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Garstka K, Bellotti D, Wątły J, Kozłowski H, Remelli M, Rowińska-Żyrek M. Metal coordination to solute binding proteins - exciting chemistry with potential biological meaning. Dalton Trans 2023; 52:16140-16150. [PMID: 37814857 DOI: 10.1039/d3dt02417b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Zn(II) is essential for bacterial survival and virulence. In host cells, its abundance is extremely limited, thus, bacteria have evolved transport mechanisms that enable them to take up this essential metal nutrient. Paracoccus denitrificans encodes two solute binding proteins (SBPs) - ZnuA and AztC, which are responsible for zinc acquisition from the host cells. We focus on understanding the interactions of Zn(II) and Ni(II) (zinc's potential competitor, which is a biologically relevant metal ion essential for various bacterial enzymes) with the extracellular ZnuA and AztC's loops from P. denitrificans that are expected to be possible Zn(II) binding sites. In the case of Zn(II) complexes with ZnuA outercellular loop regions, the numerous histidines act as anchoring donors, forming complexes with up to four coordinated His residues, while in the AztC region, three imidazole nitrogens and one water molecule are involved in Zn(II) binding. In Zn(II) complexes with ZnuA His-rich loop regions, so-called polymorphic binding sites are observed. The large number of available imidazoles and carboxylic side chains also strongly affects the structure of Ni(II) complexes; the more histidines in the studied peptide, the higher the affinity to bind Ni(II) and the higher the pH value at which amide nitrogens start to participate in Ni(II) binding. Additionally, for Ni(II)-ZnuA complexes, a more rare octahedral geometry is observed and such complexes are more stable than the corresponding Zn(II) ones, in contrast to what was observed in the AztC region, suggesting that the numerous histidyl and glutamic acid side chains are more tempting for Ni(II) than for Zn(II).The general strong affinity of Zn(II)-zincophore complexes is also discussed.
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Affiliation(s)
- Kinga Garstka
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland.
| | - Denise Bellotti
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland.
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Joanna Wątły
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland.
| | - Henryk Kozłowski
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland.
- Institute of Health Sciences, University of Opole, Katowicka 68 St, 45-060 Opole, Poland
| | - Maurizio Remelli
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
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Structure and Function of the Zinc Binding Protein ZrgA from Vibrio cholerae. Int J Mol Sci 2022; 24:ijms24010548. [PMID: 36613986 PMCID: PMC9820375 DOI: 10.3390/ijms24010548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/16/2022] [Accepted: 12/27/2022] [Indexed: 12/30/2022] Open
Abstract
ATP binding cassette (ABC) transporters are the primary means by which bacteria acquire trace elements from the environment. They rely on solute binding proteins (SBPs) to bind the relevant substrate and deliver it to the integral membrane permease for ATP-powered import into the cytoplasm. SBPs of cluster A-I are known to facilitate the transport of essential metals zinc, manganese, and iron, and many have been characterized to date. A group of ABC transporter operons dubbed zinc-regulated genes (zrg) have recently been shown to transport zinc with putative SBPs (zrgA) bearing no homology to the classical cluster A-I family, and a recent crystal structure of a representative protein from Pseudomonas aeruginosa shows no structural similarity to classical SBPs. Thus, the ZrgA proteins appear to represent a newly discovered family of zinc SBPs widespread among Gram-negative bacteria, including human pathogens. Here, we have determined the crystal structure of ZrgA from Vibrio cholerae and characterized its zinc binding in vitro and function in vivo. We also assessed the role of a histidine-rich sequence that appears to be a hallmark of ZrgA proteins that is particularly long in V. cholerae ZrgA. The results show that the zrgA gene is critical to the function of the operon, consistent with a function as an SBP in this system. Further, the His-rich region is not essential to the function of ZrgA, but it does provide additional zinc binding sites in vitro. The structure and zinc binding data for ZrgA reveal interesting differences between it and its homologue from P. aeruginosa, illustrating diversity within this little-studied protein family.
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3
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Yekwa EL, Serrano FA, Yukl E. Conformational flexibility in the zinc solute-binding protein ZnuA. Acta Crystallogr F Struct Biol Commun 2022; 78:128-134. [PMID: 35234138 PMCID: PMC8900738 DOI: 10.1107/s2053230x22001662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/10/2022] [Indexed: 11/10/2022] Open
Abstract
Zinc is an essential metal for all kingdoms of life, making its transport across the cell membrane a critical function. In bacteria, high-affinity zinc import is accomplished by ATP-binding cassette (ABC) transporters, which rely on extracellular solute-binding proteins (SBPs) of cluster A-I to acquire the metal and deliver it to the membrane permease. These systems are important for survival and virulence, making them attractive targets for the development of novel antibiotics. Citrobacter koseri is an emerging pathogen with extensive antibiotic resistance. High-affinity zinc binding to the C. koseri cluster A-I SBP ZnuA has been characterized and the structure of the zinc-bound (holo) form has been determined by X-ray crystallography. Remarkably, despite 95% sequence identity to the ZnuA homologue from Salmonella enterica, C. koseri ZnuA exhibits a different zinc-coordination environment and a closed rather than an open conformation. Comparison with structures of another close ZnuA homologue from Escherichia coli suggests a surprisingly flexible conformational landscape that may be important for efficient zinc binding and/or delivery to the membrane permease.
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4
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Structural and biochemical characterization of Acinetobacter baumannii ZnuA. J Inorg Biochem 2022; 231:111787. [DOI: 10.1016/j.jinorgbio.2022.111787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/27/2022] [Accepted: 03/06/2022] [Indexed: 11/19/2022]
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Serrano FA, Yukl ET. Contributions of Conformational Flexibility to High-Affinity Zinc Binding in the Solute Binding Protein AztC. ACS OMEGA 2022; 7:3768-3774. [PMID: 35128285 PMCID: PMC8811889 DOI: 10.1021/acsomega.1c06639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Bacteria rely on ATP binding cassette (ABC) transporters for the import of various nutrients. Bacterial ABC importers utilize an extracellular solute binding protein (SBP) to bind the substrate with high affinity and specificity and deliver it to the membrane permease for transport. The essential metals iron, manganese, and zinc are bound and transported by the cluster A-I SBPs. Crystal structures exist for the metal-bound and metal-free forms of several cluster A-I SBPs that show relatively subtle conformational changes that accompany metal binding. Recent solution studies and molecular dynamics simulations indicate a more complex conformational landscape for the cluster A-I SBPs, suggesting that changes in protein dynamics upon metal binding may have an important role in recognition by the membrane permease and effective transport. Here, we investigate conformational states and dynamics in the cluster A-I SBP AztC fromParacoccus denitrificans, characterizing its unusual intrinsic fluorescence behavior and thermodynamics of zinc binding. These data suggest a dynamic equilibrium of at least two conformational states in the apo form and compensatory changes in the holo that provide for a significant entropic contribution to zinc binding. Correlation with available crystal structures suggests that the formation of a Trp-Phe π-stacking interaction in the metal-bound form may mediate the observed changes in fluorescence. The conformational dynamics identified here for AztC are likely applicable to other cluster A-I SBPs with relevance to their exploitation as potential antibiotic drug targets.
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Affiliation(s)
- Fred A. Serrano
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, United States
| | - Erik T. Yukl
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, United States
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Meni A, Yukl ET. Structural Features Mediating Zinc Binding and Transfer in the AztABCD Zinc Transporter System. Biomolecules 2020; 10:biom10081156. [PMID: 32781785 PMCID: PMC7463823 DOI: 10.3390/biom10081156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 12/27/2022] Open
Abstract
Many bacteria require ATP binding cassette (ABC) transporters for the import of the essential metal zinc from limited environments. These systems rely on a periplasmic or cell-surface solute binding protein (SBP) to bind zinc with high affinity and specificity. AztABCD is one such zinc transport system recently identified in a large group of diverse bacterial species. In addition to a classical SBP (AztC), the operon also includes a periplasmic metallochaperone (AztD) shown to transfer zinc directly to AztC. Crystal structures of both proteins from Paracoccus denitrificans have been solved and suggest several structural features on each that may be important for zinc binding and transfer. Here we determine zinc binding affinity, dissociation kinetics, and transfer kinetics for several deletion mutants as well as a crystal structure for one of them. The results indicate specific roles for loop structures on AztC and an N-terminal motif on AztD in zinc binding and transfer. These data are consistent with a structural transfer model proposed previously and provide further mechanistic insight into the processes of zinc binding and transfer.
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Neupane DP, Fullam SH, Chacón KN, Yukl ET. Crystal structures of AztD provide mechanistic insights into direct zinc transfer between proteins. Commun Biol 2019; 2:308. [PMID: 31428696 PMCID: PMC6689063 DOI: 10.1038/s42003-019-0542-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/15/2019] [Indexed: 12/19/2022] Open
Abstract
Zinc acquisition from limited environments is critical for bacterial survival and pathogenesis. AztD has been identified as a periplasmic or cell surface zinc-binding protein in numerous bacterial species. In Paracoccus denitrificans, AztD can transfer zinc directly to AztC, the solute binding protein for a zinc-specific ATP-binding cassette transporter system, suggesting a role in zinc acquisition and homeostasis. Here, we present the first cry stal structures of AztD from P. denitrificans and tbe human pathogen Citrobacter koseri, revealing a beta-propeller fold and two high-affinity zinc-binding sites that are highly conserved among AztD homologs. These structures combined with transfer assays using WT and mutant proteins provide rare insight into the mechanism of direct zinc transfer from one protein to another. Given the importance of zinc import to bacterial pathogenesis, these insights may prove valuable to the development of zinc transfer inhibitors as antibiotics.
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Affiliation(s)
- Durga Prasad Neupane
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003 USA
| | - Stephanie Hope Fullam
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003 USA
| | | | - Erik Thomas Yukl
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003 USA
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Tanaka KJ, Pinkett HW. Oligopeptide-binding protein from nontypeable Haemophilus influenzae has ligand-specific sites to accommodate peptides and heme in the binding pocket. J Biol Chem 2018; 294:1070-1082. [PMID: 30455346 DOI: 10.1074/jbc.ra118.004479] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/14/2018] [Indexed: 11/06/2022] Open
Abstract
In nontypeable Haemophilus influenzae (NTHi), the oligopeptide-binding protein (OppA) serves as the substrate-binding protein (SBP) of the oligopeptide transport system responsible for the import of peptides. We solved the crystal structure of nthiOppA in complex with hydrophobic peptides of various sizes. Our novel hexapeptide complex demonstrates the flexibility of the nthiOppA-binding cavity to expand and accommodate the longer peptide while maintaining similar protein-peptide interactions of smaller peptide complexes. In addition to acquiring peptides from the host environment, as a heme auxotroph NTHi utilizes host hemoproteins as a source of essential iron. OppA is a member of the Cluster C SBP family, and unlike other SBP families, some members recognize two distinctly different substrates. DppA (dipeptide), MppA (murein tripeptide), and SapA (antimicrobial peptides) are Cluster C proteins known to also transport heme. We observed nthiOppA shares this heme-binding characteristic and established heme specificity and affinity by surface plasmon resonance (SPR) of the four Cluster C proteins in NTHi. Ligand-docking studies predicted a distinct heme-specific cleft in the binding pocket, and using SPR competition assays, we observed that heme does not directly compete with peptide in the substrate-binding pocket. Additionally, we identified that the individual nthiOppA domains differentially contribute to substrate binding, with one domain playing a dominant role in heme binding and the other in peptide binding. Our results demonstrate the multisubstrate specificity of nthiOppA and the role of NTHi Cluster C proteins in the heme-uptake pathway for this pathogen.
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Affiliation(s)
- Kari J Tanaka
- From the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Heather W Pinkett
- From the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
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Neupane DP, Kumar S, Yukl ET. Two ABC Transporters and a Periplasmic Metallochaperone Participate in Zinc Acquisition in Paracoccus denitrificans. Biochemistry 2018; 58:126-136. [PMID: 30353723 PMCID: PMC6824839 DOI: 10.1021/acs.biochem.8b00854] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Bacteria must acquire the essential
element zinc from extremely
limited environments, and this function is performed largely by ATP
binding cassette (ABC) transporters. These systems rely on a periplasmic
or extracellular solute binding protein (SBP) to bind zinc specifically
with a high affinity and deliver it to the membrane permease for import
into the cytoplasm. However, zinc acquisition systems in bacteria
may be more complex, involving multiple transporters and other periplasmic
or extracellular zinc binding proteins. Here we describe the zinc
acquisition functions of two zinc SBPs (ZnuA and AztC) and a novel
periplasmic metallochaperone (AztD) in Paracoccus denitrificans. ZnuA was characterized in vitro and demonstrated
to bind as many as 5 zinc ions with a high affinity. It does not interact
with AztD, in contrast to what has been demonstrated for AztC, which
is able to acquire a single zinc ion through associative transfer
from AztD. Deletions of the corresponding genes singly and in combination
show that either AztC or ZnuA is sufficient and essential for robust
growth in zinc-limited media. Although AztD cannot support transport
of zinc into the cytoplasm, it likely functions to store zinc in the
periplasm for transfer through the AztABCD system.
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Affiliation(s)
- Durga P Neupane
- Department of Chemistry and Biochemistry , New Mexico State University , Las Cruces , New Mexico 88003 , United States
| | - Santosh Kumar
- Department of Biological Sciences , University of Texas at Dallas , Richardson , Texas 75080 , United States
| | - Erik T Yukl
- Department of Chemistry and Biochemistry , New Mexico State University , Las Cruces , New Mexico 88003 , United States
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10
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Sridharan U, Ragunathan P, Spellerberg B, Ponnuraj K. Molecular dynamics simulation of metal free structure of Lmb, a laminin-binding adhesin of Streptococcus agalactiae: metal removal and its structural implications. J Biomol Struct Dyn 2018; 37:714-725. [PMID: 29421962 DOI: 10.1080/07391102.2018.1438923] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Metal-binding receptors are one of the extracellular components of ATP-binding cassette transporters that are essential for regulation of metal homeostasis in bacteria. Laminin-binding adhesin (Lmb) of Streptococcus agalactiae falls under this class of solute binding proteins. It binds to zinc with a high affinity. Crystal structure of Lmb solved previously by our group reveals that the zinc is tetrahedrally coordinated by three histidines and a glutamate at the interdomain cleft. Lmb contains a long disordered loop close to the metal-binding site whose precise function is unknown. Several experimental attempts to produce apo-Lmb failed and this prompted us to carry out in silico studies to analyse the structural importance of the metal in Lmb. Here, we present the results of the molecular dynamics (MD) simulation studies of native, apo-(metal removed) and the long loop truncated Lmb models along with a homologous protein, TroA from Treponema pallidum that was taken up for validating the MD results of Lmb. Absence of a metal results in significant structural changes in Lmb, particularly at the metal-binding pocket and with the long loop, although the overall fold is retained. This study thus revealed that the Lmb can exist in different conformational states with subtle differences in the overall fold based on the presence or absence of the metal. This could be functionally important for a putative metal uptake and release and also for the adhesive function of Lmb in recognizing laminin, which contains a high number of zinc finger motifs.
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Affiliation(s)
- Upasana Sridharan
- a Centre of Advanced Study in Crystallography and Biophysics , University of Madras, Guindy Campus , Chennai , India
| | - Preethi Ragunathan
- a Centre of Advanced Study in Crystallography and Biophysics , University of Madras, Guindy Campus , Chennai , India
| | - Barbara Spellerberg
- b Institute for Medical Microbiology and Hygiene , University of Ulm , Ulm , Germany
| | - Karthe Ponnuraj
- a Centre of Advanced Study in Crystallography and Biophysics , University of Madras, Guindy Campus , Chennai , India
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11
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Radka CD, Chen D, DeLucas LJ, Aller SG. The crystal structure of the Yersinia pestis iron chaperone YiuA reveals a basic triad binding motif for the chelated metal. Acta Crystallogr D Struct Biol 2017; 73:921-939. [PMID: 29095164 PMCID: PMC5683015 DOI: 10.1107/s2059798317015236] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/18/2017] [Indexed: 12/25/2022] Open
Abstract
Biological chelating molecules called siderophores are used to sequester iron and maintain its ferric state. Bacterial substrate-binding proteins (SBPs) bind iron-siderophore complexes and deliver these complexes to ATP-binding cassette (ABC) transporters for import into the cytoplasm, where the iron can be transferred from the siderophore to catalytic enzymes. In Yersinia pestis, the causative agent of plague, the Yersinia iron-uptake (Yiu) ABC transporter has been shown to improve iron acquisition under iron-chelated conditions. The Yiu transporter has been proposed to be an iron-siderophore transporter; however, the precise siderophore substrate is unknown. Therefore, the precise role of the Yiu transporter in Y. pestis survival remains uncharacterized. To better understand the function of the Yiu transporter, the crystal structure of YiuA (YPO1310/y2875), an SBP which functions to present the iron-siderophore substrate to the transporter for import into the cytoplasm, was determined. The 2.20 and 1.77 Å resolution X-ray crystal structures reveal a basic triad binding motif at the YiuA canonical substrate-binding site, indicative of a metal-chelate binding site. Structural alignment and computational docking studies support the function of YiuA in binding chelated metal. Additionally, YiuA contains two mobile helices, helix 5 and helix 10, that undergo 2-3 Å shifts across crystal forms and demonstrate structural breathing of the c-clamp architecture. The flexibility in both c-clamp lobes suggest that YiuA substrate transfer resembles the Venus flytrap mechanism that has been proposed for other SBPs.
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Affiliation(s)
- Christopher D. Radka
- Graduate Biomedical Sciences Microbiology Theme, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Dongquan Chen
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Lawrence J. DeLucas
- Office of the Provost, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Stephen G. Aller
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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12
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Neupane DP, Avalos D, Fullam S, Roychowdhury H, Yukl ET. Mechanisms of zinc binding to the solute-binding protein AztC and transfer from the metallochaperone AztD. J Biol Chem 2017; 292:17496-17505. [PMID: 28887302 DOI: 10.1074/jbc.m117.804799] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/16/2017] [Indexed: 01/22/2023] Open
Abstract
Bacteria can acquire the essential metal zinc from extremely zinc-limited environments by using ATP-binding cassette (ABC) transporters. These transporters are critical virulence factors, relying on specific and high-affinity binding of zinc by a periplasmic solute-binding protein (SBP). As such, the mechanisms of zinc binding and release among bacterial SBPs are of considerable interest as antibacterial drug targets. Zinc SBPs are characterized by a flexible loop near the high-affinity zinc-binding site. The function of this structure is not always clear, and its flexibility has thus far prevented structural characterization by X-ray crystallography. Here, we present intact structures for the zinc-specific SBP AztC from the bacterium Paracoccus denitrificans in the zinc-bound and apo-states. A comparison of these structures revealed that zinc loss prompts significant structural rearrangements, mediated by the formation of a sodium-binding site in the apo-structure. We further show that the AztC flexible loop has no impact on zinc-binding affinity, stoichiometry, or protein structure, yet is essential for zinc transfer from the metallochaperone AztD. We also found that 3 His residues in the loop appear to temporarily coordinate zinc and then convey it to the high-affinity binding site. Thus, mutation of any of these residues to Ala abrogated zinc transfer from AztD. Our structural and mechanistic findings conclusively identify a role for the AztC flexible loop in zinc acquisition from the metallochaperone AztD, yielding critical insights into metal binding by AztC from both solution and AztD. These proteins are highly conserved in human pathogens, making this work potentially useful for the development of novel antibiotics.
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Affiliation(s)
- Durga P Neupane
- From the Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003
| | - Dante Avalos
- From the Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003
| | - Stephanie Fullam
- From the Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003
| | - Hridindu Roychowdhury
- From the Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003
| | - Erik T Yukl
- From the Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003
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13
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Neupane DP, Jacquez B, Sundararajan A, Ramaraj T, Schilkey FD, Yukl ET. Zinc-Dependent Transcriptional Regulation in Paracoccus denitrificans. Front Microbiol 2017; 8:569. [PMID: 28443074 PMCID: PMC5387054 DOI: 10.3389/fmicb.2017.00569] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/20/2017] [Indexed: 01/20/2023] Open
Abstract
Zinc homeostasis is critical for bacterial survival and is mediated largely at the transcriptional level by the regulation of zinc uptake and efflux genes. Here we use RNA-seq to assess transcriptional changes as a result of zinc limitation in the denitrifying bacterium Paracoccus denitrificans. The results identify the differential expression of 147 genes, most of which were upregulated in zinc-depleted medium. Included in this set of genes are a large number of transition metal transporters, several transcription factors, and hypothetical proteins. Intriguingly, genes encoding nitric oxide reductase (norCB) and nitrite reductase (nirS) were also upregulated. A Zur consensus binding motif was identified in the promoters of the most highly upregulated genes. The zinc uptake regulator (Zur) from this organism was also characterized and shown to bind to the Zur motif in a zinc-dependent manner. This work expands our current understanding of the transcriptional response of gram-negative bacteria to zinc limitation and identifies genes involved in denitrification as part of the Zur regulon.
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Affiliation(s)
- Durga P Neupane
- Department of Chemistry and Biochemistry, New Mexico State UniversityLas Cruces, NM, USA
| | - Belkis Jacquez
- Department of Chemistry and Biochemistry, New Mexico State UniversityLas Cruces, NM, USA
| | | | | | | | - Erik T Yukl
- Department of Chemistry and Biochemistry, New Mexico State UniversityLas Cruces, NM, USA
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14
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Capdevila DA, Wang J, Giedroc DP. Bacterial Strategies to Maintain Zinc Metallostasis at the Host-Pathogen Interface. J Biol Chem 2016; 291:20858-20868. [PMID: 27462080 DOI: 10.1074/jbc.r116.742023] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Among the biologically required first row, late d-block metals from MnII to ZnII, the catalytic and structural reach of ZnII ensures that this essential micronutrient touches nearly every major metabolic process or pathway in the cell. Zn is also toxic in excess, primarily because it is a highly competitive divalent metal and will displace more weakly bound transition metals in the active sites of metalloenzymes if left unregulated. The vertebrate innate immune system uses several strategies to exploit this "Achilles heel" of microbial physiology, but bacterial evolution has responded in kind. This review highlights recent insights into transcriptional, transport, and trafficking mechanisms that pathogens use to "win the fight" over zinc and thrive in an otherwise hostile environment.
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Affiliation(s)
- Daiana A Capdevila
- From the Departments of Chemistry and the Departamento de Quimica Inorganica, Analitica y Quimica Fisica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
| | - Jiefei Wang
- From the Departments of Chemistry and Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405-7102 and
| | - David P Giedroc
- From the Departments of Chemistry and Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405-7102 and
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15
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Krężel A, Maret W. The biological inorganic chemistry of zinc ions. Arch Biochem Biophys 2016; 611:3-19. [PMID: 27117234 PMCID: PMC5120989 DOI: 10.1016/j.abb.2016.04.010] [Citation(s) in RCA: 388] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/14/2016] [Accepted: 04/20/2016] [Indexed: 12/21/2022]
Abstract
The solution and complexation chemistry of zinc ions is the basis for zinc biology. In living organisms, zinc is redox-inert and has only one valence state: Zn(II). Its coordination environment in proteins is limited by oxygen, nitrogen, and sulfur donors from the side chains of a few amino acids. In an estimated 10% of all human proteins, zinc has a catalytic or structural function and remains bound during the lifetime of the protein. However, in other proteins zinc ions bind reversibly with dissociation and association rates commensurate with the requirements in regulation, transport, transfer, sensing, signalling, and storage. In contrast to the extensive knowledge about zinc proteins, the coordination chemistry of the “mobile” zinc ions in these processes, i.e. when not bound to proteins, is virtually unexplored and the mechanisms of ligand exchange are poorly understood. Knowledge of the biological inorganic chemistry of zinc ions is essential for understanding its cellular biology and for designing complexes that deliver zinc to proteins and chelating agents that remove zinc from proteins, for detecting zinc ion species by qualitative and quantitative analysis, and for proper planning and execution of experiments involving zinc ions and nanoparticles such as zinc oxide (ZnO). In most investigations, reference is made to zinc or Zn2+ without full appreciation of how biological zinc ions are buffered and how the d-block cation Zn2+ differs from s-block cations such as Ca2+ with regard to significantly higher affinity for ligands, preference for the donor atoms of ligands, and coordination dynamics. Zinc needs to be tightly controlled. The interaction with low molecular weight ligands such as water and inorganic and organic anions is highly relevant to its biology but in contrast to its coordination in proteins has not been discussed in the biochemical literature. From the discussion in this article, it is becoming evident that zinc ion speciation is important in zinc biochemistry and for biological recognition as a variety of low molecular weight zinc complexes have already been implicated in biological processes, e.g. with ATP, glutathione, citrate, ethylenediaminedisuccinic acid, nicotianamine, or bacillithiol. Zinc ions not bound to proteins have critical roles in cell biology. Zinc has a unique coordination chemistry, poorly appreciated in the biosciences. Its coordination chemistry is significantly different from that of calcium ions. Specific conditions apply for buffering cellular zinc ions. Investigations with zinc need to consider solution chemistry and metal buffering.
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Affiliation(s)
- Artur Krężel
- Laboratory of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14A, 50-383 Wroclaw, Poland.
| | - Wolfgang Maret
- King's College London, Metal Metabolism Group, Division of Diabetes and Nutritional Sciences, Department of Biochemistry, Faculty of Life Sciences of Medicine, 150 Stamford Street, London, SE1 9NH, UK.
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