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Yao H, Alli S, Liu L, Soldano A, Cooper A, Fontenot L, Verdin D, Battaile KP, Lovell S, Rivera M. The crystal structure of Acinetobacter baumannii bacterioferritin reveals a heteropolymer of bacterioferritin and ferritin subunits. Sci Rep 2024; 14:18242. [PMID: 39107474 PMCID: PMC11303784 DOI: 10.1038/s41598-024-69156-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024] Open
Abstract
Iron storage proteins, e.g., vertebrate ferritin, and the ferritin-like bacterioferritin (Bfr) and bacterial ferritin (Ftn), are spherical, hollow proteins that catalyze the oxidation of Fe2+ at binuclear iron ferroxidase centers (FOC) and store the Fe3+ in their interior, thus protecting cells from unwanted Fe3+/Fe2+ redox cycling and storing iron at concentrations far above the solubility of Fe3+. Vertebrate ferritins are heteropolymers of H and L subunits with only the H subunits having FOC. Bfr and Ftn were thought to coexist in bacteria as homopolymers, but recent evidence indicates these molecules are heteropolymers assembled from Bfr and Ftn subunits. Despite the heteropolymeric nature of vertebrate and bacterial ferritins, structures have been determined only for recombinant proteins constituted by a single subunit type. Herein we report the structure of Acinetobacter baumannii bacterioferritin, the first structural example of a heteropolymeric ferritin or ferritin-like molecule, assembled from completely overlapping Ftn homodimers harboring FOC and Bfr homodimers devoid of FOC but binding heme. The Ftn homodimers function by catalyzing the oxidation of Fe2+ to Fe3+, while the Bfr homodimers bind a cognate ferredoxin (Bfd) which reduces the stored Fe3+ by transferring electrons via the heme, enabling Fe2+ mobilization to the cytosol for incorporation in metabolism.
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Affiliation(s)
- Huili Yao
- Department of Chemistry, Louisiana State University, Baton Rouge, 70803, USA
| | - Suliat Alli
- Department of Chemistry, Louisiana State University, Baton Rouge, 70803, USA
| | - Lijun Liu
- Protein Structure and X-Ray Crystallography Laboratory, University of Kansas, Lawrence, 66047, USA
| | - Anabel Soldano
- Department of Chemistry, Louisiana State University, Baton Rouge, 70803, USA
| | - Anne Cooper
- Protein Structure and X-Ray Crystallography Laboratory, University of Kansas, Lawrence, 66047, USA
| | - Leo Fontenot
- Department of Chemistry, Louisiana State University, Baton Rouge, 70803, USA
| | - Dristen Verdin
- Department of Chemistry, Louisiana State University, Baton Rouge, 70803, USA
| | | | - Scott Lovell
- Protein Structure and X-Ray Crystallography Laboratory, University of Kansas, Lawrence, 66047, USA.
| | - Mario Rivera
- Department of Chemistry, Louisiana State University, Baton Rouge, 70803, USA.
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Sinha PR, Balasubramanian R, Hegde SR. Integrated sequence and -omic features reveal novel small proteome of Mycobacterium tuberculosis. Front Microbiol 2024; 15:1335310. [PMID: 38812687 PMCID: PMC11133741 DOI: 10.3389/fmicb.2024.1335310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/15/2024] [Indexed: 05/31/2024] Open
Abstract
Bioinformatic studies on small proteins are under-represented due to difficulties in annotation posed by their small size. However, recent discoveries emphasize the functional significance of small proteins in cellular processes including cell signaling, metabolism, and adaptation to stress. In this study, we utilized a Random Forest classifier trained on sequence features, RNA-Seq, and Ribo-Seq data to uncover small proteins (smORFs) in M. tuberculosis. Independent predictions for the exponential and starvation conditions resulted in 695 potential smORFs. We examined the functional implications of these smORFs using homology searches, LC-MS/MS, and ChIP-seq data, testing their expression in diverse growth conditions, and identifying protein domains. We provide evidence that some of these smORFs could be part of operons, or exist as upstream ORFs. This expanded data resource for the proteins of M. tuberculosis would aid in fine-tuning the existing protein and gene regulatory networks, thereby improving system-wide studies. The primary goal of this study was to uncover and characterize smORFs in M. tuberculosis through bioinformatic analysis, shedding light on their functional roles and genomic organization. Further investigation of these potential smORFs would provide valuable insights into the genome organization and functional diversity of the M. tuberculosis proteome.
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Affiliation(s)
| | | | - Shubhada R. Hegde
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, India
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Rivera M. Mobilization of iron stored in bacterioferritin, a new target for perturbing iron homeostasis and developing antibacterial and antibiofilm molecules. J Inorg Biochem 2023; 247:112306. [PMID: 37451083 DOI: 10.1016/j.jinorgbio.2023.112306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/08/2023] [Accepted: 06/24/2023] [Indexed: 07/18/2023]
Abstract
Antibiotic resistance is a global public health threat. The care of chronic infections is complicated by bacterial biofilms. Biofilm embedded cells can be up to 1000-fold more tolerant to antibiotic treatment than planktonic cells. Antibiotic tolerance is a condition which does not involve mutation and enables bacteria to survive in the presence of antibiotics. The antibiotic tolerance of biofilm-cells often renders antibiotics ineffective, even against strains that do not carry resistance-impairing mutations. This review discusses bacterial iron homeostasis and the strategies being developed to target this bacterial vulnerability, with emphasis on a recently proposed approach which aims at targeting the iron storage protein bacterioferritin (Bfr) and its physiological partner, the ferredoxin Bfd. Bfr regulates cytosolic iron concentrations by oxidizing Fe2+ and storing Fe3+ in its internal cavity, and by forming a complex with Bfd to reduce Fe3+ in the internal cavity and release Fe2+ to the cytosol. Blocking the Bfr-Bfd complex in P. aeruginosa cells causes an irreversible accumulation of Fe3+ in BfrB and simultaneous cytosolic iron depletion, which leads to impaired biofilm maintenance and biofilm cell death. Recently discovered small molecule inhibitors of the Bfr-Bfd complex, which bind Bfr at the Bfd binding site, inhibit iron mobilization, and elicit biofilm cell death.
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Affiliation(s)
- Mario Rivera
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803, USA.
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Bacterioferritin nanocage: Structure, biological function, catalytic mechanism, self-assembly and potential applications. Biotechnol Adv 2022; 61:108057. [DOI: 10.1016/j.biotechadv.2022.108057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/22/2022]
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Pseudomonas aeruginosa Bacterioferritin Is Assembled from FtnA and BfrB Subunits with the Relative Proportions Dependent on the Environmental Oxygen Availability. Biomolecules 2022; 12:biom12030366. [PMID: 35327558 PMCID: PMC8945002 DOI: 10.3390/biom12030366] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 12/14/2022] Open
Abstract
Ferritins are iron storage proteins assembled from 24 subunits into a spherical and hollow structure. The genomes of many bacteria harbor genes encoding two types of ferritin-like proteins, the bacterial ferritins (Ftn) and the bacterioferritins (Bfr), which bind heme. The genome of P. aeruginosa PAO1 (like the genomes of many bacteria) contains genes coding for two different types of ferritin-like molecules, ftnA (PA4235) and bfrB (PA3531). The reasons for requiring the presence of two distinct types of iron storage protein in bacterial cells have remained largely unexplained. Attempts to understand this issue in P. aeruginosa through the recombinant expression of the ftnA and bfrB genes in E. coli host cells, coupled to the biochemical and structural characterization of the recombinant 24-mer FtnA and 24-mer BfrB molecules, have shown that each of the recombinant molecules can form an Fe3+-mineral core. These observations led to the suggestion that 24-mer FtnA and 24-mer BfrB molecules coexist in P. aeruginosa cells where they share iron storage responsibilities. Herein, we demonstrate that P. aeruginosa utilizes a single heterooligomeric 24-mer Bfr assembled from FtnA and BfrB subunits. The relative content of the FtnA and BfrB subunits in Bfr depends on the O2 availability during cell culture, such that Bfr isolated from aerobically cultured P. aeruginosa is assembled from a majority of BfrB subunits. In contrast, when the cells are cultured in O2-limiting conditions, the proportion of FtnA subunits in the isolated Bfr increases significantly and can become the most abundant subunit. Despite the variability in the subunit composition of Bfr, the 24-mer assembly is consistently arranged from FtnA subunit dimers devoid of heme and BfrB subunit dimers each containing a heme molecule.
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Soldano A, Yao H, Punchi Hewage AND, Meraz K, Annor-Gyamfi JK, Bunce RA, Battaile KP, Lovell S, Rivera M. Small Molecule Inhibitors of the Bacterioferritin (BfrB)-Ferredoxin (Bfd) Complex Kill Biofilm-Embedded Pseudomonas aeruginosa Cells. ACS Infect Dis 2021; 7:123-140. [PMID: 33269912 PMCID: PMC7802073 DOI: 10.1021/acsinfecdis.0c00669] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Indexed: 01/05/2023]
Abstract
Bacteria depend on a well-regulated iron homeostasis to survive adverse environments. A key component of the iron homeostasis machinery is the compartmentalization of Fe3+ in bacterioferritin and its subsequent mobilization as Fe2+ to satisfy metabolic requirements. In Pseudomonas aeruginosa Fe3+ is compartmentalized in bacterioferritin (BfrB), and its mobilization to the cytosol requires binding of a ferredoxin (Bfd) to reduce the stored Fe3+ and release the soluble Fe2+. Blocking the BfrB-Bfd complex in P. aeruginosa by deletion of the bfd gene triggers an irreversible accumulation of Fe3+ in BfrB, concomitant cytosolic iron deficiency and significant impairment of biofilm development. Herein we report that small molecules developed to bind BfrB at the Bfd binding site block the BfrB-Bfd complex, inhibit the mobilization of iron from BfrB in P. aeruginosa cells, elicit a bacteriostatic effect on planktonic cells, and are bactericidal to cells embedded in mature biofilms.
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Affiliation(s)
- Anabel Soldano
- Department
of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| | - Huili Yao
- Department
of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| | | | - Kevin Meraz
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Joel K. Annor-Gyamfi
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Richard A. Bunce
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Kevin P. Battaile
- NYX, New York Structural Biology Center, Upton, New York 11973, United States
| | - Scott Lovell
- Protein
Structure Laboratory, University of Kansas, 2034 Becker Drive, Lawrence, Kansas 66047, United States
| | - Mario Rivera
- Department
of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
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Soldano A, Yao H, Chandler JR, Rivera M. Inhibiting Iron Mobilization from Bacterioferritin in Pseudomonas aeruginosa Impairs Biofilm Formation Irrespective of Environmental Iron Availability. ACS Infect Dis 2020; 6:447-458. [PMID: 31898890 PMCID: PMC7076691 DOI: 10.1021/acsinfecdis.9b00398] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
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Although iron is
essential for bacteria, the nutrient presents problems of toxicity
and solubility. Bacteria circumvent these problems with the aid of
iron storage proteins where Fe3+ is deposited and, when
necessary, mobilized as Fe2+ for metabolic requirements.
In Pseudomonas aeruginosa, Fe3+ is compartmentalized
in bacterioferritin (BfrB), and its mobilization as Fe2+ requires specific binding of a ferredoxin (Bfd) to reduce the stored
Fe3+. Blocking the BfrB-Bfd complex leads to irreversible
iron accumulation in BfrB and cytosolic iron deprivation. Consequently,
given the intracellular iron sufficiency requirement for biofilm development,
we hypothesized that blocking the BfrB-Bfd interaction in P. aeruginosa would impair biofilm development. Our results
show that planktonic and biofilm-embedded cells where the BfrB-Bfd
complex is blocked exhibit cytosolic iron deficiency, and poorly developed
biofilms, even in iron-sufficient culture conditions. These results
underscore inhibition of the BfrB-Bfd complex as a rational target
to dysregulate iron homeostasis and possibly control biofilms.
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Affiliation(s)
- Anabel Soldano
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| | - Huili Yao
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| | - Josephine R. Chandler
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas 66045, United States
| | - Mario Rivera
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
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Punchi Hewage AND, Yao H, Nammalwar B, Gnanasekaran KK, Lovell S, Bunce RA, Eshelman K, Phaniraj SM, Lee MM, Peterson BR, Battaile KP, Reitz AB, Rivera M. Small Molecule Inhibitors of the BfrB-Bfd Interaction Decrease Pseudomonas aeruginosa Fitness and Potentiate Fluoroquinolone Activity. J Am Chem Soc 2019; 141:8171-8184. [PMID: 31038945 PMCID: PMC6535718 DOI: 10.1021/jacs.9b00394] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
The iron storage
protein bacterioferritin (BfrB) is central to
bacterial iron homeostasis. The mobilization of iron from BfrB, which
requires binding by a cognate ferredoxin (Bfd), is essential to the
regulation of cytosolic iron levels in P. aeruginosa. This paper describes the structure-guided development of small
molecule inhibitors of the BfrB–Bfd protein–protein
interaction. The process was initiated by screening a fragment library
and followed by obtaining the structure of a fragment hit bound to
BfrB. The structural insights were used to develop a series of 4-(benzylamino)-
and 4-((3-phenylpropyl)amino)-isoindoline-1,3-dione analogs that selectively
bind BfrB at the Bfd binding site. Challenging P. aeruginosa cells with the 4-substituted isoindoline analogs revealed a dose-dependent
growth phenotype. Further investigation determined that the analogs
elicit a pyoverdin hyperproduction phenotype that is consistent with
blockade of the BfrB–Bfd interaction and ensuing irreversible
accumulation of iron in BfrB, with concomitant depletion of iron in
the cytosol. The irreversible accumulation of iron in BfrB prompted
by the 4-substituted isoindoline analogs was confirmed by visualization
of BfrB-iron in P. aeruginosa cell lysates separated
on native PAGE gels and stained for iron with Ferene S. Challenging P. aeruginosa cultures with a combination of commercial
fluoroquinolone and our isoindoline analogs results in significantly
lower cell survival relative to treatment with either antibiotic or
analog alone. Collectively, these findings furnish proof of concept
for the usefulness of small molecule probes designed to dysregulate
bacterial iron homeostasis by targeting a protein–protein interaction
pivotal for iron storage in the bacterial cell.
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Affiliation(s)
- Achala N D Punchi Hewage
- Department of Chemistry , University of Kansas , 2030 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Huili Yao
- Department of Chemistry , Louisiana State University , 229A Choppin Hall , Baton Rouge , Louisiana 70803 , United States
| | - Baskar Nammalwar
- Department of Chemistry , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | | | - Scott Lovell
- Protein Structure Laboratory , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Richard A Bunce
- Department of Chemistry , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Kate Eshelman
- Department of Chemistry , University of Kansas , 2030 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Sahishna M Phaniraj
- Department of Medicinal Chemistry , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Molly M Lee
- Department of Medicinal Chemistry , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Blake R Peterson
- Department of Medicinal Chemistry , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Kevin P Battaile
- IMCA-CAT , Hauptman Woodward Medical Research Institute , 9700 South Cass Avenue, Building 435A , Argonne , Illinois 60439 , United States
| | - Allen B Reitz
- Fox Chase Chemical Diversity Center, Inc. , 3805 Old Easton Road , Doylestown , Pennsylvania 18902 , United States
| | - Mario Rivera
- Department of Chemistry , Louisiana State University , 229A Choppin Hall , Baton Rouge , Louisiana 70803 , United States
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