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Chen M, Wu B, Huang Y, Wang W, Zheng Y, Shabbir S, Liu P, Dai Y, Xia M, Hu G, He M. Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation. Nucleic Acids Res 2024; 52:5643-5657. [PMID: 38716861 PMCID: PMC11162768 DOI: 10.1093/nar/gkae318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 04/09/2024] [Accepted: 04/24/2024] [Indexed: 06/11/2024] Open
Abstract
Genomic mutations allow bacteria to adapt rapidly to adverse stress environments. The three-dimensional conformation of the genome may also play an important role in transcriptional regulation and environmental adaptation. Here, using chromosome conformation capture, we investigate the high-order architecture of the Zymomonas mobilis chromosome in response to genomic mutation and ambient stimuli (acetic acid and furfural, derived from lignocellulosic hydrolysate). We find that genomic mutation only influences the local chromosome contacts, whereas stress of acetic acid and furfural restrict the long-range contacts and significantly change the chromosome organization at domain scales. Further deciphering the domain feature unveils the important transcription factors, Ferric uptake regulator (Fur) proteins, which act as nucleoid-associated proteins to promote long-range (>200 kb) chromosomal communications and regulate the expression of genes involved in stress response. Our work suggests that ubiquitous transcription factors in prokaryotes mediate chromosome organization and regulate stress-resistance genes in bacterial adaptation.
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Affiliation(s)
- Mao Chen
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
- Graduate School of Chinese Academy of Agricultural Sciences; Beijing 100081, PR China
| | - Bo Wu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Yuhuan Huang
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
- Graduate School of Chinese Academy of Agricultural Sciences; Beijing 100081, PR China
| | - Weiting Wang
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Yudi Zheng
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
- Graduate School of Chinese Academy of Agricultural Sciences; Beijing 100081, PR China
| | - Samina Shabbir
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Panting Liu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Yonghua Dai
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Mengli Xia
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Guoquan Hu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Mingxiong He
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
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Choi Y, Koh J, Cha SS, Roe JH. Activation of zinc uptake regulator by zinc binding to three regulatory sites. Nucleic Acids Res 2024; 52:4185-4197. [PMID: 38349033 PMCID: PMC11077047 DOI: 10.1093/nar/gkae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 05/09/2024] Open
Abstract
Zur is a Fur-family metalloregulator that is widely used to control zinc homeostasis in bacteria. In Streptomyces coelicolor, Zur (ScZur) acts as both a repressor for zinc uptake (znuA) gene and an activator for zinc exporter (zitB) gene. Previous structural studies revealed three zinc ions specifically bound per ScZur monomer; a structural one to allow dimeric architecture and two regulatory ones for DNA-binding activity. In this study, we present evidence that Zur contains a fourth specific zinc-binding site with a key histidine residue (H36), widely conserved among actinobacteria, for regulatory function. Biochemical, genetic, and calorimetric data revealed that H36 is critical for hexameric binding of Zur to the zitB zurbox and further binding to its upstream region required for full activation. A comprehensive thermodynamic model demonstrated that the DNA-binding affinity of Zur to both znuA and zitB zurboxes is remarkably enhanced upon saturation of all three regulatory zinc sites. The model also predicts that the strong coupling between zinc binding and DNA binding equilibria of Zur drives a biphasic activation of the zitB gene in response to a wide concentration change of zinc. Similar mechanisms may be pertinent to other metalloproteins, expanding their response spectrum through binding multiple regulatory metals.
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Affiliation(s)
- Yunchan Choi
- Laboratory of Molecular Microbiology, School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Junseock Koh
- Laboratory of Biophysical Chemistry, School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Sun-Shin Cha
- Protein Research Laboratory, Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jung-Hye Roe
- Laboratory of Molecular Microbiology, School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Republic of Korea
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Gu Y, Liu Y, Mao W, Peng Y, Han X, Jin H, Xu J, Chang L, Hou Y, Shen X, Liu X, Yang Y. Functional versatility of Zur in metal homeostasis, motility, biofilm formation, and stress resistance in Yersinia pseudotuberculosis. Microbiol Spectr 2024; 12:e0375623. [PMID: 38534119 PMCID: PMC11064496 DOI: 10.1128/spectrum.03756-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/13/2024] [Indexed: 03/28/2024] Open
Abstract
Zur (zinc uptake regulator) is a significant member of the Fur (ferric uptake regulator) superfamily, which is widely distributed in bacteria. Zur plays crucial roles in zinc homeostasis and influences cell development and environmental adaptation in various species. Yersinia pseudotuberculosis is a Gram-negative enteric that pathogen usually serves as a model organism in pathogenicity studies. The regulatory effects of Zur on the zinc transporter ZnuABC and the protein secretion system T6SS have been documented in Y. pseudotuberculosis. In this study, a comparative transcriptomics analysis between a ∆zur mutant and the wild-type (WT) strain of Y. pseudotuberculosis was conducted using RNA-seq. This analysis revealed global regulation by Zur across multiple functional categories, including membrane transport, cell motility, and molecular and energy metabolism. Additionally, Zur mediates the homeostasis not only of zinc but also ferric and magnesium in vivo. There was a notable decrease in 35 flagellar biosynthesis and assembly-related genes, leading to reduced swimming motility in the ∆zur mutant strain. Furthermore, Zur upregulated multiple simple sugar and oligopeptide transport system genes by directly binding to their promoters. The absence of Zur inhibited biofilm formation as well as reduced resistance to chloramphenicol and acidic stress. This study illustrates the comprehensive regulatory functions of Zur, emphasizing its importance in stress resistance and pathogenicity in Y. pseudotuberculosis. IMPORTANCE Bacteria encounter diverse stresses in the environment and possess essential regulators to modulate the expression of genes in responding to the stresses for better fitness and survival. Zur (zinc uptake regulator) plays a vital role in zinc homeostasis. Studies of Zur from multiple species reviewed that it influences cell development, stress resistance, and virulence of bacteria. Y. pseudotuberculosis is an enteric pathogen that serves a model organism in the study of pathogenicity, virulence factors, and mechanism of environmental adaptation. In this study, transcriptomics analysis of Zur's regulons was conducted in Y. pseudotuberculosis. The functions of Zur as a global regulator in metal homeostasis, motility, nutrient acquisition, glycan metabolism, and nucleotide metabolism, in turn, increasing the biofilm formation, stress resistance, and virulence were reviewed. The importance of Zur in environmental adaptation and pathogenicity of Y. pseudotuberculosis was emphasized.
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Affiliation(s)
- Yanchao Gu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Yongde Liu
- Qingyang Longfeng Sponge City Construction Management and Operation Co., Ltd, Qingyang, China
| | - Wei Mao
- Qingyang Longfeng Sponge City Construction Management and Operation Co., Ltd, Qingyang, China
| | - Ying Peng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xiaoru Han
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Han Jin
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Jingling Xu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Liyang Chang
- College of Enology, Northwest A&F University, Yangling, China
| | - Yixin Hou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xihui Shen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xingyu Liu
- General Research Institute for Nonferrous Metals, Beijing, China
| | - Yantao Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
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Olczak T, Śmiga M, Antonyuk SV, Smalley JW. Hemophore-like proteins of the HmuY family in the oral and gut microbiome: unraveling the mystery of their evolution. Microbiol Mol Biol Rev 2024; 88:e0013123. [PMID: 38305743 PMCID: PMC10966948 DOI: 10.1128/mmbr.00131-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Abstract
SUMMARY Heme (iron protoporphyrin IX, FePPIX) is the main source of iron and PPIX for host-associated pathogenic bacteria, including members of the Bacteroidota (formerly Bacteroidetes) phylum. Porphyromonas gingivalis, a keystone oral pathogen, uses a unique heme uptake (Hmu) system, comprising a hemophore-like protein, designated as the first member of the novel HmuY family. Compared to classical, secreted hemophores utilized by Gram-negative bacteria or near-iron transporter domain-based hemophores utilized by Gram-positive bacteria, the HmuY family comprises structurally similar proteins that have undergone diversification during evolution. The best characterized are P. gingivalis HmuY and its homologs from Tannerella forsythia (Tfo), Prevotella intermedia (PinO and PinA), Bacteroides vulgatus (Bvu), and Bacteroides fragilis (BfrA, BfrB, and BfrC). In contrast to the two histidine residues coordinating heme iron in P. gingivalis HmuY, Tfo, PinO, PinA, Bvu, and BfrA preferentially use two methionine residues. Interestingly, BfrB, despite conserved methionine residue, binds the PPIX ring without iron coordination. BfrC binds neither heme nor PPIX in keeping with the lack of conserved histidine or methionine residues used by other members of the HmuY family. HmuY competes for heme binding and heme sequestration from host hemoproteins with other members of the HmuY family to increase P. gingivalis competitiveness. The participation of HmuY in the host immune response confirms its relevance in relation to the survival of P. gingivalis and its ability to induce dysbiosis not only in the oral microbiome but also in the gut microbiome or other host niches, leading to local injuries and involvement in comorbidities.
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Affiliation(s)
- Teresa Olczak
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Michał Śmiga
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, the University of Liverpool, Liverpool, United Kingdom
| | - John W. Smalley
- Institute of Life Course and Medical Sciences, School of Dentistry, the University of Liverpool, Liverpool, United Kingdom
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Hou J, Yang M, Wu X, Chen Q, Lu Y, Zhang J, Lin D. Epidermal microorganisms contributed to the toxic mechanism of nZVI and TCEP in earthworms by robbing metal elements and nutrients. ECO-ENVIRONMENT & HEALTH (ONLINE) 2024; 3:80-88. [PMID: 38323088 PMCID: PMC10844675 DOI: 10.1016/j.eehl.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Indexed: 02/08/2024]
Abstract
Disrupting effects of pollutants on symbiotic microbiota have been regarded as an important mechanism of host toxicity, with most current research focusing on the intestinal microbiota. In fact, the epidermal microbiota, which participates in the nutrient exchange between hosts and environments, could play a crucial role in host toxicity via community changes. To compare the contributions of intestinal and epidermal symbiotic microorganisms to host toxicity, this study designed single and combined scenarios of soil contamination [nano zero-valent iron (nZVI) and tris (2-chloroethyl) phosphate (TCEP)], and revealed the coupling mechanisms between intestinal/epidermal symbiotic bacterial communities and earthworm toxicological endpoints. Microbiome analysis showed that 15% of intestinal microbes were highly correlated with host endpoints, compared to 45% of epidermal microbes showing a similar correlation. Functional comparisons revealed that key species on the epidermis were mainly heterotrophic microbes with genetic abilities to utilize metal elements and carbohydrate nutrients. Further verifications demonstrated that when facing the co-contamination of nZVI and TCEP, certain symbiotic microorganisms became dominant and consumed zinc, copper, and manganese along with saccharides and amino acids, which may be responsible for the nutritional deficiencies in the host earthworms. The findings can enrich the understanding of the coupling relationship between symbiotic microorganisms and host toxicity, highlighting the importance of epidermal microorganisms in host resistance to environmental pollution.
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Affiliation(s)
- Jie Hou
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Meirui Yang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Xinyue Wu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Qiqi Chen
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Yuqi Lu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Jianying Zhang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- National Demonstration Center for Experimental Environment and Resources Education (Zhejiang University), Hangzhou 310058, China
| | - Daohui Lin
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Zhejiang Ecological Civilization Academy, Anji 313300, China
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6
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Sarasa-Buisan C, Ochoa de Alda JAG, Velázquez-Suárez C, Rubio MÁ, Gómez-Baena G, Fillat MF, Luque I. An ancient bacterial zinc acquisition system identified from a cyanobacterial exoproteome. PLoS Biol 2024; 22:e3002546. [PMID: 38466754 PMCID: PMC10957091 DOI: 10.1371/journal.pbio.3002546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 03/21/2024] [Accepted: 02/12/2024] [Indexed: 03/13/2024] Open
Abstract
Bacteria have developed fine-tuned responses to cope with potential zinc limitation. The Zur protein is a key player in coordinating this response in most species. Comparative proteomics conducted on the cyanobacterium Anabaena highlighted the more abundant proteins in a zur mutant compared to the wild type. Experimental evidence showed that the exoprotein ZepA mediates zinc uptake. Genomic context of the zepA gene and protein structure prediction provided additional insights on the regulation and putative function of ZepA homologs. Phylogenetic analysis suggests that ZepA represents a primordial system for zinc acquisition that has been conserved for billions of years in a handful of species from distant bacterial lineages. Furthermore, these results show that Zur may have been one of the first regulators of the FUR family to evolve, consistent with the scarcity of zinc in the ecosystems of the Archean eon.
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Affiliation(s)
- Cristina Sarasa-Buisan
- Departamento de Bioquímica y Biología Molecular y Celular e Instituto de Biocomputación y Física de Sistemas Complejos (Bifi), Universidad de Zaragoza, Zaragoza, Spain
| | - Jesús A. G. Ochoa de Alda
- Didáctica de las Ciencias Experimentales y la Matemáticas, Universidad de Extremadura, Cáceres, Spain
| | | | - Miguel Ángel Rubio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Guadalupe Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain
| | - María F. Fillat
- Departamento de Bioquímica y Biología Molecular y Celular e Instituto de Biocomputación y Física de Sistemas Complejos (Bifi), Universidad de Zaragoza, Zaragoza, Spain
| | - Ignacio Luque
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
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Hubert T, Madec M, Schalk IJ. Experimental and computational methods to highlight behavioural variations in TonB-dependent transporter expression in Pseudomonas aeruginosa versus siderophore concentration. Sci Rep 2023; 13:20015. [PMID: 37974013 PMCID: PMC10654771 DOI: 10.1038/s41598-023-46585-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
Iron is a key nutrient for bacterial growth. The source can be either heme or siderophore-Fe complexes. Siderophores are small molecules synthesized by bacteria to scavenge iron from the bacterial environment. The pathogen Pseudomonas aeruginosa can express at least 15 different iron uptake pathways and all but one involve a TonB-dependent transporter (TBDT) for the uptake of iron across the outer membrane. Little is known about how bacteria modulate and adapt the expression of their different iron import pathways according to their environment. Here, we have developed fluorescent reporters between the promoter region of genes encoding a TBDT and the fluorescent reporter mCherry. With these constructs, we can follow the expression of TBDTs under different growth conditions. Mathematical modelling of the data obtained showed the transcription and expression of the gene encoding the TBDT PfeA to have a sigmoidal shape, whereas it was logarithmic for the TBDT gene foxA. Maximum transcription for pfeA was reached in the presence of 3 µM enterobactin, the siderophore recognized by PfeA, whereas the maximum was not reached for foxA with 100 µM nocardamine, the siderophore of FoxA.
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Affiliation(s)
- Thibaut Hubert
- CNRS, UMR7242, ESBS, University of Strasbourg, Bld Sébastien Brant, 67412, Illkirch, Strasbourg, France
- ICube Laboratory, CNRS, UMR 7357, University of Strasbourg, Bld Sébastien Brant, 67412, Illkirch, Strasbourg, France
| | - Morgan Madec
- ICube Laboratory, CNRS, UMR 7357, University of Strasbourg, Bld Sébastien Brant, 67412, Illkirch, Strasbourg, France.
| | - Isabelle J Schalk
- CNRS, UMR7242, ESBS, University of Strasbourg, Bld Sébastien Brant, 67412, Illkirch, Strasbourg, France.
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Williams MT, Yee E, Larson GW, Apiche EA, Rama Damodaran A, Bhagi-Damodaran A. Metalloprotein enabled redox signal transduction in microbes. Curr Opin Chem Biol 2023; 76:102331. [PMID: 37311385 PMCID: PMC10524656 DOI: 10.1016/j.cbpa.2023.102331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/21/2023] [Accepted: 04/26/2023] [Indexed: 06/15/2023]
Abstract
Microbes utilize numerous metal cofactor-containing proteins to recognize and respond to constantly fluctuating redox stresses in their environment. Gaining an understanding of how these metalloproteins sense redox events, and how they communicate such information downstream to DNA to modulate microbial metabolism, is a topic of great interest to both chemists and biologists. In this article, we review recently characterized examples of metalloprotein sensors, focusing on the coordination and oxidation state of the metals involved, how these metals are able to recognize redox stimuli, and how the signal is transmitted beyond the metal center. We discuss specific examples of iron, nickel, and manganese-based microbial sensors, and identify gaps in knowledge in the field of metalloprotein-based signal transduction pathways.
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Affiliation(s)
- Murphi T Williams
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Eaindra Yee
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Grant W Larson
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Elizabeth A Apiche
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Anoop Rama Damodaran
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA.
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Fan X, Zhao B, Zhang W, Li N, Mi K, Wang B. Coevolution of furA-Regulated Hyper-Inflammation and Mycobacterial Resistance to Oxidative Killing through Adaptation to Hydrogen Peroxide. Microbiol Spectr 2023; 11:e0536722. [PMID: 37358434 PMCID: PMC10433983 DOI: 10.1128/spectrum.05367-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 05/25/2023] [Indexed: 06/27/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is highly resistant to host oxidative killing. We hypothesized that the evolutionary adaptation of M. smegmatis to hydrogen peroxide (H2O2) would endow the nonpathogenic Mycobacterium persistent in a host. In the study, we screened a highly H2O2-resistant strain (mc2114) via evolutionary H2O2 adaptation in vitro. The MIC of mc2114 to H2O2 is 320 times that of wild-type mc2155. Mouse infection experiments showed that mc2114, similar to Mtb, was persistent in the lungs and caused high lethality in mice with restricted responses of NOX2, ROS, IFN-γ, decreased macrophage apoptosis, and overexpressed inflammatory cytokines in the lungs. Whole-genome sequencing analysis revealed that mc2114 harbored 29 single nucleotide polymorphisms in multiple genes; one of them was on the furA gene that caused FurA deficiency-mediated overexpression of KatG, a catalase-peroxidase to detoxify ROS. Complementation of mc2114 with a wild-type furA gene reversed lethality and hyper-inflammatory response in mice with rescued overexpression of KatG and inflammatory cytokines, whereas NOX2, ROS, IFN-γ, and macrophage apoptosis remained reduced. The results indicate that although FurA regulates KatG expression, it does not contribute significantly to the restriction of ROS response. Instead, FurA deficiency is responsible for the detrimental pulmonary inflammation that contributes to the severity of the infection, a previously nonrecognized function of FurA in mycobacterial pathogenesis. The study also indicates that mycobacterial resistance to oxidative burst results from complex mechanisms involving adaptive genetic changes in multiple genes. IMPORTANCE Mycobacterium tuberculosis (Mtb) causes human tuberculosis (TB), which has killed more people in human history than any other microorganism. However, the mechanisms underlying Mtb pathogenesis and related genes have not yet been fully elucidated, which impedes the development of effective strategies for containing and eradicating TB. In the study, we generated a mutant of M. smegmatis (mc2114) with multiple mutations by an adaptive evolutionary screen with H2O2. One of the mutations in furA caused a deficiency of FurA, which mediated severe inflammatory lung injury and higher lethality in mice by overexpression of inflammatory cytokines. Our results indicate that FurA-regulated pulmonary inflammation plays a critical role in mycobacterial pathogenesis in addition to the known downregulation of NOX2, ROS, IFN-γ responses, and macrophage apoptosis. Further analysis of the mutations in mc2114 would identify more genes related to the increased pathogenicity and help in devising new strategies for containing and eradicating TB.
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Affiliation(s)
- Xin Fan
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bei Zhao
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Weishan Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Ning Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Kaixia Mi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Beinan Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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10
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Sarasa-Buisan C, Guío J, Peleato ML, Fillat MF, Sevilla E. Expanding the FurC (PerR) regulon in Anabaena (Nostoc) sp. PCC 7120: Genome-wide identification of novel direct targets uncovers FurC participation in central carbon metabolism regulation. PLoS One 2023; 18:e0289761. [PMID: 37549165 PMCID: PMC10406281 DOI: 10.1371/journal.pone.0289761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023] Open
Abstract
FurC (PerR, Peroxide Response Regulator) from Anabaena sp. PCC 7120 (also known as Nostoc sp. PCC 7120) is a master regulator engaged in the modulation of relevant processes including the response to oxidative stress, photosynthesis and nitrogen fixation. Previous differential gene expression analysis of a furC-overexpressing strain (EB2770FurC) allowed the inference of a putative FurC DNA-binding consensus sequence. In the present work, more data concerning the regulon of the FurC protein were obtained through the searching of the putative FurC-box in the whole Anabaena sp. PCC 7120 genome. The total amount of novel FurC-DNA binding sites found in the promoter regions of genes with known function was validated by electrophoretic mobility shift assays (EMSA) identifying 22 new FurC targets. Some of these identified targets display relevant roles in nitrogen fixation (hetR and hgdC) and carbon assimilation processes (cmpR, glgP1 and opcA), suggesting that FurC could be an additional player for the harmonization of carbon and nitrogen metabolisms. Moreover, differential gene expression of a selection of newly identified FurC targets was measured by Real Time RT-PCR in the furC-overexpressing strain (EB2770FurC) comparing to Anabaena sp. PCC 7120 revealing that in most of these cases FurC could act as a transcriptional activator.
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Affiliation(s)
- Cristina Sarasa-Buisan
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
| | - Jorge Guío
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
| | - M. Luisa Peleato
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
| | - María F. Fillat
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
| | - Emma Sevilla
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
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11
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Abanoz-Seçgin B, Otur Ç, Okay S, Kurt-Kızıldoğan A. The regulatory role of Fur-encoding SCLAV_3199 in iron homeostasis in Streptomyces clavuligerus. Gene 2023:147594. [PMID: 37364696 DOI: 10.1016/j.gene.2023.147594] [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: 03/14/2023] [Revised: 06/09/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Iron homeostasis is strictly regulated by complex cascades connected with secondary metabolism in bacteria. Ferric uptake regulators ('Fur's), siderophores, efflux systems, and two-component signal transduction systems are the leading players in response stimuli. However, these regulatory mechanisms remain to be elucidated in Streptomyces clavuligerus. Our study focused on unraveling a possible role of SCLAV_3199 which encodes a Fur family transcriptional regulator, particularly in iron regulation and at the global level in this species. We deleted the SCLAV_3199 gene in S. clavuligerus and compared gene expression differences with the wild-type strain based on iron availability by RNA-seq. We found a potential regulatory effect of SCLAV_3199 on many transcriptional regulators and transporters. Besides, the genes encoding iron sulfur binding proteins were overexpressed in the mutant in the presence of iron. Notably, catechol (SCLAV_5397), and hydroxamate-type (SCLAV_1952, SCLAV_4680) siderophore-related genes were upregulated in the mutant strain in iron scarcity. Concomitantly, S. clavuligerus Δ3199 produced 1.65 and 1.9 times more catechol and hydroxamate-type siderophores, respectively, than that of the wild type strain under iron depletion. Iron containing chemically defined medium did not favor antibiotic production in S. clavuligerus Δ3199 while fermentation in starch-asparagine medium led to improved cephamycin C (2.23-fold) and clavulanic acid (2.56-fold) production in the mutant compared to the control. However, better tunicamycin yield (2.64-fold) was obtained in trypticase soy broth-grown cultures of S. clavuligerus Δ3199. Our findings demonstrate that the SCLAV_3199 gene plays a significant role in regulating both iron homeostasis and secondary metabolite biosynthesis in S. clavuligerus.
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Affiliation(s)
- Büşra Abanoz-Seçgin
- Department of Agricultural Biotechnology, Ondokuz Mayıs University, Samsun 55139, Türkiye
| | - Çiğdem Otur
- Department of Agricultural Biotechnology, Ondokuz Mayıs University, Samsun 55139, Türkiye
| | - Sezer Okay
- Department of Vaccine Technology, Vaccine Institute, Hacettepe University, Ankara, 06230, Türkiye
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12
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Hammerstad M, Rugtveit AK, Dahlen S, Andersen HK, Hersleth HP. Functional Diversity of Homologous Oxidoreductases-Tuning of Substrate Specificity by a FAD-Stacking Residue for Iron Acquisition and Flavodoxin Reduction. Antioxidants (Basel) 2023; 12:1224. [PMID: 37371954 DOI: 10.3390/antiox12061224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Although bacterial thioredoxin reductase-like ferredoxin/flavodoxin NAD(P)+ oxidoreductases (FNRs) are similar in terms of primary sequences and structures, they participate in diverse biological processes by catalyzing a range of different redox reactions. Many of the reactions are critical for the growth, survival of, and infection by pathogens, and insight into the structural basis for substrate preference, specificity, and reaction kinetics is crucial for the detailed understanding of these redox pathways. Bacillus cereus (Bc) encodes three FNR paralogs, two of which have assigned distinct biological functions in bacillithiol disulfide reduction and flavodoxin (Fld) reduction. Bc FNR2, the endogenous reductase of the Fld-like protein NrdI, belongs to a distinct phylogenetic cluster of homologous oxidoreductases containing a conserved His residue stacking the FAD cofactor. In this study, we have assigned a function to FNR1, in which the His residue is replaced by a conserved Val, in the reduction of the heme-degrading monooxygenase IsdG, ultimately facilitating the release of iron in an important iron acquisition pathway. The Bc IsdG structure was solved, and IsdG-FNR1 interactions were proposed through protein-protein docking. Mutational studies and bioinformatics analyses confirmed the importance of the conserved FAD-stacking residues on the respective reaction rates, proposing a division of FNRs into four functionally unique sequence similarity clusters likely related to the nature of this residue.
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Affiliation(s)
- Marta Hammerstad
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Anne Kristine Rugtveit
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Sondov Dahlen
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Hilde Kristin Andersen
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Hans-Petter Hersleth
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
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13
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Nandavaram A, Nandakumar A, Kashif GM, Sagar AL, Shailaja G, Ramesh A, Siddavattam D. Unusual Relationship between Iron Deprivation and Organophosphate Hydrolase Expression. Appl Environ Microbiol 2023; 89:e0190322. [PMID: 37074175 PMCID: PMC10231211 DOI: 10.1128/aem.01903-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/08/2023] [Indexed: 04/20/2023] Open
Abstract
Organophosphate hydrolases (OPH), hitherto known to hydrolyze the third ester bond of organophosphate (OP) insecticides and nerve agents, have recently been shown to interact with outer membrane transport components, namely, TonB and ExbB/ExbD. In an OPH negative background, Sphingopyxis wildii cells failed to transport ferric enterobactin and showed retarded growth under iron-limiting conditions. We now show the OPH-encoding organophosphate degradation (opd) gene from Sphingobium fuliginis ATCC 27551 to be part of the iron regulon. A fur-box motif found to be overlapping with the transcription start site (TSS) of the opd gene coordinates with an iron responsive element (IRE) RNA motif identified in the 5' coding region of the opd mRNA to tightly regulate opd gene expression. The fur-box motif serves as a target for the Fur repressor in the presence of iron. A decrease in iron concentration leads to the derepression of opd. IRE RNA inhibits the translation of opd mRNA and serves as a target for apo-aconitase (IRP). The IRP recruited by the IRE RNA abrogates IRE-mediated translational inhibition. Our findings establish a novel, multilayered, iron-responsive regulation that is crucial for OPH function in the transport of siderophore-mediated iron uptake. IMPORTANCE Sphingobium fuliginis, a soil-dwelling microbe isolated from agricultural soils, was shown to degrade a variety of insecticides and pesticides. These synthetic chemicals function as potent neurotoxins, and they belong to a class of chemicals termed organophosphates. S. fuliginis codes for OPH, an enzyme that has been shown to be involved in the metabolism of several organophosphates and their derivatives. Interestingly, OPH has also been shown to facilitate siderophore-mediated iron uptake in S. fuliginis and in another Sphingomonad, namely, Sphingopyxis wildii, implying that this organophosphate-metabolizing protein has a role in iron homeostasis, as well. Our research dissects the underlying molecular mechanisms linking iron to the expression of OPH, prompting a reconsideration of the role of OPH in Sphingomonads and a reevaluation of the evolutionary origins of the OPH proteins from soil bacteria.
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Affiliation(s)
- Aparna Nandavaram
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Anirudh Nandakumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bengaluru, India
- The University of Trans-Disciplinary Health Sciences & Technology (TDU), Bengaluru, Karnataka, India
| | - G. M. Kashif
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | | | - G. Shailaja
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Arati Ramesh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bengaluru, India
| | - Dayananda Siddavattam
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
- Department of Biochemistry, School of Sciences, GITAM University, Visakhapatnam, India
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14
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Marcos-Torres FJ, Juniar L, Griese JJ. The molecular mechanisms of the bacterial iron sensor IdeR. Biochem Soc Trans 2023:233013. [PMID: 37140254 DOI: 10.1042/bst20221539] [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: 03/09/2023] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 05/05/2023]
Abstract
Life came to depend on iron as a cofactor for many essential enzymatic reactions. However, once the atmosphere was oxygenated, iron became both scarce and toxic. Therefore, complex mechanisms have evolved to scavenge iron from an environment in which it is poorly bioavailable, and to tightly regulate intracellular iron contents. In bacteria, this is typically accomplished with the help of one key regulator, an iron-sensing transcription factor. While Gram-negative bacteria and Gram-positive species with low guanine-cytosine (GC) content generally use Fur (ferric uptake regulator) proteins to regulate iron homeostasis, Gram-positive species with high GC content use the functional homolog IdeR (iron-dependent regulator). IdeR controls the expression of iron acquisition and storage genes, repressing the former, and activating the latter in an iron-dependent manner. In bacterial pathogens such as Corynebacterium diphtheriae and Mycobacterium tuberculosis, IdeR is also involved in virulence, whereas in non-pathogenic species such as Streptomyces, it regulates secondary metabolism as well. Although in recent years the focus of research on IdeR has shifted towards drug development, there is much left to learn about the molecular mechanisms of IdeR. Here, we summarize our current understanding of how this important bacterial transcriptional regulator represses and activates transcription, how it is allosterically activated by iron binding, and how it recognizes its DNA target sites, highlighting the open questions that remain to be addressed.
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Affiliation(s)
- Francisco Javier Marcos-Torres
- Department of Cell and Molecular Biology, Uppsala University, 751 24 Uppsala, Sweden
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-CSIC, 18011 Granada, Spain
| | - Linda Juniar
- Department of Cell and Molecular Biology, Uppsala University, 751 24 Uppsala, Sweden
| | - Julia J Griese
- Department of Cell and Molecular Biology, Uppsala University, 751 24 Uppsala, Sweden
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15
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Steingard CH, Helmann JD. Meddling with Metal Sensors: Fur-Family Proteins as Signaling Hubs. J Bacteriol 2023; 205:e0002223. [PMID: 37010421 PMCID: PMC10127796 DOI: 10.1128/jb.00022-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
The ferric uptake regulator (Fur) protein is the founding member of the FUR superfamily of metalloregulatory proteins that control metal homeostasis in bacteria. FUR proteins regulate metal homeostasis in response to the binding of iron (Fur), zinc (Zur), manganese (Mur), or nickel (Nur). FUR family proteins are generally dimers in solution, but the DNA-bound complex can involve a single dimer, a dimer-of-dimers, or an extended array of bound protein. Elevated FUR levels due to changes in cell physiology increase DNA occupancy and may also kinetically facilitate protein dissociation. Interactions between FUR proteins and other regulators are commonplace, often including cooperative and competitive DNA-binding interactions within the regulatory region. Further, there are many emerging examples of allosteric regulators that interact directly with FUR family proteins. Here, we focus on newly uncovered examples of allosteric regulation by diverse Fur antagonists (Escherichia coli YdiV/SlyD, Salmonella enterica EIIANtr, Vibrio parahaemolyticus FcrX, Acinetobacter baumannii BlsA, Bacillus subtilis YlaN, and Pseudomonas aeruginosa PacT) as well as one Zur antagonist (Mycobacterium bovis CmtR). Small molecules and metal complexes may also serve as regulatory ligands, with examples including heme binding to Bradyrhizobium japonicum Irr and 2-oxoglutarate binding to Anabaena FurA. How these protein-protein and protein-ligand interactions act in conjunction with regulatory metal ions to facilitate signal integration is an active area of investigation.
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Affiliation(s)
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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16
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Lee JW. Bacterial Regulatory Mechanisms for the Control of Cellular Processes: Simple Organisms' Complex Regulation. J Microbiol 2023; 61:273-276. [PMID: 37010794 DOI: 10.1007/s12275-023-00036-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2023] [Indexed: 04/04/2023]
Affiliation(s)
- Jin-Won Lee
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
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17
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Navale GR, Singh S, Ghosh K. NO donors as the wonder molecules with therapeutic potential: Recent trends and future perspectives. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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18
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Grassmann AA, Tokarz R, Golino C, McLain MA, Groshong AM, Radolf JD, Caimano MJ. BosR and PlzA reciprocally regulate RpoS function to sustain Borrelia burgdorferi in ticks and mammals. J Clin Invest 2023; 133:e166710. [PMID: 36649080 PMCID: PMC9974103 DOI: 10.1172/jci166710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
The RNA polymerase alternative σ factor RpoS in Borrelia burgdorferi (Bb), the Lyme disease pathogen, is responsible for programmatic-positive and -negative gene regulation essential for the spirochete's dual-host enzootic cycle. RpoS is expressed during tick-to-mammal transmission and throughout mammalian infection. Although the mammalian-phase RpoS regulon is well described, its counterpart during the transmission blood meal is unknown. Here, we used Bb-specific transcript enrichment by tick-borne disease capture sequencing (TBDCapSeq) to compare the transcriptomes of WT and ΔrpoS Bb in engorged nymphs and following mammalian host-adaptation within dialysis membrane chambers. TBDCapSeq revealed dramatic changes in the contours of the RpoS regulon within ticks and mammals and further confirmed that RpoS-mediated repression is specific to the mammalian-phase of Bb's enzootic cycle. We also provide evidence that RpoS-dependent gene regulation, including repression of tick-phase genes, is required for persistence in mice. Comparative transcriptomics of engineered Bb strains revealed that the Borrelia oxidative stress response regulator (BosR), a noncanonical Fur family member, and the cyclic diguanosine monophosphate (c-di-GMP) effector PlzA reciprocally regulate the function of RNA polymerase complexed with RpoS. BosR is required for RpoS-mediated transcription activation and repression in addition to its well-defined role promoting transcription of rpoS by the RNA polymerase alternative σ factor RpoN. During transmission, ligand-bound PlzA antagonizes RpoS-mediated repression, presumably acting through BosR.
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Affiliation(s)
| | - Rafal Tokarz
- Center for Infection and Immunity and
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Caroline Golino
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
| | | | - Ashley M. Groshong
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Pediatrics
| | - Justin D. Radolf
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Pediatrics
- Department of Molecular Biology and Biophysics
- Department of Genetics and Genome Sciences, and
- Department of Immunology, UConn Health, Farmington, Connecticut, USA
| | - Melissa J. Caimano
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Pediatrics
- Department of Molecular Biology and Biophysics
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19
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Sánchez-Jiménez A, Marcos-Torres FJ, Llamas MA. Mechanisms of iron homeostasis in Pseudomonas aeruginosa and emerging therapeutics directed to disrupt this vital process. Microb Biotechnol 2023. [PMID: 36857468 DOI: 10.1111/1751-7915.14241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/13/2023] [Indexed: 03/03/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen able to infect any human tissue. One of the reasons for its high adaptability and colonization of host tissues is its capacity of maintaining iron homeostasis through a wide array of iron acquisition and removal mechanisms. Due to their ability to cause life-threatening acute and chronic infections, especially among cystic fibrosis and immunocompromised patients, and their propensity to acquire resistance to many antibiotics, the World Health Organization (WHO) has encouraged the scientific community to find new strategies to eradicate this pathogen. Several recent strategies to battle P. aeruginosa focus on targeting iron homeostasis mechanisms, turning its greatest advantage into an exploitable weak point. In this review, we discuss the different mechanisms used by P. aeruginosa to maintain iron homeostasis and the strategies being developed to fight this pathogen by blocking these mechanisms. Among others, the use of iron chelators and mimics, as well as disruption of siderophore production and uptake, have shown promising results in reducing viability and/or virulence of this pathogen. The so-called 'Trojan-horse' strategy taking advantage of the siderophore uptake systems is emerging as an efficient method to improve delivery of antibiotics into the bacterial cells. Moreover, siderophore transporters are considered promising targets for the developing of P. aeruginosa vaccines.
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Affiliation(s)
- Ana Sánchez-Jiménez
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Francisco J Marcos-Torres
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - María A Llamas
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
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20
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Steingard CH, Pinochet-Barros A, Wendel BM, Helmann JD. Iron homeostasis in Bacillus subtilis relies on three differentially expressed efflux systems. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001289. [PMID: 36748638 PMCID: PMC9993123 DOI: 10.1099/mic.0.001289] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In Bacillus subtilis, iron homeostasis is maintained by the ferric uptake regulator (Fur) and manganese homeostasis relies on the manganese transport regulator (MntR). Both Fur and MntR function as bi-functional metalloregulators that repress import and activate metal ion efflux systems. The ferrous iron efflux ATPase, PfeT, is derepressed by hydrogen peroxide (H2O2) as sensed by PerR and induced by iron as sensed by Fur. Mutants lacking PfeT are sensitive to iron intoxication. Here, we show that mntR mutants are also iron-sensitive, largely due to decreased expression of the MntR-activated MneP and MneS cation diffusion facilitator (CDF) proteins previously defined for their role in Mn2+ export. The ability of MneP and MneS to export iron is apparent even when their expression is not induced by Mn2+. Our results demonstrate that PfeT, MneP and MneS each contribute to iron homeostasis, and a triple mutant lacking all three is more iron-sensitive than any single mutant. We further show that sensitivity to H2O2 does not correlate with iron sensitivity. For example, an mntR mutant is H2O2-sensitive due to elevated Mn(II) that increases PerR-mediated repression of peroxide resistance genes, and this repression is antagonized by elevated Fe2+ in an mntR pfeT mutant. Thus, H2O2-sensitivity reflects the relative levels of Mn2+ and Fe2+ as sensed by the PerR regulatory protein. These results underscore the complex interplay between manganese, iron and oxidative stress in B. subtilis.
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Affiliation(s)
- Caroline H Steingard
- Department of Microbiology, Cornell University, Ithaca, New York 14853-8101, USA
| | - Azul Pinochet-Barros
- Department of Microbiology, Cornell University, Ithaca, New York 14853-8101, USA
| | - Brian M Wendel
- Department of Microbiology, Cornell University, Ithaca, New York 14853-8101, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, New York 14853-8101, USA
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21
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Identification of the Preferred DNA-Binding Sequence and Transcription Regulatory Network for the Thermophilic Zinc Uptake Regulator TTHA1292. J Bacteriol 2022; 204:e0030322. [PMID: 36286513 PMCID: PMC9664954 DOI: 10.1128/jb.00303-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Discovering how organisms sense and adapt to their environments is paramount to understanding biology. Thermophilic organisms have adapted to survive at elevated temperatures (>50°C); however, our understanding of how these organisms adapt to changes in their environment is limited.
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22
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Reitz ZL, Medema MH. Genome mining strategies for metallophore discovery. Curr Opin Biotechnol 2022; 77:102757. [PMID: 35914390 DOI: 10.1016/j.copbio.2022.102757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 11/03/2022]
Abstract
Many bacteria use small-molecule chelators called metallophores to acquire trace metals from their environment. These molecules play a central role in interactions between bacteria, plants, and animals. Hence, knowing their full diversity is key to combatting infectious diseases as well as harnessing beneficial microbial communities. Metallophore discovery has been streamlined by advances in genome mining, where genomes are scanned for genes involved in metallophore biosynthesis. This review highlights recent trends and advances in predicting the presence and structure of metallophores based solely on genomic information. Recent work suggests new families of metallophores remain hidden from current homology-based approaches. Their discovery will require new genome mining approaches that move beyond biosynthesis to consider metallophore transporters, regulation, and evolution.
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Affiliation(s)
- Zachary L Reitz
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands.
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23
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Iron Homeostasis in Pseudomonas aeruginosa: Targeting Iron Acquisition and Storage as an Antimicrobial Strategy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:29-68. [DOI: 10.1007/978-3-031-08491-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Charbonnier M, González-Espinoza G, Kehl-Fie TE, Lalaouna D. Battle for Metals: Regulatory RNAs at the Front Line. Front Cell Infect Microbiol 2022; 12:952948. [PMID: 35865816 PMCID: PMC9294342 DOI: 10.3389/fcimb.2022.952948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Metal such as iron, zinc, manganese, and nickel are essential elements for bacteria. These nutrients are required in crucial structural and catalytic roles in biological processes, including precursor biosynthesis, DNA replication, transcription, respiration, and oxidative stress responses. While essential, in excess these nutrients can also be toxic. The immune system leverages both of these facets, to limit bacterial proliferation and combat invaders. Metal binding immune proteins reduce the bioavailability of metals at the infection sites starving intruders, while immune cells intoxicate pathogens by providing metals in excess leading to enzyme mismetallation and/or reactive oxygen species generation. In this dynamic metal environment, maintaining metal homeostasis is a critical process that must be precisely coordinated. To achieve this, bacteria utilize diverse metal uptake and efflux systems controlled by metalloregulatory proteins. Recently, small regulatory RNAs (sRNAs) have been revealed to be critical post-transcriptional regulators, working in conjunction with transcription factors to promote rapid adaptation and to fine-tune bacterial adaptation to metal abundance. In this mini review, we discuss the expanding role for sRNAs in iron homeostasis, but also in orchestrating adaptation to the availability of other metals like manganese and nickel. Furthermore, we describe the sRNA-mediated interdependency between metal homeostasis and oxidative stress responses, and how regulatory networks controlled by sRNAs contribute to survival and virulence.
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Affiliation(s)
- Mathilde Charbonnier
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | | | - Thomas E Kehl-Fie
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana IL, United States.,Carl R. Woese Institute for Genomic Biology University of Illinois Urbana-Champaign, Urbana IL, United States
| | - David Lalaouna
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
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25
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Metal utilization in genome-reduced bacteria: Do human mycoplasmas rely on iron? Comput Struct Biotechnol J 2021; 19:5752-5761. [PMID: 34765092 PMCID: PMC8566771 DOI: 10.1016/j.csbj.2021.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 12/04/2022] Open
Abstract
Mycoplasmas are parasitic bacteria with streamlined genomes and complex nutritional requirements. Although iron is vital for almost all organisms, its utilization by mycoplasmas is controversial. Despite its minimalist nature, mycoplasmas can survive and persist within the host, where iron availability is rigorously restricted through nutritional immunity. In this review, we describe the putative iron-enzymes, transporters, and metalloregulators of four relevant human mycoplasmas. This work brings in light critical differences in the mycoplasma-iron interplay. Mycoplasma penetrans, the species with the largest genome (1.36 Mb), shows a more classic repertoire of iron-related proteins, including different enzymes using iron-sulfur clusters as well as iron storage and transport systems. In contrast, the iron requirement is less apparent in the three species with markedly reduced genomes, Mycoplasma genitalium (0.58 Mb), Mycoplasma hominis (0.67 Mb) and Mycoplasma pneumoniae (0.82 Mb), as they exhibit only a few proteins possibly involved in iron homeostasis. The multiple facets of iron metabolism in mycoplasmas illustrate the remarkable evolutive potential of these minimal organisms when facing nutritional immunity and question the dependence of several human-infecting species for iron. Collectively, our data contribute to better understand the unique biology and infective strategies of these successful pathogens.
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Key Words
- ABC, ATP-binding cassette
- ECF transporter
- ECF, energy-coupling factor
- Fur, ferric uptake regulator
- Hrl, histidine-rich lipoprotein
- Iron homeostasis
- Metal acquisition
- Metalloenzyme
- Mge, Mycoplasma genitalium
- Mho, Mycoplasma hominis
- Mollicutes
- Mpe, Mycoplasma penetrans
- Mpn, Mycoplasma pneumonia
- Mycoplasmas
- PDB, protein data bank
- RNR, ribonucleotide reductase
- XRF, X-ray fluorescence
- ZIP, zinc-iron permease
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