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Yang C, Cui C, Deng F. The mntH gene of Burkholderia cenocepacia influences motility and quorum sensing to control virulence. Braz J Microbiol 2024:10.1007/s42770-024-01506-8. [PMID: 39230636 DOI: 10.1007/s42770-024-01506-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 08/25/2024] [Indexed: 09/05/2024] Open
Abstract
Quorum sensing (QS) signals widely exist in bacteria to control biological functions in response to populations of cells. Burkholderia cenocepacia, an important opportunistic pathogen in patients with cystic fibrosis (CF), is commonly found in the environment and mostly utilizes the N-acylhomoserine lactone (AHL) and cis-2-dodecenoic acid (BDSF) QS systems to control biological functions. Our previous study illuminated the detailed mechanism by which B.cenocepacia integrates BDSF and cyclic diguanosine monophosphate (c-di-GMP) signals to control virulence. Here, we employed Tn5 transposon mutagenesis to identify genes related to the BDSF QS system. One of the most significantly attenuated mutants had an insertion in the mntH gene. Here, we showed that MntH (Bcam0836), a manganese transport protein, controls QS-regulated phenotypes, including motility, biofilm formation and virulence. We also found that. BDSF production was attenuated at both the gene and signaling levels in the Bcam0836 mutant, and that Bcam0836 influenced the expression of some genes regulated by the BDSF receptor RpfR and the downstream regulator GtrR. These results show that the manganese transport protein. MntH modulates a subset of genes and functions regulated by the QS system in B. cenocepacia.
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Affiliation(s)
- Chunxi Yang
- Institute of Clinical Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, 330006, China.
| | - Chaoyu Cui
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China
| | - Fengyi Deng
- Institute of Clinical Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, 330006, China
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2
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Wang P, He Y, Zhou G. Iron-based mixotrophic denitrification for enhancing nitrate removal from municipal secondary effluent: Performance, microbial community dynamics, and economic feasibility. BIORESOURCE TECHNOLOGY 2024; 406:130989. [PMID: 38885725 DOI: 10.1016/j.biortech.2024.130989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024]
Abstract
High nitrate content limits the recycling of the secondary effluent of wastewater treatment plants. In the research, one biomass-iron mixture (BIM) filter material based on mixotrophic denitrification mode (heterotrophic and iron-driven autotrophic denitrification) was developed and used to construct a novel denitrification biological filter (BIM-DNBF) for the nitrogen removal of secondary effluent. BIM-DNBF had a short start-up time (approximately 9 days), and high total nitrogen removal (81 %-89 %) without external addition of organic carbon sources during the whole operation. The coexistence of dominant heterotrophic-denitrification-like Pseudomonas and Erysipelothrix as well as iron-driven autotrophic-denitrification-like Citrobacter, Acidovorax, etc. were found in the BIM-DNBF. Moreover, biomass was recognized as one key player in promoting the reduction of Fe3+ to Fe2+, thereby facilitating the occurrence of iron-driven autotrophic denitrification. In addition, BIM-DNBF was assessed to be affordable. These findings provide evidence that BIM-DNBF can be an efficient technology for nitrogen removal of secondary effluent.
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Affiliation(s)
- Pengcheng Wang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, East China Normal University, Shanghai 200241, China; State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yan He
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, East China Normal University, Shanghai 200241, China.
| | - Gongming Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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3
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Golaz D, Papenfuhs CK, Bellés-Sancho P, Eberl L, Egli M, Pessi G. RNA-seq analysis in simulated microgravity unveils down-regulation of the beta-rhizobial siderophore phymabactin. NPJ Microgravity 2024; 10:44. [PMID: 38570513 PMCID: PMC10991261 DOI: 10.1038/s41526-024-00391-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/25/2024] [Indexed: 04/05/2024] Open
Abstract
Exploiting the symbiotic interaction between crops and nitrogen-fixing bacteria is a simple and ecological method to promote plant growth in prospective extraterrestrial human outposts. In this study, we performed an RNA-seq analysis to investigate the adaptation of the legume symbiont Paraburkholderia phymatum STM815T to simulated microgravity (s0-g) at the transcriptome level. The results revealed a drastic effect on gene expression, with roughly 23% of P. phymatum genes being differentially regulated in s0-g. Among those, 951 genes were upregulated and 858 downregulated in the cells grown in s0-g compared to terrestrial gravity (1 g). Several genes involved in posttranslational modification, protein turnover or chaperones encoding were upregulated in s0-g, while those involved in translation, ribosomal structure and biosynthesis, motility or inorganic ions transport were downregulated. Specifically, the whole phm gene cluster, previously bioinformatically predicted to be involved in the production of a hypothetical malleobactin-like siderophore, phymabactin, was 20-fold downregulated in microgravity. By constructing a mutant strain (ΔphmJK) we confirmed that the phm gene cluster codes for the only siderophore secreted by P. phymatum as assessed by the complete lack of iron chelating activity of the P. phymatum ΔphmJK mutant on chrome azurol S (CAS) agar plates. These results not only provide a deeper understanding of the physiology of symbiotic organisms exposed to space-like conditions, but also increase our knowledge of iron acquisition mechanisms in rhizobia.
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Affiliation(s)
- Daphné Golaz
- Department of Plant and Microbial biology, University of Zurich, Zurich, Switzerland
| | - Chad K Papenfuhs
- Department of Plant and Microbial biology, University of Zurich, Zurich, Switzerland
| | - Paula Bellés-Sancho
- Department of Plant and Microbial biology, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial biology, University of Zurich, Zurich, Switzerland
| | - Marcel Egli
- School of Engineering and Architecture, Institute of Medical Engineering, Space Biology Group, Lucerne University of Applied Sciences and Arts, Hergiswil, Switzerland
- National Center for Biomedical Research in Space, Innovation Cluster Space and Aviation, University of Zurich, Zurich, Switzerland
| | - Gabriella Pessi
- Department of Plant and Microbial biology, University of Zurich, Zurich, Switzerland.
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4
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Jia J, Lu SE. Comparative Genome Analyses Provide Insight into the Antimicrobial Activity of Endophytic Burkholderia. Microorganisms 2024; 12:100. [PMID: 38257926 PMCID: PMC10821513 DOI: 10.3390/microorganisms12010100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Endophytic bacteria are endosymbionts that colonize a portion of plants without harming the plant for at least a part of its life cycle. Bacterial endophytes play an essential role in promoting plant growth using multiple mechanisms. The genus Burkholderia is an important member among endophytes and encompasses bacterial species with high genetic versatility and adaptability. In this study, the endophytic characteristics of Burkholderia species are investigated via comparative genomic analyses of several endophytic Burkholderia strains with pathogenic Burkholderia strains. A group of bacterial genes was identified and predicted as the putative endophytic behavior genes of Burkholderia. Multiple antimicrobial biosynthesis genes were observed in these endophytic bacteria; however, certain important pathogenic and virulence genes were absent. The majority of resistome genes were distributed relatively evenly among the endophytic and pathogenic bacteria. All known types of secretion systems were found in the studied bacteria. This includes T3SS and T4SS, which were previously thought to be disproportionately represented in endophytes. Additionally, questionable CRISPR-Cas systems with an orphan CRISPR array were prevalent, suggesting that intact CRISPR-Cas systems may not exist in symbiotes of Burkholderia. This research not only sheds light on the antimicrobial activities that contribute to biocontrol but also expands our understanding of genomic variations in Burkholderia's endophytic and pathogenic bacteria.
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Affiliation(s)
| | - Shi-En Lu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA;
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5
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Hussein SM, Sofoluwe A, Paleja A, Duhme-Klair A, Thomas MS. Identification of a system for hydroxamate xenosiderophore-mediated iron transport in Burkholderia cenocepacia. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001425. [PMID: 38189440 PMCID: PMC10866019 DOI: 10.1099/mic.0.001425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/19/2023] [Indexed: 01/09/2024]
Abstract
One of the mechanisms employed by the opportunistic pathogen Burkholderia cenocepacia to acquire the essential element iron is the production and release of two ferric iron chelating compounds (siderophores), ornibactin and pyochelin. Here we show that B. cenocepacia is also able to take advantage of a range of siderophores produced by other bacteria and fungi ('xenosiderophores') that chelate iron exclusively by means of hydroxamate groups. These include the tris-hydroxamate siderophores ferrioxamine B, ferrichrome, ferricrocin and triacetylfusarinine C, the bis-hydroxamates alcaligin and rhodotorulic acid, and the monohydroxamate siderophore cepabactin. We also show that of the 24 TonB-dependent transporters encoded by the B. cenocepacia genome, two (FhuA and FeuA) are involved in the uptake of hydroxamate xenosiderophores, with FhuA serving as the exclusive transporter of iron-loaded ferrioxamine B, triacetylfusarinine C, alcaligin and rhodotorulic acid, while both FhuA and FeuA are able to translocate ferrichrome-type siderophores across the outer membrane. Finally, we identified FhuB, a putative cytoplasmic membrane-anchored ferric-siderophore reductase, as being obligatory for utilization of all of the tested bis- and tris-hydroxamate xenosiderophores apart from alcaligin.
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Affiliation(s)
- Syakira Mohammed Hussein
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Medical School, Beech Hill Road, Sheffield S10 2RX, UK
| | - Aderonke Sofoluwe
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Medical School, Beech Hill Road, Sheffield S10 2RX, UK
- Department of Immunobiology, School of Immunology & Microbial Sciences, King’s College London, London WC2R 2LS, UK
| | - Ameya Paleja
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Medical School, Beech Hill Road, Sheffield S10 2RX, UK
| | - Anne Duhme-Klair
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Mark S. Thomas
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Medical School, Beech Hill Road, Sheffield S10 2RX, UK
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6
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Blanco Nouche C, Paris C, Dhalleine T, Oger P, Turpault MP, Uroz S. The non-ribosomal peptide synthetase-independent siderophore (NIS) rhizobactin produced by Caballeronia mineralivorans PML1(12) confers the ability to weather minerals. Appl Environ Microbiol 2023; 89:e0045323. [PMID: 37800940 PMCID: PMC10617554 DOI: 10.1128/aem.00453-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/16/2023] [Indexed: 10/07/2023] Open
Abstract
To mobilize nutrients entrapped into minerals and rocks, heterotrophic bacteria living in nutrient-poor environments have developed different mechanisms based mainly on acidolysis and chelation. However, the genetic bases of these mechanisms remain unidentified. To fill this gap, we considered the model strain Caballeronia mineralivorans PML1(12) known to be effective at weathering. Based on its transcriptomics and proteomics responses in Fe-depleted conditions, we pointed a cluster of genes differentially expressed and putatively involved in the production of siderophores. In this study, we report the characterization of this gene region coding for the production of a non-ribosomal peptide synthetase-independent siderophore (NIS). Targeted mutagenesis associated with functional assays and liquid chromatography coupled to high-resolution tandem mass spectrometry demonstrated the production of a single siderophore, identified as rhizobactin. This siderophore represents the first NIS containing malic acid in its structure. The evidence for the implication of rhizobactin in mineral weathering was demonstrated during a hematite dissolution assay. This study provides the first demonstration of the synthesis of a NIS in the genus Caballeronia and its involvement in mineral weathering. Our conclusions reinforce the idea that strain PML1(12) is particularly well adapted to nutrient-poor environments. IMPORTANCE This work deciphers the molecular and genetic bases used by strain PML1(12) of Caballeronia mineralivorans to mobilize iron and weather minerals. Through the combination of bioinformatics, chemical, and phylogenetic analyses, we characterized the siderophore produced by strain PML1(12) and the related genes. This siderophore was identified as rhizobactin and classified as a non-ribosomal peptide synthetase-independent siderophore (NIS). Contrary to the previously identified NIS synthetases that form siderophores containing citric acid, α-ketoglutarate, or succinic acid, our analyses revealed that rhizobactin contains malic acid in its structure, representing, therefore, the first identified NIS with such an acid and probably a new NIS category. Last, this work demonstrates for the first time the effectiveness at weathering minerals of a siderophore of the NIS family. Our findings offer relevant information for different fields of research, such as environmental genomics, microbiology, chemistry, and soil sciences.
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Affiliation(s)
- Cintia Blanco Nouche
- Université de Lorraine, INRAE, UMR1136 Interactions Arbres-Microorganismes, Nancy, France
- INRAE, UR1138 Biogéochimie des Ecosystèmes Forestiers, Champenoux, France
| | - Cédric Paris
- Université de Lorraine, EA 4367 Laboratoire d’Ingénierie des Biomolécules, Ecole Nationale Supérieure d’Agronomie et des Industries Alimentaires (ENSAIA), Vandœuvre-lès-Nancy, France
| | - Tiphaine Dhalleine
- Université de Lorraine, INRAE, UMR1136 Interactions Arbres-Microorganismes, Nancy, France
| | - Philippe Oger
- INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Villeurbanne, France
| | | | - Stéphane Uroz
- Université de Lorraine, INRAE, UMR1136 Interactions Arbres-Microorganismes, Nancy, France
- INRAE, UR1138 Biogéochimie des Ecosystèmes Forestiers, Champenoux, France
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7
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Iron acquisition strategies in pseudomonads: mechanisms, ecology, and evolution. Biometals 2022:10.1007/s10534-022-00480-8. [PMID: 36508064 PMCID: PMC10393863 DOI: 10.1007/s10534-022-00480-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
AbstractIron is important for bacterial growth and survival, as it is a common co-factor in essential enzymes. Although iron is very abundant in the earth crust, its bioavailability is low in most habitats because ferric iron is largely insoluble under aerobic conditions and at neutral pH. Consequently, bacteria have evolved a plethora of mechanisms to solubilize and acquire iron from environmental and host stocks. In this review, I focus on Pseudomonas spp. and first present the main iron uptake mechanisms of this taxa, which involve the direct uptake of ferrous iron via importers, the production of iron-chelating siderophores, the exploitation of siderophores produced by other microbial species, and the use of iron-chelating compounds produced by plants and animals. In the second part of this review, I elaborate on how these mechanisms affect interactions between bacteria in microbial communities, and between bacteria and their hosts. This is important because Pseudomonas spp. live in diverse communities and certain iron-uptake strategies might have evolved not only to acquire this essential nutrient, but also to gain relative advantages over competitors in the race for iron. Thus, an integrative understanding of the mechanisms of iron acquisition and the eco-evolutionary dynamics they drive at the community level might prove most useful to understand why Pseudomonas spp., in particular, and many other bacterial species, in general, have evolved such diverse iron uptake repertoires.
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8
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Li W, He E, Zhang P, Li Y, Qiu H. Multiomics analyses uncover nanoceria triggered oxidative injury and nutrient imbalance in earthworm Eisenia fetida. JOURNAL OF HAZARDOUS MATERIALS 2022; 437:129354. [PMID: 35717815 DOI: 10.1016/j.jhazmat.2022.129354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/24/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
The toxic stress caused by nanoceria remains vague owing to the limited efforts scrutinizing its molecular mechanisms. Herein, we investigated the impacts of nanoceria on earthworm Eisenia fetida, at the molecular level using the multiomics-based profiling approaches (transcriptomics, metabolomics, and 16 S rRNA sequencing). Nanoceria (50 and 500 mg/kg) significantly increased the contents of malondialdehyde (MDA), Fe, and K in worms, suggesting oxidative injury and nutrient imbalance. This was corroborated by the transcriptomic and metabolomic analyses. Nanoceria decreased the levels of certain genes and metabolites associated with glycerolipid and glycerophospholipid metabolisms, suggesting the production of reactive oxygen species and subsequent oxidative stress. Additionally, the ABCD3 gene belonging to ABC transporter family was upregulated, facilitating Fe uptake by worms. Moreover, the higher contents of MDA, Fe, and K after exposure were tightly associated with the imbalanced intestinal flora. Specifically, a higher relative abundance of Actinobacteriota and a lower relative abundance of Proteobacteria and Patescibacteria were induced. This study, for the first time, revealed that nanoceria at nonlethal levels caused oxidative stress and nutrient imbalance of earthworms from the perspective of genes, metabolites, and gut microbiome perturbations, and also established links between the gut microbiome and the overall physiological responses of the host.
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Affiliation(s)
- Wenxing Li
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Erkai He
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Peihua Zhang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yinsheng Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Qiu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
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9
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Steunou AS, Vigouroux A, Aumont‐Nicaise M, Plancqueel S, Boussac A, Ouchane S, Moréra S. New insights into the mechanism of iron transport through the bacterial Ftr system present in pathogens. FEBS J 2022; 289:6286-6307. [DOI: 10.1111/febs.16476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/11/2022] [Accepted: 05/06/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Anne Soisig Steunou
- Université Paris‐Saclay, CEA CNRS Institute for Integrative Biology of the Cell (I2BC) Gif‐sur‐Yvette France
| | - Armelle Vigouroux
- Université Paris‐Saclay, CEA CNRS Institute for Integrative Biology of the Cell (I2BC) Gif‐sur‐Yvette France
| | - Magali Aumont‐Nicaise
- Université Paris‐Saclay, CEA CNRS Institute for Integrative Biology of the Cell (I2BC) Gif‐sur‐Yvette France
| | - Stéphane Plancqueel
- Université Paris‐Saclay, CEA CNRS Institute for Integrative Biology of the Cell (I2BC) Gif‐sur‐Yvette France
| | - Alain Boussac
- Université Paris‐Saclay, CEA CNRS Institute for Integrative Biology of the Cell (I2BC) Gif‐sur‐Yvette France
| | - Soufian Ouchane
- Université Paris‐Saclay, CEA CNRS Institute for Integrative Biology of the Cell (I2BC) Gif‐sur‐Yvette France
| | - Solange Moréra
- Université Paris‐Saclay, CEA CNRS Institute for Integrative Biology of the Cell (I2BC) Gif‐sur‐Yvette France
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10
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Nakei MD, Venkataramana PB, Ndakidemi PA. Soybean-Nodulating Rhizobia: Ecology, Characterization, Diversity, and Growth Promoting Functions. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.824444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The worldwide increase in population continues to threaten the sustainability of agricultural systems since agricultural output must be optimized to meet the global rise in food demand. Sub-Saharan Africa (SSA) is among the regions with a fast-growing population but decreasing crop productivity. Pests and diseases, as well as inadequate nitrogen (N) levels in soils, are some of the biggest restrictions to agricultural production in SSA. N is one of the most important plant-limiting elements in agricultural soils, and its deficit is usually remedied by using nitrogenous fertilizers. However, indiscriminate use of these artificial N fertilizers has been linked to environmental pollution calling for alternative N fertilization mechanisms. Soybean (Glycine max) is one of the most important legumes in the world. Several species of rhizobia from the four genera, Bardyrhizobium, Rhizobium, Mesorhizobium, and Ensifer (formerly Sinorhizobium), are observed to effectively fix N with soybean as well as perform various plant-growth promoting (PGP) functions. The efficiency of the symbiosis differs with the type of rhizobia species, soybean cultivar, and biotic factors. Therefore, a complete understanding of the ecology of indigenous soybean-nodulating rhizobia concerning their genetic diversity and the environmental factors associated with their localization and dominance in the soil is important. This review aimed to understand the potential of indigenous soybean-nodulating rhizobia through a synthesis of the literature regarding their characterization using different approaches, genetic diversity, symbiotic effectiveness, as well as their functions in biological N fixation (BNF) and biocontrol of soybean soil-borne pathogens.
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11
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Banerjee S, Chanakira MN, Hall J, Kerkan A, Dasgupta S, Martin DW. A review on bacterial redox dependent iron transporters and their evolutionary relationship. J Inorg Biochem 2022; 229:111721. [PMID: 35033753 DOI: 10.1016/j.jinorgbio.2022.111721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/05/2023]
Abstract
Iron is an essential yet toxic micronutrient and its transport across biological membranes is tightly regulated in all living organisms. One such iron transporter, the Ftr-type permeases, is found in both eukaryotic and prokaryotic cells. These Ftr-type transporters are required for iron transport, predicted to form α-helical transmembrane structures, and conserve two ArgGluxxGlu (x = any amino acid) motifs. In the yeast Ftr transporter (Ftr1p), a ferroxidase (Fet3p) is required for iron transport in an oxidation coupled transport step. None of the bacterial Ftr-type transporters (EfeU and FetM from E. coli; cFtr from Campylobacter jejuni; FtrC from Brucella, Bordetella, and Burkholderia spp.) contain a ferroxidase protein. Bioinformatics report predicted periplasmic EfeO and FtrB (from the EfeUOB and FtrABCD systems) as novel cupredoxins. The Cu2+ binding and the ferrous oxidation properties of these proteins are uncharacterized and the other two bacterial Ftr-systems are expressed without any ferroxidase/cupredoxin, leading to controversy about the mode of function of these transporters. Here, we review published data on Ftr-type transporters to gain insight into their functional diversity. Based on original bioinformatics data presented here evolutionary relations between these systems are presented.
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Affiliation(s)
- Sambuddha Banerjee
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA.
| | - Mina N Chanakira
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Jonathan Hall
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Alexa Kerkan
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Saumya Dasgupta
- Department of Chemistry, Amity Institute of Applied Sciences, Amity University Kolkata, WB 700135, India
| | - Daniel W Martin
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
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12
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Zhang J, Xiao Q, Wang P. Phosphate-solubilizing bacterium Burkholderia sp. strain N3 facilitates the regulation of gene expression and improves tomato seedling growth under cadmium stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 217:112268. [PMID: 33930768 DOI: 10.1016/j.ecoenv.2021.112268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/11/2021] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
Cadmium (Cd) is among the most toxic heavy metals in soils. The ways by which tomato plants inoculated with a phosphate-solubilizing bacterium (PSB) respond to Cd and regulate gene expression remain unclear. We investigated hormone metabolism and genes involved in Cd resistance in tomato seedlings inoculated with the PSB strain N3. Cd inhibited tomato plant growth and nutrient uptake and increase in dry weight. Compared with Cd treatment, N3 inoculation inhibited the accumulation of Cd in the shoots and roots, and the root dry weight significantly increased by 30.50% (P < 0.05). The nitrogen and potassium contents in the roots of seedlings treated with N3 increased, and the phosphorus levels were the same as those in the control. N3 decreased the rate of Zn2+ absorption but increased Fe3+ absorption in the roots, and the amount of accumulated Cd increased with Zn2+ uptake. The concentrations of hormones (indole-3-acetic acid, IAA; zeatin, ZEA; and jasmonic acid, JA) increased under Cd stress, whereas inoculation with N3 reduced IAA and ZEA levels. In the comparison between N3 + Cd and Cd treatments, the highest number of up- and downregulated genes was obtained. Pathways involved in signaling response, photosynthesis, phenylpropanoid biosynthesis, and DNA replication and the photosynthesis-antenna proteins pathway play important roles in the responses and adaptation of seedlings to Cd. Inoculation with N3 alleviates Cd stress in tomato seedlings. The present study provides new insights into the differentially expressed genes related to interaction between PSB and tomato exposed to Cd in soils.
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Affiliation(s)
- Jian Zhang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230031 Anhui Province, China.
| | - Qingqing Xiao
- School of Biology, Food and Environment, Hefei University, 230601 Anhui Province, China
| | - Pengcheng Wang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230031 Anhui Province, China
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13
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Picard L, Paris C, Dhalleine T, Morin E, Oger P, Turpault MP, Uroz S. The mineral weathering ability of Collimonas pratensis PMB3(1) involves a Malleobactin-mediated iron acquisition system. Environ Microbiol 2021; 24:784-802. [PMID: 33817942 DOI: 10.1111/1462-2920.15508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/23/2021] [Accepted: 04/03/2021] [Indexed: 11/27/2022]
Abstract
Mineral weathering by microorganisms is considered to occur through a succession of mechanisms based on acidification and chelation. While the role of acidification is established, the role of siderophores is difficult to disentangle from the effect of the acidification. We took advantage of the ability of strain Collimonas pratensis PMB3(1) to weather minerals but not to acidify depending on the carbon source to address the role of siderophores in mineral weathering. We identified a single non-ribosomal peptide synthetase (NRPS) responsible for siderophore biosynthesis in the PMB3(1) genome. By combining iron-chelating assays, targeted mutagenesis and chemical analyses (HPLC and LC-ESI-HRMS), we identified the siderophore produced as malleobactin X and how its production depends on the concentration of available iron. Comparison with the genome sequences of other collimonads evidenced that malleobactin production seems to be a relatively conserved functional trait, though some collimonads harboured other siderophore synthesis systems. We also revealed by comparing the wild-type strain and its mutant impaired in the production of malleobactin that the ability to produce this siderophore is essential to allow the dissolution of hematite under non-acidifying conditions. This study represents the first characterization of the siderophore produced by collimonads and its role in mineral weathering.
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Affiliation(s)
- Laura Picard
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, F-54280, France.,INRAE, UR1138 « Biogéochimie des Ecosystèmes Forestiers », Champenoux, F-54280, France
| | - Cédric Paris
- Université de Lorraine, EA 4367 « Laboratoire d'Ingénierie des Biomolécules », Ecole Nationale Supérieure d'Agronomie et des Industries Alimentaires (ENSAIA), Vandœuvre-lès-Nancy, F-54505, France.,Plateau d'Analyse Structurale et Métabolomique (PASM) - SF4242 EFABA, Vandœuvre-lès-Nancy, F-54505, France
| | - Tiphaine Dhalleine
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, F-54280, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, F-54280, France
| | - Philippe Oger
- Université de Lyon, INSA de Lyon, CNRS UMR 5240 « Microbiologie, Adaptation et Pathogénie », Villeurbanne, F-69621, France
| | - Marie-Pierre Turpault
- INRAE, UR1138 « Biogéochimie des Ecosystèmes Forestiers », Champenoux, F-54280, France
| | - Stéphane Uroz
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, F-54280, France.,INRAE, UR1138 « Biogéochimie des Ecosystèmes Forestiers », Champenoux, F-54280, France
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14
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Liu J, Yin F, Liu T, Li S, Tan C, Li L, Zhou R, Huang Q. The Tat system and its dependent cell division proteins are critical for virulence of extra-intestinal pathogenic Escherichia coli. Virulence 2020; 11:1279-1292. [PMID: 32962530 PMCID: PMC7549933 DOI: 10.1080/21505594.2020.1817709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/23/2020] [Accepted: 08/28/2020] [Indexed: 11/29/2022] Open
Abstract
The twin-arginine translocation (Tat) system is involved in a variety of important bacterial physiological processes. Conserved among bacteria and crucial for virulence, the Tat system is deemed as a promising anti-microbial drug target. However, the mechanism of how the Tat system functions in bacterial pathogenesis has not been fully understood. In this study, we showed that the Tat system was critical for the virulence of an extra-intestinal pathogenic E. coli (ExPEC) strain PCN033. A total of 20 Tat-related mutant strains were constructed, and competitive infection assays were performed to evaluate the relative virulence of these mutants. The results demonstrated that several Tat substrate mutants, including the ΔsufI, ΔamiAΔamiC double mutant as well as each single mutant, ΔyahJ, ΔcueO, and ΔnapG, were significantly outcompeted by the WT strain, among which the ΔsufI and ΔamiAΔamiC strains showed the lowest competitive index (CI) value. Results of individual mouse infection assay, in vitro cell adhesion assay, whole blood bactericidal assay, and serum bactericidal assay further confirmed the virulence attenuation phenotype of the ΔsufI and ΔamiAΔamiC strains. Moreover, the two mutants displayed chained morphology in the log phase resembling the Δtat and were defective in stress response. Our results suggest that the Tat system and its dependent cell division proteins SufI, AmiA, and AmiC play critical roles during ExPEC pathogenesis.
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Affiliation(s)
- Jinjin Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Fan Yin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Te Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Shaowen Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Chen Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of China, Wuhan, China
| | - Lu Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of China, Wuhan, China
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of China, Wuhan, China
| | - Qi Huang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of China, Wuhan, China
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15
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Dashti Y, Nakou IT, Mullins AJ, Webster G, Jian X, Mahenthiralingam E, Challis GL. Discovery and Biosynthesis of Bolagladins: Unusual Lipodepsipeptides from Burkholderia gladioli Clinical Isolates*. Angew Chem Int Ed Engl 2020; 59:21553-21561. [PMID: 32780452 PMCID: PMC7756342 DOI: 10.1002/anie.202009110] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Indexed: 01/01/2023]
Abstract
Two Burkholderia gladioli strains isolated from the lungs of cystic fibrosis patients were found to produce unusual lipodepsipeptides containing a unique citrate-derived fatty acid and a rare dehydro-β-alanine residue. The gene cluster responsible for their biosynthesis was identified by bioinformatics and insertional mutagenesis. In-frame deletions and enzyme activity assays were used to investigate the functions of several proteins encoded by the biosynthetic gene cluster, which was found in the genomes of about 45 % of B. gladioli isolates, suggesting that its metabolic products play an important role in the growth and/or survival of the species. The Chrome Azurol S assay indicated that these metabolites bind ferric iron, which suppresses their production when added to the growth medium. Moreover, a gene encoding a TonB-dependent ferric-siderophore receptor is adjacent to the biosynthetic genes, suggesting that these metabolites may function as siderophores in B. gladioli.
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Affiliation(s)
- Yousef Dashti
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Current address: The Centre for Bacterial Cell BiologyBiosciences InstituteMedical SchoolNewcastle UniversityNewcastle upon TyneNE2 4AXUK
| | - Ioanna T. Nakou
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
| | - Alex J. Mullins
- Microbiomes, Microbes and Informatics GroupOrganisms and Environment DivisionSchool of BiosciencesCardiff UniversityCardiffCF103 ATUK
| | - Gordon Webster
- Microbiomes, Microbes and Informatics GroupOrganisms and Environment DivisionSchool of BiosciencesCardiff UniversityCardiffCF103 ATUK
| | - Xinyun Jian
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Warwick Integrative Synthetic Biology CentreUniversity of WarwickCoventryCV4 7ALUK
| | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics GroupOrganisms and Environment DivisionSchool of BiosciencesCardiff UniversityCardiffCF103 ATUK
| | - Gregory L. Challis
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Warwick Integrative Synthetic Biology CentreUniversity of WarwickCoventryCV4 7ALUK
- Department of Biochemistry and Molecular Biology, ARC Centre of Excellence for Innovations in Peptide and Protein ScienceMonash UniversityClaytonVIC3800Australia
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16
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Dashti Y, Nakou IT, Mullins AJ, Webster G, Jian X, Mahenthiralingam E, Challis GL. Discovery and Biosynthesis of Bolagladins: Unusual Lipodepsipeptides from
Burkholderia gladioli
Clinical Isolates**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yousef Dashti
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Current address: The Centre for Bacterial Cell Biology Biosciences Institute Medical School Newcastle University Newcastle upon Tyne NE2 4AX UK
| | - Ioanna T. Nakou
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
| | - Alex J. Mullins
- Microbiomes, Microbes and Informatics Group Organisms and Environment Division School of Biosciences Cardiff University Cardiff CF103 AT UK
| | - Gordon Webster
- Microbiomes, Microbes and Informatics Group Organisms and Environment Division School of Biosciences Cardiff University Cardiff CF103 AT UK
| | - Xinyun Jian
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Warwick Integrative Synthetic Biology Centre University of Warwick Coventry CV4 7AL UK
| | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics Group Organisms and Environment Division School of Biosciences Cardiff University Cardiff CF103 AT UK
| | - Gregory L. Challis
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Warwick Integrative Synthetic Biology Centre University of Warwick Coventry CV4 7AL UK
- Department of Biochemistry and Molecular Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton VIC 3800 Australia
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17
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Sathe S, Kümmerli R. Antagonistic interactions subdue inter-species green-beard cooperation in bacteria. J Evol Biol 2020; 33:1245-1255. [PMID: 32946129 DOI: 10.1111/jeb.13666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 12/16/2022]
Abstract
Cooperation can be favoured through the green-beard mechanism, where a set of linked genes encodes both a cooperative trait and a phenotypic marker (green beard), which allows carriers of the trait to selectively direct cooperative acts to other carriers. In theory, the green-beard mechanism should favour cooperation even when interacting partners are totally unrelated at the genome level. Here, we explore such an extreme green-beard scenario between two unrelated bacterial species-Pseudomonas aeruginosa and Burkholderia cenocepacia, which share a cooperative locus encoding the public good pyochelin (an iron-scavenging siderophore) and its cognate receptor (green beard) required for iron-pyochelin uptake. We show that pyochelin, when provided in cell-free supernatants, can be mutually exchanged between species and provide fitness benefits under iron limitation. However, in co-culture we observed that these cooperative benefits vanished and communities were dominated by P. aeruginosa, regardless of strain background and species starting frequencies. Our results further suggest that P. aeruginosa engages in interference competition to suppress B. cenocepacia, indicating that inter-species conflict arising from dissimilarities at the genome level overrule the aligned cooperative interests at the pyochelin locus. Thus, green-beard cooperation is subdued by competition, indicating that interspecific siderophore cooperation is difficult to evolve and to be maintained.
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Affiliation(s)
- Santosh Sathe
- Department of Quantitative Biomedicine, University of Zürich, Zürich, Switzerland.,Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland.,Indian Institute of Science Education and Research (IISER) Pune, Maharashtra, India
| | - Rolf Kümmerli
- Department of Quantitative Biomedicine, University of Zürich, Zürich, Switzerland.,Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
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18
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Corretto E, Antonielli L, Sessitsch A, Höfer C, Puschenreiter M, Widhalm S, Swarnalakshmi K, Brader G. Comparative Genomics of Microbacterium Species to Reveal Diversity, Potential for Secondary Metabolites and Heavy Metal Resistance. Front Microbiol 2020; 11:1869. [PMID: 32903828 PMCID: PMC7438953 DOI: 10.3389/fmicb.2020.01869] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/16/2020] [Indexed: 12/11/2022] Open
Abstract
Microbacterium species have been isolated from a wide range of hosts and environments, including heavy metal-contaminated sites. Here, we present a comprehensive analysis on the phylogenetic distribution and the genetic potential of 70 Microbacterium belonging to 20 different species isolated from heavy metal-contaminated and non-contaminated sites with particular attention to secondary metabolites gene clusters. The analyzed Microbacterium species are divided in three main functional clades. They share a small core genome (331 gene families covering basic functions) pointing to high genetic diversity. The most common secondary metabolite gene clusters encode pathways for the production of terpenoids, type III polyketide synthases and non-ribosomal peptide synthetases, potentially responsible of the synthesis of siderophore-like compounds. In vitro tests showed that many Microbacterium strains produce siderophores, ACC deaminase, auxins (IAA) and are able to solubilize phosphate. Microbacterium isolates from heavy metal contaminated sites are on average more resistant to heavy metals and harbor more genes related to metal homeostasis (e.g., metalloregulators). On the other hand, the ability to increase the metal mobility in a contaminated soil through the secretion of specific molecules seems to be widespread among all. Despite the widespread capacity of strains to mobilize several metals, plants inoculated with selected Microbacterium isolates showed only slightly increased iron concentrations, whereas concentrations of zinc, cadmium and lead were decreased.
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Affiliation(s)
- Erika Corretto
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Livio Antonielli
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Angela Sessitsch
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Christoph Höfer
- Institute of Soil Research, Department of Forest- and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Markus Puschenreiter
- Institute of Soil Research, Department of Forest- and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Siegrid Widhalm
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | | | - Günter Brader
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
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19
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Burkholderia pseudomallei pathogenesis and survival in different niches. Biochem Soc Trans 2020; 48:569-579. [PMID: 32167134 DOI: 10.1042/bst20190836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 01/16/2023]
Abstract
Burkholderia pseudomallei (Bp) is the causative agent of melioidosis, a disease of the tropics with high clinical mortality rates. To date, no vaccines are approved for melioidosis and current treatment relies on antibiotics. Conversely, common misdiagnosis and high pathogenicity of Bp hamper efforts to fight melioidosis. This bacterium can be isolated from a wide range of niches such as waterlogged fields, stagnant water bodies, salt water bodies and from human and animal clinical specimens. Although extensive studies have been undertaken to elucidate pathogenesis mechanisms of Bp, little is known about how a harmless soil bacterium adapts to different environmental conditions, in particular, the shift to a human host to become a highly virulent pathogen. The bacterium has a large genome encoding an armory of factors that assist the pathogen in surviving under stressful conditions and assuming its role as a deadly intracellular pathogen. This review presents an overview of what is currently known about how the pathogen adapts to different environments. With in-depth understanding of Bp adaptation and survival, more effective therapies for melioidosis can be developed by targeting related genes or proteins that play a major role in the bacteria's survival.
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20
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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: 409] [Impact Index Per Article: 102.3] [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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21
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Sathe S, Mathew A, Agnoli K, Eberl L, Kümmerli R. Genetic architecture constrains exploitation of siderophore cooperation in the bacterium Burkholderia cenocepacia. Evol Lett 2019; 3:610-622. [PMID: 31844554 PMCID: PMC6906993 DOI: 10.1002/evl3.144] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Explaining how cooperation can persist in the presence of cheaters, exploiting the cooperative acts, is a challenge for evolutionary biology. Microbial systems have proved extremely useful to test evolutionary theory and identify mechanisms maintaining cooperation. One of the most widely studied system is the secretion and sharing of iron‐scavenging siderophores by Pseudomonas bacteria, with many insights gained from this system now being considered as hallmarks of bacterial cooperation. Here, we introduce siderophore secretion by the bacterium Burkholderia cenocepacia H111 as a novel parallel study system, and show that this system behaves differently. For ornibactin, the main siderophore of this species, we discovered a novel mechanism of how cheating can be prevented. Particularly, we found that secreted ornibactin cannot be exploited by ornibactin‐defective mutants because ornibactin receptor and synthesis genes are co‐expressed from the same operon, such that disruptive mutations in synthesis genes compromise receptor availability required for siderophore uptake and cheating. For pyochelin, the secondary siderophore of this species, we found that cheating was possible, but the relative success of cheaters was positive frequency dependent, thus diametrically opposite to the Pseudomonas and other microbial systems. Altogether, our results highlight that expanding our repertoire of microbial study systems leads to new discoveries and suggest that there is an enormous diversity of social interactions out there in nature, and we might have only looked at the tip of the iceberg so far.
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Affiliation(s)
- Santosh Sathe
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland.,Department of Quantitative Biomedicine, University of Zürich, Zürich, Switzerland
| | - Anugraha Mathew
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Kirsty Agnoli
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Rolf Kümmerli
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland.,Department of Quantitative Biomedicine, University of Zürich, Zürich, Switzerland
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22
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Torres Perez MP, Romero Deimer V, Cordero Alexander P. Biorremediación de mercurio y níquel por bacterias endófitas de macrófitas acuáticas. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2019. [DOI: 10.15446/rev.colomb.biote.v21n2.79975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
La contaminación ambiental se ha categorizado como uno de los principales problemas que afecta la salud de las diferentes formas de vida. Las bacterias endófitas (BE), son capaces de mejorar el estado nutricional de las plantas y remover contaminantes del suelo. La subregión la Mojana funciona como zona de amortización de ríos. En este estudio, se colectaron muestras de macrófitas acuáticas de las ciénagas de Ayapel, San Marcos y San Benito Abad, de los cuales se aislaron bacterias endófitas. Se cuantificó las densidades poblacional de estas bacterias y su respectiva tolerancia a los metales pesados níquel y mercurio. Posteriormente, las cepas tolerantes fueron identificadas molecularmente y se les evaluó su capacidad de promover el crecimiento vegetal. Un total de 182 morfotipos de bacterias endófitas fueron aislados, los mayores promedios de densidad poblacional se obtuvieron en las macrófitas de la ciénaga de San Benito Abad ubicada en las coordenadas coordenadas 8°55´32.81´´ N y 75°1´13.72” O. Los mayores promedios de morfotipos tolerantes a mercurio y níquel se encontraron en la ciénaga de Ayapel en las coordenadas 8°18´51.10´´ N y 75°8´8.26” O. Los resultados muestran que los aislados con mayor potencial biotecnológico son BAT6, BAR2 y PAT2, donde los dos primeros tienen una homología del 100% con la especie Lysinibacillus fusifomis y el género Enterobacter, respectivamente, mientras que el tercer aislamiento tuvo una homología del 96% con la especie Burkholderia cepacia. El presente estudio reporta por primera vez la presencia de Lysinibacillus fusifomis y Burkholderia cepacia asociadas a macrófitas en cuerpos cenagosos de Sucre y Córdoba.
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23
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Ohkura M, Cotty PJ, Orbach MJ. Comparative Genomics of Aspergillus flavus S and L Morphotypes Yield Insights into Niche Adaptation. G3 (BETHESDA, MD.) 2018; 8:3915-3930. [PMID: 30361280 PMCID: PMC6288828 DOI: 10.1534/g3.118.200553] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/15/2018] [Indexed: 02/08/2023]
Abstract
Aspergillus flavus, the primary causal agent for aflatoxin contamination on crops, consists of isolates with two distinct morphologies: isolates of the S morphotype produce numerous small sclerotia and lower numbers of conidia while isolates of the L morphotype produce fewer large sclerotia and abundant conidia. The morphotypes also differ in aflatoxin production with S isolates consistently producing high concentrations of aflatoxin, whereas L isolates range from atoxigenic to highly toxigenic. The production of abundant sclerotia by the S morphotype suggests adaptation for long-term survival in the soil, whereas the production of abundant conidia by the L morphotype suggests adaptation for aerial dispersal to the phyllosphere. To identify genomic changes that support differential niche adaption, the sequences of three S and three L morphotype isolates were compared. Differences in genome structure and gene content were identified between the morphotypes. A >530 kb inversion between the morphotypes affect a secondary metabolite gene cluster and a cutinase gene. The morphotypes also differed in proteins predicted to be involved in carbon/nitrogen metabolism, iron acquisition, antimicrobial defense, and evasion of host immunity. The S morphotype genomes contained more intact secondary metabolite clusters indicating there is higher selection pressure to maintain secondary metabolism in the soil and that it is not limited to aflatoxin production. The L morphotype genomes were enriched in amino acid transporters, suggesting efficient nitrogen transport may be critical in the nutrient limited phyllosphere. These findings indicate the genomes of the two morphotypes differ beyond developmental genes and have diverged as they adapted to their respective niches.
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Affiliation(s)
- Mana Ohkura
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | - Peter J Cotty
- USDA-ARS, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | - Marc J Orbach
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
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24
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Chitarra CS, Oliveira Filho JXD, Morés N, Silva MIVD, Cândido SL, Cezarino PG, Nakazato L, Dutra V. Identification of Pasteurella multocida transcribed genes in porcine lungs through RNAseq. Microb Pathog 2018; 122:180-183. [PMID: 29890333 DOI: 10.1016/j.micpath.2018.06.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 05/11/2018] [Accepted: 06/08/2018] [Indexed: 11/16/2022]
Abstract
Pasteurella multocida is one of the most important pathogen that causes pneumonia in swine. Although several virulence factors are known, the pathogenesis of this bacterium is not well-studied. Therefore, to study the pathogenesis of P. multocida infection in porcine lung, next-generation RNA sequencing was used to compare the transcriptomes of P. multocida grown in vivo and in vitro, respectively. After P. multocida infection a total of 704 genes were expressed in vitro, 1422 genes were expressed in vivo, and 237 genes were differentially expressed based on statistical analyses, padj of ≤0.1. Genes encoding ribosomal proteins or other products that function in the regulation of transcription and translation were downregulated, whereas genes whose products affected cellular processes (protein transport and RNA degradation) and metabolic pathways, such as those of amino acid metabolism and nucleotide metabolism, were upregulated in vitro compared with in vivo. This study shows that differentially expressed genes in P. multocida regulate pathways that operate during stress, iron capture, heat shock, and nitrogen regulation. However, extensive investigation of the pathogenic mechanism of P. multocida is still required.
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Affiliation(s)
- Cristiane Silva Chitarra
- Avenida Fernando Corrêa da Costa, nº 2367 - Bairro Boa Esperança, Cuiabá, Mato Grosso, CEP: 78060-900, Brazil.
| | | | - Nelson Morés
- Rodovia BR-153, Km 110, Distrito de Tamanduá Caixa Postal: 321, Concórdia, Santa Catarina, CEP: 89715-899, Brazil
| | | | - Stefhano Luis Cândido
- Avenida Fernando Corrêa da Costa, nº 2367 - Bairro Boa Esperança, Cuiabá, Mato Grosso, CEP: 78060-900, Brazil
| | - Paula Gabriela Cezarino
- Avenida Fernando Corrêa da Costa, nº 2367 - Bairro Boa Esperança, Cuiabá, Mato Grosso, CEP: 78060-900, Brazil
| | - Luciano Nakazato
- Avenida Fernando Corrêa da Costa, nº 2367 - Bairro Boa Esperança, Cuiabá, Mato Grosso, CEP: 78060-900, Brazil
| | - Valéria Dutra
- Avenida Fernando Corrêa da Costa, nº 2367 - Bairro Boa Esperança, Cuiabá, Mato Grosso, CEP: 78060-900, Brazil
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25
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Leinweber A, Weigert M, Kümmerli R. The bacterium Pseudomonas aeruginosa senses and gradually responds to interspecific competition for iron. Evolution 2018; 72:1515-1528. [PMID: 29665015 PMCID: PMC6314444 DOI: 10.1111/evo.13491] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 04/07/2018] [Indexed: 12/20/2022]
Abstract
Phenotypic plasticity in response to competition is a well-described phenomenon in higher organisms. Here, we show that also bacteria have the ability to sense the presence of competitors and mount fine-tuned responses to match prevailing levels of competition. In our experiments, we studied interspecific competition for iron between the bacterium Pseudomonas aeruginosa (PA) and its competitor Burkholderia cenocepacia (BC). We focused on the ability of PA to phenotypically adjust the production of pyoverdine, an iron-scavenging siderophore. We found that PA upregulates pyoverdine production early on during competition under condition of low iron availability. This plastic upregulation was fine-tuned in response to the level of competition imposed by BC, and seems to confer a relative fitness benefit to PA in the form of an earlier initiation of growth. At later time points, however, PA showed reduced growth in mixed compared to monoculture, suggesting that competitive responses are costly. Altogether, our results demonstrate that phenotypic plasticity in siderophore production plays an important role in interspecific competition for iron. Upregulating siderophore production may be a powerful strategy to lock iron away from competing species, and to reserve this nutrient for strain members possessing the compatible receptor for uptake.
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Affiliation(s)
- Anne Leinweber
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Michael Weigert
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Rolf Kümmerli
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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26
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Butt AT, Thomas MS. Iron Acquisition Mechanisms and Their Role in the Virulence of Burkholderia Species. Front Cell Infect Microbiol 2017; 7:460. [PMID: 29164069 PMCID: PMC5681537 DOI: 10.3389/fcimb.2017.00460] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/18/2017] [Indexed: 11/19/2022] Open
Abstract
Burkholderia is a genus within the β-Proteobacteriaceae that contains at least 90 validly named species which can be found in a diverse range of environments. A number of pathogenic species occur within the genus. These include Burkholderia cenocepacia and Burkholderia multivorans, opportunistic pathogens that can infect the lungs of patients with cystic fibrosis, and are members of the Burkholderia cepacia complex (Bcc). Burkholderia pseudomallei is also an opportunistic pathogen, but in contrast to Bcc species it causes the tropical human disease melioidosis, while its close relative Burkholderia mallei is the causative agent of glanders in horses. For these pathogens to survive within a host and cause disease they must be able to acquire iron. This chemical element is essential for nearly all living organisms due to its important role in many enzymes and metabolic processes. In the mammalian host, the amount of accessible free iron is negligible due to the low solubility of the metal ion in its higher oxidation state and the tight binding of this element by host proteins such as ferritin and lactoferrin. As with other pathogenic bacteria, Burkholderia species have evolved an array of iron acquisition mechanisms with which to capture iron from the host environment. These mechanisms include the production and utilization of siderophores and the possession of a haem uptake system. Here, we summarize the known mechanisms of iron acquisition in pathogenic Burkholderia species and discuss the evidence for their importance in the context of virulence and the establishment of infection in the host. We have also carried out an extensive bioinformatic analysis to identify which siderophores are produced by each Burkholderia species that is pathogenic to humans.
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Affiliation(s)
- Aaron T Butt
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, United Kingdom
| | - Mark S Thomas
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, United Kingdom
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27
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Burkholderia cepacia Complex Regulation of Virulence Gene Expression: A Review. Genes (Basel) 2017; 8:genes8010043. [PMID: 28106859 PMCID: PMC5295037 DOI: 10.3390/genes8010043] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 12/31/2022] Open
Abstract
Burkholderia cepacia complex (Bcc) bacteria emerged as opportunistic pathogens in cystic fibrosis and immunocompromised patients. Their eradication is very difficult due to the high level of intrinsic resistance to clinically relevant antibiotics. Bcc bacteria have large and complex genomes, composed of two to four replicons, with variable numbers of insertion sequences. The complexity of Bcc genomes confers a high genomic plasticity to these bacteria, allowing their adaptation and survival to diverse habitats, including the human host. In this work, we review results from recent studies using omics approaches to elucidate in vivo adaptive strategies and virulence gene regulation expression of Bcc bacteria when infecting the human host or subject to conditions mimicking the stressful environment of the cystic fibrosis lung.
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28
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Sankari S, O'Brian MR. The Bradyrhizobium japonicum Ferrous Iron Transporter FeoAB Is Required for Ferric Iron Utilization in Free Living Aerobic Cells and for Symbiosis. J Biol Chem 2016; 291:15653-62. [PMID: 27288412 PMCID: PMC4957049 DOI: 10.1074/jbc.m116.734129] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/07/2016] [Indexed: 01/02/2023] Open
Abstract
The bacterium Bradyrhizobium japonicum USDA110 does not synthesize siderophores for iron utilization in aerobic environments, and the mechanism of iron uptake within symbiotic soybean root nodules is unknown. An mbfA bfr double mutant defective in iron export and storage activities cannot grow aerobically in very high iron medium. Here, we found that this phenotype was suppressed by loss of function mutations in the feoAB operon encoding ferrous (Fe(2+)) iron uptake proteins. Expression of the feoAB operon genes was elevated under iron limitation, but mutants defective in either gene were unable to grow aerobically over a wide external ferric (Fe(3+)) iron (FeCl3) concentration range. Thus, FeoAB accommodates iron acquisition under iron limited and iron replete conditions. Incorporation of radiolabel from either (55)Fe(2+) or (59)Fe(3+) into cells was severely defective in the feoA and feoB strains, suggesting Fe(3+) reduction to Fe(2+) prior to traversal across the cytoplasmic membrane by FeoAB. The feoA or feoB deletion strains elicited small, ineffective nodules on soybean roots, containing few bacteria and lacking nitrogen fixation activity. A feoA(E40K) mutant contained partial iron uptake activity in culture that supported normal growth and established an effective symbiosis. The feoA(E40K) strain had partial iron uptake activity in situ within nodules and in isolated cells, indicating that FeoAB is the iron transporter in symbiosis. We conclude that FeoAB supports iron acquisition under limited conditions of soil and in the iron-rich environment of a symbiotic nodule.
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Affiliation(s)
- Siva Sankari
- From the Department of Biochemistry, State University of New York, Buffalo, New York 14214
| | - Mark R O'Brian
- From the Department of Biochemistry, State University of New York, Buffalo, New York 14214
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Ribolzi O, Rochelle-Newall E, Dittrich S, Auda Y, Newton PN, Rattanavong S, Knappik M, Soulileuth B, Sengtaheuanghoung O, Dance DAB, Pierret A. Land use and soil type determine the presence of the pathogen Burkholderia pseudomallei in tropical rivers. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:7828-7839. [PMID: 26758304 PMCID: PMC4846699 DOI: 10.1007/s11356-015-5943-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/07/2015] [Indexed: 06/05/2023]
Abstract
Burkholderia pseudomallei is the bacterium that causes melioidosis in humans. While B. pseudomallei is known to be endemic in South East Asia (SEA), the occurrence of the disease in other parts of the tropics points towards a potentially large global distribution. We investigated the environmental factors that influence the presence (and absence) of B. pseudomallei in a tropical watershed in SEA. Our main objective was to determine whether there is a link between the presence of the organism in the hydrographic network and the upstream soil and land-use type. The presence of B. pseudomallei was determined using a specific quantitative real-time PCR assay following enrichment culture. Land use, soil, geomorphology, and environmental data were then analyzed using partial least squares discriminant analysis (PLSDA) to compare the B. pseudomallei positive and negative sites. Soil type in the surrounding catchment and turbidity had a strong positive influence on the presence (acrisols and luvisols) or absence (ferralsols) of B. pseudomallei. Given the strong apparent links between soil characteristics, water turbidity, and the presence/absence of B. pseudomallei, actions to raise public awareness about factors increasing the risk of exposure should be undertaken in order to reduce the incidence of melioidosis in regions of endemicity.
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Affiliation(s)
- Olivier Ribolzi
- Géosciences Environnement Toulouse (GET), UMR 5563, (IRD, CNRS, UPS), Université de Toulouse, UPS (OMP), CNRS, Toulouse, France.
| | - Emma Rochelle-Newall
- iEES-Paris (IRD-UPMC-CNRS-INRA-UDD-UPEC), Sorbonne Universités, UPMC Univ Paris 06, Institut de Recherche pour le Développement (IRD), case 23, 4 place Jussieu, Paris cedex, 75252, France
| | - Sabine Dittrich
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Yves Auda
- Géosciences Environnement Toulouse (GET), UMR 5563, (IRD, CNRS, UPS), Université de Toulouse, UPS (OMP), CNRS, Toulouse, France
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sayaphet Rattanavong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Michael Knappik
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bounsamai Soulileuth
- Institute of Ecology and Environmental Science-Paris, Institut de Recherche pour le Développement (IRD), Vientiane, Lao People's Democratic Republic
| | - Oloth Sengtaheuanghoung
- Department of Agricultural Land Management (DALaM), P.O. Box 4199, Ban Nogviengkham, Xaythany District, Vientiane, Lao People's Democratic Republic
| | - David A B Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alain Pierret
- Institute of Ecology and Environmental Science-Paris, Institut de Recherche pour le Développement (IRD), Vientiane, Lao People's Democratic Republic
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30
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Genetic and Functional Analysis of the Biosynthesis of a Non-Ribosomal Peptide Siderophore in Burkholderia xenovorans LB400. PLoS One 2016; 11:e0151273. [PMID: 26963250 PMCID: PMC4786211 DOI: 10.1371/journal.pone.0151273] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 02/25/2016] [Indexed: 11/26/2022] Open
Abstract
B. xenovorans LB400 is a model bacterium for the study of the metabolism of aromatic compounds. The aim of this study was the genomic and functional characterization of a non-ribosomal peptide synthetase containing gene cluster that encodes a siderophore in B. xenovorans LB400. The mba gene cluster from strain LB400 encodes proteins involved in the biosynthesis and transport of a hydroxamate-type siderophore. Strain LB400 has a unique mba gene organization, although mba gene clusters have been observed in diverse Burkholderiales. Bioinformatic analysis revealed the presence of promoters in the mba gene cluster that strongly suggest regulation by the ferric uptake regulator protein (Fur) and by the alternative RNA polymerase extracytoplasmic function sigma factor MbaF. Reverse transcriptase PCR analyses showed the expression of iron-regulated transcriptional units mbaFGHIJKL, mbaN, mbaABCE, mbaO, mbaP and mbaD genes under iron limitation. Chrome azurol S (CAS) assay strongly suggests that strain LB400 synthesized a siderophore under iron limitation. Mass spectrometry ESI-MS and MALDI-TOF-MS analyses revealed that the siderophore is a non-ribosomal peptide, and forms an iron complex with a molecular mass of 676 Da. Based on bioinformatic prediction, CAS assay and MS analyses, we propose that the siderophore is L-Nδ-hydroxy-Nδ-formylOrn-D-β-hydroxyAsp-L-Ser-L-Nδ-hydroxy-Nδ-formylOrn-1,4-diaminobutane that is closely related to malleobactin-type siderophores reported in B. thailandensis.
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31
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Multi-omics analysis of niche specificity provides new insights into ecological adaptation in bacteria. ISME JOURNAL 2016; 10:2072-5. [PMID: 26859773 DOI: 10.1038/ismej.2015.251] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 11/30/2015] [Indexed: 12/13/2022]
Abstract
Different lifestyles, ranging from a saprophyte to a pathogen, have been reported in bacteria of one species. Here, we performed genome-wide survey of the ecological adaptation in four Burkholderia seminalis strains, distinguished by their origin as part of the saprophytic microbial community of soil or water but also including human and plant pathogens. The results indicated that each strain is separated from the others by increased fitness in medium simulating its original niche corresponding to the difference between strains in metabolic capacities. Furthermore, strain-specific metabolism and niche survival was generally linked with genomic variants and niche-dependent differential expression of the corresponding genes. In particular, the importance of iron, trehalose and d-arabitol utilization was highlighted by the involvement of DNA-methylation and horizontal gene transfer in niche-adapted regulation of the corresponding operons based on the integrated analysis of our multi-omics data. Overall, our results provided insights of niche-specific adaptation in bacteria.
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32
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Mathew A, Jenul C, Carlier AL, Eberl L. The role of siderophores in metal homeostasis of members of the genus Burkholderia. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:103-109. [PMID: 26621188 DOI: 10.1111/1758-2229.12357] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 06/05/2023]
Abstract
Although members of the genus Burkholderia can utilize a high-affinity iron uptake system to sustain growth under iron-limiting conditions, many strains also produce siderophores, suggesting that they may serve alternative functions. Here we demonstrate that the two Burkholderia siderophores pyochelin and ornibactin can protect the cells from metal toxicity and thus play an alternative role in metal homeostasis. We also demonstrate that metals such as copper and zinc induce the production of ornibactin.
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Affiliation(s)
- Anugraha Mathew
- Department of Microbiology, Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | - Christian Jenul
- Department of Microbiology, Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | - Aurelien L Carlier
- Department of Microbiology, Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Microbiology, Institute of Plant Biology, University of Zurich, Zurich, Switzerland
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33
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Carlier A, Fehr L, Pinto-Carbó M, Schäberle T, Reher R, Dessein S, König G, Eberl L. The genome analysis of Candidatus Burkholderia crenata reveals that secondary metabolism may be a key function of the Ardisia crenata leaf nodule symbiosis. Environ Microbiol 2016; 18:2507-22. [PMID: 26663534 DOI: 10.1111/1462-2920.13184] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 12/08/2015] [Indexed: 11/30/2022]
Abstract
A majority of Ardisia species harbour Burkholderia sp. bacteria within specialized leaf nodules. The bacteria are transmitted hereditarily and have not yet been cultured outside of their host. Because the plants cannot develop beyond the seedling stage without their symbionts, the symbiosis is considered obligatory. We sequenced for the first time the genome of Candidatus Burkholderia crenata (Ca. B. crenata), the leaf nodule symbiont of Ardisia crenata. The genome of Ca. B. crenata is the smallest Burkholderia genome to date. It contains a large amount of insertion sequences and pseudogenes and displays features consistent with reductive genome evolution. The genome does not encode functions commonly associated with plant symbioses such as nitrogen fixation and plant hormone metabolism. However, we identified unique genes with a predicted role in secondary metabolism in the genome of Ca. B. crenata. Specifically, we provide evidence that the bacterial symbionts are responsible for the synthesis of compound FR900359, a cyclic depsipeptide with biomedical properties previously isolated from leaves of A. crenata.
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Affiliation(s)
- Aurelien Carlier
- Department of Microbiology, University of Zurich, CH-8008, Zurich, Switzerland.,Department of Microbiology, University of Ghent, 9000, Gent, Belgium
| | - Linda Fehr
- Department of Microbiology, University of Zurich, CH-8008, Zurich, Switzerland
| | - Marta Pinto-Carbó
- Department of Microbiology, University of Zurich, CH-8008, Zurich, Switzerland
| | - Till Schäberle
- Institute for Pharmaceutical Biology, University of Bonn, 53115, Bonn, Germany
| | - Raphael Reher
- Institute for Pharmaceutical Biology, University of Bonn, 53115, Bonn, Germany
| | - Steven Dessein
- Plant Conservation and Population Biology, KU Leuven, 3001, Leuven, Belgium.,National Botanic Garden of Belgium, 1860, Meise, Belgium
| | - Gabriele König
- Institute for Pharmaceutical Biology, University of Bonn, 53115, Bonn, Germany
| | - Leo Eberl
- Department of Microbiology, University of Zurich, CH-8008, Zurich, Switzerland
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34
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Rosconi F, Trovero MF, de Souza EM, Fabiano E. Serobactins-mediated iron acquisition systems optimize competitive fitness of Herbaspirillum seropedicae inside rice plants. Environ Microbiol 2015; 18:2523-33. [PMID: 26715074 DOI: 10.1111/1462-2920.13202] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 12/27/2015] [Indexed: 02/02/2023]
Abstract
Herbaspirillum seropedicae Z67 is a diazotrophic endophyte able to colonize the interior of many economically relevant crops such as rice, wheat, corn and sorghum. Under iron-deficient conditions, this organism secretes serobactins, a suite of lipopetide siderophores. The role of siderophores in the interaction between endophytes and their plant hosts are not well understood. In this work, we aimed to determine the importance of serobactins-mediated iron acquisition systems in the interaction of H. seropedicae with rice plants. First we provide evidence, by using a combination of genome analysis, proteomic and genetic studies, that the Hsero_2345 gene encodes a TonB-dependent receptor involved in iron-serobactin complex internalization when iron bioavailability is low. Our results show that survival of the Hsero_2345 mutant inside rice plants was not significantly different from that of the wild-type strain. However, when plants were co-inoculated at equal ratios with the wild-type strain and with a double mutant defective in serobactins synthesis and internalization, recovery of mutant was significantly impaired after 8 days post-inoculation. These results demonstrate that serobactins-mediated iron acquisition contributes to competitive fitness of H. seropedicae inside host plants.
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Affiliation(s)
- Federico Rosconi
- Departamento de Bioquímica y Genómica Microbianas, IIBCE, Montevideo, Uruguay
| | - María F Trovero
- Departamento de Bioquímica y Genómica Microbianas, IIBCE, Montevideo, Uruguay
| | | | - Elena Fabiano
- Departamento de Bioquímica y Genómica Microbianas, IIBCE, Montevideo, Uruguay
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35
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Tyrrell J, Callaghan M. Iron acquisition in the cystic fibrosis lung and potential for novel therapeutic strategies. MICROBIOLOGY-SGM 2015; 162:191-205. [PMID: 26643057 DOI: 10.1099/mic.0.000220] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Iron acquisition is vital to microbial survival and is implicated in the virulence of many of the pathogens that reside in the cystic fibrosis (CF) lung. The multifaceted nature of iron acquisition by both bacterial and fungal pathogens encompasses a range of conserved and species-specific mechanisms, including secretion of iron-binding siderophores, utilization of siderophores from other species, release of iron from host iron-binding proteins and haemoproteins, and ferrous iron uptake. Pathogens adapt and deploy specific systems depending on iron availability, bioavailability of the iron pool, stage of infection and presence of competing pathogens. Understanding the dynamics of pathogen iron acquisition has the potential to unveil new avenues for therapeutic intervention to treat both acute and chronic CF infections. Here, we examine the range of strategies utilized by the primary CF pathogens to acquire iron and discuss the different approaches to targeting iron acquisition systems as an antimicrobial strategy.
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Affiliation(s)
- Jean Tyrrell
- Centre of Microbial Host Interactions, Institute of Technology Tallaght, Dublin D24KT9, Ireland
| | - Máire Callaghan
- Centre of Microbial Host Interactions, Institute of Technology Tallaght, Dublin D24KT9, Ireland
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36
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Tyrrell J, Whelan N, Wright C, Sá-Correia I, McClean S, Thomas M, Callaghan M. Investigation of the multifaceted iron acquisition strategies of Burkholderia cenocepacia. Biometals 2015; 28:367-80. [DOI: 10.1007/s10534-015-9840-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 02/18/2015] [Indexed: 10/23/2022]
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