Pseudomonas aeruginosa gene PA4880 encodes a Dps-like protein with a Dps fold, bacterioferritin-type ferroxidase centers, and endonuclease activity

Rajapaksha, Nimesha; Yao, Huili; Cook, Aisha; Seibold, Steve; Liu, Lijun; Battaile, Kevin P.; Fontenot, Leo; Donnarumma, Fabrizio; Lovell, Scott; Rivera, Mario

doi:10.3389/fmolb.2024.1390745

Title: Pseudomonas aeruginosa gene PA4880 encodes a Dps-like protein with a Dps fold, bacterioferritin-type ferroxidase centers, and endonuclease activity

Journal Article · 22 May 2024 · Frontiers in Molecular Biosciences

DOI: https://doi.org/10.3389/fmolb.2024.1390745 · OSTI ID:2473104

Rajapaksha, Nimesha ^[1]; Yao, Huili ^[1]; Cook, Aisha ^[1]; Seibold, Steve ^[2]; Liu, Lijun ^[2]; Battaile, Kevin P. ^[3]; Fontenot, Leo ^[1]; Donnarumma, Fabrizio ^[1]; Lovell, Scott ^[2]; Rivera, Mario ^[1]

Louisiana State Univ., Baton Rouge, LA (United States)
Univ. of Kansas, Lawrence, KS (United States)
City College of New York, NY (United States). New York Structural Biology Center

We report the biochemical, structural, and functional characterization of the protein coded by gene PA4880 in the P. aeruginosa PAO1 genome. The PA4880 gene had been annotated as coding a probable bacterioferritin. Our structural work shows that the product of gene PA4880 is a protein that adopts the Dps subunit fold, which oligomerizes into a 12-mer quaternary structure. Unlike Dps, however, the ferroxidase di-iron centers and iron coordinating ligands are buried within each subunit, in a manner identical to that observed in the ferroxidase center of P. aeruginosa bacterioferritin. Since these structural characteristics correspond to Dps-like proteins, we term the protein as P. aeruginosa Dps-like, or Pa DpsL. The ferroxidase centers in Pa DpsL catalyze the oxidation of Fe²⁺ utilizing O₂ or H₂O₂ as oxidant, and the resultant Fe³⁺ is compartmentalized in the interior cavity. Interestingly, incubating Pa DpsL with plasmid DNA results in efficient nicking of the DNA and at higher concentrations of Pa DpsL the DNA is linearized and eventually degraded. The nickase and endonuclease activities suggest that Pa DpsL, in addition to participating in the defense of P. aeruginosa cells against iron-induced toxicity, may also participate in the innate immune mechanisms consisting of restriction endonucleases and cognate methyl transferases.

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Research Organization:: Brookhaven National Laboratory (BNL), Upton, NY (United States). National Synchrotron Light Source II (NSLS-II)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: SC0012704

OSTI ID:: 2473104

Journal Information:: Frontiers in Molecular Biosciences, Journal Name: Frontiers in Molecular Biosciences Vol. 11; ISSN 2296-889X

Publisher:: Frontiers Media S.A.Copyright Statement

Country of Publication:: United States

Language:: English

References (54)

Transcriptome analysis of the Pseudomonas aeruginosa response to iron Palma, Marco; Worgall, Stefan; Quadri, Luis E. N. Archives of Microbiology, Vol. 180, Issue 5 https://doi.org/10.1007/s00203-003-0602-z	journal	November 2003
Identification and characterization of a new HNH restriction endonuclease with unusual properties Santoshi, Meghna; Engleng, Bharat; Eligar, Sachin M. Applied Microbiology and Biotechnology, Vol. 107, Issue 20 https://doi.org/10.1007/s00253-023-12717-8	journal	August 2023
Ferritins: furnishing proteins with iron Bradley, Justin M.; Le Brun, Nick E.; Moore, Geoffrey R. JBIC Journal of Biological Inorganic Chemistry, Vol. 21, Issue 1 https://doi.org/10.1007/s00775-016-1336-0	journal	January 2016
Multicomponent mixtures for cryoprotection and ligand solubilization Ciccone, Lidia; Vera, Laura; Tepshi, Livia Biotechnology Reports, Vol. 7 https://doi.org/10.1016/j.btre.2015.05.008	journal	September 2015
Miniferritins: Small multifunctional protein cages Guerra, João P. L.; Jacinto, João P.; Tavares, Pedro Coordination Chemistry Reviews, Vol. 449 https://doi.org/10.1016/j.ccr.2021.214187	journal	December 2021
Mobilization of iron stored in bacterioferritin, a new target for perturbing iron homeostasis and developing antibacterial and antibiofilm molecules Rivera, Mario Journal of Inorganic Biochemistry, Vol. 247 https://doi.org/10.1016/j.jinorgbio.2023.112306	journal	October 2023
Bacterioferritin: Structure, Dynamics, and Protein–Protein Interactions at Play in Iron Storage and Mobilization Rivera, Mario Accounts of Chemical Research, Vol. 50, Issue 2 https://doi.org/10.1021/acs.accounts.6b00514	journal	January 2017
Small Molecule Inhibitors of the Bacterioferritin (BfrB)–Ferredoxin (Bfd) Complex Kill Biofilm-Embedded Pseudomonas aeruginosa Cells Soldano, Anabel; Yao, Huili; Punchi Hewage, Achala N. D. ACS Infectious Diseases, Vol. 7, Issue 1 https://doi.org/10.1021/acsinfecdis.0c00669	journal	December 2020
The Therapeutic Pipeline for Pseudomonas aeruginosa Infections Burrows, Lori L. ACS Infectious Diseases, Vol. 4, Issue 7 https://doi.org/10.1021/acsinfecdis.8b00112	journal	May 2018
Inhibiting Iron Mobilization from Bacterioferritin in Pseudomonas aeruginosa Impairs Biofilm Formation Irrespective of Environmental Iron Availability Soldano, Anabel; Yao, Huili; Chandler, Josephine R. ACS Infectious Diseases, Vol. 6, Issue 3 https://doi.org/10.1021/acsinfecdis.9b00398	journal	January 2020
Structure of the DPS-Like Protein from Sulfolobus solfataricus Reveals a Bacterioferritin-Like Dimetal Binding Site within a DPS-Like Dodecameric Assembly ^† ^, ^‡ Gauss, George H.; Benas, Philippe; Wiedenheft, Blake Biochemistry, Vol. 45, Issue 36 https://doi.org/10.1021/bi060782u	journal	September 2006
Two Distinct Ferritin-like Molecules in Pseudomonas aeruginosa : The Product of the bfrA Gene Is a Bacterial Ferritin (FtnA) and Not a Bacterioferritin (Bfr) Yao, Huili; Jepkorir, Grace; Lovell, Scott Biochemistry, Vol. 50, Issue 23 https://doi.org/10.1021/bi2004119	journal	June 2011
Binding of Pseudomonas aeruginosa Apobacterioferritin-Associated Ferredoxin to Bacterioferritin B Promotes Heme Mediation of Electron Delivery and Mobilization of Core Mineral Iron Weeratunga, Saroja K.; Gee, Casey E.; Lovell, Scott Biochemistry, Vol. 48, Issue 31 https://doi.org/10.1021/bi900561a	journal	August 2009
Structural Studies of Bacterioferritin B from Pseudomonas aeruginosa Suggest a Gating Mechanism for Iron Uptake via the Ferroxidase Center, Weeratunga, Saroja K.; Lovell, Scott; Yao, Huili Biochemistry, Vol. 49, Issue 6 https://doi.org/10.1021/bi9015204	journal	February 2010
The Structure of the BfrB–Bfd Complex Reveals Protein–Protein Interactions Enabling Iron Release from Bacterioferritin Yao, Huili; Wang, Yan; Lovell, Scott Journal of the American Chemical Society, Vol. 134, Issue 32 https://doi.org/10.1021/ja305180n	journal	August 2012
Small Molecule Inhibitors of the BfrB–Bfd Interaction Decrease Pseudomonas aeruginosa Fitness and Potentiate Fluoroquinolone Activity Punchi Hewage, Achala N. D.; Yao, Huili; Nammalwar, Baskar Journal of the American Chemical Society https://doi.org/10.1021/jacs.9b00394	journal	May 2019
The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site Chiancone, Emilia; Ilari, Andrea; Stefanini, Simonetta Nature Structural Biology, Vol. 7, Issue 1, p. 38-43 https://doi.org/10.1038/71236	journal	January 2000
Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 Langer, Gerrit; Cohen, Serge X.; Lamzin, Victor S. Nature Protocols, Vol. 3, Issue 7 https://doi.org/10.1038/nprot.2008.91	journal	June 2008
Regulation of Bacterial DNA Packaging in Early Stationary Phase by Competitive DNA Binding of Dps and IHF Lee, Sin Yi; Lim, Ci Ji; Dröge, Peter Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep18146	journal	December 2015
Evidence for Direct Control of Virulence and Defense Gene Circuits by the Pseudomonas aeruginosa Quorum Sensing Regulator, MvfR Maura, Damien; Hazan, Ronen; Kitao, Tomoe Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep34083	journal	September 2016
Inhibiting the BfrB:Bfd interaction in Pseudomonas aeruginosa causes irreversible iron accumulation in bacterioferritin and iron deficiency in the bacterial cytosol Eshelman, Kate; Yao, Huili; Punchi Hewage, Achala N. D. Metallomics, Vol. 9, Issue 6 https://doi.org/10.1039/c7mt00042a	journal	January 2017
GeneChip® expression analysis of the iron starvation response in Pseudomonas aeruginosa: identification of novel pyoverdine biosynthesis genes: GeneChip® expression analysis of iron starvation Ochsner, Urs A.; Wilderman, Paula J.; Vasil, Adriana I. Molecular Microbiology, Vol. 45, Issue 5 https://doi.org/10.1046/j.1365-2958.2002.03084.x	journal	September 2002
Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis Wilderman, Paula J.; Sowa, Nathaniel A.; FitzGerald, David J. Proceedings of the National Academy of Sciences, Vol. 101, Issue 26 https://doi.org/10.1073/pnas.0403423101	journal	June 2004
From The Cover: An archaeal antioxidant: Characterization of a Dps-like protein from Sulfolobus solfataricus Wiedenheft, B.; Mosolf, J.; Willits, D. Proceedings of the National Academy of Sciences, Vol. 102, Issue 30 https://doi.org/10.1073/pnas.0501497102	journal	July 2005
Use of Structural Phylogenetic Networks for Classification of the Ferritin-like Superfamily Lundin, Daniel; Poole, Anthony M.; Sjöberg, Britt-Marie Journal of Biological Chemistry, Vol. 287, Issue 24 https://doi.org/10.1074/jbc.M112.367458	journal	June 2012
Iron Incorporation into Escherichia coli Dps Gives Rise to a Ferritin-like Microcrystalline Core Ilari, Andrea; Ceci, Pierpaolo; Ferrari, Davide Journal of Biological Chemistry, Vol. 277, Issue 40 https://doi.org/10.1074/jbc.M206186200	journal	October 2002
Codon usage and tRNA content in unicellular and multicellular organisms. Ikemura, T. Molecular Biology and Evolution, 13–34 https://doi.org/10.1093/oxfordjournals.molbev.a040335	journal	January 1985
A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli. Almiron, M.; Link, A. J.; Furlong, D. Genes & Development, Vol. 6, Issue 12b https://doi.org/10.1101/gad.6.12b.2646	journal	December 1992
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Experimental phasing with SHELXC / D / E : combining chain tracing with density modification Sheldrick, George M. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444909038360	journal	March 2010
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Integration, scaling, space-group assignment and post-refinement Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 133-144 https://doi.org/10.1107/S0907444909047374	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
An introduction to data reduction: space-group determination, scaling and intensity statistics Evans, Philip R. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S090744491003982X	journal	March 2011
Presenting your structures: the CCP 4 mg molecular-graphics software McNicholas, S.; Potterton, E.; Wilson, K. S. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911007281	journal	March 2011
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/S2059798319011471	journal	October 2019
The CCP4 suite: integrative software for macromolecular crystallography Agirre, Jon; Atanasova, Mihaela; Bagdonas, Haroldas Acta Crystallographica Section D Structural Biology, Vol. 79, Issue 6 https://doi.org/10.1107/S2059798323003595	journal	May 2023
The environmental occurrence of Pseudomonas aeruginosa Crone, Stephanie; Vives‐Flórez, Martha; Kvich, Lasse APMIS, Vol. 128, Issue 3 https://doi.org/10.1111/apm.13010	journal	December 2019
Structure, function and regulation of the DNA-binding protein Dps and its role in acid and oxidative stress resistance in Escherichia coli: a review: Escherichia coli Dps protein Calhoun, L. N.; Kwon, Y. M. Journal of Applied Microbiology, Vol. 110, Issue 2 https://doi.org/10.1111/j.1365-2672.2010.04890.x	journal	December 2010
Epidemiology and Treatment of Multidrug-Resistant and Extensively Drug-Resistant Pseudomonas aeruginosa Infections Horcajada, Juan P.; Montero, Milagro; Oliver, Antonio Clinical Microbiology Reviews, Vol. 32, Issue 4 https://doi.org/10.1128/CMR.00031-19	journal	September 2019
Links between Anr and Quorum Sensing in Pseudomonas aeruginosa Biofilms Hammond, John H.; Dolben, Emily F.; Smith, T. Jarrod Journal of Bacteriology, Vol. 197, Issue 17 https://doi.org/10.1128/JB.00182-15	journal	September 2015
Proteomic Analysis of the Pseudomonas aeruginosa Iron Starvation Response Reveals PrrF Small Regulatory RNA-Dependent Iron Regulation of Twitching Motility, Amino Acid Metabolism, and Zinc Homeostasis Proteins Nelson, Cassandra E.; Huang, Weiliang; Brewer, Luke K. Journal of Bacteriology, Vol. 201, Issue 12 https://doi.org/10.1128/JB.00754-18	journal	April 2019
Characterization of the Bacteroides fragilis bfr Gene Product Identifies a Bacterial DPS-Like Protein and Suggests Evolutionary Links in the Ferritin Superfamily Gauss, G. H.; Reott, M. A.; Rocha, E. R. Journal of Bacteriology, Vol. 194, Issue 1 https://doi.org/10.1128/JB.05260-11	journal	October 2011
Dps Protects Cells against Multiple Stresses during Stationary Phase Nair, S.; Finkel, S. E. Journal of Bacteriology, Vol. 186, Issue 13 https://doi.org/10.1128/JB.186.13.4192-4198.2004	journal	June 2004
Microarray Analysis of the Osmotic Stress Response inPseudomonas aeruginosa Aspedon, Arden; Palmer, Kelli; Whiteley, Marvin Journal of Bacteriology, Vol. 188, Issue 7 https://doi.org/10.1128/JB.188.7.2721-2725.2006	journal	April 2006
Identification, Timing, and Signal Specificity of Pseudomonas aeruginosa Quorum-Controlled Genes: a Transcriptome Analysis Schuster, M.; Lostroh, C. P.; Ogi, T. Journal of Bacteriology, Vol. 185, Issue 7 https://doi.org/10.1128/jb.185.7.2066-2079.2003	journal	April 2003
Gene regulation of plasmid- and chromosome-determined inorganic ion transport in bacteria Silver, S.; Walderhaug, M. Microbiological Reviews, Vol. 56, Issue 1 https://doi.org/10.1128/mr.56.1.195-228.1992	journal	March 1992
Nicking endonucleases Zheleznaya, L. A.; Kachalova, G. S.; Artyukh, R. I. Biochemistry (Moscow), Vol. 74, Issue 13 https://doi.org/10.1134/s0006297909130033	journal	December 2009
Transport of Magnesium by a Bacterial Nramp-Related Gene Shin, Jung-Ho; Wakeman, Catherine A.; Goodson, Jonathan R. PLoS Genetics, Vol. 10, Issue 6 https://doi.org/10.1371/journal.pgen.1004429	journal	June 2014
Pseudomonas aeruginosa Bacterioferritin Is Assembled from FtnA and BfrB Subunits with the Relative Proportions Dependent on the Environmental Oxygen Availability Yao, Huili; Soldano, Anabel; Fontenot, Leo Biomolecules, Vol. 12, Issue 3 https://doi.org/10.3390/biom12030366	journal	February 2022
Pseudomonas aeruginosa Dps (PA0962) Functions in H2O2 Mediated Oxidative Stress Defense and Exhibits In Vitro DNA Cleaving Activity Rajapaksha, Nimesha; Soldano, Anabel; Yao, Huili International Journal of Molecular Sciences, Vol. 24, Issue 5 https://doi.org/10.3390/ijms24054669	journal	February 2023
In Vitro and In Vivo Antimicrobial Activities of Vancomycin and Rifampin against Elizabethkingia anophelis Lin, I-Fan; Lai, Chung-Hsu; Lin, Shang-Yi International Journal of Molecular Sciences, Vol. 24, Issue 23 https://doi.org/10.3390/ijms242317012	journal	November 2023
Mobilization of Iron Stored in Bacterioferritin Is Required for Metabolic Homeostasis in Pseudomonas aeruginosa Punchi Hewage, Achala N. D.; Fontenot, Leo; Guidry, Jessie Pathogens, Vol. 9, Issue 12 https://doi.org/10.3390/pathogens9120980	journal	November 2020

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Title: Pseudomonas aeruginosa gene PA4880 encodes a Dps-like protein with a Dps fold, bacterioferritin-type ferroxidase centers, and endonuclease activity

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