng
- College of Food Science, Southwest University, Chongqing 400715, PR China; Food Storage and Logistics Research Center, Southwest University, Chongqing 400715, PR China.
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23
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Li YP, Fekih IB, Fru EC, Moraleda-Munoz A, Li X, Rosen BP, Yoshinaga M, Rensing C. Antimicrobial Activity of Metals and Metalloids. Annu Rev Microbiol 2021; 75:175-197. [PMID: 34343021 DOI: 10.1146/annurev-micro-032921-123231] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Competition shapes evolution. Toxic metals and metalloids have exerted selective pressure on life since the rise of the first organisms on the Earth, which has led to the evolution and acquisition of resistance mechanisms against them, as well as mechanisms to weaponize them. Microorganisms exploit antimicrobial metals and metalloids to gain competitive advantage over other members of microbial communities. This exerts a strong selective pressure that drives evolution of resistance. This review describes, with a focus on arsenic and copper, how microorganisms exploit metals and metalloids for predation and how metal- and metalloid-dependent predation may have been a driving force for evolution of microbial resistance against metals and metalloids. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Yuan Ping Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 35002, China;
| | - Ibtissem Ben Fekih
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 35002, China;
| | - Ernest Chi Fru
- Centre for Geobiology and Geochemistry, School of Earth and Ocean Sciences, Cardiff University, CF10 3AT Cardiff, United Kingdom
| | - Aurelio Moraleda-Munoz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Granada 18071, Spain
| | - Xuanji Li
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Barry P Rosen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, USA
| | - Masafumi Yoshinaga
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, USA
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 35002, China;
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24
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Wang Y, Cao Q, Cao Q, Gan J, Sun N, Yang CG, Bae T, Wu M, Lan L. Histamine activates HinK to promote the virulence of Pseudomonas aeruginosa. Sci Bull (Beijing) 2021; 66:1101-1118. [PMID: 36654344 DOI: 10.1016/j.scib.2021.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/25/2020] [Accepted: 12/28/2020] [Indexed: 01/20/2023]
Abstract
During infections, bacteria stimulate host cells to produce and release histamine, which is a key mediator of vital cellular processes in animals. However, the mechanisms underlying the bacterial cell's ability to sense and respond to histamine are poorly understood. Herein, we show that HinK, a LysR-type transcriptional regulator, is required to evoke responses to histamine in Pseudomonas aeruginosa, an important human pathogen. HinK directly binds to and activates the promoter of genes involved in histamine uptake and metabolism, iron acquisition, and Pseudomonas quinolone signal (PQS) biosynthesis. The transcriptional regulatory activity of HinK is induced when histamine is present, and it occurs when HinK binds with imidazole-4-acetic acid (ImAA), a histamine metabolite whose production in P. aeruginosa depends on the HinK-activated histamine uptake and utilization operon hinDAC-pa0222. Importantly, the inactivation of HinK inhibits diverse pathogenic phenotypes of P. aeruginosa. These results suggest that histamine acts as an interkingdom signal and provide insights into the mechanism used by pathogenic bacteria to exploit host regulatory signals to promote virulence.
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Affiliation(s)
- Yaya Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qiao Cao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; College of Life Science, Northwest University, Xi'an 710069, China
| | - Qin Cao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Shanghai Public Health Clinical Center, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201438, China
| | - Ning Sun
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary IN 46408, USA
| | - Min Wu
- Department of Biomedical Sciences, University of North Dakota, Grand Forks ND 58203-9037, USA
| | - Lefu Lan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai 201203, China.
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25
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González-Fernández D, Nemeth E, Pons EDC, Rueda D, Sinisterra OT, Murillo E, Sangkhae V, Starr LM, Scott ME, Koski KG. INTERGROWTH-21 Identifies High Prevalence of Low Symphysis-Fundal Height in Indigenous Pregnant Women Experiencing Multiple Infections, Nutrient Deficiencies, and Inflammation: The Maternal Infections, Nutrient Deficiencies, and Inflammation (MINDI) Cohort. Curr Dev Nutr 2021; 5:nzab012. [PMID: 33898918 PMCID: PMC8053398 DOI: 10.1093/cdn/nzab012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/20/2021] [Accepted: 02/17/2021] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND In the absence of ultrasound, symphysis-fundal height (SFH) can assess maternal-fetal well-being as it is associated with gestational age, fetal weight, and amniotic fluid volume. However, other modifiers of SFH, including maternal infections, nutrient deficiencies, and inflammation (MINDI), have not been widely explored. OBJECTIVES Our objectives were 2-fold: 1) to assess prevalence of low SFH in indigenous Panamanian women using both Pan-American Health Organization (PAHO) and INTERGROWTH-21 standards and 2) to explore associations of SFH with maternal health indicators: infections (oral, skin, urogenital, nematode infections), nutrient deficiencies [protein and iron indicators (ferritin, serum iron, serum transferrin receptor, hepcidin), folate, and vitamins A, D, and B-12], and inflammation [leukocytes, C-reactive protein (CRP), cytokines]. METHODS For this cross-sectional study, low-SFH-for-gestational-age was assessed using PAHO and INTERGROWTH <10th centile in 174 women at ≥16 weeks of gestation. Bootstrapping selected MINDI variables for inclusion in multivariable fractional polynomial (MFP) logistic regressions for low SFH. Associations of MINDI variables with hepcidin were also investigated. RESULTS Prevalence of low SFH was 8% using PAHO, but using INTERGROWTH, 50.6% had SFH <10th centile, including 37.9% <3rd centile. Both PAHO-SFH <10th centile and INTERGROWTH-SFH <3rd centile were associated with higher hepcidin (OR = 1.12, P = 0.008, and OR = 3.04, P = 0.001, respectively) and with lower TNF-α (OR = 0.73, P = 0.012, and OR = 0.93, P = 0.015, respectively). Wood-smoke exposure increased the odds of PAHO-SFH <10th centile (OR = 1.19, P = 0.009), whereas higher BMI decreased the odds of INTERGROWTH-SFH <3rd centile (OR = 0.87, P = 0.012). Lower pulse pressure (OR = 0.90, P = 0.009) and lower inflammatory responses [lower lymphocytes (OR = 0.21, P = 0.026), IL-17 (OR = 0.89, P = 0.011)] distinguished SFH <3rd centile from SFH ≥3rd to <10th centiles using INTERGROWTH-21 standards. The MFP regression for hepcidin controlling for SFH (adjusted R 2 = 0.40, P = 0.001) revealed associations with indicators of inflammation (CRP, P < 0.0001; IL-17, P = 0.012), acidic urinary pH (P = 0.008), and higher intake of supplements (P = 0.035). CONCLUSIONS Associations of low SFH with MINDI variables, including hepcidin, highlight its potential for early detection of multicausal in utero growth faltering.
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Affiliation(s)
- Doris González-Fernández
- School of Human Nutrition, McGill University (Macdonald Campus), Ste-Anne-de-Bellevue, Quebec, Canada
| | - Elizabeta Nemeth
- Center for Iron Disorders, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | | | - Delfina Rueda
- “Comarca Ngäbe-Buglé” Health Region, Ministry of Health, San Félix, Chiriquí Province, Panama
| | | | - Enrique Murillo
- Department of Biochemistry, University of Panama, Panama City, Panama
| | - Veena Sangkhae
- Center for Iron Disorders, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Lisa M Starr
- Institute of Parasitology, McGill University (Macdonald Campus), Ste-Anne-de-Bellevue, Quebec, Canada
| | - Marilyn E Scott
- Institute of Parasitology, McGill University (Macdonald Campus), Ste-Anne-de-Bellevue, Quebec, Canada
| | - Kristine G Koski
- School of Human Nutrition, McGill University (Macdonald Campus), Ste-Anne-de-Bellevue, Quebec, Canada
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26
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Thomas MD, Ewunkem AJ, Boyd S, Williams DK, Moore A, Rhinehardt KL, Van Beveren E, Yang B, Tapia A, Han J, Harrison SH, Graves JL. Too much of a good thing: Adaption to iron (II) intoxication in Escherichia coli. EVOLUTION MEDICINE AND PUBLIC HEALTH 2021; 9:53-67. [PMID: 33717488 PMCID: PMC7937436 DOI: 10.1093/emph/eoaa051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 11/30/2020] [Indexed: 12/22/2022]
Abstract
Background There has been an increased usage of metallic antimicrobial materials to control pathogenic and multi-drug resistant bacteria. Yet, there is a corresponding need to know if this usage leads to genetic adaptations that could produce more harmful strains. Methodology Experimental evolution was used to adapt Escherichia coli K-12 MG1655 to excess iron (II) with subsequent genomic analysis. Phenotypic assays and gene expression studies were conducted to demonstrate pleiotropic effects associated with this adaptation and to elucidate potential cellular responses. Results After 200 days of adaptation, populations cultured in excess iron (II), showed a significant increase in 24-h optical densities compared to controls. Furthermore, these populations showed increased resistance toward other metals [iron (III) and gallium (III)] and to traditional antibiotics (bacitracin, rifampin, chloramphenicol and sulfanilamide). Genomic analysis identified selective sweeps in three genes; fecA, ptsP and ilvG unique to the iron (II) resistant populations, and gene expression studies demonstrated that their cellular response may be to downregulate genes involved in iron transport (cirA and fecA) while increasing the oxidative stress response (oxyR, soxS and soxR) prior to FeSO4 exposure. Conclusions and implications Together, this indicates that the selected populations can quickly adapt to stressful levels of iron (II). This study is unique in that it demonstrates that E. coli can adapt to environments that contain excess levels of an essential micronutrient while also demonstrating the genomic foundations of the response and the pleiotropic consequences. The fact that adaptation to excess iron also causes increases in general antibiotic resistance is a serious concern. Lay summary: The evolution of iron resistance in E. coli leads to multi-drug and general metal resistance through the acquisition of mutations in three genes (fecA, ptsP and ilvG) while also initiating cellular defenses as part of their normal growth process.
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Affiliation(s)
- Misty D Thomas
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
| | - Akamu J Ewunkem
- BEACON, Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA
| | - Sada Boyd
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University and UNC Greensboro, 2907 E. Gate City Blvd., Greensboro, NC 27401, USA
| | - Danielle K Williams
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
| | - Adiya Moore
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
| | - Kristen L Rhinehardt
- Computational Data Science and Engineering, North Carolina Agricultural and Technical State University, 1601 E. Market Street, Greensboro, NC 27411, USA
| | - Emma Van Beveren
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University and UNC Greensboro, 2907 E. Gate City Blvd., Greensboro, NC 27401, USA
| | - Bobi Yang
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University and UNC Greensboro, 2907 E. Gate City Blvd., Greensboro, NC 27401, USA
| | - Anna Tapia
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University and UNC Greensboro, 2907 E. Gate City Blvd., Greensboro, NC 27401, USA
| | - Jian Han
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
| | - Scott H Harrison
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
| | - Joseph L Graves
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market St, Greensboro, NC 27411, USA
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27
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Extracellular Metabolism Sets the Table for Microbial Cross-Feeding. Microbiol Mol Biol Rev 2021; 85:85/1/e00135-20. [PMID: 33441489 DOI: 10.1128/mmbr.00135-20] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.
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28
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Gaston JR, Johnson AO, Bair KL, White AN, Armbruster CE. Polymicrobial interactions in the urinary tract: is the enemy of my enemy my friend? Infect Immun 2021; 89:IAI.00652-20. [PMID: 33431702 DOI: 10.1128/iai.00652-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The vast majority of research pertaining to urinary tract infection has focused on a single pathogen in isolation, and predominantly Escherichia coli. However, polymicrobial urine colonization and infection are prevalent in several patient populations, including individuals with urinary catheters. The progression from asymptomatic colonization to symptomatic infection and severe disease is likely shaped by interactions between traditional pathogens as well as constituents of the normal urinary microbiota. Recent studies have begun to experimentally dissect the contribution of polymicrobial interactions to disease outcomes in the urinary tract, including their role in development of antimicrobial-resistant biofilm communities, modulating the innate immune response, tissue damage, and sepsis. This review aims to summarize the epidemiology of polymicrobial urine colonization, provide an overview of common urinary tract pathogens, and present key microbe-microbe and host-microbe interactions that influence infection progression, persistence, and severity.
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Affiliation(s)
- Jordan R Gaston
- Department of Medicine, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo
| | - Alexandra O Johnson
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo
| | - Kirsten L Bair
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo
| | - Ashley N White
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo
| | - Chelsie E Armbruster
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo
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29
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Crespi B, Alcock J. Conflicts over calcium and the treatment of COVID-19. EVOLUTION MEDICINE AND PUBLIC HEALTH 2020; 9:149-156. [PMID: 33732462 PMCID: PMC7717197 DOI: 10.1093/emph/eoaa046] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022]
Abstract
Several recent studies have provided evidence that use of calcium channel blockers (CCBs), especially amlodipine and nifedipine, can reduce mortality from coronavirus disease 2019 (COVID-19). Moreover, hypocalcemia (a reduced level of serum ionized calcium) has been shown to be strongly positively associated with COVID-19 severity. Both effectiveness of CCBs as antiviral therapy, and positive associations of hypocalcemia with mortality, have been demonstrated for many other viruses as well. We evaluate these findings in the contexts of virus–host evolutionary conflicts over calcium metabolism, and hypocalcemia as either pathology, viral manipulation or host defence against pathogens. Considerable evidence supports the hypothesis that hypocalcemia represents a host defence. Indeed, hypocalcemia may exert antiviral effects in a similar manner as do CCBs, through interference with calcium metabolism in virus-infected cells. Prospective clinical studies that address the efficacy of CCBs and hypocalcemia should provide novel insights into the pathogenicity and treatment of COVID-19 and other viruses.
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Affiliation(s)
- Bernard Crespi
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Joe Alcock
- Department of Emergency Medicine, University of New Mexico, Albuquerque, NM, USA
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30
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Phenotypic Adaptation of Pseudomonas aeruginosa in the Presence of Siderophore-Antibiotic Conjugates during Epithelial Cell Infection. Microorganisms 2020; 8:microorganisms8111820. [PMID: 33218210 PMCID: PMC7699141 DOI: 10.3390/microorganisms8111820] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/12/2020] [Accepted: 11/15/2020] [Indexed: 12/14/2022] Open
Abstract
Iron acquisition pathways have often been considered to be gateways for the uptake of antibiotics into bacteria. Bacteria excrete chelators, called siderophores, to access iron. Antibiotic molecules can be covalently attached to siderophores for their transport into pathogens during the iron-uptake process. P. aeruginosa produces two siderophores and is also able to use many siderophores produced by other bacteria. We investigated the phenotypic plasticity of iron-uptake pathway expression in an epithelial cell infection assay in the presence of two different siderophore-antibiotic conjugates, one with a hydroxamate siderophore and the second with a tris-catechol. Proteomic and RT-qPCR approaches showed that P. aeruginosa was able to sense the presence of both compounds in its environment and adapt the expression of its iron uptake pathways to access iron via them. Moreover, the catechol-type siderophore-antibiotic was clearly more efficient in inducing the expression of its corresponding transporter than the hydroxamate compound when both were simultaneously present. In parallel, the expression of the proteins of the two iron uptake pathways using siderophores produced by P. aeruginosa was significantly repressed in the presence of both conjugates. Altogether, the data indicate that catechol-type siderophores are more promising vectors for antibiotic vectorization using a Trojan-horse strategy.
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31
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Normant V, Josts I, Kuhn L, Perraud Q, Fritsch S, Hammann P, Mislin GLA, Tidow H, Schalk IJ. Nocardamine-Dependent Iron Uptake in Pseudomonas aeruginosa: Exclusive Involvement of the FoxA Outer Membrane Transporter. ACS Chem Biol 2020; 15:2741-2751. [PMID: 32902248 DOI: 10.1021/acschembio.0c00535] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Iron is a key nutrient for almost all living organisms. Paradoxically, it is poorly soluble and consequently poorly bioavailable. Bacteria have thus developed multiple strategies to access this metal. One of the most common consists of the use of siderophores, small compounds that chelate ferric iron with very high affinity. Many bacteria are able to produce their own siderophores or use those produced by other microorganisms (exosiderophores) in a piracy strategy. Pseudomonas aeruginosa produces two siderophores, pyoverdine and pyochelin, and is also able to use a large panel of exosiderophores. We investigated the ability of P. aeruginosa to use nocardamine (NOCA) and ferrioxamine B (DFOB) as exosiderophores under iron-limited planktonic growth conditions. Proteomic and RT-qPCR approaches showed induction of the transcription and expression of the outer membrane transporter FoxA in the presence of NOCA or DFOB in the bacterial environment. Expression of the proteins of the heme- or pyoverdine- and pyochelin-dependent iron uptake pathways was not affected by the presence of these two tris-hydroxamate siderophores. 55Fe uptake assays using foxA mutants showed ferri-NOCA to be exclusively transported by FoxA, whereas ferri-DFOB was transported by FoxA and at least one other unidentified transporter. The crystal structure of FoxA complexed with NOCA-Fe revealed very similar siderophore binding sites between NOCA-Fe and DFOB-Fe. We discuss iron uptake by hydroxamate exosiderophores in P. aeruginosa cells in light of these results.
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Affiliation(s)
- Vincent Normant
- CNRS, UMR7242, ESBS, Université de Strasbourg, Bld Sébastien Brant, F-67412 Illkirch, France
| | - 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
| | - Lauriane Kuhn
- Plateforme Proteomique Strasbourg - Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS, FR1589, 15 rue Descartes, F-67084 Strasbourg Cedex, France
| | - Quentin Perraud
- CNRS, UMR7242, ESBS, Université de Strasbourg, Bld Sébastien Brant, F-67412 Illkirch, France
| | - Sarah Fritsch
- CNRS, UMR7242, ESBS, Université de Strasbourg, Bld Sébastien Brant, F-67412 Illkirch, France
| | - Philippe Hammann
- Plateforme Proteomique Strasbourg - Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS, FR1589, 15 rue Descartes, F-67084 Strasbourg Cedex, France
| | - Gaëtan L. A. Mislin
- CNRS, UMR7242, ESBS, Université de Strasbourg, Bld Sébastien Brant, F-67412 Illkirch, France
| | - 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
| | - Isabelle J. Schalk
- CNRS, UMR7242, ESBS, Université de Strasbourg, Bld Sébastien Brant, F-67412 Illkirch, France
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32
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Weber JJ, Kanost MR, Gorman MJ. Iron binding and release properties of transferrin-1 from Drosophila melanogaster and Manduca sexta: Implications for insect iron homeostasis. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 125:103438. [PMID: 32735914 PMCID: PMC7501197 DOI: 10.1016/j.ibmb.2020.103438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/11/2020] [Indexed: 05/20/2023]
Abstract
Transferrins belong to an ancient family of extracellular proteins. The best-characterized transferrins are mammalian proteins that function in iron sequestration or iron transport; they accomplish these functions by having a high-affinity iron-binding site in each of their two homologous lobes. Insect hemolymph transferrins (Tsf1s) also function in iron sequestration and transport; however, sequence-based predictions of their iron-binding residues have suggested that most Tsf1s have a single, lower-affinity iron-binding site. To reconcile the apparent contradiction between the known physiological functions and predicted biochemical properties of Tsf1s, we purified and characterized the iron-binding properties of Drosophila melanogaster Tsf1 (DmTsf1), Manduca sexta Tsf1 (MsTsf1), and the amino-lobe of DmTsf1 (DmTsf1N). Using UV-Vis spectroscopy, we found that these proteins bind iron, but they exhibit shifts in their spectra compared to mammalian transferrins. Through equilibrium dialysis experiments, we determined that DmTsf1 and MsTsf1 bind only one ferric ion; their affinity for iron is high (log K' = 18), but less than that of the well-characterized mammalian transferrins (log K' ~ 20); and they release iron under moderately acidic conditions (pH50 = 5.5). Iron release analysis of DmTsf1N suggested that iron binding in the amino-lobe is stabilized by the carboxyl-lobe. These findings will be critical for elucidating the mechanisms of Tsf1 function in iron sequestration and transport in insects.
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Affiliation(s)
- Jacob J Weber
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
| | - Michael R Kanost
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
| | - Maureen J Gorman
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
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Antelo GT, Vila AJ, Giedroc DP, Capdevila DA. Molecular Evolution of Transition Metal Bioavailability at the Host-Pathogen Interface. Trends Microbiol 2020; 29:441-457. [PMID: 32951986 DOI: 10.1016/j.tim.2020.08.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/01/2020] [Accepted: 08/19/2020] [Indexed: 12/21/2022]
Abstract
The molecular evolution of the adaptive response at the host-pathogen interface has been frequently referred to as an 'arms race' between the host and bacterial pathogens. The innate immune system employs multiple strategies to starve microbes of metals. Pathogens, in turn, develop successful strategies to maintain access to bioavailable metal ions under conditions of extreme restriction of transition metals, or nutritional immunity. However, the processes by which evolution repurposes or re-engineers host and pathogen proteins to perform or refine new functions have been explored only recently. Here we review the molecular evolution of several human metalloproteins charged with restricting bacterial access to transition metals. These include the transition metal-chelating S100 proteins, natural resistance-associated macrophage protein-1 (NRAMP-1), transferrin, lactoferrin, and heme-binding proteins. We examine their coevolution with bacterial transition metal acquisition systems, involving siderophores and membrane-spanning metal importers, and the biological specificity of allosteric transcriptional regulatory proteins tasked with maintaining bacterial metallostasis. We also discuss the evolution of metallo-β-lactamases; this illustrates how rapid antibiotic-mediated evolution of a zinc metalloenzyme obligatorily occurs in the context of host-imposed nutritional immunity.
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Affiliation(s)
- Giuliano T Antelo
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405BWE Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo and Esmeralda, S2002LRK Rosario, Argentina; Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
| | - Daiana A Capdevila
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405BWE Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.
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Herlihy JH, Long TA, McDowell JM. Iron homeostasis and plant immune responses: Recent insights and translational implications. J Biol Chem 2020; 295:13444-13457. [PMID: 32732287 DOI: 10.1074/jbc.rev120.010856] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/29/2020] [Indexed: 12/16/2022] Open
Abstract
Iron metabolism and the plant immune system are both critical for plant vigor in natural ecosystems and for reliable agricultural productivity. Mechanistic studies of plant iron home-ostasis and plant immunity have traditionally been carried out in isolation from each other; however, our growing understanding of both processes has uncovered significant connections. For example, iron plays a critical role in the generation of reactive oxygen intermediates during immunity and has been recently implicated as a critical factor for immune-initiated cell death via ferroptosis. Moreover, plant iron stress triggers immune activation, suggesting that sensing of iron depletion is a mechanism by which plants recognize a pathogen threat. The iron deficiency response engages hormone signaling sectors that are also utilized for plant immune signaling, providing a probable explanation for iron-immunity cross-talk. Finally, interference with iron acquisition by pathogens might be a critical component of the immune response. Efforts to address the global burden of iron deficiency-related anemia have focused on classical breeding and transgenic approaches to develop crops biofortified for iron content. However, our improved mechanistic understanding of plant iron metabolism suggests that such alterations could promote or impede plant immunity, depending on the nature of the alteration and the virulence strategy of the pathogen. Effects of iron biofortification on disease resistance should be evaluated while developing plants for iron biofortification.
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Affiliation(s)
- John H Herlihy
- School of Plant and Environmental Sciences, Virginia Tech, Latham Hall, Blacksburg, Virginia, USA
| | - Terri A Long
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA.
| | - John M McDowell
- School of Plant and Environmental Sciences, Virginia Tech, Latham Hall, Blacksburg, Virginia, USA.
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Abstract
Cell-autonomous immunity relies on the rapid detection of invasive pathogens by host proteins. Guanylate binding proteins (GBPs) have emerged as key mediators of vertebrate immune defense through their ability to recognize a diverse array of intracellular pathogens and pathogen-containing cellular compartments. Human and mouse GBPs have been shown to target distinct groups of microbes, although the molecular determinants of pathogen specificity remain unclear. We show that rapid diversification of a C-terminal polybasic motif (PBM) in primate GBPs controls recognition of the model cytosolic bacterial pathogen Shigella flexneri By swapping this membrane-binding motif between primate GBP orthologs, we found that the ability to target S. flexneri has been enhanced and lost in specific lineages of New World primates. Single substitutions in rapidly evolving sites of the GBP1 PBM are sufficient to abolish or restore bacterial detection abilities, illustrating a role for epistasis in the evolution of pathogen recognition. We further demonstrate that the squirrel monkey GBP2 C-terminal domain recently gained the ability to target S. flexneri through a stepwise process of convergent evolution. These findings reveal a mechanism by which accelerated evolution of a PBM shifts GBP target specificity and aid in resolving the molecular basis of GBP function in cell-autonomous immune defense.IMPORTANCE Many infectious diseases are caused by microbes that enter and survive within host cells. Guanylate binding proteins (GBPs) are a group of immune proteins which recognize and inhibit a variety of intracellular pathogenic microbes. We discovered that a short sequence within GBPs required for the detection of bacteria, the polybasic motif (PBM), has been rapidly evolving between primate species. By swapping PBMs between primate GBP1 genes, we were able to show that specific sequences can both reduce and improve the ability of GBP1 to target intracellular bacteria. We also show that the ability to envelop bacteria has independently evolved in GBP2 of South American monkeys. Taking the results together, this report illustrates how primate GBPs have adapted to defend against infectious pathogens.
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Gu S, Wei Z, Shao Z, Friman VP, Cao K, Yang T, Kramer J, Wang X, Li M, Mei X, Xu Y, Shen Q, Kümmerli R, Jousset A. Competition for iron drives phytopathogen control by natural rhizosphere microbiomes. Nat Microbiol 2020; 5:1002-1010. [PMID: 32393858 DOI: 10.1038/s41564-020-0719-8] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 04/03/2020] [Indexed: 01/26/2023]
Abstract
Plant pathogenic bacteria cause high crop and economic losses to human societies1-3. Infections by such pathogens are challenging to control as they often arise through complex interactions between plants, pathogens and the plant microbiome4,5. Experimental studies of this natural ecosystem at the microbiome-wide scale are rare, and consequently we have a poor understanding of how the taxonomic and functional microbiome composition and the resulting ecological interactions affect pathogen growth and disease outbreak. Here, we combine DNA-based soil microbiome analysis with in vitro and in planta bioassays to show that competition for iron via secreted siderophore molecules is a good predictor of microbe-pathogen interactions and plant protection. We examined the ability of 2,150 individual bacterial members of 80 rhizosphere microbiomes, covering all major phylogenetic lineages, to suppress the bacterium Ralstonia solanacearum, a global phytopathogen capable of infecting various crops6,7. We found that secreted siderophores altered microbiome-pathogen interactions from complete pathogen suppression to strong facilitation. Rhizosphere microbiome members with growth-inhibitory siderophores could often suppress the pathogen in vitro as well as in natural and greenhouse soils, and protect tomato plants from infection. Conversely, rhizosphere microbiome members with growth-promotive siderophores were often inferior in competition and facilitated plant infection by the pathogen. Because siderophores are a chemically diverse group of molecules, with each siderophore type relying on a compatible receptor for iron uptake8-12, our results suggest that pathogen-suppressive microbiome members produce siderophores that the pathogen cannot use. Our study establishes a causal mechanistic link between microbiome-level competition for iron and plant protection and opens promising avenues to use siderophore-mediated interactions as a tool for microbiome engineering and pathogen control.
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Affiliation(s)
- Shaohua Gu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China.
| | - Zhengying Shao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China
| | - Ville-Petri Friman
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China.,Department of Biology, University of York, York, UK
| | - Kehao Cao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China
| | - Tianjie Yang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China
| | - Jos Kramer
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Xiaofang Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China
| | - Mei Li
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China
| | - Xinlan Mei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China
| | - Rolf Kümmerli
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China.,Institute of Environmental Biology, Ecology and Biodiversity, Utrecht University, Utrecht, The Netherlands
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Vu-Khac H, Trinh TTH, Nguyen TTG, Nguyen XT, Nguyen TT. Prevalence of virulence factor, antibiotic resistance, and serotype genes of Pasteurella multocida strains isolated from pigs in Vietnam. Vet World 2020; 13:896-904. [PMID: 32636585 PMCID: PMC7311876 DOI: 10.14202/vetworld.2020.896-904] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 04/07/2020] [Indexed: 11/16/2022] Open
Abstract
AIM The study was conducted to determine the prevalence and characterization of the Pasteurella multocida isolates from suspected pigs in Vietnam. MATERIALS AND METHODS A total of 83 P. multocida strains were isolated from lung samples and nasal swabs collected from pigs associated with pneumonia, progressive atrophic rhinitis, or reproductive and respiratory symptoms. Isolates were subjected to multiplex polymerase chain reaction (PCR) for capsular typing, detection of virulence-associated genes and antibiotic resistance genes by PCR. The antimicrobial sensitivity profiles of the isolates were tested by disk diffusion method. RESULTS All the isolates 83/83 (100%) were identified as P. multocida by PCR: serogroup A was obtained from 40/83 (48.19%), serogroup D was detected from 24/83 strains (28.91%), and serogroup B was found in 19/83 (22.35%) isolates. The presence of 14 virulence genes was reported including adhesins group (ptfA - 93.97%, pfhA - 93.97%, and fimA - 90.36%), iron acquisition (exbB - 100%, and exbD - 85.54%), hyaluronidase (pmHAS - 84.33%), and protectins (ompA - 56.62%, ompH 68.67%, and oma87 - 100%). The dermonecrotoxin toxA had low prevalence (19.28%). The antimicrobial susceptibility testing revealed that cephalexin, cefotaxime, ceftriaxone, ofloxacin, pefloxacin, ciprofloxacin, and enrofloxacin were the drugs most likely active against P. multocida while amoxicillin and tetracycline were inactive. The usage of PCR revealed that 63/83 isolates were carrying at least one of the drug resistance genes. CONCLUSION Unlike other parts of the word, serotype B was prevalent among Vietnamese porcine P. multocida strains. The high antibiotic resistance detected among these isolates gives us an alert about the current state of imprudent antibiotic usage in controlling the pathogenic bacteria.
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Affiliation(s)
- Hung Vu-Khac
- Department of Biotechnology, Institute of Veterinary Research and Development of Central Vietnam, Nha Trang City, Vietnam
| | - T. T. Hang Trinh
- Department of Biotechnology, Institute of Veterinary Research and Development of Central Vietnam, Nha Trang City, Vietnam
| | - T. T. Giang Nguyen
- Department of Biotechnology, Institute of Veterinary Research and Development of Central Vietnam, Nha Trang City, Vietnam
| | - X. Truong Nguyen
- Department of Biotechnology, Institute of Veterinary Research and Development of Central Vietnam, Nha Trang City, Vietnam
| | - Thi Thinh Nguyen
- Department of Biotechnology, Institute of Veterinary Research and Development of Central Vietnam, Nha Trang City, Vietnam
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38
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Criscitiello MF, Kraev I, Lange S. Post-Translational Protein Deimination Signatures in Serum and Serum-Extracellular Vesicles of Bos taurus Reveal Immune, Anti-Pathogenic, Anti-Viral, Metabolic and Cancer-Related Pathways for Deimination. Int J Mol Sci 2020; 21:E2861. [PMID: 32325910 PMCID: PMC7215346 DOI: 10.3390/ijms21082861] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 12/14/2022] Open
Abstract
The bovine immune system is known for its unusual traits relating to immunoglobulin and antiviral responses. Peptidylarginine deiminases (PADs) are phylogenetically conserved enzymes that cause post-translational deimination, contributing to protein moonlighting in health and disease. PADs also regulate extracellular vesicle (EV) release, forming a critical part of cellular communication. As PAD-mediated mechanisms in bovine immunology and physiology remain to be investigated, this study profiled deimination signatures in serum and serum-EVs in Bos taurus. Bos EVs were poly-dispersed in a 70-500 nm size range and showed differences in deiminated protein cargo, compared with whole sera. Key immune, metabolic and gene regulatory proteins were identified to be post-translationally deiminated with some overlapping hits in sera and EVs (e.g., immunoglobulins), while some were unique to either serum or serum-EVs (e.g., histones). Protein-protein interaction network analysis of deiminated proteins revealed KEGG pathways common for serum and serum-EVs, including complement and coagulation cascades, viral infection (enveloped viruses), viral myocarditis, bacterial and parasitic infections, autoimmune disease, immunodeficiency intestinal IgA production, B-cell receptor signalling, natural killer cell mediated cytotoxicity, platelet activation and hematopoiesis, alongside metabolic pathways including ferroptosis, vitamin digestion and absorption, cholesterol metabolism and mineral absorption. KEGG pathways specific to EVs related to HIF-1 signalling, oestrogen signalling and biosynthesis of amino acids. KEGG pathways specific for serum only, related to Epstein-Barr virus infection, transcription mis-regulation in cancer, bladder cancer, Rap1 signalling pathway, calcium signalling pathway and ECM-receptor interaction. This indicates differences in physiological and pathological pathways for deiminated proteins in serum-EVs, compared with serum. Our findings may shed light on pathways underlying a number of pathological and anti-pathogenic (viral, bacterial, parasitic) pathways, with putative translatable value to human pathologies, zoonotic diseases and development of therapies for infections, including anti-viral therapies.
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Affiliation(s)
- Michael F. Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA;
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX 77843, USA
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes MK7 6AA, UK;
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6XH, UK
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Kramer J, Özkaya Ö, Kümmerli R. Bacterial siderophores in community and host interactions. Nat Rev Microbiol 2020; 18:152-163. [PMID: 31748738 PMCID: PMC7116523 DOI: 10.1038/s41579-019-0284-4] [Citation(s) in RCA: 380] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2019] [Indexed: 01/06/2023]
Abstract
Iron is an essential trace element for most organisms. A common way for bacteria to acquire this nutrient is through the secretion of siderophores, which are secondary metabolites that scavenge iron from environmental stocks and deliver it to cells via specific receptors. While there has been tremendous interest in understanding the molecular basis of siderophore synthesis, uptake and regulation, questions about the ecological and evolutionary consequences of siderophore secretion have only recently received increasing attention. In this Review, we outline how eco-evolutionary questions can complement the mechanistic perspective and help to obtain a more integrated view of siderophores. In particular, we explain how secreted diffusible siderophores can affect other community members, leading to cooperative, exploitative and competitive interactions between individuals. These social interactions in turn can spur co-evolutionary arms races between strains and species, lead to ecological dependencies between them and potentially contribute to the formation of stable communities. In brief, this Review shows that siderophores are much more than just iron carriers: they are important mediators of interactions between members of microbial assemblies and the eukaryotic hosts they inhabit.
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Affiliation(s)
- Jos Kramer
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Özhan Özkaya
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Rolf Kümmerli
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
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Dauner M, Skerra A. Scavenging Bacterial Siderophores with Engineered Lipocalin Proteins as an Alternative Antimicrobial Strategy. Chembiochem 2019; 21:601-606. [PMID: 31613035 PMCID: PMC7079049 DOI: 10.1002/cbic.201900564] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Indexed: 12/30/2022]
Abstract
Iron acquisition mediated by siderophores, high-affinity chelators for which bacteria have evolved specific synthesis and uptake mechanisms, plays a crucial role in microbiology and in host-pathogen interactions. In the ongoing fight against bacterial infections, this area has attracted biomedical interest. Beyond several approaches to interfere with siderophore-mediated iron uptake from medicinal and immunochemistry, the development of high-affinity protein scavengers that tightly complex the siderophores produced by pathogenic bacteria has appeared as a novel strategy. Such binding proteins have been engineered based on siderocalin-also known as lipocalin 2-an endogenous human scavenger of enterobactin and bacillibactin that controls the systemic spreading of commensal bacteria such as Escherichia coli. By using combinatorial protein design, siderocalin was reshaped to bind several siderophores from Pseudomonas aeruginosa and, in particular, petrobactin from Bacillus anthracis, none of which is recognized by the natural protein. Such engineered versions of siderocalin effectively suppress the growth of corresponding pathogenic bacteria by depriving them of their iron supply and offer the potential to complement antibiotic therapy in situations of acute or persistent infection.
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Affiliation(s)
- Martin Dauner
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120, Halle/Saale, Germany
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany
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Gianquinto E, Moscetti I, De Bei O, Campanini B, Marchetti M, Luque FJ, Cannistraro S, Ronda L, Bizzarri AR, Spyrakis F, Bettati S. Interaction of human hemoglobin and semi-hemoglobins with the Staphylococcus aureus hemophore IsdB: a kinetic and mechanistic insight. Sci Rep 2019; 9:18629. [PMID: 31819099 PMCID: PMC6901573 DOI: 10.1038/s41598-019-54970-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/21/2019] [Indexed: 12/21/2022] Open
Abstract
Among multidrug-resistant bacteria, methicillin-resistant Staphylococcus aureus is emerging as one of the most threatening pathogens. S. aureus exploits different mechanisms for its iron supply, but the preferred one is acquisition of organic iron through the expression of hemoglobin (Hb) receptors. One of these, IsdB, belonging to the Isd (Iron-Regulated Surface Determinant) system, was shown to be essential for bacterial growth and virulence. Therefore, interaction of IsdB with Hb represents a promising target for the rational design of a new class of antibacterial molecules. However, despite recent investigations, many structural and mechanistic details of complex formation and heme extraction process are still elusive. By combining site-directed mutagenesis, absorption spectroscopy, surface plasmon resonance and molecular dynamics simulations, we tackled most of the so far unanswered questions: (i) the exact complex stoichiometry, (ii) the microscopic kinetic rates of complex formation, (iii) the IsdB selectivity for binding to, and extracting heme from, α and β subunits of Hb, iv) the role of specific amino acid residues and structural regions in driving complex formation and heme transfer, and (v) the structural/dynamic effect played by the hemophore on Hb.
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Affiliation(s)
- Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Turin, 10125, Italy
| | - Ilaria Moscetti
- Department of Environmental and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
| | - Omar De Bei
- Department of Food and Drug, University of Parma, Parma, 43124, Italy
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, Parma, 43124, Italy.,Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy
| | - Marialaura Marchetti
- Department of Drug Science and Technology, University of Turin, Turin, 10125, Italy.,Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Santa Coloma de Gramenet, 08921, Spain
| | - Salvatore Cannistraro
- Department of Environmental and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
| | - Luca Ronda
- Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy.,Department of Medicine and Surgery, University of Parma, Parma, 43126, Italy.,Institute of Biophysics, National Research Council, Pisa, 56124, Italy
| | - Anna Rita Bizzarri
- Department of Environmental and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy.
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Turin, 10125, Italy.
| | - Stefano Bettati
- Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy. .,Department of Medicine and Surgery, University of Parma, Parma, 43126, Italy. .,Institute of Biophysics, National Research Council, Pisa, 56124, Italy.
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Rodríguez-Arce I, Al-Jubair T, Euba B, Fernández-Calvet A, Gil-Campillo C, Martí S, Törnroth-Horsefield S, Riesbeck K, Garmendia J. Moonlighting of Haemophilus influenzae heme acquisition systems contributes to the host airway-pathogen interplay in a coordinated manner. Virulence 2019; 10:315-333. [PMID: 30973092 PMCID: PMC6550540 DOI: 10.1080/21505594.2019.1596506] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/18/2019] [Accepted: 03/12/2019] [Indexed: 01/30/2023] Open
Abstract
Nutrient iron sequestration is the most significant form of nutritional immunity and causes bacterial pathogens to evolve strategies of host iron scavenging. Cigarette smoking contains iron particulates altering lung and systemic iron homeostasis, which may enhance colonization in the lungs of patients suffering chronic obstructive pulmonary disease (COPD) by opportunistic pathogens such as nontypeable. NTHi is a heme auxotroph, and the NTHi genome contains multiple heme acquisition systems whose role in pulmonary infection requires a global understanding. In this study, we determined the relative contribution to NTHi airway infection of the four heme-acquisition systems HxuCBA, PE, SapABCDFZ, and HbpA-DppBCDF that are located at the bacterial outer membrane or the periplasm. Our computational studies provided plausible 3D models for HbpA, SapA, PE, and HxuA interactions with heme. Generation and characterization of single mutants in the hxuCBA, hpe, sapA, and hbpA genes provided evidence for participation in heme binding-storage and inter-bacterial donation. The hxuA, sapA, hbpA, and hpe genes showed differential expression and responded to heme. Moreover, HxuCBA, PE, SapABCDFZ, and HbpA-DppBCDF presented moonlighting properties related to resistance to antimicrobial peptides or glutathione import, together likely contributing to the NTHi-host airway interplay, as observed upon cultured airway epithelia and in vivo lung infection. The observed multi-functionality was shown to be system-specific, thus limiting redundancy. Together, we provide evidence for heme uptake systems as bacterial factors that act in a coordinated and multi-functional manner to subvert nutritional- and other sources of host innate immunity during NTHi airway infection.
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Affiliation(s)
| | - Tamim Al-Jubair
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Begoña Euba
- Instituto de Agrobiotecnología, CSIC-Gobierno, Navarra, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | | | | | - Sara Martí
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Departamento Microbiología, Hospital Universitari Bellvitge, University of Barcelona, IDIBELL, Barcelona, Spain
| | - Susanna Törnroth-Horsefield
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Lund, Sweden
| | - Kristian Riesbeck
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Junkal Garmendia
- Instituto de Agrobiotecnología, CSIC-Gobierno, Navarra, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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Protease-associated import systems are widespread in Gram-negative bacteria. PLoS Genet 2019; 15:e1008435. [PMID: 31613892 PMCID: PMC6793856 DOI: 10.1371/journal.pgen.1008435] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/19/2019] [Indexed: 01/25/2023] Open
Abstract
Bacteria have evolved sophisticated uptake machineries in order to obtain the nutrients required for growth. Gram-negative plant pathogens of the genus Pectobacterium obtain iron from the protein ferredoxin, which is produced by their plant hosts. This iron-piracy is mediated by the ferredoxin uptake system (Fus), a gene cluster encoding proteins that transport ferredoxin into the bacterial cell and process it proteolytically. In this work we show that gene clusters related to the Fus are widespread in bacterial species. Through structural and biochemical characterisation of the distantly related Fus homologues YddB and PqqL from Escherichia coli, we show that these proteins are analogous to components of the Fus from Pectobacterium. The membrane protein YddB shares common structural features with the outer membrane ferredoxin transporter FusA, including a large extracellular substrate binding site. PqqL is an active protease with an analogous periplasmic localisation and iron-dependent expression to the ferredoxin processing protease FusC. Structural analysis demonstrates that PqqL and FusC share specific features that distinguish them from other members of the M16 protease family. Taken together, these data provide evidence that protease associated import systems analogous to the Fus are widespread in Gram-negative bacteria. To grow and cause infection bacteria must obtain essential nutrients from their environment or host. The element iron is one such nutrient and is often contained inside proteins, the building blocks of hosts cells. Bacteria that cause disease in plants are able to extract iron from plant proteins, by importing the protein and cutting it up once inside the bacterial cell. While it was known that specific bacteria that infect plants can do this, it was unclear if other bacteria that infect humans and animals are also able to import host proteins. In this work we analysed the genetic sequences of bacteria and found that genes responsible for importing and processing proteins are widespread in bacteria that cause disease in humans, animals and plants. We analysed the structure and chemistry of the protein products of these genes and found that they possess characteristics that are necessary and sufficient for importing and processing proteins. Our conclusion from this work is that the ability to import host proteins to gain nutrients is common in bacteria.
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Gude S, Taga ME. Multi-faceted approaches to discovering and predicting microbial nutritional interactions. Curr Opin Biotechnol 2019; 62:58-64. [PMID: 31597114 DOI: 10.1016/j.copbio.2019.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/08/2019] [Accepted: 08/20/2019] [Indexed: 01/07/2023]
Abstract
Nearly all microbes rely on other species in their environment to provide nutrients they are unable to produce. Nutritional interactions include not only the exchange of carbon and nitrogen compounds, but also amino acids and cofactors. Interactions involving cross-feeding of cobamides, the vitamin B12 family of cofactors, have been developed as a model for nutritional interactions across species and environments. In addition to experimental studies, new developments in culture-independent methodologies such as genomics and modeling now enable the prediction of nutritional interactions in a broad range of organisms including those that cannot be cultured in the laboratory. New insights into the mechanisms and evolution of microbial nutritional interactions are beginning to emerge by combining experimental, genomic, and modeling approaches.
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Affiliation(s)
- Sebastian Gude
- Department of Plant & Microbial Biology, University of California, Berkeley, CA USA
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, CA USA.
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Lewis RW, Islam A, Opdahl L, Davenport JR, Sullivan TS. Comparative Genomics, Siderophore Production, and Iron Scavenging Potential of Root Zone Soil Bacteria Isolated from 'Concord' Grape Vineyards. MICROBIAL ECOLOGY 2019; 78:699-713. [PMID: 30770943 DOI: 10.1007/s00248-019-01324-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 01/10/2019] [Indexed: 06/09/2023]
Abstract
Iron (Fe) deficiency in crop production is a worldwide problem which often results in chlorosis in grapevines, particularly in calcareous soils. Siderophores secreted by microorganisms and Strategy II plants can chelate Fe and other metals in soil solution, and siderophore-Fe complexes can then be utilized by plants and microbes. Plants may also shift rhizosphere conditions to favor siderophore-producing microbes, which can increase plant available Fe. Between-row cover crops (barley, rye, wheat, wheat/vetch) were planted as living mulch to address grapevine chlorosis by enhancing soil health in two vineyards in central Washington. The objectives of the current study were to (1) enrich for siderophore-producing organisms from within the indigenous rooting zone community of 'Concord' grapevines, and (2) perform comparative genomics on putative siderophore producing organisms to assess potentially important Fe acquisition-related functional domains and protein families. A high-throughput, chrome azurol S (CAS)-based enrichment assay was used to select siderophore-producing microbes from 'Concord' grapevine root zone soil. Next-generation whole genome sequencing allowed the assembly and annotation of ten full genomes. Phylogenetic analysis revealed two distinct clades among the genomes using the 40 nearest neighbors available in the public database, all of which were of the Pseudomonas genus. Significant differences in functional domain abundances were observed between the clades including iron acquisition and metabolism of amino acids, carbon, nitrogen, phosphate, and sulfur. Diverse mechanisms of Fe uptake and siderophore production/uptake were identified in the protein families of the genomes. The sequenced organisms are likely pseudomonads which are well-suited for iron scavenging, suggesting a potential role in Fe turnover in vineyard systems.
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Affiliation(s)
- Ricky W Lewis
- Department of Crop and Soil Sciences, Washington State University, PO Box 646420, Pullman, WA, USA
| | - Anjuman Islam
- Department of Crop and Soil Sciences, Washington State University, PO Box 646420, Pullman, WA, USA
| | - Lee Opdahl
- Department of Crop and Soil Sciences, Washington State University, PO Box 646420, Pullman, WA, USA
| | - Joan R Davenport
- Irrigated Agriculture Research and Extension Center, Washington State University, 24106 N. Bunn Road, Prosser, WA, USA
| | - Tarah S Sullivan
- Department of Crop and Soil Sciences, Washington State University, PO Box 646420, Pullman, WA, USA.
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Freimoser FM, Rueda-Mejia MP, Tilocca B, Migheli Q. Biocontrol yeasts: mechanisms and applications. World J Microbiol Biotechnol 2019; 35:154. [PMID: 31576429 PMCID: PMC6773674 DOI: 10.1007/s11274-019-2728-4] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/17/2019] [Indexed: 01/10/2023]
Abstract
Yeasts occur in all environments and have been described as potent antagonists of various plant pathogens. Due to their antagonistic ability, undemanding cultivation requirements, and limited biosafety concerns, many of these unicellular fungi have been considered for biocontrol applications. Here, we review the fundamental research on the mechanisms (e.g., competition, enzyme secretion, toxin production, volatiles, mycoparasitism, induction of resistance) by which biocontrol yeasts exert their activity as plant protection agents. In a second part, we focus on five yeast species (Candida oleophila, Aureobasidium pullulans, Metschnikowia fructicola, Cryptococcus albidus, Saccharomyces cerevisiae) that are or have been registered for the application as biocontrol products. These examples demonstrate the potential of yeasts for commercial biocontrol usage, but this review also highlights the scarcity of fundamental studies on yeast biocontrol mechanisms and of registered yeast-based biocontrol products. Yeast biocontrol mechanisms thus represent a largely unexplored field of research and plentiful opportunities for the development of commercial, yeast-based applications for plant protection exist.
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Affiliation(s)
- Florian M Freimoser
- Agroscope, Research Division Plant Protection, Müller-Thurgau-Strasse 29, 8820, Wädenswil, Switzerland.
| | - Maria Paula Rueda-Mejia
- Agroscope, Research Division Plant Protection, Müller-Thurgau-Strasse 29, 8820, Wädenswil, Switzerland
| | - Bruno Tilocca
- Dipartimento di Agraria, Università degli Studi di Sassari, Viale Italia 39, 07100, Sassari, Italy
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Quirico Migheli
- Dipartimento di Agraria, Università degli Studi di Sassari, Viale Italia 39, 07100, Sassari, Italy
- Istituto Nazionale di Biostrutture e Biosistemi and NRD - Nucleo di Ricerca sulla Desertificazione, Università degli Studi di Sassari, Viale Italia 39, 07100, Sassari, Italy
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New Shuttle Vectors for Real-Time Gene Expression Analysis in Multidrug-Resistant Acinetobacter Species: In Vitro and In Vivo Responses to Environmental Stressors. Appl Environ Microbiol 2019; 85:AEM.01334-19. [PMID: 31324623 DOI: 10.1128/aem.01334-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 07/06/2019] [Indexed: 11/20/2022] Open
Abstract
The Acinetobacter genus includes species of opportunistic pathogens and harmless saprophytes. The type species, Acinetobacter baumannii, is a nosocomial pathogen renowned for being multidrug resistant (MDR). Despite the clinical relevance of infections caused by MDR A. baumannii and a few other Acinetobacter spp., the regulation of their pathogenicity remains elusive due to the scarcity of adequate genetic tools, including vectors for gene expression analysis. Here, we report the generation and testing of a series of Escherichia coli-Acinetobacter promoter-probe vectors suitable for gene expression analysis in Acinetobacter spp. These vectors, named pLPV1Z, pLPV2Z, and pLPV3Z, carry both gentamicin and zeocin resistance markers and contain lux, lacZ, and green fluorescent protein (GFP) reporter systems downstream of an extended polylinker, respectively. The presence of a toxin-antitoxin gene system and the high copy number allow pLPV plasmids to be stably maintained even without antibiotic selection. The pLPV plasmids can easily be introduced by electroporation into MDR A. baumannii belonging to the major international lineages as well as into species of the Acinetobacter calcoaceticus-A. baumannii complex. The pLPV vectors have successfully been employed to study the regulation of stress-responsive A. baumannii promoters, including the DNA damage-inducible uvrABC promoter, the ethanol-inducible adhP and yahK promoters, and the iron-repressible promoter of the acinetobactin siderophore biosynthesis gene basA A lux-tagged A. baumannii ATCC 19606T strain, carrying the iron-responsive pLPV1Z::PbasA promoter fusion, allowed in vivo and ex vivo monitoring of the bacterial burden in the Galleria mellonella infection model.IMPORTANCE The short-term adaptive response to environmental cues greatly contributes to the ecological success of bacteria, and profound alterations in bacterial gene expression occur in response to physical, chemical, and nutritional stresses. Bacteria belonging to the Acinetobacter genus are ubiquitous inhabitants of soil and water though some species, such as Acinetobacter baumannii, are pathogenic and cause serious concern due to antibiotic resistance. Understanding A. baumannii pathobiology requires adequate genetic tools for gene expression analysis, and to this end we developed user-friendly shuttle vectors to probe the transcriptional responses to different environmental stresses. Vectors were constructed to overcome the problem of antibiotic selection in multidrug-resistant strains and were equipped with suitable reporter systems to facilitate signal detection. By means of these vectors, the transcriptional response of A. baumannii to DNA damage, ethanol exposure, and iron starvation was investigated both in vitro and in vivo, providing insights into A. baumannii adaptation during stress and infection.
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Selective pressures during chronic infection drive microbial competition and cooperation. NPJ Biofilms Microbiomes 2019; 5:16. [PMID: 31263568 PMCID: PMC6555799 DOI: 10.1038/s41522-019-0089-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/15/2019] [Indexed: 12/14/2022] Open
Abstract
Chronic infections often contain complex mixtures of pathogenic and commensal microorganisms ranging from aerobic and anaerobic bacteria to fungi and viruses. The microbial communities present in infected tissues are not passively co-existing but rather actively interacting with each other via a spectrum of competitive and/or cooperative mechanisms. Competition versus cooperation in these microbial interactions can be driven by both the composition of the microbial community as well as the presence of host defense strategies. These interactions are typically mediated via the production of secreted molecules. In this review, we will explore the possibility that microorganisms competing for nutrients at the host–pathogen interface can evolve seemingly cooperative mechanisms by controlling the production of subsets of secreted virulence factors. We will also address interspecies versus intraspecies utilization of community resources and discuss the impact that this phenomenon might have on co-evolution at the host–pathogen interface.
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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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50
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Grinter R, Lithgow T. Determination of the molecular basis for coprogen import by Gram-negative bacteria. IUCRJ 2019; 6:401-411. [PMID: 31098021 PMCID: PMC6503915 DOI: 10.1107/s2052252519002926] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
In order to survive in mixed microbial communities, some species of fungi secrete coprogens, siderophores that facilitate capture of the scarce nutrient iron. The TonB-dependent transporter FhuE is integrated in the outer membrane of Gram-negative bacteria and has been reported to scavenge these fungally produced coprogens. In this work, an Escherichia coli strain was engineered that is dependent solely on FhuE for its access to siderophore-sequestered iron. Using this tool, it is shown that while FhuE is highly active in the import of coprogens, it has some level of promiscuity, acting as a low-affinity transporter for related siderophores. The crystal structure of FhuE in complex with coprogen was determined, providing a structural basis to explain this selective promiscuity. The structural data, in combination with functional analysis, presented in this work show that FhuE has evolved to specifically engage with planar siderophores. A potential evolutionary driver, and a critical consequence of this selectivity, is that it allows FhuE to exclude antibiotics that mimic nonplanar hydroxamate siderophores: these toxic molecules could otherwise cross the outer membrane barrier through a Trojan horse mechanism.
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Affiliation(s)
- Rhys Grinter
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Monash, Victoria 3800, Australia
- School of Biology, Monash University, Monash, Victoria 3800, Australia
- Institute of Microbiology and Infection, School of Immunity and Infection, University of Birmingham, Birmingham B15 2TT, England
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Monash, Victoria 3800, Australia
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