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Thompson MEH, Raizada MN. The Microbiome of Fertilization-Stage Maize Silks (Style) Encodes Genes and Expresses Traits That Potentially Promote Survival in Pollen/Style Niches and Host Reproduction. Microorganisms 2024; 12:1473. [PMID: 39065240 PMCID: PMC11278993 DOI: 10.3390/microorganisms12071473] [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: 06/27/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Within flowers, the style channel receives pollen and transmits male gametes inside elongating pollen tubes to ovules. The styles of maize/corn are called silks. Fertilization-stage silks possess complex microbiomes, which may partially derive from pollen. These microbiomes lack functional analysis. We hypothesize that fertilization-stage silk microbiomes promote host fertilization to ensure their own vertical transmission. We further hypothesize that these microbes encode traits to survive stresses within the silk (water/nitrogen limitation) and pollen (dehydration/aluminum) habitats. Here, bacteria cultured from fertilization-stage silks of 14 North American maize genotypes underwent genome mining and functional testing, which revealed osmoprotection, nitrogen-fixation, and aluminum-tolerance traits. Bacteria contained auxin biosynthesis genes, and testing confirmed indole compound secretion, which is relevant, since pollen delivers auxin to silks to stimulate egg cell maturation. Some isolates encoded biosynthetic/transport compounds known to regulate pollen tube guidance/growth. The isolates encoded ACC deaminase, which degrades the precursor for ethylene that otherwise accelerates silk senescence. The findings suggest that members of the microbiome of fertilization-stage silks encode adaptations to survive the stress conditions of silk/pollen and have the potential to express signaling compounds known to impact reproduction. Overall, whereas these microbial traits have traditionally been assumed to primarily promote vegetative plant growth, this study proposes they may also play selfish roles during host reproduction.
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Affiliation(s)
| | - Manish N. Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada;
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2
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Li X, Li Z. What determines symbiotic nitrogen fixation efficiency in rhizobium: recent insights into Rhizobium leguminosarum. Arch Microbiol 2023; 205:300. [PMID: 37542687 DOI: 10.1007/s00203-023-03640-7] [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: 06/01/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/07/2023]
Abstract
Symbiotic nitrogen fixation (SNF) by rhizobium, a Gram-negative soil bacterium, is an essential component in the nitrogen cycle and is a sustainable green way to maintain soil fertility without chemical energy consumption. SNF, which results from the processes of nodulation, rhizobial infection, bacteroid differentiation and nitrogen-fixing reaction, requires the expression of various genes from both symbionts with adaptation to the changing environment. To achieve successful nitrogen fixation, rhizobia and their hosts cooperate closely for precise regulation of symbiotic genes, metabolic processes and internal environment homeostasis. Many researches have progressed to reveal the ample information about regulatory aspects of SNF during recent decades, but the major bottlenecks regarding improvement of nitrogen-fixing efficiency has proven to be complex. In this mini-review, we summarize recent advances that have contributed to understanding the rhizobial regulatory aspects that determine SNF efficiency, focusing on the coordinated regulatory mechanism of symbiotic genes, oxygen, carbon metabolism, amino acid metabolism, combined nitrogen, non-coding RNAs and internal environment homeostasis. Unraveling regulatory determinants of SNF in the nitrogen-fixing protagonist rhizobium is expected to promote an improvement of nitrogen-fixing efficiency in crop production.
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Affiliation(s)
- Xiaofang Li
- Institute of Biopharmaceuticals, Taizhou University, 1139 Shifu Avenue, Taizhou, 318000, China.
- School of Pharmaceutical Sciences, Taizhou University, 1139 Shifu Avenue, Taizhou, 318000, China.
| | - Zhangqun Li
- School of Pharmaceutical Sciences, Taizhou University, 1139 Shifu Avenue, Taizhou, 318000, China
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3
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Mihelj P, Abreu I, Moreyra T, González-Guerrero M, Raimunda D. Functional Characterization of the Co 2+ Transporter AitP in Sinorhizobium meliloti: A New Player in Fe 2+ Homeostasis. Appl Environ Microbiol 2023; 89:e0190122. [PMID: 36853042 PMCID: PMC10057888 DOI: 10.1128/aem.01901-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/27/2023] [Indexed: 03/01/2023] Open
Abstract
Co2+ induces the increase of the labile-Fe pool (LIP) by Fe-S cluster damage, heme synthesis inhibition, and "free" iron import, which affects cell viability. The N2-fixing bacteria, Sinorhizobium meliloti, is a suitable model to determine the roles of Co2+-transporting cation diffusion facilitator exporters (Co-eCDF) in Fe2+ homeostasis because it has a putative member of this subfamily, AitP, and two specific Fe2+-export systems. An insertional mutant of AitP showed Co2+ sensitivity and accumulation, Fe accumulation and hydrogen peroxide sensitivity, but not Fe2+ sensitivity, despite AitP being a bona fide low affinity Fe2+ exporter as demonstrated by the kinetic analyses of Fe2+ uptake into everted membrane vesicles. Suggesting concomitant Fe2+-dependent induced stress, Co2+ sensitivity was increased in strains carrying mutations in AitP and Fe2+ exporters which did not correlate with the Co2+ accumulation. Growth in the presence of sublethal Fe2+ and Co2+ concentrations suggested that free Fe-import might contribute to Co2+ toxicity. Supporting this, Co2+ induced transcription of Fe-import system and genes associated with Fe homeostasis. Analyses of total protoporphyrin content indicates Fe-S cluster attack as the major source for LIP. AitP-mediated Fe2+-export is likely counterbalanced via a nonfutile Fe2+-import pathway. Two lines of evidence support this: (i) an increased hemin uptake in the presence of Co2+ was observed in wild-type (WT) versus AitP mutant, and (ii) hemin reversed the Co2+ sensitivity in the AitP mutant. Thus, the simultaneous detoxification mediated by AitP aids cells to orchestrate an Fe-S cluster salvage response, avoiding the increase in the LIP caused by the disassembly of Fe-S clusters or free iron uptake. IMPORTANCE Cross-talk between iron and cobalt has been long recognized in biological systems. This is due to the capacity of cobalt to interfere with proper iron utilization. Cells can detoxify cobalt by exporting mechanisms involving membrane proteins known as exporters. Highlighting the cross-talk, the capacity of several cobalt exporters to also export iron is emerging. Although biologically less important than Fe2+, Co2+ induces toxicity by promoting intracellular Fe release, which ultimately causes additional toxic effects. In this work, we describe how the rhizobia cells solve this perturbation by clearing Fe through a Co2+ exporter, in order to reestablish intracellular Fe levels by importing nonfree Fe, heme. This piggyback-ride type of transport may aid bacterial cells to survive in free-living conditions where high anthropogenic Co2+ content may be encountered.
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Affiliation(s)
- Paula Mihelj
- Instituto de Investigación Médica Mercedes y Martín Ferreyra-INIMEC-CONICET, UNC, Córdoba, Argentina
| | - Isidro Abreu
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
| | - Tomás Moreyra
- Instituto de Investigación Médica Mercedes y Martín Ferreyra-INIMEC-CONICET, UNC, Córdoba, Argentina
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Daniel Raimunda
- Instituto de Investigación Médica Mercedes y Martín Ferreyra-INIMEC-CONICET, UNC, Córdoba, Argentina
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Zhao Y, Kong M, Yang J, Zhao X, Shi Y, Zhai Y, Qiu J, Zheng C. The DmeRF System Is Involved in Maintaining Cobalt Homeostasis in Vibrio parahaemolyticus. Int J Mol Sci 2022; 24:ijms24010414. [PMID: 36613858 PMCID: PMC9820535 DOI: 10.3390/ijms24010414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/18/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Although cobalt (Co) is indispensable for life, it is toxic to cells when accumulated in excess. The DmeRF system is a well-characterized metal-response system that contributes to Co and nickel resistance in certain bacterial species. The Vibrio parahaemolyticus RIMD 2210633 genome also harbors a dmeRF operon that encodes a multiple antibiotic resistance regulator family transcriptional regulator and a cation diffusion facilitator family protein. Quantitative real-time PCR, growth curves analysis, inductively coupled plasma-mass spectrometry, β-galactosidase activity assays, electrophoretic mobility shift assays, and a mouse infection experiment were performed to characterize the function of the DmeRF system in V. parahaemolyticus. Zinc, copper, and Co significantly increase dmeF expression, with Co inducing the greatest increase. DmeF promotes V. parahaemolyticus growth under high-Co conditions. Additionally, increased accumulation of cellular Co in the ΔdmeF mutant indicates that DmeF is potentially involved in Co efflux. Moreover, DmeR represses the dmeRF operon by binding directly to its promoter in the absence of Co. Finally, the DmeRF system was not required for V. parahaemolyticus virulence in mice. Collectively, our data indicate that the DmeRF system is involved in maintaining Co homeostasis in V. parahaemolyticus and DmeR functioning as a repressor of the operon.
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Affiliation(s)
- Yuxuan Zhao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of MOE, Yangzhou University, Yangzhou 225009, China
| | - Mengyao Kong
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of MOE, Yangzhou University, Yangzhou 225009, China
| | - Jiaxue Yang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of MOE, Yangzhou University, Yangzhou 225009, China
| | - Xiaoxian Zhao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of MOE, Yangzhou University, Yangzhou 225009, China
| | - Yiran Shi
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of MOE, Yangzhou University, Yangzhou 225009, China
| | - Yimeng Zhai
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of MOE, Yangzhou University, Yangzhou 225009, China
| | - Jun Qiu
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of MOE, Yangzhou University, Yangzhou 225009, China
| | - Chengkun Zheng
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of MOE, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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Signaling and Detoxification Strategies in Plant-Microbes Symbiosis under Heavy Metal Stress: A Mechanistic Understanding. Microorganisms 2022; 11:microorganisms11010069. [PMID: 36677361 PMCID: PMC9865731 DOI: 10.3390/microorganisms11010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Plants typically interact with a variety of microorganisms, including bacteria, mycorrhizal fungi, and other organisms, in their above- and below-ground parts. In the biosphere, the interactions of plants with diverse microbes enable them to acquire a wide range of symbiotic advantages, resulting in enhanced plant growth and development and stress tolerance to toxic metals (TMs). Recent studies have shown that certain microorganisms can reduce the accumulation of TMs in plants through various mechanisms and can reduce the bioavailability of TMs in soil. However, relevant progress is lacking in summarization. This review mechanistically summarizes the common mediating pathways, detoxification strategies, and homeostatic mechanisms based on the research progress of the joint prevention and control of TMs by arbuscular mycorrhizal fungi (AMF)-plant and Rhizobium-plant interactions. Given the importance of tripartite mutualism in the plant-microbe system, it is necessary to further explore key signaling molecules to understand the role of plant-microbe mutualism in improving plant tolerance under heavy metal stress in the contaminated soil environments. It is hoped that our findings will be useful in studying plant stress tolerance under a broad range of environmental conditions and will help in developing new technologies for ensuring crop health and performance in future.
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6
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The Cell Membrane of a Novel Rhizobium phaseoli Strain Is the Crucial Target for Aluminium Toxicity and Tolerance. Cells 2022; 11:cells11050873. [PMID: 35269493 PMCID: PMC8909678 DOI: 10.3390/cells11050873] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/17/2022] [Accepted: 02/28/2022] [Indexed: 01/01/2023] Open
Abstract
Soils with low pH and high aluminium (Al) contamination restrict common bean production, mainly due to adverse effects on rhizobia. We isolated a novel rhizobium strain, B3, from Kenyan soil which is more tolerant to Al stress than the widely used commercial strain CIAT899. B3 was resistant to 50 µM Al and recovered from 100 µM Al stress, while CIAT899 did not. Calcein labeling showed that less Al binds to the B3 membranes and less ATP and mScarlet-1 protein, a cytoplasmic marker, leaked out of B3 than CIAT899 cells in Al-containing media. Expression profiles showed that the primary targets of Al are genes involved in membrane biogenesis, metal ions binding and transport, carbohydrate, and amino acid metabolism and transport. The identified differentially expressed genes suggested that the intracellular γ-aminobutyric acid (GABA), glutathione (GSH), and amino acid levels, as well as the amount of the extracellular exopolysaccharide (EPS), might change during Al stress. Altered EPS levels could also influence biofilm formation. Therefore, these parameters were investigated in more detail. The GABA levels, extracellular EPS production, and biofilm formation increased, while GSH and amino acid level decreased. In conclusion, our comparative analysis identified genes that respond to Al stress in R. phaseoli. It appears that a large portion of the identified genes code for proteins stabilizing the plasma membrane. These genes might be helpful for future studies investigating the molecular basis of Al tolerance and the characterization of candidate rhizobial isolates that perform better in Al-contaminated soils than commercial strains.
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Osman D, Cooke A, Young TR, Deery E, Robinson NJ, Warren MJ. The requirement for cobalt in vitamin B 12: A paradigm for protein metalation. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2021; 1868:118896. [PMID: 33096143 PMCID: PMC7689651 DOI: 10.1016/j.bbamcr.2020.118896] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022]
Abstract
Vitamin B12, cobalamin, is a cobalt-containing ring-contracted modified tetrapyrrole that represents one of the most complex small molecules made by nature. In prokaryotes it is utilised as a cofactor, coenzyme, light sensor and gene regulator yet has a restricted role in assisting only two enzymes within specific eukaryotes including mammals. This deployment disparity is reflected in another unique attribute of vitamin B12 in that its biosynthesis is limited to only certain prokaryotes, with synthesisers pivotal in establishing mutualistic microbial communities. The core component of cobalamin is the corrin macrocycle that acts as the main ligand for the cobalt. Within this review we investigate why cobalt is paired specifically with the corrin ring, how cobalt is inserted during the biosynthetic process, how cobalt is made available within the cell and explore the cellular control of cobalt and cobalamin levels. The partitioning of cobalt for cobalamin biosynthesis exemplifies how cells assist metalation.
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Affiliation(s)
- Deenah Osman
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Anastasia Cooke
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Tessa R Young
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Nigel J Robinson
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; Biomedical Research Centre, University of East Anglia, Norwich NR4 7TJ, UK.
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Abreu I, Mihelj P, Raimunda D. Transition metal transporters in rhizobia: tuning the inorganic micronutrient requirements to different living styles. Metallomics 2020; 11:735-755. [PMID: 30734808 DOI: 10.1039/c8mt00372f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A group of bacteria known as rhizobia are key players in symbiotic nitrogen fixation (SNF) in partnership with legumes. After a molecular exchange, the bacteria end surrounded by a plant membrane forming symbiosomes, organelle-like structures, where they differentiate to bacteroids and fix nitrogen. This symbiotic process is highly dependent on dynamic nutrient exchanges between the partners. Among these are transition metals (TM) participating as inorganic and organic cofactors of fundamental enzymes. While the understanding of how plant transporters facilitate TMs to the very near environment of the bacteroid is expanding, our knowledge on how bacteroid transporters integrate to TM homeostasis mechanisms in the plant host is still limited. This is significantly relevant considering the low solubility and scarcity of TMs in soils, and the in crescendo gradient of TM bioavailability rhizobia faces during the infection and bacteroid differentiation processes. In the present work, we review the main metal transporter families found in rhizobia, their role in free-living conditions and, when known, in symbiosis. We focus on discussing those transporters which could play a significant role in TM-dependent biochemical and physiological processes in the bacteroid, thus paving the way towards an optimized SNF.
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Affiliation(s)
- Isidro Abreu
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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9
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Abstract
Nickel is essential for the survival of many pathogenic bacteria. E. coli and H. pylori require nickel for [NiFe]-hydrogenases. H. pylori also requires nickel for urease. At high concentrations nickel can be toxic to the cell, therefore, nickel concentrations are tightly regulated. Metalloregulators help to maintain nickel concentration in the cell by regulating the expression of the genes associated with nickel import and export. Nickel import into the cell, delivery of nickel to target proteins, and export of nickel from the cell is a very intricate and well-choreographed process. The delivery of nickel to [NiFe]-hydrogenase and urease is complex and involves several chaperones and accessory proteins. A combination of biochemical, crystallographic, and spectroscopic techniques has been utilized to study the structures of these proteins, as well as protein-protein interactions resulting in an expansion of our knowledge regarding how these proteins sense and bind nickel. In this review, recent advances in the field will be discussed, focusing on the metal site structures of nickel bound to metalloregulators and chaperones.
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Huang HT, Maroney MJ. Ni(II) Sensing by RcnR Does Not Require an FrmR-Like Intersubunit Linkage. Inorg Chem 2019; 58:13639-13653. [PMID: 31247878 DOI: 10.1021/acs.inorgchem.9b01096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
E. coli RcnR (resistance to cobalt and nickel regulator) is a homotetrameric DNA binding protein that regulates the expression of a Ni(II) and Co(II) exporter (RcnAB) by derepressing expression of rcnA and rcnB in response to binding Co(II) or Ni(II). Prior studies have shown that the cognate metal ions, Ni(II) and Co(II), bind in six-coordinate sites at subunit interfaces and are distinguished from noncognate metals (Cu(I), Cu(II), and Zn(II)) by coordination number and ligand selection. In analogy with FrmR, a formaldehyde-responsive transcriptional regulator in the RcnR/CsoR family, the interfacial site allows the metal ions to "cross-link" the N-terminal domain of one subunit with the invariant Cys35 residue in another, which has been deemed to be key to mediating the allosteric response of the tetrameric protein to metal binding. Through the use of mutagenesis to disconnect one subunit from the metal-mediated cross-link, X-ray absorption spectroscopy (XAS) as a structural probe, LacZ reporter assays, and metal binding studies using isothermal titration calorimetry (ITC), the work presented here shows that neither the interfacial binding site nor the coordination number of Ni(II) is important to the allosteric response to binding of this cognate metal ion. The opposite is found for the other cognate metal ion, Co(II), with respect to the interfacial binding site, suggesting that the molecular mechanisms for transcriptional regulation by the two ions are distinct. The metal binding studies reveal that tight metal binding is maintained in the variant. XAS is further used to demonstrate that His33 is not a ligand for Co(II), Ni(II), or Zn(II) in WT-RcnR. The results are discussed in the context of the overall understanding of the molecular mechanisms of metallosensors.
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Fagorzi C, Checcucci A, diCenzo GC, Debiec-Andrzejewska K, Dziewit L, Pini F, Mengoni A. Harnessing Rhizobia to Improve Heavy-Metal Phytoremediation by Legumes. Genes (Basel) 2018; 9:genes9110542. [PMID: 30413093 PMCID: PMC6266702 DOI: 10.3390/genes9110542] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/05/2018] [Accepted: 11/06/2018] [Indexed: 12/15/2022] Open
Abstract
Rhizobia are bacteria that can form symbiotic associations with plants of the Fabaceae family, during which they reduce atmospheric di-nitrogen to ammonia. The symbiosis between rhizobia and leguminous plants is a fundamental contributor to nitrogen cycling in natural and agricultural ecosystems. Rhizobial microsymbionts are a major reason why legumes can colonize marginal lands and nitrogen-deficient soils. Several leguminous species have been found in metal-contaminated areas, and they often harbor metal-tolerant rhizobia. In recent years, there have been numerous efforts and discoveries related to the genetic determinants of metal resistance by rhizobia, and on the effectiveness of such rhizobia to increase the metal tolerance of host plants. Here, we review the main findings on the metal resistance of rhizobia: the physiological role, evolution, and genetic determinants, and the potential to use native and genetically-manipulated rhizobia as inoculants for legumes in phytoremediation practices.
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Affiliation(s)
- Camilla Fagorzi
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - Alice Checcucci
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - George C diCenzo
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - Klaudia Debiec-Andrzejewska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Francesco Pini
- Department of Agri-food Production and Environmental Science, University of Florence, 50144 Florence, Italy.
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
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12
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Li Z, Song X, Wang J, Bai X, Gao E, Wei G. Nickel and cobalt resistance properties of Sinorhizobium meliloti isolated from Medicago lupulina growing in gold mine tailing. PeerJ 2018; 6:e5202. [PMID: 30018859 PMCID: PMC6044271 DOI: 10.7717/peerj.5202] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/18/2018] [Indexed: 12/20/2022] Open
Abstract
Sinorhizobium meliloti CCNWSX0020, isolated from root nodules of Medicago lupulina growing in gold mine tailings in the northwest of China, displayed multiple heavy metal resistance and growth promotion of M. lupulina. In our previous work, the expression level of dmeR and dmeF genes were induced by Cu2+ through comparative transcriptome approach. Based on protein analysis, the dmeF encoded for a protein which showed a 37% similarity to the cation transporter DmeF of Cupriavidus metallidurans, whereas dmeR encoded transcriptional regulator which was highly homologous with DmeR belonging to RcnR/CsoR family metal-responsive transcriptional regulator. In addition to copper, quantitative real-time PCR analysis showed that dmeR and dmeF were also induced by nickel and cobalt. To investigate the functions of dmeR and dmeF in S. meliloti CCNWSX0020, the dmeR and dmeF deletion mutants were constructed. The dmeF mutant was more sensitive to Co2 + and Ni2 + than the wild type strain. Pot experiments were carried out to determine whether the growth of M. lupulina was affected when the dmeF gene was knocked out in the presence of nickel or cobalt. Results indicated that the nodule number of the host plant inoculated with the dmeF deletion mutant was significantly less than the S. meliloti CCNWSX0020 wild-type in the presence of Co2 + or Ni2 +. However, when standardized by nodule fresh weight, the nitrogenase activities of nodules infected by the dmeF deletion mutant was similar to nitrogenase activity of the wild type nodule.
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Affiliation(s)
- Zhefei Li
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shannxi, China
| | - Xiuyong Song
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shannxi, China
| | - Juanjuan Wang
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shannxi, China
| | - Xiaoli Bai
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shannxi, China
| | - Engting Gao
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shannxi, China
| | - Gehong Wei
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shannxi, China.,Northwest A and F University, State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling, Shaanxi, China
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13
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Sánchez-Cañizares C, Jorrín B, Durán D, Nadendla S, Albareda M, Rubio-Sanz L, Lanza M, González-Guerrero M, Prieto RI, Brito B, Giglio MG, Rey L, Ruiz-Argüeso T, Palacios JM, Imperial J. Genomic Diversity in the Endosymbiotic Bacterium Rhizobium leguminosarum. Genes (Basel) 2018; 9:E60. [PMID: 29364862 PMCID: PMC5852556 DOI: 10.3390/genes9020060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/16/2018] [Accepted: 01/22/2018] [Indexed: 12/22/2022] Open
Abstract
Rhizobium leguminosarum bv. viciae is a soil α-proteobacterium that establishes a diazotrophic symbiosis with different legumes of the Fabeae tribe. The number of genome sequences from rhizobial strains available in public databases is constantly increasing, although complete, fully annotated genome structures from rhizobial genomes are scarce. In this work, we report and analyse the complete genome of R. leguminosarum bv. viciae UPM791. Whole genome sequencing can provide new insights into the genetic features contributing to symbiotically relevant processes such as bacterial adaptation to the rhizosphere, mechanisms for efficient competition with other bacteria, and the ability to establish a complex signalling dialogue with legumes, to enter the root without triggering plant defenses, and, ultimately, to fix nitrogen within the host. Comparison of the complete genome sequences of two strains of R. leguminosarum bv. viciae, 3841 and UPM791, highlights the existence of different symbiotic plasmids and a common core chromosome. Specific genomic traits, such as plasmid content or a distinctive regulation, define differential physiological capabilities of these endosymbionts. Among them, strain UPM791 presents unique adaptations for recycling the hydrogen generated in the nitrogen fixation process.
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Affiliation(s)
- Carmen Sánchez-Cañizares
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, UK
| | - Beatriz Jorrín
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, UK
| | - David Durán
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid (UAM), Ciudad Universitaria de Cantoblanco, Calle Francisco Tomás y Valiente 7, 28049 Madrid, Spain
| | - Suvarna Nadendla
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD 21201, USA; (S.N.); (M.G.G.)
| | - Marta Albareda
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Laura Rubio-Sanz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Mónica Lanza
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Rosa Isabel Prieto
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Belén Brito
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Michelle G. Giglio
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD 21201, USA; (S.N.); (M.G.G.)
| | - Luis Rey
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Tomás Ruiz-Argüeso
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - José M. Palacios
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Juan Imperial
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 115 bis, 28006 Madrid, Spain
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Rubio-Sanz L, Brito B, Palacios J. Analysis of metal tolerance in Rhizobium leguminosarum strains isolated from an ultramafic soil. FEMS Microbiol Lett 2018; 365:4813332. [DOI: 10.1093/femsle/fny010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/16/2018] [Indexed: 11/12/2022] Open
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Jaiswal SK, Naamala J, Dakora FD. Nature and mechanisms of aluminium toxicity, tolerance and amelioration in symbiotic legumes and rhizobia. BIOLOGY AND FERTILITY OF SOILS 2018; 54:309-318. [PMID: 31258230 PMCID: PMC6560468 DOI: 10.1007/s00374-018-1262-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/14/2017] [Accepted: 01/01/2018] [Indexed: 05/18/2023]
Abstract
Recent findings on the effect of aluminium (Al) on the functioning of legumes and their associated microsymbionts are reviewed here. Al represents 7% of solid matter in the Earth's crust and is an important abiotic factor that alters microbial and plant functioning at very early stages. The trivalent Al (Al3+) dominates at pH < 5 in soils and becomes a constraint to legume productivity through its lethal effect on rhizobia, the host plant and their interaction. Al3+ has lethal effects on many aspects of the rhizobia/legume symbiosis, which include a decrease in root elongation and root hair formation, lowered soil rhizobial population, and suppression of nitrogen metabolism involving nitrate reduction, nitrite reduction, nitrogenase activity and the functioning of uptake of hydrogenases (Hup), ultimately impairing the N2 fixation process. At the molecular level, Al is known to suppress the expression of nodulation genes in symbiotic rhizobia, as well as the induction of genes for the formation of hexokinase, phosphodiesterase, phosphooxidase and acid/alkaline phosphatase. Al toxicity can also induce the accumulation of reactive oxygen species and callose, in addition to lipoperoxidation in the legume root elongation zone. Al tolerance in plants can be achieved through over-expression of citrate synthase gene in roots and/or the synthesis and release of organic acids that reverse Al-induced changes in proteins, as well as metabolic regulation by plant-secreted microRNAs. In contrast, Al tolerance in symbiotic rhizobia is attained via the production of exopolysaccharides, the synthesis of siderophores that reduce Al uptake, induction of efflux pumps resistant to heavy metals and the expression of metal-inducible (dmeRF) gene clusters in symbiotic Rhizobiaceae. In soils, Al toxicity is usually ameliorated through liming, organic matter supply and use of Al-tolerant species. Our current understanding of crop productivity in high Al soils suggests that a much greater future accumulation of Al is likely to occur in agricultural soils globally if crop irrigation is increased under a changing climate.
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Affiliation(s)
- Sanjay K. Jaiswal
- Department of Chemistry, Tshwane University of Technology, Arcadia campus, 175 Nelson Mandela Drive, Private Bag X680, Pretoria, 0001 South Africa
| | - Judith Naamala
- Department of Crop Sciences, Tshwane University of Technology, Arcadia campus, 175 Nelson Mandela Drive, Private Bag X680, Pretoria, 0001 South Africa
| | - Felix D. Dakora
- Department of Chemistry, Tshwane University of Technology, Arcadia campus, 175 Nelson Mandela Drive, Private Bag X680, Pretoria, 0001 South Africa
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Liang J, Zhang M, Lu M, Li Z, Shen X, Chou M, Wei G. Functional characterization of a csoR-cueA divergon in Bradyrhizobium liaoningense CCNWSX0360, involved in copper, zinc and cadmium cotolerance. Sci Rep 2016; 6:35155. [PMID: 27725778 PMCID: PMC5057107 DOI: 10.1038/srep35155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/26/2016] [Indexed: 12/14/2022] Open
Abstract
Random mutagenesis in a symbiotic nitrogen-fixing Bradyrhizobium liaoningense CCNWSX0360 (Bln0360) using Tn5 identified five copper (Cu) resistance-related genes. They were functionally sorted into three groups: transmembrane transport (cueA and tolC); oxidation (copA); and protection of the membrane barrier (lptE and ctpA). The gene cueA, together with the upstream csoR (Cu-sensitive operon repressor), constituted a csoR-cueA divergon which plays a crucial role in Cu homeostasis. Deletion of cueA decreased the Cu tolerance of cells, and complementation of this mutant restored comparable Cu resistance to that of the wild-type. Transcriptional and fusion expression analysis demonstrated that csoR-cueA divergon was up-regulated by both the monovalent Cu+ and divalent Zn2+/Cd2+, and negatively regulated by transcriptional repressor CsoR, via a bidirectional promoter. Deletion of csoR renders the cell hyper-resistant to Cu, Zn and Cd. Although predicted to encode a Cu transporting P-type ATPase (CueA), cueA also conferred resistance to zinc and cadmium; two putative N-MBDs (N-terminal metal binding domains) of CueA were required for the Cu/Zn/Cd tolerance. Moreover, cueA is needed for nodulation competitiveness of B. liaoningense in Cu rich conditions. Together, the results demonstrated a crucial role for the csoR-cueA divergon as a component of the multiple-metal resistance machinery in B. liaoningense.
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Affiliation(s)
- Jianqiang Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Mingzhe Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Mingmei Lu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhefei Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xihui Shen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Minxia Chou
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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Osman D, Piergentili C, Chen J, Sayer LN, Usón I, Huggins TG, Robinson NJ, Pohl E. The Effectors and Sensory Sites of Formaldehyde-responsive Regulator FrmR and Metal-sensing Variant. J Biol Chem 2016; 291:19502-16. [PMID: 27474740 PMCID: PMC5016687 DOI: 10.1074/jbc.m116.745174] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/21/2016] [Indexed: 11/29/2022] Open
Abstract
The DUF156 family of DNA-binding transcriptional regulators includes metal sensors that respond to cobalt and/or nickel (RcnR, InrS) or copper (CsoR) plus CstR, which responds to persulfide, and formaldehyde-responsive FrmR. Unexpectedly, the allosteric mechanism of FrmR from Salmonella enterica serovar Typhimurium is triggered by metals in vitro, and variant FrmR(E64H) gains responsiveness to Zn(II) and cobalt in vivo Here we establish that the allosteric mechanism of FrmR is triggered directly by formaldehyde in vitro Sensitivity to formaldehyde requires a cysteine (Cys(35) in FrmR) conserved in all DUF156 proteins. A crystal structure of metal- and formaldehyde-sensing FrmR(E64H) reveals that an FrmR-specific amino-terminal Pro(2) is proximal to Cys(35), and these residues form the deduced formaldehyde-sensing site. Evidence is presented that implies that residues spatially close to the conserved cysteine tune the sensitivities of DUF156 proteins above or below critical thresholds for different effectors, generating the semblance of specificity within cells. Relative to FrmR, RcnR is less responsive to formaldehyde in vitro, and RcnR does not sense formaldehyde in vivo, but reciprocal mutations FrmR(P2S) and RcnR(S2P), respectively, impair and enhance formaldehyde reactivity in vitro Formaldehyde detoxification by FrmA requires S-(hydroxymethyl)glutathione, yet glutathione inhibits formaldehyde detection by FrmR in vivo and in vitro Quantifying the number of FrmR molecules per cell and modeling formaldehyde modification as a function of [formaldehyde] demonstrates that FrmR reactivity is optimized such that FrmR is modified and frmRA is derepressed at lower [formaldehyde] than required to generate S-(hydroxymethyl)glutathione. Expression of FrmA is thereby coordinated with the accumulation of its substrate.
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Affiliation(s)
- Deenah Osman
- From the Department of Chemistry, School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Cecilia Piergentili
- From the Department of Chemistry, School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Junjun Chen
- Procter and Gamble, Mason Business Center, Cincinnati, Ohio 45040
| | | | - Isabel Usón
- the Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, 08028 Barcelona, Spain, and the Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Thomas G Huggins
- Procter and Gamble, Mason Business Center, Cincinnati, Ohio 45040
| | - Nigel J Robinson
- From the Department of Chemistry, School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom,
| | - Ehmke Pohl
- From the Department of Chemistry, School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
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González-Guerrero M, Escudero V, Saéz Á, Tejada-Jiménez M. Transition Metal Transport in Plants and Associated Endosymbionts: Arbuscular Mycorrhizal Fungi and Rhizobia. FRONTIERS IN PLANT SCIENCE 2016; 7:1088. [PMID: 27524990 PMCID: PMC4965479 DOI: 10.3389/fpls.2016.01088] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 07/11/2016] [Indexed: 05/03/2023]
Abstract
Transition metals such as iron, copper, zinc, or molybdenum are essential nutrients for plants. These elements are involved in almost every biological process, including photosynthesis, tolerance to biotic and abiotic stress, or symbiotic nitrogen fixation. However, plants often grow in soils with limiting metallic oligonutrient bioavailability. Consequently, to ensure the proper metal levels, plants have developed a complex metal uptake and distribution system, that not only involves the plant itself, but also its associated microorganisms. These microorganisms can simply increase metal solubility in soils and making them more accessible to the host plant, as well as induce the plant metal deficiency response, or directly deliver transition elements to cortical cells. Other, instead of providing metals, can act as metal sinks, such as endosymbiotic rhizobia in legume nodules that requires relatively large amounts to carry out nitrogen fixation. In this review, we propose to do an overview of metal transport mechanisms in the plant-microbe system, emphasizing the role of arbuscular mycorrhizal fungi and endosymbiotic rhizobia.
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Affiliation(s)
- Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Madrid, Spain
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Regulation of the Cobalt/Nickel Efflux Operon dmeRF in Agrobacterium tumefaciens and a Link between the Iron-Sensing Regulator RirA and Cobalt/Nickel Resistance. Appl Environ Microbiol 2016; 82:4732-4742. [PMID: 27235438 DOI: 10.1128/aem.01262-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 05/20/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The Agrobacterium tumefaciens C58 genome harbors an operon containing the dmeR (Atu0890) and dmeF (Atu0891) genes, which encode a transcriptional regulatory protein belonging to the RcnR/CsoR family and a metal efflux protein belonging to the cation diffusion facilitator (CDF) family, respectively. The dmeRF operon is specifically induced by cobalt and nickel, with cobalt being the more potent inducer. Promoter-lacZ transcriptional fusion, an electrophoretic mobility shift assay, and DNase I footprinting assays revealed that DmeR represses dmeRF transcription through direct binding to the promoter region upstream of dmeR A strain lacking dmeF showed increased accumulation of intracellular cobalt and nickel and exhibited hypersensitivity to these metals; however, this strain displayed full virulence, comparable to that of the wild-type strain, when infecting a Nicotiana benthamiana plant model under the tested conditions. Cobalt, but not nickel, increased the expression of many iron-responsive genes and reduced the induction of the SoxR-regulated gene sodBII Furthermore, control of iron homeostasis via RirA is important for the ability of A. tumefaciens to cope with cobalt and nickel toxicity. IMPORTANCE The molecular mechanism of the regulation of dmeRF transcription by DmeR was demonstrated. This work provides evidence of a direct interaction of apo-DmeR with the corresponding DNA operator site in vitro The recognition site for apo-DmeR consists of 10-bp AT-rich inverted repeats separated by six C bases (5'-ATATAGTATACCCCCCTATAGTATAT-3'). Cobalt and nickel cause DmeR to dissociate from the dmeRF promoter, which leads to expression of the metal efflux gene dmeF This work also revealed a connection between iron homeostasis and cobalt/nickel resistance in A. tumefaciens.
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Osman D, Piergentili C, Chen J, Chakrabarti B, Foster AW, Lurie-Luke E, Huggins TG, Robinson NJ. Generating a Metal-responsive Transcriptional Regulator to Test What Confers Metal Sensing in Cells. J Biol Chem 2015; 290:19806-22. [PMID: 26109070 PMCID: PMC4528141 DOI: 10.1074/jbc.m115.663427] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Indexed: 11/06/2022] Open
Abstract
FrmR from Salmonella enterica serovar typhimurium (a CsoR/RcnR-like transcriptional de-repressor) is shown to repress the frmRA operator-promoter, and repression is alleviated by formaldehyde but not manganese, iron, cobalt, nickel, copper, or Zn(II) within cells. In contrast, repression by a mutant FrmRE64H (which gains an RcnR metal ligand) is alleviated by cobalt and Zn(II). Unexpectedly, FrmR was found to already bind Co(II), Zn(II), and Cu(I), and moreover metals, as well as formaldehyde, trigger an allosteric response that weakens DNA affinity. However, the sensory metal sites of the cells' endogenous metal sensors (RcnR, ZntR, Zur, and CueR) are all tighter than FrmR for their cognate metals. Furthermore, the endogenous metal sensors are shown to out-compete FrmR. The metal-sensing FrmRE64H mutant has tighter metal affinities than FrmR by approximately 1 order of magnitude. Gain of cobalt sensing by FrmRE64H remains enigmatic because the cobalt affinity of FrmRE64H is substantially weaker than that of the endogenous cobalt sensor. Cobalt sensing requires glutathione, which may assist cobalt access, conferring a kinetic advantage. For Zn(II), the metal affinity of FrmRE64H approaches the metal affinities of cognate Zn(II) sensors. Counter-intuitively, the allosteric coupling free energy for Zn(II) is smaller in metal-sensing FrmRE64H compared with nonsensing FrmR. By determining the copies of FrmR and FrmRE64H tetramers per cell, then estimating promoter occupancy as a function of intracellular Zn(II) concentration, we show how a modest tightening of Zn(II) affinity, plus weakened DNA affinity of the apoprotein, conspires to make the relative properties of FrmRE64H (compared with ZntR and Zur) sufficient to sense Zn(II) inside cells.
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Affiliation(s)
- Deenah Osman
- From the School of Biological and Biomedical Sciences and Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Cecilia Piergentili
- From the School of Biological and Biomedical Sciences and Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Junjun Chen
- Procter and Gamble, Mason Business Centre, Cincinnati, Ohio 45040, and
| | - Buddhapriya Chakrabarti
- From the School of Biological and Biomedical Sciences and Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Andrew W Foster
- From the School of Biological and Biomedical Sciences and Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Elena Lurie-Luke
- Life Sciences Open Innovation, London Innovation Centre, Procter and Gamble Technical Centres, Ltd., Egham TW20 9NW, United Kingdom
| | - Thomas G Huggins
- Procter and Gamble, Mason Business Centre, Cincinnati, Ohio 45040, and
| | - Nigel J Robinson
- From the School of Biological and Biomedical Sciences and Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom,
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22
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Cation Diffusion Facilitator family: Structure and function. FEBS Lett 2015; 589:1283-95. [PMID: 25896018 DOI: 10.1016/j.febslet.2015.04.007] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/01/2015] [Accepted: 04/08/2015] [Indexed: 01/13/2023]
Abstract
The Cation Diffusion Facilitators (CDFs) form a family of membrane-bound proteins capable of transporting zinc and other heavy metal ions. Involved in metal tolerance/resistance by efflux of ions, CDF proteins share a two-modular architecture consisting of a transmembrane domain (TMD) and C-terminal domain (CTD) that protrudes into the cytoplasm. Discovery of a Zn²⁺ and Cd²⁺ CDF transporter from a marine bacterium Maricaulis maris that does not possess the CTD questions current perceptions regarding this family of proteins. This article describes a new, CTD-lacking subfamily of CDFs and our current knowledge about this family of proteins in the view of these findings.
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23
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Hao X, Xie P, Zhu YG, Taghavi S, Wei G, Rensing C. Copper tolerance mechanisms of Mesorhizobium amorphae and its role in aiding phytostabilization by Robinia pseudoacacia in copper contaminated soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:2328-2340. [PMID: 25594414 DOI: 10.1021/es504956a] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The legume-rhizobium symbiosis has been proposed as an important system for phytoremediation of heavy metal contaminated soils due to its beneficial activity of symbiotic nitrogen fixation. However, little is known about metal resistant mechanism of rhizobia and the role of metal resistance determinants in phytoremediation. In this study, copper resistance mechanisms were investigated for a multiple metal resistant plant growth promoting rhizobium, Mesorhizobium amorphae 186. Three categories of determinants involved in copper resistance were identified through transposon mutagenesis, including genes encoding a P-type ATPase (CopA), hypothetical proteins, and other proteins (a GTP-binding protein and a ribosomal protein). Among these determinants, copA played the dominant role in copper homeostasis of M. amorphae 186. Mutagenesis of a hypothetical gene lipA in mutant MlipA exhibited pleiotropic phenotypes including sensitivity to copper, blocked symbiotic capacity and inhibited growth. In addition, the expression of cusB encoding part of an RND-type efflux system was induced by copper. To explore the possible role of copper resistance mechanism in phytoremediation of copper contaminated soil, the symbiotic nodulation and nitrogen fixation abilities were compared using a wild-type strain, a copA-defective mutant, and a lipA-defective mutant. Results showed that a copA deletion did not affect the symbiotic capacity of rhizobia under uncontaminated condition, but the protective role of copA in symbiotic processes at high copper concentration is likely concentration-dependent. In contrast, inoculation of a lipA-defective strain led to significant decreases in the functional nodule numbers, total N content, plant biomass and leghemoglobin expression level of Robinia pseudoacacia even under conditions of uncontaminated soil. Moreover, plants inoculated with lipA-defective strain accumulated much less copper than both the wild-type strain and the copA-defective strain, suggesting an important role of a healthy symbiotic relationship between legume and rhizobia in phytostabilization.
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Affiliation(s)
- Xiuli Hao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100, China
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24
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Musiani F, Zambelli B, Bazzani M, Mazzei L, Ciurli S. Nickel-responsive transcriptional regulators. Metallomics 2015; 7:1305-18. [DOI: 10.1039/c5mt00072f] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The structural features, metal coordination modes and metal binding thermodynamics of known Ni(ii)-dependent transcriptional regulators are highlighted and discussed.
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Affiliation(s)
- Francesco Musiani
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- 40127 Bologna, Italy
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- 40127 Bologna, Italy
| | - Micaela Bazzani
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- 40127 Bologna, Italy
| | - Luca Mazzei
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- 40127 Bologna, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- 40127 Bologna, Italy
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25
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Albareda M, Rodrigue A, Brito B, Ruiz-Argüeso T, Imperial J, Mandrand-Berthelot MA, Palacios J. Rhizobium leguminosarum HupE is a highly-specific diffusion facilitator for nickel uptake. Metallomics 2015; 7:691-701. [DOI: 10.1039/c4mt00298a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Functional and topological analysis ofRhizobium leguminosarumHupE, the founding member of the HupE/UreJ family of nickel permeases, provides new hints on how bacteria manage nickel provision for metalloenzyme synthesis.
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Affiliation(s)
- Marta Albareda
- Departamento de Biotecnología
- Escuela Técnica Superior de Ingenieros Agrónomos and Centro de Biotecnología y Genómica de Plantas (C.B.G.P.)
- Universidad Politécnica de Madrid
- Campus de Montegancedo
- 28223 Pozuelo de Alarcón, Spain
| | - Agnès Rodrigue
- Microbiologie
- Adaptation et Pathogénie
- F-69622 Villeurbanne Cedex, France
| | - Belén Brito
- Departamento de Biotecnología
- Escuela Técnica Superior de Ingenieros Agrónomos and Centro de Biotecnología y Genómica de Plantas (C.B.G.P.)
- Universidad Politécnica de Madrid
- Campus de Montegancedo
- 28223 Pozuelo de Alarcón, Spain
| | - Tomás Ruiz-Argüeso
- Departamento de Biotecnología
- Escuela Técnica Superior de Ingenieros Agrónomos and Centro de Biotecnología y Genómica de Plantas (C.B.G.P.)
- Universidad Politécnica de Madrid
- Campus de Montegancedo
- 28223 Pozuelo de Alarcón, Spain
| | - Juan Imperial
- Departamento de Biotecnología
- Escuela Técnica Superior de Ingenieros Agrónomos and Centro de Biotecnología y Genómica de Plantas (C.B.G.P.)
- Universidad Politécnica de Madrid
- Campus de Montegancedo
- 28223 Pozuelo de Alarcón, Spain
| | | | - Jose Palacios
- Departamento de Biotecnología
- Escuela Técnica Superior de Ingenieros Agrónomos and Centro de Biotecnología y Genómica de Plantas (C.B.G.P.)
- Universidad Politécnica de Madrid
- Campus de Montegancedo
- 28223 Pozuelo de Alarcón, Spain
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26
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Furnholm TR, Tisa LS. The ins and outs of metal homeostasis by the root nodule actinobacterium Frankia. BMC Genomics 2014; 15:1092. [PMID: 25495525 PMCID: PMC4531530 DOI: 10.1186/1471-2164-15-1092] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Frankia are actinobacteria that form a symbiotic nitrogen-fixing association with actinorhizal plants, and play a significant role in actinorhizal plant colonization of metal contaminated areas. Many Frankia strains are known to be resistant to several toxic metals and metalloids including Pb(2+), Al(+3), SeO2, Cu(2+), AsO4, and Zn(2+). With the availability of eight Frankia genome databases, comparative genomics approaches employing phylogeny, amino acid composition analysis, and synteny were used to identify metal homeostasis mechanisms in eight Frankia strains. Characterized genes from the literature and a meta-analysis of 18 heavy metal gene microarray studies were used for comparison. RESULTS Unlike most bacteria, Frankia utilize all of the essential trace elements (Ni, Co, Cu, Se, Mo, B, Zn, Fe, and Mn) and have a comparatively high percentage of metalloproteins, particularly in the more metal resistant strains. Cation diffusion facilitators, being one of the few known metal resistance mechanisms found in the Frankia genomes, were strong candidates for general divalent metal resistance in all of the Frankia strains. Gene duplication and amino acid substitutions that enhanced the metal affinity of CopA and CopCD proteins may be responsible for the copper resistance found in some Frankia strains. CopA and a new potential metal transporter, DUF347, may be involved in the particularly high lead tolerance in Frankia. Selenite resistance involved an alternate sulfur importer (CysPUWA) that prevents sulfur starvation, and reductases to produce elemental selenium. The pattern of arsenate, but not arsenite, resistance was achieved by Frankia using the novel arsenite exporter (AqpS) previously identified in the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Based on the presence of multiple tellurite resistance factors, a new metal resistance (tellurite) was identified and confirmed in Frankia. CONCLUSIONS Each strain had a unique combination of metal import, binding, modification, and export genes that explain differences in patterns of metal resistance between strains. Frankia has achieved similar levels of metal and metalloid resistance as bacteria from highly metal-contaminated sites. From a bioremediation standpoint, it is important to understand mechanisms that allow the endosymbiont to survive and infect actinorhizal plants in metal contaminated soils.
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Affiliation(s)
- Teal R Furnholm
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
| | - Louis S Tisa
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
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27
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Higgins KA, Giedroc D. Insights into Protein Allostery in the CsoR/RcnR Family of Transcriptional Repressors. CHEM LETT 2014; 43:20-25. [PMID: 24695963 DOI: 10.1246/cl.130965] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
CsoR/RcnR transcriptional repressors adopt a disc-shaped, all α-helical dimer of dimers tetrameric architecture, with a four-helix bundle the key structural feature of the dimer. Individual members of this large family of repressors coordinate Cu(I) or Ni(II)/Co(II) or perform cysteine sulfur chemistry in mitigating the effects of metal or metabolite toxicity, respectively. Here we highlight recent insights into the functional diversity of this fascinating family of repressors.
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Affiliation(s)
- Khadine A Higgins
- Department of Chemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405, USA
| | - David Giedroc
- Department of Chemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405, USA
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