1
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Mettert EL, Kiley PJ. Fe-S cluster homeostasis and beyond: The multifaceted roles of IscR. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119749. [PMID: 38763301 DOI: 10.1016/j.bbamcr.2024.119749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/29/2024] [Accepted: 05/08/2024] [Indexed: 05/21/2024]
Abstract
The role of IscR in regulating the transcription of genes involved in Fe-S cluster homeostasis has been well established for the model organism Escherichia coli K12. In this bacterium, IscR coordinates expression of the Isc and Suf Fe-S cluster assembly pathways to meet cellular Fe-S cluster demands shaped by a variety of environmental cues. However, since its initial discovery nearly 25 years ago, there has been growing evidence that IscR function extends well beyond Fe-S cluster homeostasis, not only in E. coli, but in bacteria of diverse lifestyles. Notably, pathogenic bacteria have exploited the ability of IscR to respond to changes in oxygen tension, oxidative and nitrosative stress, and iron availability to navigate their trajectory in their respective hosts as changes in these cues are frequently encountered during host infection. In this review, we highlight these broader roles of IscR in different cellular processes and, in particular, discuss the importance of IscR as a virulence factor for many bacterial pathogens.
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Affiliation(s)
- Erin L Mettert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Patricia J Kiley
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
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2
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Repair of Iron Center Proteins—A Different Class of Hemerythrin-like Proteins. Molecules 2022; 27:molecules27134051. [PMID: 35807291 PMCID: PMC9268430 DOI: 10.3390/molecules27134051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 01/27/2023] Open
Abstract
Repair of Iron Center proteins (RIC) form a family of di-iron proteins that are widely spread in the microbial world. RICs contain a binuclear nonheme iron site in a four-helix bundle fold, two basic features of hemerythrin-like proteins. In this work, we review the data on microbial RICs including how their genes are regulated and contribute to the survival of pathogenic bacteria. We gathered the currently available biochemical, spectroscopic and structural data on RICs with a particular focus on Escherichia coli RIC (also known as YtfE), which remains the best-studied protein with extensive biochemical characterization. Additionally, we present novel structural data for Escherichia coli YtfE harboring a di-manganese site and the protein’s affinity for this metal. The networking of protein interactions involving YtfE is also described and integrated into the proposed physiological role as an iron donor for reassembling of stress-damaged iron-sulfur centers.
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3
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Crack JC, Balasiny BK, Bennett SP, Rolfe MD, Froes A, MacMillan F, Green J, Cole JA, Le Brun NE. The Di-Iron Protein YtfE Is a Nitric Oxide-Generating Nitrite Reductase Involved in the Management of Nitrosative Stress. J Am Chem Soc 2022; 144:7129-7145. [PMID: 35416044 PMCID: PMC9052748 DOI: 10.1021/jacs.1c12407] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Previously characterized
nitrite reductases fall into three classes:
siroheme-containing enzymes (NirBD), cytochrome c hemoproteins (NrfA and NirS), and copper-containing enzymes (NirK).
We show here that the di-iron protein YtfE represents a physiologically
relevant new class of nitrite reductases. Several functions have been
previously proposed for YtfE, including donating iron for the repair
of iron–sulfur clusters that have been damaged by nitrosative
stress, releasing nitric oxide (NO) from nitrosylated iron, and reducing
NO to nitrous oxide (N2O). Here, in vivo reporter assays confirmed that Escherichia coli YtfE increased cytoplasmic NO production from nitrite. Spectroscopic
and mass spectrometric investigations revealed that the di-iron site
of YtfE exists in a mixture of forms, including nitrosylated and nitrite-bound,
when isolated from nitrite-supplemented, but not nitrate-supplemented,
cultures. Addition of nitrite to di-ferrous YtfE resulted in nitrosylated
YtfE and the release of NO. Kinetics of nitrite reduction were dependent
on the nature of the reductant; the lowest Km, measured for the di-ferrous form, was ∼90 μM,
well within the intracellular nitrite concentration range. The vicinal
di-cysteine motif, located in the N-terminal domain of YtfE, was shown
to function in the delivery of electrons to the di-iron center. Notably,
YtfE exhibited very low NO reductase activity and was only able to
act as an iron donor for reconstitution of apo-ferredoxin under conditions
that damaged its di-iron center. Thus, YtfE is a high-affinity, low-capacity
nitrite reductase that we propose functions to relieve nitrosative
stress by acting in combination with the co-regulated NO-consuming
enzymes Hmp and Hcp.
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Affiliation(s)
- Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Basema K Balasiny
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Sophie P Bennett
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Matthew D Rolfe
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Afonso Froes
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Fraser MacMillan
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Jeffrey Green
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Jeffrey A Cole
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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4
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Defenses of multidrug resistant pathogens against reactive nitrogen species produced in infected hosts. Adv Microb Physiol 2022; 80:85-155. [PMID: 35489794 DOI: 10.1016/bs.ampbs.2022.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Bacterial pathogens have sophisticated systems that allow them to survive in hosts in which innate immunity is the frontline of defense. One of the substances produced by infected hosts is nitric oxide (NO) that together with its derived species leads to the so-called nitrosative stress, which has antimicrobial properties. In this review, we summarize the current knowledge on targets and protective systems that bacteria have to survive host-generated nitrosative stress. We focus on bacterial pathogens that pose serious health concerns due to the growing increase in resistance to currently available antimicrobials. We describe the role of nitrosative stress as a weapon for pathogen eradication, the detoxification enzymes, protein/DNA repair systems and metabolic strategies that contribute to limiting NO damage and ultimately allow survival of the pathogen in the host. Additionally, this systematization highlights the lack of available data for some of the most important human pathogens, a gap that urgently needs to be addressed.
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5
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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6
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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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7
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Carvalho SM, Freitas CS, Oliveira AS, Saraiva LM. Staphylococcus aureus flavohaemoglobin contributes to early stage biofilm development under nitrosative stress. FEMS Microbiol Lett 2021; 368:6402901. [PMID: 34665259 DOI: 10.1093/femsle/fnab131] [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] [Received: 05/18/2021] [Accepted: 10/14/2021] [Indexed: 02/07/2023] Open
Abstract
Staphylococcus aureus is a Gram-positive bacterium with capacity to form biofilms, which constitute an important resistance mechanism and virulence factor. Flavohaemoglobin (Hmp) is a major nitric oxide (NO) detoxifier of several bacteria, including S. aureus. Although Hmp has a well-known physiological role linked to response of planktonic cells to nitrosative stress, its contribution to biofilm formation remains unaddressed. Hence, in this work, we investigated the role of Hmp in biofilm development of a methicillin-resistant S. aureus strain. For this purpose, we exposed the hmp mutant to nitrosative stress and examined its behaviour along biofilm development. We observed that cells inactivated in hmp and grown under nitrosative stress conditions have significantly impaired capacity to develop early stage biofilms. Furthermore, the wild-type biofilm phenotype was fully restored by trans-complementation of hmp in the hmp mutant. Coculture studies of NO-producing macrophages with S. aureus revealed that the hmp mutant has significantly lower capacity to develop biofilm biomass when compared with the wild type. Thus, we concluded that the pathogen S. aureus relies on Hmp to establish viable biofilms in the presence of cells of the host innate immune system.
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Affiliation(s)
- Sandra M Carvalho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Cláudia S Freitas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Ana S Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Lígia M Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
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8
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Patterson DC, Ruiz MP, Yoon H, Walker JA, Armache JP, Yennawar NH, Weinert EE. Differential ligand-selective control of opposing enzymatic activities within a bifunctional c-di-GMP enzyme. Proc Natl Acad Sci U S A 2021; 118:e2100657118. [PMID: 34475207 PMCID: PMC8433548 DOI: 10.1073/pnas.2100657118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/02/2021] [Indexed: 01/23/2023] Open
Abstract
Cyclic dimeric guanosine monophosphate (c-di-GMP) serves as a second messenger that modulates bacterial cellular processes, including biofilm formation. While proteins containing both c-di-GMP synthesizing (GGDEF) and c-di-GMP hydrolyzing (EAL) domains are widely predicted in bacterial genomes, it is poorly understood how domains with opposing enzymatic activity are regulated within a single polypeptide. Herein, we report the characterization of a globin-coupled sensor protein (GCS) from Paenibacillus dendritiformis (DcpG) with bifunctional c-di-GMP enzymatic activity. DcpG contains a regulatory sensor globin domain linked to diguanylate cyclase (GGDEF) and phosphodiesterase (EAL) domains that are differentially regulated by gas binding to the heme; GGDEF domain activity is activated by the Fe(II)-NO state of the globin domain, while EAL domain activity is activated by the Fe(II)-O2 state. The in vitro activity of DcpG is mimicked in vivo by the biofilm formation of P. dendritiformis in response to gaseous environment, with nitric oxide conditions leading to the greatest amount of biofilm formation. The ability of DcpG to differentially control GGDEF and EAL domain activity in response to ligand binding is likely due to the unusual properties of the globin domain, including rapid ligand dissociation rates and high midpoint potentials. Using structural information from small-angle X-ray scattering and negative stain electron microscopy studies, we developed a structural model of DcpG, providing information about the regulatory mechanism. These studies provide information about full-length GCS protein architecture and insight into the mechanism by which a single regulatory domain can selectively control output domains with opposing enzymatic activities.
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Affiliation(s)
- Dayna C Patterson
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Myrrh Perez Ruiz
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Hyerin Yoon
- Department of Chemistry, Emory University, Atlanta, GA 30322
| | | | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Emily E Weinert
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802;
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
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9
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The Amino Acids Motif -32GSSYN36- in the Catalytic Domain of E. coli Flavorubredoxin NO Reductase Is Essential for Its Activity. Catalysts 2021. [DOI: 10.3390/catal11080926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Flavodiiron proteins (FDPs) are a family of modular and soluble enzymes endowed with nitric oxide and/or oxygen reductase activities, producing N2O or H2O, respectively. The FDP from Escherichia coli, which, apart from the two core domains, possesses a rubredoxin-like domain at the C-terminus (therefore named flavorubredoxin (FlRd)), is a bona fide NO reductase, exhibiting O2 reducing activity that is approximately ten times lower than that for NO. Among the flavorubredoxins, there is a strictly conserved amino acids motif, -G[S,T]SYN-, close to the catalytic diiron center. To assess its role in FlRd’s activity, we designed several site-directed mutants, replacing the conserved residues with hydrophobic or anionic ones. The mutants, which maintained the general characteristics of the wild type enzyme, including cofactor content and integrity of the diiron center, revealed a decrease of their oxygen reductase activity, while the NO reductase activity—specifically, its physiological function—was almost completely abolished in some of the mutants. Molecular modeling of the mutant proteins pointed to subtle changes in the predicted structures that resulted in the reduction of the hydration of the regions around the conserved residues, as well as in the elimination of hydrogen bonds, which may affect proton transfer and/or product release.
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10
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Silva LSO, Matias PM, Romão CV, Saraiva LM. Structural Basis of RICs Iron Donation for Iron-Sulfur Cluster Biogenesis. Front Microbiol 2021; 12:670681. [PMID: 33995335 PMCID: PMC8117158 DOI: 10.3389/fmicb.2021.670681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli YtfE is a di-iron protein of the widespread Repair of Iron Centers proteins (RIC) family that has the capacity to donate iron, which is a crucial component of the biogenesis of the ubiquitous family of iron-sulfur proteins. In this work we identify in E. coli a previously unrecognized link between the YtfE protein and the major bacterial system for iron-sulfur cluster (ISC) assembly. We show that YtfE establishes protein-protein interactions with the scaffold IscU, where the transient cluster is formed, and the cysteine desulfurase IscS. Moreover, we found that promotion by YtfE of the formation of an Fe-S cluster in IscU requires two glutamates, E125 and E159 in YtfE. Both glutamates form part of the entrance of a protein channel in YtfE that links the di-iron center to the surface. In particular, E125 is crucial for the exit of iron, as a single mutation to leucine closes the channel rendering YtfE inactive for the build-up of Fe-S clusters. Hence, we provide evidence for the key role of RICs as bacterial iron donor proteins involved in the biogenesis of Fe-S clusters.
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Affiliation(s)
- Liliana S O Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Pedro M Matias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.,iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Lígia M Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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11
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Porrini C, Ramarao N, Tran SL. Dr. NO and Mr. Toxic - the versatile role of nitric oxide. Biol Chem 2021; 401:547-572. [PMID: 31811798 DOI: 10.1515/hsz-2019-0368] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/04/2019] [Indexed: 12/25/2022]
Abstract
Nitric oxide (NO) is present in various organisms from humans, to plants, fungus and bacteria. NO is a fundamental signaling molecule implicated in major cellular functions. The role of NO ranges from an essential molecule to a potent mediator of cellular damages. The ability of NO to react with a broad range of biomolecules allows on one hand its regulation and a gradient concentration and on the other hand to exert physiological as well as pathological functions. In humans, NO is implicated in cardiovascular homeostasis, neurotransmission and immunity. However, NO can also contribute to cardiovascular diseases (CVDs) or septic shock. For certain denitrifying bacteria, NO is part of their metabolism as a required intermediate of the nitrogen cycle. However, for other bacteria, NO is toxic and harmful. To survive, those bacteria have developed processes to resist this toxic effect and persist inside their host. NO also contributes to maintain the host/microbiota homeostasis. But little is known about the impact of NO produced during prolonged inflammation on microbiota integrity, and some pathogenic bacteria take advantage of the NO response to colonize the gut over the microbiota. Taken together, depending on the environmental context (prolonged production, gradient concentration, presence of partners for interaction, presence of oxygen, etc.), NO will exert its beneficial or detrimental function. In this review, we highlight the dual role of NO for humans, pathogenic bacteria and microbiota, and the mechanisms used by each organism to produce, use or resist NO.
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Affiliation(s)
- Constance Porrini
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Nalini Ramarao
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Seav-Ly Tran
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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12
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Porrini C, Guérin C, Tran SL, Dervyn R, Nicolas P, Ramarao N. Implication of a Key Region of Six Bacillus cereus Genes Involved in Siroheme Synthesis, Nitrite Reductase Production and Iron Cluster Repair in the Bacterial Response to Nitric Oxide Stress. Int J Mol Sci 2021; 22:ijms22105079. [PMID: 34064887 PMCID: PMC8151001 DOI: 10.3390/ijms22105079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 12/30/2022] Open
Abstract
Bacterial response to nitric oxide (NO) is of major importance for bacterial survival. NO stress is a main actor of the eukaryotic immune response and several pathogenic bacteria have developed means for detoxification and repair of the damages caused by NO. However, bacterial mechanisms of NO resistance by Gram-positive bacteria are poorly described. In the opportunistic foodborne pathogen Bacillus cereus, genome sequence analyses did not identify homologs to known NO reductases and transcriptional regulators, such as NsrR, which orchestrate the response to NO of other pathogenic or non-pathogenic bacteria. Using a transcriptomic approach, we investigated the adaptation of B. cereus to NO stress. A cluster of 6 genes was identified to be strongly up-regulated in the early phase of the response. This cluster contains an iron-sulfur cluster repair enzyme, a nitrite reductase and three enzymes involved in siroheme biosynthesis. The expression pattern and close genetic localization suggest a functional link between these genes, which may play a pivotal role in the resistance of B. cereus to NO stress during infection.
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Affiliation(s)
- Constance Porrini
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.P.); (S.-L.T.); (R.D.)
| | - Cyprien Guérin
- MaIAGE, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.G.); (P.N.)
| | - Seav-Ly Tran
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.P.); (S.-L.T.); (R.D.)
| | - Rozenn Dervyn
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.P.); (S.-L.T.); (R.D.)
| | - Pierre Nicolas
- MaIAGE, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.G.); (P.N.)
| | - Nalini Ramarao
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.P.); (S.-L.T.); (R.D.)
- Correspondence:
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13
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Cole JA. Anaerobic bacterial response to nitric oxide stress: Widespread misconceptions and physiologically relevant responses. Mol Microbiol 2021; 116:29-40. [PMID: 33706420 DOI: 10.1111/mmi.14713] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 11/27/2022]
Abstract
How anaerobic bacteria protect themselves against nitric oxide-induced stress is controversial, not least because far higher levels of stress were used in the experiments on which most of the literature is based than bacteria experience in their natural environments. This results in chemical damage to enzymes that inactivates their physiological function. This review illustrates how transcription control mechanisms reveal physiological roles of the encoded gene products. Evidence that the hybrid cluster protein, Hcp, is a major high affinity NO reductase in anaerobic bacteria is reviewed: if so, its trans-nitrosation activity is a nonspecific secondary consequence of chemical inactivation. Whether the flavorubredoxin, NorV, is equally effective at such low [NO] is unknown. YtfE is proposed to be an enzyme rather than a source of iron for the repair of iron-sulfur proteins damaged by nitrosative stress. Any reaction catalyzed by YtfE needs to be revealed. The concentration of NO that accumulates in the cytoplasm of anaerobic bacteria is unknown, but indirect evidence indicates that it is in the pM to low nM range. Also unknown are the functions of the NO-inducible cytoplasmic proteins YgbA, YeaR, or YoaG. Experiments to resolve some of these questions are proposed.
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Affiliation(s)
- J A Cole
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
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14
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Naïli I, Gardette M, Garrivier A, Daniel J, Desvaux M, Pizza M, Gobert A, Marchal T, Loukiadis E, Jubelin G. Interplay between enterohaemorrhagic Escherichia coli and nitric oxide during the infectious process. Emerg Microbes Infect 2021; 9:1065-1076. [PMID: 32459575 PMCID: PMC7336997 DOI: 10.1080/22221751.2020.1768804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Enterohaemorrhagic Escherichia coli (EHEC) are bacterial pathogens responsible for life-threatening diseases in humans such as bloody diarrhoea and the hemolytic and uremic syndrome. To date, no specific therapy is available and treatments remain essentially symptomatic. In recent years, we demonstrated in vitro that nitric oxide (NO), a major mediator of the intestinal immune response, strongly represses the synthesis of the two cardinal virulence factors in EHEC, namely Shiga toxins (Stx) and the type III secretion system, suggesting NO has a great potential to protect against EHEC infection. In this study, we investigated the interplay between NO and EHEC in vivo using mouse models of infection. Using a NO-sensing reporter strain, we determined that EHEC sense NO in the gut of infected mice. Treatment of infected mice with a specific NOS inhibitor increased EHEC adhesion to the colonic mucosa but unexpectedly decreased Stx activity in the gastrointestinal tract, protecting mice from renal failure. Taken together, our data indicate that NO can have both beneficial and detrimental consequences on the outcome of an EHEC infection, and underline the importance of in vivo studies to increase our knowledge in host–pathogen interactions.
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Affiliation(s)
- Ilham Naïli
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France.,GSK, Siena, Italy
| | - Marion Gardette
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France.,Université de Lyon, CNRS, INRAE, Université Claude Bernard Lyon 1, VetAgro Sup, Laboratoire d'Ecologie Microbienne, F-63280 Marcy l'Etoile, France
| | - Annie Garrivier
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Julien Daniel
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Mickaël Desvaux
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | | | - Alain Gobert
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Thierry Marchal
- VetAgro Sup, Laboratoire vétérinaire d'histopathologie, F-63280 Marcy-l'Etoile, France
| | - Estelle Loukiadis
- Université de Lyon, CNRS, INRAE, Université Claude Bernard Lyon 1, VetAgro Sup, Laboratoire d'Ecologie Microbienne, F-63280 Marcy l'Etoile, France.,VetAgro Sup, Laboratoire national de référence des E. coli, F-63280 Marcy-l'Etoile, France
| | - Grégory Jubelin
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
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15
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Transcriptional Landscape of Waddlia chondrophila Aberrant Bodies Induced by Iron Starvation. Microorganisms 2020; 8:microorganisms8121848. [PMID: 33255276 PMCID: PMC7760296 DOI: 10.3390/microorganisms8121848] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/05/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022] Open
Abstract
Chronic infections caused by obligate intracellular bacteria belonging to the Chlamydiales order are related to the formation of persistent developmental forms called aberrant bodies (ABs), which undergo DNA replication without cell division. These enlarged bacteria develop and persist upon exposure to different stressful conditions such as β-lactam antibiotics, iron deprivation and interferon-γ. However, the mechanisms behind ABs biogenesis remain uncharted. Using an RNA-sequencing approach, we compared the transcriptional profile of ABs induced by iron starvation to untreated bacteria in the Chlamydia-related species Waddliachondrophila, a potential agent of abortion in ruminants and miscarriage in humans. Consistent with the growth arrest observed following iron depletion, our results indicate a significant reduction in the expression of genes related to energy production, carbohydrate and amino acid metabolism and cell wall/envelope biogenesis, compared to untreated, actively replicating bacteria. Conversely, three putative toxin-antitoxin modules were among the most up-regulated genes upon iron starvation, suggesting that their activation might be involved in growth arrest in adverse conditions, an uncommon feature in obligate intracellular bacteria. Our work represents the first complete transcriptomic profile of a Chlamydia-related species in stressful conditions and sets the grounds for further investigations on the mechanisms underlying chlamydial persistence.
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16
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Role of the Nitric Oxide Reductase NorVW in the Survival and Virulence of Enterohaemorrhagic Escherichia coli during Infection. Pathogens 2020; 9:pathogens9090683. [PMID: 32825770 PMCID: PMC7558590 DOI: 10.3390/pathogens9090683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 01/20/2023] Open
Abstract
Enterohaemorrhagic Escherichia coli (EHEC) are bacterial pathogens responsible for life-threatening diseases in humans, such as hemolytic and uremic syndrome. It has been previously demonstrated that the interplay between EHEC and nitric oxide (NO), a mediator of the host immune innate response, is critical for infection outcome, since NO affects both Shiga toxin (Stx) production and adhesion to enterocytes. In this study, we investigated the role of the NO reductase NorVW in the virulence and fitness of two EHEC strains in a murine model of infection. We determined that the deletion of norVW in the strain O91:H21 B2F1 has no impact on its virulence, whereas it reduces the ability of the strain O157:H7 620 to persist in the mouse gut and to produce Stx. We also revealed that the fitness defect of strain 620 ΔnorVW is strongly attenuated when mice are treated with an NO synthase inhibitor. Altogether, these results demonstrate that the NO reductase NorVW participates in EHEC resistance against NO produced by the host and promotes virulence through the modulation of Stx synthesis. The contribution of NorVW in the EHEC infectious process is, however, strain-dependent and suggests that the EHEC response to nitrosative stress is complex and multifactorial.
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17
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Chlamydomonas reinhardtii, an Algal Model in the Nitrogen Cycle. PLANTS 2020; 9:plants9070903. [PMID: 32708782 PMCID: PMC7412212 DOI: 10.3390/plants9070903] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 02/06/2023]
Abstract
Nitrogen (N) is an essential constituent of all living organisms and the main limiting macronutrient. Even when dinitrogen gas is the most abundant form of N, it can only be used by fixing bacteria but is inaccessible to most organisms, algae among them. Algae preferentially use ammonium (NH4+) and nitrate (NO3−) for growth, and the reactions for their conversion into amino acids (N assimilation) constitute an important part of the nitrogen cycle by primary producers. Recently, it was claimed that algae are also involved in denitrification, because of the production of nitric oxide (NO), a signal molecule, which is also a substrate of NO reductases to produce nitrous oxide (N2O), a potent greenhouse gas. This review is focused on the microalga Chlamydomonas reinhardtii as an algal model and its participation in different reactions of the N cycle. Emphasis will be paid to new actors, such as putative genes involved in NO and N2O production and their occurrence in other algae genomes. Furthermore, algae/bacteria mutualism will be considered in terms of expanding the N cycle to ammonification and N fixation, which are based on the exchange of carbon and nitrogen between the two organisms.
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18
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Rochman ND, Raciti D, Takaesu F, Sun SX. Prolonged culture in aerobic environments alters Escherichia coli H 2 production capacity. ENGINEERING REPORTS : OPEN ACCESS 2020; 2:e12161. [PMID: 38586583 PMCID: PMC10997342 DOI: 10.1002/eng2.12161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/04/2020] [Indexed: 04/09/2024]
Abstract
Growing interest in renewable energy continues to motivate new work on microbial biohydrogen production and in particular utilizing Escherichia coli a well-studied, facultative anaerobe. Here we characterize, for the first time the H2 production rate and capacity, of E coli isolates from the 50 000th generation of the Long-Term Evolution Experiment. Under these reaction conditions, peak production rates near or above 5 mL per hour for 100 mL of lysogeny broth (LB media) was established for the ancestral strains and batch efficiencies between 0.15 and 0.22 mL H2 produced per 1 mL LB media were achieved. All 11 isolates studied, which had been aerobically cultured in minimal media since 1988, exhibited a decreased H2 production rate or capacity with many strains unable to grow under anaerobic conditions at all. The genomes of these strains have been sequenced and a preliminary analysis of the correlations between genotype and phenotype shows that mutations in gene ydjO are exclusively observed in the two isolates which produce H2, potentially suggesting a role for this gene in the maintenance of wild type metabolic pathways in the context of diverse mutational backgrounds. These results provide hints towards uncovering new genetic targets for the pursuit of bacterial strains with increased capacity for H2 production as well as a case study in speciation and the control of phenotypic switching.
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Affiliation(s)
- Nash D. Rochman
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland
| | - David Raciti
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Felipe Takaesu
- Department of Biology, Johns Hopkins University, Baltimore, Maryland
| | - Sean X. Sun
- Departments of Mechanical Engineering and Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
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19
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Seth D, Hausladen A, Stamler JS. Anaerobic Transcription by OxyR: A Novel Paradigm for Nitrosative Stress. Antioxid Redox Signal 2020; 32:803-816. [PMID: 31691575 PMCID: PMC7074925 DOI: 10.1089/ars.2019.7921] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Significance: S-nitrosylation, the post-translational modification by nitric oxide (NO) to form S-nitrosothiols (SNOs), regulates diverse aspects of cellular function, and aberrant S-nitrosylation (nitrosative stress) is implicated in disease, from neurodegeneration to cancer. Essential roles for S-nitrosylation have been demonstrated in microbes, plants, and animals; notably, bacteria have often served as model systems for elucidation of general principles. Recent Advances: Recent conceptual advances include the idea of a molecular code through which proteins sense and differentiate S-nitrosothiol (SNO) from alternative oxidative modifications, providing the basis for specificity in SNO signaling. In Escherichia coli, S-nitrosylation relies on an enzymatic cascade that regulates, and is regulated by, the transcription factor OxyR under anaerobic conditions. S-nitrosylated OxyR activates an anaerobic regulon of >100 genes that encode for enzymes that both mediate S-nitrosylation and protect against nitrosative stress. Critical Issues: Mitochondria originated from endosymbiotic bacteria and generate NO under hypoxic conditions, analogous to conditions in E. coli. Nitrosative stress in mitochondria has been implicated in Alzheimer's and Parkinson's disease, among others. Many proteins that are S-nitrosylated in mitochondria are also S-nitrosylated in E. coli. Insights into enzymatic regulation of S-nitrosylation in E. coli may inform the identification of disease-relevant regulatory machinery in mammalian systems. Future Directions: Using E. coli as a model system, in-depth analysis of the anaerobic response controlled by OxyR may lead to the identification of enzymatic mechanisms regulating S-nitrosylation in particular, and hypoxic signaling more generally, providing novel insights into analogous mechanisms in mammalian cells and within dysfunctional mitochondria that characterize neurodegenerative diseases.
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Affiliation(s)
- Divya Seth
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Alfred Hausladen
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Jonathan S Stamler
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio
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20
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Folgosa F, Martins MC, Teixeira M. Diversity and complexity of flavodiiron NO/O2 reductases. FEMS Microbiol Lett 2019; 365:4733271. [PMID: 29240952 DOI: 10.1093/femsle/fnx267] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/11/2017] [Indexed: 11/14/2022] Open
Abstract
Flavodiiron proteins (FDPs) are a family of enzymes endowed with nitric oxide (NO) or oxygen reductase activities, forming the innocuous nitrous oxide (N2O) or water molecules, respectively. FDPs are widespread in the three life kingdoms, and have a modular nature, being each monomer minimally constituted by a metallo-β-lactamase-like domain containing a catalytic diiron centre, followed by a flavodoxin one, with a flavin mononucleotide. Since their discovery, additional domains have been found in FDPs, attached to the C-terminus, and containing either extra metal (iron) centers or extra flavin binding modules. Following an extensive analysis of genomic databases, we identified novel domain compositions, and proposed a new classification of FDPs in eight classes based on the nature and number of extra domains.
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21
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Martins MC, Romão CV, Folgosa F, Borges PT, Frazão C, Teixeira M. How superoxide reductases and flavodiiron proteins combat oxidative stress in anaerobes. Free Radic Biol Med 2019; 140:36-60. [PMID: 30735841 DOI: 10.1016/j.freeradbiomed.2019.01.051] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/14/2019] [Accepted: 01/31/2019] [Indexed: 12/31/2022]
Abstract
Microbial anaerobes are exposed in the natural environment and in their hosts, even if transiently, to fluctuating concentrations of oxygen and its derived reactive species, which pose a considerable threat to their anoxygenic lifestyle. To counteract these stressful conditions, they contain a multifaceted array of detoxifying systems that, in conjugation with cellular repairing mechanisms and in close crosstalk with metal homeostasis, allow them to survive in the presence of O2 and reactive oxygen species. Some of these systems are shared with aerobes, but two families of enzymes emerged more recently that, although not restricted to anaerobes, are predominant in anaerobic microbes. These are the iron-containing superoxide reductases, and the flavodiiron proteins, endowed with O2 and/or NO reductase activities, which are the subject of this Review. A detailed account of their physicochemical, physiological and molecular mechanisms will be presented, highlighting their unique properties in allowing survival of anaerobes in oxidative stress conditions, and comparing their properties with the most well-known detoxifying systems.
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Affiliation(s)
- Maria C Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Filipe Folgosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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22
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Abstract
The global regulatory protein CsrA coordinates gene expression in response to physiological cues reflecting cellular stress and nutrition. CsrA binding to the 5' segments of mRNA targets affects their translation, RNA stability, and/or transcript elongation. Recent studies identified probable mRNA targets of CsrA that are involved in iron uptake and storage in Escherichia coli, suggesting an unexplored role for CsrA in regulating iron homeostasis. Here, we assessed the impact of CsrA on iron-related gene expression, cellular iron, and growth under various iron levels. We investigated five new targets of CsrA regulation, including the genes for 4 ferritin or ferritin-like iron storage proteins (ISPs) and the stress-inducible Fe-S repair protein, SufA. CsrA bound with high affinity and specificity to ftnB, bfr, and dps mRNAs and inhibited their translation, while it modestly activated ftnA expression. Furthermore, CsrA was found to regulate cellular iron levels and support growth by repressing the expression of genes for ISPs, most importantly, ferritin B (FtnB) and bacterioferritin (Bfr). Iron starvation did not substantially affect cellular levels of CsrA or its small RNA (sRNA) antagonists, CsrB and CsrC. csrA disruption led to increased resistance to the lethal effects of H2O2 during exponential growth, consistent with a regulatory role in oxidative stress resistance. We propose that during exponential growth and under minimal stress, CsrA represses the deleterious expression of the ISPs that function under oxidative stress and stationary-phase conditions (FtnB, Bfr, and Dps), thus ensuring that cellular iron is available to processes that are required for growth.IMPORTANCE Iron is an essential micronutrient for nearly all living organisms but is toxic in excess. Consequently, the maintenance of iron homeostasis is a critical biological process, and the genes involved in this function are tightly regulated. Here, we explored a new role for the bacterial RNA binding protein CsrA in the regulation of iron homeostasis. CsrA was shown to be a key regulator of iron storage genes in Escherichia coli, with consequential effects on cellular iron levels and growth. Our findings establish a model in which robust CsrA activity during the exponential phase of growth leads to repression of genes whose products sequester iron or divert it to unnecessary stress response processes. In so doing, CsrA supports E. coli growth under iron-limiting laboratory conditions and may promote fitness in the competitive iron-limited environment of the host large intestine.
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23
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Hoeksema M, Jonker MJ, Bel K, Brul S, Ter Kuile BH. Genome rearrangements in Escherichia coli during de novo acquisition of resistance to a single antibiotic or two antibiotics successively. BMC Genomics 2018; 19:973. [PMID: 30591014 PMCID: PMC6307192 DOI: 10.1186/s12864-018-5353-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/07/2018] [Indexed: 11/25/2022] Open
Abstract
Background The ability of bacteria to acquire resistance to antibiotics relies to a large extent on their capacity for genome modification. Prokaryotic genomes are highly plastic and can utilize horizontal gene transfer, point mutations, and gene deletions or amplifications to realize genome expansion and rearrangements. The contribution of point mutations to de novo acquisition of antibiotic resistance is well-established. In this study, the internal genome rearrangement of Escherichia coli during to de novo acquisition of antibiotic resistance was investigated using whole-genome sequencing. Results Cells were made resistant to one of the four antibiotics and subsequently to one of the three remaining. This way the initial genetic rearrangements could be documented together with the effects of an altered genetic background on subsequent development of resistance. A DNA fragment including ampC was amplified by a factor sometimes exceeding 100 as a result of exposure to amoxicillin. Excision of prophage e14 was observed in many samples with a double exposure history, but not in cells exposed to a single antibiotic, indicating that the activation of the SOS stress response alone, normally the trigger for excision, was not sufficient to cause excision of prophage e14. Partial deletion of clpS and clpA occurred in strains exposed to enrofloxacin and tetracycline. Other deletions were observed in some strains, but not in replicates with the exact same exposure history. Various insertion sequence transpositions correlated with exposure to specific antibiotics. Conclusions Many of the genome rearrangements have not been reported before to occur during resistance development. The observed correlation between genome rearrangements and specific antibiotic pressure, as well as their presence in independent replicates indicates that these events do not occur randomly. Taken together, the observed genome rearrangements illustrate the plasticity of the E. coli genome when exposed to antibiotic stress. Electronic supplementary material The online version of this article (10.1186/s12864-018-5353-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marloes Hoeksema
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Martijs J Jonker
- RNA Biology & Applied Bioinformatics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Keshia Bel
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Benno H Ter Kuile
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands. .,Netherlands Food and Consumer Product Safety Authority, Office for Risk Assessment, Utrecht, The Netherlands.
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24
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Lu TT, Wang YM, Hung CH, Chiou SJ, Liaw WF. Bioinorganic Chemistry of the Natural [Fe(NO)2] Motif: Evolution of a Functional Model for NO-Related Biomedical Application and Revolutionary Development of a Translational Model. Inorg Chem 2018; 57:12425-12443. [DOI: 10.1021/acs.inorgchem.8b01818] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | - Yun-Ming Wang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30013, Taiwan
| | | | - Show-Jen Chiou
- Department of Applied Chemistry, National Chiayi University, Chiayi 60004, Taiwan
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25
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Abstract
Urinary tract infection (UTI) is one of the most common bacterial infections in humans, and the majority are caused by uropathogenic Escherichia coli (UPEC). The rising antibiotic resistance among UPEC and the frequent failure of antibiotics to effectively treat recurrent UTI and catheter-associated UTI motivate research on alternative ways of managing UTI. Abundant evidence indicates that the toxic radical nitric oxide (NO), formed by activation of the inducible nitric oxide synthase, plays an important role in host defence to bacterial infections, including UTI. The major source of NO production during UTI is from inflammatory cells, especially neutrophils, and from the uroepithelial cells that are known to orchestrate the innate immune response during UTI. NO and reactive nitrogen species have a wide range of antibacterial targets, including DNA, heme proteins, iron-sulfur clusters, and protein thiol groups. However, UPEC have acquired a variety of defence mechanisms for protection against NO, such as the NO-detoxifying enzyme flavohemoglobin and the NO-tolerant cytochrome bd-I respiratory oxidase. The cytotoxicity of NO-derived intermediates is nonspecific and may be detrimental to host cells, and a balanced NO production is crucial to maintain the tissue integrity of the urinary tract. In this review, we will give an overview of how NO production from host cells in the urinary tract is activated and regulated, the effect of NO on UPEC growth and colonization, and the ability of UPEC to protect themselves against NO. We also discuss the attempts that have been made to develop NO-based therapeutics for UTI treatment.
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26
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Ercan U, Sen B, Brooks A, Joshi S. Escherichia coli
cellular responses to exposure to atmospheric‐pressure dielectric barrier discharge plasma‐treated N‐acetylcysteine solution. J Appl Microbiol 2018; 125:383-397. [DOI: 10.1111/jam.13777] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 03/15/2018] [Accepted: 03/27/2018] [Indexed: 12/30/2022]
Affiliation(s)
- U.K. Ercan
- College of Medicine Center for Surgical Infection and Biofilm Drexel University Philadelphia PA USA
| | - B. Sen
- College of Medicine Center for Surgical Infection and Biofilm Drexel University Philadelphia PA USA
| | - A.D. Brooks
- College of Medicine Center for Surgical Infection and Biofilm Drexel University Philadelphia PA USA
| | - S.G. Joshi
- College of Medicine Center for Surgical Infection and Biofilm Drexel University Philadelphia PA USA
- School of Biomedical Engineering, Science and Health Systems Drexel University Philadelphia PA USA
- A.J. Drexel Plasma Institute, Drexel University Philadelphia PA USA
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27
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Balasiny B, Rolfe MD, Vine C, Bradley C, Green J, Cole J. Release of nitric oxide by the Escherichia coli YtfE (RIC) protein and its reduction by the hybrid cluster protein in an integrated pathway to minimize cytoplasmic nitrosative stress. Microbiology (Reading) 2018; 164:563-575. [DOI: 10.1099/mic.0.000629] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Basema Balasiny
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Matthew D. Rolfe
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Claire Vine
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Charlene Bradley
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Jeffrey Green
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jeff Cole
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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28
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Abstract
This chapter provides an overview of current knowledge of how anaerobic bacteria protect themselves against nitrosative stress. Nitric oxide (NO) is the primary source of this stress. Aerobically its removal is an oxidative process, whereas reduction is required anaerobically. Mechanisms required to protect aerobic and anaerobic bacteria are therefore different. Several themes recur in the review. First, how gene expression is regulated often provides clues to the physiological function of the gene products. Second, the physiological significance of reports based upon experiments under extreme conditions that bacteria do not encounter in their natural environment requires reassessment. Third, responses to the primary source of stress need to be distinguished from secondary consequences of chemical damage due to failure of repair mechanisms to cope with extreme conditions. NO is generated by many mechanisms, some of which remain undefined. An example is the recent demonstration that the hybrid cluster protein combines with YtfE (or RIC protein, for repair of iron centres damaged by nitrosative stress) in a new pathway to repair key iron-sulphur proteins damaged by nitrosative stress. The functions of many genes expressed in response to nitrosative stress remain either controversial or are completely unknown. The concentration of NO that accumulates in the bacterial cytoplasm is essentially unknown, so dogmatic statements cannot be made that damage to transcription factors (Fur, FNR, SoxRS, MelR, OxyR) occurs naturally as part of a physiologically relevant signalling mechanism. Such doubts can be resolved by simple experiments to meet six proposed criteria.
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29
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Jarboe LR. Improving the success and impact of the metabolic engineering design, build, test, learn cycle by addressing proteins of unknown function. Curr Opin Biotechnol 2018; 53:93-98. [PMID: 29306676 DOI: 10.1016/j.copbio.2017.12.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 12/12/2017] [Accepted: 12/17/2017] [Indexed: 12/20/2022]
Abstract
Rational, predictive metabolic engineering of organisms requires an ability to associate biological activity to the corresponding gene(s). Despite extensive advances in the 20 years since the Escherichia coli genome was published, there are still gaps in our knowledge of protein function. The substantial amount of data that has been published, such as: omics-level characterization in a myriad of conditions; genome-scale libraries; and evolution and genome sequencing, provide means of identifying and prioritizing proteins for characterization. This review describes the scale of this knowledge gap, demonstrates the benefit of addressing the knowledge gap, and demonstrates the availability of interesting candidates for characterization.
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Affiliation(s)
- Laura R Jarboe
- Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, United States; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA 50011, United States.
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Silva LO, Nobre LS, Mil-Homens D, Fialho A, Saraiva LM. Repair of Iron Centers RIC protein contributes to the virulence of Staphylococcus aureus. Virulence 2018; 9:312-317. [PMID: 29020514 PMCID: PMC5955197 DOI: 10.1080/21505594.2017.1389829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
RICs are a family of bacterial proteins involved in the repair of iron centers containing proteins damaged by the antimicrobial reactive species liberated by the innate immune system of infected hosts. Staphylococcus aureus is a human pathogen with increasing antibiotic resistance that also contains a RIC-like protein. In this work, we show that the survival of S. aureus within macrophages decreases upon inactivation of ric, and that the viability was restored to levels similar to the wild-type strain by reintroduction of ric via in trans complementation. Importantly, in macrophages that do not produce reactive oxygen species, the lower survival of the ric mutant was no longer observed. In lung epithelial cells, the intracellular viability of the S. aureus ric mutant was also shown to be lower than that of the wild-type. The wax moth larvae Galleria mellonella infected with S. aureus ric mutant presented an approximately 2.5-times higher survival when compared to the wild-type strain. Moreover, significantly lower bacterial loads were determined in the larvae hemolymph infected with strains not expressing ric, and complementation assays confirmed that this behavior was related to RIC. Furthermore, expression of the S. aureus ric gene within the larvae increased along the course of infection with a ~20-fold increase after 8 h of infection. Altogether, the data show that RIC is important for the virulence of S. aureus.
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Affiliation(s)
- Liliana O Silva
- a Instituto de Tecnologia Química e Biológica NOVA , Av. da República Oeiras , Portugal
| | - Lígia S Nobre
- a Instituto de Tecnologia Química e Biológica NOVA , Av. da República Oeiras , Portugal
| | - Dalila Mil-Homens
- b Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico , Av. Rovisco Pais, 1, Lisboa , Portugal
| | - Arsénio Fialho
- b Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico , Av. Rovisco Pais, 1, Lisboa , Portugal
| | - Lígia M Saraiva
- a Instituto de Tecnologia Química e Biológica NOVA , Av. da República Oeiras , Portugal
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Iwadate Y, Kato JI. Involvement of the ytfK gene from the PhoB regulon in stationary-phase H 2 O 2 stress tolerance in Escherichia coli. Microbiology (Reading) 2017; 163:1912-1923. [DOI: 10.1099/mic.0.000534] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yumi Iwadate
- Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Jun-ichi Kato
- Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Tokyo 192-0397, Japan
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Nitrosative stress defences of the enterohepatic pathogenic bacterium Helicobacter pullorum. Sci Rep 2017; 7:9909. [PMID: 28855660 PMCID: PMC5577044 DOI: 10.1038/s41598-017-10375-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/07/2017] [Indexed: 01/28/2023] Open
Abstract
Helicobacter pullorum is an avian bacterium that causes gastroenteritis, intestinal bowel and hepatobiliary diseases in humans. Although H. pullorum has been shown to activate the mammalian innate immunity with release of nitric oxide (NO), the proteins that afford protection against NO and reactive nitrogen species (RNS) remain unknown. Here several protein candidates of H. pullorum, namely a truncated (TrHb) and a single domain haemoglobin (SdHb), and three peroxiredoxin-like proteins (Prx1, Prx2 and Prx3) were investigated. We report that the two haemoglobin genes are induced by RNS, and that SdHb confers resistance to nitrosative stress both in vitro and in macrophages. For peroxiredoxins, the prx2 and prx3 expression is enhanced by peroxynitrite and hydrogen peroxide, respectively. Mutation of prx1 does not alter the resistance to these stresses, while the single ∆prx2 and double ∆prx1∆prx2 mutants have decreased viability. To corroborate the physiological data, the biochemical analysis of the five recombinant enzymes was done, namely by stopped-flow spectrophotometry. It is shown that H. pullorum SdHb reacts with NO much more quickly than TrHb, and that the three Prxs react promptly with peroxynitrite, Prx3 displaying the highest reactivity. Altogether, the results unveil SdHb and Prx3 as major protective systems of H. pullorum against nitrosative stress.
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Galia W, Leriche F, Cruveiller S, Garnier C, Navratil V, Dubost A, Blanquet-Diot S, Thevenot-Sergentet D. Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat. BMC Genomics 2017; 18:574. [PMID: 28774270 PMCID: PMC5543532 DOI: 10.1186/s12864-017-3957-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/24/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Enterohemorrhagic Escherichia coli (EHEC) are zoonotic agents associated with outbreaks worldwide. Growth of EHEC strains in ground beef could be inhibited by background microbiota that is present initially at levels greater than that of the pathogen E. coli. However, how the microbiota outcompetes the pathogenic bacteria is unknown. Our objective was to identify metabolic pathways of EHEC that were altered by natural microbiota in order to improve our understanding of the mechanisms controlling the growth and survival of EHECs in ground beef. RESULTS Based on 16S metagenomics analysis, we identified the microbial community structure in our beef samples which was an essential preliminary for subtractively analyzing the gene expression of the EHEC strains. Then, we applied strand-specific RNA-seq to investigate the effects of this microbiota on the global gene expression of EHEC O2621765 and O157EDL933 strains by comparison with their behavior in beef meat without microbiota. In strain O2621765, the expression of genes connected with nitrate metabolism and nitrite detoxification, DNA repair, iron and nickel acquisition and carbohydrate metabolism, and numerous genes involved in amino acid metabolism were down-regulated. Further, the observed repression of ftsL and murF, involved respectively in building the cytokinetic ring apparatus and in synthesizing the cytoplasmic precursor of cell wall peptidoglycan, might help to explain the microbiota's inhibitory effect on EHECs. For strain O157EDL933, the induced expression of the genes implicated in detoxification and the general stress response and the repressed expression of the peR gene, a gene negatively associated with the virulence phenotype, might be linked to the survival and virulence of O157:H7 in ground beef with microbiota. CONCLUSION In the present study, we show how RNA-Seq coupled with a 16S metagenomics analysis can be used to identify the effects of a complex microbial community on relevant functions of an individual microbe within it. These findings add to our understanding of the behavior of EHECs in ground beef. By measuring transcriptional responses of EHEC, we could identify putative targets which may be useful to develop new strategies to limit their shedding in ground meat thus reducing the risk of human illnesses.
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Affiliation(s)
- Wessam Galia
- UMR 5557 Ecologie Microbienne, Research Group on Bacterial Opportunistic Pathogens and Environment, CNRS, VetAgro Sup and Université de Lyon, Lyon, France.
- Université Clermont Auvergne, INRA, UMRF, F-15000, Aurillac, France.
- UMR UCA INRA 454 MEDIS Microbiota Digestive environment and Health, Université Clermont Auvergne, 63000, Clermont-Ferrand, France.
- VetAgro Sup, Campus Agronomique de Lempdes, Lempdes, France.
| | - Francoise Leriche
- Université Clermont Auvergne, INRA, UMRF, F-15000, Aurillac, France
- VetAgro Sup, Campus Agronomique de Lempdes, Lempdes, France
| | - Stéphane Cruveiller
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute Genoscope & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism, Evry, France
| | - Cindy Garnier
- UMR 5557 Ecologie Microbienne, Research Group on Bacterial Opportunistic Pathogens and Environment, CNRS, VetAgro Sup and Université de Lyon, Lyon, France
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Lyon1, Université de Lyon, Lyon, France
| | - Audrey Dubost
- UMR 5557 Ecologie Microbienne, CNRS, Université de Lyon, Lyon, France
| | - Stéphanie Blanquet-Diot
- UMR UCA INRA 454 MEDIS Microbiota Digestive environment and Health, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Delphine Thevenot-Sergentet
- UMR 5557 Ecologie Microbienne, Research Group on Bacterial Opportunistic Pathogens and Environment, CNRS, VetAgro Sup and Université de Lyon, Lyon, France
- Reference Laboratory for Escherichia coli including Shiga Toxin-Producing E. coli, VetAgro Sup, Campus Vétérinaire de Lyon, Université de Lyon, Marcy l'Etoile, Lyon, France
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Flint A, Stintzi A, Saraiva LM. Oxidative and nitrosative stress defences of Helicobacter and Campylobacter species that counteract mammalian immunity. FEMS Microbiol Rev 2016; 40:938-960. [PMID: 28201757 PMCID: PMC5091033 DOI: 10.1093/femsre/fuw025] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/29/2016] [Accepted: 07/02/2016] [Indexed: 12/18/2022] Open
Abstract
Helicobacter and Campylobacter species are Gram-negative microaerophilic host-associated heterotrophic bacteria that invade the digestive tract of humans and animals. Campylobacter jejuni is the major worldwide cause of foodborne gastroenteritis in humans, while Helicobacter pylori is ubiquitous in over half of the world's population causing gastric and duodenal ulcers. The colonisation of the gastrointestinal system by Helicobacter and Campylobacter relies on numerous cellular defences to sense the host environment and respond to adverse conditions, including those imposed by the host immunity. An important antimicrobial tool of the mammalian innate immune system is the generation of harmful oxidative and nitrosative stresses to which pathogens are exposed during phagocytosis. This review summarises the regulators, detoxifying enzymes and subversion mechanisms of Helicobacter and Campylobacter that ultimately promote the successful infection of humans.
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Affiliation(s)
- Annika Flint
- Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Alain Stintzi
- Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Lígia M. Saraiva
- Instituto de Tecnologia Química e Biológica, NOVA, Av. da República, 2780-157 Oeiras, Portugal
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Romão CV, Vicente JB, Borges PT, Victor BL, Lamosa P, Silva E, Pereira L, Bandeiras TM, Soares CM, Carrondo MA, Turner D, Teixeira M, Frazão C. Structure of Escherichia coli Flavodiiron Nitric Oxide Reductase. J Mol Biol 2016; 428:4686-4707. [PMID: 27725182 DOI: 10.1016/j.jmb.2016.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/02/2016] [Accepted: 10/04/2016] [Indexed: 01/08/2023]
Abstract
Flavodiiron proteins (FDPs) are present in organisms from all domains of life and have been described so far to be involved in the detoxification of oxygen or nitric oxide (NO), acting as O2 and/or NO reductases. The Escherichia coli FDP, named flavorubredoxin (FlRd), is the most extensively studied FDP. Biochemical and in vivo studies revealed that FlRd is involved in NO detoxification as part of the bacterial defense mechanisms against reactive nitrogen species. E. coli FlRd has a clear preference for NO as a substrate in vitro, exhibiting a very low reactivity toward O2. To contribute to the understanding of the structural features defining this substrate selectivity, we determined the crystallographic structure of E. coli FlRd, both in the isolated and reduced states. The overall tetrameric structure revealed a highly conserved flavodiiron core domain, with a metallo-β-lactamase-like domain containing a diiron center, and a flavodoxin domain with a flavin mononucleotide cofactor. The metal center in the oxidized state has a μ-hydroxo bridge coordinating the two irons, while in the reduced state, this moiety is not detected. Since only the flavodiiron domain was observed in these crystal structures, the structure of the rubredoxin domain was determined by NMR. Tunnels for the substrates were identified, and through molecular dynamics simulations, no differences for O2 or NO permeation were found. The present data represent the first structure for a NO-selective FDP.
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Affiliation(s)
- Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - João B Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - Bruno L Victor
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - Pedro Lamosa
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - Elísio Silva
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - Luís Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - Tiago M Bandeiras
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal; Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
| | - Cláudio M Soares
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - Maria A Carrondo
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - David Turner
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal.
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal.
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Abstract
Iron-sulfur (Fe-S) clusters are fundamental to numerous biological processes in most organisms, but these protein cofactors can be prone to damage by various oxidants (e.g., O2, reactive oxygen species, and reactive nitrogen species) and toxic levels of certain metals (e.g., cobalt and copper). Furthermore, their synthesis can also be directly influenced by the level of available iron in the environment. Consequently, the cellular need for Fe-S cluster biogenesis varies with fluctuating growth conditions. To accommodate changes in Fe-S demand, microorganisms employ diverse regulatory strategies to tailor Fe-S cluster biogenesis according to their surroundings. Here, we review the mechanisms that regulate Fe-S cluster formation in bacteria, primarily focusing on control of the Isc and Suf Fe-S cluster biogenesis systems in the model bacterium Escherichia coli.
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Affiliation(s)
- Erin L Mettert
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, ,
| | - Patricia J Kiley
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, ,
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37
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Lo FC, Hsieh CC, Maestre-Reyna M, Chen CY, Ko TP, Horng YC, Lai YC, Chiang YW, Chou CM, Chiang CH, Huang WN, Lin YH, Bohle DS, Liaw WF. Crystal Structure Analysis of the Repair of Iron Centers Protein YtfE and Its Interaction with NO. Chemistry 2016; 22:9768-76. [DOI: 10.1002/chem.201600990] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Feng-Chun Lo
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
| | - Chang-Chih Hsieh
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
| | | | - Chin-Yu Chen
- Department of Life Sciences; National Central University; Taoyuan Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry; Academia Sinica; Taipei Taiwan
| | - Yih-Chern Horng
- Department of Chemistry; National Changhua University of Education; Changhua Taiwan
| | - Yei-Chen Lai
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
| | - Chih-Mao Chou
- Department of Life Sciences; National Central University; Taoyuan Taiwan
| | | | - Wei-Ning Huang
- Department of Biotechnology; Yuanpei University; Hsinchu Taiwan
| | - Yi-Hung Lin
- National Synchrotron Radiation Research Center Hsinchu; Taiwan
| | - D. Scott Bohle
- Department of Chemistry; McGill University; 801 Sherbrooke Street West Montreal QC H3A2K6 Canada
| | - Wen-Feng Liaw
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
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38
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Nobre LS, Meloni D, Teixeira M, Viscogliosi E, Saraiva LM. Trichomonas vaginalis Repair of Iron Centres Proteins: The Different Role of Two Paralogs. Protist 2016; 167:222-33. [PMID: 27124376 DOI: 10.1016/j.protis.2016.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/28/2016] [Accepted: 03/15/2016] [Indexed: 01/04/2023]
Abstract
Trichomonas vaginalis, the causative parasite of one of the most prevalent sexually transmitted diseases is, so far, the only protozoan encoding two putative Repair of Iron Centres (RIC) proteins. Homologs of these proteins have been shown to protect bacteria from the chemical stress imposed by mammalian immunity. In this work, the biochemical and functional characterisation of the T. vaginalis RICs revealed that the two proteins have different properties. Expression of ric1 is induced by nitrosative stress but not by hydrogen peroxide, while ric2 transcription remained unaltered under similar conditions. T. vaginalis RIC1 contains a di-iron centre, but RIC2 apparently does not. Only RIC1 resembles bacterial RICs on spectroscopic profiling and repairing ability of oxidatively-damaged iron-sulfur clusters. Unexpectedly, RIC2 was found to bind DNA plasmid and T. vaginalis genomic DNA, a function proposed to be related with its leucine zipper domain. The two proteins also differ in their cellular localization: RIC1 is expressed in the cytoplasm only, and RIC2 occurs both in the nucleus and cytoplasm. Therefore, we concluded that the two RIC paralogs have different roles in T. vaginalis, with RIC2 showing an unprecedented DNA binding ability when compared with all other until now studied RICs.
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Affiliation(s)
- Lígia S Nobre
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República (EAN), 2780-157 Oeiras, Portugal
| | - Dionigia Meloni
- University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, 1 rue du Professeur Calmette, BP 245, 59019 Lille Cedex, France
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República (EAN), 2780-157 Oeiras, Portugal
| | - Eric Viscogliosi
- University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, 1 rue du Professeur Calmette, BP 245, 59019 Lille Cedex, France
| | - Lígia M Saraiva
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República (EAN), 2780-157 Oeiras, Portugal.
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Runkel S, Wells HC, Rowley G. Living with Stress: A Lesson from the Enteric Pathogen Salmonella enterica. ADVANCES IN APPLIED MICROBIOLOGY 2016; 83:87-144. [PMID: 23651595 DOI: 10.1016/b978-0-12-407678-5.00003-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The ability to sense and respond to the environment is essential for the survival of all living organisms. Bacterial pathogens such as Salmonella enterica are of particular interest due to their ability to sense and adapt to the diverse range of conditions they encounter, both in vivo and in environmental reservoirs. During this cycling from host to non-host environments, Salmonella encounter a variety of environmental insults ranging from temperature fluctuations, nutrient availability and changes in osmolarity, to the presence of antimicrobial peptides and reactive oxygen/nitrogen species. Such fluctuating conditions impact on various areas of bacterial physiology including virulence, growth and antimicrobial resistance. A key component of the success of any bacterial pathogen is the ability to recognize and mount a suitable response to the discrete chemical and physical stresses elicited by the host. Such responses occur through a coordinated and complex programme of gene expression and protein activity, involving a range of transcriptional regulators, sigma factors and two component regulatory systems. This review briefly outlines the various stresses encountered throughout the Salmonella life cycle and the repertoire of regulatory responses with which Salmonella counters. In particular, how these Gram-negative bacteria are able to alleviate disruption in periplasmic envelope homeostasis through a group of stress responses, known collectively as the Envelope Stress Responses, alongside the mechanisms used to overcome nitrosative stress, will be examined in more detail.
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Affiliation(s)
- Sebastian Runkel
- School of Biological Sciences, University of East Anglia, Norwich, UK
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40
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Wang J, Vine CE, Balasiny BK, Rizk J, Bradley CL, Tinajero-Trejo M, Poole RK, Bergaust LL, Bakken LR, Cole JA. The roles of the hybrid cluster protein, Hcp and its reductase, Hcr, in high affinity nitric oxide reduction that protects anaerobic cultures ofEscherichia coliagainst nitrosative stress. Mol Microbiol 2016; 100:877-92. [DOI: 10.1111/mmi.13356] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2016] [Indexed: 01/24/2023]
Affiliation(s)
- Jing Wang
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham; Birmingham B15 2TT UK
| | - Claire E. Vine
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham; Birmingham B15 2TT UK
| | - Basema K. Balasiny
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham; Birmingham B15 2TT UK
| | - John Rizk
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham; Birmingham B15 2TT UK
| | - Charlene L. Bradley
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham; Birmingham B15 2TT UK
| | - Mariana Tinajero-Trejo
- Department of Molecular Biology & Biotechnology; University of Sheffield, Firth Court, Western Bank; Sheffield S10 2TN UK
| | - Robert K. Poole
- Department of Molecular Biology & Biotechnology; University of Sheffield, Firth Court, Western Bank; Sheffield S10 2TN UK
| | | | - Lars R. Bakken
- Norwegian University of Life Science; PO box 5003 N-1432 Ås Norway
| | - Jeffrey A. Cole
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham; Birmingham B15 2TT UK
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41
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Li D, Zeng S, He M, Gu AZ. Water Disinfection Byproducts Induce Antibiotic Resistance-Role of Environmental Pollutants in Resistance Phenomena. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:3193-201. [PMID: 26928861 PMCID: PMC6321747 DOI: 10.1021/acs.est.5b05113] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The spread of antibiotic resistance represents a global threat to public health, and has been traditionally attributed to extensive antibiotic uses in clinical and agricultural applications. As a result, researchers have mostly focused on clinically relevant high-level resistance enriched by antibiotics above the minimal inhibitory concentrations (MICs). Here, we report that two common water disinfection byproducts (chlorite and iodoacetic acid) had antibiotic-like effects that led to the evolution of resistant E. coli strains under both high (near MICs) and low (sub-MIC) exposure concentrations. The subinhibitory concentrations of DBPs selected strains with resistance higher than those evolved under above-MIC exposure concentrations. In addition, whole-genome analysis revealed distinct mutations in small sets of genes known to be involved in multiple drug and drug-specific resistance, as well as in genes not yet identified to play role in antibiotic resistance. The number and identities of genetic mutations were distinct for either the high versus low sub-MIC concentrations exposure scenarios. This study provides evidence and mechanistic insight into the sub-MIC selection of antibiotic resistance by antibiotic-like environmental pollutants such as disinfection byproducts in water, which may be important contributors to the spread of global antibiotic resistance. The results from this study open an intriguing and profound question on the roles of large amount and various environmental contaminants play in selecting and spreading the antibiotics resistance in the environment.
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Affiliation(s)
- Dan Li
- Environmental Simulation and Pollution Control (ESPC) State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing, 100084, China
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts 02115, United States
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, China
| | - Siyu Zeng
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miao He
- Environmental Simulation and Pollution Control (ESPC) State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing, 100084, China
| | - April Z. Gu
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts 02115, United States
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42
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Romão CV, Vicente JB, Borges PT, Frazão C, Teixeira M. The dual function of flavodiiron proteins: oxygen and/or nitric oxide reductases. J Biol Inorg Chem 2016; 21:39-52. [PMID: 26767750 DOI: 10.1007/s00775-015-1329-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/28/2015] [Indexed: 12/27/2022]
Abstract
Flavodiiron proteins have emerged in the last two decades as a newly discovered family of oxygen and/or nitric oxide reductases widespread in the three life domains, and present in both aerobic and anaerobic organisms. Herein we present the main features of these fascinating enzymes, with a particular emphasis on the metal sites, as more appropriate for this special issue in memory of the exceptional bioinorganic scientist R. J. P. Williams who pioneered the notion of (metal) element availability-driven evolution. We also compare the flavodiiron proteins with the other oxygen and nitric oxide reductases known until now, highlighting how throughout evolution Nature arrived at different solutions for similar functions, in some cases adding extra features, such as energy conservation. These enzymes are an example of the (bioinorganic) unpredictable diversity of the living world.
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Affiliation(s)
- Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - João B Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal.
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Abstract
Nitrate reduction to ammonia via nitrite occurs widely as an anabolic process through which bacteria, archaea, and plants can assimilate nitrate into cellular biomass. Escherichia coli and related enteric bacteria can couple the eight-electron reduction of nitrate to ammonium to growth by coupling the nitrate and nitrite reductases involved to energy-conserving respiratory electron transport systems. In global terms, the respiratory reduction of nitrate to ammonium dominates nitrate and nitrite reduction in many electron-rich environments such as anoxic marine sediments and sulfide-rich thermal vents, the human gastrointestinal tract, and the bodies of warm-blooded animals. This review reviews the regulation and enzymology of this process in E. coli and, where relevant detail is available, also in Salmonella and draws comparisons with and implications for the process in other bacteria where it is pertinent to do so. Fatty acids may be present in high levels in many of the natural environments of E. coli and Salmonella in which oxygen is limited but nitrate is available to support respiration. In E. coli, nitrate reduction in the periplasm involves the products of two seven-gene operons, napFDAGHBC, encoding the periplasmic nitrate reductase, and nrfABCDEFG, encoding the periplasmic nitrite reductase. No bacterium has yet been shown to couple a periplasmic nitrate reductase solely to the cytoplasmic nitrite reductase NirB. The cytoplasmic pathway for nitrate reduction to ammonia is restricted almost exclusively to a few groups of facultative anaerobic bacteria that encounter high concentrations of environmental nitrate.
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44
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Abstract
This review describes the two main systems, namely the Isc (iron-sulfur cluster) and Suf (sulfur assimilation) systems, utilized by Escherichia coli and Salmonella for the biosynthesis of iron-sulfur (Fe-S) clusters, as well as other proteins presumably participating in this process. In the case of Fe-S cluster biosynthesis, it is assumed that the sulfur atoms from the cysteine desulfurase end up at cysteine residues of the scaffold protein, presumably waiting for iron atoms for cluster assembly. The review discusses the various potential iron donor proteins. For in vitro experiments, in general, ferrous salts are used during the assembly of Fe-S clusters, even though this approach is unlikely to reflect the physiological conditions. The fact that sulfur atoms can be directly transferred from cysteine desulfurases to scaffold proteins supports a mechanism in which the latter bind sulfur atoms first and iron atoms afterwards. In E. coli, fdx gene inactivation results in a reduced growth rate and reduced Fe-S enzyme activities. Interestingly, the SufE structure resembles that of IscU, strengthening the notion that the two proteins share the property of acting as acceptors of sulfur atoms provided by cysteine desulfurases. Several other factors have been suggested to participate in cluster assembly and repair in E. coli and Salmonella. Most of them were identified by their abilities to act as extragenic and/or multicopy suppressors of mutations in Fe-S cluster metabolism, while others possess biochemical properties that are consistent with a role in Fe-S cluster biogenesis.
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45
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Mehta HH, Liu Y, Zhang MQ, Spiro S. Genome-wide analysis of the response to nitric oxide in uropathogenic Escherichia coli CFT073. Microb Genom 2015; 1:e000031. [PMID: 28348816 PMCID: PMC5320621 DOI: 10.1099/mgen.0.000031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/07/2015] [Indexed: 12/30/2022] Open
Abstract
Uropathogenic Escherchia coli (UPEC) is the causative agent of urinary tract infections. Nitric oxide (NO) is a toxic water-soluble gas that is encountered by UPEC in the urinary tract. Therefore, UPEC probably requires mechanisms to detoxify NO in the host environment. Thus far, flavohaemoglobin (Hmp), an NO denitrosylase, is the only demonstrated NO detoxification system in UPEC. Here we show that, in E. coli strain CFT073, the NADH-dependent NO reductase flavorubredoxin (FlRd) also plays a major role in NO scavenging. We generated a mutant that lacks all known and candidate NO detoxification pathways (Hmp, FlRd and the respiratory nitrite reductase, NrfA). When grown and assayed anaerobically, this mutant expresses an NO-inducible NO scavenging activity, pointing to the existence of a novel detoxification mechanism. Expression of this activity is inducible by both NO and nitrate, and the enzyme is membrane-associated. Genome-wide transcriptional profiling of UPEC grown under anaerobic conditions in the presence of nitrate (as a source of NO) highlighted various aspects of the response of the pathogen to nitrate and NO. Several virulence-associated genes are upregulated, suggesting that host-derived NO is a potential regulator of UPEC virulence. Chromatin immunoprecipitation and sequencing was used to evaluate the NsrR regulon in CFT073. We identified 49 NsrR binding sites in promoter regions in the CFT073 genome, 29 of which were not previously identified in E. coli K-12. NsrR may regulate some CFT073 genes that do not have homologues in E. coli K-12.
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Affiliation(s)
- Heer H. Mehta
- Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
| | - Yuxuan Liu
- Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
- Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
| | - Michael Q. Zhang
- Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
- Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
| | - Stephen Spiro
- Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
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46
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Chhabra S, Spiro S. Inefficient translation of nsrR constrains behaviour of the NsrR regulon in Escherichia coli. Microbiology (Reading) 2015; 161:2029-2038. [DOI: 10.1099/mic.0.000151] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Shivani Chhabra
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Stephen Spiro
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
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47
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Park YM, Lee HJ, Jeong JH, Kook JK, Choy HE, Hahn TW, Bang IS. Branched-chain amino acid supplementation promotes aerobic growth of Salmonella Typhimurium under nitrosative stress conditions. Arch Microbiol 2015; 197:1117-27. [PMID: 26374245 DOI: 10.1007/s00203-015-1151-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 09/03/2015] [Accepted: 09/11/2015] [Indexed: 12/31/2022]
Abstract
Nitric oxide (NO) inactivates iron-sulfur enzymes in bacterial amino acid biosynthetic pathways, causing amino acid auxotrophy. We demonstrate that exogenous supplementation with branched-chain amino acids (BCAA) can restore the NO resistance of hmp mutant Salmonella Typhimurium lacking principal NO-metabolizing enzyme flavohemoglobin, and of mutants further lacking iron-sulfur enzymes dihydroxy-acid dehydratase (IlvD) and isopropylmalate isomerase (LeuCD) that are essential for BCAA biosynthesis, in an oxygen-dependent manner. BCAA supplementation did not affect the NO consumption rate of S. Typhimurium, suggesting the BCAA-promoted NO resistance independent of NO metabolism. BCAA supplementation also induced intracellular survival of ilvD and leuCD mutants at wild-type levels inside RAW 264.7 macrophages that produce constant amounts of NO regardless of varied supplemental BCAA concentrations. Our results suggest that the NO-induced BCAA auxotrophy of Salmonella, due to inactivation of iron-sulfur enzymes for BCAA biosynthesis, could be rescued by bacterial taking up exogenous BCAA available in oxic environments.
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Affiliation(s)
- Yoon Mee Park
- Department of Microbiology and Immunology, Chosun University School of Dentistry, Gwangju, 501-759, Republic of Korea
| | - Hwa Jeong Lee
- Department of Microbiology and Immunology, Chosun University School of Dentistry, Gwangju, 501-759, Republic of Korea
| | - Jae-Ho Jeong
- Department of Microbiology, Chonnam National University Medical School, Gwangju, 501-746, Republic of Korea
| | - Joong-Ki Kook
- Department of Oral Biochemistry, Chosun University School of Dentistry, Gwangju, 501-759, Republic of Korea
| | - Hyon E Choy
- Department of Microbiology, Chonnam National University Medical School, Gwangju, 501-746, Republic of Korea
| | - Tae-Wook Hahn
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, 200-701, Republic of Korea
| | - Iel Soo Bang
- Department of Microbiology and Immunology, Chosun University School of Dentistry, Gwangju, 501-759, Republic of Korea.
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48
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Li X, Tao J, Hu X, Chan J, Xiao J, Mi K. A bacterial hemerythrin-like protein MsmHr inhibits the SigF-dependent hydrogen peroxide response in mycobacteria. Front Microbiol 2015; 5:800. [PMID: 25642228 PMCID: PMC4295536 DOI: 10.3389/fmicb.2014.00800] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/27/2014] [Indexed: 12/05/2022] Open
Abstract
Hydrogen peroxide (H2O2) is one of a variety of reactive oxygen species (ROS) produced by aerobic organisms. Host production of toxic H2O2 in response to pathogen infection is an important classical innate defense mechanism against invading microbes. Understanding the mechanisms by which pathogens, in response to oxidative stress, mediate defense against toxic ROS, can reveal anti-microbial targets and shed light on pathogenic mechanisms. In this study, we provide evidence that a Mycobacterium smegmatis hemerythrin-like protein MSMEG_2415, designated MsmHr, is a H2O2-modulated repressor of the SigF-mediated response to H2O2. Circular dichroism and spectrophotometric analysis of MsmHr revealed properties characteristic of a typical hemerythrin-like protein. An msmHr knockout strain of M. smegmatis mc2155 (ΔmsmHr) was more resistant to H2O2 than its parental strain, and overexpression of MsmHr increased mycobacterial susceptibility to H2O2. Mutagenesis studies revealed that the hemerythrin domain of MsmHr is required for the regulation of the H2O2 response observed in the overexpression study. We show that MsmHr inhibits the expression of SigF (MSMEG_1804), an alternative sigma factor that plays an important role in bacterial oxidative stress responses, including those elicited by H2O2, thus providing a mechanistic link between ΔmsmHr and its enhanced resistance to H2O2. Together, these results strongly suggest that MsmHr is involved in the response of mycobacteria to H2O2 by negatively regulating a sigma factor, a function not previously described for hemerythrins.
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Affiliation(s)
- Xiaojing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Jun Tao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Xinling Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - John Chan
- Departments of Medicine and Microbiology and Immunology, Albert Einstein College of Medicine Bronx, NY, USA
| | - Jing Xiao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Kaixia Mi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences Beijing, China ; Beijing Key Laboratory of Microbial Drug Resistance and Resistome Beijing, China
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49
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Nobre LS, Lousa D, Pacheco I, Soares CM, Teixeira M, Saraiva LM. Insights into the structure of the diiron site of RIC fromEscherichia coli. FEBS Lett 2015; 589:426-31. [DOI: 10.1016/j.febslet.2014.12.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 12/17/2014] [Accepted: 12/22/2014] [Indexed: 11/30/2022]
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50
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Mettert EL, Kiley PJ. Fe-S proteins that regulate gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1284-93. [PMID: 25450978 DOI: 10.1016/j.bbamcr.2014.11.018] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 10/24/2014] [Accepted: 11/13/2014] [Indexed: 02/06/2023]
Abstract
Iron-sulfur (Fe-S) cluster containing proteins that regulate gene expression are present in most organisms. The innate chemistry of their Fe-S cofactors makes these regulatory proteins ideal for sensing environmental signals, such as gases (e.g. O2 and NO), levels of Fe and Fe-S clusters, reactive oxygen species, and redox cycling compounds, to subsequently mediate an adaptive response. Here we review the recent findings that have provided invaluable insight into the mechanism and function of these highly significant Fe-S regulatory proteins. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- Erin L Mettert
- University of Wisconsin-Madison, Department of Biomolecular Chemistry, 440 Henry Mall, Biochemical Sciences Building, Room 4204C, Madison, WI 53706, USA.
| | - Patricia J Kiley
- University of Wisconsin-Madison, Department of Biomolecular Chemistry, 440 Henry Mall, Biochemical Sciences Building, Room 4204C, Madison, WI 53706, USA.
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