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Garcia PS, Gribaldo S, Barras F. When iron and sulfur met on an anoxic planet and eventually made clusters essential for life. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119730. [PMID: 38631441 DOI: 10.1016/j.bbamcr.2024.119730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/11/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024]
Abstract
[FeS] clusters are co-factors that are essential for life and are synthesized by dedicated multiprotein cellular machineries. In this review, we present the current scenario for the emergence and the diversification of the [FeS] cluster biosynthesis machineries. In addition to well-known NIF, ISC and SUF machineries, two alternative minimal systems, SMS, and MIS, were recently identified. Taxonomic distribution and phylogeny analyses indicate that SMS and MIS were present in the Last Universal Common Ancestor (LUCA), well before the increase of oxygen on Earth. ISC, SUF and NIF systems emerged later in the history of life. The possible reasons for the emergence and diversification of these machineries are discussed.
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Affiliation(s)
- Pierre Simon Garcia
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Department of Microbiology, Unit Stress Adaptation and Metabolism in Enterobacteria, Paris, France; Institut Pasteur, Université Paris Cité, Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Frédéric Barras
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Department of Microbiology, Unit Stress Adaptation and Metabolism in Enterobacteria, Paris, France.
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2
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Vannini A, Pinatel E, Costantini PE, Pelliciari S, Roncarati D, Puccio S, De Bellis G, Scarlato V, Peano C, Danielli A. (Re)-definition of the holo- and apo-Fur direct regulons of Helicobacter pylori. J Mol Biol 2024; 436:168573. [PMID: 38626867 DOI: 10.1016/j.jmb.2024.168573] [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: 12/13/2023] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024]
Abstract
Iron homeostasis is a critical process for living organisms because this metal is an essential co-factor for fundamental biochemical activities, like energy production and detoxification, albeit its excess quickly leads to cell intoxication. The protein Fur (ferric uptake regulator) controls iron homeostasis in bacteria by switching from its apo- to holo-form as a function of the cytoplasmic level of ferrous ions, thereby modulating gene expression. The Helicobacter pylori HpFur protein has the rare ability to operate as a transcriptional commutator; apo- and holo-HpFur function as two different repressors with distinct DNA binding recognition properties for specific sets of target genes. Although the regulation of apo- and holo-HpFur in this bacterium has been extensively investigated, we propose a genome-wide redefinition of holo-HpFur direct regulon in H. pylori by integration of RNA-seq and ChIP-seq data, and a large extension of the apo-HpFur direct regulon. We show that in response to iron availability, new coding sequences, non-coding RNAs, toxin-antitoxin systems, and transcripts within open reading frames are directly regulated by apo- or holo-HpFur. These new targets and the more thorough validation and deeper characterization of those already known provide a complete and updated picture of the direct regulons of this two-faced transcriptional regulator.
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Affiliation(s)
- Andrea Vannini
- University of Bologna Department of Pharmacy and Biotechnology, Via Selmi 3, 40126 Bologna, Italy.
| | - Eva Pinatel
- Institute of Biomedical Technologies - National Research Council, Via Fratelli Cervi 93, 20054 Segrate (MI), Italy.
| | - Paolo Emidio Costantini
- University of Bologna Department of Pharmacy and Biotechnology, Via Selmi 3, 40126 Bologna, Italy.
| | - Simone Pelliciari
- Human Genetic Unit, Institute of Genetic and Cancer - University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.
| | - Davide Roncarati
- University of Bologna Department of Pharmacy and Biotechnology, Via Selmi 3, 40126 Bologna, Italy.
| | - Simone Puccio
- Institute of Genetics and Biomedical Research, UoS Milan - National Research Council, Via Manzoni 113, 20089 Rozzano (MI), Italy; Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano (MI), Italy.
| | - Gianluca De Bellis
- Institute of Biomedical Technologies - National Research Council, Via Fratelli Cervi 93, 20054 Segrate (MI), Italy.
| | - Vincenzo Scarlato
- University of Bologna Department of Pharmacy and Biotechnology, Via Selmi 3, 40126 Bologna, Italy.
| | - Clelia Peano
- Institute of Genetics and Biomedical Research, UoS Milan - National Research Council, Via Manzoni 113, 20089 Rozzano (MI), Italy; Human Technopole, Via Rita Levi Montalcini 1, 20157 Milan, Italy.
| | - Alberto Danielli
- University of Bologna Department of Pharmacy and Biotechnology, Via Selmi 3, 40126 Bologna, Italy.
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3
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Denic M, Turlin E, Zamble DB, Betton JM, Vinella D, De Reuse H. The SlyD metallochaperone targets iron-sulfur biogenesis pathways and the TCA cycle. mBio 2023; 14:e0096723. [PMID: 37584558 PMCID: PMC10653786 DOI: 10.1128/mbio.00967-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/26/2023] [Indexed: 08/17/2023] Open
Abstract
IMPORTANCE Correct folding of proteins represents a crucial step for their functions. Among the chaperones that control protein folding, the ubiquitous PPIases catalyze the cis/trans-isomerization of peptidyl-prolyl bonds. Only few protein targets of PPIases have been reported in bacteria. To fill this knowledge gap, we performed a large-scale two-hybrid screen to search for targets of the Escherichia coli and Helicobacter pylori SlyD PPIase-metallochaperone. SlyD from both organisms interacts with enzymes (i) containing metal cofactors, (ii) from the central metabolism tricarboxylic acid (TCA) cycle, and (iii) involved in the formation of the essential and ancestral Fe-S cluster cofactor. E. coli and H. pylori ∆slyD mutants present similar phenotypes of diminished susceptibility to antibiotics and to oxidative stress. In H. pylori, measurements of the intracellular ATP content, proton motive force, and activity of TCA cycle proteins suggest that SlyD regulates TCA cycle enzymes by controlling the formation of their indispensable Fe-S clusters.
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Affiliation(s)
- Milica Denic
- Unité Pathogenèse de Helicobacter, Département de Microbiologie, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Evelyne Turlin
- Unité Pathogenèse de Helicobacter, Département de Microbiologie, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
| | - Deborah B. Zamble
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jean-Michel Betton
- Unité Adaptation au stress et Métabolisme chez les entérobactéries, Département de Microbiologie, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
| | - Daniel Vinella
- Unité Pathogenèse de Helicobacter, Département de Microbiologie, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
| | - Hilde De Reuse
- Unité Pathogenèse de Helicobacter, Département de Microbiologie, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
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4
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Ryan ME, Damke PP, Bryant C, Sheedlo MJ, Shaffer CL. Architectural asymmetry enables DNA transport through the Helicobacter pylori cag type IV secretion system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550604. [PMID: 37546756 PMCID: PMC10402047 DOI: 10.1101/2023.07.25.550604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Structural asymmetry within secretion system architecture is fundamentally important for apparatus diversification and biological function. However, the mechanism by which symmetry mismatch contributes to nanomachine assembly and interkingdom effector translocation are undefined. Here, we show that architectural asymmetry orchestrates dynamic substrate selection and enables trans-kingdom DNA conjugation through the Helicobacter pylori cag type IV secretion system (cag T4SS). Structural analyses of asymmetric units within the cag T4SS periplasmic ring complex (PRC) revealed intermolecular π-π stacking interactions that coordinate DNA binding and license trans-kingdom conjugation without disrupting the translocation of protein and peptidoglycan effector molecules. Additionally, we identified a novel proximal translocation channel gating mechanism that regulates cargo loading and governs substrate transport across the outer membrane. We thus propose a model whereby the organization and geometry of architectural symmetry mismatch exposes π-π interfaces within the PRC to facilitate DNA transit through the cag T4SS translocation channel.
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Affiliation(s)
- Mackenzie E. Ryan
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, 40506, USA
| | - Prashant P. Damke
- Department of Veterinary Sciences, University of Kentucky College of Agriculture, Lexington, KY, 40546, USA
| | - Caitlynn Bryant
- Department of Veterinary Sciences, University of Kentucky College of Agriculture, Lexington, KY, 40546, USA
| | - Michael J. Sheedlo
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Carrie L. Shaffer
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, 40506, USA
- Department of Veterinary Sciences, University of Kentucky College of Agriculture, Lexington, KY, 40546, USA
- Department of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, KY, 40536, USA
- Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40506, USA
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5
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Román-Camacho JJ, Mauricio JC, Santos-Dueñas IM, García-Martínez T, García-García I. Unraveling the Role of Acetic Acid Bacteria Comparing Two Acetification Profiles From Natural Raw Materials: A Quantitative Approach in Komagataeibacter europaeus. Front Microbiol 2022; 13:840119. [PMID: 35572698 PMCID: PMC9100681 DOI: 10.3389/fmicb.2022.840119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
The industrial production of vinegar is carried out by the activity of a complex microbiota of acetic acid bacteria (AAB) working, mainly, within bioreactors providing a quite specific and hard environment. The “omics” sciences can facilitate the identification and characterization analyses of these microbial communities, most of which are difficult to cultivate by traditional methods, outside their natural medium. In this work, two acetification profiles coming from the same AAB starter culture but using two natural raw materials of different alcoholic origins (fine wine and craft beer), were characterized and compared and the emphasis of this study is the effect of these raw materials. For this purpose, the composition and natural behavior of the microbiota present throughout these profiles were analyzed by metaproteomics focusing, mainly, on the quantitative protein profile of Komagataeibacter europaeus. This species provided a protein fraction significantly higher (73.5%) than the others. A submerged culture system and semi-continuous operating mode were employed for the acetification profiles and liquid chromatography with tandem mass spectrometry (LC-MS/MS) for the protein analyses. The results showed that neither of two raw materials barely modified the microbiota composition of the profiles, however, they had an effect on the protein expression changes in different biological process. A molecular strategy in which K. europaeus would prevail over other species by taking advantage of the different features offered by each raw material has been suggested. First, by assimilating the excess of inner acetic acid through the TCA cycle and supplying biosynthetic precursors to replenish the cellular material losses; second, by a previous assimilation of the excess of available glucose, mainly in the beer medium, through the glycolysis and the pentose phosphate pathway (PPP); and third, by triggering membrane mechanisms dependent on proton motive force to detoxify the cell at the final moments of acetification. This study could complement the current knowledge of these bacteria as well as to expand the use of diverse raw materials and optimize operating conditions to obtain quality vinegars.
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Affiliation(s)
- Juan J. Román-Camacho
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, Spain
| | - Juan C. Mauricio
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, Spain
- *Correspondence: Juan C. Mauricio,
| | - Inés M. Santos-Dueñas
- Department of Inorganic Chemistry and Chemical Engineering, Institute of Nanochemistry (IUNAN), University of Córdoba, Córdoba, Spain
| | - Teresa García-Martínez
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, Spain
| | - Isidoro García-García
- Department of Inorganic Chemistry and Chemical Engineering, Institute of Nanochemistry (IUNAN), University of Córdoba, Córdoba, Spain
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Fujishiro T, Nakamura R, Kunichika K, Takahashi Y. Structural diversity of cysteine desulfurases involved in iron-sulfur cluster biosynthesis. Biophys Physicobiol 2022; 19:1-18. [PMID: 35377584 PMCID: PMC8918507 DOI: 10.2142/biophysico.bppb-v19.0001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/02/2022] [Indexed: 12/04/2022] Open
Abstract
Cysteine desulfurases are pyridoxal-5'-phosphate (PLP)-dependent enzymes that mobilize sulfur derived from the l-cysteine substrate to the partner sulfur acceptor proteins. Three cysteine desulfurases, IscS, NifS, and SufS, have been identified in ISC, NIF, and SUF/SUF-like systems for iron-sulfur (Fe-S) cluster biosynthesis, respectively. These cysteine desulfurases have been investigated over decades, providing insights into shared/distinct catalytic processes based on two types of enzymes (type I: IscS and NifS, type II: SufS). This review summarizes the insights into the structural/functional varieties of bacterial and eukaryotic cysteine desulfurases involved in Fe-S cluster biosynthetic systems. In addition, an inactive cysteine desulfurase IscS paralog, which contains pyridoxamine-5'-phosphate (PMP), instead of PLP, is also described to account for its hypothetical function in Fe-S cluster biosynthesis involving this paralog. The structural basis for cysteine desulfurase functions will be a stepping stone towards understanding the diversity and evolution of Fe-S cluster biosynthesis.
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Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Ryosuke Nakamura
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Kouhei Kunichika
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Yasuhiro Takahashi
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
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7
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Benoit SL, Maier RJ. Copper toxicity towards Campylobacter jejuni is enhanced by the nickel chelator dimethylglyoxime. Metallomics 2021; 14:6486457. [PMID: 34963007 DOI: 10.1093/mtomcs/mfab076] [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: 09/01/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022]
Abstract
The nickel (Ni)-chelator dimethylglyoxime (DMG) was found to be bacteriostatic towards Campylobacter jejuni. Supplementation of nickel to DMG-containing media restored bacterial growth, whereas supplementation of cobalt or zinc had no effect on the growth inhibition. Unexpectedly, the combination of millimolar levels of DMG with micromolar levels of copper (Cu) was bactericidal, an effect not seen in select Gram-negative pathogenic bacteria. Both the cytoplasmic Ni-binding chaperone SlyD and the twin arginine translocation (Tat)-dependent periplasmic copper oxidase CueO were found to play a central role in the Cu-DMG hypersensitivity phenotype. Ni-replete SlyD is needed for Tat-dependent CueO translocation to the periplasm, whereas Ni-depleted (DMG-treated) SlyD is unable to interact with the CueO Tat signal peptide, leading to mislocalization of CueO and increased copper sensitivity. In support of this model, C. jejuni ΔslyD and ΔcueO mutants were more sensitive to copper than the wild-type (WT); CueO was less abundant in the periplasmic fraction of ΔslyD or DMG-grown WT cells, compared to WT cells grown on plain medium; SlyD binds the CueO signal sequence peptide, with DMG inhibiting and nickel enhancing the binding, respectively. Injection of Cu-DMG into Galleria mellonella before C. jejuni inoculation significantly increased the insect survival rate compared to the control group. In chickens, oral administration of DMG or Cu-DMG decreased and even abolished C. jejuni colonization in some cases, compared to both water-only and Cu-only control groups. The latter finding is important, since campylobacteriosis is the leading bacterial foodborne infection, and chicken meat constitutes the major foodborne source.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology.,Center for Metalloenzyme Studies, The University of Georgia, Athens, Georgia, 30602
| | - Robert J Maier
- Department of Microbiology.,Center for Metalloenzyme Studies, The University of Georgia, Athens, Georgia, 30602
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8
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Abstract
Building iron-sulfur (Fe-S) clusters and assembling Fe-S proteins are essential actions for life on Earth. The three processes that sustain life, photosynthesis, nitrogen fixation, and respiration, require Fe-S proteins. Genes coding for Fe-S proteins can be found in nearly every sequenced genome. Fe-S proteins have a wide variety of functions, and therefore, defective assembly of Fe-S proteins results in cell death or global metabolic defects. Compared to alternative essential cellular processes, there is less known about Fe-S cluster synthesis and Fe-S protein maturation. Moreover, new factors involved in Fe-S protein assembly continue to be discovered. These facts highlight the growing need to develop a deeper biological understanding of Fe-S cluster synthesis, holo-protein maturation, and Fe-S cluster repair. Here, we outline bacterial strategies used to assemble Fe-S proteins and the genetic regulation of these processes. We focus on recent and relevant findings and discuss future directions, including the proposal of using Fe-S protein assembly as an antipathogen target.
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9
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Molecular Biology and Genetic Tools to Investigate Functional Redundancy Among Fe-S Cluster Carriers in E. coli. Methods Mol Biol 2021. [PMID: 34292541 DOI: 10.1007/978-1-0716-1605-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Iron-sulfur (Fe-S) clusters are among the oldest protein cofactors, and Fe-S cluster-based chemistry has shaped the cellular metabolism of all living organisms. Over the last 30 years, thanks to molecular biology and genetic approaches, numerous actors for Fe-S cluster assembly and delivery to apotargets have been uncovered. In prokaryotes, Escherichia coli is the best-studied for its convenience of growth and its genetic amenability. During evolution, redundant ways to secure the supply of Fe-S clusters to the client proteins have emerged in E. coli. Disrupting gene expression is essential for gene function exploration, but redundancy can blur the interpretations as it can mask the role of important biogenesis components. This chapter describes molecular biology and genetic strategies that have permitted to reveal the E. coli Fe-S cluster conveying component network, composition, organization, and plasticity. In this chapter, we will describe the following genetic methods to investigate the importance of E. coli Fe-S cluster carriers: one-step inactivation of chromosomal genes in E. coli using polymerase chain reaction (PCR) products, P1 transduction, arabinose-inducible expression system, mevalonate (MVA) genetic by-pass, sensitivity tests to oxidative stress and iron starvation, β-galactosidase assay, gentamicin survival test, and Hot Fusion cloning method.
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10
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Benoit SL, Agudelo S, Maier RJ. A two-hybrid system reveals previously uncharacterized protein-protein interactions within the Helicobacter pylori NIF iron-sulfur maturation system. Sci Rep 2021; 11:10794. [PMID: 34031459 PMCID: PMC8144621 DOI: 10.1038/s41598-021-90003-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/26/2021] [Indexed: 11/10/2022] Open
Abstract
Iron-sulfur (Fe-S) proteins play essential roles in all living organisms. The gastric pathogen Helicobacter pylori relies exclusively on the NIF system for biosynthesis and delivery of Fe-S clusters. Previously characterized components include two essential proteins, NifS (cysteine desulfurase) and NifU (scaffold protein), and a dispensable Fe-S carrier, Nfu. Among 38 proteins previously predicted to coordinate Fe-S clusters, two proteins, HP0207 (a member of the Nbp35/ApbC ATPase family) and HP0277 (previously annotated as FdxA, a member of the YfhL ferredoxin-like family) were further studied, using a bacterial two-hybrid system approach to identify protein-protein interactions. ApbC was found to interact with 30 proteins, including itself, NifS, NifU, Nfu and FdxA, and alteration of the conserved ATPase motif in ApbC resulted in a significant (50%) decrease in the number of protein interactions, suggesting the ATpase activity is needed for some ApbC-target protein interactions. FdxA was shown to interact with 21 proteins, including itself, NifS, ApbC and Nfu, however no interactions between NifU and FdxA were detected. By use of cross-linking studies, a 51-kDa ApbC-Nfu heterodimer complex was identified. Attempts to generate apbC chromosomal deletion mutants in H. pylori were unsuccessful, therefore indirectly suggesting the hp0207 gene is essential. In contrast, mutants in the fdxA gene were obtained, albeit only in one parental strain (26695). Taken together, these results suggest both ApbC and FdxA are important players in the H. pylori NIF maturation system.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, The University of Georgia, 30602, Athens, Georgia.,Center for Metalloenzyme Studies, The University of Georgia, 30602, Athens, Georgia
| | - Stephanie Agudelo
- Department of Microbiology, The University of Georgia, 30602, Athens, Georgia
| | - Robert J Maier
- Department of Microbiology, The University of Georgia, 30602, Athens, Georgia. .,Center for Metalloenzyme Studies, The University of Georgia, 30602, Athens, Georgia.
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Azam T, Przybyla-Toscano J, Vignols F, Couturier J, Rouhier N, Johnson MK. [4Fe-4S] cluster trafficking mediated by Arabidopsis mitochondrial ISCA and NFU proteins. J Biol Chem 2020; 295:18367-18378. [PMID: 33122194 PMCID: PMC7939391 DOI: 10.1074/jbc.ra120.015726] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/12/2020] [Indexed: 12/17/2022] Open
Abstract
Numerous iron-sulfur (Fe-S) proteins with diverse functions are present in the matrix and respiratory chain complexes of mitochondria. Although [4Fe-4S] clusters are the most common type of Fe-S cluster in mitochondria, the molecular mechanism of [4Fe-4S] cluster assembly and insertion into target proteins by the mitochondrial iron-sulfur cluster (ISC) maturation system is not well-understood. Here we report a detailed characterization of two late-acting Fe-S cluster-carrier proteins from Arabidopsis thaliana, NFU4 and NFU5. Yeast two-hybrid and bimolecular fluorescence complementation studies demonstrated interaction of both the NFU4 and NFU5 proteins with the ISCA class of Fe-S carrier proteins. Recombinant NFU4 and NFU5 were purified as apo-proteins after expression in Escherichia coliIn vitro Fe-S cluster reconstitution led to the insertion of one [4Fe-4S]2+ cluster per homodimer as determined by UV-visible absorption/CD, resonance Raman and EPR spectroscopy, and analytical studies. Cluster transfer reactions, monitored by UV-visible absorption and CD spectroscopy, showed that a [4Fe-4S]2+ cluster-bound ISCA1a/2 heterodimer is effective in transferring [4Fe-4S]2+ clusters to both NFU4 and NFU5 with negligible back reaction. In addition, [4Fe-4S]2+ cluster-bound ISCA1a/2, NFU4, and NFU5 were all found to be effective [4Fe-4S]2+ cluster donors for maturation of the mitochondrial apo-aconitase 2 as assessed by enzyme activity measurements. The results demonstrate rapid, unidirectional, and quantitative [4Fe-4S]2+ cluster transfer from ISCA1a/2 to NFU4 or NFU5 that further delineates their respective positions in the plant ISC machinery and their contributions to the maturation of client [4Fe-4S] cluster-containing proteins.
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Affiliation(s)
- Tamanna Azam
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia, USA
| | | | - Florence Vignols
- BPMP, Université de Montpellier, INRAE, CNRS, SupAgro, Montpellier, France
| | | | | | - Michael K Johnson
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia, USA.
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12
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Braymer JJ, Freibert SA, Rakwalska-Bange M, Lill R. Mechanistic concepts of iron-sulfur protein biogenesis in Biology. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118863. [PMID: 33007329 DOI: 10.1016/j.bbamcr.2020.118863] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 02/08/2023]
Abstract
Iron-sulfur (Fe/S) proteins are present in virtually all living organisms and are involved in numerous cellular processes such as respiration, photosynthesis, metabolic reactions, nitrogen fixation, radical biochemistry, protein synthesis, antiviral defense, and genome maintenance. Their versatile functions may go back to the proposed role of their Fe/S cofactors in the origin of life as efficient catalysts and electron carriers. More than two decades ago, it was discovered that the in vivo synthesis of cellular Fe/S clusters and their integration into polypeptide chains requires assistance by complex proteinaceous machineries, despite the fact that Fe/S proteins can be assembled chemically in vitro. In prokaryotes, three Fe/S protein biogenesis systems are known; ISC, SUF, and the more specialized NIF. The former two systems have been transferred by endosymbiosis from bacteria to mitochondria and plastids, respectively, of eukaryotes. In their cytosol, eukaryotes use the CIA machinery for the biogenesis of cytosolic and nuclear Fe/S proteins. Despite the structural diversity of the protein constituents of these four machineries, general mechanistic concepts underlie the complex process of Fe/S protein biogenesis. This review provides a comprehensive and comparative overview of the various known biogenesis systems in Biology, and summarizes their common or diverging molecular mechanisms, thereby illustrating both the conservation and diverse adaptions of these four machineries during evolution and under different lifestyles. Knowledge of these fundamental biochemical pathways is not only of basic scientific interest, but is important for the understanding of human 'Fe/S diseases' and can be used in biotechnology.
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Affiliation(s)
- Joseph J Braymer
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany
| | - Sven A Freibert
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany
| | | | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany; SYNMIKRO Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany.
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13
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Benoit SL, Maier RJ, Sawers RG, Greening C. Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists. Microbiol Mol Biol Rev 2020; 84:e00092-19. [PMID: 31996394 PMCID: PMC7167206 DOI: 10.1128/mmbr.00092-19] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H2). Here, we comprehensively review the distribution, biochemistry, and physiology of H2 metabolism in pathogens. Over 200 pathogens and pathobionts carry genes for hydrogenases, the enzymes responsible for H2 oxidation and/or production. Furthermore, at least 46 of these species have been experimentally shown to consume or produce H2 Several major human pathogens use the large amounts of H2 produced by colonic microbiota as an energy source for aerobic or anaerobic respiration. This process has been shown to be critical for growth and virulence of the gastrointestinal bacteria Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Campylobacter concisus, and Helicobacter pylori (including carcinogenic strains). H2 oxidation is generally a facultative trait controlled by central regulators in response to energy and oxidant availability. Other bacterial and protist pathogens produce H2 as a diffusible end product of fermentation processes. These include facultative anaerobes such as Escherichia coli, S Typhimurium, and Giardia intestinalis, which persist by fermentation when limited for respiratory electron acceptors, as well as obligate anaerobes, such as Clostridium perfringens, Clostridioides difficile, and Trichomonas vaginalis, that produce large amounts of H2 during growth. Overall, there is a rich literature on hydrogenases in growth, survival, and virulence in some pathogens. However, we lack a detailed understanding of H2 metabolism in most pathogens, especially obligately anaerobic bacteria, as well as a holistic understanding of gastrointestinal H2 transactions overall. Based on these findings, we also evaluate H2 metabolism as a possible target for drug development or other therapies.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Robert J Maier
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - R Gary Sawers
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
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14
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Roland M, Przybyla-Toscano J, Vignols F, Berger N, Azam T, Christ L, Santoni V, Wu HC, Dhalleine T, Johnson MK, Dubos C, Couturier J, Rouhier N. The plastidial Arabidopsis thaliana NFU1 protein binds and delivers [4Fe-4S] clusters to specific client proteins. J Biol Chem 2020; 295:1727-1742. [PMID: 31911438 PMCID: PMC7008376 DOI: 10.1074/jbc.ra119.011034] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/03/2020] [Indexed: 11/06/2022] Open
Abstract
Proteins incorporating iron-sulfur (Fe-S) co-factors are required for a plethora of metabolic processes. Their maturation depends on three Fe-S cluster assembly machineries in plants, located in the cytosol, mitochondria, and chloroplasts. After de novo formation on scaffold proteins, transfer proteins load Fe-S clusters onto client proteins. Among the plastidial representatives of these transfer proteins, NFU2 and NFU3 are required for the maturation of the [4Fe-4S] clusters present in photosystem I subunits, acting upstream of the high-chlorophyll fluorescence 101 (HCF101) protein. NFU2 is also required for the maturation of the [2Fe-2S]-containing dihydroxyacid dehydratase, important for branched-chain amino acid synthesis. Here, we report that recombinant Arabidopsis thaliana NFU1 assembles one [4Fe-4S] cluster per homodimer. Performing co-immunoprecipitation experiments and assessing physical interactions of NFU1 with many [4Fe-4S]-containing plastidial proteins in binary yeast two-hybrid assays, we also gained insights into the specificity of NFU1 for the maturation of chloroplastic Fe-S proteins. Using bimolecular fluorescence complementation and in vitro Fe-S cluster transfer experiments, we confirmed interactions with two proteins involved in isoprenoid and thiamine biosynthesis, 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate synthase and 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase, respectively. An additional interaction detected with the scaffold protein SUFD enabled us to build a model in which NFU1 receives its Fe-S cluster from the SUFBC2D scaffold complex and serves in the maturation of specific [4Fe-4S] client proteins. The identification of the NFU1 partner proteins reported here more clearly defines the role of NFU1 in Fe-S client protein maturation in Arabidopsis chloroplasts among other SUF components.
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Affiliation(s)
- Mélanie Roland
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
| | | | - Florence Vignols
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Nathalie Berger
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Tamanna Azam
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602
| | - Loick Christ
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
| | - Véronique Santoni
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Hui-Chen Wu
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | | | - Michael K Johnson
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602
| | - Christian Dubos
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
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Abstract
Nickel is an essential cofactor for some pathogen virulence factors. Due to its low availability in hosts, pathogens must efficiently transport the metal and then balance its ready intracellular availability for enzyme maturation with metal toxicity concerns. The most notable virulence-associated components are the Ni-enzymes hydrogenase and urease. Both enzymes, along with their associated nickel transporters, storage reservoirs, and maturation enzymes have been best-studied in the gastric pathogen Helicobacter pylori, a bacterium which depends heavily on nickel. Molecular hydrogen utilization is associated with efficient host colonization by the Helicobacters, which include both gastric and liver pathogens. Translocation of a H. pylori carcinogenic toxin into host epithelial cells is powered by H2 use. The multiple [NiFe] hydrogenases of Salmonella enterica Typhimurium are important in host colonization, while ureases play important roles in both prokaryotic (Proteus mirabilis and Staphylococcus spp.) and eukaryotic (Cryptoccoccus genus) pathogens associated with urinary tract infections. Other Ni-requiring enzymes, such as Ni-acireductone dioxygenase (ARD), Ni-superoxide dismutase (SOD), and Ni-glyoxalase I (GloI) play important metabolic or detoxifying roles in other pathogens. Nickel-requiring enzymes are likely important for virulence of at least 40 prokaryotic and nine eukaryotic pathogenic species, as described herein. The potential for pathogenic roles of many new Ni-binding components exists, based on recent experimental data and on the key roles that Ni enzymes play in a diverse array of pathogens.
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16
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Benoit SL, Maier RJ. Site-directed mutagenesis of Campylobacter concisus respiratory genes provides insight into the pathogen's growth requirements. Sci Rep 2018; 8:14203. [PMID: 30242194 PMCID: PMC6155014 DOI: 10.1038/s41598-018-32509-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/10/2018] [Indexed: 12/30/2022] Open
Abstract
Campylobacter concisus is an emerging human pathogen found throughout the entire human oral-gastrointestinal tract. The ability of C. concisus to colonize diverse niches of the human body indicates the pathogen is metabolically versatile. C. concisus is able to grow under both anaerobic conditions and microaerophilic conditions. Hydrogen (H2) has been shown to enhance growth and may even be required. Analysis of several C. concisus genome sequences reveals the presence of two sets of genes encoding for distinct hydrogenases: a H2-uptake-type ("Hyd") complex and a H2-evolving hydrogenase ("Hyf"). Whole cells hydrogenase assays indicate that the former (H2-uptake) activity is predominant in C. concisus, with activity among the highest we have found for pathogenic bacteria. Attempts to generate site-directed chromosomal mutants were partially successful, as we could disrupt hyfB, but not hydB, suggesting that H2-uptake, but not H2-evolving activity, is an essential respiratory pathway in C. concisus. Furthermore, the tetrathionate reductase ttrA gene was inactivated in various C. concisus genomospecies. Addition of tetrathionate to the medium resulted in a ten-fold increase in cell yield for the WT, while it had no effect on the ttrA mutant growth. To our knowledge, this is the first report of mutants in C. concisus.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, University of Georgia, Athens, 30602, Georgia.
- Center for Metalloenzyme Studies, University of Georgia, Athens, 30602, Georgia.
| | - Robert J Maier
- Department of Microbiology, University of Georgia, Athens, 30602, Georgia
- Center for Metalloenzyme Studies, University of Georgia, Athens, 30602, Georgia
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17
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Abstract
In this review, we highlight progress in the last year in characterizing known virulence factors like flagella and the Cag type IV secretion system with sophisticated structural and biochemical approaches to yield new insight on the assembly and functions of these critical virulence determinants. Several aspects of Helicobacter pylori physiology were newly explored this year and evaluated for their functions during stomach colonization, including a fascinating role for the essential protease HtrA in allowing access of H. pylori to the basolateral side of the gastric epithelium through cleavage of the tight junction protein E-cadherin to facilitate CagA delivery. Molecular biology tools standard in model bacteria, including regulated gene expression during animal infection and fluorescent reporter gene fusions, were newly applied to H. pylori to explore functions for urease beyond initial colonization and establish high salt consumption as a mediator of gene expression changes. New sequencing technologies enabled validation of long postulated roles for DNA methylation in regulating H. pylori gene expression. On the cell biology side, elegant work using lineage tracing in the murine model and organoid primary cell culture systems has provided new insights into how H. pylori manipulates gastric tissue functions, locally and at a distance, to promote its survival in the stomach and induce pathologic changes. Finally, new work has bolstered the case for genomic variation as an important mechanism to generate phenotypic diversity during changing environmental conditions in the context of diet manipulation in animal infection models and during human experimental infection after vaccination.
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Affiliation(s)
- Langgeng Agung Waskito
- Faculty of Medicine, Department of Environmental and Preventive Medicine, Oita University, Yufu-City, Oita, Japan.,Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Nina R Salama
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Yoshio Yamaoka
- Faculty of Medicine, Department of Environmental and Preventive Medicine, Oita University, Yufu-City, Oita, Japan.,Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, Texas
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18
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Peña-Diaz P, Lukeš J. Fe-S cluster assembly in the supergroup Excavata. J Biol Inorg Chem 2018; 23:521-541. [PMID: 29623424 PMCID: PMC6006210 DOI: 10.1007/s00775-018-1556-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 03/29/2018] [Indexed: 12/21/2022]
Abstract
The majority of established model organisms belong to the supergroup Opisthokonta, which includes yeasts and animals. While enlightening, this focus has neglected protists, organisms that represent the bulk of eukaryotic diversity and are often regarded as primitive eukaryotes. One of these is the “supergroup” Excavata, which comprises unicellular flagellates of diverse lifestyles and contains species of medical importance, such as Trichomonas, Giardia, Naegleria, Trypanosoma and Leishmania. Excavata exhibits a continuum in mitochondrial forms, ranging from classical aerobic, cristae-bearing mitochondria to mitochondria-related organelles, such as hydrogenosomes and mitosomes, to the extreme case of a complete absence of the organelle. All forms of mitochondria house a machinery for the assembly of Fe–S clusters, ancient cofactors required in various biochemical activities needed to sustain every extant cell. In this review, we survey what is known about the Fe–S cluster assembly in the supergroup Excavata. We aim to bring attention to the diversity found in this group, reflected in gene losses and gains that have shaped the Fe–S cluster biogenesis pathways.
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Affiliation(s)
- Priscila Peña-Diaz
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
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