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Chen J, Wang L, Li W, Zheng X, Li X. Genomic Insights Into Cadmium Resistance of a Newly Isolated, Plasmid-Free Cellulomonas sp. Strain Y8. Front Microbiol 2022; 12:784575. [PMID: 35154027 PMCID: PMC8832061 DOI: 10.3389/fmicb.2021.784575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Our current knowledge on bacterial cadmium (Cd) resistance is mainly based on the functional exploration of specific Cd-resistance genes. In this study, we carried out a genomic study on Cd resistance of a newly isolated Cellulomonas strain with a MIC of 5 mM Cd. Full genome of the strain, with a genome size of 4.47 M bp and GC-content of 75.35%, was obtained through high-quality sequencing. Genome-wide annotations identified 54 heavy metal-related genes. Four potential Cd-resistance genes, namely zntAY8, copAY8, HMTY8, and czcDY8, were subjected to functional exploration. Quantitative PCR determination of in vivo expression showed that zntAY8, copAY8, and HMTY8 were strongly Cd-inducible. Expression of the three inducible genes against time and Cd concentrations were further quantified. It is found that zntAY8 responded more strongly to higher Cd concentrations, while expression of copAY8 and HMTY8 increased over time at lower Cd concentrations. Heterologous expression of the four genes in Cd-sensitive Escherichia coli led to different impacts on hosts’ Cd sorption, with an 87% reduction by zntAY8 and a 3.7-fold increase by HMTY8. In conclusion, a Cd-resistant Cellulomonas sp. strain was isolated, whose genome harbors a diverse panel of metal-resistance genes. Cd resistance in the strain is not controlled by a dedicated gene alone, but by several gene systems collectively whose roles are probably time- and dose-dependent. The plasmid-free, high-GC strain Y8 may provide a platform for exploring heavy metal genomics of the Cellulomonas genus.
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Affiliation(s)
- Jinghao Chen
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Likun Wang
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Wenjun Li
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Zheng
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Xiaofang Li
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- *Correspondence: Xiaofang Li,
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Ly K, Bartho JD, Eicher T, Pos KM, Mitra AK. A novel packing arrangement of AcrB in the lipid bilayer membrane. FEBS Lett 2014; 588:4776-83. [PMID: 25451234 DOI: 10.1016/j.febslet.2014.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 10/20/2014] [Accepted: 11/05/2014] [Indexed: 12/01/2022]
Abstract
The central component AcrB of the Escherichia coli drug efflux complex AcrA-AcrB-TolC has been extensively investigated by X-ray crystallography of detergent-protein 3-D crystals. In these crystals, AcrB packs as trimers - the functional unit. We visualized the AcrB-AcrB interaction in its native environment by examining E. coli lipid reconstituted 2-D crystals, which were overwhelmingly formed by asymmetric trimers stabilized by strongly-interacting monomers from adjacent trimers. Most interestingly, we observed lattices formed by an arrangement of AcrB monomers distinct from that in traditional trimers. This hitherto unobserved packing, might play a role in the biogenesis of trimeric AcrB.
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Affiliation(s)
- K Ly
- School of Biological Sciences, Private Bag 92019, University of Auckland, Auckland, New Zealand
| | - J D Bartho
- School of Biological Sciences, Private Bag 92019, University of Auckland, Auckland, New Zealand
| | - T Eicher
- Institute of Biochemistry, Max-von-Laue-Str. 9, Goethe-University Frankfurt am Main, Germany(1)
| | - K M Pos
- Institute of Biochemistry, Max-von-Laue-Str. 9, Goethe-University Frankfurt am Main, Germany(1)
| | - A K Mitra
- School of Biological Sciences, Private Bag 92019, University of Auckland, Auckland, New Zealand
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3
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Ferrandez Y, Dezi M, Bosco M, Urvoas A, Valerio-Lepiniec M, Le Bon C, Giusti F, Broutin I, Durand G, Polidori A, Popot JL, Picard M, Minard P. Amphipol-mediated screening of molecular orthoses specific for membrane protein targets. J Membr Biol 2014; 247:925-40. [PMID: 25086771 DOI: 10.1007/s00232-014-9707-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 07/14/2014] [Indexed: 12/11/2022]
Abstract
Specific, tight-binding protein partners are valuable helpers to facilitate membrane protein (MP) crystallization, because they can i) stabilize the protein, ii) reduce its conformational heterogeneity, and iii) increase the polar surface from which well-ordered crystals can grow. The design and production of a new family of synthetic scaffolds (dubbed αReps, for "artificial alpha repeat protein") have been recently described. The stabilization and immobilization of MPs in a functional state are an absolute prerequisite for the screening of binders that recognize specifically their native conformation. We present here a general procedure for the selection of αReps specific of any MP. It relies on the use of biotinylated amphipols, which act as a universal "Velcro" to stabilize, and immobilize MP targets onto streptavidin-coated solid supports, thus doing away with the need to tag the protein itself.
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Affiliation(s)
- Yann Ferrandez
- Laboratoire de Modélisation et Ingénierie des Protéines, IBBMC UMR 8619, CNRS/Université Paris Sud, 91405, Orsay, France
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4
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Mealman TD, Zhou M, Affandi T, Chacón KN, Aranguren ME, Blackburn NJ, Wysocki VH, McEvoy MM. N-terminal region of CusB is sufficient for metal binding and metal transfer with the metallochaperone CusF. Biochemistry 2012; 51:6767-75. [PMID: 22812620 DOI: 10.1021/bi300596a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Gram-negative bacteria, such as Escherichia coli, utilize efflux resistance systems in order to expel toxins from their cells. Heavy-metal resistance is mediated by resistance nodulation cell division (RND)-based efflux pumps composed of a tripartite complex that includes an RND-transporter, an outer-membrane factor (OMF), and a membrane fusion protein (MFP) that spans the periplasmic space. MFPs are necessary for complex assembly and have been hypothesized to play an active role in substrate efflux. Crystal structures of MFPs are available, however incomplete, as large portions of the apparently disordered N- and C-termini are unresolved. Such is the case for CusB, the MFP of the E. coli Cu(I)/Ag(I) efflux pump CusCFBA. In this work, we have investigated the structure and function of the N-terminal region of CusB, which includes the metal-binding site and is missing from previously determined crystal structures. Results from mass spectrometry and X-ray absorption spectroscopy show that the isolated N-terminal 61 residues (CusB-NT) bind metal in a 1:1 stoichiometry with a coordination site composed of M21, M36, and M38, consistent with full-length CusB. NMR spectra show that CusB-NT is mostly disordered in the apo state; however, some slight structure is adopted upon metal binding. Much of the intact protein's function is maintained in this fragment as CusB-NT binds metal in vivo and in vitro, and metal is transferred between the metallochaperone CusF and CusB-NT in vitro. Functional analysis in vivo shows that full-length CusB is necessary in an intact polypeptide for full metal resistance, though CusB-NT alone can contribute partial metal resistance. These findings reinforce the theory that the role of CusB is not only to bind metal but also to play an active role in efflux.
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Affiliation(s)
- Tiffany D Mealman
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
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5
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Mealman TD, Blackburn NJ, McEvoy MM. Metal export by CusCFBA, the periplasmic Cu(I)/Ag(I) transport system of Escherichia coli. CURRENT TOPICS IN MEMBRANES 2012; 69:163-96. [PMID: 23046651 DOI: 10.1016/b978-0-12-394390-3.00007-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
High levels of metal ions have the potential to cause cellular toxicity through a variety of mechanisms; therefore, cells have developed numerous systems that regulate their intracellular concentrations. The Cus resistance system aids in protection of Escherichia coli from high levels of Cu(I) and Ag(I) by actively transporting these metal ions to the extracellular environment. The Cus system forms a continuous complex, CusCBA, that spans the inner membrane, periplasm, and outer membrane of Gram-negative bacteria, together with a novel fourth component, the periplasmic metallochaperone, CusF. The metal-binding sites of CusA, CusB, and CusF are exquisitely tuned for Cu(I) and Ag(I), and thus effectively discriminate these ions for transport from other metals that may be required in the cell. Furthermore, direct transfer of metal from protein to protein within the Cus system during the transport process is likely to reduce the potential toxicity posed by the free metal ions. Here we review the wealth of structural, biochemical, and genetic information on the Cus system, which demonstrates the many intriguing aspects of function for metal-transporting efflux systems.
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Affiliation(s)
- Tiffany D Mealman
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
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Sequential mechanism of assembly of multidrug efflux pump AcrAB-TolC. ACTA ACUST UNITED AC 2011; 18:454-63. [PMID: 21513882 DOI: 10.1016/j.chembiol.2011.02.011] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 02/16/2011] [Accepted: 02/28/2011] [Indexed: 01/29/2023]
Abstract
Multidrug efflux pumps adversely affect both the clinical effectiveness of existing antibiotics and the discovery process to find new ones. In this study, we reconstituted and characterized by surface plasmon resonance the assembly of AcrAB-TolC, the archetypal multidrug efflux pump from Escherichia coli. We report that the periplasmic AcrA and the outer membrane channel TolC assemble high-affinity complexes with AcrB transporter independently from each other. Antibiotic novobiocin and MC-207,110 inhibitor bind to the immobilized AcrB but do not affect interactions between components of the complex. In contrast, DARPin inhibits interactions between AcrA and AcrB. Mutational opening of TolC channel decreases stability of interactions and promotes disassembly of the complex. The conformation of the membrane proximal domain of AcrA is critical for the formation of AcrAB-TolC and could be targeted for the development of new inhibitors.
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Lu W, Zhong M, Wei Y. Folding of AcrB Subunit Precedes Trimerization. J Mol Biol 2011; 411:264-74. [DOI: 10.1016/j.jmb.2011.05.042] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 05/20/2011] [Accepted: 05/26/2011] [Indexed: 10/18/2022]
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Analysis of AcrB and AcrB/DARPin ligand complexes by LILBID MS. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2189-96. [PMID: 21616055 DOI: 10.1016/j.bbamem.2011.05.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2011] [Revised: 04/15/2011] [Accepted: 05/10/2011] [Indexed: 12/24/2022]
Abstract
The AcrA/AcrB/TolC complex is responsible for intrinsic multidrug resistance (MDR) in Escherichia coli. Together with the periplasmic adaptor protein AcrA and the outer membrane channel TolC, the inner membrane component AcrB forms an efflux complex that spans both the inner and outer membrane and bridges the periplasm of the Gram-negative cell. Within the entire tripartite complex, homotrimeric AcrB plays a central role in energy transduction and substrate selection. In vitro selected designed ankyrin repeat proteins (DARPin) that specifically bind to the periplasmic domain of AcrB were shown to ameliorate diffraction resolution of AcrB/DARPin protein co-crystals (G. Sennhauser, P. Amstutz, C. Briand, O. Storchenegger, M.G. Grutter, Drug export pathway of multidrug exporter AcrB revealed by DARPin inhibitors, PLoS Biol 5 (2007) e7). Structural analysis by X-ray crystallography revealed that 2 DARPin molecules were bound to the trimeric AcrB wildtype protein in the crystal, whereas the V612F and G616N AcrB variant crystal structures show 3 DARPin molecules bound to the trimer. These specific stoichiometric differences were analyzed in solution via densitometry after microchannel electrophoresis, analytical ultracentrifugation and via laser-induced liquid bead ion desorption mass spectrometry (LILBID-MS). Using the latter technology, we investigated the gradual disassembly of the AcrB trimer and bound DARPin ligands in dependence on laser intensity in solution. At low laser intensity, the release of the detergent molecule micelle from the AcrB/DARPin complex was observed. By increasing laser intensity, dimeric and monomeric AcrB species with bound DARPin molecules were detected showing the high affinity binding of DARPin to monomeric AcrB species. High laser intensity LILBID MS experiments indicated a spectral shift of the monomeric AcrB peak of 3.1kDa, representing a low molecular weight ligand in all detergent-solubilized AcrB samples and in the AcrB crystal. The identity of this ligand was further investigated using phospholipid analysis of purified AcrB and AcrB variant samples, and indicated the presence of phosphatidylethanolamine and possibly cardiolipin, both constituents of the Escherichia coli membrane.
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9
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Ebel C. Sedimentation velocity to characterize surfactants and solubilized membrane proteins. Methods 2011; 54:56-66. [DOI: 10.1016/j.ymeth.2010.11.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 11/18/2010] [Accepted: 11/19/2010] [Indexed: 02/07/2023] Open
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Deniaud A, Goulielmakis A, Covès J, Pebay-Peyroula E. Differences between CusA and AcrB crystallisation highlighted by protein flexibility. PLoS One 2009; 4:e6214. [PMID: 19593437 PMCID: PMC2704858 DOI: 10.1371/journal.pone.0006214] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Accepted: 06/08/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Until very recently, AcrB was the only Resistance Nodulation and cell Division transporter for which the structure has been elucidated. Towards a general understanding of this protein family, CusA and AcrB were compared. METHODOLOGY/PRINCIPAL FINDINGS In dodecylmaltoside, AcrB crystallised in many different conditions, while CusA does not. This could be due to the difference in dynamic between these proteins as judged from limited proteolysis assays. Addition of various compounds, in particular heavy metal cations, stabilises CusA. CONCLUSION/SIGNIFICANCE This approach could constitute a first step towards CusA crystallisation.
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Affiliation(s)
- Aurélien Deniaud
- Institut de Biologie Structurale Jean Pierre Ebel, UMR5075 CEA-CNRS-Université Joseph Fourier, Grenoble, France
| | - Aurélie Goulielmakis
- Institut de Biologie Structurale Jean Pierre Ebel, UMR5075 CEA-CNRS-Université Joseph Fourier, Grenoble, France
| | - Jacques Covès
- Institut de Biologie Structurale Jean Pierre Ebel, UMR5075 CEA-CNRS-Université Joseph Fourier, Grenoble, France
| | - Eva Pebay-Peyroula
- Institut de Biologie Structurale Jean Pierre Ebel, UMR5075 CEA-CNRS-Université Joseph Fourier, Grenoble, France
- * E-mail:
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Scherer J, Nies DH. CzcP is a novel efflux system contributing to transition metal resistance in Cupriavidus metallidurans CH34. Mol Microbiol 2009; 73:601-21. [PMID: 19602147 DOI: 10.1111/j.1365-2958.2009.06792.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cupriavidus metallidurans CH34 possesses a multitude of metal efflux systems. Here, the function of the novel P(IB4)-type ATPase CzcP is characterized, which belongs to the plasmid pMOL30-mediated cobalt-zinc-cadmium (Czc) resistance system. Contribution of CzcP to transition metal resistance in C. metallidurans was compared with that of three P(IB2)-type ATPases (CadA, ZntA, PrbA) and to other efflux proteins by construction and characterization of multiple deletion mutants. These data also yielded additional evidence for an export of metal cations from the periplasm to the outside of the cell rather than from the cytoplasm to the outside. Moreover, metal-sensitive Escherichia coli strains were functionally substituted in trans with CzcP and the three P(IB2)-type ATPases. Metal transport kinetics performed with inside-out vesicles identified the main substrates for these four exporters, the K(m) values and apparent turn-over numbers. In combination with the mutant data, transport kinetics indicated that CzcP functions as 'resistance enhancer': this P(IB4)-type ATPase exports transition metals Zn(2+), Cd(2+) and Co(2+) much more rapidly than the three P(IB2)-type proteins. However, a basic resistance level has to be provided by the P(IB2)-type efflux pumps because CzcP may not be able to reach all different speciations of these metals in the cytoplasm.
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Affiliation(s)
- Judith Scherer
- Molecular Microbiology, Institute for Biology/Microbiology, Martin-Luther-University, Halle-Wittenberg, Germany
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Lin HT, Bavro VN, Barrera NP, Frankish HM, Velamakanni S, van Veen HW, Robinson CV, Borges-Walmsley MI, Walmsley AR. MacB ABC transporter is a dimer whose ATPase activity and macrolide-binding capacity are regulated by the membrane fusion protein MacA. J Biol Chem 2008; 284:1145-54. [PMID: 18955484 PMCID: PMC2613632 DOI: 10.1074/jbc.m806964200] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Gram-negative bacteria utilize specialized machinery to translocate drugs
and protein toxins across the inner and outer membranes, consisting of a
tripartite complex composed of an inner membrane secondary or primary active
transporter (IMP), a periplasmic membrane fusion protein, and an outer
membrane channel. We have investigated the assembly and function of the
MacAB/TolC system that confers resistance to macrolides in Escherichia
coli. The membrane fusion protein MacA not only stabilizes the tripartite
assembly by interacting with both the inner membrane protein MacB and the
outer membrane protein TolC, but also has a role in regulating the function of
MacB, apparently increasing its affinity for both erythromycin and ATP.
Analysis of the kinetic behavior of ATP hydrolysis indicated that MacA
promotes and stabilizes the ATP-binding form of the MacB transporter. For the
first time, we have established unambiguously the dimeric nature of a
noncanonic ABC transporter, MacB that has an N-terminal nucleotide binding
domain, by means of nondissociating mass spectrometry, analytical
ultracentrifugation, and atomic force microscopy. Structural studies of ABC
transporters indicate that ATP is bound between a pair of nucleotide binding
domains to stabilize a conformation in which the substrate-binding site is
outward-facing. Consequently, our data suggest that in the presence of ATP the
same conformation of MacB is promoted and stabilized by MacA. Thus, MacA would
facilitate the delivery of drugs by MacB to TolC by enhancing the binding of
drugs to it and inducing a conformation of MacB that is primed and competent
for binding TolC. Our structural studies are an important first step in
understanding how the tripartite complex is assembled.
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Affiliation(s)
- Hong Ting Lin
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK
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