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Xie P, Hao X, Herzberg M, Luo Y, Nies DH, Wei G. Genomic analyses of metal resistance genes in three plant growth promoting bacteria of legume plants in Northwest mine tailings, China. J Environ Sci (China) 2015; 27:179-187. [PMID: 25597676 DOI: 10.1016/j.jes.2014.07.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/11/2014] [Accepted: 07/31/2014] [Indexed: 06/04/2023]
Abstract
To better understand the diversity of metal resistance genetic determinant from microbes that survived at metal tailings in northwest of China, a highly elevated level of heavy metal containing region, genomic analyses was conducted using genome sequence of three native metal-resistant plant growth promoting bacteria (PGPB). It shows that: Mesorhizobium amorphae CCNWGS0123 contains metal transporters from P-type ATPase, CDF (Cation Diffusion Facilitator), HupE/UreJ and CHR (chromate ion transporter) family involved in copper, zinc, nickel as well as chromate resistance and homeostasis. Meanwhile, the putative CopA/CueO system is expected to mediate copper resistance in Sinorhizobium meliloti CCNWSX0020 while ZntA transporter, assisted with putative CzcD, determines zinc tolerance in Agrobacterium tumefaciens CCNWGS0286. The greenhouse experiment provides the consistent evidence of the plant growth promoting effects of these microbes on their hosts by nitrogen fixation and/or indoleacetic acid (IAA) secretion, indicating a potential in-site phytoremediation usage in the mining tailing regions of China.
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Affiliation(s)
- Pin Xie
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China; Molecular Microbiology, Institute for Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), 06120, Germany.
| | - Xiuli Hao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Martin Herzberg
- Molecular Microbiology, Institute for Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Yantao Luo
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dietrich H Nies
- Molecular Microbiology, Institute for Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Gehong Wei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China.
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52
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Lu M, Jiang YL, Wang S, Jin H, Zhang RG, Virolle MJ, Chen Y, Zhou CZ. Streptomyces coelicolor SCO4226 is a nickel binding protein. PLoS One 2014; 9:e109660. [PMID: 25285530 PMCID: PMC4186839 DOI: 10.1371/journal.pone.0109660] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/03/2014] [Indexed: 12/03/2022] Open
Abstract
The open reading frame SCO4226 of Streptomyces coelicolor A3(2) encodes an 82-residue hypothetical protein. Biochemical assays revealed that each SCO4226 dimer binds four nickel ions. To decipher the molecular function, we solved the crystal structures of SCO4226 in both apo- and nickel-bound (Ni-SCO4226) forms at 1.30 and 2.04 Å resolution, respectively. Each subunit of SCO4226 dimer adopts a canonical ferredoxin-like fold with five β-strands flanked by two α-helices. In the structure of Ni-SCO4226, four nickel ions are coordinated at the surface of the dimer. Further biochemical assays suggested that the binding of Ni2+ triggers the self-aggregation of SCO4226 in vitro. In addition, RT-qPCR assays demonstrated that the expression of SCO4226 gene in S. coelicolor is specifically up-regulated by the addition of Ni2+, but not other divalent ions such as Cu2+, Mn2+ or Co2+. All these results suggested that SCO4226 acts as a nickel binding protein, probably required for nickel sequestration and/or detoxification.
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Affiliation(s)
- Mo Lu
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
- Department of Biology, South University of Sciences and Technology of China, Shenzhen, Guangdong, People's Republic of China
| | - Yong-Liang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
- * E-mail: (YLJ); (CZZ)
| | - Shu Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Hua Jin
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Rong-Guang Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Marie-Joelle Virolle
- Institut de Génétique et Microbiologie, UMR8621 CNRS Université Paris Sud, Orsay, France
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
- * E-mail: (YLJ); (CZZ)
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53
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Lebrette H, Brochier-Armanet C, Zambelli B, de Reuse H, Borezée-Durant E, Ciurli S, Cavazza C. Promiscuous nickel import in human pathogens: structure, thermodynamics, and evolution of extracytoplasmic nickel-binding proteins. Structure 2014; 22:1421-32. [PMID: 25199691 DOI: 10.1016/j.str.2014.07.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/16/2014] [Accepted: 07/13/2014] [Indexed: 10/24/2022]
Abstract
In human pathogenic bacteria, nickel is required for the activation of two enzymes, urease and [NiFe]-hydrogenase, necessary for host infection. Acquisition of Ni(II) is mediated by either permeases or ABC-importers, the latter including a subclass that involves an extracytoplasmic nickel-binding protein, Ni-BP. This study reports on the structure of three Ni-BPs from a diversity of human pathogens and on the existence of three new nickel-binding motifs. These are different from that previously described for Escherichia coli Ni-BP NikA, known to bind nickel via a nickelophore, and indicate a variegated ligand selectivity for Ni-BPs. The structures are consistent with ligand affinities measured in solution by calorimetry and challenge the hypothesis of a general requirement of nickelophores for nickel uptake by canonical ABC importers. Phylogenetic analyses showed that Ni-BPs have different evolutionary origins and emerged independently from peptide-binding proteins, possibly explaining the promiscuous behavior of this class of Ni(II) carriers.
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Affiliation(s)
- Hugo Lebrette
- University Grenoble Alpes, Institut de Biologie Structurale (IBS), 38044 Grenoble, France; CNRS, IBS, 38044 Grenoble, France; CEA, IBS, 38044 Grenoble, France
| | - Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin, 40, 40127 Bologna, Italy
| | - Hilde de Reuse
- Département de Microbiologie, Unité Pathogenèse de Helicobacter, Institut Pasteur, 75724 Paris Cedex 15, France
| | - Elise Borezée-Durant
- INRA, UMR 1319 Micalis, 78350 Jouy en Josas, France; Agro ParisTech, UMR Micalis, 78350 Jouy en Josas, France
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin, 40, 40127 Bologna, Italy.
| | - Christine Cavazza
- University Grenoble Alpes, LCBM, 17, Avenue des Martyrs, 38054 Grenoble Cedex 09, France.
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Hynninen A, Virta M. Whole-cell bioreporters for the detection of bioavailable metals. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 118:31-63. [PMID: 19543702 DOI: 10.1007/10_2009_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Whole-cell bioreporters are living microorganisms that produce a specific, quantifiable output in response to target chemicals. Typically, whole-cell bioreporters combine a sensor element for the substance of interest and a reporter element coding for an easily detectable protein. The sensor element is responsible for recognizing the presence of an analyte. In the case of metal bioreporters, the sensor element consists of a DNA promoter region for a metal-binding transcription factor fused to a promoterless reporter gene that encodes a signal-producing protein. In this review, we provide an overview of specific whole-cell bioreporters for heavy metals. Because the sensing of metals by bioreporter microorganisms is usually based on heavy metal resistance/homeostasis mechanisms, the basis of these mechanisms will also be discussed. The goal here is not to present a comprehensive summary of individual metal-specific bioreporters that have been constructed, but rather to express views on the theory and applications of metal-specific bioreporters and identify some directions for future research and development.
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Affiliation(s)
- Anu Hynninen
- Department of Applied Chemistry and Microbiology, University of Helsinki, 56, 00014, Helsinki, Finland
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Boer JL, Mulrooney SB, Hausinger RP. Nickel-dependent metalloenzymes. Arch Biochem Biophys 2014; 544:142-52. [PMID: 24036122 PMCID: PMC3946514 DOI: 10.1016/j.abb.2013.09.002] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 08/31/2013] [Accepted: 09/03/2013] [Indexed: 11/29/2022]
Abstract
This review describes the functions, structures, and mechanisms of nine nickel-containing enzymes: glyoxalase I, acireductone dioxygenase, urease, superoxide dismutase, [NiFe]-hydrogenase, carbon monoxide dehydrogenase, acetyl-coenzyme A synthase/decarbonylase, methyl-coenzyme M reductase, and lactate racemase. These enzymes catalyze their various chemistries by using metallocenters of diverse structures, including mononuclear nickel, dinuclear nickel, nickel-iron heterodinuclear sites, more complex nickel-containing clusters, and nickel-tetrapyrroles. Selected other enzymes are active with nickel, but the physiological relevance of this metal specificity is unclear. Additional nickel-containing proteins of undefined function have been identified.
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Affiliation(s)
- Jodi L Boer
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Scott B Mulrooney
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
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56
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Ge RG, Wang DX, Hao MC, Sun XS. Nickel trafficking system responsible for urease maturation in Helicobacter pylori. World J Gastroenterol 2013; 19:8211-8218. [PMID: 24363511 PMCID: PMC3857443 DOI: 10.3748/wjg.v19.i45.8211] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/17/2013] [Accepted: 11/03/2013] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori (H. pylori) is a common human pathogen responsible for various gastric diseases. This bacterium relies on the production of urease and hydrogenase to inhabit the acidic environment of the stomach. Nickel is an essential cofactor for urease and hydrogenase. H. pylori has to uptake sufficient nickel ions for the maturation of urease, and on the other way, to prevent the toxic effects of excessive nickel ions. Therefore, H. pylori has to strike a delicate balance between the import of nickel ions, its efficient intracellular storage, and delivery to nickel-dependent metalloenzymes when required. The assembly and maturation of the urease enzyme is a complex and timely ordered process, requiring various regulatory, uptake, chaperone and accessory proteins. In this review, we focus on several nickel trafficking proteins involved in urease maturation: NikR, NixA, HypAB, UreEFGH, HspA, Hpn and Hpnl. The work will deepen our understanding of how this pathogenic bacterium adapts to severe habitant environments in the host.
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57
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Structural basis for a homodimeric ATPase subunit of an ECF transporter. Protein Cell 2013; 4:793-801. [PMID: 24104393 DOI: 10.1007/s13238-013-3915-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 09/09/2013] [Indexed: 01/25/2023] Open
Abstract
The transition metal cobalt, an essential cofactor for many enzymes in prokaryotes, is taken up by several specific transport systems. The CbiMNQO protein complex belongs to type-1 energy-coupling factor (ECF) transporters and is a widespread group of microbial cobalt transporters. CbiO is the ATPase subunit (A-component) of the cobalt transporting system in the gram-negative thermophilic bacterium Thermoanaerobacter tengcongensis. Here we report the crystal structure of a nucleotide-free CbiO at a resolution of 2.3 Å. CbiO contains an N-terminal canonical nucleotide-binding domain (NBD) and C-terminal helical domain. Structural and biochemical data show that CbiO forms a homodimer mediated by the NBD and the C-terminal domain. Interactions mainly via conserved hydrophobic amino acids between the two C-terminal domains result in formation of a four-helix bundle. Structural comparison with other ECF transporters suggests that non-conserved residues outside the T-component binding groove in the A component likely act as a specificity determinant for T components. Together, our data provide information on understanding of the structural organization and interaction of the CbiMNQO system.
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58
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Ray P, Girard V, Gault M, Job C, Bonneu M, Mandrand-Berthelot MA, Singh SS, Job D, Rodrigue A. Pseudomonas putida KT2440 response to nickel or cobalt induced stress by quantitative proteomics. Metallomics 2013; 5:68-79. [DOI: 10.1039/c2mt20147j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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60
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61
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Abstract
Biological trace metals are needed in small quantities, but used by all living organisms. They are employed in key cellular functions in a variety of biological processes, resulting in the various degree of dependence of organisms on metals. Most effort in the field has been placed on experimental studies of metal utilization pathways and metal-dependent proteins. On the other hand, systemic level analyses of metalloproteomes (or metallomes) have been limited for most metals. In this chapter, we focus on the recent advances in comparative genomics, which provides many insights into evolution and function of metal utilization. These studies suggested that iron and zinc are widely used in biology (presumably by all organisms), whereas some other metals such as copper, molybdenum, nickel, and cobalt, show scattered occurrence in various groups of organisms. For these metals, most user proteins are well characterized and their dependence on a specific element is evolutionarily conserved. We also discuss evolutionary dynamics of the dependence of user proteins on different metals. Overall, comparative genomics analysis of metallomes provides a foundation for the systemic level understanding of metal utilization as well as for investigating the general features, functions, and evolutionary dynamics of metal use in the three domains of life.
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62
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Remy L, Carrière M, Derré-Bobillot A, Martini C, Sanguinetti M, Borezée-Durant E. The Staphylococcus aureus Opp1 ABC transporter imports nickel and cobalt in zinc-depleted conditions and contributes to virulence. Mol Microbiol 2012; 87:730-43. [PMID: 23279021 DOI: 10.1111/mmi.12126] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2012] [Indexed: 11/27/2022]
Abstract
Metals are common enzymatic cofactors, and their acquisition must be assured under the various conditions encountered in the host. Although some strategies for acquisition of common metals such as iron and manganese have been elucidated, little is known about the conditions and mechanisms used to capture trace metals. Nickel is a transition metal required as a cofactor for several bacterial enzymes, including urease. Staphylococcus aureus does express a nickel ABC transporter, Nik, which functions in metal-replete medium and is necessary for nickel urease activity and urinary tract colonization. In this work, we identified a novel cobalt and nickel transporter, which we named Cnt (previously annotated Opp1), in the major opportunistic pathogen S. aureus. Metal transport activity was revealed by growing cells in a chemically defined medium devoid of metals. Zinc specifically inhibits Cnt-mediated nickel and cobalt uptake, on both functional and transcriptional levels. Mortality due to S. aureus cnt mutant in systemic infection and colonization of the bladder and kidneys in ascending urinary tract infection model were reduced compared to the parent strain. This study identifies a novel S. aureus trace metal transporter and its restricted conditions of activity, and establishes its role in infection.
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Affiliation(s)
- Laetitia Remy
- UMR1319 Micalis, INRA, F-78350, Jouy en Josas, France
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63
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Nair S, Joshi-Saha A, Singh S, Ramachandran V, Singh S, Thorat V, Kaushik CP, Eapen S, D'Souza SF. Evaluation of transgenic tobacco plants expressing a bacterial Co-Ni transporter for acquisition of cobalt. J Biotechnol 2012; 161:422-8. [PMID: 22898176 DOI: 10.1016/j.jbiotec.2012.07.191] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Revised: 06/23/2012] [Accepted: 07/15/2012] [Indexed: 11/21/2022]
Abstract
Phytoremediation is a viable strategy for management of toxic wastes in a large area/volume with low concentrations of toxic elemental pollutants. With increased industrial use of cobalt and its alloys, it has become a major metal contaminant in soils and water bodies surrounding these industries and mining sites with adverse effects on the biota. A bacterial Co-Ni permease was cloned from Rhodopseudomonas palustris and introduced into Nicotiana tabacum to explore its potential for phytoremediation and was found to be specific for cobalt and nickel. The transgenic plants accumulated more cobalt and nickel as compared to control, whereas no significant difference in accumulation of other divalent ions was observed. The transgenic plants were evaluated for cobalt content and showed increased acquisition of cobalt (up to 5 times) as compared to control. The plants were also assessed for accumulation of nickel and found to accumulate up to 2 times more nickel than control. At the same initial concentration of cobalt and nickel, transgenic plant preferentially accumulated cobalt as compared to nickel. The present study is perhaps the first attempt to develop transgenic plants expressing heterologous Co transporter with an improved capacity to uptake cobalt.
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Affiliation(s)
- Smitha Nair
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
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64
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Higgins KA, Carr CE, Maroney MJ. Specific metal recognition in nickel trafficking. Biochemistry 2012; 51:7816-32. [PMID: 22970729 DOI: 10.1021/bi300981m] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nickel is an essential metal for a number of bacterial species that have developed systems for acquiring, delivering, and incorporating the metal into target enzymes and controlling the levels of nickel in cells to prevent toxic effects. As with other transition metals, these trafficking systems must be able to distinguish between the desired metal and other transition metal ions with similar physical and chemical properties. Because there are few enzymes (targets) that require nickel for activity (e.g., Escherichia coli transports nickel for hydrogenases made under anaerobic conditions, and Helicobacter pylori requires nickel for hydrogenase and urease that are essential for acid viability), the "traffic pattern" for nickel is relatively simple, and nickel trafficking therefore presents an opportunity to examine a system for the mechanisms that are used to distinguish nickel from other metals. In this review, we describe the details known for examples of uptake permeases, metallochaperones and proteins involved in metallocenter assembly, and nickel metalloregulators. We also illustrate a variety of mechanisms, including molecular recognition in the case of NikA protein and examples of allosteric regulation for HypA, NikR, and RcnR, employed to generate specific biological responses to nickel ions.
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Affiliation(s)
- Khadine A Higgins
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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65
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Enhanced co-production of hydrogen and poly-(R)-3-hydroxybutyrate by recombinant PHB producing E. coli over-expressing hydrogenase 3 and acetyl-CoA synthetase. Metab Eng 2012; 14:496-503. [DOI: 10.1016/j.ymben.2012.07.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 06/29/2012] [Accepted: 07/19/2012] [Indexed: 11/24/2022]
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Genetic identification of a high-affinity Ni transporter and the transcriptional response to Ni deprivation in Synechococcus sp. strain WH8102. Appl Environ Microbiol 2012; 78:7822-32. [PMID: 22904052 DOI: 10.1128/aem.01739-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
One biological need for Ni in marine cyanobacteria stems from the utilization of the Ni metalloenzyme urease for the assimilation of urea as a nitrogen source. In many of the same cyanobacteria, including Synechococcus sp. strain WH8102, an additional and obligate nutrient requirement for Ni results from usage of a Ni superoxide dismutase (Ni-SOD), which is encoded by sodN. To better understand the effects of Ni deprivation on WH8102, parallel microarray-based analysis of gene expression and gene knockout experiments were conducted. The global transcriptional response to Ni deprivation depends upon the nitrogen source provided for growth; fewer than 1% of differentially expressed genes for Ni deprivation on ammonium or urea were concordantly expressed. Surprisingly, genes for putative Ni transporters, including one colocalized on the genome with sodN, sodT, were not induced despite an increase in Ni transport. Knockouts of the putative Ni transporter gene sodT appeared to be lethal in WH8102, so the genes for sodT and sodN in WH8102 were interrupted with the gene for Fe-SOD, sodB, and its promoter from Synechococcus sp. strain WH7803. The sodT::sodB exconjugants were unable to grow at low Ni concentrations, confirming that SodT is a Ni transporter. The sodN::sodB exconjugants displayed higher growth rates at low Ni concentrations than did the wild type, presumably due to a relaxed competition between urease and Ni-SOD for Ni. Both sodT::sodB and sodN::sodB lines exhibited an impaired ability to grow at low Fe concentrations. We propose a posttranslational allosteric SodT regulation involving the binding of Ni to a histidine-rich intracellular protein loop.
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67
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Bioaccumulation of 137Cs and 60Co by bacteria isolated from spent nuclear fuel pools. J Radioanal Nucl Chem 2012. [DOI: 10.1007/s10967-012-1932-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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68
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Witkowska D, Rowinska-Zyrek M, Valensin G, Kozlowski H. Specific poly-histidyl and poly-cysteil protein sites involved in Ni2+ homeostasis in Helicobacter pylori. Impact of Bi3+ ions on Ni2+ binding to proteins. Structural and thermodynamic aspects. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.06.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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69
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Macomber L, Elsey SP, Hausinger RP. Fructose-1,6-bisphosphate aldolase (class II) is the primary site of nickel toxicity in Escherichia coli. Mol Microbiol 2011; 82:1291-300. [PMID: 22014167 DOI: 10.1111/j.1365-2958.2011.07891.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nickel is toxic to all forms of life, but the mechanisms of cell damage are unknown. Indeed, environmentally relevant nickel levels (8 µM) inhibit wild-type Escherichia coli growth on glucose minimal medium. The same concentration of nickel also inhibits growth on fructose, but not succinate, lactate or glycerol; these results suggest that fructose-1,6-bisphosphate aldolase (FbaA) is a target of nickel toxicity. Cells stressed by 8 µM Ni(II) for 20 min lost 75% of their FbaA activity, demonstrating that FbaA is inactivated during nickel stress. Furthermore, overexpression of fbaA restored growth of an rcnA mutant in glucose minimal medium supplemented with 4 µM Ni(II), thus confirming that FbaA is a primary target of nickel toxicity. This class II aldolase has an active site zinc and a non-catalytic zinc nearby. Purified FbaA lost 80 % of its activity within 2 min when challenged with 8 µM Ni(II). Nickel-challenged FbaA lost 0.8 zinc and gained 0.8 nickel per inactivated monomer. FbaA mutants (D144A and E174A) affecting the non-catalytic zinc were resistant to nickel inhibition. These results define the primary site of nickel toxicity in E. coli as the class II aldolase FbaA through binding to the non-catalytic zinc site.
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Affiliation(s)
- Lee Macomber
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA
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70
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Abstract
Nickel has long been known to be an important human toxicant, including having the ability to form carcinomas, but until recently nickel was believed to be an issue only to microorganisms living in nickel-rich serpentine soils or areas contaminated by industrial pollution. This assumption was overturned by the discovery of a nickel defense system (RcnR/RcnA) found in microorganisms that live in a wide range of environmental niches, suggesting that nickel homeostasis is a general biological concern. To date, the mechanisms of nickel toxicity in microorganisms and higher eukaryotes are poorly understood. In this review, we summarize nickel homeostasis processes used by microorganisms and highlight in vivo and in vitro effects of exposure to elevated concentrations of nickel. On the basis of this evidence we propose four mechanisms of nickel toxicity: (1) nickel replaces the essential metal of metalloproteins, (2) nickel binds to catalytic residues of non-metalloenzymes; (3) nickel binds outside the catalytic site of an enzyme to inhibit allosterically and (4) nickel indirectly causes oxidative stress.
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Affiliation(s)
- Lee Macomber
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, USA
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
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Contributions of five secondary metal uptake systems to metal homeostasis of Cupriavidus metallidurans CH34. J Bacteriol 2011; 193:4652-63. [PMID: 21742896 DOI: 10.1128/jb.05293-11] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cupriavidus metallidurans is adapted to high concentrations of transition metal cations and is a model system for studying metal homeostasis in difficult environments. The elemental composition of C. metallidurans cells cultivated under various conditions was determined, revealing the ability of the bacterium to shield homeostasis of one essential metal from the toxic action of another. The contribution of metal uptake systems to this ability was studied. C. metallidurans contains three CorA members of the metal inorganic transport (MIT) protein family of putative magnesium uptake systems, ZupT of the ZRT/IRT protein, or ZIP, family, and PitA, which imports metal phosphate complexes. Expression of the genes for all these transporters was regulated by zinc availability, as shown by reporter gene fusions. While expression of zupT was upregulated under conditions of zinc starvation, expression of the other genes was downregulated at high zinc concentrations. Only corA(1) expression was influenced by magnesium starvation. Deletion mutants were constructed to characterize the contribution of each system to transition metal import. This identified ZupT as the main zinc uptake system under conditions of low zinc availability, CorA(1) as the main secondary magnesium uptake system, and CorA(2) and CorA(3) as backup systems for metal cation import. PitA may function as a cation-phosphate uptake system, the main supplier of divalent metal cations and phosphate in phosphate-rich environments. Thus, metal homeostasis in C. metallidurans is achieved by highly redundant metal uptake systems, which have only minimal cation selectivity and are in combination with efflux systems that "worry later" about surplus cations.
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72
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An ABC-type cobalt transport system is essential for growth of Sinorhizobium meliloti at trace metal concentrations. J Bacteriol 2011; 193:4405-16. [PMID: 21725018 DOI: 10.1128/jb.05045-11] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We report expression and mutant phenotypes for a gene cluster in Sinorhizobium meliloti, designated cbtJKL, that has been shown to encode an ABC-type cobalt transport system. Transcription of cbtJKL initiated 384 nucleotides upstream from the cbtJ translation start codon, and the resulting 5' region contained a putative B(12)riboswitch. Expression of the cbtJKL genes appeared to be controlled by (cobalt-loaded) cobalamin interacting at the B(12)riboswitch, since (i) a putative B(12)riboswitch was located within this large upstream region, (ii) cbtJ transcription was repressed upon addition of cobalt or vitamin B(12), and (iii) deletions in the B(12)riboswitch resulted in constitutive cbtJKL transcription. Insertion mutants in cbtJKL failed to grow in LB medium, and growth was restored through the addition of cobalt but not other metals. This growth phenotype appeared to be due to the chelation of cobalt present in LB, and cbtJKL mutants also failed to grow in minimal medium containing the chelating agent EDTA unless the medium was supplemented with additional or excess cobalt. In uptake experiments, (57)Co(2+)accumulation was high in wild-type cells expressing the cbtJKL genes, whereas wild-type cells in which cbtJKL expression was repressed showed reduced accumulation. In cbtJKL mutant cells, (57)Co(2+)accumulation was reduced relative to that of the wild type, and presumably, this residual cobalt transport occurred via an alternate ion uptake system(s) that is not specific to cobalt. In symbiosis, the alternate system(s) appeared to mediate cobalt transport into bacteroid cells, as low cbtJKL expression was detected in bacteroids and cbtJKL mutants formed N(2)-fixing nodules on alfalfa.
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73
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Lau SK, Fan RY, Ho TC, Wong GK, Tsang AK, Teng JL, Chen W, Watt RM, Curreem SO, Tse H, Yuen KY, Woo PC. Environmental adaptability and stress tolerance of Laribacter hongkongensis: a genome-wide analysis. Cell Biosci 2011; 1:22. [PMID: 21711489 PMCID: PMC3135505 DOI: 10.1186/2045-3701-1-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 06/14/2011] [Indexed: 12/31/2022] Open
Abstract
Background Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler's diarrhea and it can reside in human, fish, frogs and water. In this study, we performed an in-depth annotation of the genes in its genome related to adaptation to the various environmental niches. Results L. hongkongensis possessed genes for DNA repair and recombination, basal transcription, alternative σ-factors and 109 putative transcription factors, allowing DNA repair and global changes in gene expression in response to different environmental stresses. For acid stress, it possessed a urease gene cassette and two arc gene clusters. For alkaline stress, it possessed six CDSs for transporters of the monovalent cation/proton antiporter-2 and NhaC Na+:H+ antiporter families. For heavy metals acquisition and tolerance, it possessed CDSs for iron and nickel transport and efflux pumps for other metals. For temperature stress, it possessed genes related to chaperones and chaperonins, heat shock proteins and cold shock proteins. For osmotic stress, 25 CDSs were observed, mostly related to regulators for potassium ion, proline and glutamate transport. For oxidative and UV light stress, genes for oxidant-resistant dehydratase, superoxide scavenging, hydrogen peroxide scavenging, exclusion and export of redox-cycling antibiotics, redox balancing, DNA repair, reduction of disulfide bonds, limitation of iron availability and reduction of iron-sulfur clusters are present. For starvation, it possessed phosphorus and, despite being asaccharolytic, carbon starvation-related CDSs. Conclusions The L. hongkongensis genome possessed a high variety of genes for adaptation to acid, alkaline, temperature, osmotic, oxidative, UV light and starvation stresses and acquisition of and tolerance to heavy metals.
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Affiliation(s)
- Susanna Kp Lau
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong.,Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Rachel Yy Fan
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Tom Cc Ho
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Gilman Km Wong
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Alan Kl Tsang
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Jade Ll Teng
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Wenyang Chen
- Faculty of Dentistry, The University of Hong Kong, Hong Kong
| | - Rory M Watt
- Faculty of Dentistry, The University of Hong Kong, Hong Kong
| | | | - Herman Tse
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong.,Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong.,Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Patrick Cy Woo
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong.,Department of Microbiology, The University of Hong Kong, Hong Kong
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74
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RcnB is a periplasmic protein essential for maintaining intracellular Ni and Co concentrations in Escherichia coli. J Bacteriol 2011; 193:3785-93. [PMID: 21665978 DOI: 10.1128/jb.05032-11] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nickel and cobalt are both essential trace elements that are toxic when present in excess. The main resistance mechanism that bacteria use to overcome this toxicity is the efflux of these cations out of the cytoplasm. RND (resistance-nodulation-cell division)- and MFS (major facilitator superfamily)-type efflux systems are known to export either nickel or cobalt. The RcnA efflux pump, which belongs to a unique family, is responsible for the detoxification of Ni and Co in Escherichia coli. In this work, the role of the gene yohN, which is located downstream of rcnA, is investigated. yohN is cotranscribed with rcnA, and its expression is induced by Ni and Co. Surprisingly, in contrast to the effect of deleting rcnA, deletion of yohN conferred enhanced resistance to Ni and Co in E. coli, accompanied by decreased metal accumulation. We show that YohN is localized to the periplasm and does not bind Ni or Co ions directly. Physiological and genetic experiments demonstrate that YohN is not involved in Ni import. YohN is conserved among proteobacteria and belongs to a new family of proteins; consequently, yohN has been renamed rcnB. We show that the enhanced resistance of rcnB mutants to Ni and Co and their decreased Ni and Co intracellular accumulation are linked to the greater efflux of these ions in the absence of rcnB. Taken together, these results suggest that RcnB is required to maintain metal ion homeostasis, in conjunction with the efflux pump RcnA, presumably by modulating RcnA-mediated export of Ni and Co to avoid excess efflux of Ni and Co ions via an unknown novel mechanism.
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75
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A novel zinc binding system, ZevAB, is critical for survival of nontypeable Haemophilus influenzae in a murine lung infection model. Infect Immun 2011; 79:3366-76. [PMID: 21576338 DOI: 10.1128/iai.05135-11] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHI) is a Gram-negative bacterial pathogen that causes upper and lower respiratory infections. Factors required for pulmonary infection by NTHI are not well understood. Previously, using high-throughput insertion tracking by deep sequencing (HITS), putative lung colonization factors were identified. Also, previous research indicates that secreted disulfide-dependent factors are important for virulence of H. influenzae. In the present study, HITS data were compared with an informatics-based list of putative substrates of the periplasmic oxidoreductase DsbA to find and characterize secreted virulence factors. This analysis resulted in identification of the "zinc binding essential for virulence" (zev) locus consisting of zevA (HI1249) and zevB (HI1248). NTHI mutants of zevA and zevB grew normally in rich medium but were defective for colonization in a mouse lung model. Mutants also exhibited severe growth defects in medium containing EDTA and were rescued by supplementation with zinc. Additionally, purified recombinant ZevA was found to bind to zinc with high affinity. Together, these data demonstrate that zevAB is a novel virulence factor important for zinc utilization of H. influenzae under conditions where zinc is limiting. Furthermore, evidence presented here suggests that zinc limitation is likely an important mechanism for host defense against pathogens during lung infection.
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76
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Hiron A, Posteraro B, Carrière M, Remy L, Delporte C, La Sorda M, Sanguinetti M, Juillard V, Borezée-Durant E. A nickel ABC-transporter of Staphylococcus aureus is involved in urinary tract infection. Mol Microbiol 2011; 77:1246-60. [PMID: 20662775 DOI: 10.1111/j.1365-2958.2010.07287.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The oligopeptide transport systems Opp belong to the nickel/peptide/opine PepT subfamily of ABC-transporters. The opportunist pathogen Staphylococcus aureus encodes four putative Opps and one orphean substrate binding protein Opp5A. Here, we report that the Opp2 permease complex (Opp2BCDF) and Opp5A are involved in nickel uptake and then renamed them NikBCDE and NikA respectively. S. aureus carries also a high-affinity nickel transporter NixA belonging to the NiCoT family of secondary transporters. The activity of these two nickel transporters determine that of urease, a multimeric nickel-dependent enzyme mainly involved in the neutralization of acidic environments. However, only the Nik system was responsible for the neutralization and deposit of pH-dependent crystals in human urine. Inactivation of the nik genes affected bacterial colonization of mouse urinary tract, as well as the 50% infective dose levels compared with the parental and nixA strains. Finally, complementation of the nik mutations restored bacterial colonization. Together, our results suggest a role for the Nik system in the urinary tract infection by S. aureus, probably due to the urease-mediated pH increase of the urine.
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Affiliation(s)
- Aurelia Hiron
- UMR1319 Micalis, Institut National de la Recherche Agronomique, 78352 Jouy en Josas, France
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77
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Eitinger T, Rodionov DA, Grote M, Schneider E. Canonical and ECF-type ATP-binding cassette importers in prokaryotes: diversity in modular organization and cellular functions. FEMS Microbiol Rev 2011; 35:3-67. [PMID: 20497229 DOI: 10.1111/j.1574-6976.2010.00230.x] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Thomas Eitinger
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Berlin, Germany
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78
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Bolchi A, Ruotolo R, Marchini G, Vurro E, di Toppi LS, Kohler A, Tisserant E, Martin F, Ottonello S. Genome-wide inventory of metal homeostasis-related gene products including a functional phytochelatin synthase in the hypogeous mycorrhizal fungus Tuber melanosporum. Fungal Genet Biol 2010; 48:573-84. [PMID: 21094264 DOI: 10.1016/j.fgb.2010.11.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 10/27/2010] [Accepted: 11/07/2010] [Indexed: 11/27/2022]
Abstract
Ectomycorrhizal fungi are thought to enhance mineral nutrition of their host plants and to confer increased tolerance toward toxic metals. However, a global view of metal homeostasis-related genes and pathways in these organisms is still lacking. Building upon the genome sequence of Tuber melanosporum and on transcriptome analyses, we set out to systematically identify metal homeostasis-related genes in this plant-symbiotic ascomycete. Candidate gene products (101) were subdivided into three major functional classes: (i) metal transport (58); (ii) oxidative stress defence (32); (iii) metal detoxification (11). The latter class includes a small-size metallothionein (TmelMT) that was functionally validated in yeast, and phytochelatin synthase (TmelPCS), the first enzyme of this kind to be described in filamentous ascomycetes. Recombinant TmelPCS was shown to support GSH-dependent, metal-activated phytochelatin synthesis in vitro and to afford increased Cd/Cu tolerance to metal hypersensitive yeast strains. Metal transporters, especially those related to Cu and Zn trafficking, displayed the highest expression levels in mycorrhizae, suggesting extensive translocation of both metals to root cells as well as to fungal metalloenzymes (e.g., laccase) that are strongly upregulated in symbiotic hyphae.
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Affiliation(s)
- Angelo Bolchi
- Department of Biochemistry and Molecular and Functional Biology, University of Parma, 43100 Parma, Italy
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79
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Siche S, Neubauer O, Hebbeln P, Eitinger T. A bipartite S unit of an ECF-type cobalt transporter. Res Microbiol 2010; 161:824-9. [PMID: 20868747 DOI: 10.1016/j.resmic.2010.09.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 07/31/2010] [Indexed: 11/25/2022]
Abstract
ECF-class transporters comprise abundant importers for micronutrients such as vitamins and transition-metal ions, and for intermediates of salvage pathways in bacteria and archaea. They are composed of ABC ATPases (A units), a conserved transmembrane protein (T unit) and a substrate-specific transmembrane protein (S unit or core transporter). Here we analyzed the function of an ECF-type Co(2+) transporter (CbiMNQO) and, in particular, the derived bipartite S unit CbiMN. CbiMN was characterized as the minimal unit that functions as a Co(2+) transporter. Neither the solitary CbiM nor a tripartite CbiMQO complex was active, indicating an essential role for CbiN. CbiN was loosely bound in CbiMNQO and CbiMN complexes, and did not copurify with its partners. Generating a contiguous reading frame resulted in a Cbi(MN) fusion protein that displayed Co(2+)-transport activity and interacted with CbiQO in vivo. Sixteen variants of Cbi(MN) with modifications in the strongly conserved N-terminal stretch of ten amino-acid residues were constructed and analyzed for transport activity. The results indicate that the length and sequence of this region are critical for functioning of the core transporter. Specifically, they point to essential roles of His₂ and the distance of His₂ to the amino group of the peptide chain in metal recognition.
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Affiliation(s)
- Stefanie Siche
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestraße 117, 10115 Berlin, Germany.
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80
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Li J, Pandeya D, Nath K, Zulfugarov IS, Yoo SC, Zhang H, Yoo JH, Cho SH, Koh HJ, Kim DS, Seo HS, Kang BC, Lee CH, Paek NC. ZEBRA-NECROSIS, a thylakoid-bound protein, is critical for the photoprotection of developing chloroplasts during early leaf development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 62:713-25. [PMID: 20202171 DOI: 10.1111/j.1365-313x.2010.04183.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The zebra-necrosis (zn) mutant of rice (Oryza sativa) produces transversely green/yellow-striped leaves. The mutant phenotype is formed by unequal impairment of chloroplast biogenesis before emergence from the leaf sheath under alternate light/dark or high/low temperatures (restrictive), but not under constant light and temperature (permissive) conditions. Map-based cloning revealed that ZN encodes a thylakoid-bound protein of unknown function. Virus-induced gene silencing of a ZN homolog in Nicotiana benthamiana causes leaf variegation with sporadic green/yellow sectors, indicating that ZN is essential for chloroplast biogenesis during early leaf development. Necrotic lesions often occur in the yellow sectors as a result of an excessive accumulation of reactive oxygen species (ROS). The phenotypic severity (leaf variegation and necrosis) and ROS levels are positively correlated with an increase in light intensity under restrictive conditions. In the mutant leaves, chlorophyll (Chl) metabolism, ROS scavenging activities, maximum quantum yield of photosystem II (PSII), and structures and functions of the photosynthetic complexes are normal in the Chl-containing cells, suggesting that ROS are mainly generated from the defective plastids of the Chl-free cells. The PSII activity of normal chloroplasts is hypersensitive to photoinhibition because the recovery rates of PSII are much slower. In the PSII repair, the degradation of damaged D1 is not impaired, suggesting a reduced activity of new D1 synthesis, possibly because of higher levels of ROS generated from the Chl-free cells by excess light. Together, we propose that ZN is required for protecting developing chloroplasts, especially during the assembly of thylakoid protein complexes, from incidental light after darkness.
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Affiliation(s)
- Jinjie Li
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
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81
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Sangari FJ, Cayón AM, Seoane A, García-Lobo JM. Brucella abortus ure2 region contains an acid-activated urea transporter and a nickel transport system. BMC Microbiol 2010; 10:107. [PMID: 20380737 PMCID: PMC2868824 DOI: 10.1186/1471-2180-10-107] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 04/10/2010] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Urease is a virulence factor that plays a role in the resistance of Brucella to low pH conditions, both in vivo and in vitro. Brucella contains two separate urease gene clusters, ure1 and ure2. Although only ure1 codes for an active urease, ure2 is also transcribed, but its contribution to Brucella biology is unknown. RESULTS Re-examination of the ure2 locus showed that the operon includes five genes downstream of ureABCEFGDT that are orthologs to a nikKMLQO cluster encoding an ECF-type transport system for nickel. ureT and nikO mutants were constructed and analyzed for urease activity and acid resistance. A non-polar ureT mutant was unaffected in urease activity at neutral pH but showed a significantly decreased activity at acidic pH. It also showed a decreased survival rate to pH 2 at low concentration of urea when compared to the wild type. The nikO mutant had decreased urease activity and acid resistance at all urea concentrations tested, and this phenotype could be reverted by the addition of nickel to the growth medium. CONCLUSIONS Based on these results, we concluded that the operon ure2 codes for an acid-activated urea transporter and a nickel transporter necessary for the maximal activity of the urease whose structural subunits are encoded exclusively by the genes in the ure1 operon.
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Affiliation(s)
- Félix J Sangari
- Departamento de Biología Molecular, Universidad de Cantabria, and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), UC-CSIC-IDICAN, Santander, Spain
| | - Ana M Cayón
- Departamento de Biología Molecular, Universidad de Cantabria, and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), UC-CSIC-IDICAN, Santander, Spain
| | - Asunción Seoane
- Departamento de Biología Molecular, Universidad de Cantabria, and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), UC-CSIC-IDICAN, Santander, Spain
| | - Juan M García-Lobo
- Departamento de Biología Molecular, Universidad de Cantabria, and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), UC-CSIC-IDICAN, Santander, Spain
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82
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Schauer K, Muller C, Carrière M, Labigne A, Cavazza C, De Reuse H. The Helicobacter pylori GroES cochaperonin HspA functions as a specialized nickel chaperone and sequestration protein through its unique C-terminal extension. J Bacteriol 2010; 192:1231-7. [PMID: 20061471 PMCID: PMC2820833 DOI: 10.1128/jb.01216-09] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Accepted: 12/27/2009] [Indexed: 02/06/2023] Open
Abstract
The transition metal nickel plays a central role in the human gastric pathogen Helicobacter pylori because it is required for two enzymes indispensable for colonization, the nickel metalloenzyme urease and [NiFe] hydrogenase. To sustain nickel availability for these metalloenzymes while providing protection from the metal's harmful effects, H. pylori is equipped with several specific nickel-binding proteins. Among these, H. pylori possesses a particular chaperone, HspA, that is a homolog of the highly conserved and essential bacterial heat shock protein GroES. HspA contains a unique His-rich C-terminal extension and was demonstrated to bind nickel in vitro. To investigate the function of this extension in H. pylori, we constructed mutants carrying either a complete deletion or point mutations in critical residues of this domain. All mutants presented a decreased intracellular nickel content measured by inductively coupled plasma mass spectrometry (ICP-MS) and reduced nickel tolerance. While urease activity was unaffected in the mutants, [NiFe] hydrogenase activity was significantly diminished when the C-terminal extension of HspA was mutated. We conclude that H. pylori HspA is involved in intracellular nickel sequestration and detoxification and plays a novel role as a specialized nickel chaperone involved in nickel-dependent maturation of hydrogenase.
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Affiliation(s)
- Kristine Schauer
- Institut Pasteur, Département de Microbiologie, Unité Postulante Pathogenèse de Helicobacter, 75724 Paris Cedex 15, France, Institut Pasteur, Département de Microbiologie, Unité de Pathogénie Bactérienne des Muqueuses, 75724 Paris Cedex 15, France, UMR3299 CEA-CNRS SIS2M, LSDRNI CEA/Saclay, 91191 Gif-sur-Yvette, France, Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale J.P. Ebel, CEA, CNRS, Université Joseph Fourier, 41, rue Jules Horowitz, 38027 Grenoble Cedex 01, France
| | - Cécile Muller
- Institut Pasteur, Département de Microbiologie, Unité Postulante Pathogenèse de Helicobacter, 75724 Paris Cedex 15, France, Institut Pasteur, Département de Microbiologie, Unité de Pathogénie Bactérienne des Muqueuses, 75724 Paris Cedex 15, France, UMR3299 CEA-CNRS SIS2M, LSDRNI CEA/Saclay, 91191 Gif-sur-Yvette, France, Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale J.P. Ebel, CEA, CNRS, Université Joseph Fourier, 41, rue Jules Horowitz, 38027 Grenoble Cedex 01, France
| | - Marie Carrière
- Institut Pasteur, Département de Microbiologie, Unité Postulante Pathogenèse de Helicobacter, 75724 Paris Cedex 15, France, Institut Pasteur, Département de Microbiologie, Unité de Pathogénie Bactérienne des Muqueuses, 75724 Paris Cedex 15, France, UMR3299 CEA-CNRS SIS2M, LSDRNI CEA/Saclay, 91191 Gif-sur-Yvette, France, Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale J.P. Ebel, CEA, CNRS, Université Joseph Fourier, 41, rue Jules Horowitz, 38027 Grenoble Cedex 01, France
| | - Agnès Labigne
- Institut Pasteur, Département de Microbiologie, Unité Postulante Pathogenèse de Helicobacter, 75724 Paris Cedex 15, France, Institut Pasteur, Département de Microbiologie, Unité de Pathogénie Bactérienne des Muqueuses, 75724 Paris Cedex 15, France, UMR3299 CEA-CNRS SIS2M, LSDRNI CEA/Saclay, 91191 Gif-sur-Yvette, France, Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale J.P. Ebel, CEA, CNRS, Université Joseph Fourier, 41, rue Jules Horowitz, 38027 Grenoble Cedex 01, France
| | - Christine Cavazza
- Institut Pasteur, Département de Microbiologie, Unité Postulante Pathogenèse de Helicobacter, 75724 Paris Cedex 15, France, Institut Pasteur, Département de Microbiologie, Unité de Pathogénie Bactérienne des Muqueuses, 75724 Paris Cedex 15, France, UMR3299 CEA-CNRS SIS2M, LSDRNI CEA/Saclay, 91191 Gif-sur-Yvette, France, Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale J.P. Ebel, CEA, CNRS, Université Joseph Fourier, 41, rue Jules Horowitz, 38027 Grenoble Cedex 01, France
| | - Hilde De Reuse
- Institut Pasteur, Département de Microbiologie, Unité Postulante Pathogenèse de Helicobacter, 75724 Paris Cedex 15, France, Institut Pasteur, Département de Microbiologie, Unité de Pathogénie Bactérienne des Muqueuses, 75724 Paris Cedex 15, France, UMR3299 CEA-CNRS SIS2M, LSDRNI CEA/Saclay, 91191 Gif-sur-Yvette, France, Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale J.P. Ebel, CEA, CNRS, Université Joseph Fourier, 41, rue Jules Horowitz, 38027 Grenoble Cedex 01, France
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Brito B, Prieto RI, Cabrera E, Mandrand-Berthelot MA, Imperial J, Ruiz-Argüeso T, Palacios JM. Rhizobium leguminosarum hupE encodes a nickel transporter required for hydrogenase activity. J Bacteriol 2010; 192:925-35. [PMID: 20023036 PMCID: PMC2812973 DOI: 10.1128/jb.01045-09] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 12/07/2009] [Indexed: 02/04/2023] Open
Abstract
Synthesis of the hydrogen uptake (Hup) system in Rhizobium leguminosarum bv. viciae requires the function of an 18-gene cluster (hupSLCDEFGHIJK-hypABFCDEX). Among them, the hupE gene encodes a protein showing six transmembrane domains for which a potential role as a nickel permease has been proposed. In this paper, we further characterize the nickel transport capacity of HupE and that of the translated product of hupE2, a hydrogenase-unlinked gene identified in the R. leguminosarum genome. HupE2 is a potential membrane protein that shows 48% amino acid sequence identity with HupE. Expression of both genes in the Escherichia coli nikABCDE mutant strain HYD723 restored hydrogenase activity and nickel transport. However, nickel transport assays revealed that HupE and HupE2 displayed different levels of nickel uptake. Site-directed mutagenesis of histidine residues in HupE revealed two motifs (HX(5)DH and FHGX[AV]HGXE) that are required for HupE functionality. An R. leguminosarum double mutant, SPF22A (hupE hupE2), exhibited reduced levels of hydrogenase activity in free-living cells, and this phenotype was complemented by nickel supplementation. Low levels of symbiotic hydrogenase activity were also observed in SPF22A bacteroid cells from lentil (Lens culinaris L.) root nodules but not in pea (Pisum sativum L.) bacteroids. Moreover, heterologous expression of the R. leguminosarum hup system in bacteroid cells of Rhizobium tropici and Mesorhizobium loti displayed reduced levels of hydrogen uptake in the absence of hupE. These data support the role of R. leguminosarum HupE as a nickel permease required for hydrogen uptake under both free-living and symbiotic conditions.
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Affiliation(s)
- Belén Brito
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40, km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain, Université Lyon, F-69622 Lyon, Université Lyon 1, Villeurbanne, INSA de Lyon, F-69621 Villeurbanne, and CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Lyon, France, Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Rosa-Isabel Prieto
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40, km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain, Université Lyon, F-69622 Lyon, Université Lyon 1, Villeurbanne, INSA de Lyon, F-69621 Villeurbanne, and CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Lyon, France, Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Ezequiel Cabrera
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40, km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain, Université Lyon, F-69622 Lyon, Université Lyon 1, Villeurbanne, INSA de Lyon, F-69621 Villeurbanne, and CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Lyon, France, Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Marie-Andrée Mandrand-Berthelot
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40, km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain, Université Lyon, F-69622 Lyon, Université Lyon 1, Villeurbanne, INSA de Lyon, F-69621 Villeurbanne, and CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Lyon, France, Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Juan Imperial
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40, km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain, Université Lyon, F-69622 Lyon, Université Lyon 1, Villeurbanne, INSA de Lyon, F-69621 Villeurbanne, and CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Lyon, France, Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Tomás Ruiz-Argüeso
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40, km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain, Université Lyon, F-69622 Lyon, Université Lyon 1, Villeurbanne, INSA de Lyon, F-69621 Villeurbanne, and CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Lyon, France, Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - José-Manuel Palacios
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40, km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain, Université Lyon, F-69622 Lyon, Université Lyon 1, Villeurbanne, INSA de Lyon, F-69621 Villeurbanne, and CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Lyon, France, Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
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84
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Ma Z, Jacobsen FE, Giedroc DP. Coordination chemistry of bacterial metal transport and sensing. Chem Rev 2009; 109:4644-81. [PMID: 19788177 PMCID: PMC2783614 DOI: 10.1021/cr900077w] [Citation(s) in RCA: 434] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Zhen Ma
- Department of Chemistry, Indiana University, Bloomington, IN 47401-7005 USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128 USA
| | - Faith E. Jacobsen
- Department of Chemistry, Indiana University, Bloomington, IN 47401-7005 USA
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47401-7005 USA
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85
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Affiliation(s)
- Yanjie Li
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Deborah B. Zamble
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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86
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Zhang Y, Gladyshev VN. Comparative Genomics of Trace Elements: Emerging Dynamic View of Trace Element Utilization and Function. Chem Rev 2009; 109:4828-61. [DOI: 10.1021/cr800557s] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yan Zhang
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0664
| | - Vadim N. Gladyshev
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0664
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87
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Chen Z, Watanabe T, Shinano T, Okazaki K, Osaki M. Rapid characterization of plant mutants with an altered ion-profile: a case study using Lotus japonicus. THE NEW PHYTOLOGIST 2009; 181:795-801. [PMID: 19140942 DOI: 10.1111/j.1469-8137.2008.02730.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Legumes are second only to cereals in their importance to humans, and study of their functional genomics of nutrition and other trace elements is crucial for agricultural production and food fortification. We describe here an ionomic screening experiment carried out to investigate the accumulation of 15 elements in shoots of mutants of Lotus japonicus, a good genetic tool for legume study.Approximately 2000 mutagenized M2 plants were cultivated in a novel low-cost high-throughput system and their elemental profiles were determined by inductively coupled plasma mass spectroscopy (ICP-MS).After triple-checking the element concentrations in M2 or M3 plant shoots, 31 mutants with altered elemental profiles were identified. Surprisingly, the number of genes regulating essential elements was similar to the number regulating nonessential elements. Magnesium (Mg) and nickel (Ni) were correlated in a number of mutants.Further investigation suggested that phosphorus (P) and cobalt (Co) might be involved in the ion homeostasis network of Mg and Ni.The results suggested that the pathways for element uptake or translocation were highly linked through the ion transport-related genes. Ionomics proved to be a powerful functional genomics tool for determining genes related to ion homeostasisin this study.
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Affiliation(s)
- Zheng Chen
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Toshihiro Watanabe
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Takuro Shinano
- National Agricultural Research Center for Hokkaido Region, Sapporo, 062-8555, Japan
| | - Keiki Okazaki
- National Agricultural Research Center for Hokkaido Region, Sapporo, 062-8555, Japan
| | - Mitsuru Osaki
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
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88
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Zhang Y, Rodionov DA, Gelfand MS, Gladyshev VN. Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics 2009; 10:78. [PMID: 19208259 PMCID: PMC2667541 DOI: 10.1186/1471-2164-10-78] [Citation(s) in RCA: 182] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2008] [Accepted: 02/10/2009] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Nickel (Ni) and cobalt (Co) are trace elements required for a variety of biological processes. Ni is directly coordinated by proteins, whereas Co is mainly used as a component of vitamin B12. Although a number of Ni and Co-dependent enzymes have been characterized, systematic evolutionary analyses of utilization of these metals are limited. RESULTS We carried out comparative genomic analyses to examine occurrence and evolutionary dynamics of the use of Ni and Co at the level of (i) transport systems, and (ii) metalloproteomes. Our data show that both metals are widely used in bacteria and archaea. Cbi/NikMNQO is the most common prokaryotic Ni/Co transporter, while Ni-dependent urease and Ni-Fe hydrogenase, and B12-dependent methionine synthase (MetH), ribonucleotide reductase and methylmalonyl-CoA mutase are the most widespread metalloproteins for Ni and Co, respectively. Occurrence of other metalloenzymes showed a mosaic distribution and a new B12-dependent protein family was predicted. Deltaproteobacteria and Methanosarcina generally have larger Ni- and Co-dependent proteomes. On the other hand, utilization of these two metals is limited in eukaryotes, and very few of these organisms utilize both of them. The Ni-utilizing eukaryotes are mostly fungi (except saccharomycotina) and plants, whereas most B12-utilizing organisms are animals. The NiCoT transporter family is the most widespread eukaryotic Ni transporter, and eukaryotic urease and MetH are the most common Ni- and B12-dependent enzymes, respectively. Finally, investigation of environmental and other conditions and identity of organisms that show dependence on Ni or Co revealed that host-associated organisms (particularly obligate intracellular parasites and endosymbionts) have a tendency for loss of Ni/Co utilization. CONCLUSION Our data provide information on the evolutionary dynamics of Ni and Co utilization and highlight widespread use of these metals in the three domains of life, yet only a limited number of user proteins.
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Affiliation(s)
- Yan Zhang
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, NE 68588-0664, USA.
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89
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Mabilleau G, Kwon YM, Pandit H, Murray DW, Sabokbar A. Metal-on-metal hip resurfacing arthroplasty: a review of periprosthetic biological reactions. Acta Orthop 2008; 79:734-47. [PMID: 19085489 DOI: 10.1080/17453670810016795] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Metal-on-metal hip resurfacing arthroplasty has undergone a recent resurgence as an alternative treatment option for young and active patients with significant osteoarthritis. The claimed advantages of metal-on-metal hip resurfacing arthroplasty include lower wear rate, preservation of bone stock for subsequent revision procedures, restoration of anatomic hip mechanics, and enhanced stability due to the larger diameter of articulation. A disadvantage, however, is that the metal-on-metal resurfacing releases large amounts of very small wear particles and metal ions. The long-term biological consequences of the exposure to these Co-Cr particles and ions remain largely unknown. The purpose of this review is to provide an overview of the current literature on the adverse periprosthetic biological reactions associated with metal-on-metal hip resurfacing arthroplasty.
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Affiliation(s)
- Guillaume Mabilleau
- Nuffield Department of Orthopaedic Surgery, Institute of Musculoskeletal Science, Botnar Research Centre, University of Oxford, Oxford, UK.
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90
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Abstract
The specific and tightly controlled transport of numerous nutrients and metabolites across cellular membranes is crucial to all forms of life. However, many of the transporter proteins involved have yet to be identified, including the vitamin transporters in various human pathogens, whose growth depends strictly on vitamin uptake. Comparative analysis of the ever-growing collection of microbial genomes coupled with experimental validation enables the discovery of such transporters. Here, we used this approach to discover an abundant class of vitamin transporters in prokaryotes with an unprecedented architecture. These transporters have energy-coupling modules comprised of a conserved transmembrane protein and two nucleotide binding proteins similar to those of ATP binding cassette (ABC) transporters, but unlike ABC transporters, they use small integral membrane proteins to capture specific substrates. We identified 21 families of these substrate capture proteins, each with a different specificity predicted by genome context analyses. Roughly half of the substrate capture proteins (335 cases) have a dedicated energizing module, but in 459 cases distributed among almost 100 gram-positive bacteria, including numerous human pathogens, different and unrelated substrate capture proteins share the same energy-coupling module. The shared use of energy-coupling modules was experimentally confirmed for folate, thiamine, and riboflavin transporters. We propose the name energy-coupling factor transporters for the new class of membrane transporters.
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91
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Cupriavidus metallidurans: evolution of a metal-resistant bacterium. Antonie van Leeuwenhoek 2008; 96:115-39. [DOI: 10.1007/s10482-008-9284-5] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Accepted: 09/17/2008] [Indexed: 10/21/2022]
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92
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Riccardi G, Milano A, Pasca MR, Nies DH. Genomic analysis of zinc homeostasis inMycobacterium tuberculosis. FEMS Microbiol Lett 2008; 287:1-7. [DOI: 10.1111/j.1574-6968.2008.01320.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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93
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94
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Nicolás MF, Barcellos FG, Nehab Hess P, Hungria M. ABC transporters in Mycoplasma hyopneumoniae and Mycoplasma synoviae: insights into evolution and pathogenicity. Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000200006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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95
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Marrero J, Auling G, Coto O, Nies DH. High-level resistance to cobalt and nickel but probably no transenvelope efflux: Metal resistance in the Cuban Serratia marcescens strain C-1. MICROBIAL ECOLOGY 2007; 53:123-33. [PMID: 17186148 DOI: 10.1007/s00248-006-9152-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Revised: 07/21/2006] [Accepted: 07/26/2006] [Indexed: 05/13/2023]
Abstract
Molecular mechanisms underlying inducible cobalt and nickel resistance of a bacterial strain isolated from a Cuban serpentine deposit were investigated. This strain C-1 was assigned to Serratia marcescens by 16S rDNA analysis and DNA/DNA hybridization. Genes involved in metal resistance were identified by transposon mutagenesis followed by selection for cobalt- and nickel-sensitive derivatives. The transposon insertion causing the highest decrease in metal resistance was located in the ncrABC determinant. The predicted NcrA product was a NreB ortholog of the major facilitator protein superfamily and central for cobalt/nickel resistance in S. marcescens strain C-1. NcrA also mediated metal resistance in Escherichia coli and caused decreased accumulation of Co(II) and Ni(II) in this heterologous host. NcrB may be a regulatory protein. NcrC was a protein of the nickel-cobalt transport (NiCoT) protein family and necessary for full metal resistance in E. coli, but only when NcrA was also present. Without NcrA, NcrC caused a slight decrease in metal resistance and mediated increased accumulation of Ni(II) and Co(II). Because the cytoplasmic metal concentration can be assumed to be the result of a flow equilibrium of uptake and efflux processes, this interplay between metal uptake system NcrC and metal efflux system NcrA may contribute to nickel and cobalt resistance in this bacterium.
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Affiliation(s)
- Jeannette Marrero
- Institut für Mikrobiologie, Martin-Luther-Universität Halle-Wittenberg, Halle/Saale, Germany
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96
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Hoffmann D, Gutekunst K, Klissenbauer M, Schulz-Friedrich R, Appel J. Mutagenesis of hydrogenase accessory genes of Synechocystis sp. PCC 6803. Additional homologues of hypA and hypB are not active in hydrogenase maturation. FEBS J 2006; 273:4516-27. [PMID: 16972939 DOI: 10.1111/j.1742-4658.2006.05460.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genes homologous to hydrogenase accessory genes are scattered over the whole genome in the cyanobacterium Synechocystis sp. PCC 6803. Deletion and insertion mutants of hypA1 (slr1675), hypB1 (sll1432), hypC, hypD, hypE and hypF were constructed and showed no hydrogenase activity. Involvement of the respective genes in maturation of the enzyme was confirmed by complementation. Deletion of the additional homologues hypA2 (sll1078) and hypB2 (sll1079) had no effect on hydrogenase activity. Thus, hypA1 and hypB1 are specific for hydrogenase maturation. We suggest that hypA2 and hypB2 are involved in a different metal insertion process. The hydrogenase activity of DeltahypA1 and DeltahypB1 could be increased by the addition of nickel, suggesting that HypA1 and HypB1 are involved in the insertion of nickel into the active site of the enzyme. The urease activity of all the hypA and hypB single- and double-mutants was the same as in wild-type cells. Therefore, there seems to be no common function for these two hyp genes in hydrogenase and urease maturation in Synechocystis. Similarity searches in the whole genome yielded Slr1876 as the best candidate for the hydrogenase-specific protease. The respective deletion mutant had no hydrogenase activity. Deletion of hupE had no effect on hydrogenase activity but resulted in a mutant unable to grow in a medium containing the metal chelator nitrilotriacetate. Growth was resumed upon the addition of cobalt or methionine. Because the latter is synthesized by a cobalt-requiring enzyme in Synechocystis, HupE is a good candidate for a cobalt transporter in cyanobacteria.
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Affiliation(s)
- Dörte Hoffmann
- Botanisches Institut, Christian-Albrechts University, Kiel, Germany
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97
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Rodionov DA, Hebbeln P, Gelfand MS, Eitinger T. Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters. J Bacteriol 2006; 188:317-27. [PMID: 16352848 PMCID: PMC1317602 DOI: 10.1128/jb.188.1.317-327.2006] [Citation(s) in RCA: 207] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The transition metals nickel and cobalt, essential components of many enzymes, are taken up by specific transport systems of several different types. We integrated in silico and in vivo methods for the analysis of various protein families containing both nickel and cobalt transport systems in prokaryotes. For functional annotation of genes, we used two comparative genomic approaches: identification of regulatory signals and analysis of the genomic positions of genes encoding candidate nickel/cobalt transporters. The nickel-responsive repressor NikR regulates many nickel uptake systems, though the NikR-binding signal is divergent in various taxonomic groups of bacteria and archaea. B(12) riboswitches regulate most of the candidate cobalt transporters in bacteria. The nickel/cobalt transporter genes are often colocalized with genes for nickel-dependent or coenzyme B(12) biosynthesis enzymes. Nickel/cobalt transporters of different families, including the previously known NiCoT, UreH, and HupE/UreJ families of secondary systems and the NikABCDE ABC-type transporters, showed a mosaic distribution in prokaryotic genomes. In silico analyses identified CbiMNQO and NikMNQO as the most widespread groups of microbial transporters for cobalt and nickel ions. These unusual uptake systems contain an ABC protein (CbiO or NikO) but lack an extracytoplasmic solute-binding protein. Experimental analysis confirmed metal transport activity for three members of this family and demonstrated significant activity for a basic module (CbiMN) of the Salmonella enterica serovar Typhimurium transporter.
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Affiliation(s)
- Dmitry A Rodionov
- The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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98
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Callahan DL, Baker AJM, Kolev SD, Wedd AG. Metal ion ligands in hyperaccumulating plants. J Biol Inorg Chem 2005; 11:2-12. [PMID: 16328457 DOI: 10.1007/s00775-005-0056-7] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2005] [Accepted: 10/27/2005] [Indexed: 12/22/2022]
Abstract
Metal-hyperaccumulating plants have the ability to take up extraordinary quantities of certain metal ions without succumbing to toxic effects. Most hyperaccumulators select for particular metals but the mechanisms of selection are not understood at the molecular level. While there are many metal-binding biomolecules, this review focuses only on ligands that have been reported to play a role in sequestering, transporting or storing the accumulated metal. These include citrate, histidine and the phytosiderophores. The metal detoxification role of metallothioneins and phytochelatins in plants is also discussed.
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Affiliation(s)
- Damien L Callahan
- School of Chemistry, The University of Melbourne, 3010 Melbourne, Victoria, Australia
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