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Beraldo C, Traverso E, Boschin M, Cendron L, Morosinotto T, Alboresi A. Physcomitrium patens flavodiiron proteins form heterotetrametric complexes. J Biol Chem 2024:107643. [PMID: 39122005 DOI: 10.1016/j.jbc.2024.107643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 07/11/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Flavodiiron proteins (FLVs) catalyze the reduction of oxygen to water by using electrons from Photosystem I (PSI). In several photosynthetic organisms such as cyanobacteria, green algae, mosses and gymnosperms, FLV-dependent electron flow protects PSI from over-reduction and consequent damage especially under fluctuating light conditions. In this work we investigated biochemical and structural properties of FLVA and FLVB from the model moss Physcomitrium patens. The two proteins, expressed and purified from Escherichia coli, bind both iron and flavin cofactors and show NAD(P)H oxidase activity as well as oxygen reductase capacities. Moreover, the co-expression of both FLVA and FLVB, coupled to a tandem affinity purification procedure with two different affinity tags, enabled the isolation of the stable and catalytically active FLVA/B hetero tetrameric protein complex with cooperative nature. The multimeric organization was shown to be stabilized by inter-subunit disulfide bonds. This investigation provides valuable new information on the biochemical properties of FLVs, with new insights into their in vivo activity.
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Affiliation(s)
- Claudia Beraldo
- Department of Biology, University of Padova, Via Ugo Bassi 58B, Padova 35121, Italy
| | - Eleonora Traverso
- Department of Biology, University of Padova, Via Ugo Bassi 58B, Padova 35121, Italy
| | - Marco Boschin
- Department of Biology, University of Padova, Via Ugo Bassi 58B, Padova 35121, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Via Ugo Bassi 58B, Padova 35121, Italy
| | - Tomas Morosinotto
- Department of Biology, University of Padova, Via Ugo Bassi 58B, Padova 35121, Italy
| | - Alessandro Alboresi
- Department of Biology, University of Padova, Via Ugo Bassi 58B, Padova 35121, Italy; National Biodiversity Future Center, Università degli Studi di Palermo, Italy.
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2
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Blomberg MRA, Ädelroth P. Reduction of molecular oxygen in flavodiiron proteins - Catalytic mechanism and comparison to heme-copper oxidases. J Inorg Biochem 2024; 255:112534. [PMID: 38552360 DOI: 10.1016/j.jinorgbio.2024.112534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
The family of flavodiiron proteins (FDPs) plays an important role in the scavenging and detoxification of both molecular oxygen and nitric oxide. Using electrons from a flavin mononucleotide cofactor molecular oxygen is reduced to water and nitric oxide is reduced to nitrous oxide and water. While the mechanism for NO reduction in FDPs has been studied extensively, there is very little information available about O2 reduction. Here we use hybrid density functional theory (DFT) to study the mechanism for O2 reduction in FDPs. An important finding is that a proton coupled reduction is needed after the O2 molecule has bound to the diferrous diiron active site and before the OO bond can be cleaved. This is in contrast to the mechanism for NO reduction, where both NN bond formation and NO bond cleavage occurs from the same starting structure without any further reduction, according to both experimental and computational results. This computational result for the O2 reduction mechanism should be possible to evaluate experimentally. Another difference between the two substrates is that the actual OO bond cleavage barrier is low, and not involved in rate-limiting the reduction process, while the barrier connected with bond cleavage/formation in the NO reduction process is of similar height as the rate-limiting steps. We suggest that these results may be part of the explanation for the generally higher activity for O2 reduction as compared to NO reduction in most FDPs. Comparisons are also made to the O2 reduction reaction in the family of heme‑copper oxidases.
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Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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3
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Martínez-Rosas V, Hernández-Ochoa B, Morales-Luna L, Ortega-Cuellar D, González-Valdez A, Arreguin-Espinosa R, Rufino-González Y, Calderón-Jaimes E, Castillo-Rodríguez RA, Wong-Baeza C, Baeza-Ramírez I, Pérez de la Cruz V, Vidal-Limón A, Gómez-Manzo S. Nitazoxanide Inhibits the Bifunctional Enzyme GlG6PD::6PGL of Giardia lamblia: Biochemical and In Silico Characterization of a New Druggable Target. Int J Mol Sci 2023; 24:11516. [PMID: 37511272 PMCID: PMC10380810 DOI: 10.3390/ijms241411516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/08/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Giardiasis, which is caused by Giardia lamblia infection, is a relevant cause of morbidity and mortality worldwide. Because no vaccines are currently available to treat giardiasis, chemotherapeutic drugs are the main options for controlling infection. Evidence has shown that the nitro drug nitazoxanide (NTZ) is a commonly prescribed treatment for giardiasis; however, the mechanisms underlying NTZ's antigiardial activity are not well-understood. Herein, we identified the glucose-6-phosphate::6-phosphogluconate dehydrogenase (GlG6PD::6PGL) fused enzyme as a nitazoxanide target, as NTZ behaves as a GlG6PD::6PGL catalytic inhibitor. Furthermore, fluorescence assays suggest alterations in the stability of GlG6PD::6PGL protein, whereas the results indicate a loss of catalytic activity due to conformational and folding changes. Molecular docking and dynamic simulation studies suggest a model of NTZ binding on the active site of the G6PD domain and near the structural NADP+ binding site. The findings of this study provide a novel mechanistic basis and strategy for the antigiardial activity of the NTZ drug.
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Affiliation(s)
- Víctor Martínez-Rosas
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Beatriz Hernández-Ochoa
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Mexico City 06720, Mexico
| | - Laura Morales-Luna
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Daniel Ortega-Cuellar
- Laboratorio de Nutrición Experimental, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Roberto Arreguin-Espinosa
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Yadira Rufino-González
- Laboratorio de Parasitología Experimental, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico
| | - Ernesto Calderón-Jaimes
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Mexico City 06720, Mexico
| | | | - Carlos Wong-Baeza
- Laboratorio de Biomembranas, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Isabel Baeza-Ramírez
- Laboratorio de Biomembranas, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Verónica Pérez de la Cruz
- Neurobiochemistry and Behavior Laboratory, National Institute of Neurology and Neurosurgery "Manuel Velasco Suárez", Mexico City 14269, Mexico
| | - Abraham Vidal-Limón
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec 351, El Haya, Xalapa 91073, Mexico
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico
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4
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DeMichele E, Sosnowski O, Buret AG, Allain T. Regulatory Functions of Hypoxia in Host-Parasite Interactions: A Focus on Enteric, Tissue, and Blood Protozoa. Microorganisms 2023; 11:1598. [PMID: 37375100 PMCID: PMC10303274 DOI: 10.3390/microorganisms11061598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Body tissues are subjected to various oxygenic gradients and fluctuations and hence can become transiently hypoxic. Hypoxia-inducible factor (HIF) is the master transcriptional regulator of the cellular hypoxic response and is capable of modulating cellular metabolism, immune responses, epithelial barrier integrity, and local microbiota. Recent reports have characterized the hypoxic response to various infections. However, little is known about the role of HIF activation in the context of protozoan parasitic infections. Growing evidence suggests that tissue and blood protozoa can activate HIF and subsequent HIF target genes in the host, helping or hindering their pathogenicity. In the gut, enteric protozoa are adapted to steep longitudinal and radial oxygen gradients to complete their life cycle, yet the role of HIF during these protozoan infections remains unclear. This review focuses on the hypoxic response to protozoa and its role in the pathophysiology of parasitic infections. We also discuss how hypoxia modulates host immune responses in the context of protozoan infections.
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Affiliation(s)
- Emily DeMichele
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada; (E.D.); (O.S.); (A.G.B.)
- Inflammation Research Network, University of Calgary, Calgary, AB T2N 1N4, Canada
- Host-Parasite Interactions, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Olivia Sosnowski
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada; (E.D.); (O.S.); (A.G.B.)
- Inflammation Research Network, University of Calgary, Calgary, AB T2N 1N4, Canada
- Host-Parasite Interactions, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Andre G. Buret
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada; (E.D.); (O.S.); (A.G.B.)
- Inflammation Research Network, University of Calgary, Calgary, AB T2N 1N4, Canada
- Host-Parasite Interactions, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Thibault Allain
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada; (E.D.); (O.S.); (A.G.B.)
- Inflammation Research Network, University of Calgary, Calgary, AB T2N 1N4, Canada
- Host-Parasite Interactions, University of Calgary, Calgary, AB T2N 1N4, Canada
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5
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Abdulaziz EN, Bell TA, Rashid B, Heacock ML, Begic T, Skinner OS, Yaseen MA, Chao LH, Mootha VK, Pierik AJ, Cracan V. A natural fusion of flavodiiron, rubredoxin, and rubredoxin oxidoreductase domains is a self-sufficient water-forming oxidase of Trichomonas vaginalis. J Biol Chem 2022; 298:102210. [PMID: 35780837 PMCID: PMC9364112 DOI: 10.1016/j.jbc.2022.102210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 11/29/2022] Open
Abstract
Microaerophilic pathogens such as Giardia lamblia, Entamoeba histolytica, and Trichomonas vaginalis have robust oxygen consumption systems to detoxify oxygen and maintain intracellular redox balance. This oxygen consumption results from H2O-forming NADH oxidase (NOX) activity of two distinct flavin-containing systems: H2O-forming NOXes and multicomponent flavodiiron proteins (FDPs). Neither system is membrane bound, and both recycle NADH into oxidized NAD+ while simultaneously removing O2 from the local environment. However, little is known about the specific contributions of these systems in T. vaginalis. In this study, we use bioinformatics and biochemical analyses to show that T. vaginalis lacks a NOX-like enzyme and instead harbors three paralogous genes (FDPF1-3), each encoding a natural fusion product between the N-terminal FDP, central rubredoxin (Rb), and C-terminal NADH:Rb oxidoreductase domains. Unlike a "stand-alone" FDP that lacks Rb and oxidoreductase domains, this natural fusion protein with fully populated flavin redox centers directly accepts reducing equivalents of NADH to catalyze the four-electron reduction of oxygen to water within a single polypeptide with an extremely high turnover. Furthermore, using single-particle cryo-EM, we present structural insights into the spatial organization of the FDP core within this multidomain fusion protein. Together, these results contribute to our understanding of systems that allow protozoan parasites to maintain optimal redox balance and survive transient exposure to oxic conditions.
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Affiliation(s)
- Evana N Abdulaziz
- Redox Biology and Metabolism Laboratory, Scintillon Institute, San Diego, California, USA
| | - Tristan A Bell
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bazlur Rashid
- Faculty of Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Mina L Heacock
- Redox Biology and Metabolism Laboratory, Scintillon Institute, San Diego, California, USA
| | - Tarik Begic
- Faculty of Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Owen S Skinner
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Mohammad A Yaseen
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Vamsi K Mootha
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Antonio J Pierik
- Faculty of Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Valentin Cracan
- Redox Biology and Metabolism Laboratory, Scintillon Institute, San Diego, California, USA; Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.
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6
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Souza JB, Tsantarlis K, Tonelli RR. Oxygen-dependent regulation of permeability in low resistance intestinal epithelial cells infected with Giardia lamblia. Exp Parasitol 2022; 240:108329. [PMID: 35868574 DOI: 10.1016/j.exppara.2022.108329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 06/22/2022] [Accepted: 07/11/2022] [Indexed: 11/26/2022]
Abstract
Intestinal epithelial cells (IECs) reside in a highly anaerobic environment that is subject to daily fluctuations in partial oxygen pressure (pO2), depending on intestinal tissue perfusion. This condition, known as physiological hypoxia, has a major impact on the maintenance of gut homeostasis, such as effects on the integrity and function of the intestinal epithelial barrier. Giardia lamblia is a microaerophilic protozoan parasite that infects and colonizes the small intestine of its host, causing watery diarrhea. The disease, known as giardiasis, is associated with enhanced intestinal permeability and disruption or reorganization of tight junction (TJ) proteins between IECs. Given the central role of oxygen in gut homeostasis, in this study, we aimed to evaluate whether pO2 affects intestinal permeability (flux of ions and macromolecules) and TJ protein expression in human IECs during G. lamblia infection. Using human cell lines HuTu-80 and Caco-2 as models of "loose" (low resistance) and "tight" (high resistance) intestines, respectively, we elucidated that low pO2 drives intestinal barrier dysfunction in IECs infected with trophozoites through dephosphorylation of protein kinase C (PKC α/β II). Additionally, we demonstrated that IECs infected with trophozoites in the presence of a pharmacological PKC activator (phorbol 12-myristate 13-acetate) partially restored the barrier function, which was correlated with increased protein expression levels of zonula occludens (ZO)-2 and occludin. Collectively, these results support the emerging theory that molecular oxygen impacts gut homeostasis during Giardia infection via direct host signaling pathways. These findings further our knowledge regarding Giardia-host interactions and the pathophysiological mechanisms of human giardiasis.
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Affiliation(s)
- Juliana Bizarri Souza
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, 04023-062, São Paulo, SP, Brazil
| | - Katherine Tsantarlis
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, 04023-062, São Paulo, SP, Brazil
| | - Renata Rosito Tonelli
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, 04023-062, São Paulo, SP, Brazil; Departamento de Ciências Farmacêuticas, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, 09913-030, Diadema, SP, Brazil.
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7
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Tachezy J, Makki A, Hrdý I. The hydrogenosomes of Trichomonas vaginalis. J Eukaryot Microbiol 2022; 69:e12922. [PMID: 35567536 DOI: 10.1111/jeu.12922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This review is dedicated to the 50th anniversary of the discovery of hydrogenosomes by Miklós Müller and Donald Lindmark, which we will celebrate the following year. It was a long journey from the first observation of enigmatic rows of granules in trichomonads at the end of the 19th century to their first biochemical characterization in 1973. The key experiments by Müller and Lindmark revealed that the isolated granules contain hydrogen-producing hydrogenase, similar to some anaerobic bacteria-a discovery that gave birth to the field of hydrogenosomes. It is also important to acknowledge the parallel work of the team of Apolena Čerkasovová, Jiří Čerkasov, and Jaroslav Kulda, who demonstrated that these granules, similar to mitochondria, produce ATP. However, the evolutionary origin of hydrogenosomes remained enigmatic until the turn of the millennium, when it was finally accepted that hydrogenosomes and mitochondria evolved from a common ancestor. After a historical introduction, the review provides an overview of hydrogenosome biogenesis, hydrogenosomal protein import, and the relationship between the peculiar structure of membrane translocases and its low inner membrane potential due to the lack of respiratory complexes. Next, it summarizes the current state of knowledge on energy metabolism, the oxygen defense system, and iron/sulfur cluster assembly.
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Affiliation(s)
- Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
| | - Abhijith Makki
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
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8
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Krakovka S, Ribacke U, Miyamoto Y, Eckmann L, Svärd S. Characterization of Metronidazole-Resistant Giardia intestinalis Lines by Comparative Transcriptomics and Proteomics. Front Microbiol 2022; 13:834008. [PMID: 35222342 PMCID: PMC8866875 DOI: 10.3389/fmicb.2022.834008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/13/2022] [Indexed: 12/13/2022] Open
Abstract
Metronidazole (MTZ) is a clinically important antimicrobial agent that is active against both bacterial and protozoan organisms. MTZ has been used extensively for more than 60 years and until now resistance has been rare. However, a recent and dramatic increase in the number of MTZ resistant bacteria and protozoa is of great concern since there are few alternative drugs with a similarly broad activity spectrum. To identify key factors and mechanisms underlying MTZ resistance, we utilized the protozoan parasite Giardia intestinalis, which is commonly treated with MTZ. We characterized two in vitro selected, metronidazole resistant parasite lines, as well as one revertant, by analyzing fitness aspects associated with increased drug resistance and transcriptomes and proteomes. We also conducted a meta-analysis using already existing data from additional resistant G. intestinalis isolates. The combined data suggest that in vitro generated MTZ resistance has a substantial fitness cost to the parasite, which may partly explain why resistance is not widespread despite decades of heavy use. Mechanistically, MTZ resistance in Giardia is multifactorial and associated with complex changes, yet a core set of pathways involving oxidoreductases, oxidative stress responses and DNA repair proteins, is central to MTZ resistance in both bacteria and protozoa.
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Affiliation(s)
- Sascha Krakovka
- Department of Cell and Molecular Biology, Biomedical Center (BMC), Uppsala University, Uppsala, Sweden
| | - Ulf Ribacke
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Yukiko Miyamoto
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Lars Eckmann
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Staffan Svärd
- Department of Cell and Molecular Biology, Biomedical Center (BMC), Uppsala University, Uppsala, Sweden.,SciLifeLab, Uppsala University, Uppsala, Sweden
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9
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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: 96] [Impact Index Per Article: 32.0] [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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10
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Oxygen levels are key to understanding "Anaerobic" protozoan pathogens with micro-aerophilic lifestyles. Adv Microb Physiol 2021; 79:163-240. [PMID: 34836611 DOI: 10.1016/bs.ampbs.2021.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Publications abound on the physiology, biochemistry and molecular biology of "anaerobic" protozoal parasites as usually grown under "anaerobic" culture conditions. The media routinely used are poised at low redox potentials using techniques that remove O2 to "undetectable" levels in sealed containers. However there is growing understanding that these culture conditions do not faithfully resemble the O2 environments these organisms inhabit. Here we review for protists lacking oxidative energy metabolism, the oxygen cascade from atmospheric to intracellular concentrations and relevant methods of measurements of O2, some well-studied parasitic or symbiotic protozoan lifestyles, their homeodynamic metabolic and redox balances, organism-drug-oxygen interactions, and the present and future prospects for improved drugs and treatment regimes.
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11
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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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12
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Miller KR, Biswas S, Jasniewski A, Follmer AH, Biswas A, Albert T, Sabuncu S, Bominaar EL, Hendrich MP, Moënne-Loccoz P, Borovik AS. Artificial Metalloproteins with Dinuclear Iron-Hydroxido Centers. J Am Chem Soc 2021; 143:2384-2393. [PMID: 33528256 DOI: 10.1021/jacs.0c12564] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Dinuclear iron centers with a bridging hydroxido or oxido ligand form active sites within a variety of metalloproteins. A key feature of these sites is the ability of the protein to control the structures around the Fe centers, which leads to entatic states that are essential for function. To simulate this controlled environment, artificial proteins have been engineered using biotin-streptavidin (Sav) technology in which Fe complexes from adjacent subunits can assemble to form [FeIII-(μ-OH)-FeIII] cores. The assembly process is promoted by the site-specific localization of the Fe complexes within a subunit through the designed mutation of a tyrosinate side chain to coordinate the Fe centers. An important outcome is that the Sav host can regulate the Fe···Fe separation, which is known to be important for function in natural metalloproteins. Spectroscopic and structural studies from X-ray diffraction methods revealed uncommonly long Fe···Fe separations that change by less than 0.3 Å upon the binding of additional bridging ligands. The structural constraints imposed by the protein host on the di-Fe cores are unique and create examples of active sites having entatic states within engineered artificial metalloproteins.
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Affiliation(s)
- Kelsey R Miller
- Department of Chemistry, 1102 Natural Sciences II, University of California, Irvine, California 92697, United States
| | - Saborni Biswas
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Andrew Jasniewski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Alec H Follmer
- Department of Chemistry, 1102 Natural Sciences II, University of California, Irvine, California 92697, United States
| | - Ankita Biswas
- Department of Chemistry, 1102 Natural Sciences II, University of California, Irvine, California 92697, United States
| | - Therese Albert
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Mail Code HRC3, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Sinan Sabuncu
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Mail Code HRC3, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Emile L Bominaar
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Michael P Hendrich
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Pierre Moënne-Loccoz
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Mail Code HRC3, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - A S Borovik
- Department of Chemistry, 1102 Natural Sciences II, University of California, Irvine, California 92697, United States
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13
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Nitroreductase Activites in Giardia lamblia: ORF 17150 Encodes a Quinone Reductase with Nitroreductase Activity. Pathogens 2021; 10:pathogens10020129. [PMID: 33513906 PMCID: PMC7912051 DOI: 10.3390/pathogens10020129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/12/2021] [Accepted: 01/22/2021] [Indexed: 02/05/2023] Open
Abstract
The intestinal diplomonadid Giardia lamblia is a causative agent of persistent diarrhea. Current treatments are based on nitro drugs, especially metronidazole. Nitro compounds are activated by reduction, yielding toxic intermediates. The enzymatic systems responsible for this activation are not completely understood. By fractionating cell free crude extracts by size exclusion chromatography followed by mass spectrometry, enzymes with nitroreductase (NR) activities are identified. The protein encoded by ORF 17150 found in two pools with NR activities is overexpressed and characterized. In pools of fractions with main NR activities, previously-known NRs are identified, as well as a previously uncharacterized protein encoded by ORF 17150. Recombinant protein 17150 is a flavoprotein with NADPH-dependent quinone reductase and NR activities. Besides a set of previously identified NRs, we have identified a novel enzyme with NR activity.
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14
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Rubredoxin from the green sulfur bacterium Chlorobaculum tepidum donates a redox equivalent to the flavodiiron protein in an NAD(P)H dependent manner via ferredoxin-NAD(P) + oxidoreductase. Arch Microbiol 2020; 203:799-808. [PMID: 33051772 DOI: 10.1007/s00203-020-02079-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/24/2020] [Accepted: 10/01/2020] [Indexed: 10/23/2022]
Abstract
The green sulfur bacterium, Chlorobaculum tepidum, is an anaerobic photoautotroph that performs anoxygenic photosynthesis. Although genes encoding rubredoxin (Rd) and a putative flavodiiron protein (FDP) were reported in the genome, a gene encoding putative NADH-Rd oxidoreductase is not identified. In this work, we expressed and purified the recombinant Rd and FDP and confirmed dioxygen reductase activity in the presence of ferredoxin-NAD(P)+ oxidoreductase (FNR). FNR from C. tepidum and Bacillus subtilis catalyzed the reduction of Rd at rates comparable to those reported for NADH-Rd oxidoreductases. Also, we observed substrate inhibition at high concentrations of NADPH similar to that observed with ferredoxins. In the presence of NADPH, B. subtilis FNR and Rd, FDP promoted dioxygen reduction at rates comparable to those reported for other bacterial FDPs. Taken together, our results suggest that Rd and FDP participate in the reduction of dioxygen in C. tepidum and that FNR can promote the reduction of Rd in this bacterium.
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15
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Abstract
Although the gastrointestinal tract is regarded as mainly anoxic, low O2 tension is present in the gut and tends to increase following antibiotic-induced disruption of the host microbiota. Two decreasing O2 gradients are observed, a longitudinal one from the small to the large intestine and a second one from the intestinal epithelium toward the colon lumen. Thus, O2 concentration fluctuations within the gastrointestinal tract are a challenge for anaerobic bacteria such as C. difficile. This enteropathogen has developed efficient strategies to detoxify O2. In this work, we identified reverse rubrerythrins and flavodiiron proteins as key actors for O2 tolerance in C. difficile. These enzymes are responsible for the reduction of O2 protecting C. difficile vegetative cells from associated damages. Original and complex detoxification pathways involving O2-reductases are crucial in the ability of C. difficile to tolerate O2 and survive to O2 concentrations encountered in the gastrointestinal tract. Clostridioides difficile is a major cause of diarrhea associated with antibiotherapy. After germination of C. difficile spores in the small intestine, vegetative cells are exposed to low oxygen (O2) tensions. While considered strictly anaerobic, C. difficile is able to grow in nonstrict anaerobic conditions (1 to 3% O2) and tolerates brief air exposure indicating that this bacterium harbors an arsenal of proteins involved in O2 detoxification and/or protection. Tolerance of C. difficile to low O2 tensions requires the presence of the alternative sigma factor, σB, involved in the general stress response. Among the genes positively controlled by σB, four encode proteins likely involved in O2 detoxification: two flavodiiron proteins (FdpA and FdpF) and two reverse rubrerythrins (revRbr1 and revRbr2). As previously observed for FdpF, we showed that both purified revRbr1 and revRbr2 harbor NADH-linked O2- and H2O2-reductase activities in vitro, while purified FdpA mainly acts as an O2-reductase. The growth of a fdpA mutant is affected at 0.4% O2, while inactivation of both revRbrs leads to a growth defect above 0.1% O2. O2-reductase activities of these different proteins are additive since the quadruple mutant displays a stronger phenotype when exposed to low O2 tensions compared to the triple mutants. Our results demonstrate a key role for revRbrs, FdpF, and FdpA proteins in the ability of C. difficile to grow in the presence of physiological O2 tensions such as those encountered in the colon.
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16
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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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17
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Ferousi C, Majer SH, DiMucci IM, Lancaster KM. Biological and Bioinspired Inorganic N-N Bond-Forming Reactions. Chem Rev 2020; 120:5252-5307. [PMID: 32108471 PMCID: PMC7339862 DOI: 10.1021/acs.chemrev.9b00629] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.
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Affiliation(s)
- Christina Ferousi
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Sean H Majer
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Ida M DiMucci
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
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18
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Jiménez-González A, Xu F, Andersson JO. Lateral Acquisitions Repeatedly Remodel the Oxygen Detoxification Pathway in Diplomonads and Relatives. Genome Biol Evol 2020; 11:2542-2556. [PMID: 31504492 PMCID: PMC6934886 DOI: 10.1093/gbe/evz188] [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] [Accepted: 08/19/2019] [Indexed: 12/13/2022] Open
Abstract
Oxygen and reactive oxygen species (ROS) are important stress factors for cells because they can oxidize many large molecules. Fornicata, a group of flagellated protists that includes diplomonads, have anaerobic metabolism but are still able to tolerate fluctuating levels of oxygen. We identified 25 protein families putatively involved in detoxification of oxygen and ROS in this group using a bioinformatics approach and propose how these interact in an oxygen detoxification pathway. These protein families were divided into a central oxygen detoxification pathway and accessory pathways for the synthesis of nonprotein thiols. We then used a phylogenetic approach to investigate the evolutionary origin of the components of this putative pathway in Diplomonadida and other Fornicata species. Our analyses suggested that the diplomonad ancestor was adapted to low-oxygen levels, was able to reduce O2 to H2O in a manner similar to extant diplomonads, and was able to synthesize glutathione and l-cysteine. Several genes involved in the pathway have complex evolutionary histories and have apparently been repeatedly acquired through lateral gene transfer and subsequently lost. At least seven genes were acquired independently in different Fornicata lineages, leading to evolutionary convergences. It is likely that acquiring these oxygen detoxification proteins helped anaerobic organisms (like the parasitic Giardia intestinalis) adapt to low-oxygen environments (such as the digestive tract of aerobic hosts).
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Affiliation(s)
- Alejandro Jiménez-González
- Uppsala Biomedicine Centre, Department of Cell and Molecular Biology, Molecular Evolution Program, Uppsala University, Sweden
| | - Feifei Xu
- Uppsala Biomedicine Centre, Department of Cell and Molecular Biology, Microbiology Program, Uppsala University, Sweden
| | - Jan O Andersson
- Uppsala Biomedicine Centre, Department of Cell and Molecular Biology, Molecular Evolution Program, Uppsala University, Sweden
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19
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Engilberge S, Wagner T, Carpentier P, Girard E, Shima S. Krypton-derivatization highlights O 2-channeling in a four-electron reducing oxidase. Chem Commun (Camb) 2020; 56:10863-10866. [DOI: 10.1039/d0cc04557h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Kr-derivatization and X-ray structures indicated O2-channel and gating-loop that prevent side-reaction in reduction of O2 to water in F420H2 oxidase.
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Affiliation(s)
| | - Tristan Wagner
- Microbial Metabolism Group
- Max-Planck-Institut für Marine Mikrobiologie
- Celsiusstraße 1
- Bremen
- Germany
| | - Philippe Carpentier
- Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Laboratoire Chimie et Biologie des Métaux (LCBM)
- Université Grenoble Alpes, CNRS, CEA
- Grenoble
- France
- European Synchrotron Radiation Facility (ESRF)
| | - Eric Girard
- Univ. Grenoble Alpes, CEA, CNRS, IBS
- F-38000 Grenoble
- France
| | - Seigo Shima
- Microbial Protein Structure Group
- Max Planck Institute for Terrestrial Microbiology
- Karl-von-Frisch Straße 10
- 35043 Marburg
- Germany
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20
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Role and regulation of class-C flavodiiron proteins in photosynthetic organisms. Biochem J 2019; 476:2487-2498. [DOI: 10.1042/bcj20180648] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 12/29/2022]
Abstract
Abstract
The regulation of photosynthesis is crucial to efficiently support the assimilation of carbon dioxide and to prevent photodamage. One key regulatory mechanism is the pseudo-cyclic electron flow (PCEF) mediated by class-C flavodiiron proteins (FLVs). These enzymes use electrons coming from Photosystem I (PSI) to reduce oxygen to water, preventing over-reduction in the acceptor side of PSI. FLVs are widely distributed among organisms performing oxygenic photosynthesis and they have been shown to be fundamental in many different conditions such as fluctuating light, sulfur deprivation and plant submersion. Moreover, since FLVs reduce oxygen they can help controlling the redox status of the cell and maintaining the microoxic environment essential for processes such as nitrogen fixation in cyanobacteria. Despite these important roles identified in various species, the genes encoding for FLV proteins have been lost in angiosperms where their activity could have been at least partially compensated by a more efficient cyclic electron flow (CEF). The present work reviews the information emerged on FLV function, analyzing recent structural data that suggest FLV could be regulated through a conformational change.
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21
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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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22
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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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23
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Zimorski V, Mentel M, Tielens AGM, Martin WF. Energy metabolism in anaerobic eukaryotes and Earth's late oxygenation. Free Radic Biol Med 2019; 140:279-294. [PMID: 30935869 PMCID: PMC6856725 DOI: 10.1016/j.freeradbiomed.2019.03.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/21/2019] [Accepted: 03/26/2019] [Indexed: 01/09/2023]
Abstract
Eukaryotes arose about 1.6 billion years ago, at a time when oxygen levels were still very low on Earth, both in the atmosphere and in the ocean. According to newer geochemical data, oxygen rose to approximately its present atmospheric levels very late in evolution, perhaps as late as the origin of land plants (only about 450 million years ago). It is therefore natural that many lineages of eukaryotes harbor, and use, enzymes for oxygen-independent energy metabolism. This paper provides a concise overview of anaerobic energy metabolism in eukaryotes with a focus on anaerobic energy metabolism in mitochondria. We also address the widespread assumption that oxygen improves the overall energetic state of a cell. While it is true that ATP yield from glucose or amino acids is increased in the presence of oxygen, it is also true that the synthesis of biomass costs thirteen times more energy per cell in the presence of oxygen than in anoxic conditions. This is because in the reaction of cellular biomass with O2, the equilibrium lies very far on the side of CO2. The absence of oxygen offers energetic benefits of the same magnitude as the presence of oxygen. Anaerobic and low oxygen environments are ancient. During evolution, some eukaryotes have specialized to life in permanently oxic environments (life on land), other eukaryotes have remained specialized to low oxygen habitats. We suggest that the Km of mitochondrial cytochrome c oxidase of 0.1-10 μM for O2, which corresponds to about 0.04%-4% (avg. 0.4%) of present atmospheric O2 levels, reflects environmental O2 concentrations that existed at the time that the eukaryotes arose.
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Affiliation(s)
- Verena Zimorski
- Institute of Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany.
| | - Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 851 04, Bratislava, Slovakia.
| | - Aloysius G M Tielens
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center Rotterdam, The Netherlands; Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany.
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24
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Santana-Sanchez A, Solymosi D, Mustila H, Bersanini L, Aro EM, Allahverdiyeva Y. Flavodiiron proteins 1-to-4 function in versatile combinations in O 2 photoreduction in cyanobacteria. eLife 2019; 8:e45766. [PMID: 31294693 PMCID: PMC6658166 DOI: 10.7554/elife.45766] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/10/2019] [Indexed: 12/15/2022] Open
Abstract
Flavodiiron proteins (FDPs) constitute a group of modular enzymes widespread in Bacteria, Archaea and Eukarya. Synechocystis sp. PCC 6803 has four FDPs (Flv1-4), which are essential for the photoprotection of photosynthesis. A direct comparison of light-induced O2 reduction (Mehler-like reaction) under high (3% CO2, HC) and low (air level CO2, LC) inorganic carbon conditions demonstrated that the Flv1/Flv3 heterodimer is solely responsible for an efficient steady-state O2 photoreduction under HC, with flv2 and flv4 expression strongly down-regulated. Conversely, under LC conditions, Flv1/Flv3 acts only as a transient electron sink, due to the competing withdrawal of electrons by the highly induced NDH-1 complex. Further, in vivo evidence is provided indicating that Flv2/Flv4 contributes to the Mehler-like reaction when naturally expressed under LC conditions, or, when artificially overexpressed under HC. The O2 photoreduction driven by Flv2/Flv4 occurs down-stream of PSI in a coordinated manner with Flv1/Flv3 and supports slow and steady-state O2 photoreduction.
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Affiliation(s)
| | - Daniel Solymosi
- Molecular Plant Biology, Department of BiochemistryUniversity of TurkuTurkuFinland
| | - Henna Mustila
- Molecular Plant Biology, Department of BiochemistryUniversity of TurkuTurkuFinland
| | - Luca Bersanini
- Molecular Plant Biology, Department of BiochemistryUniversity of TurkuTurkuFinland
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of BiochemistryUniversity of TurkuTurkuFinland
| | - Yagut Allahverdiyeva
- Molecular Plant Biology, Department of BiochemistryUniversity of TurkuTurkuFinland
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25
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Saghaug CS, Klotz C, Kallio JP, Brattbakk HR, Stokowy T, Aebischer T, Kursula I, Langeland N, Hanevik K. Genetic variation in metronidazole metabolism and oxidative stress pathways in clinical Giardia lamblia assemblage A and B isolates. Infect Drug Resist 2019; 12:1221-1235. [PMID: 31190910 PMCID: PMC6519707 DOI: 10.2147/idr.s177997] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/16/2019] [Indexed: 12/12/2022] Open
Abstract
Purpose: Treatment-refractory Giardia cases have increased rapidly within the last decade. No markers of resistance nor a standardized susceptibility test have been established yet, but several enzymes and their pathways have been associated with metronidazole (MTZ) resistant Giardia. Very limited data are available regarding genetic variation in these pathways. We aimed to investigate genetic variation in metabolic pathway genes proposed to be involved in MTZ resistance in recently acquired, cultured clinical isolates. Methods: Whole genome sequencing of 12 assemblage A2 and 8 assemblage B isolates was done, to decipher genomic variation in Giardia. Twenty-nine genes were identified in a literature search and investigated for their single nucleotide variants (SNVs) in the coding/non-coding regions of the genes, either as amino acid changing (non-synonymous SNVs) or non-changing SNVs (synonymous). Results: In Giardia assemblage B, several genes involved in MTZ activation or oxidative stress management were found to have higher numbers of non-synonymous SNVs (thioredoxin peroxidase, nitroreductase 1, ferredoxin 2, NADH oxidase, nitroreductase 2, alcohol dehydrogenase, ferredoxin 4 and ferredoxin 1) than the average variation. For Giardia assemblage A2, the highest genetic variability was found in the ferredoxin 2, ferredoxin 6 and in nicotinamide adenine dinucleotide phosphate (NADPH) oxidoreductase putative genes. SNVs found in the ferredoxins and nitroreductases were analyzed further by alignment and homology modeling. SNVs close to the iron-sulfur cluster binding sites in nitroreductase-1 and 2 and ferredoxin 2 and 4 could potentially affect protein function. Flavohemoprotein seems to be a variable-copy gene, due to higher, but variable coverage compared to other genes investigated. Conclusion: In clinical Giardia isolates, genetic variability is common in important genes in the MTZ metabolizing pathway and in the management of oxidative and nitrosative stress and includes high numbers of non-synonymous SNVs. Some of the identified amino acid changes could potentially affect the respective proteins important in the MTZ metabolism.
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Affiliation(s)
- Christina S Saghaug
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway
| | - Christian Klotz
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Juha P Kallio
- Department of Biomedicine, University of Bergen, Bergen, Hordaland, Norway
| | - Hans-Richard Brattbakk
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway
| | - Tomasz Stokowy
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway
| | - Toni Aebischer
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Inari Kursula
- Department of Biomedicine, University of Bergen, Bergen, Hordaland, Norway.,Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway.,Department of Medicine, Haraldsplass Deaconess Hospital, Bergen, Hordaland, Norway
| | - Kurt Hanevik
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway
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26
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Pernil R, Schleiff E. Metalloproteins in the Biology of Heterocysts. Life (Basel) 2019; 9:E32. [PMID: 30987221 PMCID: PMC6616624 DOI: 10.3390/life9020032] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/18/2019] [Accepted: 03/28/2019] [Indexed: 12/15/2022] Open
Abstract
Cyanobacteria are photoautotrophic microorganisms present in almost all ecologically niches on Earth. They exist as single-cell or filamentous forms and the latter often contain specialized cells for N₂ fixation known as heterocysts. Heterocysts arise from photosynthetic active vegetative cells by multiple morphological and physiological rearrangements including the absence of O₂ evolution and CO₂ fixation. The key function of this cell type is carried out by the metalloprotein complex known as nitrogenase. Additionally, many other important processes in heterocysts also depend on metalloproteins. This leads to a high metal demand exceeding the one of other bacteria in content and concentration during heterocyst development and in mature heterocysts. This review provides an overview on the current knowledge of the transition metals and metalloproteins required by heterocysts in heterocyst-forming cyanobacteria. It discusses the molecular, physiological, and physicochemical properties of metalloproteins involved in N₂ fixation, H₂ metabolism, electron transport chains, oxidative stress management, storage, energy metabolism, and metabolic networks in the diazotrophic filament. This provides a detailed and comprehensive picture on the heterocyst demands for Fe, Cu, Mo, Ni, Mn, V, and Zn as cofactors for metalloproteins and highlights the importance of such metalloproteins for the biology of cyanobacterial heterocysts.
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Affiliation(s)
- Rafael Pernil
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straβe 9, 60438 Frankfurt am Main, Germany.
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straβe 9, 60438 Frankfurt am Main, Germany.
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straβe 15, 60438 Frankfurt am Main, Germany.
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27
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Degli Esposti M, Mentel M, Martin W, Sousa FL. Oxygen Reductases in Alphaproteobacterial Genomes: Physiological Evolution From Low to High Oxygen Environments. Front Microbiol 2019; 10:499. [PMID: 30936856 PMCID: PMC6431628 DOI: 10.3389/fmicb.2019.00499] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/27/2019] [Indexed: 01/24/2023] Open
Abstract
Oxygen reducing terminal oxidases differ with respect to their subunit composition, heme groups, operon structure, and affinity for O2. Six families of terminal oxidases are currently recognized, all of which occur in alphaproteobacterial genomes, two of which are also present in mitochondria. Many alphaproteobacteria encode several different terminal oxidases, likely reflecting ecological versatility with respect to oxygen levels. Terminal oxidase evolution likely started with the advent of O2 roughly 2.4 billion years ago and terminal oxidases diversified in the Proterozoic, during which oxygen levels remained low, around the Pasteur point (ca. 2 μM O2). Among the alphaproteobacterial genomes surveyed, those from members of the Rhodospirillaceae reveal the greatest diversity in oxygen reductases. Some harbor all six terminal oxidase types, in addition to many soluble enzymes typical of anaerobic fermentations in mitochondria and hydrogenosomes of eukaryotes. Recent data have it that O2 levels increased to current values (21% v/v or ca. 250 μM) only about 430 million years ago. Ecological adaptation brought forth different lineages of alphaproteobacteria and different lineages of eukaryotes that have undergone evolutionary specialization to high oxygen, low oxygen, and anaerobic habitats. Some have remained facultative anaerobes that are able to generate ATP with or without the help of oxygen and represent physiological links to the ancient proteobacterial lineage at the origin of mitochondria and eukaryotes. Our analysis reveals that the genomes of alphaproteobacteria appear to retain signatures of ancient transitions in aerobic metabolism, findings that are relevant to mitochondrial evolution in eukaryotes as well.
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Affiliation(s)
| | - Marek Mentel
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Bratislava, Slovakia
| | - William Martin
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Filipa L Sousa
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
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28
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Müller J, Braga S, Heller M, Müller N. Resistance formation to nitro drugs in Giardia lamblia: No common markers identified by comparative proteomics. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2019; 9:112-119. [PMID: 30889439 PMCID: PMC6423486 DOI: 10.1016/j.ijpddr.2019.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/15/2019] [Accepted: 03/12/2019] [Indexed: 02/07/2023]
Abstract
In order to elucidate the question whether resistance to nitro drugs in G. lamblia is due to common resistance markers, trophozoites of three resistant G. lamblia strains, namely C4, 1062ID10, and 713M3 were grown in the presence of the two nitro drugs metronidazole and nitazoxanide and compared to their corresponding wild-types WBC6, 106, and 713 by mass spectometry shotgun analysis of their proteomes. Depending on the strain and the nitro drug, more than 200 to 500 differentially expressed proteins were identified, but there were no common patterns across strains and drugs. All resistant strains underwent antigenic variation with distinct surface antigens like variant surface proteins or cysteine rich proteins depending on strain and nitro compound. A closer look on enzymes involved in nitroreduction and detoxification of nitro radicals, NO or O2 suggested the existence of distinct strategies for each drug and each strain. Therefore, we conclude that resistance to nitro drugs in G. lamblia is not correlated with a specific pattern of differentially expressed proteins and therefore seems not to be the result of a directed process. Is resistance to nitro drugs in G. lamblia due to common resistance markers? Three resistant strains were grown in the presence of two nitro drugs separately and compared to wild-types by MS shotgun analysis. More than 200 to 500 differentially expressed proteins identified depending on strain and drug. No common patterns across strains and drugs. Strain specific antigenic variation and strategies linked to nitro reduction.
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Affiliation(s)
- Joachim Müller
- Institute of Parasitology, Vetsuisse Faculty, University of Berne, Länggass-Strasse 122, CH-3012, Berne, Switzerland.
| | - Sophie Braga
- Proteomics & Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Berne, Freiburgstrasse 15, CH-3010, Berne, Switzerland.
| | - Manfred Heller
- Proteomics & Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Berne, Freiburgstrasse 15, CH-3010, Berne, Switzerland.
| | - Norbert Müller
- Institute of Parasitology, Vetsuisse Faculty, University of Berne, Länggass-Strasse 122, CH-3012, Berne, Switzerland.
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29
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Stairs CW, Kokla A, Ástvaldsson Á, Jerlström-Hultqvist J, Svärd S, Ettema TJG. Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida. BMC Biol 2019; 17:19. [PMID: 30823887 PMCID: PMC6397501 DOI: 10.1186/s12915-019-0634-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/06/2019] [Indexed: 01/01/2023] Open
Abstract
Background Spironucleus salmonicida is an anaerobic parasite that can cause systemic infections in Atlantic salmon. Unlike other diplomonad parasites, such as the human pathogen Giardia intestinalis, Spironucleus species can infiltrate the blood stream of their hosts eventually colonizing organs, skin and gills. How this presumed anaerobe can persist and invade oxygenated tissues, despite having a strictly anaerobic metabolism, remains elusive. Results To investigate how S. salmonicida response to oxygen stress, we performed RNAseq transcriptomic analyses of cells grown in the presence of oxygen or antioxidant-free medium. We found that over 20% of the transcriptome is differentially regulated in oxygen (1705 genes) and antioxidant-depleted (2280 genes) conditions. These differentially regulated transcripts encode proteins related to anaerobic metabolism, cysteine and Fe-S cluster biosynthesis, as well as a large number of proteins of unknown function. S. salmonicida does not encode genes involved in the classical elements of oxygen metabolism (e.g., catalases, superoxide dismutase, glutathione biosynthesis, oxidative phosphorylation). Instead, we found that genes encoding bacterial-like oxidoreductases were upregulated in response to oxygen stress. Phylogenetic analysis revealed some of these oxygen-responsive genes (e.g., nadh oxidase, rubrerythrin, superoxide reductase) are rare in eukaryotes and likely derived from lateral gene transfer (LGT) events into diplomonads from prokaryotes. Unexpectedly, we observed that many host evasion- and invasion-related genes were also upregulated under oxidative stress suggesting that oxygen might be an important signal for pathogenesis. Conclusion While oxygen is toxic for related organisms, such as G. intestinalis, we find that oxygen is likely a gene induction signal for host invasion- and evasion-related pathways in S. salmonicida. These data provide the first molecular evidence for how S. salmonicida could tolerate oxic host environments and demonstrate how LGT can have a profound impact on the biology of anaerobic parasites. Electronic supplementary material The online version of this article (10.1186/s12915-019-0634-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Courtney W Stairs
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
| | - Anna Kokla
- Present Address: Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Almas Allé 5, BioCentrum, room D-444, Uppsala, Sweden
| | - Ásgeir Ástvaldsson
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Jon Jerlström-Hultqvist
- Present Address: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Staffan Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
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30
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Borges PT, Romão CV, Saraiva LM, Gonçalves VL, Carrondo MA, Teixeira M, Frazão C. Analysis of a new flavodiiron core structural arrangement in Flv1-ΔFlR protein from Synechocystis sp. PCC6803. J Struct Biol 2019; 205:91-102. [DOI: 10.1016/j.jsb.2018.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/24/2018] [Accepted: 11/09/2018] [Indexed: 12/11/2022]
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31
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Dubourg A, Xia D, Winpenny JP, Al Naimi S, Bouzid M, Sexton DW, Wastling JM, Hunter PR, Tyler KM. Giardia secretome highlights secreted tenascins as a key component of pathogenesis. Gigascience 2018; 7:1-13. [PMID: 29385462 PMCID: PMC5887430 DOI: 10.1093/gigascience/giy003] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 01/17/2018] [Indexed: 11/13/2022] Open
Abstract
Background Giardia is a protozoan parasite of public health relevance that causes gastroenteritis in a wide range of hosts. Two genetically distinct lineages (assemblages A and B) are responsible for the human disease. Although it is clear that differences in virulence occur, the pathogenesis and virulence of Giardia remain poorly understood. Results The genome of Giardia is believed to contain open reading frames that could encode as many as 6000 proteins. By successfully applying quantitative proteomic analyses to the whole parasite and to the supernatants derived from parasite culture of assemblages A and B, we confirm expression of ∼1600 proteins from each assemblage, the vast majority of which are common to both lineages. To look for signature enrichment of secreted proteins, we considered the ratio of proteins in the supernatant compared with the pellet, which defined a small group of enriched proteins, putatively secreted at a steady state by cultured growing trophozoites of both assemblages. This secretome is enriched with proteins annotated to have N-terminal signal peptide. The most abundant secreted proteins include known virulence factors such as cathepsin B cysteine proteases and members of a Giardia superfamily of cysteine-rich proteins that comprise variant surface proteins, high-cysteine membrane proteins, and a new class of virulence factors, the Giardia tenascins. We demonstrate that physiological function of human enteric epithelial cells is disrupted by such soluble factors even in the absence of the trophozoites. Conclusions We are able to propose a straightforward model of Giardia pathogenesis incorporating key roles for the major Giardia-derived soluble mediators.
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Affiliation(s)
- Audrey Dubourg
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Dong Xia
- Department of Infection Biology, Institute of Infection and Global Health, Faculty of Health and Life Sciences, University of Liverpool, Liverpool Science Park IC2, 146 Brownlow Hill, Liverpool, L3 5RF, UK.,Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, University of London, London, NW1 0TU, UK
| | - John P Winpenny
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Suha Al Naimi
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Department of Science and Technology, Faculty of Health and Science, James Hehir Building, Neptune Quay, University of Suffolk, Ipswich, IP4 1QJ, UK
| | - Maha Bouzid
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Darren W Sexton
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Jonathan M Wastling
- Department of Infection Biology, Institute of Infection and Global Health, Faculty of Health and Life Sciences, University of Liverpool, Liverpool Science Park IC2, 146 Brownlow Hill, Liverpool, L3 5RF, UK.,Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - Paul R Hunter
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Kevin M Tyler
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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32
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Shimakawa G, Miyake C. Oxidation of P700 Ensures Robust Photosynthesis. FRONTIERS IN PLANT SCIENCE 2018; 9:1617. [PMID: 30459798 PMCID: PMC6232666 DOI: 10.3389/fpls.2018.01617] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/18/2018] [Indexed: 05/18/2023]
Abstract
In the light, photosynthetic cells can potentially suffer from oxidative damage derived from reactive oxygen species. Nevertheless, a variety of oxygenic photoautotrophs, including cyanobacteria, algae, and plants, manage their photosynthetic systems successfully. In the present article, we review previous research on how these photoautotrophs safely utilize light energy for photosynthesis without photo-oxidative damage to photosystem I (PSI). The reaction center chlorophyll of PSI, P700, is kept in an oxidized state in response to excess light, under high light and low CO2 conditions, to tune the light utilization and dissipate the excess photo-excitation energy in PSI. Oxidation of P700 is co-operatively regulated by a number of molecular mechanisms on both the electron donor and acceptor sides of PSI. The strategies to keep P700 oxidized are diverse among a variety of photoautotrophs, which are evolutionarily optimized for their ecological niche.
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Affiliation(s)
- Ginga Shimakawa
- Department of Biological and Environmental Science, Faculty of Agriculture, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Chikahiro Miyake
- Department of Biological and Environmental Science, Faculty of Agriculture, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- Core Research for Environmental Science and Technology, Japan Science and Technology Agency, Tokyo, Japan
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33
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The multidomain flavodiiron protein from Clostridium difficile 630 is an NADH:oxygen oxidoreductase. Sci Rep 2018; 8:10164. [PMID: 29977056 PMCID: PMC6033852 DOI: 10.1038/s41598-018-28453-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/20/2018] [Indexed: 01/05/2023] Open
Abstract
Flavodiiron proteins (FDPs) are enzymes with a minimal core of two domains: a metallo-β-lactamase-like, harbouring a diiron center, and a flavodoxin, FMN containing, domains. FDPs are O2 or NO reducing enzymes; for many pathogens, they help mitigate the NO produced by the immune system of the host, and aid survival during fluctuating concentrations concentrations of oxygen. FDPs have a mosaic structure, being predicted to contain multiple extra domains. Clostridium difficile, a threatening human pathogen, encodes two FDPs: one with the two canonical domains, and another with a larger polypeptide chain of 843 amino acids, CD1623, with two extra domains, predicted to be a short-rubredoxin-like and an NAD(P)H:rubredoxin oxidoreductase. This multi-domain protein is the most complex FDP characterized thus far. Each of the predicted domains was characterized and the presence of the predicted cofactors confirmed by biochemical and spectroscopic analysis. Results show that this protein operates as a standalone FDP, receiving electrons directly from NADH, and reducing oxygen to water, precluding the need for extra partners. CD1623 displayed negligible NO reductase activity, and is thus considered an oxygen selective FDP, that may contribute to the survival of C. difficile in the human gut and in the environment.
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34
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Leitsch D, Williams CF, Hrdý I. Redox Pathways as Drug Targets in Microaerophilic Parasites. Trends Parasitol 2018; 34:576-589. [PMID: 29807758 DOI: 10.1016/j.pt.2018.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 01/06/2023]
Abstract
The microaerophilic parasites Entamoeba histolytica, Trichomonas vaginalis, and Giardia lamblia jointly cause hundreds of millions of infections in humans every year. Other microaerophilic parasites such as Tritrichomonas foetus and Spironucleus spp. pose a relevant health problem in veterinary medicine. Unfortunately, vaccines against these pathogens are unavailable, but their microaerophilic lifestyle opens opportunities for specifically developed chemotherapeutics. In particular, their high sensitivity towards oxygen can be exploited by targeting redox enzymes. This review focusses on the redox pathways of microaerophilic parasites and on drugs, either already in use or currently in the state of development, which target these pathways.
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Affiliation(s)
- David Leitsch
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Austria.
| | - Catrin F Williams
- School of Engineering, Cardiff University, Cardiff, Wales, United Kingdom
| | - Ivan Hrdý
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
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35
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Müller J, Hemphill A, Müller N. Physiological aspects of nitro drug resistance in Giardia lamblia. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2018; 8:271-277. [PMID: 29738984 PMCID: PMC6039359 DOI: 10.1016/j.ijpddr.2018.04.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/24/2018] [Accepted: 04/26/2018] [Indexed: 11/01/2022]
Abstract
For over 50 years, metronidazole and other nitro compounds such as nitazoxanide have been used as a therapy of choice against giardiasis and more and more frequently, resistance formation has been observed. Model systems allowing studies on biochemical aspects of resistance formation to nitro drugs are, however, scarce since resistant strains are often unstable in culture. In order to fill this gap, we have generated a stable metronidazole- and nitazoxanide-resistant Giardia lamblia WBC6 clone, the strain C4. Previous studies on strain C4 and the corresponding wild-type strain WBC6 revealed marked differences in the transcriptomes of both strains. Here, we present a physiological comparison between trophozoites of both strains with respect to their ultrastructure, whole cell activities such as oxygen consumption and resazurin reduction assays, key enzyme activities, and several metabolic key parameters such as NAD(P)+/NAD(P)H and ADP/ATP ratios and FAD contents. We show that nitro compound-resistant C4 trophozoites exhibit lower nitroreductase activities, lower oxygen consumption and resazurin reduction rates, lower ornithine-carbamyl-transferase activity, reduced FAD and NADP(H) pool sizes and higher ADP/ATP ratios than wildtype trophozoites. The present results suggest that resistance formation against nitro compounds is correlated with metabolic adaptations resulting in a reduction of the activities of FAD-dependent oxidoreductases.
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Affiliation(s)
- Joachim Müller
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, CH-3012 Bern, Switzerland
| | - Andrew Hemphill
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, CH-3012 Bern, Switzerland
| | - Norbert Müller
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, CH-3012 Bern, Switzerland.
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36
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Pham JK, Nosala C, Scott EY, Nguyen KF, Hagen KD, Starcevich HN, Dawson SC. Transcriptomic Profiling of High-Density Giardia Foci Encysting in the Murine Proximal Intestine. Front Cell Infect Microbiol 2017; 7:227. [PMID: 28620589 PMCID: PMC5450421 DOI: 10.3389/fcimb.2017.00227] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/16/2017] [Indexed: 12/15/2022] Open
Abstract
Giardia is a highly prevalent, understudied protistan parasite causing significant diarrheal disease worldwide. Its life cycle consists of two stages: infectious cysts ingested from contaminated food or water sources, and motile trophozoites that colonize and attach to the gut epithelium, later encysting to form new cysts that are excreted into the environment. Current understanding of parasite physiology in the host is largely inferred from transcriptomic studies using Giardia grown axenically or in co-culture with mammalian cell lines. The dearth of information about the diversity of host-parasite interactions occurring within distinct regions of the gastrointestinal tract has been exacerbated by a lack of methods to directly and non-invasively interrogate disease progression and parasite physiology in live animal hosts. By visualizing Giardia infections in the mouse gastrointestinal tract using bioluminescent imaging (BLI) of tagged parasites, we recently showed that parasites colonize the gut in high-density foci. Encystation is initiated in these foci throughout the entire course of infection, yet how the physiology of parasites within high-density foci in the host gut differs from that of cells in laboratory culture is unclear. Here we use BLI to precisely select parasite samples from high-density foci in the proximal intestine to interrogate in vivo Giardia gene expression in the host. Relative to axenic culture, we noted significantly higher expression (>10-fold) of oxidative stress, membrane transporter, and metabolic and structural genes associated with encystation in the high-density foci. These differences in gene expression within parasite foci in the host may reflect physiological changes associated with high-density growth in localized regions of the gut. We also identified and verified six novel cyst-specific proteins, including new components of the cyst wall that were highly expressed in these foci. Our in vivo transcriptome data support an emerging view that parasites encyst early in localized regions in the gut, possibly as a consequence of nutrient limitation, and also impact local metabolism and physiology.
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Affiliation(s)
- Jonathan K Pham
- Department of Microbiology and Molecular Genetics, University of California, DavisDavis, CA, United States
| | - Christopher Nosala
- Department of Microbiology and Molecular Genetics, University of California, DavisDavis, CA, United States
| | - Erica Y Scott
- Department of Animal Science, University of California, DavisDavis, CA, United States
| | - Kristofer F Nguyen
- Department of Microbiology and Molecular Genetics, University of California, DavisDavis, CA, United States
| | - Kari D Hagen
- Department of Microbiology and Molecular Genetics, University of California, DavisDavis, CA, United States
| | - Hannah N Starcevich
- Department of Microbiology and Molecular Genetics, University of California, DavisDavis, CA, United States
| | - Scott C Dawson
- Department of Microbiology and Molecular Genetics, University of California, DavisDavis, CA, United States
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37
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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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Solomon EI, Park K. Structure/function correlations over binuclear non-heme iron active sites. J Biol Inorg Chem 2016; 21:575-88. [PMID: 27369780 PMCID: PMC5010389 DOI: 10.1007/s00775-016-1372-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/14/2016] [Indexed: 11/30/2022]
Abstract
Binuclear non-heme iron enzymes activate O2 to perform diverse chemistries. Three different structural mechanisms of O2 binding to a coupled binuclear iron site have been identified utilizing variable-temperature, variable-field magnetic circular dichroism spectroscopy (VTVH MCD). For the μ-OH-bridged Fe(II)2 site in hemerythrin, O2 binds terminally to a five-coordinate Fe(II) center as hydroperoxide with the proton deriving from the μ-OH bridge and the second electron transferring through the resulting μ-oxo superexchange pathway from the second coordinatively saturated Fe(II) center in a proton-coupled electron transfer process. For carboxylate-only-bridged Fe(II)2 sites, O2 binding as a bridged peroxide requires both Fe(II) centers to be coordinatively unsaturated and has good frontier orbital overlap with the two orthogonal O2 π* orbitals to form peroxo-bridged Fe(III)2 intermediates. Alternatively, carboxylate-only-bridged Fe(II)2 sites with only a single open coordination position on an Fe(II) enable the one-electron formation of Fe(III)-O2 (-) or Fe(III)-NO(-) species. Finally, for the peroxo-bridged Fe(III)2 intermediates, further activation is necessary for their reactivities in one-electron reduction and electrophilic aromatic substitution, and a strategy consistent with existing spectral data is discussed.
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Affiliation(s)
- Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, CA, 94305-5080, USA.
| | - Kiyoung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, 34141, Republic of Korea
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39
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Abstract
Mitochondrion-related organelles (MROs) have arisen independently in a wide range of anaerobic protist lineages. Only a few of these organelles and their functions have been investigated in detail, and most of what is known about MROs comes from studies of parasitic organisms such as the parabasalid Trichomonas vaginalis. Here, we describe the MRO of a free-living anaerobic jakobid excavate, Stygiella incarcerata. We report an RNAseq-based reconstruction of S. incarcerata’s MRO proteome, with an associated biochemical map of the pathways predicted to be present in this organelle. The pyruvate metabolism and oxidative stress response pathways are strikingly similar to those found in the MROs of other anaerobic protists, such as Pygsuia and Trichomonas. This elegant example of convergent evolution is suggestive of an anaerobic biochemical ‘module’ of prokaryotic origins that has been laterally transferred among eukaryotes, enabling them to adapt rapidly to anaerobiosis. We also identified genes corresponding to a variety of mitochondrial processes not found in Trichomonas, including intermembrane space components of the mitochondrial protein import apparatus, and enzymes involved in amino acid metabolism and cardiolipin biosynthesis. In this respect, the MROs of S. incarcerata more closely resemble those of the much more distantly related free-living organisms Pygsuia biforma and Cantina marsupialis, likely reflecting these organisms’ shared lifestyle as free-living anaerobes.
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Affiliation(s)
- Michelle M Leger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Laura Eme
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Laura A Hug
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
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40
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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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41
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Reduction potential and heme-pocket polarity in low potential cytochrome b5 of Giardia intestinalis. J Inorg Biochem 2016; 158:110-114. [PMID: 27048807 DOI: 10.1016/j.jinorgbio.2016.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 12/24/2015] [Accepted: 02/23/2016] [Indexed: 11/20/2022]
Abstract
Although it lacks mitochondria and the ability to synthesize heme, the protozoan parasite Giardia intestinalis encodes several heme proteins. This includes four members of the cytochrome b5 family, three of which are of similar size to mammalian cytochromes b5 but with reduction potentials that are 140 to 180mV lower. While no structures have yet been determined for any of these proteins, homology modeling points to an increase in heme pocket polarity as a reason for their low potentials. To test this we measured the reduction potentials of four mutants of Giardia cytochrome b5 isotype-I (gCYTB5-I) in which polar residues at two candidate positions (C84, Y51) in the heme pocket were changed to nonpolar ones (C84A, C84F; Y51L, Y51F). All mutants were expressed with comparable levels of heme incorporation and had UV-visible spectra consistent with low spin bis-histidyl coordination. These mutations increased the reduction potential by 18 to 57mV and highlight the influence of C84, which is a residue unique to gCYTB5-I and whose mutation to alanine caused the largest increase. The influence of these two residues plus that of Y61 reported previously accounts for much of the reduction potential difference between gCYTB5-I and microsomal cytochrome b5. A complementary triple mutant of the latter with the hydrophilic residues found in gCYTB5-I bound heme less effectively but nonetheless had a reduction potential that was 135mV lower than wild type.
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42
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Fischer WW, Hemp J, Valentine JS. How did life survive Earth's great oxygenation? Curr Opin Chem Biol 2016; 31:166-78. [PMID: 27043270 DOI: 10.1016/j.cbpa.2016.03.013] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/11/2016] [Accepted: 03/15/2016] [Indexed: 12/26/2022]
Abstract
Life on Earth originated and evolved in anoxic environments. Around 2.4 billion-years-ago, ancestors of Cyanobacteria invented oxygenic photosynthesis, producing substantial amounts of O2 as a byproduct of phototrophic water oxidation. The sudden appearance of O2 would have led to significant oxidative stress due to incompatibilities with core cellular biochemical processes. Here we examine this problem through the lens of Cyanobacteria-the first taxa to observe significant fluxes of intracellular dioxygen. These early oxygenic organisms likely adapted to the oxidative stress by co-opting preexisting systems (exaptation) with fortuitous antioxidant properties. Over time more advanced antioxidant systems evolved, allowing Cyanobacteria to adapt to an aerobic lifestyle and become the most important environmental engineers in Earth history.
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Affiliation(s)
- Woodward W Fischer
- Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, United States.
| | - James Hemp
- Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, United States
| | - Joan Selverstone Valentine
- Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, United States; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, United States.
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43
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Antioxidant defence systems in the protozoan pathogen Giardia intestinalis. Mol Biochem Parasitol 2016; 206:56-66. [DOI: 10.1016/j.molbiopara.2015.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/26/2015] [Accepted: 12/01/2015] [Indexed: 01/03/2023]
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44
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Emery SJ, Mirzaei M, Vuong D, Pascovici D, Chick JM, Lacey E, Haynes PA. Induction of virulence factors in Giardia duodenalis independent of host attachment. Sci Rep 2016; 6:20765. [PMID: 26867958 PMCID: PMC4751611 DOI: 10.1038/srep20765] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 01/04/2016] [Indexed: 02/06/2023] Open
Abstract
Giardia duodenalis is responsible for the majority of parasitic gastroenteritis in humans worldwide. Host-parasite interaction models in vitro provide insights into disease and virulence and help us to understand pathogenesis. Using HT-29 intestinal epithelial cells (IEC) as a model we have demonstrated that initial sensitisation by host secretions reduces proclivity for trophozoite attachment, while inducing virulence factors. Host soluble factors triggered up-regulation of membrane and secreted proteins, including Tenascins, Cathepsin-B precursor, cystatin, and numerous Variant-specific Surface Proteins (VSPs). By comparison, host-cell attached trophozoites up-regulated intracellular pathways for ubiquitination, reactive oxygen species (ROS) detoxification and production of pyridoxal phosphate (PLP). We reason that these results demonstrate early pathogenesis in Giardia involves two independent host-parasite interactions. Motile trophozoites respond to soluble secreted signals, which deter attachment and induce expression of virulence factors. Trophozoites attached to host cells, in contrast, respond by up-regulating intracellular pathways involved in clearance of ROS, thus anticipating the host defence response.
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Affiliation(s)
- Samantha J Emery
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Pty, Ltd, Smithfield, NSW 2165, Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility (APAF), Macquarie University, North Ryde, NSW, 2109, Australia
| | - Joel M Chick
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ernest Lacey
- Microbial Screening Technologies, Pty, Ltd, Smithfield, NSW 2165, Australia
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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45
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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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46
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Ansell BRE, McConville MJ, Baker L, Korhonen PK, Young ND, Hall RS, Rojas CAA, Svärd SG, Gasser RB, Jex AR. Time-Dependent Transcriptional Changes in Axenic Giardia duodenalis Trophozoites. PLoS Negl Trop Dis 2015; 9:e0004261. [PMID: 26636323 PMCID: PMC4670223 DOI: 10.1371/journal.pntd.0004261] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/03/2015] [Indexed: 12/27/2022] Open
Abstract
Giardia duodenalis is the most common gastrointestinal protozoan parasite of humans and a significant contributor to the global burden of both diarrheal disease and post-infectious chronic disorders. Although G. duodenalis can be cultured axenically, significant gaps exist in our understanding of the molecular biology and metabolism of this pathogen. The present study employed RNA sequencing to characterize the mRNA transcriptome of G. duodenalis trophozoites in axenic culture, at log (48 h of growth), stationary (60 h), and declining (96 h) growth phases. Using ~400-times coverage of the transcriptome, we identified 754 differentially transcribed genes (DTGs), mainly representing two large DTG groups: 438 that were down-regulated in the declining phase relative to log and stationary phases, and 281 that were up-regulated. Differential transcription of prominent antioxidant and glycolytic enzymes implicated oxygen tension as a key factor influencing the transcriptional program of axenic trophozoites. Systematic bioinformatic characterization of numerous DTGs encoding hypothetical proteins of unknown function was achieved using structural homology searching. This powerful approach greatly informed the differential transcription analysis and revealed putative novel antioxidant-coding genes, and the presence of a near-complete two-component-like signaling system that may link cytosolic redox or metabolite sensing to the observed transcriptional changes. Motif searching applied to promoter regions of the two large DTG groups identified different putative transcription factor-binding motifs that may underpin global transcriptional regulation. This study provides new insights into the drivers and potential mediators of transcriptional variation in axenic G. duodenalis and provides context for static transcriptional studies.
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Affiliation(s)
- Brendan R. E. Ansell
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Malcolm J. McConville
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Louise Baker
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K. Korhonen
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Neil D. Young
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Ross S. Hall
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Cristian A. A. Rojas
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Staffan G. Svärd
- Department of Cell & Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Robin B. Gasser
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Aaron R. Jex
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
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47
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Transcriptional profiling of Giardia intestinalis in response to oxidative stress. Int J Parasitol 2015; 45:925-38. [DOI: 10.1016/j.ijpara.2015.07.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/17/2015] [Accepted: 07/24/2015] [Indexed: 12/20/2022]
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48
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Rafferty SP, Dayer G. Heme proteins of Giardia intestinalis. Exp Parasitol 2015; 159:13-23. [PMID: 26297679 DOI: 10.1016/j.exppara.2015.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 08/09/2015] [Accepted: 08/10/2015] [Indexed: 10/23/2022]
Abstract
Among the few organisms that cannot make the iron cofactor heme, some nonetheless possess heme proteins. This includes the protozoan parasite Giardia intestinalis, which encodes five known heme proteins: a flavohemoglobin and four members of the cytochrome b5 family. Giardia flavohemoglobin closely resembles those of the Enterobacteriaceae in structure and function, acting as a nitric oxide dioxygenase that is induced when trophozoites are exposed to reactive nitrogen species. The Giardia cytochromes b5 are soluble proteins having relatively low reduction potentials and lack several features that are expected to promote rapid electron transfer with redox partners. Only one potential electron donor, and no electron acceptors, have yet been identified in the Giardia genome, and the roles of these cytochromes are presently unknown. The answer may lie in the sequences that flank the heme-binding core of these proteins which could serve to localize them within the cell through reversible post-translational modifications and to promote specific protein-protein interactions.
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Affiliation(s)
- Steven Patrick Rafferty
- Department of Chemistry, Trent University, 1600 West Bank Drive, Peterborough, Ontario, Canada, K9J 7B8; Environmental and Life Sciences Graduate Program, Trent University, 1600 West Bank Drive, Peterborough, Ontario, Canada, K9J 7B8.
| | - Guillem Dayer
- Environmental and Life Sciences Graduate Program, Trent University, 1600 West Bank Drive, Peterborough, Ontario, Canada, K9J 7B8
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49
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Ansell BRE, McConville MJ, Ma'ayeh SY, Dagley MJ, Gasser RB, Svärd SG, Jex AR. Drug resistance in Giardia duodenalis. Biotechnol Adv 2015; 33:888-901. [PMID: 25922317 DOI: 10.1016/j.biotechadv.2015.04.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 04/21/2015] [Accepted: 04/21/2015] [Indexed: 02/07/2023]
Abstract
Giardia duodenalis is a microaerophilic parasite of the human gastrointestinal tract and a major contributor to diarrheal and post-infectious chronic gastrointestinal disease world-wide. Treatment of G. duodenalis infection currently relies on a small number of drug classes. Nitroheterocyclics, in particular metronidazole, have represented the front line treatment for the last 40 years. Nitroheterocyclic-resistant G. duodenalis have been isolated from patients and created in vitro, prompting considerable research into the biomolecular mechanisms of resistance. These compounds are redox-active and are believed to damage proteins and DNA after being activated by oxidoreductase enzymes in metabolically active cells. In this review, we explore the molecular phenotypes of nitroheterocyclic-resistant G. duodenalis described to date in the context of the protist's unusual glycolytic and antioxidant systems. We propose that resistance mechanisms are likely to extend well beyond currently described resistance-associated enzymes (i.e., pyruvate ferredoxin oxidoreductases and nitroreductases), to include NAD(P)H- and flavin-generating pathways, and possibly redox-sensitive epigenetic regulation. Mechanisms that allow G. duodenalis to tolerate oxidative stress may lead to resistance against both oxygen and nitroheterocyclics, with implications for clinical control. The present review highlights the potential for systems biology tools and advanced bioinformatics to further investigate the multifaceted mechanisms of nitroheterocyclic resistance in this important pathogen.
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Affiliation(s)
- Brendan R E Ansell
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Cnr Park Dr and Flemington Rd, Parkville, VIC 3010, Australia.
| | - Malcolm J McConville
- Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC 3010, Australia
| | - Showgy Y Ma'ayeh
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Michael J Dagley
- Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC 3010, Australia
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Cnr Park Dr and Flemington Rd, Parkville, VIC 3010, Australia
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Aaron R Jex
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Cnr Park Dr and Flemington Rd, Parkville, VIC 3010, Australia
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50
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Argüello-García R, Cruz-Soto M, González-Trejo R, Paz-Maldonado LMT, Bazán-Tejeda ML, Mendoza-Hernández G, Ortega-Pierres G. An antioxidant response is involved in resistance of Giardia duodenalis to albendazole. Front Microbiol 2015; 6:286. [PMID: 25914688 PMCID: PMC4392323 DOI: 10.3389/fmicb.2015.00286] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 03/23/2015] [Indexed: 12/16/2022] Open
Abstract
Albendazole (ABZ) is a therapeutic benzimidazole used to treat giardiasis that targets β-tubulin. However, the molecular bases of ABZ resistance in Giardia duodenalis are not understood because β-tubulin in ABZ-resistant clones lacks mutations explaining drug resistance. In previous work we compared ABZ-resistant (1.35, 8, and 250 μM) and ABZ-susceptible clones by proteomic analysis and eight proteins involved in energy metabolism, cytoskeleton dynamics, and antioxidant response were found as differentially expressed among the clones. Since ABZ is converted into sulphoxide (ABZ-SO) and sulphone (ABZ-SOO) metabolites we measured the levels of these metabolites, the antioxidant enzymes and free thiols in the susceptible and resistant clones. Production of reactive oxygen species (ROS) and levels of ABZ-SO/ABZ-SOO induced by ABZ were determined by fluorescein diacetate-based fluorescence and liquid chromatography respectively. The mRNA and protein levels of antioxidant enzymes (NADH oxidase, peroxiredoxin 1a, superoxide dismutase and flavodiiron protein) in these clones were determined by RT-PCR and proteomic analysis. The intracellular sulfhydryl (R-SH) pool was quantified using dinitrobenzoic acid. The results showed that ABZ induced ROS accumulation in the ABZ-susceptible Giardia cultures but not in the resistant ones whilst the accumulation of ABZ-SO and ABZ-SOO was lower in all ABZ-resistant cultures. Consistent with these findings, all the antioxidant enzymes detected and analyzed were upregulated in ABZ-resistant clones. Likewise the R-SH pool increased concomitantly to the degree of ABZ-resistance. These results indicate an association between accumulation of ABZ metabolites and a pro-oxidant effect of ABZ in Giardia-susceptible clones. Furthermore the antioxidant response involving ROS-metabolizing enzymes and intracellular free thiols in ABZ-resistant parasites suggest that this response may contribute to overcome the pro-oxidant cytotoxicity of ABZ.
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Affiliation(s)
- Raúl Argüello-García
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados Instituto Politécnico Nacional, Mexico City Mexico
| | | | - Rolando González-Trejo
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados Instituto Politécnico Nacional, Mexico City Mexico
| | - Luz María T Paz-Maldonado
- Ingeniería de Biorreactores, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí Mexico
| | - M Luisa Bazán-Tejeda
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados Instituto Politécnico Nacional, Mexico City Mexico
| | - Guillermo Mendoza-Hernández
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City Mexico
| | - Guadalupe Ortega-Pierres
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados Instituto Politécnico Nacional, Mexico City Mexico
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