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Gustafsson TN, Sahlin M, Lu J, Sjöberg BM, Holmgren A. Bacillus anthracis thioredoxin systems, characterization and role as electron donors for ribonucleotide reductase. J Biol Chem 2012; 287:39686-97. [PMID: 23012357 DOI: 10.1074/jbc.m112.413427] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bacillus anthracis is the causative agent of anthrax, which is associated with a high mortality rate. Like several medically important bacteria, B. anthracis lacks glutathione but encodes many genes annotated as thioredoxins, thioredoxin reductases, and glutaredoxin-like proteins. We have cloned, expressed, and characterized three potential thioredoxins, two potential thioredoxin reductases, and three glutaredoxin-like proteins. Of these, thioredoxin 1 (Trx1) and NrdH reduced insulin, 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB), and the manganese-containing type Ib ribonucleotide reductase (RNR) from B. anthracis in the presence of NADPH and thioredoxin reductase 1 (TR1), whereas thioredoxin 2 (Trx2) could only reduce DTNB. Potential TR2 was verified as an FAD-containing protein reducible by dithiothreitol but not by NAD(P)H. The recently discovered monothiol bacillithiol did not work as a reductant for RNR, either directly or via any of the redoxins. The catalytic efficiency of Trx1 was 3 and 20 times higher than that of Trx2 and NrdH, respectively, as substrates for TR1. Additionally, the catalytic efficiency of Trx1 as an electron donor for RNR was 7-fold higher than that of NrdH. In extracts of B. anthracis, Trx1 was responsible for almost all of the disulfide reductase activity, whereas Western blots showed that the level of Trx1 was 15 and 60 times higher than that of Trx2 and NrdH, respectively. Our findings demonstrate that the most important general disulfide reductase system in B. anthracis is TR1/Trx1 and that Trx1 is the physiologically relevant electron donor for RNR. This information may provide a basis for the development of novel antimicrobial therapies targeting this severe pathogen.
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Affiliation(s)
- Tomas N Gustafsson
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet SE-17177 Stockholm, Sweden
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Chen C, Ai L, Zhou F, Ren J, Sun K, Zhang H, Chen W, Guo B. Complete nucleotide sequence of plasmid pST-III from Lactobacillus plantarum ST-III. Plasmid 2011; 67:236-44. [PMID: 22209721 DOI: 10.1016/j.plasmid.2011.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Revised: 12/07/2011] [Accepted: 12/15/2011] [Indexed: 10/14/2022]
Abstract
The complete nucleotide sequence of the 53,560-bp plasmid pST-III from Lactobacillus plantarum ST-III has been determined. The plasmid contains 42 predicted protein-coding sequences, and the functions of 34 coding sequences could be assigned. Homology analysis for the replication protein and the typical features of the origin of replication suggested that pST-III replicates via the theta-type mechanism. Among the predicted genes, we identified a kdp gene cluster (a high-affinity K(+)-transport system) for the first time in the Lactobacillus genus and a system for osmolyte transport. Analysis of the plasmid-encoded functions and the plasmid-cured experiment showed that the genes of pST-III could serve for the niche adaptations of L. plantarum ST-III and make significant contributions to its viability under hyperosmotic conditions. Furthermore, the relative copy number of pST-III was determined to be 6.79±1.55 copies per cell.
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Affiliation(s)
- Chen Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
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Cotruvo JA, Stubbe J. Class I ribonucleotide reductases: metallocofactor assembly and repair in vitro and in vivo. Annu Rev Biochem 2011; 80:733-67. [PMID: 21456967 DOI: 10.1146/annurev-biochem-061408-095817] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Incorporation of metallocofactors essential for the activity of many enyzmes is a major mechanism of posttranslational modification. The cellular machinery required for these processes in the case of mono- and dinuclear nonheme iron and manganese cofactors has remained largely elusive. In addition, many metallocofactors can be converted to inactive forms, and pathways for their repair have recently come to light. The class I ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides and require dinuclear metal clusters for activity: an Fe(III)Fe(III)-tyrosyl radical (Y•) cofactor (class Ia), a Mn(III)Mn(III)-Y• cofactor (class Ib), and a Mn(IV)Fe(III) cofactor (class Ic). The class Ia, Ib, and Ic RNRs are structurally homologous and contain almost identical metal coordination sites. Recent progress in our understanding of the mechanisms by which the cofactor of each of these RNRs is generated in vitro and in vivo and by which the damaged cofactors are repaired is providing insight into how nature prevents mismetallation and orchestrates active cluster formation in high yields.
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Affiliation(s)
- Joseph A Cotruvo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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Crona M, Torrents E, Røhr AK, Hofer A, Furrer E, Tomter AB, Andersson KK, Sahlin M, Sjöberg BM. NrdH-redoxin protein mediates high enzyme activity in manganese-reconstituted ribonucleotide reductase from Bacillus anthracis. J Biol Chem 2011; 286:33053-60. [PMID: 21832039 PMCID: PMC3190916 DOI: 10.1074/jbc.m111.278119] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacillus anthracis is a severe mammalian pathogen encoding a class Ib ribonucleotide reductase (RNR). RNR is a universal enzyme that provides the four essential deoxyribonucleotides needed for DNA replication and repair. Almost all Bacillus spp. encode both class Ib and class III RNR operons, but the B. anthracis class III operon was reported to encode a pseudogene, and conceivably class Ib RNR is necessary for spore germination and proliferation of B. anthracis upon infection. The class Ib RNR operon in B. anthracis encodes genes for the catalytic NrdE protein, the tyrosyl radical metalloprotein NrdF, and the flavodoxin protein NrdI. The tyrosyl radical in NrdF is stabilized by an adjacent Mn(2)(III) site (Mn-NrdF) formed by the action of the NrdI protein or by a Fe(2)(III) site (Fe-NrdF) formed spontaneously from Fe(2+) and O(2). In this study, we show that the properties of B. anthracis Mn-NrdF and Fe-NrdF are in general similar for interaction with NrdE and NrdI. Intriguingly, the enzyme activity of Mn-NrdF was approximately an order of magnitude higher than that of Fe-NrdF in the presence of the class Ib-specific physiological reductant NrdH, strongly suggesting that the Mn-NrdF form is important in the life cycle of B. anthracis. Whether the Fe-NrdF form only exists in vitro or whether the NrdF protein in B. anthracis is a true cambialistic enzyme that can work with either manganese or iron remains to be established.
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Affiliation(s)
- Mikael Crona
- Department of Molecular Biology and Functional Genomics, Arrhenius Laboratories for Natural Sciences, Stockholm University SE-10691 Stockholm, Sweden
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Zhang Y, Stubbe J. Bacillus subtilis class Ib ribonucleotide reductase is a dimanganese(III)-tyrosyl radical enzyme. Biochemistry 2011; 50:5615-23. [PMID: 21561096 DOI: 10.1021/bi200348q] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacillus subtilis class Ib ribonucleotide reductase (RNR) catalyzes the conversion of nucleotides to deoxynucleotides, providing the building blocks for DNA replication and repair. It is composed of two proteins: α (NrdE) and β (NrdF). β contains the metallo-cofactor, essential for the initiation of the reduction process. The RNR genes are organized within the nrdI-nrdE-nrdF-ymaB operon. Each protein has been cloned, expressed, and purified from Escherichia coli. As isolated, recombinant NrdF (rNrdF) contained a diferric-tyrosyl radical [Fe(III)(2)-Y(•)] cofactor. Alternatively, this cluster could be self-assembled from apo-rNrdF, Fe(II), and O(2). Apo-rNrdF loaded using 4 Mn(II)/β(2), O(2), and reduced NrdI (a flavodoxin) can form a dimanganese(III)-Y(•) [Mn(III)(2)-Y(•)] cofactor. In the presence of rNrdE, ATP, and CDP, Mn(III)(2)-Y(•) and Fe(III)(2)-Y(•) rNrdF generate dCDP at rates of 132 and 10 nmol min(-1) mg(-1), respectively (both normalized for 1 Y(•)/β(2)). To determine the endogenous cofactor of NrdF in B. subtilis, the entire operon was placed behind a Pspank(hy) promoter and integrated into the B. subtilis genome at the amyE site. All four genes were induced in cells grown in Luria-Bertani medium, with levels of NrdE and NrdF elevated 35-fold relative to that of the wild-type strain. NrdE and NrdF were copurified in a 1:1 ratio from this engineered B. subtilis. The visible, EPR, and atomic absorption spectra of the purified NrdENrdF complex (eNrdF) exhibited characteristics of a Mn(III)(2)-Y(•) center with 2 Mn/β(2) and 0.5 Y(•)/β(2) and an activity of 318-363 nmol min(-1) mg(-1) (normalized for 1 Y(•)/β(2)). These data strongly suggest that the B. subtilis class Ib RNR is a Mn(III)(2)-Y(•) enzyme.
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Affiliation(s)
- Yan Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Barh D, Jain N, Tiwari S, Parida BP, D'Afonseca V, Li L, Ali A, Santos AR, Guimarães LC, de Castro Soares S, Miyoshi A, Bhattacharjee A, Misra AN, Silva A, Kumar A, Azevedo V. A novel comparative genomics analysis for common drug and vaccine targets in Corynebacterium pseudotuberculosis and other CMN group of human pathogens. Chem Biol Drug Des 2011; 78:73-84. [PMID: 21443692 DOI: 10.1111/j.1747-0285.2011.01118.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Caseous lymphadenitis is a chronic goat and sheep disease caused by Corynebacterium pseudotuberculosis (Cp) that accounts for a huge economic loss worldwide. Proper vaccination or medication is not available because of the lack of understanding of molecular biology of the pathogen. In a recent approach, four Cp (CpFrc41, Cp1002, CpC231, and CpI-19) genomes were sequenced to elucidate the molecular pathology of the bacteria. In this study, using these four genome sequences along with other eight genomes (total 12 genomes) and a novel subtractive genomics approach (first time ever applied to a veterinary pathogen), we identified potential conserved common drug and vaccine targets of these four Cp strains along with other Corybacterium, Mycobacterium and Nocardia (CMN) group of human pathogens (Corynebacterium diphtheriae and Mycobacterium tuberculosis) considering goat, sheep, bovine, horse, and human as the most affected hosts. The minimal genome of Cp1002 was found to consist of 724 genes, and 20 conserved common targets (to all Cp strains as well as CMN group of pathogens) from various metabolic pathways (13 from host-pathogen common and seven from pathogen's unique pathways) are potential targets irrespective of all hosts considered. ubiA from host-pathogen common pathway and an ABC-like transporter from unique pathways may serve dual (drug and vaccine) targets. Two Corynebacterium-specific (mscL and resB) and one broad-spectrum (rpmB) novel targets were also identified. Strain-specific targets are also discussed. Six important targets were subjected to virtual screening, and one compound was found to be potent enough to render two targets (cdc and nrdL). We are currently validating all identified targets and lead compounds.
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Affiliation(s)
- Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, India.
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Martin JE, Imlay JA. The alternative aerobic ribonucleotide reductase of Escherichia coli, NrdEF, is a manganese-dependent enzyme that enables cell replication during periods of iron starvation. Mol Microbiol 2011; 80:319-34. [PMID: 21338418 DOI: 10.1111/j.1365-2958.2011.07593.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The genome of Escherichia coli encodes two class I ribonucleotide reductases. The first, NrdAB, is a well-studied iron-dependent enzyme that is essential for aerobic growth. The second, NrdEF, is not functional under routine conditions, and its role is obscure. Recent studies demonstrated that NrdEF can be activated in vitro by manganese as well as iron. Since iron enzymes are potential targets for hydrogen peroxide, and since the nrdHIEF operon is induced during H(2) O(2) stress, we hypothesized that H(2) O(2) might inactivate NrdAB and that NrdEF might be induced to compensate. This idea was tested using E. coli mutants that are chronically stressed by H(2) O(2) . Contrary to expectation, NrdAB remained active. Its resistance to H(2) O(2) depended upon YfaE, which helps to activate NrdB. The induction of NrdEF during H(2) O(2) stress was mediated by the inactivation of Fur, an iron-dependent repressor. This regulatory arrangement implied that NrdEF has a physiological role during periods of iron starvation. Indeed, NrdEF supported cell replication in iron-depleted cells. Iron bound to NrdF when it was expressed in iron-rich cells, but NrdEF was functional only in cells that were both iron-depleted and manganese-rich. Thus NrdEF supports DNA replication when iron is unavailable to activate the housekeeping NrdAB enzyme.
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Affiliation(s)
- Julia E Martin
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
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Stubbe J, Cotruvo JA. Control of metallation and active cofactor assembly in the class Ia and Ib ribonucleotide reductases: diiron or dimanganese? Curr Opin Chem Biol 2011; 15:284-90. [PMID: 21216656 DOI: 10.1016/j.cbpa.2010.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 11/27/2010] [Accepted: 12/01/2010] [Indexed: 12/28/2022]
Abstract
Ribonucleotide reductases (RNRs) convert nucleotides to deoxynucleotides in all organisms. Activity of the class Ia and Ib RNRs requires a stable tyrosyl radical (Yⁱ), which can be generated by the reaction of O2 with a diferrous cluster on the β subunit to form active diferric-Yⁱ cofactor. Recent experiments have demonstrated, however, that in vivo the class Ib RNR contains an active dimanganese(III)-Yⁱ cofactor. The similar metal binding sites of the class Ia and Ib RNRs, their ability to bind both MnII and FeII, and the activity of the class Ib RNR with both diferric-Yⁱ and dimanganese(III)-Y cofactors raise the intriguing question of how the cell prevents mismetallation of these essential enzymes. The presence of the class Ib RNR in numerous pathogenic bacteria also highlights the importance of manganese for these organisms' growth and virulence.
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Affiliation(s)
- JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
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Johansson R, Torrents E, Lundin D, Sprenger J, Sahlin M, Sjöberg BM, Logan DT. High-resolution crystal structures of the flavoprotein NrdI in oxidized and reduced states--an unusual flavodoxin. Structural biology. FEBS J 2010; 277:4265-77. [PMID: 20831589 DOI: 10.1111/j.1742-4658.2010.07815.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The small flavoprotein NrdI is an essential component of the class Ib ribonucleotide reductase system in many bacteria. NrdI interacts with the class Ib radical generating protein NrdF. It is suggested to be involved in the rescue of inactivated diferric centres or generation of active dimanganese centres in NrdF. Although NrdI bears a superficial resemblance to flavodoxin, its redox properties have been demonstrated to be strikingly different. In particular, NrdI is capable of two-electron reduction, whereas flavodoxins are exclusively one-electron reductants. This has been suggested to depend on a lesser destabilization of the negatively-charged hydroquinone state than in flavodoxins. We have determined the crystal structures of NrdI from Bacillus anthracis, the causative agent of anthrax, in the oxidized and semiquinone forms, at resolutions of 0.96 and 1.4 Å, respectively. These structures, coupled with analysis of all curated NrdI sequences, suggest that NrdI defines a new structural family within the flavodoxin superfamily. The conformational behaviour of NrdI in response to FMN reduction is very similar to that of flavodoxins, involving a peptide flip in a loop near the N5 atom of the flavin ring. However, NrdI is much less negatively charged than flavodoxins, which is expected to affect its redox properties significantly. Indeed, sequence analysis shows a remarkable spread in the predicted isoelectric points of NrdIs, from approximately pH 4-10. The implications of these observations for class Ib ribonucleotide reductase function are discussed.
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Affiliation(s)
- Renzo Johansson
- Department of Biochemistry and Structural Biology, Lund University, Sweden
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Staphylococcus aureus NrdH redoxin is a reductant of the class Ib ribonucleotide reductase. J Bacteriol 2010; 192:4963-72. [PMID: 20675493 DOI: 10.1128/jb.00539-10] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococci contain a class Ib NrdEF ribonucleotide reductase (RNR) that is responsible, under aerobic conditions, for the synthesis of deoxyribonucleotide precursors for DNA synthesis and repair. The genes encoding that RNR are contained in an operon consisting of three genes, nrdIEF, whereas many other class Ib RNR operons contain a fourth gene, nrdH, that determines a thiol redoxin protein, NrdH. We identified a 77-amino-acid open reading frame in Staphylococcus aureus that resembles NrdH proteins. However, S. aureus NrdH differs significantly from the canonical NrdH both in its redox-active site, C-P-P-C instead of C-M/V-Q-C, and in the absence of the C-terminal [WF]SGFRP[DE] structural motif. We show that S. aureus NrdH is a thiol redox protein. It is not essential for aerobic or anaerobic growth and appears to have a marginal role in protection against oxidative stress. In vitro, S. aureus NrdH was found to be an efficient reductant of disulfide bonds in low-molecular-weight substrates and proteins using dithiothreitol as the source of reducing power and an effective reductant for the homologous class Ib RNR employing thioredoxin reductase and NADPH as the source of the reducing power. Its ability to reduce NrdEF is comparable to that of thioredoxin-thioredoxin reductase. Hence, S. aureus contains two alternative thiol redox proteins, NrdH and thioredoxin, with both proteins being able to function in vitro with thioredoxin reductase as the immediate hydrogen donors for the class Ib RNR. It remains to be clarified under which in vivo physiological conditions the two systems are used.
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Leiting W, Jianping X. Comparative genomics analysis of Mycobacterium NrdH-redoxins. Microb Pathog 2010; 48:97-102. [DOI: 10.1016/j.micpath.2010.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 01/10/2010] [Accepted: 01/14/2010] [Indexed: 10/19/2022]
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Lundin D, Torrents E, Poole AM, Sjöberg BM. RNRdb, a curated database of the universal enzyme family ribonucleotide reductase, reveals a high level of misannotation in sequences deposited to Genbank. BMC Genomics 2009; 10:589. [PMID: 19995434 PMCID: PMC2795772 DOI: 10.1186/1471-2164-10-589] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 12/08/2009] [Indexed: 11/10/2022] Open
Abstract
Background Ribonucleotide reductases (RNRs) catalyse the only known de novo pathway for deoxyribonucleotide synthesis, and are therefore essential to DNA-based life. While ribonucleotide reduction has a single evolutionary origin, significant differences between RNRs nevertheless exist, notably in cofactor requirements, subunit composition and allosteric regulation. These differences result in distinct operational constraints (anaerobicity, iron/oxygen dependence and cobalamin dependence), and form the basis for the classification of RNRs into three classes. Description In RNRdb (Ribonucleotide Reductase database), we have collated and curated all known RNR protein sequences with the aim of providing a resource for exploration of RNR diversity and distribution. By comparing expert manual annotations with annotations stored in Genbank, we find that significant inaccuracies exist in larger databases. To our surprise, only 23% of protein sequences included in RNRdb are correctly annotated across the key attributes of class, role and function, with 17% being incorrectly annotated across all three categories. This illustrates the utility of specialist databases for applications where a high degree of annotation accuracy may be important. The database houses information on annotation, distribution and diversity of RNRs, and links to solved RNR structures, and can be searched through a BLAST interface. RNRdb is accessible through a public web interface at http://rnrdb.molbio.su.se. Conclusion RNRdb is a specialist database that provides a reliable annotation and classification resource for RNR proteins, as well as a tool to explore distribution patterns of RNR classes. The recent expansion in available genome sequence data have provided us with a picture of RNR distribution that is more complex than believed only a few years ago; our database indicates that RNRs of all three classes are found across all three cellular domains. Moreover, we find a number of organisms that encode all three classes.
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Affiliation(s)
- Daniel Lundin
- Department of Molecular Biology and Functional Genomics, Stockholm University, Stockholm, Sweden.
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Jacquot JP, Eklund H, Rouhier N, Schürmann P. Structural and evolutionary aspects of thioredoxin reductases in photosynthetic organisms. TRENDS IN PLANT SCIENCE 2009; 14:336-43. [PMID: 19446492 DOI: 10.1016/j.tplants.2009.03.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 03/27/2009] [Accepted: 03/31/2009] [Indexed: 05/24/2023]
Abstract
Thioredoxins (Trxs) are small oxidoreductases that are involved in redox homeostasis and are found in large numbers in the subcellular compartments of eukaryotic plant cells, including the chloroplasts. Also present in chloroplasts are two forms of thioredoxin reductase (TR), which use either NADPH or ferredoxin as an electron donor. In other compartments, two additional TR forms also use NADPH: one is distributed in all photosynthetic organisms and is similar to prokaryotic enzymes, whereas the other is restricted to algae and is similar to mammalian selenoproteins. Here, we review current knowledge of the different forms of TRs across organisms and discuss the possible evolutionary fate of this class of enzymes, which provide an example of convergent functional evolution.
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Affiliation(s)
- Jean-Pierre Jacquot
- Interactions Arbres Microorganismes UMR 1136, IFR 110, Nancy University, BP 239, 54506 Vandoeuvre Cedex, France.
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65
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Alves R, Vilaprinyo E, Sorribas A, Herrero E. Evolution based on domain combinations: the case of glutaredoxins. BMC Evol Biol 2009; 9:66. [PMID: 19321008 PMCID: PMC2679010 DOI: 10.1186/1471-2148-9-66] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Accepted: 03/25/2009] [Indexed: 11/12/2022] Open
Abstract
Background Protein domains represent the basic units in the evolution of proteins. Domain duplication and shuffling by recombination and fusion, followed by divergence are the most common mechanisms in this process. Such domain fusion and recombination events are predicted to occur only once for a given multidomain architecture. However, other scenarios may be relevant in the evolution of specific proteins, such as convergent evolution of multidomain architectures. With this in mind, we study glutaredoxin (GRX) domains, because these domains of approximately one hundred amino acids are widespread in archaea, bacteria and eukaryotes and participate in fusion proteins. GRXs are responsible for the reduction of protein disulfides or glutathione-protein mixed disulfides and are involved in cellular redox regulation, although their specific roles and targets are often unclear. Results In this work we analyze the distribution and evolution of GRX proteins in archaea, bacteria and eukaryotes. We study over one thousand GRX proteins, each containing at least one GRX domain, from hundreds of different organisms and trace the origin and evolution of the GRX domain within the tree of life. Conclusion Our results suggest that single domain GRX proteins of the CGFS and CPYC classes have, each, evolved through duplication and divergence from one initial gene that was present in the last common ancestor of all organisms. Remarkably, we identify a case of convergent evolution in domain architecture that involves the GRX domain. Two independent recombination events of a TRX domain to a GRX domain are likely to have occurred, which is an exception to the dominant mechanism of domain architecture evolution.
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Affiliation(s)
- Rui Alves
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, IRBLleida, Lleida, Spain.
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66
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Lillig CH, Berndt C, Holmgren A. Glutaredoxin systems. Biochim Biophys Acta Gen Subj 2008; 1780:1304-17. [DOI: 10.1016/j.bbagen.2008.06.003] [Citation(s) in RCA: 416] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 06/11/2008] [Accepted: 06/11/2008] [Indexed: 12/15/2022]
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NrdI, a flavodoxin involved in maintenance of the diferric-tyrosyl radical cofactor in Escherichia coli class Ib ribonucleotide reductase. Proc Natl Acad Sci U S A 2008; 105:14383-8. [PMID: 18799738 DOI: 10.1073/pnas.0807348105] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribonucleotide reductase (RNR) catalyzes the conversion of nucleotides to deoxynucleotides and is essential in all organisms. Class I RNRs consist of two homodimeric subunits: alpha2 and beta2. The alpha subunit contains the site of nucleotide reduction, and the beta subunit contains the essential diferric-tyrosyl radical (Y*) cofactor. Escherichia coli contains genes encoding two class I RNRs (Ia and Ib) and a class III RNR, which is active only under anaerobic conditions. Its class Ia RNR, composed of NrdA (alpha) and NrdB (beta), is expressed under normal aerobic growth conditions. The class Ib RNR, composed of NrdE (alpha) and NrdF (beta), is expressed under oxidative stress and iron-limited growth conditions. Our laboratory is interested in pathways of cofactor biosynthesis and maintenance in class I RNRs and modulation of Y* levels as a means of regulating RNR activity. Our recent studies have implicated a [2Fe2S]-ferredoxin, YfaE, in the NrdB diferric-Y* maintenance pathway and possibly in the biosynthetic and regulatory pathways. Here, we report that NrdI is a flavodoxin counterpart to YfaE for the class Ib RNR. It possesses redox properties unprecedented for a flavodoxin (E(ox/sq) = -264 +/- 17 mV and E(sq/hq) = -255 +/- 17 mV) that allow it to mediate a two-electron reduction of the diferric cluster of NrdF via two successive one-electron transfers. Data presented support the presence of a distinct maintenance pathway for NrdEF, orthogonal to that for NrdAB involving YfaE.
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NrdI essentiality for class Ib ribonucleotide reduction in Streptococcus pyogenes. J Bacteriol 2008; 190:4849-58. [PMID: 18502861 DOI: 10.1128/jb.00185-08] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The Streptococcus pyogenes genome harbors two clusters of class Ib ribonucleotide reductase genes, nrdHEF and nrdF*I*E*, and a second stand-alone nrdI gene, designated nrdI2. We show that both clusters are expressed simultaneously as two independent operons. The NrdEF enzyme is functionally active in vitro, while the NrdE*F* enzyme is not. The NrdF* protein lacks three of the six highly conserved iron-liganding side chains and cannot form a dinuclear iron site or a tyrosyl radical. In vivo, on the other hand, both operons are functional in heterologous complementation in Escherichia coli. The nrdF*I*E* operon requires the presence of the nrdI* gene, and the nrdHEF operon gained activity upon cotranscription of the heterologous nrdI gene from Streptococcus pneumoniae, while neither nrdI* nor nrdI2 from S. pyogenes rendered it active. Our results highlight the essential role of the flavodoxin NrdI protein in vivo, and we suggest that it is needed to reduce met-NrdF, thereby enabling the spontaneous reformation of the tyrosyl radical. The NrdI* flavodoxin may play a more direct role in ribonucleotide reduction by the NrdF*I*E* system. We discuss the possibility that the nrdF*I*E* operon has been horizontally transferred to S. pyogenes from Mycoplasma spp.
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69
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Vlamis-Gardikas A. The multiple functions of the thiol-based electron flow pathways of Escherichia coli: Eternal concepts revisited. Biochim Biophys Acta Gen Subj 2008; 1780:1170-200. [PMID: 18423382 DOI: 10.1016/j.bbagen.2008.03.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2007] [Revised: 03/18/2008] [Accepted: 03/22/2008] [Indexed: 10/22/2022]
Abstract
Electron flow via thiols is a theme with many variations in all kingdoms of life. The favourable physichochemical properties of the redox active couple of two cysteines placed in the optimised environment of the thioredoxin fold allow for two electron transfers in between top biological reductants and ultimate oxidants. The reduction of ribonucleotide reductases by thioredoxin and thioredoxin reductase of Escherichia coli (E. coli) was one of the first pathways to be elucidated. Diverse functions such as protein folding in the periplasm, maturation of respiratory enzymes, detoxification of hydrogen peroxide and prevention of oxidative damage may be based on two electron transfers via thiols. A growing field is the relation of thiol reducing pathways and the interaction of E. coli with different organisms. This concept combined with the sequencing of the genomes of different bacteria may allow for the identification of fine differences in the systems employing thiols for electron flow between pathogens and their corresponding mammalian hosts. The emerging possibility is the development of novel antibiotics.
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Affiliation(s)
- Alexios Vlamis-Gardikas
- Center of Basic Research I-Biochemistry Division, Biomedical Research Foundation (BRFAA), Academy of Athens, Soranou Efessiou 4, GR-11527 Athens, Greece.
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70
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Kannan G, Wilks JC, Fitzgerald DM, Jones BD, Bondurant SS, Slonczewski JL. Rapid acid treatment of Escherichia coli: transcriptomic response and recovery. BMC Microbiol 2008; 8:37. [PMID: 18302792 PMCID: PMC2270276 DOI: 10.1186/1471-2180-8-37] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Accepted: 02/26/2008] [Indexed: 11/10/2022] Open
Abstract
Background Many E. coli genes show pH-dependent expression during logarithmic growth in acid (pH 5–6) or in base (pH 8–9). The effect of rapid pH change, however, has rarely been tested. Rapid acid treatment could distinguish between genes responding to external pH, and genes responding to cytoplasmic acidification, which occurs transiently following rapid external acidification. It could reveal previously unknown acid-stress genes whose effects are transient, as well as show which acid-stress genes have a delayed response. Results Microarray hybridization was employed to observe the global gene expression of E. coli K-12 W3110 following rapid acidification of the external medium, from pH 7.6 to pH 5.5. Fluorimetric observation of pH-dependent tetR-YFP showed that rapid external acidification led to a half-unit drop in cytoplasmic pH (from pH 7.6 to pH 6.4) which began to recover within 20 s. Following acid treatment, 630 genes were up-regulated and 586 genes were down-regulated. Up-regulated genes included amino-acid decarboxylases (cadA, adiY, gadA), succinate dehydrogenase (sdhABCD), biofilm-associated genes (bdm, gatAB, and ymgABC), and the Gad, Fur and Rcs regulons. Genes with response patterns consistent with cytoplasmic acid stress were revealed by addition of benzoate, a membrane-permeant acid that permanently depresses cytoplasmic pH without affecting external pH. Several genes (yagU, ygiN, yjeI, and yneI) were up-regulated specifically by external acidification, while other genes (fimB, ygaC, yhcN, yhjX, ymgABC, yodA) presented a benzoate response consistent with cytoplasmic pH stress. Other genes (the nuo operon for NADH dehydrogenase I, and the HslUV protease) showed delayed up-regulation by acid, with expression rising by 10 min following the acid shift. Conclusion Transcriptomic profiling of E. coli K-12 distinguished three different classes of change in gene expression following rapid acid treatment: up-regulation with or without recovery, and delayed response to acid. For eight genes showing acid response and recovery (fimB, ygaC, yhcN, yhjX, ymgABC, yodA), responses to the permeant acid benzoate revealed expression patterns consistent with sensing of cytoplasmic pH. The delayed acid response of nuo genes shows that NADH dehydrogenase I is probably induced as a secondary result of acid-associated metabolism, not as a direct response to cytoplasmic acidification.
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Affiliation(s)
- Geetha Kannan
- Department of Biology, Kenyon College, Gambier, OH, 43022 USA.
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71
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Akyol I. Regulation of the ribonucleotide reductases in Lactococcus lactis subsp. cremoris. ACTA BIOLOGICA HUNGARICA 2007; 58:105-14. [PMID: 17385548 DOI: 10.1556/abiol.58.2007.1.10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Lactococcus lactis has two essential ribonucleotide reductases for DNA biosynthesis and repair which are affected in the presence or absence of oxygen. Expression of glutaredoxin like protein (NrdH), the hydrogen donor for ribonucleotide reductase, was found to be regulated by the FNR like proteins (FlpA and FlpB). Proteomics study demonstrated that expression level of NrdH significantly decreased in the flpA and flpAB deletion mutants. The nrdH gene is located in an nrdHIEF operon and encoding the NrdEF ribonucleotide reductase, which is active under aerobic and anaerobic conditions. Regulation of expression of the nrdHIEF operons was investigated using beta-galactosidase as a reporter gene. The 588 bp fragment containing the nrdH promoter and gene cloned into the pORI vector immediately upstream of a promoterless lacZ gene. Constructed plasmid was transferred into wild type (MG1363), single mutant (flpA orflpB) and double mutant (flpAB). Aerobically, nrdH promoter activity is 15-fold higher than anaerobic expression.
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Affiliation(s)
- I Akyol
- Animal Science Department, Agriculture Faculty, Kahramanmaras Sutcu Imam University, 46060, Kahramanmaras, Turkey.
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72
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Porat A, Lillig CH, Johansson C, Fernandes AP, Nilsson L, Holmgren A, Beckwith J. The reducing activity of glutaredoxin 3 toward cytoplasmic substrate proteins is restricted by methionine 43. Biochemistry 2007; 46:3366-77. [PMID: 17305371 PMCID: PMC2518409 DOI: 10.1021/bi6024353] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reducing proteins glutaredoxin 3 (Grx3) and glutaredoxin 1 (Grx1) are structurally similar but exhibit different specificities toward substrates. Grx1 efficiently reduces ribonucleotide reductase and PAPS reductase, while Grx3 reduces these enzymes inefficiently or not at all. We previously described a selection for Grx3 mutants with increased activity toward substrates of Grx1 in vivo. Remarkably, we repeatedly isolated mutants with changes in only one of the amino acids of Grx3, methionine 43, converting it to either valine, leucine, or isoleucine. In this paper we present additional genetic studies and a biochemical characterization of Grx3-Met43Val, the most efficient mutant. We show that Grx3-Met43Val is able to reduce ribonucleotide reductae and PAPS reductase much more efficiently than the wild-type protein in vitro. The altered protein has an increased Vmax over that of Grx3, nearly the same Vmax as Grx1 while the Km remains high. Molecular dynamics simulations suggest that the Met43Val substitution results in changes in properties of the N-terminal cysteine of the active site leading to a considerably lower pKa. Furthermore, Grx3-Met43Val shows an 11 mV lower redox potential than the wild-type Grx3. These findings provide biochemical and structural explanations for the increased reductive efficiency of the mutant Grx3.
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Affiliation(s)
- Amir Porat
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, USA
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73
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Härtig E, Hartmann A, Schätzle M, Albertini AM, Jahn D. The Bacillus subtilis nrdEF genes, encoding a class Ib ribonucleotide reductase, are essential for aerobic and anaerobic growth. Appl Environ Microbiol 2006; 72:5260-5. [PMID: 16885274 PMCID: PMC1538738 DOI: 10.1128/aem.00599-06] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ribonucleotide reductases (RNRs) are essential for the biosynthesis of the deoxyribonucleoside triphosphates of DNA. Recently, it was proposed that externally supplied deoxyribonucleosides or DNA is required for the growth of Bacillus subtilis under strict anaerobic conditions (M. J. Folmsbee, M. J. McInerney, and D. P. Nagle, Appl. Environ. Microbiol. 70:5252-5257, 2004). Cultivation of B. subtilis on minimal medium in the presence of oxygen indicators in combination with oxygen electrode measurements and viable cell counting demonstrated that growth occurred under strict anaerobic conditions in the absence of externally supplied deoxyribonucleosides. The nrdEF genes encode the only obvious RNR in B. subtilis. A temperature-sensitive nrdE mutant failed to grow under aerobic and anaerobic conditions, indicating that this oxygen-dependent class I RNR has an essential role under both growth conditions. Aerobic growth and anaerobic growth of the nrdE mutant were rescued by addition of deoxynucleotides. The nrd locus consists of an nrdI-nrdE-nrdF-ymaB operon. The 5' end of the corresponding mRNA revealed transcriptional start sites 45 and 48 bp upstream of the translational start of nrdI. Anaerobic transcription of the operon was found to be dependent on the presence of intact genes for the ResDE two-component redox regulatory system. Two potential ResD binding sites were identified approximately 62 bp (site A) and 50 bp (site B) upstream of the transcriptional start sites by a bioinformatic approach. Only mutation of site B eliminated nrd expression. Aerobic transcription was ResDE independent but required additional promoter elements localized between 88 and 275 bp upstream of the transcriptional start.
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Affiliation(s)
- Elisabeth Härtig
- Institute of Microbiology, Technical University of Braunschweig, D-38106 Braunschweig, Germany.
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74
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Abstract
DNA microarrays were used to probe the transcriptional response of Escherichia coli to N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine (TPEN). Fifty-five transcripts were significantly up-regulated, including all of the genes that are regulated by Zur and many that are regulated by Fur. In the same TPEN-treated cells, 46 transcripts were significantly down-regulated.
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Affiliation(s)
- Tara K Sigdel
- Department of Chemistry and Biochemistry, 160 Hughes Hall, Miami University, Oxford, OH 45056, USA
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75
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Abstract
Ribonucleotide reductases (RNRs) transform RNA building blocks to DNA building blocks by catalyzing the substitution of the 2'OH-group of a ribonucleotide with a hydrogen by a mechanism involving protein radicals. Three classes of RNRs employ different mechanisms for the generation of the protein radical. Recent structural studies of members from each class have led to a deeper understanding of their catalytic mechanism and allosteric regulation by nucleoside triphosphates. The main emphasis of this review is on regulation of RNR at the molecular and cellular level. Conformational transitions induced by nucleotide binding determine the regulation of substrate specificity. An intricate interplay between gene activation, enzyme inhibition, and protein degradation regulates, together with the allosteric effects, enzyme activity and provides the appropriate amount of deoxynucleotides for DNA replication and repair. In spite of large differences in the amino acid sequences, basic structural features are remarkably similar and suggest a common evolutionary origin for the three classes.
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Affiliation(s)
- Pär Nordlund
- Division of Biophysics and 2Division of Biochemistry, Medical Nobel Institute, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden.
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76
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Gon S, Faulkner MJ, Beckwith J. In vivo requirement for glutaredoxins and thioredoxins in the reduction of the ribonucleotide reductases of Escherichia coli. Antioxid Redox Signal 2006; 8:735-42. [PMID: 16771665 DOI: 10.1089/ars.2006.8.735] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Escherichia coli expresses three types of ribonucleotide reductases (RNRs) that utilize the redox chemistry of cysteine to catalyze the reduction of ribonucleotides. Upon reduction, the cysteines form a disulfide bond and must be reduced. The authors present in vivo studies that shed light on the mechanism by which these enzymes are regenerated. The class Ia enzyme, NrdAB, can be reduced by either the thioredoxins 1 and 2 or by glutaredoxin 1. The class Ib enzyme, NrdEF, is reduced in vivo by a dedicated glutaredoxin-like protein, NrdH. Despite its similarities to glutaredoxins, this protein is itself reduced by thioredoxin reductase in vivo. However, in the absence of thioredoxin reductase and NrdH, glutaredoxin 1 can partially replace NrdH. Despite their similar structures, the NrdEF and NrdAB RNRs differ in their abilities to function under low oxygen conditions. With only traces of oxygen present, NrdAB can allow some growth in the absence of the anaerobic enzyme NrdDG. NrdEF cannot. Furthermore, in anaerobiosis, E. coli is dependent for growth on class III RNR, NrdDG, and on having at least one of the two reductive systems, thioredoxin reductase or glutathione reductase. These findings indicate a role for these enzymes either for NrdDG reactivation or some other essential anaerobic process.
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Affiliation(s)
- Stéphanie Gon
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, USA.
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77
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Kim Y, Subramaniam S. Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships. Proteins 2006; 62:1115-24. [PMID: 16385560 DOI: 10.1002/prot.20830] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Phylogenetic profiles encode patterns of presence or absence of genes across genomes, and these profiles can be used to assign functional relationships to nonhomologous pairs of proteins (Pellegrini et al., Proc Natl Acad Sci USA 1999;96:4284-4288). Although it is well known that many proteins were created from combinations of domains, most of the existing implementations of phylogenetic profiles do not consider this fact. Here, we introduce an extension that considers the multidomain nature of proteins and test the method against the known interaction data sets. Whereas earlier implementations associated one entire sequence with one protein phylogenetic profile (Single-Profile), our method instead breaks the sequence into a set of segments of predetermined size and constructs a separate profile for each segment (Multiple-Profile). The results show that the Multiple-Profile method performs as well as the Single-Profile method. However, the two methods share, surprisingly, a small fraction of their predictions, indicating that the Multiple-Profile method can detect known interactions missed by the Single-Profile method. Thus, the Multiple-Profile method can be used with other methods to determine functional relationships on a genome scale with wider coverage.
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Affiliation(s)
- Yohan Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0505, USA
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78
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Kilstrup M, Hammer K, Ruhdal Jensen P, Martinussen J. Nucleotide metabolism and its control in lactic acid bacteria. FEMS Microbiol Rev 2005. [DOI: 10.1016/j.fmrre.2005.04.006] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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79
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Discola KF, de Oliveira MA, Monteiro Silva G, Barcena JA, Porras P, Padilla A, Netto LES, Guimarães BG. Crystallization and preliminary X-ray crystallographic studies of glutaredoxin 2 from Saccharomyces cerevisiae in different oxidation states. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:445-7. [PMID: 16511065 PMCID: PMC1952414 DOI: 10.1107/s1744309105008730] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2005] [Accepted: 03/17/2005] [Indexed: 01/17/2023]
Abstract
Glutaredoxins are small (9-12 kDa) heat-stable proteins that are highly conserved throughout evolution; the glutaredoxin active site (Cys-Pro-Tyr-Cys) is conserved in most species. Five glutaredoxin genes have been identified in Saccharomyces cerevisiae; however, Grx2 is responsible for the majority of oxidoreductase activity in the cell, suggesting that its primary function may be the detoxification of mixed disulfides generated by reactive oxygen species (ROS). Recombinant Grx2 was expressed in Escherichia coli as a 6xHis-tagged fusion protein and purified by nickel-affinity chromatography. Prior to crystallization trials, the enzyme was submitted to various treatments with reducing agents and peroxides. Crystals suitable for X-ray diffraction experiments were obtained from untreated protein and protein oxidized with t-butyl hydroperoxide (10 mM). Complete data sets were collected to resolutions 2.15 and 2.05 A for untreated and oxidized Grx2, respectively, using a synchrotron-radiation source. The crystals belong to space group P4(1)2(1)2, with similar unit-cell parameters.
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Affiliation(s)
- Karen Fulan Discola
- Departamento de Biologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo, SP, Brazil
| | - Marcos Antonio de Oliveira
- Departamento de Biologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo, SP, Brazil
| | - Gustavo Monteiro Silva
- Departamento de Biologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo, SP, Brazil
| | - José Antonio Barcena
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Edificio ‘Severo Ochoa’, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Pablo Porras
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Edificio ‘Severo Ochoa’, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Alicia Padilla
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Edificio ‘Severo Ochoa’, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Luis Eduardo Soares Netto
- Departamento de Biologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo, SP, Brazil
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80
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Stehr M, Lindqvist Y. NrdH-redoxin of Corynebacterium ammoniagenes forms a domain-swapped dimer. Proteins 2004; 55:613-9. [PMID: 15103625 DOI: 10.1002/prot.20126] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
NrdH-redoxins constitute a family of small redox proteins, which contain a conserved CXXC sequence motif, and are characterized by a glutaredoxin-like amino acid sequence but a thioredoxin-like activity profile. Here we report the structure of Corynebacterium ammoniagenes NrdH at 2.7 A resolution, determined by molecular replacement using E. coli NrdH as model. The structure is the first example of a domain-swapped dimer from the thioredoxin family. The domain-swapped structure is formed by an inter-chain two-stranded anti-parallel beta-sheet and is stabilized by electrostatic interactions at the dimer interface. Size exclusion chromatography, and MALDI-ESI experiments revealed however, that the protein exists as a monomer in solution. Similar to E. coli NrdH-redoxin and thioredoxin, C. ammoniagenes NrdH-redoxin has a wide hydrophobic pocket at the surface that could be involved in binding to thioredoxin reductase. However, the loop between alpha2 and beta3, which is complementary to a crevice in the reductase in the thioredoxin-thioredoxin reductase complex, is the hinge for formation of the swapped dimer in C. ammoniagenes NrdH-redoxin. C. ammoniagenes NrdH-redoxin has the highly conserved sequence motif W61-S-G-F-R-P-[DE]67 which is unique to the NrdH-redoxins and which determines the orientation of helix alpha3. An extended hydrogen-bond network, similar to that in E. coli NrdH-redoxin, determines the conformation of the loop formed by the conserved motif.
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Affiliation(s)
- Matthias Stehr
- Division of Molecular Structural Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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81
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Fernandes AP, Holmgren A. Glutaredoxins: glutathione-dependent redox enzymes with functions far beyond a simple thioredoxin backup system. Antioxid Redox Signal 2004; 6:63-74. [PMID: 14713336 DOI: 10.1089/152308604771978354] [Citation(s) in RCA: 480] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Most cells contain high levels of glutathione and multiple glutaredoxins, which utilize the reducing power of glutathione to catalyze disulfide reductions in the presence of NADPH and glutathione reductase (the glutaredoxin system). Glutaredoxins, like thioredoxins, may operate as dithiol reductants and are involved as alternative pathways in cellular functions such as formation of deoxyribonucleotides for DNA synthesis (by reducing the essential enzyme ribonucleotide reductase), the generation of reduced sulfur (via 3'-phosphoadenylylsulfate reductase), signal transduction, and the defense against oxidative stress. The three dithiol glutaredoxins of E. coli with the active-site sequence CPYC and a glutathione binding site in a thioredoxin/glutaredoxin fold display surprisingly different properties. These include the inducible OxyR-regulated 10-kDa Grx1 or the highly abundant 24-kDa glutathione S-transferase-like Grx2 (with Grx3 it accounts for 1% of total protein). Glutaredoxins uniquely reduce mixed disulfides with glutathione via a monothiol mechanism where only an N-terminal low pKa Cys residue is required, by using their glutathione binding site. Glutaredoxins also catalyze formation of mixed disulfides (glutathionylation), which is an important redox regulatory mechanism, particularly in mammalian cells under oxidative stress conditions, to sense cellular redox potential.
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Affiliation(s)
- Aristi Potamitou Fernandes
- Medical Nobel Institute for Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
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82
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Kashima Y, Ishikawa K. A hyperthermostable novel protein-disulfide oxidoreductase is reduced by thioredoxin reductase from hyperthermophilic archaeon Pyrococcus horikoshii. Arch Biochem Biophys 2003; 418:179-85. [PMID: 14522589 DOI: 10.1016/j.abb.2003.08.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A redox protein gene (PH0178) with high sequence homology to a glutaredoxin from Pyrococcus furiosus and a thioredoxin reductase homologue gene (PH1426) were found in the genome sequence of Pyrococcus horikoshii. These two genes were cloned and the corresponding expressed proteins were characterized. The redox protein from PH0178 had strong thioredoxin-like activity, but no glutaredoxin activity. The protein from PH1426 had some reductase activity against thioredoxin from Escherichia coli as well as the redox protein (PH0178). The protein from PH1426 was a typical, homodimeric flavoprotein. These results indicate that the redox protein (PH0178) is not a glutaredoxin but, rather, a new protein-disulfide oxidoreductase that is involved in a thioredoxin-like system with thioredoxin reductase (PH1426) in P. horikoshii. The redox protein and thioredoxin reductase retained their full activities for over 1h at 100 degrees C. The redox potential of the redox protein was similar to that of thioredoxin from E. coli and lower than that of glutathione. Site-directed mutagenesis studies revealed that the active site of the redox protein corresponds to a CPYC sequence, located in the middle of the sequence.
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Affiliation(s)
- Yasuhiro Kashima
- The special division for Human Life Technology, National Institute of Advanced Industrial Science and Technology (AIST Kansai), 1-8-31 Midorigaoka, 563-8577, Ikeda, Osaka, Japan
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83
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Boston T, Atlung T. FNR-mediated oxygen-responsive regulation of the nrdDG operon of Escherichia coli. J Bacteriol 2003; 185:5310-3. [PMID: 12923108 PMCID: PMC180968 DOI: 10.1128/jb.185.17.5310-5313.2003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcription of the nrdDG operon, which encodes the class III nucleotide reductase, which is only active under anaerobic conditions, was strongly induced after a shift to anaerobiosis. The induction was completely dependent on the transcriptional activator FNR and was independent of the ArcA-ArcB two-component response regulator system. The nrdD transcript start site was mapped to a position immediately downstream of two FNR binding sites. Transcription of the other two nucleotide reductase operons, nrdAB and nrdEF, did not respond to oxygen conditions in a wild-type background, but nrdAB expression was increased in the fnr mutant under anaerobic conditions.
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Affiliation(s)
- T Boston
- Department of Life Sciences and Chemistry, Roskilde University, DK-4000 Roskilde, Denmark
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84
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Kern R, Malki A, Holmgren A, Richarme G. Chaperone properties of Escherichia coli thioredoxin and thioredoxin reductase. Biochem J 2003; 371:965-72. [PMID: 12549977 PMCID: PMC1223331 DOI: 10.1042/bj20030093] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2003] [Accepted: 01/28/2003] [Indexed: 11/17/2022]
Abstract
Thioredoxin, thioredoxin reductase and NADPH form the thioredoxin system and are the major cellular protein disulphide reductase. We report here that Escherichia coli thioredoxin and thioredoxin reductase interact with unfolded and denatured proteins, in a manner similar to that of molecular chaperones that are involved in protein folding and protein renaturation after stress. Thioredoxin and/or thioredoxin reductase promote the functional folding of citrate synthase and alpha-glucosidase after urea denaturation. They also promote the functional folding of the bacterial galactose receptor, a protein without any cysteines. Furthermore, redox cycling of thioredoxin/thioredoxin reductase in the presence of NADPH and cystine stimulates the renaturation of the galactose receptor, suggesting that the thioredoxin system functions like a redox-powered chaperone machine. Thioredoxin reductase prevents the aggregation of citrate synthase under heat-shock conditions. It forms complexes that are more stable than those formed by thioredoxin with several unfolded proteins such as reduced carboxymethyl alpha-lactalbumin and unfolded bovine pancreatic trypsin inhibitor. These results suggest that the thioredoxin system, in addition to its protein disulphide isomerase activity possesses chaperone-like properties, and that its thioredoxin reductase component plays a major role in this function.
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Affiliation(s)
- Renée Kern
- Stress Molecules, Institut Jacques Monod, Université Paris 7, 2 place Jussieu, 75005 Paris, France
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85
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Affiliation(s)
- Daniel Ritz
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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86
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Abstract
Disulfide bonds in proteins play various important roles. They are either formed as structural features to stabilize the protein or are found only transiently as part of a catalytic or regulatory cycle. In vivo, the formation and reduction of disulfide bonds is catalyzed by specialized thiol-disulfide exchanging enzymes that contain an active site with the sequence motif Cys-X-X-Cys. These proteins have structurally evolved to catalyze predominantly either oxidative reactions or reductive steps. There is mounting evidence that, in addition to the thiol redox potential, the spatial distribution within different cell compartments and the overall redox state of the cell are equally important. In the cytoplasm, multiple pathways play overlapping roles in the reduction of disulfide bonds and additionally, the expression of several components of thiol-redox pathways was shown to respond to the changes in the cellular thiol-redox equilibrium. In the periplasm, two systems coexist, one catalyzing thiol oxidation and the other disulfide reduction. Recent results suggest that two different mechanisms are used to translocate reducing power from the cytoplasm or to dissipate the electrons after oxidation.
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Affiliation(s)
- D Ritz
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
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87
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Masalha M, Borovok I, Schreiber R, Aharonowitz Y, Cohen G. Analysis of transcription of the Staphylococcus aureus aerobic class Ib and anaerobic class III ribonucleotide reductase genes in response to oxygen. J Bacteriol 2001; 183:7260-72. [PMID: 11717286 PMCID: PMC95576 DOI: 10.1128/jb.183.24.7260-7272.2001] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a gram-positive facultative aerobe that can grow in the absence of oxygen by fermentation or by using an alternative electron acceptor. To investigate the mechanism by which S. aureus is able to adapt to changes in oxygen concentration, we analyzed the transcriptional regulation of genes that encode the aerobic class Ib and anaerobic class III ribonucleotide reductase (RNR) systems that are responsible for the synthesis of deoxyribonucleotides needed for DNA synthesis. The S. aureus class Ib RNR nrdIEF and class III RNR nrdDG genes and their regulatory regions were cloned and sequenced. Inactivation of the nrdDG genes showed that the class III RNR is essential for anaerobic growth. Inhibition of aerobic growth by hydroxyurea showed that the class Ib RNR is an oxygen-dependent enzyme. Northern blot analysis and primer extension analysis demonstrated that transcription of class III nrdDG genes is regulated by oxygen concentration and was at least 10-fold higher under anaerobic than under aerobic conditions. In contrast, no significant effect of oxygen concentration was found on the transcription of class Ib nrdIEF genes. Disruption or deletion of S. aureus nrdDG genes caused up to a fivefold increase in nrdDG and nrdIEF transcription under anaerobic conditions but not under aerobic conditions. Similarly, hydroxyurea, an inhibitor of the class I RNRs, resulted in increased transcription of class Ib and class III RNR genes under aerobic conditions. These findings establish that transcription of class Ib and class III RNR genes is upregulated under conditions that cause the depletion of deoxyribonucleotide. Promoter analysis of class Ib and class III RNR operons identified several inverted-repeat elements that may account for the transcriptional response of the nrdIEF and nrdDG genes to oxygen.
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Affiliation(s)
- M Masalha
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
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88
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Andersson J, Bodevin S, Westman M, Sahlin M, Sjöberg BM. Two active site asparagines are essential for the reaction mechanism of the class III anaerobic ribonucleotide reductase from bacteriophage T4. J Biol Chem 2001; 276:40457-63. [PMID: 11526118 DOI: 10.1074/jbc.m106863200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Class III ribonucleotide reductase is an anaerobic enzyme that uses a glycyl radical to catalyze the reduction of ribonucleotides to deoxyribonucleotides and formate as ultimate reductant. The reaction mechanism of class III ribonucleotide reductases requires two cysteines within the active site, Cys-79 and Cys-290 in bacteriophage T4 NrdD numbering. Cys-290 is believed to form a transient thiyl radical that initiates the reaction with substrate and Cys-79 to take part as a transient thiyl radical in later steps of the reductive reaction. The recently solved three-dimensional structure of class III ribonucleotide reductase (RNR) from bacteriophage T4 shows that two highly conserved asparagines, Asn-78 and Asn-311, are positioned close to the essential Cys-79. We have investigated the function of Asn-78 and Asn-311 by site-directed mutagenesis and measured enzyme activity and glycyl radical formation in five single (N78(A/C/D) and N311(A/C)) and one double (N78A/N311A) mutant proteins. Our results suggest that both asparagines are important for the catalytic mechanism of class III RNR and that one asparagine can partially compensate for the lack of the other functional group in the single Asn --> Ala mutant proteins. A plausible role for these two asparagines could be in positioning formate in the active site to orient it toward the proposed thiyl radical of Cys-79. This would also control the highly reactive carbon dioxide radical anion form of formate within the active site before it is released as carbon dioxide. A detailed reaction scheme including the function of the two asparagines and two formate molecules is proposed for class III RNRs.
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Affiliation(s)
- J Andersson
- Department of Molecular Biology and Functional Genomics, Stockholm University, SE-10691 Stockholm, Sweden
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89
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Rahlfs S, Fischer M, Becker K. Plasmodium falciparum possesses a classical glutaredoxin and a second, glutaredoxin-like protein with a PICOT homology domain. J Biol Chem 2001; 276:37133-40. [PMID: 11479312 DOI: 10.1074/jbc.m105524200] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The genes coding for two different proteins with homologies to glutaredoxins have been identified in the genome of the malarial parasite Plasmodium falciparum. Both genes were amplified from a gametocytic cDNA and overexpressed in Escherichia coli. The smaller protein (named PfGrx-1) with 12.4 kDa in size exhibits the typical glutaredoxin active site motif "CPYC," shows glutathione-dependent glutaredoxin activity in the beta-hydroxyethyl disulfide (HEDS) assay, and reduces Trypanosoma brucei ribonucleotide reductase. Glutathione:HEDS transhydrogenase activity (approximately 60 milliunits/mg of protein) was clearly detectable in trophozoite extracts from eight different P. falciparum strains and did not differ between chloroquine-resistant and -sensitive parasites. Five different antimalarial drugs at 100 microm did not significantly influence isolated PfGrx-1 activity. In contrast, the second protein (deduced mass 19.9 kDa) with homology to glutaredoxins (31% identity to Schizosaccharomyces pombe in a 140-amino acid overlap) was not active in the HEDS assay; however, its general dithiol reducing activity was demonstrated in the insulin assay in the presence of dithiothreitol. Interestingly, the sequence contains a PICOT (for protein kinase C-interacting cousin of thioredoxin) homology domain, which might suggest regulatory functions of the protein. We named this protein PfGLP-1, for P. falciparum 1-Cys-glutaredoxin-like protein-1. In contrast to glutaredoxins, PfGLP-1 could not be reduced by glutathione. This is the first report on glutaredoxin-like proteins in the family of Plasmodia.
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Affiliation(s)
- S Rahlfs
- Interdisciplinary Research Center, Justus Liebig University, 35392 Giessen, Germany
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90
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Stehr M, Schneider G, Aslund F, Holmgren A, Lindqvist Y. Structural basis for the thioredoxin-like activity profile of the glutaredoxin-like NrdH-redoxin from Escherichia coli. J Biol Chem 2001; 276:35836-41. [PMID: 11441020 DOI: 10.1074/jbc.m105094200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterized by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. The crystal structure of recombinant Escherichia coli NrdH-redoxin in the oxidized state has been determined at 1.7 A resolution by multiwavelength anomalous diffraction. NrdH-redoxin belongs to the thioredoxin superfamily and is structurally most similar to E. coli glutaredoxin 3 and phage T4 glutaredoxin. The angle between the C-terminal helix alpha3 and strand beta4, which differs between thioredoxin and glutaredoxin, has an intermediate value in NrdH-redoxin. The orientation of this helix is to a large extent determined by an extended hydrogen-bond network involving the highly conserved sequence motif (61)WSGFRP(D/E)(67), which is unique to this subclass of the thioredoxin superfamily. Residues that bind glutathione in glutaredoxins are in general not conserved in NrdH-redoxin, and no glutathione-binding cleft is present. Instead, NrdH-redoxin contains a wide hydrophobic pocket at the surface, similar to thioredoxin. Modeling studies suggest that NrdH-redoxin can interact with E. coli thioredoxin reductase at this pocket and also via a loop that is complementary to a crevice in the reductase in a similar manner as observed in the E. coli thioredoxin-thioredoxin reductase complex.
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Affiliation(s)
- M Stehr
- Division of Molecular Structural Biology and the Medical Nobel Institute for Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, S-171 77 Sweden
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91
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Skamrov A, Feoktistova E, Goldman M, Beabealashvilli R. Gene re-arrangement and fusion in Mycoplasma gallisepticum thyA-nrdFEI locus. FEMS Microbiol Lett 2001; 200:31-5. [PMID: 11410345 DOI: 10.1111/j.1574-6968.2001.tb10688.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Sequencing of Mycoplasma gallisepticum genome fragment containing thymidylate synthase and ribonucleotide reductase gene clusters reveals both its unusual organization and gene content. Sequence analysis indicates the presence of a gene whose product can be considered as a fusion of two full size proteins: the N-terminal part shows significant similarity to mycoplasmal dihydrofolate reductases, while the C-terminal part of the polypeptide chain shows significant similarity to eukaryotic deoxycytidylate deaminase. Phylogenetic analysis has suggested that the C-terminal part of the M. gallisepticum fusion gene and eukaryotic deoxycytidylate deaminase genes are xenologous. No chromosomal regions encoding peptides similar to the C-terminal part of this fusion protein were found in completely sequenced genomes of Mycoplasma genitalium and Mycoplasma pneumoniae. Genes for ribonucleoside diphosphate reductase alpha chain (nrdE), NrdI protein (nrdI), and ribonucleoside diphosphate reductase beta chain (nrdF) have an opposite direction of transcription with respect to genes for thymidylate synthase (thyA), and dihydrofolate reductase-deoxycytidylate deaminase fusion protein.
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Affiliation(s)
- A Skamrov
- National Cardiology Research Center, Ministry of Health of the Russian Federation, 3rd Cherepkovskaya Str. 15A, 121552 Moscow, Russia.
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92
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Monje-Casas F, Jurado J, Prieto-Alamo MJ, Holmgren A, Pueyo C. Expression analysis of the nrdHIEF operon from Escherichia coli. Conditions that trigger the transcript level in vivo. J Biol Chem 2001; 276:18031-7. [PMID: 11278973 DOI: 10.1074/jbc.m011728200] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli has two aerobic ribonucleotide reductases encoded by the nrdAB and nrdHIEF operons. While NrdAB is active during aerobiosis, NrdEF is considered a cryptic enzyme with no obvious function. Here, we present evidence that nrdHIEF expression might be important under certain circumstances. Basal transcript levels were dramatically enhanced (25-75-fold), depending on the growth-phase and the growth-medium composition. Likewise, a large increase of >100-fold in nrdHIEF mRNA was observed in bacteria lacking Trx1 and Grx1, the two main NrdAB reductants. Moreover, nrdHIEF expression was triggered in response to oxidative stress, particularly in mutants missing hydroperoxidase I and alkyl-hydroperoxide reductase activities (69.7-fold) and in cells treated with oxidants (up to 23.4-fold over the enhanced transcript level possessed by cells grown on minimal medium). The mechanism(s) that triggers nrdHIEF expression remains unknown, but our findings exclude putative global regulators like RpoS, Fis, cAMP, OxyR, SoxR/S, or RecA. What we have learned about nrdHIEF expression indicates strong differences between its regulation and that of the nrdAB operon and of genes coding for components of both thioredoxin/glutaredoxin pathways. We propose that E. coli might optimize the responses to different stimuli by co-evolving the expression levels for its multiple reductases and electron donors.
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Affiliation(s)
- F Monje-Casas
- Departamento de Bioquimica y Biologia Molecular, Universidad de Córdoba, 14071-Córdoba, Spain
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93
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Sahlin M, Sjöberg BM. Ribonucleotide reductase. A virtual playground for electron transfer reactions. Subcell Biochem 2001; 35:405-43. [PMID: 11192729 DOI: 10.1007/0-306-46828-x_12] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- M Sahlin
- Department of Molecular Biology, Stockholm University, SE-10691 Stockholm, Sweden
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94
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Carmel-Harel O, Storz G. Roles of the glutathione- and thioredoxin-dependent reduction systems in the Escherichia coli and saccharomyces cerevisiae responses to oxidative stress. Annu Rev Microbiol 2001; 54:439-61. [PMID: 11018134 DOI: 10.1146/annurev.micro.54.1.439] [Citation(s) in RCA: 536] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The glutathione- and thioredoxin-dependent reduction systems are responsible for maintaining the reduced environment of the Escherichia coli and Saccharomyces cerevisiae cytosol. Here we examine the roles of these two cellular reduction systems in the bacterial and yeast defenses against oxidative stress. The transcription of a subset of the genes encoding glutathione biosynthetic enzymes, glutathione reductases, glutaredoxins, thioredoxins, and thioredoxin reductases, as well as glutathione- and thioredoxin-dependent peroxidases is clearly induced by oxidative stress in both organisms. However, only some strains carrying mutations in single genes are hypersensitive to oxidants. This is due, in part, to the redundant effects of the gene products and the overlap between the two reduction systems. The construction of strains carrying mutations in multiple genes is helping to elucidate the different roles of glutathione and thioredoxin, and studies with such strains have recently revealed that these two reduction systems modulate the activities of the E. coli OxyR and SoxR and the S. cerevisiae Yap1p transcriptional regulators of the adaptive responses to oxidative stress.
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Affiliation(s)
- O Carmel-Harel
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA.
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95
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Cave JW, Cho HS, Batchelder AM, Yokota H, Kim R, Wemmer DE. Solution nuclear magnetic resonance structure of a protein disulfide oxidoreductase from Methanococcus jannaschii. Protein Sci 2001; 10:384-96. [PMID: 11266624 PMCID: PMC2373935 DOI: 10.1110/ps.35101] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The solution structure of the protein disulfide oxidoreductase Mj0307 in the reduced form has been solved by nuclear magnetic resonance. The secondary and tertiary structure of this protein from the archaebacterium Methanococcus jannaschii is similar to the structures that have been solved for the glutaredoxin proteins from Escherichia coli, although Mj0307 also shows features that are characteristic of thioredoxin proteins. Some aspects of Mj0307's unique behavior can be explained by comparing structure-based sequence alignments with mesophilic bacterial and eukaryotic glutaredoxin and thioredoxin proteins. It is proposed that Mj0307, and similar archaebacterial proteins, may be most closely related to the mesophilic bacterial NrdH proteins. Together these proteins may form a unique subgroup within the family of protein disulfide oxidoreductases.
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Affiliation(s)
- J W Cave
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720-1460, USA
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96
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Arnér ES, Holmgren A. Physiological functions of thioredoxin and thioredoxin reductase. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:6102-9. [PMID: 11012661 DOI: 10.1046/j.1432-1327.2000.01701.x] [Citation(s) in RCA: 1762] [Impact Index Per Article: 73.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Thioredoxin, thioredoxin reductase and NADPH, the thioredoxin system, is ubiquitous from Archea to man. Thioredoxins, with a dithiol/disulfide active site (CGPC) are the major cellular protein disulfide reductases; they therefore also serve as electron donors for enzymes such as ribonucleotide reductases, thioredoxin peroxidases (peroxiredoxins) and methionine sulfoxide reductases. Glutaredoxins catalyze glutathione-disulfide oxidoreductions overlapping the functions of thioredoxins and using electrons from NADPH via glutathione reductase. Thioredoxin isoforms are present in most organisms and mitochondria have a separate thioredoxin system. Plants have chloroplast thioredoxins, which via ferredoxin-thioredoxin reductase regulates photosynthetic enzymes by light. Thioredoxins are critical for redox regulation of protein function and signaling via thiol redox control. A growing number of transcription factors including NF-kappaB or the Ref-1-dependent AP1 require thioredoxin reduction for DNA binding. The cytosolic mammalian thioredoxin, lack of which is embryonically lethal, has numerous functions in defense against oxidative stress, control of growth and apoptosis, but is also secreted and has co-cytokine and chemokine activities. Thioredoxin reductase is a specific dimeric 70-kDa flavoprotein in bacteria, fungi and plants with a redox active site disulfide/dithiol. In contrast, thioredoxin reductases of higher eukaryotes are larger (112-130 kDa), selenium-dependent dimeric flavoproteins with a broad substrate specificity that also reduce nondisulfide substrates such as hydroperoxides, vitamin C or selenite. All mammalian thioredoxin reductase isozymes are homologous to glutathione reductase and contain a conserved C-terminal elongation with a cysteine-selenocysteine sequence forming a redox-active selenenylsulfide/selenolthiol active site and are inhibited by goldthioglucose (aurothioglucose) and other clinically used drugs.
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Affiliation(s)
- E S Arnér
- Medical Nobel Institute for Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
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97
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Huynen M, Snel B, Lathe W, Bork P. Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res 2000; 10:1204-10. [PMID: 10958638 PMCID: PMC310926 DOI: 10.1101/gr.10.8.1204] [Citation(s) in RCA: 347] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Various new methods have been proposed to predict functional interactions between proteins based on the genomic context of their genes. The types of genomic context that they use are Type I: the fusion of genes; Type II: the conservation of gene-order or co-occurrence of genes in potential operons; and Type III: the co-occurrence of genes across genomes (phylogenetic profiles). Here we compare these types for their coverage, their correlations with various types of functional interaction, and their overlap with homology-based function assignment. We apply the methods to Mycoplasma genitalium, the standard benchmarking genome in computational and experimental genomics. Quantitatively, conservation of gene order is the technique with the highest coverage, applying to 37% of the genes. By combining gene order conservation with gene fusion (6%), the co-occurrence of genes in operons in absence of gene order conservation (8%), and the co-occurrence of genes across genomes (11%), significant context information can be obtained for 50% of the genes (the categories overlap). Qualitatively, we observe that the functional interactions between genes are stronger as the requirements for physical neighborhood on the genome are more stringent, while the fraction of potential false positives decreases. Moreover, only in cases in which gene order is conserved in a substantial fraction of the genomes, in this case six out of twenty-five, does a single type of functional interaction (physical interaction) clearly dominate (>80%). In other cases, complementary function information from homology searches, which is available for most of the genes with significant genomic context, is essential to predict the type of interaction. Using a combination of genomic context and homology searches, new functional features can be predicted for 10% of M. genitalium genes.
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Affiliation(s)
- M Huynen
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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98
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Prieto-Alamo MJ, Jurado J, Gallardo-Madueno R, Monje-Casas F, Holmgren A, Pueyo C. Transcriptional regulation of glutaredoxin and thioredoxin pathways and related enzymes in response to oxidative stress. J Biol Chem 2000; 275:13398-405. [PMID: 10788450 DOI: 10.1074/jbc.275.18.13398] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We examined the in vivo expression of up to 16 genes encoding for components of both glutaredoxin and thioredoxin systems and for members of the OxyR and SoxRS regulons. We demonstrated that grxA (Grx1) transcription is triggered in bacteria lacking Trx1 (trxA) and GSH (gshA) in an OxyR-dependent manner. We also indicated that, unlike OxyR, SoxR is not constitutively activated in the oxidizing environment of trxA gshA mutants. We discovered that the lack of Trx1 plus GSH increases the steady-state levels of Trx reductase (trxB) and Trx2 (trxC) transcripts. This increase and the trxB and trxC up-regulation caused by the constitutive oxyR2 allele indicate that OxyR also plays a role in the regulation of the thioredoxin pathway. On the contrary, no change in the expression of genes for Trx1, Grx2, and Grx3 was observed. Transcription of nrdAB (RRase) was not induced by oxidative stress yet was induced by hydroxyurea (RRase inhibitor). Induction level was as the enhanced nrdAB basal expression of trxA grxA mutants, indicating that RRase operation without Trx1 and Grx1 must lead to disturbances sensed as those caused by hydroxyurea. We also demonstrated an inverse relation between nrdAB expression and that of genes coding for components of both glutaredoxin (grxA, gorA) and thioredoxin (trxB, trxC) systems.
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Affiliation(s)
- M J Prieto-Alamo
- Departamento de Bioquimica y Biologia Molecular, Universidad de Córdoba, 14071-Córdoba, España
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99
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Abstract
This review summarizes evidence that most of cell protein degradation is maintained by pathways transferring energy from glucose to reduction of enzymic and nonenzymic proteins (redox-responsive). In contrast, a major subcomponent of proteolysis is simultaneously independent of the cell redox network (redox-unresponsive). Thus far, direct and indirect redox-responsive proteolytic effector mechanisms characterized by various investigators include: several classes of proteases, some peptide protease inhibitors, substrate conjugation systems, substrate redox and folding status, cytoskeletal-membrane kinesis, metal homeostasis, and others. The present focus involves redox control of sulfhydryl proteases and proteolytic pathways of mammalian muscle; however, other mechanisms, cell types, and species are also surveyed. The diversity of redox-responsive catabolic mechanisms reveals that the machinery of protein turnover evolved with fundamental dependencies upon the cell redox network, as observed in many species. The net redox status of a reversible proteolytic effector mechanism represents the balance between combined oxidative inactivating influences versus reductive activating influences. Similar to other proteins, redox-responsive proteolytic effectors appear to be oxidized by mixed disulfide formation, nitrosation, reactive oxygen species, and associations or reactions with metal ions and various pro-oxidative metabolites. Systems reducing the proteolytic machinery include major redox enzyme chains, such as thioredoxins or glutaredoxins, and perhaps various reductive metabolites, including glutathione and dihydrolipoic acid. Much of mammalian intracellular protein degradation is reversibly responsive to noninjurious experimental intervention in the reductive energy supply-demand balance. Proteolysis is reversibly inhibited by diamide or dehydroascorbic acid; and such antiproteolytic actions are strongly dependent on the cell glucose supply. However, gross redox-responsive proteolysis is not accompanied by ATP depletion or vice versa. Redox-responsive proteolysis includes Golgi-endoplasmic reticulum degradation, lysosomal degradation, and some amount of extravesicular degradation, all comprising more than half of total cell proteolysis. Speculatively, redox-dependent proteolysis exhibits features expected of a controlling influence coordinating distinct proteolytic processes under some intracellular conditions.
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Affiliation(s)
- T D Lockwood
- Department of Pharmacology and Toxicology, School of Medicine, Wright State University, Dayton, OH 45435, USA
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100
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Shi J, Vlamis-Gardikas A, Aslund F, Holmgren A, Rosen BP. Reactivity of glutaredoxins 1, 2, and 3 from Escherichia coli shows that glutaredoxin 2 is the primary hydrogen donor to ArsC-catalyzed arsenate reduction. J Biol Chem 1999; 274:36039-42. [PMID: 10593884 DOI: 10.1074/jbc.274.51.36039] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Escherichia coli ArsC catalyzes the reduction of arsenate to arsenite using GSH with glutaredoxin as electron donors. E. coli has three glutaredoxins: 1, 2, and 3, each with a classical -Cys-Pro-Tyr-Cys- active site. Glutaredoxin 2 is the major glutathione disulfide oxidoreductase in E. coli, but its function remains unknown. In this report glutaredoxin 2 is shown to be the most effective hydrogen donor for the reduction of arsenate by ArsC. Analysis of single or double cysteine-to-serine substitutions in the active site of the three glutaredoxins indicated that only the N-terminal cysteine residue is essential for activity. This suggests that, during the catalytic cycle, ArsC forms a mixed disulfide with GSH before being reduced by glutaredoxin to regenerate the active ArsC reductase.
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Affiliation(s)
- J Shi
- Department of Biochemistry and Molecular Biology, Wayne State University, School of Medicine, Detroit, Michigan 48201, USA
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