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Dussouchaud M, Barras F, de Choudens SO. Fe-S biogenesis by SMS and SUF pathways: A focus on the assembly step. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024:119772. [PMID: 38838856 DOI: 10.1016/j.bbamcr.2024.119772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/07/2024]
Abstract
FeS clusters are prosthetic groups present in all organisms. Proteins with FeS centers are involved in most cellular processes. ISC and SUF are machineries necessary for the formation and insertion of FeS in proteins. Recently, a phylogenetic analysis on more than 10,000 genomes of prokaryotes have uncovered two new systems, MIS and SMS, which were proposed to be ancestral to ISC and SUF. SMS is composed of SmsBC, two homologs of SufBC(D), the scaffolding complex of SUF. In this review, we will specifically focus on the current knowledge of the SUF system and on the new perspectives given by the recent discovery of its ancestor, the SMS system.
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Affiliation(s)
- Macha Dussouchaud
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Department of Microbiology, Unit Stress Adaptation and Metabolism in enterobacteria, 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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Wongdontree P, Millan-Oropeza A, Upfold J, Lavergne JP, Halpern D, Lambert C, Page A, Kénanian G, Grangeasse C, Henry C, Fouet A, Gloux K, Anba-Mondoloni J, Gruss A. Oxidative stress is intrinsic to staphylococcal adaptation to fatty acid synthesis antibiotics. iScience 2024; 27:109505. [PMID: 38577105 PMCID: PMC10993138 DOI: 10.1016/j.isci.2024.109505] [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: 07/26/2023] [Revised: 12/08/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
Antibiotics inhibiting the fatty acid synthesis pathway (FASII) of the major pathogen Staphylococcus aureus reach their enzyme targets, but bacteria continue growth by using environmental fatty acids (eFAs) to produce phospholipids. We assessed the consequences and effectors of FASII-antibiotic (anti-FASII) adaptation. Anti-FASII induced lasting expression changes without genomic rearrangements. Several identified regulators affected the timing of adaptation outgrowth. Adaptation resulted in decreased expression of major virulence factors. Conversely, stress responses were globally increased and adapted bacteria were more resistant to peroxide killing. Importantly, pre-exposure to peroxide led to faster anti-FASII-adaptation by stimulating eFA incorporation. This adaptation differs from reports of peroxide-stimulated antibiotic efflux, which leads to tolerance. In vivo, anti-FASII-adapted S. aureus killed the insect host more slowly but continued multiplying. We conclude that staphylococcal adaptation to FASII antibiotics involves reprogramming, which decreases virulence and increases stress resistance. Peroxide, produced by the host to combat infection, favors anti-FASII adaptation.
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Affiliation(s)
- Paprapach Wongdontree
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Aaron Millan-Oropeza
- PAPPSO Platform, Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Jennifer Upfold
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Jean-Pierre Lavergne
- Bacterial Pathogens and Protein Phosphorylation, Molecular Microbiology and Structural Biology, UMR 5086 - CNRS / Université de Lyon, Building IBCP, 7 Passage du Vercors, Lyon, France
| | - David Halpern
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Clara Lambert
- Université Paris Cité, Institut Cochin, INSERM, U1016, CNRS, UMR8104, Paris, France
| | - Adeline Page
- Protein Science Facility, SFR BioSciences, CNRS, UMS3444, INSERM US8, Université de Lyon, Lyon, France
| | - Gérald Kénanian
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Christophe Grangeasse
- Bacterial Pathogens and Protein Phosphorylation, Molecular Microbiology and Structural Biology, UMR 5086 - CNRS / Université de Lyon, Building IBCP, 7 Passage du Vercors, Lyon, France
| | - Céline Henry
- PAPPSO Platform, Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Agnès Fouet
- Université Paris Cité, Institut Cochin, INSERM, U1016, CNRS, UMR8104, Paris, France
| | - Karine Gloux
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Jamila Anba-Mondoloni
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Alexandra Gruss
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
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Gorityala N, Baidya AS, Sagurthi SR. Genome mining of Mycobacterium tuberculosis: targeting SufD as a novel drug candidate through in silico characterization and inhibitor screening. Front Microbiol 2024; 15:1369645. [PMID: 38686111 PMCID: PMC11057465 DOI: 10.3389/fmicb.2024.1369645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/15/2024] [Indexed: 05/02/2024] Open
Abstract
Tuberculosis (TB) stands as the second most fatal infectious disease globally, causing 1.3 million deaths in 2022. The resurgence of TB and the alarming rise of antibiotic resistance demand urgent call to develop novel antituberculosis drugs. Despite concerted efforts to control TB, the disease persists and spreads rapidly on a global scale. Targeting stress response pathways in Mycobacterium tuberculosis (Mtb) has become imperative to achieve complete eradication. This study employs subtractive genomics to identify and prioritize potential drug targets among the hypothetical proteins of Mtb, focusing on indispensable pathways. Amongst 177 essential hypothetical proteins, 152 were nonhomologous to human. These proteins participated in 34 pathways, and a 20-fold enrichment of SUF pathway genes led to its selection as a target pathway. Fe-S clusters are fundamental, widely distributed protein cofactors involved in vital cellular processes. The survival of Mtb in a hypoxic environment relies on the iron-sulfur (Fe-S) cluster biogenesis pathway for the repair of damaged Fe-S clusters. It also protects pathogen against drugs, ensuring controlled iron utilization and contributing to drug resistance. In Mtb, six proteins of Fe-S cluster assembly pathway are encoded by the suf operon. The present study was focused on SufD because of its role in iron acquisition and prevention of Fenton reaction. The research further delves into the in silico characterization of SufD, utilizing bioinformatics tools for sequence and structure based analysis. The protein's structural features, including the identification of conserved regions, motifs, and 3D structure prediction enhanced functional annotation. Target based virtual screening of compounds from the ChEMBL database resulted in 12 inhibitors with best binding affinities. Drug likeness and ADMET profiling of potential inhibitors identified promising compounds with favorable drug-like properties. The study also involved cloning in SUMO-pRSF-Duet1 expression vector, overexpression, and purification of recombinant SufD from E. coli BL21 (DE3) cells. Optimization of expression conditions resulted in soluble production, and subsequent purification highlighting the efficacy of the SUMO fusion system for challenging Mtb proteins in E. coli. These findings provide valuable insights into pharmacological targets for future experimental studies, holding promise for the development of targeted therapy against Mtb.
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Affiliation(s)
- Neelima Gorityala
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Anthony Samit Baidya
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Someswar R Sagurthi
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, Telangana, India
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Xu L, Wu Y, Yang X, Pang X, Wu Y, Li X, Liu X, Zhao Y, Yu L, Wang P, Ye B, Jiang S, Ma J, Zhang X. The Fe-S cluster biosynthesis in Enterococcus faecium is essential for anaerobic growth and gastrointestinal colonization. Gut Microbes 2024; 16:2359665. [PMID: 38831611 DOI: 10.1080/19490976.2024.2359665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/21/2024] [Indexed: 06/05/2024] Open
Abstract
The facultative anaerobic Gram-positive bacterium Enterococcus faecium is a ubiquitous member of the human gut microbiota. However, it has gradually evolved into a pathogenic and multidrug resistant lineage that causes nosocomial infections. The establishment of high-level intestinal colonization by enterococci represents a critical step of infection. The majority of current research on Enterococcus has been conducted under aerobic conditions, while limited attention has been given to its physiological characteristics in anaerobic environments, which reflects its natural colonization niche in the gut. In this study, a high-density transposon mutant library containing 26,620 distinct insertion sites was constructed. Tn-seq analysis identified six genes that significantly contribute to growth under anaerobic conditions. Under anaerobic conditions, deletion of sufB (encoding Fe-S cluster assembly protein B) results in more extensive and significant impairments on carbohydrate metabolism compared to aerobic conditions. Consistently, the pathways involved in this utilization-restricted carbohydrates were mostly expressed at significantly lower levels in mutant compared to wild-type under anaerobic conditions. Moreover, deletion of sufB or pflA (encoding pyruvate formate lyase-activating protein A) led to failure of gastrointestinal colonization in mice. These findings contribute to our understanding of the mechanisms by which E. faecium maintains proliferation under anaerobic conditions and establishes colonization in the gut.
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Affiliation(s)
- Linan Xu
- College of Agriculture and Forestry, Linyi University, Linyi, China
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Yajing Wu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Xiangpeng Yang
- College of Agriculture and Forestry, Linyi University, Linyi, China
| | - Xinxin Pang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yansha Wu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xingshuai Li
- College of Agriculture and Forestry, Linyi University, Linyi, China
| | - Xiayu Liu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Yuzhong Zhao
- College of Agriculture and Forestry, Linyi University, Linyi, China
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Lumin Yu
- College of Agriculture and Forestry, Linyi University, Linyi, China
| | - Peikun Wang
- College of Agriculture and Forestry, Linyi University, Linyi, China
| | - Bin Ye
- College of Agriculture and Forestry, Linyi University, Linyi, China
| | - Shijin Jiang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Junfei Ma
- College of Agriculture and Forestry, Linyi University, Linyi, China
| | - Xinglin Zhang
- College of Agriculture and Forestry, Linyi University, Linyi, China
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Giulieri SG, Guérillot R, Holmes NE, Baines SL, Hachani A, Hayes AS, Daniel DS, Seemann T, Davis JS, Van Hal S, Tong SYC, Stinear TP, Howden BP. A statistical genomics framework to trace bacterial genomic predictors of clinical outcomes in Staphylococcus aureus bacteremia. Cell Rep 2023; 42:113069. [PMID: 37703880 DOI: 10.1016/j.celrep.2023.113069] [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: 12/01/2022] [Revised: 06/29/2023] [Accepted: 08/18/2023] [Indexed: 09/15/2023] Open
Abstract
Outcomes of severe bacterial infections are determined by the interplay between host, pathogen, and treatments. While human genomics has provided insights into host factors impacting Staphylococcus aureus infections, comparatively little is known about S. aureus genotypes and disease severity. Building on the hypothesis that bacterial pathoadaptation is a key outcome driver, we developed a genome-wide association study (GWAS) framework to identify adaptive mutations associated with treatment failure and mortality in S. aureus bacteremia (1,358 episodes). Our research highlights the potential of vancomycin-selected mutations and vancomycin minimum inhibitory concentration (MIC) as key explanatory variables to predict infection severity. The contribution of bacterial variation was much lower for clinical outcomes (heritability <5%); however, GWASs allowed us to identify additional, MIC-independent candidate pathogenesis loci. Using supervised machine learning, we were able to quantify the predictive potential of these adaptive signatures. Our statistical genomics framework provides a powerful means to capture adaptive mutations impacting severe bacterial infections.
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Affiliation(s)
- Stefano G Giulieri
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Victorian Infectious Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia.
| | - Romain Guérillot
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Natasha E Holmes
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Ashleigh S Hayes
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Diane S Daniel
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Torsten Seemann
- Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Joshua S Davis
- Department of Infectious Diseases, John Hunter Hospital, New Lambton Heights, NSW 2305, Australia; Menzies School of Health Research, Charles Darwin University, Casuarina, NT 0810, Australia
| | - Sebastiaan Van Hal
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; Central Clinical School, University of Sydney, Camperdown, NSW 2050, Australia
| | - Steven Y C Tong
- Victorian Infectious Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia; Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC 3000, Australia
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6
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Saini J, Deere TM, Lessner DJ. The minimal SUF system is not required for Fe-S cluster biogenesis in the methanogenic archaeon Methanosarcina acetivorans. Sci Rep 2023; 13:15120. [PMID: 37704679 PMCID: PMC10500019 DOI: 10.1038/s41598-023-42400-x] [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: 08/03/2023] [Accepted: 09/09/2023] [Indexed: 09/15/2023] Open
Abstract
Iron-sulfur (Fe-S) proteins are essential for the ability of methanogens to carry out methanogenesis and biological nitrogen fixation (diazotrophy). Nonetheless, the factors involved in Fe-S cluster biogenesis in methanogens remain largely unknown. The minimal SUF Fe-S cluster biogenesis system (i.e., SufBC) is postulated to serve as the primary system in methanogens. Here, the role of SufBC in Methanosarcina acetivorans, which contains two sufCB gene clusters, was investigated. The CRISPRi-dCas9 and CRISPR-Cas9 systems were utilized to repress or delete sufC1B1 and sufC2B2, respectively. Neither the dual repression of sufC1B1 and sufC2B2 nor the deletion of both sufC1B1 and sufC2B2 affected the growth of M. acetivorans under any conditions tested, including diazotrophy. Interestingly, deletion of only sufC1B1 led to a delayed-growth phenotype under all growth conditions, suggesting that the deletion of sufC2B2 acts as a suppressor mutation in the absence of sufC1B1. In addition, the deletion of sufC1B1 and/or sufC2B2 did not affect the total Fe-S cluster content in M. acetivorans cells. Overall, these results reveal that the minimal SUF system is not required for Fe-S cluster biogenesis in M. acetivorans and challenge the universal role of SufBC in Fe-S cluster biogenesis in methanogens.
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Affiliation(s)
- Jasleen Saini
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, USA
| | - Thomas M Deere
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, USA
| | - Daniel J Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, USA.
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Norambuena J, Al-Tameemi H, Bovermann H, Kim J, Beavers WN, Skaar EP, Parker D, Boyd JM. Copper ions inhibit pentose phosphate pathway function in Staphylococcus aureus. PLoS Pathog 2023; 19:e1011393. [PMID: 37235600 PMCID: PMC10249872 DOI: 10.1371/journal.ppat.1011393] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 06/08/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
To gain a better insight of how Copper (Cu) ions toxify cells, metabolomic analyses were performed in S. aureus strains that lacks the described Cu ion detoxification systems (ΔcopBL ΔcopAZ; cop-). Exposure of the cop- strain to Cu(II) resulted in an increase in the concentrations of metabolites utilized to synthesize phosphoribosyl diphosphate (PRPP). PRPP is created using the enzyme phosphoribosylpyrophosphate synthetase (Prs) which catalyzes the interconversion of ATP and ribose 5-phosphate to PRPP and AMP. Supplementing growth medium with metabolites requiring PRPP for synthesis improved growth in the presence of Cu(II). A suppressor screen revealed that a strain with a lesion in the gene coding adenine phosphoribosyltransferase (apt) was more resistant to Cu. Apt catalyzes the conversion of adenine with PRPP to AMP. The apt mutant had an increased pool of adenine suggesting that the PRPP pool was being redirected. Over-production of apt, or alternate enzymes that utilize PRPP, increased sensitivity to Cu(II). Increasing or decreasing expression of prs resulted in decreased and increased sensitivity to growth in the presence of Cu(II), respectively. We demonstrate that Prs is inhibited by Cu ions in vivo and in vitro and that treatment of cells with Cu(II) results in decreased PRPP levels. Lastly, we establish that S. aureus that lacks the ability to remove Cu ions from the cytosol is defective in colonizing the airway in a murine model of acute pneumonia, as well as the skin. The data presented are consistent with a model wherein Cu ions inhibits pentose phosphate pathway function and are used by the immune system to prevent S. aureus infections.
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Affiliation(s)
- Javiera Norambuena
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Hassan Al-Tameemi
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Hannah Bovermann
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Jisun Kim
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
| | - William N. Beavers
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Dane Parker
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
| | - Jeffrey M. Boyd
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, United States of America
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8
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Elchennawi I, Carpentier P, Caux C, Ponge M, Ollagnier de Choudens S. Structural and Biochemical Characterization of Mycobacterium tuberculosis Zinc SufU-SufS Complex. Biomolecules 2023; 13:biom13050732. [PMID: 37238602 DOI: 10.3390/biom13050732] [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: 02/28/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/28/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters are inorganic prosthetic groups in proteins composed exclusively of iron and inorganic sulfide. These cofactors are required in a wide range of critical cellular pathways. Iron-sulfur clusters do not form spontaneously in vivo; several proteins are required to mobilize sulfur and iron, assemble and traffic-nascent clusters. Bacteria have developed several Fe-S assembly systems, such as the ISC, NIF, and SUF systems. Interestingly, in Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), the SUF machinery is the primary Fe-S biogenesis system. This operon is essential for the viability of Mtb under normal growth conditions, and the genes it contains are known to be vulnerable, revealing the Mtb SUF system as an interesting target in the fight against tuberculosis. In the present study, two proteins of the Mtb SUF system were characterized for the first time: Rv1464(sufS) and Rv1465(sufU). The results presented reveal how these two proteins work together and thus provide insights into Fe-S biogenesis/metabolism by this pathogen. Combining biochemistry and structural approaches, we showed that Rv1464 is a type II cysteine-desulfurase enzyme and that Rv1465 is a zinc-dependent protein interacting with Rv1464. Endowed with a sulfurtransferase activity, Rv1465 significantly enhances the cysteine-desulfurase activity of Rv1464 by transferring the sulfur atom from persulfide on Rv1464 to its conserved Cys40 residue. The zinc ion is important for the sulfur transfer reaction between SufS and SufU, and His354 in SufS plays an essential role in this reaction. Finally, we showed that Mtb SufS-SufU is more resistant to oxidative stress than E. coli SufS-SufE and that the presence of zinc in SufU is likely responsible for this improved resistance. This study on Rv1464 and Rv1465 will help guide the design of future anti-tuberculosis agents.
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Affiliation(s)
- Ingie Elchennawi
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 38000 Grenoble, France
| | - Philippe Carpentier
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 38000 Grenoble, France
- European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - Christelle Caux
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 38000 Grenoble, France
| | - Marine Ponge
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 38000 Grenoble, France
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9
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Ramírez-Hernández M, Norambuena J, Hu H, Thomas B, Tang C, Boyd JM, Asefa T. Repurposing Anthelmintics: Rafoxanide- and Copper-Functionalized SBA-15 Carriers against Methicillin-Resistant Staphylococcus aureus. ACS APPLIED MATERIALS & INTERFACES 2023; 15:17459-17469. [PMID: 36975176 DOI: 10.1021/acsami.2c19899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The development of materials that can more efficiently administer antimicrobial agents in a controlled manner is urgently needed due to the rise in microbial resistance to traditional antibiotics. While new classes of antibiotics are developed and put into widespread usage, existing, inexpensive compounds can be repurposed to fight bacterial infections. Here, we present the synthesis of amine-functionalized SBA-15 mesoporous silica nanomaterials with physisorbed rafoxanide (RFX), a commonly used salicylanilide anthelmintic, and anchored Cu(II) ions that exhibit enhanced antimicrobial efficacy against the pathogenic bacterium Staphylococcus aureus. The synthesized nanomaterials are structurally characterized by a combination of physicochemical, thermal, and optical methods. Additionally, release studies are carried out in vitro to determine the effects of pH and the synthetic sequence used to produce the materials on Cu(II) ion release. Our results indicate that SBA-15 mesoporous silica nanocarriers loaded with Cu(II) and RFX exhibit 10 times as much bactericidal action against wild-type S. aureus as the nanocarrier loaded with only RFX. Furthermore, the synthetic sequence used to produce the nanomaterials could significantly affect (enhance) their bactericidal efficacy.
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Affiliation(s)
- Maricely Ramírez-Hernández
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, New Jersey 08854, United States
| | - Javiera Norambuena
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, 76 Lipman Drive, New Brunswick, New Jersey 08901, United States
| | - Hongnan Hu
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, New Jersey 08854, United States
| | - Belvin Thomas
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Chaoyun Tang
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, New Jersey 08854, United States
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
- Hoffman Institute of Advanced Materials, Shenzhen Polytechnic, 7098 Liuxian Boulevard, Shenzhen 518060, China
| | - Jeffrey M Boyd
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, 76 Lipman Drive, New Brunswick, New Jersey 08901, United States
| | - Tewodros Asefa
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, New Jersey 08854, United States
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
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10
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Hudspeth J, Boncella AE, Sabo ET, Andrews T, Boyd JM, Morrison CN. Structural and Biochemical Characterization of Staphylococcus aureus Cysteine Desulfurase Complex SufSU. ACS OMEGA 2022; 7:44124-44133. [PMID: 36506149 PMCID: PMC9730764 DOI: 10.1021/acsomega.2c05576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/09/2022] [Indexed: 06/01/2023]
Abstract
In this work, we provide the first in vitro characterization of two essential proteins from Staphylococcus aureus (S. aureus) involved in iron-sulfur (Fe-S) cluster biogenesis: the cysteine desulfurase SufS and the sulfurtransferase SufU. Together, these proteins form the transient SufSU complex and execute the first stage of Fe-S cluster biogenesis in the SUF-like pathway in Gram-positive bacteria. The proteins involved in the SUF-like pathway, such as SufS and SufU, are essential in Gram-positive bacteria since these bacteria tend to lack redundant Fe-S cluster biogenesis pathways. Most previous work characterizing the SUF-like pathway has focused on Bacillus subtilis (B. subtilis). We focus on the SUF-like pathway in S. aureus because of its potential to serve as a therapeutic target to treat S. aureus infections. Herein, we characterize S. aureus SufS (SaSufS) by X-ray crystallography and UV-vis spectroscopy, and we characterize S. aureus SufU (SaSufU) by a zinc binding fluorescence assay and small-angle X-ray scattering. We show that SaSufS is a type II cysteine desulfurase and that SaSufU is a Zn2+-containing sulfurtransferase. Additionally, we evaluated the cysteine desulfurase activity of the SaSufSU complex and compared its activity to that of B. subtilis SufSU. Subsequent cross-species activity analysis reveals a surprising result: SaSufS is significantly less stimulated by SufU than BsSufS. Our results set a basis for further characterization of SaSufSU as well as the development of new therapeutic strategies for treating infections caused by S. aureus by inhibiting the SUF-like pathway.
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Affiliation(s)
- Jesse
D. Hudspeth
- Department
of Chemistry, Colorado School of Mines, 1500 Illinois St, Golden, Colorado 80401, United States
| | - Amy E. Boncella
- Department
of Chemistry, Colorado School of Mines, 1500 Illinois St, Golden, Colorado 80401, United States
| | - Emily T. Sabo
- Department
of Chemistry, Colorado School of Mines, 1500 Illinois St, Golden, Colorado 80401, United States
| | - Taylor Andrews
- Department
of Biochemistry and Microbiology, Rutgers
University, 76 Lipman Dr., New Brunswick, New Jersey 08901, United States
| | - Jeffrey M. Boyd
- Department
of Biochemistry and Microbiology, Rutgers
University, 76 Lipman Dr., New Brunswick, New Jersey 08901, United States
| | - Christine N. Morrison
- Department
of Chemistry, Colorado School of Mines, 1500 Illinois St, Golden, Colorado 80401, United States
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11
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Allan DS, Holbein BE. Iron Chelator DIBI Suppresses Formation of Ciprofloxacin-Induced Antibiotic Resistance in Staphylococcus aureus. Antibiotics (Basel) 2022; 11:1642. [PMID: 36421286 PMCID: PMC9687013 DOI: 10.3390/antibiotics11111642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 09/30/2023] Open
Abstract
Antibiotic resistance of bacterial pathogens results from their exposure to antibiotics and this has become a serious growing problem that limits effective use of antibiotics. Resistance can arise from mutations induced by antibiotic-mediated damage with these mutants possessing reduced target sensitivity. We have studied ciprofloxacin (CIP)-mediated killing of Staphylococcus aureus and the influence of the Reactive Oxygen Species (ROS) inactivator, thiourea and the iron chelator DIBI, on initial killing by CIP and their effects on survival and outgrowth upon prolonged exposure to CIP. CIP at 2× MIC caused a rapid initial killing which was not influenced by initial bacterial iron status and which was followed by robust recovery growth over 96 h exposure. Thiourea and DIBI did slow the initial rate of CIP killing but the overall extent of kill by 24 h exposure was like CIP alone. Thiourea permitted recovery growth whereas this was strongly suppressed by DIBI. Small Colony Variant (SCV) survivors were progressively enriched in the survivor population during CIP exposure, and these were found to have stable slow-growth phenotype and acquired resistance to CIP and moxifloxacin but not to other non-related antibiotics. DIBI totally suppressed SCV formation with all survivors remaining sensitive to CIP and to DIBI. DIBI exposure did not promote resistance to DIBI. Our evidence indicates a high potential for DIBI as an adjunct to CIP and other antibiotics to both improve antibiotic efficacy and to thwart antibiotic resistance development.
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Affiliation(s)
| | - Bruce E. Holbein
- Fe Pharmaceuticals Canada Inc. #58, The Labs at Innovacorp, 1344 Summer Street, Halifax, NS B3H O8A, Canada
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12
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Iron–Sulfur Clusters toward Stresses: Implication for Understanding and Fighting Tuberculosis. INORGANICS 2022. [DOI: 10.3390/inorganics10100174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB) remains the leading cause of death due to a single pathogen, accounting for 1.5 million deaths annually on the global level. Mycobacterium tuberculosis, the causative agent of TB, is persistently exposed to stresses such as reactive oxygen species (ROS), reactive nitrogen species (RNS), acidic conditions, starvation, and hypoxic conditions, all contributing toward inhibiting bacterial proliferation and survival. Iron–sulfur (Fe-S) clusters, which are among the most ancient protein prosthetic groups, are good targets for ROS and RNS, and are susceptible to Fe starvation. Mtb holds Fe-S containing proteins involved in essential biological process for Mtb. Fe-S cluster assembly is achieved via complex protein machineries. Many organisms contain several Fe-S assembly systems, while the SUF system is the only one in some pathogens such as Mtb. The essentiality of the SUF machinery and its functionality under the stress conditions encountered by Mtb underlines how it constitutes an attractive target for the development of novel anti-TB.
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13
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Stephens AC, Richardson AR. Recent developments in our understanding of the physiology and nitric oxide-resistance of Staphylococcus aureus. Adv Microb Physiol 2022; 81:111-135. [PMID: 36167441 DOI: 10.1016/bs.ampbs.2022.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Staphylococcus aureus is an important human pathogen causing a wide range of disease presentations. It harbors a vast array of virulence factors and drug-resistance determinants. All of these factors are coordinately regulated by a hand full of key transcriptional regulators. The regulation and expression of these factors are tightly intertwined with the metabolic state of the cell. Furthermore, alterations in central metabolism are also key to the ability of S. aureus to resist clearance by the host innate immune response, including nitric oxide (NO·) production. Given the fact that central metabolism directly influences virulence, drug resistance and immune tolerance in S. aureus, a better understanding of the metabolic capabilities of this pathogen is critical. This work highlights some of the major findings within the last five years surrounding S. aureus central metabolism, both organic and inorganic. These are also put in the context of the unique NO·-resistance associated with this pathogen as well as their contributions to virulence. The more we understand the intersection between central metabolism and virulence capabilities in S. aureus, the better the chances of developing novel therapeutics so desperately needed to treat this pathogen.
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Affiliation(s)
- Amelia C Stephens
- Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Anthony R Richardson
- Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, United States.
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14
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Pfanzelt M, Maher TE, Absmeier RM, Schwarz M, Sieber SA. Tailored Pyridoxal Probes Unravel Novel Cofactor-Dependent Targets and Antibiotic Hits in Critical Bacterial Pathogens. Angew Chem Int Ed Engl 2022; 61:e202117724. [PMID: 35199904 PMCID: PMC9321722 DOI: 10.1002/anie.202117724] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Indexed: 01/21/2023]
Abstract
Unprecedented bacterial targets are urgently needed to overcome the resistance crisis. Herein we systematically mine pyridoxal phosphate‐dependent enzymes (PLP‐DEs) in bacteria to focus on a target class which is involved in crucial metabolic processes. For this, we tailored eight pyridoxal (PL) probes bearing modifications at various positions. Overall, the probes exceeded the performance of a previous generation and provided a detailed map of PLP‐DEs in clinically relevant pathogens including challenging Gram‐negative strains. Putative PLP‐DEs with unknown function were exemplarily characterized via in‐depth enzymatic assays. Finally, we screened a panel of PLP binders for antibiotic activity and unravelled the targets of hit molecules. Here, an uncharacterized enzyme, essential for bacterial growth, was assigned as PLP‐dependent cysteine desulfurase and confirmed to be inhibited by the marketed drug phenelzine. Our approach provides a basis for deciphering novel PLP‐DEs as essential antibiotic targets along with corresponding ways to decipher small molecule inhibitors.
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Affiliation(s)
- Martin Pfanzelt
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Thomas E Maher
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany.,Department of Chemistry, Molecular Sciences Research Hub, White City Campus and Institute of Chemical Biology, Molecular Sciences Research Hub, White City Campus, Imperial College London, 82 Wood Lane, London, W12 0BZ, UK
| | - Ramona M Absmeier
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Markus Schwarz
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Stephan A Sieber
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
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15
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Tailored Pyridoxal Probes Unravel Novel Cofactor‐Dependent Targets and Antibiotic Hits in Critical Bacterial Pathogens. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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16
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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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17
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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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18
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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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19
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Tools, Strains, and Strategies To Effectively Conduct Anaerobic and Aerobic Transcriptional Reporter Screens and Assays in Staphylococcus aureus. Appl Environ Microbiol 2021; 87:e0110821. [PMID: 34406831 DOI: 10.1128/aem.01108-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Transcriptional reporters are reliable and time-tested tools to study gene regulation. In Staphylococcus aureus, β-galactosidase (lacZ)-based genetic screens are not widely used because of the necessity of selectable markers for strain construction and the production of staphyloxanthin pigment, which obfuscates results. We describe a series of vectors that allow for markerless insertion of codon-optimized lacZ-based transcriptional reporters. The vectors code for different ribosomal binding sites, allowing for tailored lacZ expression. A ΔcrtM::kanR deletion insertion mutant was constructed that prevents the synthesis of staphyloxanthin, thereby permitting blue-white screening without the interference of carotenoid production. We demonstrate the utility of these vectors to monitor aerobic and anaerobic transcriptional activities. For the latter, we describe the use of a ferrocyanide-ferricyanide redox system [Fe(CN)63-/4-] permitting blue-white screening in the absence of oxygen. We also describe additional reporter systems and methods for monitoring transcriptional activity during anaerobic culture, including an FAD-binding fluorescent protein (EcFbFP), alpha-hemolysin (hla), or lipase (geh). The systems and methods described are compatible with vectors utilized to create and screen high-density transposon mutant libraries. IMPORTANCE Staphylococcus aureus is a human pathogen and a leading cause of infectious disease-related illness and death worldwide. For S. aureus to successfully colonize and invade host tissues, it must tightly control the expression of genes encoding virulence factors. Oxygen tension varies greatly at infection sites, and many abscesses are devoid of oxygen. In this study, we have developed novel tools and methods to study how and when S. aureus alters transcription of genes. A key advantage of these methods and tools is that they can be utilized in the presence and absence of oxygen. A better understanding of anaerobic gene expression in S. aureus will provide important insights into the regulation of genes in low-oxygen environments.
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20
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Abstract
Staphylococcus aureus is a common cause of both superficial and invasive infections of humans and animals. Despite a potent host response and apparently appropriate antibiotic therapy, staphylococcal infections frequently become chronic or recurrent, demonstrating a remarkable ability of S. aureus to withstand the hostile host environment. There is growing evidence that staphylococcal DNA repair makes important contributions to the survival of the pathogen in host tissues, as well as promoting the emergence of mutants that resist host defenses and antibiotics. While much of what we know about DNA repair in S. aureus is inferred from studies with model organisms, the roles of specific repair mechanisms in infection are becoming clear and differences with Bacillus subtilis and Escherichia coli have been identified. Furthermore, there is growing interest in staphylococcal DNA repair as a target for novel therapeutics that sensitize the pathogen to host defenses and antibiotics. In this review, we discuss what is known about staphylococcal DNA repair and its role in infection, examine how repair in S. aureus is similar to, or differs from, repair in well-characterized model organisms, and assess the potential of staphylococcal DNA repair as a novel therapeutic target.
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21
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Chattagul S, Khan MM, Scott AJ, Nita-Lazar A, Ernst RK, Goodlett DR, Sermswan RW. Transcriptomics Analysis Uncovers Transient Ceftazidime Tolerance in Burkholderia Biofilms. ACS Infect Dis 2021; 7:2324-2336. [PMID: 34138549 DOI: 10.1021/acsinfecdis.1c00003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Burkholderia pseudomallei is an etiological agent of melioidosis, a severe community-acquired infectious disease. B. pseudomallei strain K96243 is sensitive to the drug ceftazidime (CAZ), but has been shown to exhibit transient CAZ tolerance when in a biofilm form. To investigate an observed shift in gene expression profile during CAZ tolerance condition and to better understand the mechanistic aspects of this transient tolerance, RNA-sequencing was performed on B. pseudomallei K96243 from the following three states: planktonic, biofilm, and planktonic shedding. Results indicated that the expression of 651 genes (10.97%) were significantly changed in both biofilm (resistant) and planktonic shedding (sensitive) cells in comparison to the planktonic state. The top four highly expressed genes identified in both states are associated with nitrosative stress response (BPSL2368), Fe-S homeostasis (BPSL2369), and nitrate respiration (BPSS1154 and BPSS1158). Additionally, five orthologous genes, BPSL2370-BPSL2374, implicated in Fe-S cluster biogenesis, and another gene, BPSL2863, involved in DNA-binding of the stress protein ferritin, were shown to increase expression by RT-qPCR. The shift in gene expression was especially prominent at the late stages of biofilm growth (72 and 96 h), specifically in the biofilm-challenged CAZ survivor cells. This suggested that in response to stress in a biofilm, differential expression of these genes may support development of the CAZ tolerance in Burkholderia. The application of iron chelator deferoxamine (DFO) to the biofilm caused a significant reduction in biofilm formation and associated CAZ tolerance. Therefore, the shift in Fe-S metabolism when B. pseudomallei is in a biofilm may help stabilize the levels of reactive oxygen species (ROS), thereby limiting tolerance to CAZ.
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Affiliation(s)
- Supaksorn Chattagul
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Melioidosis Research Center, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Mohd M. Khan
- University of Maryland School of Medicine, Baltimore, Maryland 21201, United States
- Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, United States
| | - Alison J. Scott
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry,Baltimore, Maryland 21201, United States
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, United States
| | - Robert K. Ernst
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry,Baltimore, Maryland 21201, United States
| | - David R. Goodlett
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry,Baltimore, Maryland 21201, United States
| | - Rasana W. Sermswan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Melioidosis Research Center, Khon Kaen University, Khon Kaen 40002, Thailand
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22
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Ellepola K, Huang X, Riley RP, Bitoun JP, Wen ZT. Streptococcus mutans Lacking sufCDSUB Is Viable, but Displays Major Defects in Growth, Stress Tolerance Responses and Biofilm Formation. Front Microbiol 2021; 12:671533. [PMID: 34248879 PMCID: PMC8264796 DOI: 10.3389/fmicb.2021.671533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/11/2021] [Indexed: 11/13/2022] Open
Abstract
Streptococcus mutans appears to possess a sole iron-sulfur (Fe-S) cluster biosynthesis system encoded by the sufCDSUB cluster. This study was designed to examine the role of sufCDSUB in S. mutans physiology. Allelic exchange mutants deficient of the whole sufCDSUB cluster and in individual genes were constructed. Compared to the wild-type, UA159, the sufCDSUB-deficient mutant, Δsuf::kanr, had a significantly reduced growth rate, especially in medium with the absence of isoleucine, leucine or glutamate/glutamine, amino acids that require Fe-S clusters for biosynthesis and when grown with medium adjusted to pH 6.0 and under oxidative and nitrosative stress conditions. Relative to UA159, Δsuf::kanr had major defects in stress tolerance responses with reduced survival rate of > 2-logs following incubation at low pH environment or after hydrogen peroxide challenge. When compared to UA159, Δsuf::kanr tended to form aggregates in broth medium and accumulated significantly less biofilm. As shown by luciferase reporter fusion assays, the expression of sufCDSUB was elevated by > 5.4-fold when the reporter strain was transferred from iron sufficient medium to iron-limiting medium. Oxidative stress induced by methyl viologen increased sufCDSUB expression by > 2-fold, and incubation in a low pH environment led to reduction of sufCDSUB expression by > 7-fold. These results suggest that lacking of SufCDSUB in S. mutans causes major defects in various cellular processes of the deficient mutant, including growth, stress tolerance responses and biofilm formation. In addition, the viability of the deficient mutant also suggests that SUF, the sole Fe-S cluster machinery identified is non-essential in S. mutans, which is not known in any other bacterium lacking the NIF and/or ISC system. However, how the bacterium compensates the Fe-S deficiency and if any novel Fe-S assembly systems exist in this bacterium await further investigation.
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Affiliation(s)
- Kassapa Ellepola
- Department of Oral and Craniofacial Biology, School of Dentistry, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Xiaochang Huang
- Department of Oral and Craniofacial Biology, School of Dentistry, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Ryan P Riley
- Department of Oral and Craniofacial Biology, School of Dentistry, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Jacob P Bitoun
- Department of Microbiology, Tulane University, New Orleans, LA, United States
| | - Zezhang Tom Wen
- Department of Oral and Craniofacial Biology, School of Dentistry, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
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23
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Jin H, Dhanasingh I, Sung J, La JW, Lee Y, Lee EM, Kang Y, Lee DY, Lee SH, Lee D. The sulfur formation system mediating extracellular cysteine-cystine recycling in Fervidobacterium islandicum AW-1 is associated with keratin degradation. Microb Biotechnol 2021; 14:938-952. [PMID: 33320434 PMCID: PMC8085985 DOI: 10.1111/1751-7915.13717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 11/27/2022] Open
Abstract
Most extremophilic anaerobes possess a sulfur formation (Suf) system for Fe-S cluster biogenesis. In addition to its essential role in redox chemistry and stress responses of Fe-S cluster proteins, the Suf system may play an important role in keratin degradation by Fervidobacterium islandicum AW-1. Comparative genomics of the order Thermotogales revealed that the feather-degrading F. islandicum AW-1 has a complete Suf-like machinery (SufCBDSU) that is highly expressed in cells grown on native feathers in the absence of elemental sulfur (S0 ). On the other hand, F. islandicum AW-1 exhibited a significant retardation in the Suf system-mediated keratin degradation in the presence of S0 . Detailed differential expression analysis of sulfur assimilation machineries unveiled the mechanism by which an efficient sulfur delivery from persulfurated SufS to SufU is achieved during keratinolysis under sulfur starvation. Indeed, addition of SufS-SufU to cell extracts containing keratinolytic proteases accelerated keratin decomposition in vitro under reducing conditions. Remarkably, mass spectrometric analysis of extracellular and intracellular levels of amino acids suggested that redox homeostasis within cells coupled to extracellular cysteine and cystine recycling might be a prerequisite for keratinolysis. Taken together, these results suggest that the Suf-like machinery including the SufS-SufU complex may contribute to sulfur availability for an extracellular reducing environment as well as intracellular redox homeostasis through cysteine released from keratin hydrolysate under starvation conditions.
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Affiliation(s)
- Hyeon‐Su Jin
- Department of BiotechnologyYonsei UniversitySeoul03722South Korea
| | - Immanuel Dhanasingh
- Department of Cellular and Molecular MedicineChosun University School of MedicineGwangju61452South Korea
| | - Jae‐Yoon Sung
- Department of BiotechnologyYonsei UniversitySeoul03722South Korea
| | - Jae Won La
- Department of BiotechnologyYonsei UniversitySeoul03722South Korea
| | - Yena Lee
- Department of BiotechnologyYonsei UniversitySeoul03722South Korea
| | - Eun Mi Lee
- Department of Agricultural BiotechnologyCenter for Food and BioconvergenceResearch Institute for Agricultural and Life SciencesSeoul National UniversitySeoul08826South Korea
| | - Yujin Kang
- Department of Bio and Fermentation Convergence TechnologyBK21 PLUS ProgramKookmin UniversitySeoul02707Korea
| | - Do Yup Lee
- Department of Agricultural BiotechnologyCenter for Food and BioconvergenceResearch Institute for Agricultural and Life SciencesSeoul National UniversitySeoul08826South Korea
| | - Sung Haeng Lee
- Department of Cellular and Molecular MedicineChosun University School of MedicineGwangju61452South Korea
| | - Dong‐Woo Lee
- Department of BiotechnologyYonsei UniversitySeoul03722South Korea
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24
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Identification of Genes Involved in Fe-S Cluster Biosynthesis of Nitrogenase in Paenibacillus polymyxa WLY78. Int J Mol Sci 2021; 22:ijms22073771. [PMID: 33916504 PMCID: PMC8038749 DOI: 10.3390/ijms22073771] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/26/2021] [Accepted: 04/01/2021] [Indexed: 11/17/2022] Open
Abstract
NifS and NifU (encoded by nifS and nifU) are generally dedicated to biogenesis of the nitrogenase Fe–S cluster in diazotrophs. However, nifS and nifU are not found in N2-fixing Paenibacillus strains, and the mechanisms involved in Fe–S cluster biosynthesis of nitrogenase is not clear. Here, we found that the genome of Paenibacillus polymyxa WLY78 contains the complete sufCDSUB operon, a partial sufC2D2B2 operon, a nifS-like gene, two nifU-like genes (nfuA-like and yutI), and two iscS genes. Deletion and complementation studies showed that the sufC, sufD, and sufB genes of the sufCDSUB operon, and nifS-like and yutI genes were involved in the Fe–S cluster biosynthesis of nitrogenase. Heterologous complementation studies demonstrated that the nifS-like gene of P. polymyxa WLY78 is interchangeable with Klebsiella oxytoca nifS, but P. polymyxa WLY78 SufCDB cannot be functionally replaced by K. oxytoca NifU. In addition, K. oxytoca nifU and Escherichia coli nfuA are able to complement the P. polymyxa WLY78 yutI mutant. Our findings thus indicate that the NifS-like and SufCDB proteins are the specific sulfur donor and the molecular scaffold, respectively, for the Fe–S cluster formation of nitrogenase in P. polymyxa WLY78. YutI can be an Fe–S cluster carrier involved in nitrogenase maturation in P. polymyxa WLY78.
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Aubourg M, Dhalluin A, Gravey F, Pottier M, Thomy N, Bernay B, Goux D, Martineau M, Giard JC. Phenotypic and proteomic approaches of the response to iron-limited condition in Staphylococcus lugdunensis. BMC Microbiol 2020; 20:328. [PMID: 33115407 PMCID: PMC7594282 DOI: 10.1186/s12866-020-02016-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/18/2020] [Indexed: 12/11/2022] Open
Abstract
Background Staphylococcus lugdunensis is a coagulase-negative Staphylococcus part of the commensal skin flora but emerge as an important opportunistic pathogen. Because iron limitation is a crucial stress during infectious process, we performed phenotypic study and compared proteomic profiles of this species incubated in absence and in presence of the iron chelator 2,2′-dipyridyl (DIP). Results No modification of cell morphology nor cell wall thickness were observed in presence of DIP. However iron-limitation condition promoted biofilm formation and reduced the ability to cope with oxidative stress (1 mM H2O2). In addition, S. lugdunensis N920143 cultured with DIP was significantly less virulent in the larvae of Galleria mellonella model of infection than that grown under standard conditions. We verified that these phenotypes were due to an iron limitation by complementation experiments with FeSO4. By mass spectrometry after trypsin digestion, we characterized the first iron-limitation stress proteome in S. lugdunensis. Among 1426 proteins identified, 349 polypeptides were differentially expressed. 222 were more and 127 less abundant in S. lugdunensis incubated in iron-limitation condition, and by RT-qPCR, some of the corresponding genes have been shown to be transcriptionally regulated. Our data revealed that proteins involved in iron metabolism and carriers were over-expressed, as well as several ABC transporters and polypeptides linked to cell wall metabolism. Conversely, enzymes playing a role in the oxidative stress response (especially catalase) were repressed. Conclusions This phenotypic and global proteomic study allowed characterization of the response of S. lugdunensis to iron-limitation. We showed that iron-limitation promoted biofilm formation, but decrease the oxidative stress resistance that may, at least in part, explained the reduced virulence of S. lugdunensis observed under low iron condition. Supplementary information Supplementary information accompanies this paper at 10.1186/s12866-020-02016-x.
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Affiliation(s)
- Marion Aubourg
- Université de Caen Normandie, EA4655 U2RM (équipe «Antibio-résistance»), CHU de Caen, Caen, France
| | - Anne Dhalluin
- Université de Caen Normandie, EA4655 U2RM (équipe «Antibio-résistance»), CHU de Caen, Caen, France
| | - François Gravey
- Université de Caen Normandie, GRAM 2.0, CHU de Caen, Service de Microbiologie, Caen, France
| | - Marine Pottier
- Université de Caen Normandie, EA4655 U2RM (équipe «Antibio-résistance»), CHU de Caen, Caen, France.,Université de Caen Normandie, GRAM 2.0, CHU de Caen, Service de Microbiologie, Caen, France
| | - Nicolas Thomy
- Université de Caen Normandie, EA4655 U2RM (équipe «Antibio-résistance»), CHU de Caen, Caen, France
| | - Benoit Bernay
- Plateforme Proteogen SFR ICORE 4206, Université de Caen Normandie, Caen, France
| | - Didier Goux
- Centre de Microscopie Appliquée à la Biologie, Université de Caen Normandie IFR ICORE, Caen, France
| | - Matthieu Martineau
- Université de Caen Normandie, EA4655 U2RM (équipe «Antibio-résistance»), CHU de Caen, Caen, France
| | - Jean-Christophe Giard
- Université de Caen Normandie, EA4655 U2RM (équipe «Antibio-résistance»), CHU de Caen, Caen, France.
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26
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Al-Tameemi H, Beavers WN, Norambuena J, Skaar EP, Boyd JM. Staphylococcus aureus lacking a functional MntABC manganese import system has increased resistance to copper. Mol Microbiol 2020; 115:554-573. [PMID: 33034093 DOI: 10.1111/mmi.14623] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/28/2020] [Accepted: 10/04/2020] [Indexed: 12/17/2022]
Abstract
S. aureus USA300 isolates utilize the copBL and copAZ gene products to prevent Cu intoxication. We created and examined a ΔcopAZ ΔcopBL mutant strain (cop-). The cop- strain was sensitive to Cu and accumulated intracellular Cu. We screened a transposon (Tn) mutant library in the cop- background and isolated strains with Tn insertions in the mntABC operon that permitted growth in the presence of Cu. The mutations were in mntA and they were recessive. Under the growth conditions utilized, MntABC functioned in manganese (Mn) import. When cultured with Cu, strains containing a mntA::Tn accumulated less Cu than the parent strain. Mn(II) supplementation improved growth when cop- was cultured with Cu and this phenotype was dependent upon the presence of MntR, which is a repressor of mntABC transcription. A ΔmntR strain had an increased Cu load and decreased growth in the presence of Cu, which was abrogated by the introduction of mntA::Tn. Over-expression of mntABC increased cellular Cu load and sensitivity to Cu. The presence of a mntA::Tn mutation protected iron-sulfur (FeS) enzymes from inactivation by Cu. The data presented are consistent with a model wherein defective MntABC results in decreased cellular Cu accumulation and protection to FeS enzymes from Cu poisoning.
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Affiliation(s)
- Hassan Al-Tameemi
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - William N Beavers
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Javiera Norambuena
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeffrey M Boyd
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
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27
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Dubovoy V, Desai P, Hao Z, Cheng CY, Verma G, Wojtas L, Brinzari TV, Boyd JM, Ma S, Asefa T, Pan L. Synthesis, Characterization, and Antimicrobial Investigation of a Novel Chlorhexidine Cyclamate Complex. CRYSTAL GROWTH & DESIGN 2020; 20:4991-4999. [PMID: 34054352 PMCID: PMC8159181 DOI: 10.1021/acs.cgd.0c00107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The synthesis, crystal structure, and antimicrobial efficacy are reported for a novel material comprising a 1:2 ratio of chlorhexidine (CHX) to N-cyclohexylsulfamate (i.e., artificial sweetener known as cyclamate). The chemical structure is unambiguously identified by incorporating a combination of single-crystal X-ray diffraction (SC-XRD), electrospray ionization mass spectrometry (ESI-MS), 1H nuclear magnetic resonance (NMR) spectroscopy, correlation spectroscopy (COSY), and attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR). The new material: 1) is amongst only several reported structures identified to date incorporating the vital chlorhexidine antimicrobial drug; 2) exhibits broad spectrum antimicrobial activity at concentrations less than 15 μg/mL; and 3) provides a unique delivery method for the essential active pharmaceutical ingredient (API). Furthermore, substitution of inactive gluconate with bioactive cyclamate counterion potentially provides the additional benefit of improving the taste profile of chlorhexidine.
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Affiliation(s)
- Viktor Dubovoy
- Colgate-Palmolive Company, 909 River Road, Piscataway, New Jersey 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Primit Desai
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, 76 Lipman Drive, New Brunswick, New Jersey 08901, United States
| | - Zhigang Hao
- Colgate-Palmolive Company, 909 River Road, Piscataway, New Jersey 08854, United States
| | - Chi-yuan Cheng
- Colgate-Palmolive Company, 909 River Road, Piscataway, New Jersey 08854, United States
| | - Gaurav Verma
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Lukasz Wojtas
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Tatiana V. Brinzari
- Colgate-Palmolive Company, 909 River Road, Piscataway, New Jersey 08854, United States
| | - Jeffrey M. Boyd
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, 76 Lipman Drive, New Brunswick, New Jersey 08901, United States
| | - Shengqian Ma
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Tewodros Asefa
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, New Jersey 08854, United States
| | - Long Pan
- Colgate-Palmolive Company, 909 River Road, Piscataway, New Jersey 08854, United States
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28
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Dubovoy V, Nawrocki S, Verma G, Wojtas L, Desai P, Al-Tameemi H, Brinzari TV, Stranick M, Chen D, Xu S, Ma S, Boyd JM, Asefa T, Pan L. Synthesis, Characterization, and Investigation of the Antimicrobial Activity of Cetylpyridinium Tetrachlorozincate. ACS OMEGA 2020; 5:10359-10365. [PMID: 32426592 PMCID: PMC7226859 DOI: 10.1021/acsomega.0c00131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Cetylpyridinium tetrachlorozincate (referred to herein as (CP)2ZnCl4) was synthesized and its solid-state structure was elucidated via single-crystal X-ray diffraction (SC-XRD), revealing a stoichiometry of C42H76Cl4N2Zn with two cetylpyridinium (CP) cations per [ZnCl4]2- tetrahedra. Crystal structures at 100 and 298 K exhibited a zig-zag pattern with alternating alkyl chains and zinc units. The material showed potential for application as a broad-spectrum antimicrobial agent, to reduce volatile sulfur compounds (VSCs) generated by bacteria, and in the fabrication of advanced functional materials. Minimum inhibitory concentration (MIC) of (CP)2ZnCl4 was 60, 6, and 6 μg mL-1 for Salmonella enterica, Staphylococcus aureus, and Streptococcus mutans, respectively. The MIC values of (CP)2ZnCl4 were comparable to that of pure cetylpyridinium chloride (CPC), despite the fact that approximately 16% of the bactericidal CPC is replaced with bacteriostatic ZnCl2 in the structure. A modified layer-by-layer deposition technique was implemented to synthesize mesoporous silica (i.e., SBA-15) loaded with approximately 9.0 wt % CPC and 8.9 wt % Zn.
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Affiliation(s)
- Viktor Dubovoy
- Department
of Chemistry and Chemical Biology, Rutgers,
The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Shiri Nawrocki
- Department
of Medicine, Rutgers Robert Wood Johnson
Medical School, 675 Hoes
Lane West, Piscataway, New
Jersey 08854, United
States
| | - Gaurav Verma
- Department
of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida33620, United States
| | - Lukasz Wojtas
- Department
of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida33620, United States
| | - Primit Desai
- Department
of Biochemistry and Microbiology, Rutgers,
The State University of New Jersey, 71 Lipman Drive, New Brunswick, New Jersey 08854, United States
| | - Hassan Al-Tameemi
- Department
of Biochemistry and Microbiology, Rutgers,
The State University of New Jersey, 71 Lipman Drive, New Brunswick, New Jersey 08854, United States
| | - Tatiana V. Brinzari
- Colgate-Palmolive
Company, 909 River Road, Piscataway, New Jersey 08854, United States
| | - Michael Stranick
- Colgate-Palmolive
Company, 909 River Road, Piscataway, New Jersey 08854, United States
| | - Dailin Chen
- Colgate-Palmolive
Company, 338 Qingnian
Road, Economic Development Zone, Guangzhou 510620, China
| | - Shaopeng Xu
- Colgate-Palmolive
Company, 338 Qingnian
Road, Economic Development Zone, Guangzhou 510620, China
| | - Shengqian Ma
- Department
of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida33620, United States
| | - Jeffrey M. Boyd
- Department
of Biochemistry and Microbiology, Rutgers,
The State University of New Jersey, 71 Lipman Drive, New Brunswick, New Jersey 08854, United States
| | - Tewodros Asefa
- Department
of Chemistry and Chemical Biology, Rutgers,
The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
- Department
of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, New Jersey 08854, United States
| | - Long Pan
- Colgate-Palmolive
Company, 909 River Road, Piscataway, New Jersey 08854, United States
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29
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Genetic Regulation of Metal Ion Homeostasis in Staphylococcus aureus. Trends Microbiol 2020; 28:821-831. [PMID: 32381454 DOI: 10.1016/j.tim.2020.04.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/16/2022]
Abstract
The acquisition of metal ions and the proper maturation of holo-metalloproteins are essential processes for all organisms. However, metal ion homeostasis is a double-edged sword. A cytosolic accumulation of metal ions can lead to mismetallation of proteins and cell death. Therefore, maintenance of proper concentrations of intracellular metals is essential for cell fitness and pathogenesis. Staphylococcus aureus, like all bacterial pathogens, uses transcriptional metalloregulatory proteins to aid in the detection and the genetic response to changes in metal ion concentrations. Herein, we review the mechanisms by which S. aureus senses and responds to alterations in the levels of cellular zinc, iron, heme, and copper. The interplay between metal ion sensing and metal-dependent expression of virulence factors is also discussed.
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30
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Wang M, Wang L, Wu P, Chen T, Zhu Y, Zhang Y, Wei Y, Qian C, Wang Y, Liu B. Genomics and Experimental Analysis Reveal a Novel Factor Contributing to the Virulence of Cronobacter sakazakii Strains Associated With Neonate Infection. J Infect Dis 2020; 220:306-315. [PMID: 30835279 DOI: 10.1093/infdis/jiz098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/02/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Cronobacter sakazakii causes meningitis and necrotizing enterocolitis in premature infants. However, its virulence determinants, especially those specific for strains associated with neonate infections, remain largely unknown. METHODS In this study, we performed a comparative genomic analysis of 209 C. sakazakii genomes, and 8 clonal groups (CGs) were revealed. RESULTS CG1 and CG2 were found to be significantly associated with neonate infections, and significantly prevalent genes in these 2 CGs were identified. Of these, a gene encoding the LysR-type regulator, CklR, was shown to contribute to bacterial pathogenicity based on animal experiments. We found that CklR directly binds and activates the suf Fe-S cluster biosynthesis operon, and high expression of the suf operon increases bacterial resistance to oxidative stress, which increases survival within the host. This leads to a high degree of bacteremia, which contributes to the development of meningitis. CONCLUSIONS Our work revealed a novel virulence factor specific to predominant pathogenic C. sakazakii strains.
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Affiliation(s)
- Min Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, People's Republic of China.,TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China.,Center for Microbial Functional Genomics and Detection Technology, Ministry of Education, Tianjin, People's Republic of China.,Tianjin Key Laboratory of Microbial Functional Genomics, People's Republic of China
| | - Lu Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, People's Republic of China.,TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Pan Wu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, People's Republic of China.,TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Tingting Chen
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, People's Republic of China.,TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Yiming Zhu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, People's Republic of China.,TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Yang Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, People's Republic of China.,TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Yi Wei
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, People's Republic of China.,TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Chengqian Qian
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, People's Republic of China.,TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Yuhui Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, People's Republic of China.,TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Bin Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, People's Republic of China.,TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China.,Center for Microbial Functional Genomics and Detection Technology, Ministry of Education, Tianjin, People's Republic of China.,Tianjin Key Laboratory of Microbial Functional Genomics, People's Republic of China
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31
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Valentin E, Bottomley AL, Chilambi GS, Harry EJ, Amal R, Sotiriou GA, Rice SA, Gunawan C. Heritable nanosilver resistance in priority pathogen: a unique genetic adaptation and comparison with ionic silver and antibiotics. NANOSCALE 2020; 12:2384-2392. [PMID: 31930233 DOI: 10.1039/c9nr08424j] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The past decade has seen the incorporation of antimicrobial nanosilver (NAg) into medical devices, and, increasingly, in everyday 'antibacterial' products. With the continued rise of antibiotic resistant bacteria, there are concerns that these priority pathogens will also develop resistance to the extensively commercialized nanoparticle antimicrobials. Herein, this work reports the emergence of stable resistance traits to NAg in the WHO-listed priority pathogen Staphylococcus aureus, which has previously been suggested to have no, or very low, capacity for silver resistance. With no native presence of genetically encoded silver defence mechanisms, the work showed that the bacterium is dependent on mutation of physiologically essential genes, including those involved in nucleotide synthesis and oxidative stress defence. While some mutations were uniquely associated with resistance to NAg, the study also found common mutations that could be protective against both NAg and ionic silver. This is consistent with the observation of NAg/ionic silver cross-resistance. These mutations were detected following withdrawal of the silver exposure, denoting heritable characteristics that allow for spread of the resistance traits even with discontinued silver use. Heritable silver resistance in priority pathogen cautions that these nanoparticle antimicrobials should only be used as needed, to preserve their efficacy for treating infections.
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Affiliation(s)
| | - Amy L Bottomley
- Ithree institute, University of Technology Sydney, NSW 2007, Australia.
| | | | - Elizabeth J Harry
- Ithree institute, University of Technology Sydney, NSW 2007, Australia.
| | - Rose Amal
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Georgios A Sotiriou
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Scott A Rice
- Ithree institute, University of Technology Sydney, NSW 2007, Australia. and Singapore Centre for Environmental Life Sciences Engineering, Singapore and School of Biological Sciences, Nanyang Technological University, Singapore
| | - Cindy Gunawan
- Ithree institute, University of Technology Sydney, NSW 2007, Australia. and School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
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Garcia PS, Gribaldo S, Py B, Barras F. The SUF system: an ABC ATPase-dependent protein complex with a role in Fe-S cluster biogenesis. Res Microbiol 2019; 170:426-434. [PMID: 31419582 DOI: 10.1016/j.resmic.2019.08.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 12/13/2022]
Abstract
Iron-sulfur (Fe-S) clusters are considered one of the most ancient and versatile inorganic cofactors present in the three domains of life. Fe-S clusters can act as redox sensors or catalysts and are found to be used by a large number of functional and structurally diverse proteins. Here, we cover current knowledge of the SUF multiprotein machinery that synthesizes and inserts Fe-S clusters into proteins. Specific focus is put on the ABC ATPase SufC, which contributes to building Fe-S clusters, and appeared early on during evolution.
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Affiliation(s)
- Pierre Simon Garcia
- Department of Microbiology, Stress Adaptation and Metabolism in Enterobacteria Unit, ERL CNRS 6002, Institut Pasteur, 25-28 Rue du Dr Roux, 75015, Paris, France; Department of Microbiology, Evolutionary Biology of the Microbial Cell Unit, Institut Pasteur, 25-28 Rue du Dr Roux, 75015, Paris, France
| | - Simonetta Gribaldo
- Department of Microbiology, Evolutionary Biology of the Microbial Cell Unit, Institut Pasteur, 25-28 Rue du Dr Roux, 75015, Paris, France
| | - Béatrice Py
- Laboratoire de Chimie Bactérienne, UMR7243 Aix-Marseille Université CNRS, 31 Chemin Joseph Aiguier, 13009, Marseille, France.
| | - Frédéric Barras
- Department of Microbiology, Stress Adaptation and Metabolism in Enterobacteria Unit, ERL CNRS 6002, Institut Pasteur, 25-28 Rue du Dr Roux, 75015, Paris, France.
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The ClpCP Complex Modulates Respiratory Metabolism in Staphylococcus aureus and Is Regulated in a SrrAB-Dependent Manner. J Bacteriol 2019; 201:JB.00188-19. [PMID: 31109995 DOI: 10.1128/jb.00188-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/17/2019] [Indexed: 01/13/2023] Open
Abstract
The staphylococcal respiratory regulator (SrrAB) modulates energy metabolism in Staphylococcus aureus Studies have suggested that regulated protein catabolism facilitates energy homeostasis. Regulated proteolysis in S. aureus is achieved through protein complexes composed of a peptidase (ClpQ or ClpP) in association with an AAA+ family ATPase (typically, ClpC or ClpX). In the present report, we tested the hypothesis that SrrAB regulates a Clp complex to facilitate energy homeostasis in S. aureus Strains deficient in one or more Clp complexes were attenuated for growth in the presence of puromycin, which causes enrichment of misfolded proteins. A ΔsrrAB strain had increased sensitivity to puromycin. Epistasis experiments suggested that the puromycin sensitivity phenotype of the ΔsrrAB strain was a result of decreased ClpC activity. Consistent with this, transcriptional activity of clpC was decreased in the ΔsrrAB mutant, and overexpression of clpC suppressed the puromycin sensitivity of the ΔsrrAB strain. We also found that ClpC positively influenced respiration and that it did so upon association with ClpP. In contrast, ClpC limited fermentative growth, while ClpP was required for optimal fermentative growth. Metabolomics studies demonstrated that intracellular metabolic profiles of the ΔclpC and ΔsrrAB mutants were distinct from those of the wild-type strain, supporting the notion that both ClpC and SrrAB affect central metabolism. We propose a model wherein SrrAB regulates energy homeostasis, in part, via modulation of regulated proteolysis.IMPORTANCE Oxygen is used as a substrate to derive energy by the bacterial pathogen Staphylococcus aureus during infection; however, S. aureus can also grow fermentatively in the absence of oxygen. To successfully cause infection, S. aureus must tailor its metabolism to take advantage of respiratory activity. Different proteins are required for growth in the presence or absence of oxygen; therefore, when cells transition between these conditions, several proteins would be expected to become unnecessary. In this report, we show that regulated proteolysis is used to modulate energy metabolism in S. aureus We report that the ClpCP protein complex is involved in specifically modulating aerobic respiratory growth but is dispensable for fermentative growth.
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Abstract
Staphylococcus aureus is clearly the most pathogenic member of the Staphylococcaceae. This is in large part due to the acquisition of an impressive arsenal of virulence factors that are coordinately regulated by a series of dedicated transcription factors. What is becoming more and more appreciated in the field is the influence of the metabolic state of S. aureus on the activity of these virulence regulators and their roles in modulating metabolic gene expression. Here I highlight recent advances in S. aureus metabolism as it pertains to virulence. Specifically, mechanisms of nutrient acquisition are outlined including carbohydrate and non-carbohydrate carbon/energy sources as well as micronutrient (Fe, Mn, Zn and S) acquisition. Additionally, energy producing strategies (respiration versus fermentation) are discussed and put in the context of pathogenesis. Finally, transcriptional regulators that coordinate metabolic gene expression are outlined, particularly those that affect the activities of major virulence factor regulators. This chapter essentially connects many recent observations that link the metabolism of S. aureus to its overall pathogenesis and hints that the mere presence of a plethora of virulence factors may not entirely explain the extraordinary pathogenic potential of S. aureus.
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35
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Contribution of YjbIH to Virulence Factor Expression and Host Colonization in Staphylococcus aureus. Infect Immun 2019; 87:IAI.00155-19. [PMID: 30885928 DOI: 10.1128/iai.00155-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 03/10/2019] [Indexed: 12/17/2022] Open
Abstract
To persist within the host and cause disease, Staphylococcus aureus relies on its ability to precisely fine-tune virulence factor expression in response to rapidly changing environments. During an unbiased transposon mutant screen, we observed that disruption of a two-gene operon, yjbIH, resulted in decreased levels of pigmentation and aureolysin (Aur) activity relative to the wild-type strain. Further analyses revealed that YjbH, a predicted thioredoxin-like oxidoreductase, is predominantly responsible for the observed yjbIH mutant phenotypes, though a minor role exists for the putative truncated hemoglobin YjbI. These differences were due to significantly decreased expression of crtOPQMN and aur Previous studies found that YjbH targets the disulfide- and oxidative stress-responsive regulator Spx for degradation by ClpXP. The absence of yjbH or yjbI resulted in altered sensitivities to nitrosative and oxidative stress and iron deprivation. Additionally, aconitase activity was altered in the yjbH and yjbI mutant strains. Decreased levels of pigmentation and aureolysin (Aur) activity in the yjbH mutant were found to be Spx dependent. Lastly, we used a murine sepsis model to determine the effect of the yjbIH deletion on pathogenesis and found that the mutant was better able to colonize the kidneys and spleens during an acute infection than the wild-type strain. These studies identified changes in pigmentation and protease activity in response to YjbIH and are the first to have shown a role for these proteins during infection.
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Rosario-Cruz Z, Eletsky A, Daigham NS, Al-Tameemi H, Swapna GVT, Kahn PC, Szyperski T, Montelione GT, Boyd JM. The copBL operon protects Staphylococcus aureus from copper toxicity: CopL is an extracellular membrane-associated copper-binding protein. J Biol Chem 2019; 294:4027-4044. [PMID: 30655293 PMCID: PMC6422080 DOI: 10.1074/jbc.ra118.004723] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 01/08/2019] [Indexed: 12/22/2022] Open
Abstract
As complications associated with antibiotic resistance have intensified, copper (Cu) is attracting attention as an antimicrobial agent. Recent studies have shown that copper surfaces decrease microbial burden, and host macrophages use Cu to increase bacterial killing. Not surprisingly, microbes have evolved mechanisms to tightly control intracellular Cu pools and protect against Cu toxicity. Here, we identified two genes (copB and copL) encoded within the Staphylococcus aureus arginine-catabolic mobile element (ACME) that we hypothesized function in Cu homeostasis. Supporting this hypothesis, mutational inactivation of copB or copL increased copper sensitivity. We found that copBL are co-transcribed and that their transcription is increased during copper stress and in a strain in which csoR, encoding a Cu-responsive transcriptional repressor, was mutated. Moreover, copB displayed genetic synergy with copA, suggesting that CopB functions in Cu export. We further observed that CopL functions independently of CopB or CopA in Cu toxicity protection and that CopL from the S. aureus clone USA300 is a membrane-bound and surface-exposed lipoprotein that binds up to four Cu+ ions. Solution NMR structures of the homologous Bacillus subtilis CopL, together with phylogenetic analysis and chemical-shift perturbation experiments, identified conserved residues potentially involved in Cu+ coordination. The solution NMR structure also revealed a novel Cu-binding architecture. Of note, a CopL variant with defective Cu+ binding did not protect against Cu toxicity in vivo Taken together, these findings indicate that the ACME-encoded CopB and CopL proteins are additional factors utilized by the highly successful S. aureus USA300 clone to suppress copper toxicity.
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Affiliation(s)
- Zuelay Rosario-Cruz
- From the Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, New Jersey 08901
| | - Alexander Eletsky
- the Department of Chemistry, State University of New York at Buffalo and Northeast Structural Genomics Consortium, Buffalo, New York 14260, and
| | - Nourhan S Daigham
- the Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854
| | - Hassan Al-Tameemi
- From the Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, New Jersey 08901
| | - G V T Swapna
- the Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854
| | - Peter C Kahn
- From the Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, New Jersey 08901
| | - Thomas Szyperski
- the Department of Chemistry, State University of New York at Buffalo and Northeast Structural Genomics Consortium, Buffalo, New York 14260, and
| | - Gaetano T Montelione
- the Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854,
- the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854
| | - Jeffrey M Boyd
- From the Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, New Jersey 08901,
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Seif Y, Monk JM, Mih N, Tsunemoto H, Poudel S, Zuniga C, Broddrick J, Zengler K, Palsson BO. A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. PLoS Comput Biol 2019; 15:e1006644. [PMID: 30625152 PMCID: PMC6326480 DOI: 10.1371/journal.pcbi.1006644] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/14/2018] [Indexed: 12/15/2022] Open
Abstract
S. aureus is classified as a serious threat pathogen and is a priority that guides the discovery and development of new antibiotics. Despite growing knowledge of S. aureus metabolic capabilities, our understanding of its systems-level responses to different media types remains incomplete. Here, we develop a manually reconstructed genome-scale model (GEM-PRO) of metabolism with 3D protein structures for S. aureus USA300 str. JE2 containing 854 genes, 1,440 reactions, 1,327 metabolites and 673 3-dimensional protein structures. Computations were in 85% agreement with gene essentiality data from random barcode transposon site sequencing (RB-TnSeq) and 68% agreement with experimental physiological data. Comparisons of computational predictions with experimental observations highlight: 1) cases of non-essential biomass precursors; 2) metabolic genes subject to transcriptional regulation involved in Staphyloxanthin biosynthesis; 3) the essentiality of purine and amino acid biosynthesis in synthetic physiological media; and 4) a switch to aerobic fermentation upon exposure to extracellular glucose elucidated as a result of integrating time-course of quantitative exo-metabolomics data. An up-to-date GEM-PRO thus serves as a knowledge-based platform to elucidate S. aureus’ metabolic response to its environment. Environmental perturbations (e.g., antibiotic stress, nutrient starvation, oxidative stress) induce systems-level perturbations of bacterial cells that vary depending on the growth environment. The generation of omics data is aimed at capturing a complete view of the organism’s response under different conditions. Genome-scale models (GEMs) of metabolism represent a knowledge-based platform for the contextualization and integration of multi-omic measurements and can serve to offer valuable insights of system-level responses. This work provides the most up to date reconstruction effort integrating recent advances in the knowledge of S. aureus molecular biology with previous annotations resulting in the first quantitatively and qualitatively validated S. aureus GEM. GEM guided predictions obtained from model analysis provided insights into the effects of medium composition on metabolic flux distribution and gene essentiality. The model can also serve as a platform to guide network reconstructions for other Staphylococci as well as direct hypothesis generation following the integration of omics data sets, including transcriptomics, proteomics, metabolomics, and multi-strain genomic data.
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Affiliation(s)
- Yara Seif
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Jonathan M. Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Nathan Mih
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Hannah Tsunemoto
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Saugat Poudel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Cristal Zuniga
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Jared Broddrick
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Karsten Zengler
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States of America
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States of America
- * E-mail:
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Metallocluster transactions: dynamic protein interactions guide the biosynthesis of Fe-S clusters in bacteria. Biochem Soc Trans 2018; 46:1593-1603. [PMID: 30381339 DOI: 10.1042/bst20180365] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/12/2018] [Accepted: 09/14/2018] [Indexed: 12/22/2022]
Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous cofactors present in all domains of life. The chemistries catalyzed by these inorganic cofactors are diverse and their associated enzymes are involved in many cellular processes. Despite the wide range of structures reported for Fe-S clusters inserted into proteins, the biological synthesis of all Fe-S clusters starts with the assembly of simple units of 2Fe-2S and 4Fe-4S clusters. Several systems have been associated with the formation of Fe-S clusters in bacteria with varying phylogenetic origins and number of biosynthetic and regulatory components. All systems, however, construct Fe-S clusters through a similar biosynthetic scheme involving three main steps: (1) sulfur activation by a cysteine desulfurase, (2) cluster assembly by a scaffold protein, and (3) guided delivery of Fe-S units to either final acceptors or biosynthetic enzymes involved in the formation of complex metalloclusters. Another unifying feature on the biological formation of Fe-S clusters in bacteria is that these systems are tightly regulated by a network of protein interactions. Thus, the formation of transient protein complexes among biosynthetic components allows for the direct transfer of reactive sulfur and Fe-S intermediates preventing oxygen damage and reactions with non-physiological targets. Recent studies revealed the importance of reciprocal signature sequence motifs that enable specific protein-protein interactions and consequently guide the transactions between physiological donors and acceptors. Such findings provide insights into strategies used by bacteria to regulate the flow of reactive intermediates and provide protein barcodes to uncover yet-unidentified cellular components involved in Fe-S metabolism.
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Laczkovich I, Teoh WP, Flury S, Grayczyk JP, Zorzoli A, Alonzo F. Increased flexibility in the use of exogenous lipoic acid by Staphylococcus aureus. Mol Microbiol 2018; 109:150-168. [PMID: 29660187 DOI: 10.1111/mmi.13970] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2018] [Indexed: 02/06/2023]
Abstract
Lipoic acid is a cofactor required for intermediary metabolism that is either synthesized de novo or acquired from environmental sources. The bacterial pathogen Staphylococcus aureus encodes enzymes required for de novo biosynthesis, but also encodes two ligases, LplA1 and LplA2, that are sufficient for lipoic acid salvage during infection. S. aureus also encodes two H proteins, GcvH of the glycine cleavage system and the homologous GcvH-L encoded in an operon with LplA2. GcvH is a recognized conduit for lipoyl transfer to α-ketoacid dehydrogenase E2 subunits, while the function of GcvH-L remains unclear. The potential to produce two ligases and two H proteins is an unusual characteristic of S. aureus that is unlike most other Gram positive Firmicutes and might allude to an expanded pathway of lipoic acid acquisition in this microorganism. Here, we demonstrate that LplA1 and LplA2 facilitate lipoic acid salvage by differentially targeting lipoyl domain-containing proteins; LplA1 targets H proteins and LplA2 targets α-ketoacid dehydrogenase E2 subunits. Furthermore, GcvH and GcvH-L both facilitate lipoyl relay to E2 subunits. Altogether, these studies identify an expanded mode of lipoic acid salvage used by S. aureus and more broadly underscore the importance of bacterial adaptations when faced with nutritional limitation.
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Affiliation(s)
- Irina Laczkovich
- Department of Microbiology and Immunology, Loyola University Chicago - Stritch School of Medicine, 2160 S. First Avenue, Maywood, IL, 60153, USA
| | - Wei Ping Teoh
- Department of Microbiology and Immunology, Loyola University Chicago - Stritch School of Medicine, 2160 S. First Avenue, Maywood, IL, 60153, USA
| | - Sarah Flury
- Department of Microbiology and Immunology, Loyola University Chicago - Stritch School of Medicine, 2160 S. First Avenue, Maywood, IL, 60153, USA
| | - James P Grayczyk
- Department of Microbiology and Immunology, Loyola University Chicago - Stritch School of Medicine, 2160 S. First Avenue, Maywood, IL, 60153, USA
| | - Azul Zorzoli
- Department of Microbiology and Immunology, Loyola University Chicago - Stritch School of Medicine, 2160 S. First Avenue, Maywood, IL, 60153, USA
| | - Francis Alonzo
- Department of Microbiology and Immunology, Loyola University Chicago - Stritch School of Medicine, 2160 S. First Avenue, Maywood, IL, 60153, USA
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Yokoyama N, Nonaka C, Ohashi Y, Shioda M, Terahata T, Chen W, Sakamoto K, Maruyama C, Saito T, Yuda E, Tanaka N, Fujishiro T, Kuzuyama T, Asai K, Takahashi Y. Distinct roles for U-type proteins in iron-sulfur cluster biosynthesis revealed by genetic analysis of the Bacillus subtilis sufCDSUB operon. Mol Microbiol 2018; 107:688-703. [PMID: 29292548 DOI: 10.1111/mmi.13907] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/24/2017] [Accepted: 12/29/2017] [Indexed: 01/09/2023]
Abstract
The biosynthesis of iron-sulfur (Fe-S) clusters in Bacillus subtilis is mediated by the SUF-like system composed of the sufCDSUB gene products. This system is unique in that it is a chimeric machinery comprising homologues of E. coli SUF components (SufS, SufB, SufC and SufD) and an ISC component (IscU). B. subtilis SufS cysteine desulfurase transfers persulfide sulfur to SufU (the IscU homologue); however, it has remained controversial whether SufU serves as a scaffold for Fe-S cluster assembly, like IscU, or acts as a sulfur shuttle protein, like E. coli SufE. Here we report that reengineering of the isoprenoid biosynthetic pathway in B. subtilis can offset the indispensability of the sufCDSUB operon, allowing the resultant Δsuf mutants to grow without detectable Fe-S proteins. Heterologous bidirectional complementation studies using B. subtilis and E. coli mutants showed that B. subtilis SufSU is interchangeable with E. coli SufSE but not with IscSU. In addition, functional similarity in SufB, SufC and SufD was observed between B. subtilis and E. coli. Our findings thus indicate that B. subtilis SufU is the protein that transfers sulfur from SufS to SufB, and that the SufBCD complex is the site of Fe-S cluster assembly.
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Affiliation(s)
- Nao Yokoyama
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Chihiro Nonaka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Yukari Ohashi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Masaharu Shioda
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Takuya Terahata
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Wen Chen
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Kotomi Sakamoto
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Chihiro Maruyama
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Takuya Saito
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Eiki Yuda
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Naoyuki Tanaka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kei Asai
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Yasuhiro Takahashi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
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Mashruwala AA, Boyd JM. Investigating the role(s) of SufT and the domain of unknown function 59 (DUF59) in the maturation of iron-sulfur proteins. Curr Genet 2017; 64:9-16. [PMID: 28589301 DOI: 10.1007/s00294-017-0716-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 05/24/2017] [Accepted: 05/26/2017] [Indexed: 01/07/2023]
Abstract
Comprehending biology at the molecular and systems levels is predicated upon understanding the functions of proteins. Proteins are typically composed of one or more functional moieties termed domains. Members of Bacteria, Eukarya, and Archaea utilize proteins containing a domain of unknown function (DUF) 59. Proteins requiring iron-sulfur (FeS) clusters containing cofactors are necessary for nearly all organisms making the assembly of functional FeS proteins essential. Recently, studies in eukaryotic and bacterial organisms have shown that proteins containing a DUF59, or those composed solely of DUF59, function in FeS protein maturation and/or intracellular Fe homeostasis. Herein, we review the current literature, discuss potential roles for DUF59, and address future studies that will help advance the field.
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Affiliation(s)
- Ameya A Mashruwala
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, 76 Lipman Dr., New Brunswick, NJ, 08901, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Jeffrey M Boyd
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, 76 Lipman Dr., New Brunswick, NJ, 08901, USA.
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