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Pedone E, Fiorentino G, Bartolucci S, Limauro D. Enzymatic Antioxidant Signatures in Hyperthermophilic Archaea. Antioxidants (Basel) 2020; 9:antiox9080703. [PMID: 32756530 PMCID: PMC7465337 DOI: 10.3390/antiox9080703] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 12/17/2022] Open
Abstract
To fight reactive oxygen species (ROS) produced by both the metabolism and strongly oxidative habitats, hyperthermophilic archaea are equipped with an array of antioxidant enzymes whose role is to protect the biological macromolecules from oxidative damage. The most common ROS, such as superoxide radical (O2-.) and hydrogen peroxide (H2O2), are scavenged by superoxide dismutase, peroxiredoxins, and catalase. These enzymes, together with thioredoxin, protein disulfide oxidoreductase, and thioredoxin reductase, which are involved in redox homeostasis, represent the core of the antioxidant system. In this review, we offer a panorama of progression of knowledge on the antioxidative system in aerobic or microaerobic (hyper)thermophilic archaea and possible industrial applications of these enzymes.
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Affiliation(s)
- Emilia Pedone
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy;
| | - Gabriella Fiorentino
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso universitario Monte S. Angelo, Via Cinthia, 80126 Napoli, Italy; (G.F.); (S.B.)
| | - Simonetta Bartolucci
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso universitario Monte S. Angelo, Via Cinthia, 80126 Napoli, Italy; (G.F.); (S.B.)
| | - Danila Limauro
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso universitario Monte S. Angelo, Via Cinthia, 80126 Napoli, Italy; (G.F.); (S.B.)
- Correspondence:
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Abstract
The formation of disulfide bonds is critical to the folding of many extracytoplasmic proteins in all domains of life. With the discovery in the early 1990s that disulfide bond formation is catalyzed by enzymes, the field of oxidative folding of proteins was born. Escherichia coli played a central role as a model organism for the elucidation of the disulfide bond-forming machinery. Since then, many of the enzymatic players and their mechanisms of forming, breaking, and shuffling disulfide bonds have become understood in greater detail. This article summarizes the discoveries of the past 3 decades, focusing on disulfide bond formation in the periplasm of the model prokaryotic host E. coli.
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Patel AK, Singhania RR, Sim SJ, Pandey A. Thermostable cellulases: Current status and perspectives. BIORESOURCE TECHNOLOGY 2019; 279:385-392. [PMID: 30685132 DOI: 10.1016/j.biortech.2019.01.049] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 05/18/2023]
Abstract
It is envisaged that the utilization of lignocellulosic biomass for ethanol production for transport sector, would make cellulases the most demanded industrial enzyme. The greatest potential of cellulolytic enzymes lies in ethanol production from biomass by enzymatic hydrolysis of cellulose but low thermostability and low titer of cellulase production resulting into high cost of the enzyme which is the major set-back. A number of research groups are working on cellulase to improve its thermostability so as to be able to perform hydrolysis at elevated temperatures which would eventually increase the efficiency of cellulose hydrolysis. The technologies developed from lignocellulosic biomass via cellulose hydrolysis promise environmental and economical sustainability in the long run along with non-dependence on nonrenewable energy source. This review deals with the important sources of thermostable cellulases, mechanism, its regulation, strategies to enhance the thermostability further with respect to its importance for biofuel applications.
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Affiliation(s)
- Anil K Patel
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | | | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Ashok Pandey
- Centre for Innovation and Translational Research, Indian Institute of Toxicological Research, Lucknow 226 001, India
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Lanzilli M, Donadio G, Fusco FA, Sarcinelli C, Limauro D, Ricca E, Isticato R. Display of the peroxiredoxin Bcp1 of Sulfolobus solfataricus on probiotic spores of Bacillus megaterium. N Biotechnol 2018; 46:38-44. [DOI: 10.1016/j.nbt.2018.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 06/15/2018] [Accepted: 06/25/2018] [Indexed: 11/16/2022]
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Reyes AM, Vazquez DS, Zeida A, Hugo M, Piñeyro MD, De Armas MI, Estrin D, Radi R, Santos J, Trujillo M. PrxQ B from Mycobacterium tuberculosis is a monomeric, thioredoxin-dependent and highly efficient fatty acid hydroperoxide reductase. Free Radic Biol Med 2016; 101:249-260. [PMID: 27751911 DOI: 10.1016/j.freeradbiomed.2016.10.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/16/2016] [Accepted: 10/06/2016] [Indexed: 12/23/2022]
Abstract
Mycobacterium tuberculosis (M. tuberculosis) is the intracellular bacterium responsible for tuberculosis disease (TD). Inside the phagosomes of activated macrophages, M. tuberculosis is exposed to cytotoxic hydroperoxides such as hydrogen peroxide, fatty acid hydroperoxides and peroxynitrite. Thus, the characterization of the bacterial antioxidant systems could facilitate novel drug developments. In this work, we characterized the product of the gene Rv1608c from M. tuberculosis, which according to sequence homology had been annotated as a putative peroxiredoxin of the peroxiredoxin Q subfamily (PrxQ B from M. tuberculosis or MtPrxQ B). The protein has been reported to be essential for M. tuberculosis growth in cholesterol-rich medium. We demonstrated the M. tuberculosis thioredoxin B/C-dependent peroxidase activity of MtPrxQ B, which acted as a two-cysteine peroxiredoxin that could function, although less efficiently, using a one-cysteine mechanism. Through steady-state and competition kinetic analysis, we proved that the net forward rate constant of MtPrxQ B reaction was 3 orders of magnitude faster for fatty acid hydroperoxides than for hydrogen peroxide (3×106vs 6×103M-1s-1, respectively), while the rate constant of peroxynitrite reduction was (0.6-1.4) ×106M-1s-1 at pH 7.4. The enzyme lacked activity towards cholesterol hydroperoxides solubilized in sodium deoxycholate. Both thioredoxin B and C rapidly reduced the oxidized form of MtPrxQ B, with rates constants of 0.5×106 and 1×106M-1s-1, respectively. Our data indicated that MtPrxQ B is monomeric in solution both under reduced and oxidized states. In spite of the similar hydrodynamic behavior the reduced and oxidized forms of the protein showed important structural differences that were reflected in the protein circular dichroism spectra.
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Affiliation(s)
- Aníbal M Reyes
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay
| | - Diego S Vazquez
- Instituto de Química y Físicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Universidad de Buenos Aires and CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ari Zeida
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Martín Hugo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay
| | - M Dolores Piñeyro
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Unidad de Biología Molecular-Institut Pasteur Montevideo, Montevideo, Uruguay
| | - María Inés De Armas
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay
| | - Darío Estrin
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay
| | - Javier Santos
- Instituto de Química y Físicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Universidad de Buenos Aires and CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay.
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Discovering Antioxidant Molecules in the Archaea Domain: Peroxiredoxin Bcp1 from Sulfolobus solfataricus Protects H9c2 Cardiomyoblasts from Oxidative Stress. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:7424870. [PMID: 27752237 PMCID: PMC5056240 DOI: 10.1155/2016/7424870] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/29/2016] [Accepted: 07/31/2016] [Indexed: 12/15/2022]
Abstract
Peroxiredoxins (Prxs) are ubiquitous thiol peroxidases that are involved in the reduction of peroxides. It has been reported that prokaryotic Prxs generally show greater structural robustness than their eukaryotic counterparts, making them less prone to inactivation by overoxidation. This difference has inspired the search for new antioxidants from prokaryotic sources that can be used as possible therapeutic biodrugs. Bacterioferritin comigratory proteins (Bcps) of the hyperthermophilic archaeon Sulfolobus solfataricus that belong to the Prx family have recently been characterized. One of these proteins, Bcp1, was chosen to determine its antioxidant effects in H9c2 rat cardiomyoblast cells. Bcp1 activity was measured in vitro under physiological temperature and pH conditions that are typical of mammalian cells; the yeast thioredoxin reductase (yTrxR)/thioredoxin (yTrx) reducing system was used to evaluate enzyme activity. A TAT-Bcp1 fusion protein was constructed to allow its internalization and verify the effect of Bcp1 on H9c2 rat cardiomyoblasts subjected to oxidative stress. The results reveal that TAT-Bcp1 is not cytotoxic and inhibits H2O2-induced apoptosis in H9c2 cells by reducing the H2O2 content inside these cells.
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Transcriptomes of the Extremely Thermoacidophilic Archaeon Metallosphaera sedula Exposed to Metal "Shock" Reveal Generic and Specific Metal Responses. Appl Environ Microbiol 2016; 82:4613-4627. [PMID: 27208114 DOI: 10.1128/aem.01176-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 05/17/2016] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED The extremely thermoacidophilic archaeon Metallosphaera sedula mobilizes metals by novel membrane-associated oxidase clusters and, consequently, requires metal resistance strategies. This issue was examined by "shocking" M. sedula with representative metals (Co(2+), Cu(2+), Ni(2+), UO2 (2+), Zn(2+)) at inhibitory and subinhibitory levels. Collectively, one-quarter of the genome (554 open reading frames [ORFs]) responded to inhibitory levels, and two-thirds (354) of the ORFs were responsive to a single metal. Cu(2+) (259 ORFs, 106 Cu(2+)-specific ORFs) and Zn(2+) (262 ORFs, 131 Zn(2+)-specific ORFs) triggered the largest responses, followed by UO2 (2+) (187 ORFs, 91 UO2 (2+)-specific ORFs), Ni(2+) (93 ORFs, 25 Ni(2+)-specific ORFs), and Co(2+) (61 ORFs, 1 Co(2+)-specific ORF). While one-third of the metal-responsive ORFs are annotated as encoding hypothetical proteins, metal challenge also impacted ORFs responsible for identifiable processes related to the cell cycle, DNA repair, and oxidative stress. Surprisingly, there were only 30 ORFs that responded to at least four metals, and 10 of these responded to all five metals. This core transcriptome indicated induction of Fe-S cluster assembly (Msed_1656-Msed_1657), tungsten/molybdenum transport (Msed_1780-Msed_1781), and decreased central metabolism. Not surprisingly, a metal-translocating P-type ATPase (Msed_0490) associated with a copper resistance system (Cop) was upregulated in response to Cu(2+) (6-fold) but also in response to UO2 (2+) (4-fold) and Zn(2+) (9-fold). Cu(2+) challenge uniquely induced assimilatory sulfur metabolism for cysteine biosynthesis, suggesting a role for this amino acid in Cu(2+) resistance or issues in sulfur metabolism. The results indicate that M. sedula employs a range of physiological and biochemical responses to metal challenge, many of which are specific to a single metal and involve proteins with yet unassigned or definitive functions. IMPORTANCE The mechanisms by which extremely thermoacidophilic archaea resist and are negatively impacted by metals encountered in their natural environments are important to understand so that technologies such as bioleaching, which leverage microbially based conversion of insoluble metal sulfides to soluble species, can be improved. Transcriptomic analysis of the cellular response to metal challenge provided both global and specific insights into how these novel microorganisms negotiate metal toxicity in natural and technological settings. As genetics tools are further developed and implemented for extreme thermoacidophiles, information about metal toxicity and resistance can be leveraged to create metabolically engineered strains with improved bioleaching characteristics.
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Bagarolo ML, Porcelli M, Martino E, Feller G, Cacciapuoti G. Multiple disulfide bridges modulate conformational stability and flexibility in hyperthermophilic archaeal purine nucleoside phosphorylase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1458-65. [DOI: 10.1016/j.bbapap.2015.06.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/27/2015] [Accepted: 06/23/2015] [Indexed: 11/25/2022]
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Reardon-Robinson ME, Osipiuk J, Chang C, Wu C, Jooya N, Joachimiak A, Das A, Ton-That H. A Disulfide Bond-forming Machine Is Linked to the Sortase-mediated Pilus Assembly Pathway in the Gram-positive Bacterium Actinomyces oris. J Biol Chem 2015; 290:21393-405. [PMID: 26170452 PMCID: PMC4571867 DOI: 10.1074/jbc.m115.672253] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Indexed: 12/30/2022] Open
Abstract
Export of cell surface pilins in Gram-positive bacteria likely occurs by the translocation of unfolded precursor polypeptides; however, how the unfolded pilins gain their native conformation is presently unknown. Here, we present physiological studies to demonstrate that the FimA pilin of Actinomyces oris contains two disulfide bonds. Alanine substitution of cysteine residues forming the C-terminal disulfide bridge abrogates pilus assembly, in turn eliminating biofilm formation and polymicrobial interaction. Transposon mutagenesis of A. oris yielded a mutant defective in adherence to Streptococcus oralis, and revealed the essential role of a vitamin K epoxide reductase (VKOR) gene in pilus assembly. Targeted deletion of vkor results in the same defects, which are rescued by ectopic expression of VKOR, but not a mutant containing an alanine substitution in its conserved CXXC motif. Depletion of mdbA, which encodes a membrane-bound thiol-disulfide oxidoreductase, abrogates pilus assembly and alters cell morphology. Remarkably, overexpression of MdbA or a counterpart from Corynebacterium diphtheriae, rescues the Δvkor mutant. By alkylation assays, we demonstrate that VKOR is required for MdbA reoxidation. Furthermore, crystallographic studies reveal that A. oris MdbA harbors a thioredoxin-like fold with the conserved CXXC active site. Consistently, each MdbA enzyme catalyzes proper disulfide bond formation within FimA in vitro that requires the catalytic CXXC motif. Because the majority of signal peptide-containing proteins encoded by A. oris possess multiple Cys residues, we propose that MdbA and VKOR constitute a major folding machine for the secretome of this organism. This oxidative protein folding pathway may be a common feature in Actinobacteria.
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Affiliation(s)
- Melissa E. Reardon-Robinson
- From the Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030
| | - Jerzy Osipiuk
- the Department of Biosciences, Midwest Center for Structural Genomics, and ,the Department of Biosciences, Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, and
| | - Chungyu Chang
- From the Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030
| | - Chenggang Wu
- From the Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030
| | - Neda Jooya
- From the Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030
| | - Andrzej Joachimiak
- the Department of Biosciences, Midwest Center for Structural Genomics, and ,the Department of Biosciences, Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, and
| | - Asis Das
- the Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030
| | - Hung Ton-That
- From the Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030,
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Limauro D, De Simone G, Pirone L, Bartolucci S, D'Ambrosio K, Pedone E. Sulfolobus solfataricus thiol redox puzzle: characterization of an atypical protein disulfide oxidoreductase. Extremophiles 2013; 18:219-28. [PMID: 24306780 DOI: 10.1007/s00792-013-0607-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 11/14/2013] [Indexed: 10/25/2022]
Abstract
Protein disulfide oxidoreductases (PDOs) are proteins involved in disulfide bond formation playing a crucial role in adaptation to extreme environment. This paper reports the functional and structural characterization of Sso1120, a PDO from the hyperthermophilic archaeon Sulfolobus solfataricus. The protein was expressed in Escherichia coli and purified to homogeneity. The functional characterization showed that the enzyme has reductase activity, as tested by insulin assay, but differently from the other PDOs, it does not present isomerase activity. In addition it is able to form a redox couple with the thioredoxin reductase that could be used in undiscovered pathways. The protein revealed a melting point of around 90 °C in CD spectroscopy-monitored thermal denaturation and high denaturant resistance. The X-ray crystallographic structure was solved at 1.80 Å resolution, showing differences with respect to other PDOs and an unexpected similarity with the N-terminal domain of the alkyl hydroperoxide reductase F component from Salmonella typhimurium. On the basis of the reported data and of bioinformatics and phylogenetic analyses, a possible involvement of this atypical PDO in a new antioxidant system of S. solfataricus has been proposed.
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Affiliation(s)
- Danila Limauro
- Dipartimento di Biologia, Università degli Studi di Napoli ''Federico II'', Complesso Universitario Monte S. Angelo, Via Cinthia, 80126, Naples, Italy
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Abstract
SIGNIFICANCE Disulfide bond formation is critical for biogenesis of many proteins. While most studies in this field are aimed at elucidating the mechanisms in the endoplasmic reticulum, intermembrane space of mitochondria, and prokaryotic periplasm, structural disulfide bond formation also occurs in other compartments including the cytoplasm. Such disulfide bond formation is essential for biogenesis of some viruses, correct epidermis biosynthesis, thermal adaptation of some extremophiles, and efficient recombinant protein production. RECENT ADVANCES The majority of work in this new field has been reported in the past decade. Within the past few years very significant new data have emerged on the catalytic and noncatalytic mechanisms for disulfide bond formation in the cytoplasm. This includes the crystal structure of a key component of viral oxidative protein folding, identification of a missing component in cytoplasmic disulfide bond formation in hyperthermophiles, and introduction of de novo dithiol oxidants in engineered oxidative folding pathways. CRITICAL ISSUES AND FUTURE DIRECTIONS While a broad picture of cytoplasmic disulfide bond formation has emerged many critical questions remain unanswered. The individual components in the natural systems are largely known, but the molecular mechanisms by which these processes occur are largely deduced from the mechanisms of analogous components in other compartments. This prevents full understanding and manipulation of these systems, including the potential for novel anti-viral drugs based on the unique features of their sulfhydryl oxidases and the generation of more efficient cell factories for the large-scale production of therapeutic and industrial proteins.
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Topological plasticity of enzymes involved in disulfide bond formation allows catalysis in either the periplasm or the cytoplasm. J Mol Biol 2013; 425:3268-76. [PMID: 23810903 DOI: 10.1016/j.jmb.2013.04.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/29/2013] [Accepted: 04/30/2013] [Indexed: 11/23/2022]
Abstract
The transmembrane enzymes disulfide bond forming enzyme B (DsbB) and vitamin K epoxide reductase (VKOR) are central to oxidative protein folding in the periplasm of prokaryotes. Catalyzed formation of structural disulfide bonds in proteins also occurs in the cytoplasm of some hyperthermophilic prokaryotes through currently, poorly defined mechanisms. We aimed to determine whether DsbB and VKOR can be inverted in the membrane with retention of activity. By rational design of inversion of membrane topology, we engineered DsbB mutants that catalyze disulfide bond formation in the cytoplasm of Escherichia coli. This represents the first engineered inversion of a transmembrane protein with demonstrated conservation of activity and substrate specificity. This successful designed engineering led us to identify two naturally occurring and oppositely oriented VKOR homologues from the hyperthermophile Aeropyrum pernix that promote oxidative protein folding in the periplasm or cytoplasm, respectively, and hence defines the probable route for disulfide bond formation in the cytoplasm of hyperthermophiles. Our findings demonstrate how knowledge on the determinants of membrane protein topology can be used to de novo engineer a metabolic pathway and to unravel an intriguingly simple evolutionary scenario where a new "adaptive" cellular process is constructed by means of membrane protein topology inversion.
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Sato Y, Inaba K. Disulfide bond formation network in the three biological kingdoms, bacteria, fungi and mammals. FEBS J 2012; 279:2262-71. [DOI: 10.1111/j.1742-4658.2012.08593.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Acharya S, Chaudhary A. Bioprospecting thermophiles for cellulase production: a review. Braz J Microbiol 2012; 43:844-56. [PMID: 24031898 PMCID: PMC3768857 DOI: 10.1590/s1517-83822012000300001] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 11/25/2011] [Accepted: 06/07/2012] [Indexed: 11/22/2022] Open
Abstract
Most of the potential bioprospecting is currently related to the study of the extremophiles and their potential use in industrial processes. Recently microbial cellulases find applications in various industries and constitute a major group of industrial enzymes. Considerable amount of work has been done on microbial cellulases, especially with resurgence of interest in biomass ethanol production employing cellulases and use of cellulases in textile and paper industry. Most efficient method of lignocellulosic biomass hydrolysis is through enzymatic saccharification using cellulases. Significant information has also been gained about the physiology of thermophilic cellulases producers and process development for enzyme production and biomass saccharification. The review discusses the current knowledge on cellulase producing thermophilic microorganisms, their physiological adaptations and control of cellulase gene expression. It discusses the industrial applications of thermophilic cellulases, their cost of production and challenges in cellulase research especially in the area of improving process economics of enzyme production.
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Affiliation(s)
- Somen Acharya
- Division of Environmental Sciences, Indian Agricultural Research Institute , New Delhi-110012 , India
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15
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Abstract
SIGNIFICANCE The biogenesis of most secreted and outer membrane proteins involves the formation of structure stabilizing disulfide bonds. Hence knowledge of the mechanisms for their formation is critical for understanding a myriad of cellular processes and associated disease states. RECENT ADVANCES Until recently it was thought that members of the Ero1 sulfhydryl oxidase family were responsible for catalyzing the majority of disulfide bond formation in the endoplasmic reticulum. However, multiple eukaryotic organisms are now known to show no or minor phenotypes when these enzymatic pathways are disrupted, suggesting that other pathways can catalyze disulfide bond formation to an extent sufficient to maintain normal physiology. CRITICAL ISSUES AND FUTURE DIRECTIONS This lack of a strong phenotype raises multiple questions regarding what pathways are acting and whether they themselves constitute the major route for disulfide bond formation. This review critically examines the potential low molecular oxidants that maybe involved in the catalyzed or noncatalyzed formation of disulfide bonds, with an emphasis on the mammalian endoplasmic reticulum, via an examination of their thermodynamics, kinetics, and availability and gives pointers to help guide future experimental work.
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Cacciapuoti G, Marabotti A, Fuccio F, Porcelli M. Unraveling the structural and functional differences between purine nucleoside phosphorylase and 5′-deoxy-5′-methylthioadenosine phosphorylase from the archaeon Pyrococcus furiosus. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1358-66. [DOI: 10.1016/j.bbapap.2011.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 05/17/2011] [Accepted: 06/01/2011] [Indexed: 10/18/2022]
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Widespread disulfide bonding in proteins from thermophilic archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2011; 2011:409156. [PMID: 21941460 PMCID: PMC3177088 DOI: 10.1155/2011/409156] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 07/16/2011] [Indexed: 11/17/2022]
Abstract
Disulfide bonds are generally not used to stabilize proteins in the cytosolic compartments of bacteria or eukaryotic cells, owing to the chemically reducing nature of those environments. In contrast, certain thermophilic archaea use disulfide bonding as a major mechanism for protein stabilization. Here, we provide a current survey of completely sequenced genomes, applying computational methods to estimate the use of disulfide bonding across the Archaea. Microbes belonging to the Crenarchaeal branch, which are essentially all hyperthermophilic, are universally rich in disulfide bonding while lesser degrees of disulfide bonding are found among the thermophilic Euryarchaea, excluding those that are methanogenic. The results help clarify which parts of the archaeal lineage are likely to yield more examples and additional specific data on protein disulfide bonding, as increasing genomic sequencing efforts are brought to bear.
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Marino SM, Gladyshev VN. Redox biology: computational approaches to the investigation of functional cysteine residues. Antioxid Redox Signal 2011; 15:135-46. [PMID: 20812876 PMCID: PMC3110093 DOI: 10.1089/ars.2010.3561] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Revised: 08/19/2010] [Accepted: 09/02/2010] [Indexed: 12/18/2022]
Abstract
Cysteine (Cys) residues serve many functions, such as catalysis, stabilization of protein structure through disulfides, metal binding, and regulation of protein function. Cys residues are also subject to numerous post-translational modifications. In recent years, various computational tools aiming at classifying and predicting different functional categories of Cys have been developed, particularly for structural and catalytic Cys. On the other hand, given complexity of the subject, bioinformatics approaches have been less successful for the investigation of regulatory Cys sites. In this review, we introduce different functional categories of Cys residues. For each category, an overview of state-of-the-art bioinformatics methods and tools is provided, along with examples of successful applications and potential limitations associated with each approach. Finally, we discuss Cys-based redox switches, which modify the view of distinct functional categories of Cys in proteins.
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Affiliation(s)
- Stefano M Marino
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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Pedone E, Limauro D, D’Ambrosio K, De Simone G, Bartolucci S. Multiple catalytically active thioredoxin folds: a winning strategy for many functions. Cell Mol Life Sci 2010; 67:3797-814. [PMID: 20625793 PMCID: PMC11115506 DOI: 10.1007/s00018-010-0449-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 06/23/2010] [Accepted: 06/28/2010] [Indexed: 10/19/2022]
Abstract
The Thioredoxin (Trx) fold is a versatile protein scaffold consisting of a four-stranded β-sheet surrounded by three α-helices. Various insertions are possible on this structural theme originating different proteins, which show a variety of functions and specificities. During evolution, the assembly of different Trx fold domains has been used many times to build new multi-domain proteins able to perform a large number of catalytic functions. To clarify the interaction mode of the different Trx domains within a multi-domain structure and how their combination can affect catalytic performances, in this review, we report on a structural and functional analysis of the most representative proteins containing more than one catalytically active Trx domain: the eukaryotic protein disulfide isomerases (PDIs), the thermophilic protein disulfide oxidoreductases (PDOs) and the hybrid peroxiredoxins (Prxs).
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Affiliation(s)
- Emilia Pedone
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Naples, Italy
| | - Danila Limauro
- Dipartimento di Biologia Strutturale e Funzionale, Università degli Studi di Napoli “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, 80126 Naples, Italy
| | - Katia D’Ambrosio
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Naples, Italy
| | - Giuseppina De Simone
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Naples, Italy
| | - Simonetta Bartolucci
- Dipartimento di Biologia Strutturale e Funzionale, Università degli Studi di Napoli “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, 80126 Naples, Italy
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D'Ambrosio K, Limauro D, Pedone E, Galdi I, Pedone C, Bartolucci S, De Simone G. Insights into the catalytic mechanism of the Bcp family: functional and structural analysis of Bcp1 from Sulfolobus solfataricus. Proteins 2009; 76:995-1006. [PMID: 19338062 DOI: 10.1002/prot.22408] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bcps constitute a group of antioxidant enzymes, belonging to the Prx family, that are widely distributed in bacteria, plants, and fungi. These proteins can contain two conserved cysteines within the CXXXXC motif. Recent studies demonstrated that though the role of the first cysteine is well defined, being the catalytic peroxidatic cysteine in all the members of this protein family, data on the function of the second cysteine are controversial and require further investigation. In this article, we report on the functional and structural characterization of Bcp1, an archaeal Bcp isolated from Sulfolobus solfataricus, which presents two conserved cysteine residues at positions 45 and 50. Functional studies revealed that this enzyme performs the catalytic reaction using an atypical 2-Cys mechanism, where Cys45 is the peroxidatic and Cys50 is the resolving cysteine. The X-ray structure of the double mutant C45S/C50S, representative of the fully reduced enzyme state, was determined at a resolution of 2.15 A, showing a Trx fold similar to that of other Prxs. Superposition with a structural homologue in the oxidized state provided, for the first time, a detailed description of the structural rearrangement necessary for a member of the Bcp family to perform the catalytic reaction. From this structural analysis, it emerges that a significant conformational change from a fully folded, to a locally unfolded form is required to form the intramolecular disulfide bond upon oxidation, according to the proposed reaction mechanism. Two residues, namely Arg53 and Asp54, which could play a role in this rearrangement, were also identified.
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Affiliation(s)
- Katia D'Ambrosio
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Naples, Italy
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Cacciapuoti G, Peluso I, Fuccio F, Porcelli M. Purine nucleoside phosphorylases from hyperthermophilic Archaea require a CXC motif for stability and folding. FEBS J 2009; 276:5799-805. [PMID: 19740110 DOI: 10.1111/j.1742-4658.2009.07247.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
5'-Deoxy-5'-methylthioadenosine phosphorylase II from Sulfolobus solfataricus (SsMTAPII) and purine nucleoside phosphorylase from Pyrococcus furiosus (PfPNP) are hyperthermophilic purine nucleoside phosphorylases stabilized by intrasubunit disulfide bonds. In their C-terminus, both enzymes harbour a CXC motif analogous to the CXXC motif present at the active site of eukaryotic protein disulfide isomerase. By monitoring the refolding of SsMTAPII, PfPNP and their mutants lacking the C-terminal cysteine pair after guanidine-induced unfolding, we demonstrated that the CXC motif is required for the folding of these enzymes. Moreover, two synthesized CXC-containing peptides with the same amino acid sequences present in the C-terminal regions of SsMTAPII and PfPNP were found to act as in vitro catalysts of oxidative folding. These small peptides are involved in the folding of partially refolded SsMTAPII, PfPNP and their CXC-lacking mutants, with a concomitant recovery of their catalytic activity, thus indicating that the CXC motif is necessary to obtain complete reversibility from the unfolded state of the two proteins. The two CXC-containing peptides are also able to reactivate scrambled RNaseA. The data obtained in the present study represent the first example of how the CXC motif improves both stability and folding in hyperthermophilic proteins with disulfide bonds.
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Affiliation(s)
- Giovanna Cacciapuoti
- Department of Biochemistry and Biophysics 'F. Cedrangolo', Second University of Naples, Italy.
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Ito K, Inaba K. The disulfide bond formation (Dsb) system. Curr Opin Struct Biol 2008; 18:450-8. [PMID: 18406599 DOI: 10.1016/j.sbi.2008.02.002] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Accepted: 02/29/2008] [Indexed: 11/16/2022]
Abstract
In oxidative folding of proteins in the bacterial periplasmic space, disulfide bonds are introduced by the oxidation system and isomerized by the reduction system. These systems utilize the oxidizing and the reducing equivalents of quinone and NADPH, respectively, that are transmitted across the cytoplasmic membrane through integral membrane components DsbB and DsbD. In both pathways, alternating interactions between a Cys-XX-Cys-containing thioredoxin domain and other regulatory domain lead to the maintenance of oxidized and reduced states of the specific terminal enzymes, DsbA that oxidizes target cysteines and DsbC that reduces an incorrect disulfide to allow its isomerization into the physiological one. Molecular details of these remarkable biochemical cascades are being rapidly unraveled by genetic, biochemical, and structural analyses in recent years.
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Affiliation(s)
- Koreaki Ito
- Institute for Virus Research, Kyoto University, Kyoto, Japan.
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Limauro D, Pedone E, Galdi I, Bartolucci S. Peroxiredoxins as cellular guardians in Sulfolobus solfataricus- characterization of Bcp1, Bcp3 and Bcp4. FEBS J 2008; 275:2067-77. [DOI: 10.1111/j.1742-4658.2008.06361.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Affiliation(s)
- Salvador Ventura
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
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