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Rosa-Núñez E, Echavarri-Erasun C, Armas AM, Escudero V, Poza-Carrión C, Rubio LM, González-Guerrero M. Iron Homeostasis in Azotobacter vinelandii. BIOLOGY 2023; 12:1423. [PMID: 37998022 PMCID: PMC10669500 DOI: 10.3390/biology12111423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023]
Abstract
Iron is an essential nutrient for all life forms. Specialized mechanisms exist in bacteria to ensure iron uptake and its delivery to key enzymes within the cell, while preventing toxicity. Iron uptake and exchange networks must adapt to the different environmental conditions, particularly those that require the biosynthesis of multiple iron proteins, such as nitrogen fixation. In this review, we outline the mechanisms that the model diazotrophic bacterium Azotobacter vinelandii uses to ensure iron nutrition and how it adapts Fe metabolism to diazotrophic growth.
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Affiliation(s)
- Elena Rosa-Núñez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Campus de Montegancedo UPM, Crta. M-40 km 38, 28223 Madrid, Spain; (E.R.-N.); (C.E.-E.); (A.M.A.); (C.P.-C.); (L.M.R.)
- Escuela Técnica de Ingeniería Agraria, Alimentaria, y de Biosistemas, Universidad Politécnica de Madrid, Avda. Puerta de Hierro, 2, 28040 Madrid, Spain
| | - Carlos Echavarri-Erasun
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Campus de Montegancedo UPM, Crta. M-40 km 38, 28223 Madrid, Spain; (E.R.-N.); (C.E.-E.); (A.M.A.); (C.P.-C.); (L.M.R.)
- Escuela Técnica de Ingeniería Agraria, Alimentaria, y de Biosistemas, Universidad Politécnica de Madrid, Avda. Puerta de Hierro, 2, 28040 Madrid, Spain
| | - Alejandro M. Armas
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Campus de Montegancedo UPM, Crta. M-40 km 38, 28223 Madrid, Spain; (E.R.-N.); (C.E.-E.); (A.M.A.); (C.P.-C.); (L.M.R.)
| | - Viviana Escudero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Campus de Montegancedo UPM, Crta. M-40 km 38, 28223 Madrid, Spain; (E.R.-N.); (C.E.-E.); (A.M.A.); (C.P.-C.); (L.M.R.)
| | - César Poza-Carrión
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Campus de Montegancedo UPM, Crta. M-40 km 38, 28223 Madrid, Spain; (E.R.-N.); (C.E.-E.); (A.M.A.); (C.P.-C.); (L.M.R.)
| | - Luis M. Rubio
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Campus de Montegancedo UPM, Crta. M-40 km 38, 28223 Madrid, Spain; (E.R.-N.); (C.E.-E.); (A.M.A.); (C.P.-C.); (L.M.R.)
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Campus de Montegancedo UPM, Crta. M-40 km 38, 28223 Madrid, Spain; (E.R.-N.); (C.E.-E.); (A.M.A.); (C.P.-C.); (L.M.R.)
- Escuela Técnica de Ingeniería Agraria, Alimentaria, y de Biosistemas, Universidad Politécnica de Madrid, Avda. Puerta de Hierro, 2, 28040 Madrid, Spain
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2
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Vind K, Brunati C, Simone M, Sosio M, Donadio S, Iorio M. Megalochelin, a Tridecapeptide Siderophore from a Talented Streptomycete. ACS Chem Biol 2023; 18:861-874. [PMID: 36920304 PMCID: PMC10127220 DOI: 10.1021/acschembio.2c00958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/06/2023] [Indexed: 03/16/2023]
Abstract
Streptomycetes are bacteria known for their extraordinary biosynthetic capabilities. Herein, we describe the genome and metabolome of a particularly talented strain, Streptomyces ID71268. Its 8.4-Mbp genome harbors 32 bioinformatically predicted biosynthetic gene clusters (BGCs), out of which 10 are expressed under a single experimental condition. In addition to five families of known metabolites with previously assigned BGCs (nigericin, azalomycin F, ectoine, SF2766, and piericidin), we were able to predict BGCs for three additional metabolites: streptochlorin, serpetene, and marinomycin. The strain also produced two families of presumably novel metabolites, one of which was associated with growth inhibitory activity against the human opportunistic pathogen Acinetobacter baumannii in an iron-dependent manner. Bioassay-guided fractionation, followed by extensive liquid chromatography-mass spectrometry (LC-MS) and NMR analyses, established that the molecule responsible for the observed antibacterial activity is an unusual tridecapeptide siderophore with a ring-and-tail structure: the heptapeptide ring is formed through a C-C bond between a 2,3-dihydroxybenzoate (DHB) cap on Gly1 and the imidazole moiety of His7, while the hexapeptide tail is sufficient for binding iron. This molecule, named megalochelin, is the largest known siderophore. The megalochelin BGC encodes a 13-module nonribosomal peptide synthetase for the synthesis of the tridecapeptide, and a copper-dependent oxidase, likely responsible for the DHB-imidazole cross-link, whereas the genes for synthesis of the DHB starter unit are apparently specified in trans by a different BGC. Our results suggest that prolific producers of specialized metabolites may conceal hidden treasures within a background of known compounds.
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Affiliation(s)
- Kristiina Vind
- NAICONS
Srl, 20139 Milan, Italy
- Host-Microbe
Interactomics Group, Wageningen University, 6708 WD Wageningen, The Netherlands
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Timofeeva AM, Galyamova MR, Sedykh SE. Bacterial Siderophores: Classification, Biosynthesis, Perspectives of Use in Agriculture. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223065. [PMID: 36432794 PMCID: PMC9694258 DOI: 10.3390/plants11223065] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 06/07/2023]
Abstract
Siderophores are synthesized and secreted by many bacteria, yeasts, fungi, and plants for Fe (III) chelation. A variety of plant-growth-promoting bacteria (PGPB) colonize the rhizosphere and contribute to iron assimilation by plants. These microorganisms possess mechanisms to produce Fe ions under iron-deficient conditions. Under appropriate conditions, they synthesize and release siderophores, thereby increasing and regulating iron bioavailability. This review focuses on various bacterial strains that positively affect plant growth and development through synthesizing siderophores. Here we discuss the diverse chemical nature of siderophores produced by plant root bacteria; the life cycle of siderophores, from their biosynthesis to the Fe-siderophore complex degradation; three mechanisms of siderophore biosynthesis in bacteria; the methods for analyzing siderophores and the siderophore-producing activity of bacteria and the methods for screening the siderophore-producing activity of bacterial colonies. Further analysis of biochemical, molecular-biological, and physiological features of siderophore synthesis by bacteria and their use by plants will allow one to create effective microbiological preparations for improving soil fertility and increasing plant biomass, which is highly relevant for sustainable agriculture.
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Affiliation(s)
- Anna M. Timofeeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia
| | - Maria R. Galyamova
- Center for Entrepreneurial Initiatives, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Sergey E. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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4
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Zhang X, Baars O, Morel FMM. Genetic, structural, and functional diversity of low and high-affinity siderophores in strains of nitrogen fixing Azotobacter chroococcum. Metallomics 2020; 11:201-212. [PMID: 30444515 DOI: 10.1039/c8mt00236c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To increase iron (Fe) bioavailability in surface soils, microbes secrete siderophores, chelators with widely varying Fe affinities. Strains of the soil bacterium Azotobacter chroococcum (AC), plant-growth promoting rhizobacteria used as agricultural inoculants, require high Fe concentrations for aerobic respiration and nitrogen fixation. Recently, A. chroococcum str. NCIMB 8003 was shown to synthesize three siderophore classes: (1) vibrioferrin, a low-affinity α-hydroxy carboxylate (pFe = 18.4), (2) amphibactins, high-affinity tris-hydroxamates, and (3) crochelin A, a high-affinity siderophore with mixed Fe-chelating groups (pFe = 23.9). The relevance and specific functions of these siderophores in AC strains remain unclear. We analyzed the genome and siderophores of a second AC strain, A. chroococcum str. B3, and found that it also produces vibrioferrin and amphibactins, but not crochelin A. Genome comparisons indicate that vibrioferrin production is a vertically inherited, conserved strategy for Fe uptake in A. chroococcum and other species of Azotobacter. Amphibactin and crochelin biosynthesis reflects a more complex evolutionary history, shaped by vertical gene transfer, gene gain and loss through recombination at a genomic hotspot. We found conserved patterns of low vs. high-affinity siderophore production across strains: the low-affinity vibrioferrin was produced by mildly Fe limited cultures. As cells became more severely Fe starved, vibrioferrin production decreased in favor of high-affinity amphibactins (str. B3, NCIMB 8003) and crochelin A (str. NCIMB 8003). Our results show the evolution of low and high-affinity siderophore families and conserved patterns for their production in response to Fe bioavailability in a common soil diazotroph.
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Affiliation(s)
- Xinning Zhang
- Department of Geosciences, Princeton University, USA.
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An effective approach of bacterial siderophore as nitrogen source triggering the desired biochemical changes in microalgae Chlorella variabilis ATCC 12198. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Nosrati R, Dehghani S, Karimi B, Yousefi M, Taghdisi SM, Abnous K, Alibolandi M, Ramezani M. Siderophore-based biosensors and nanosensors; new approach on the development of diagnostic systems. Biosens Bioelectron 2018; 117:1-14. [DOI: 10.1016/j.bios.2018.05.057] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/19/2018] [Accepted: 05/29/2018] [Indexed: 02/06/2023]
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Khan A, Singh P, Srivastava A. Synthesis, nature and utility of universal iron chelator - Siderophore: A review. Microbiol Res 2017; 212-213:103-111. [PMID: 29103733 DOI: 10.1016/j.micres.2017.10.012] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 10/10/2017] [Accepted: 10/27/2017] [Indexed: 12/16/2022]
Abstract
Siderophores, the secondary metabolite of various microorganisms are ferric ion specific chelators secreted under iron stressed condition. These non-ribosomal peptides have been classified as catecholate, hydroxamate, carboxylate and mixed types. Recent studies focus on discovery of possible mammalian siderophores. The biosynthesis pathway including non-ribosomal dependent as well as non-ribosomal independent pathways are of great interest now a days. Many significant roles of siderophores such as virulence in pathogens, oxidative stress tolerance, classification of organisms etc. are being discovered. Studies on siderophore utilization in bioremediation and other heavy metal chelation have increased in past decade. The iron chelation ability of siderophores is being recently studied with regards to malignant cancerous cells. Not only this, it has been found that they possess antimicrobial properties which can be utilized against number of microbes. This review covers all recent aspects of siderophore and its applications.
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Affiliation(s)
- Azmi Khan
- Life Science Programme, Centre for Biological Sciences, Central University of South Bihar, Patna 800014, India
| | - Pratika Singh
- Life Science Programme, Centre for Biological Sciences, Central University of South Bihar, Patna 800014, India
| | - Amrita Srivastava
- Life Science Programme, Centre for Biological Sciences, Central University of South Bihar, Patna 800014, India.
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Transcriptional Analysis of an Ammonium-Excreting Strain of Azotobacter vinelandii Deregulated for Nitrogen Fixation. Appl Environ Microbiol 2017; 83:AEM.01534-17. [PMID: 28802272 DOI: 10.1128/aem.01534-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 08/07/2017] [Indexed: 11/20/2022] Open
Abstract
Biological nitrogen fixation is accomplished by a diverse group of organisms known as diazotrophs and requires the function of the complex metalloenzyme nitrogenase. Nitrogenase and many of the accessory proteins required for proper cofactor biosynthesis and incorporation into the enzyme have been characterized, but a complete picture of the reaction mechanism and key cellular changes that accompany biological nitrogen fixation remain to be fully elucidated. Studies have revealed that specific disruptions of the antiactivator-encoding gene nifL result in the deregulation of the nif transcriptional activator NifA in the nitrogen-fixing bacterium Azotobacter vinelandii, triggering the production of extracellular ammonium levels approaching 30 mM during the stationary phase of growth. In this work, we have characterized the global patterns of gene expression of this high-ammonium-releasing phenotype. The findings reported here indicated that cultures of this high-ammonium-accumulating strain may experience metal limitation when grown using standard Burk's medium, which could be amended by increasing the molybdenum levels to further increase the ammonium yield. In addition, elevated levels of nitrogenase gene transcription are not accompanied by a corresponding dramatic increase in hydrogenase gene transcription levels or hydrogen uptake rates. Of the three potential electron donor systems for nitrogenase, only the rnf1 gene cluster showed a transcriptional correlation to the increased yield of ammonium. Our results also highlight several additional genes that may play a role in supporting elevated ammonium production in this aerobic nitrogen-fixing model bacterium.IMPORTANCE The transcriptional differences found during stationary-phase ammonium accumulation show a strong contrast between the deregulated (nifL-disrupted) and wild-type strains and what was previously reported for the wild-type strain under exponential-phase growth conditions. These results demonstrate that further improvement of the ammonium yield in this nitrogenase-deregulated strain can be obtained by increasing the amount of available molybdenum in the medium. These results also indicate a potential preference for one of two ATP synthases present in A. vinelandii as well as a prominent role for the membrane-bound hydrogenase over the soluble hydrogenase in hydrogen gas recycling. These results should inform future studies aimed at elucidating the important features of this phenotype and at maximizing ammonium production by this strain.
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McRose DL, Baars O, Morel FMM, Kraepiel AML. Siderophore production in
Azotobacter vinelandii
in response to Fe‐, Mo‐ and V‐limitation. Environ Microbiol 2017; 19:3595-3605. [DOI: 10.1111/1462-2920.13857] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/08/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Darcy L. McRose
- Department of GeosciencesPrinceton UniversityPrinceton NJ 08544 USA
| | - Oliver Baars
- Department of GeosciencesPrinceton UniversityPrinceton NJ 08544 USA
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10
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Eberhart LJ, Knutson CM, Barney BM. A methodology for markerless genetic modifications in Azotobacter vinelandii. J Appl Microbiol 2017; 120:1595-604. [PMID: 26854474 DOI: 10.1111/jam.13091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 01/29/2016] [Accepted: 01/30/2016] [Indexed: 01/03/2023]
Abstract
AIMS Efficient manipulation of multiple regions within a genome can be improved by counter-selection approaches. In this work, we sought to develop a method to manipulate Azotobacter vinelandii using a counter-selection approach based on the presence of the pyrF gene. METHODS AND RESULTS A background uracil auxotroph of A. vinelandii was first constructed by deleting the pyrF gene coding orotidine-5'-phosphate decarboxylase. The pyrF gene and promoter were also incorporated together with an antibiotic marker to create a selection and counter-selection cassette to shuttle into various plasmids. The constructed cassette could then be removed using a plasmid lacking the pyrF gene via counter-selection resulting from the production of 5-fluorouracil. The process could be repeated multiple times using the same procedure for selection and counter-selection. Following completion, the pyrF gene may be reintroduced to the genome in its original location, leaving a completed strain devoid of any antibiotic markers. CONCLUSIONS Utilization of the pyrF gene for counter-selection is a powerful tool that can be used effectively to make multiple gene deletions in A. vinelandii. SIGNIFICANCE AND IMPACT OF THE STUDY This study demonstrates the successful application of a counter-selection approach to yield markerless genetic modifications to A. vinelandii, which should be of interest for a range of applications in this important model bacterium.
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Affiliation(s)
- L J Eberhart
- Department of Bioproducts and Biosystems Engineering, Biotechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - C M Knutson
- Department of Bioproducts and Biosystems Engineering, Biotechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - B M Barney
- Department of Bioproducts and Biosystems Engineering, Biotechnology Institute, University of Minnesota, St. Paul, MN, USA
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Puopolo G, Tomada S, Sonego P, Moretto M, Engelen K, Perazzolli M, Pertot I. The Lysobacter capsici AZ78 Genome Has a Gene Pool Enabling it to Interact Successfully with Phytopathogenic Microorganisms and Environmental Factors. Front Microbiol 2016; 7:96. [PMID: 26903975 PMCID: PMC4742617 DOI: 10.3389/fmicb.2016.00096] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/18/2016] [Indexed: 01/26/2023] Open
Abstract
Lysobacter capsici AZ78 has considerable potential for biocontrol of phytopathogenic microorganisms. However, lack of information about genetic cues regarding its biological characteristics may slow down its exploitation as a biofungicide. In order to obtain a comprehensive overview of genetic features, the L. capsici AZ78 genome was sequenced, annotated and compared with the phylogenetically related pathogens Stenotrophomonas malthophilia K729a and Xanthomonas campestris pv. campestris ATCC 33913. Whole genome comparison, supported by functional analysis, indicated that L. capsici AZ78 has a larger number of genes responsible for interaction with phytopathogens and environmental stress than S. malthophilia K729a and X. c. pv. campestris ATCC 33913. Genes involved in the production of antibiotics, lytic enzymes and siderophores were specific for L. capsici AZ78, as well as genes involved in resistance to antibiotics, environmental stressors, fungicides and heavy metals. The L. capsici AZ78 genome did not encompass genes involved in infection of humans and plants included in the S. malthophilia K729a and X. c. pv. campestris ATCC 33913 genomes, respectively. The L. capsici AZ78 genome provides a genetic framework for detailed analysis of other L. capsici members and the development of novel biofungicides based on this bacterial strain.
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Affiliation(s)
- Gerardo Puopolo
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach San Michele all'Adige, Italy
| | - Selena Tomada
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy; Department of Agricultural and Environmental Science (DISA), PhD School of Agricultural Science and Biotechnology, University of UdineUdine, Italy
| | - Paolo Sonego
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach San Michele all'Adige, Italy
| | - Marco Moretto
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach San Michele all'Adige, Italy
| | - Kristof Engelen
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach San Michele all'Adige, Italy
| | - Michele Perazzolli
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach San Michele all'Adige, Italy
| | - Ilaria Pertot
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach San Michele all'Adige, Italy
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13
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Baars O, Zhang X, Morel FMM, Seyedsayamdost MR. The Siderophore Metabolome of Azotobacter vinelandii. Appl Environ Microbiol 2016; 82:27-39. [PMID: 26452553 PMCID: PMC4702634 DOI: 10.1128/aem.03160-15] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 10/02/2015] [Indexed: 12/14/2022] Open
Abstract
In this study, we performed a detailed characterization of the siderophore metabolome, or "chelome," of the agriculturally important and widely studied model organism Azotobacter vinelandii. Using a new high-resolution liquid chromatography-mass spectrometry (LC-MS) approach, we found over 35 metal-binding secondary metabolites, indicative of a vast chelome in A. vinelandii. These include vibrioferrin, a siderophore previously observed only in marine bacteria. Quantitative analyses of siderophore production during diazotrophic growth with different sources and availabilities of Fe showed that, under all tested conditions, vibrioferrin was present at the highest concentration of all siderophores and suggested new roles for vibrioferrin in the soil environment. Bioinformatic searches confirmed the capacity for vibrioferrin production in Azotobacter spp. and other bacteria spanning multiple phyla, habitats, and lifestyles. Moreover, our studies revealed a large number of previously unreported derivatives of all known A. vinelandii siderophores and rationalized their origins based on genomic analyses, with implications for siderophore diversity and evolution. Together, these insights provide clues as to why A. vinelandii harbors multiple siderophore biosynthesis gene clusters. Coupled with the growing evidence for alternative functions of siderophores, the vast chelome in A. vinelandii may be explained by multiple, disparate evolutionary pressures that act on siderophore production.
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Affiliation(s)
- Oliver Baars
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
| | - Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
| | - François M M Morel
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
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Robson RL, Jones R, Robson RM, Schwartz A, Richardson TH. Azotobacter Genomes: The Genome of Azotobacter chroococcum NCIMB 8003 (ATCC 4412). PLoS One 2015; 10:e0127997. [PMID: 26061173 PMCID: PMC4465626 DOI: 10.1371/journal.pone.0127997] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 04/22/2015] [Indexed: 11/18/2022] Open
Abstract
The genome of the soil-dwelling heterotrophic N2-fixing Gram-negative bacterium Azotobacter chroococcum NCIMB 8003 (ATCC 4412) (Ac-8003) has been determined. It consists of 7 circular replicons totalling 5,192,291 bp comprising a circular chromosome of 4,591,803 bp and six plasmids pAcX50a, b, c, d, e, f of 10,435 bp, 13,852, 62,783, 69,713, 132,724, and 311,724 bp respectively. The chromosome has a G+C content of 66.27% and the six plasmids have G+C contents of 58.1, 55.3, 56.7, 59.2, 61.9, and 62.6% respectively. The methylome has also been determined and 5 methylation motifs have been identified. The genome also contains a very high number of transposase/inactivated transposase genes from at least 12 of the 17 recognised insertion sequence families. The Ac-8003 genome has been compared with that of Azotobacter vinelandii ATCC BAA-1303 (Av-DJ), a derivative of strain O, the only other member of the Azotobacteraceae determined so far which has a single chromosome of 5,365,318 bp and no plasmids. The chromosomes show significant stretches of synteny throughout but also reveal a history of many deletion/insertion events. The Ac-8003 genome encodes 4628 predicted protein-encoding genes of which 568 (12.2%) are plasmid borne. 3048 (65%) of these show > 85% identity to the 5050 protein-encoding genes identified in Av-DJ, and of these 99 are plasmid-borne. The core biosynthetic and metabolic pathways and macromolecular architectures and machineries of these organisms appear largely conserved including genes for CO-dehydrogenase, formate dehydrogenase and a soluble NiFe-hydrogenase. The genetic bases for many of the detailed phenotypic differences reported for these organisms have also been identified. Also many other potential phenotypic differences have been uncovered. Properties endowed by the plasmids are described including the presence of an entire aerobic corrin synthesis pathway in pAcX50f and the presence of genes for retro-conjugation in pAcX50c. All these findings are related to the potentially different environmental niches from which these organisms were isolated and to emerging theories about how microbes contribute to their communities.
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Affiliation(s)
- Robert L. Robson
- School of Biological Sciences, University of Reading, Whiteknights, Reading, United Kingdom
| | - Robert Jones
- Craic Computing LLC, Seattle, Washington, United States of America
| | - R. Moyra Robson
- School of Biological Sciences, University of Reading, Whiteknights, Reading, United Kingdom
| | - Ariel Schwartz
- Synthetic Genomics, La Jolla, California, United States of America
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Johnstone TC, Nolan EM. Beyond iron: non-classical biological functions of bacterial siderophores. Dalton Trans 2015; 44:6320-39. [PMID: 25764171 PMCID: PMC4375017 DOI: 10.1039/c4dt03559c] [Citation(s) in RCA: 245] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bacteria secrete small molecules known as siderophores to acquire iron from their surroundings. For over 60 years, investigations into the bioinorganic chemistry of these molecules, including fundamental coordination chemistry studies, have provided insight into the crucial role that siderophores play in bacterial iron homeostasis. The importance of understanding the fundamental chemistry underlying bacterial life has been highlighted evermore in recent years because of the emergence of antibiotic-resistant bacteria and the need to prevent the global rise of these superbugs. Increasing reports of siderophores functioning in capacities other than iron transport have appeared recently, but reports of "non-classical" siderophore functions have long paralleled those of iron transport. One particular non-classical function of these iron chelators, namely antibiotic activity, was documented before the role of siderophores in iron transport was established. In this Perspective, we present an exposition of past and current work into non-classical functions of siderophores and highlight the directions in which we anticipate that this research is headed. Examples include the ability of siderophores to function as zincophores, chalkophores, and metallophores for a variety of other metals, sequester heavy metal toxins, transport boron, act as signalling molecules, regulate oxidative stress, and provide antibacterial activity.
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Affiliation(s)
- Timothy C Johnstone
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Villa JA, Ray EE, Barney BM. Azotobacter vinelandiisiderophore can provide nitrogen to support the culture of the green algaeNeochloris oleoabundansandScenedesmussp. BA032. FEMS Microbiol Lett 2014; 351:70-77. [DOI: 10.1111/1574-6968.12347] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 11/24/2013] [Accepted: 11/24/2013] [Indexed: 11/30/2022] Open
Affiliation(s)
- Juan A. Villa
- Biotechnology Institute; University of Minnesota; St. Paul MN USA
| | - Erin E. Ray
- Department of Bioproducts and Biosystems Engineering; University of Minnesota; St. Paul MN USA
| | - Brett M. Barney
- Biotechnology Institute; University of Minnesota; St. Paul MN USA
- Department of Bioproducts and Biosystems Engineering; University of Minnesota; St. Paul MN USA
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Deicke M, Bellenger JP, Wichard T. Direct quantification of bacterial molybdenum and iron metallophores with ultra-high-performance liquid chromatography coupled to time-of-flight mass spectrometry. J Chromatogr A 2013; 1298:50-60. [DOI: 10.1016/j.chroma.2013.05.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 04/30/2013] [Accepted: 05/02/2013] [Indexed: 10/26/2022]
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