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Ran C, Zhang Y, Chang F, Yang X, Liu Y, Wang Q, Zhu W. Genome-Wide Analyses of SlFWL Family Genes and Their Expression Profiles under Cold, Heat, Salt and Drought Stress in Tomato. Int J Mol Sci 2023; 24:11783. [PMID: 37511542 PMCID: PMC10380795 DOI: 10.3390/ijms241411783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/04/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
PLAC8 is a cysteine-rich protein that serves as a central mediator of tumor evolution in mammals. PLAC8 motif-containing proteins widely distribute in fungi, algae, higher plants and animals that have been described to be implicated in fruit size, cell number and the transport of heavy metals such as cadmium or zinc. In tomatoes, FW2.2 is a PLAC8 motif-containing gene that negatively controls fruit size by regulating cell division and expansion in the carpel ovary during fruit development. However, despite FW2.2, other FWL (FW2.2-Like) genes in tomatoes have not been investigated. In this study, we identified the 21 SlFWL genes, including FW2.2, examined their expression profiles under various abiotic adversity-related conditions. The SlFWL gene structures and motif compositions are conserved, indicating that tomato SlFWL genes may have similar roles. Cis-acting element analysis revealed that the SlFWL genes may participate in light and abiotic stress responses, and they also interacted with a variety of phytohormone-responsive proteins and plant development elements. Phylogenetic analyses were performed on five additional plant species, including Arabidopsis, pepper, soybean, rice and maize, these genes were classified into five subfamilies. Based on the results of collinearity analyses, the SlFWL genes have a tighter homologous evolutionary relationship with soybean, and these orthologous FWL gene pairs might have the common ancestor. Expression profiling of SlFWL genes show that they were all responsive to abiotic stresses, each subgroup of genes exhibited a different expression trend. Our findings provide a strong foundation for investigating the function and abiotic stress responses of the SlFWL family genes.
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Affiliation(s)
- Chunxia Ran
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Yingying Zhang
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Feifei Chang
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Xuedong Yang
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Yahui Liu
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Quanhua Wang
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Weimin Zhu
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
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2
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Dervisi I, Valassakis C, Koletti A, Kouvelis VN, Flemetakis E, Ouzounis CA, Roussis A. Evolutionary Aspects of Selenium Binding Protein (SBP). J Mol Evol 2023:10.1007/s00239-023-10105-4. [PMID: 37039856 DOI: 10.1007/s00239-023-10105-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/21/2023] [Indexed: 04/12/2023]
Abstract
Selenium-binding proteins represent a ubiquitous protein family and recently SBP1 was described as a new stress response regulator in plants. SBP1 has been characterized as a methanethiol oxidase, however its exact role remains unclear. Moreover, in mammals, it is involved in the regulation of anti-carcinogenic growth and progression as well as reduction/oxidation modulation and detoxification. In this work, we delineate the functional potential of certain motifs of SBP in the context of evolutionary relationships. The phylogenetic profiling approach revealed the absence of SBP in the fungi phylum as well as in most non eukaryotic organisms. The phylogenetic tree also indicates the differentiation and evolution of characteristic SBP motifs. Main evolutionary events concern the CSSC motif for which Acidobacteria, Fungi and Archaea carry modifications. Moreover, the CC motif is harbored by some bacteria and remains conserved in Plants, while modified to CxxC in Animals. Thus, the characteristic sequence motifs of SBPs mainly appeared in Archaea and Bacteria and retained in Animals and Plants. Our results demonstrate the emergence of SBP from bacteria and most likely as a methanethiol oxidase.
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Affiliation(s)
- Irene Dervisi
- Section of Botany, Department of Biology, National & Kapodistrian University of Athens, 15784, Athens, Greece
| | - Chrysanthi Valassakis
- Section of Botany, Department of Biology, National & Kapodistrian University of Athens, 15784, Athens, Greece
| | - Aikaterini Koletti
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855, Athens, Greece
| | - Vassilis N Kouvelis
- Section of Genetics and Biotechnology, Department of Biology, National & Kapodistrian University of Athens, 15784, Athens, Greece
| | - Emmanouil Flemetakis
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855, Athens, Greece
| | - Christos A Ouzounis
- Biological Computation & Process Laboratory, Centre for Research & Technology Hellas, Chemical Process & Energy Resources Institute, 54124, Thessaloníki, Greece
- Biological Computation & Computational Biology Group, AIIA Lab, School of Informatics, Aristotle University of Thessalonica, 57001, Thessaloníki, Greece
| | - Andreas Roussis
- Section of Botany, Department of Biology, National & Kapodistrian University of Athens, 15784, Athens, Greece.
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He J, Liu S, Fang Q, Gu H, Hu Y. The Thioredoxin System in Edwardsiella piscicida Contributes to Oxidative Stress Tolerance, Motility, and Virulence. Microorganisms 2023; 11:microorganisms11040827. [PMID: 37110252 PMCID: PMC10145099 DOI: 10.3390/microorganisms11040827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
Edwardsiella piscicida is an important fish pathogen that causes substantial economic losses. In order to understand its pathogenic mechanism, additional new virulence factors need to be identified. The bacterial thioredoxin system is a major disulfide reductase system, but its function is largely unknown in E. piscicida. In this study, we investigated the roles of the thioredoxin system in E. piscicida (named TrxBEp, TrxAEp, and TrxCEp, respectively) by constructing a correspondingly markerless in-frame mutant strain: ΔtrxB, ΔtrxA, and ΔtrxC, respectively. We found that (i) TrxBEp is confirmed as an intracellular protein, which is different from the prediction made by the Protter illustration; (ii) compared to the wild-type strain, ΔtrxB exhibits resistance against H2O2 stress but high sensitivity to thiol-specific diamide stress, while ΔtrxA and ΔtrxC are moderately sensitive to both H2O2 and diamide conditions; (iii) the deletions of trxBEp, trxAEp, and trxCEp damage E. piscicida's flagella formation and motility, and trxBEp plays a decisive role; (iv) deletions of trxBEp, trxAEp, and trxCEp substantially abate bacterial resistance against host serum, especially trxBEp deletion; (v) trxAEp and trxCEp, but not trxBEp, are involved in bacterial survival and replication in phagocytes; (vi) the thioredoxin system participates in bacterial dissemination in host immune tissues. These findings indicate that the thioredoxin system of E. piscicida plays an important role in stress resistance and virulence, which provides insight into the pathogenic mechanism of E. piscicida.
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Affiliation(s)
- Jiaojiao He
- School of Life Sciences, Hainan University, Haikou 570228, China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Su Liu
- School of Life Sciences, Hainan University, Haikou 570228, China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Qingjian Fang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Hanjie Gu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-Resources, Haikou 571101, China
| | - Yonghua Hu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-Resources, Haikou 571101, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China
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Shi X, Li C, Cheng L, Ullah H, Sha S, Kang J, Ma X, Ma Y. Mycobacterium tuberculosis Rv1324 Protein Contributes to Mycobacterial Persistence and Causes Pathological Lung Injury in Mice by Inducing Ferroptosis. Microbiol Spectr 2023; 11:e0252622. [PMID: 36625672 PMCID: PMC9927160 DOI: 10.1128/spectrum.02526-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the pathogenic agent of tuberculosis (TB). Intracellular survival plays a central role in the pathogenesis of Mtb, a process that depends on an array of virulence factors for Mtb to colonize and proliferate within a host. Reactive nitrogen and oxygen species (RNS and ROS) are among the most effective antimycobacterial molecules generated by the host during infection. However, Mtb has evolved a number of proteins and enzymes to detoxify ROS and RNS. Secretory protein Rv1324, as a possible thioredoxin, might also have oxidoreductase activity against ROS and RNS during Mtb infection, and it is a potential virulence factor of Mtb. In this study, we investigated the biochemical properties of Mtb Rv1324 and its role in mycobacterial survival and virulence. The results showed that the Rv1324 protein had antioxidant activity and increased the survival of M. smegmatis that was exposed to ROS and RNS. In addition, Rv1324 enhanced the colonization ability of M. smegmatis in the lungs of mice. Further, mice infected with M. smegmatis harboring Rv1324 exhibited pathological injury and inflammation in the lung, which was mediated by ferroptosis. In summary, this study advances our understanding of the mechanisms of mycobacterial survival and pathogenesis, and it reveals a novel target for TB treatment. IMPORTANCE The intracellular survival of M. tuberculosis (Mtb) plays a crucial role in its pathogenesis, which depends on various Mtb oxidoreductases that are resistant to reactive oxygen and nitrogen species (ROS and RNS) that are generated by the host during Mtb infection. Secretory protein Rv1324 is a potential virulence factor of Mtb and is a possible thioredoxin that has oxidoreductase activity against ROS and RNS during Mtb infection. We investigated the biochemical properties of Mtb Rv1324 and its role in mycobacterial survival and virulence. It was confirmed that the Rv1324 protein had antioxidant activity and an increased mycobacterial resistance to ROS and RNS. In addition, Rv1324 enhanced mycobacterial persistence and induced pathological injury and inflammation in the lungs of mice by activating ferroptosis. This study advances our understanding of the mechanisms of mycobacterial survival and pathogenesis, and it reveals a novel target for TB treatment.
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Affiliation(s)
- Xiaoxia Shi
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, China
- Department of Experimental Teaching Center of Public Health, Dalian Medical University, Dalian, China
| | - Chunyu Li
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, China
| | - Lin Cheng
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, China
| | - Hayan Ullah
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, China
| | - Shanshan Sha
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, China
| | - Jian Kang
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, China
| | - Xiaochi Ma
- College of Integrative Medicine, Dalian Medical University, Dalian, China
- Pharmaceutical Research Center, The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Yufang Ma
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, China
- Department of Microbiology, Dalian Medical University, Dalian, China
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Hanchapola HACR, Liyanage DS, Omeka WKM, Lim C, Kim G, Jeong T, Lee J. Thioredoxin domain-containing protein 12 (TXNDC12) in red spotted grouper (Epinephelus akaara): Molecular characteristics, disulfide reductase activities, and immune responses. FISH & SHELLFISH IMMUNOLOGY 2023; 132:108449. [PMID: 36436687 DOI: 10.1016/j.fsi.2022.11.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
Thioredoxins are small ubiquitous redox proteins that are involved in many biological processes. Proteins with thiol-disulfide bonds are essential regulators of cellular redox homeostasis and diagnostic markers for redox-dependent diseases. Here, we identified and characterized the thioredoxin domain-containing protein 12 (EaTXNDC12) gene in red spotted grouper (Epinephelus akaara), evaluated transcriptional responses, and investigated the activity of the recombinant protein using functional assays. EaTXNDC12 is a 19.22-kDa endoplasmic reticulum (ER)-resident protein with a 522-bp open reading frame and 173 amino acids, including a signal peptide. We identified a conserved active motif (66WCGAC70) and ER retention motif (170GDEL173) in the EaTXNDC12 amino acid sequence. Relative EaTXNDC12 mRNA expression was analyzed using 12 different tissues, with the highest expression seen in brain tissue, while skin tissue showed the lowest expression level. Furthermore, mRNA expression in response to immune challenges was analyzed in the head kidney, blood, and gill tissues. EaTXNDC12 was significantly modulated in response to bacterial endotoxin lipopolysaccharide (LPS), nervous necrosis virus (NNV), and polyinosinic:polycytidylic acid (poly(I:C)) challenges in all of the tested tissues. Recombinant EaTXNDC12 (rEaTXNDC12) displayed antioxidant ability in an insulin reductase assay, and a capacity for free radical inhibition in a 2,2-diphenyl-1-picryl-hydrazyl-hydrate assay. In addition, a DNA nicking assay revealed that purified rEaTXNDC12 exhibited concentration-dependent DNA protection activity, while results from 2-hydroxyethyl disulfide and L-dehydroascorbic assays indicated that rEaTXNDC12a possesses reducing ability. Furthermore, fathead minnow (FHM) cells transfected with EaTXNDC12-pcDNA demonstrated significantly upregulated cell survival against H2O2-induced apoptosis. Collectively, the results of this study strengthen our knowledge of EaTXNDC12 with respect to cellular redox hemostasis and immune regulation in Epinephelus akaara.
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Affiliation(s)
- H A C R Hanchapola
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - D S Liyanage
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - W K M Omeka
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - Chaehyeon Lim
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - Gaeun Kim
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - Taehyug Jeong
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju, 63333, Republic of Korea.
| | - Jehee Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju, 63333, Republic of Korea.
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6
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Willems P, Huang J, Messens J, Van Breusegem F. Functionally annotating cysteine disulfides and metal binding sites in the plant kingdom using AlphaFold2 predicted structures. Free Radic Biol Med 2023; 194:220-229. [PMID: 36493985 DOI: 10.1016/j.freeradbiomed.2022.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/14/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Deep learning algorithms such as AlphaFold2 predict three-dimensional protein structure with high confidence. The recent release of more than 200 million structural models provides an unprecedented resource for functional protein annotation. Here, we used AlphaFold2 predicted structures of fifteen plant proteomes to functionally and evolutionary analyze cysteine residues in the plant kingdom. In addition to identification of metal ligands coordinated by cysteine residues, we systematically analyzed cysteine disulfides present in these structural predictions. Our analysis demonstrates most of these predicted disulfides are trustworthy due their high agreement (∼96%) with those present in X-ray and NMR protein structures, their characteristic disulfide stereochemistry, the biased subcellular distribution of their proteins and a higher degree of oxidation of their respective cysteines as measured by proteomics. Adopting an evolutionary perspective, zinc binding sites are increasingly present at the expense of iron-sulfur clusters in plants. Interestingly, disulfide formation is increased in secreted proteins of land plants, likely promoting sequence evolution to adapt to changing environments encountered by plants. In summary, Alphafold2 predicted structural models are a rich source of information for studying the role of cysteines residues in proteins of interest and for protein redox biology in general.
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Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium.
| | - Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
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Kojasoy V, Tantillo DJ. Impacts of noncovalent interactions involving sulfur atoms on protein stability, structure, folding, and bioactivity. Org Biomol Chem 2022; 21:11-23. [PMID: 36345987 DOI: 10.1039/d2ob01602h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This review discusses the various types of noncovalent interactions in which sulfur atoms participate and their effects on protein stability, structure, folding and bioactivity. Current approaches and recommendations for modelling these noncovalent interactions (in terms of both geometries and interaction energies) are highlighted.
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Affiliation(s)
- Volga Kojasoy
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
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Koletti A, Dervisi I, Kalloniati C, Zografaki ME, Rennenberg H, Roussis A, Flemetakis E. Selenium-binding Protein 1 (SBD1): A stress response regulator in Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2022; 189:2368-2381. [PMID: 35579367 PMCID: PMC9342975 DOI: 10.1093/plphys/kiac230] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/04/2022] [Indexed: 05/20/2023]
Abstract
Selenium-binding proteins (SBPs) represent a ubiquitous protein family implicated in various environmental stress responses, although the exact molecular and physiological role of the SBP family remains elusive. In this work, we report the identification and characterization of CrSBD1, an SBP homolog from the model microalgae Chlamydomonas reinhardtii. Growth analysis of the C. reinhardtii sbd1 mutant strain revealed that the absence of a functional CrSBD1 resulted in increased growth under mild oxidative stress conditions, although cell viability rapidly declined at higher hydrogen peroxide (H2O2) concentrations. Furthermore, a combined global transcriptomic and metabolomic analysis indicated that the sbd1 mutant exhibited a dramatic quenching of the molecular and biochemical responses upon H2O2-induced oxidative stress when compared to the wild-type. Our results indicate that CrSBD1 represents a cell regulator, which is involved in the modulation of C. reinhardtii early responses to oxidative stress. We assert that CrSBD1 acts as a member of an extensive and conserved protein-protein interaction network including Fructose-bisphosphate aldolase 3, Cysteine endopeptidase 2, and Glutaredoxin 6 proteins, as indicated by yeast two-hybrid assays.
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Affiliation(s)
- Aikaterini Koletti
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens 11855, Greece
| | - Irene Dervisi
- Department of Botany, Faculty of Biology, National & Kapodistrian University of Athens, Athens 15784, Greece
| | - Chrysanthi Kalloniati
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens 11855, Greece
| | - Maria-Eleftheria Zografaki
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens 11855, Greece
| | - Heinz Rennenberg
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Chongqing 400715, China
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West JD. Experimental Approaches for Investigating Disulfide-Based Redox Relays in Cells. Chem Res Toxicol 2022; 35:1676-1689. [PMID: 35771680 DOI: 10.1021/acs.chemrestox.2c00123] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Reversible oxidation of cysteine residues within proteins occurs naturally during normal cellular homeostasis and can increase during oxidative stress. Cysteine oxidation often leads to the formation of disulfide bonds, which can impact protein folding, stability, and function. Work in both prokaryotic and eukaryotic models over the past five decades has revealed several multiprotein systems that use thiol-dependent oxidoreductases to mediate disulfide bond reduction, formation, and/or rearrangement. Here, I provide an overview of how these systems operate to carry out disulfide exchange reactions in different cellular compartments, with a focus on their roles in maintaining redox homeostasis, transducing redox signals, and facilitating protein folding. Additionally, I review thiol-independent and thiol-dependent approaches for interrogating what proteins partner together in such disulfide-based redox relays. While the thiol-independent approaches rely either on predictive measures or standard procedures for monitoring protein-protein interactions, the thiol-dependent approaches include direct disulfide trapping methods as well as thiol-dependent chemical cross-linking. These strategies may prove useful in the systematic characterization of known and newly discovered disulfide relay mechanisms and redox switches involved in oxidant defense, protein folding, and cell signaling.
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Affiliation(s)
- James D West
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
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Comparative Genomics of Cyclic di-GMP Metabolism and Chemosensory Pathways in Shewanella algae Strains: Novel Bacterial Sensory Domains and Functional Insights into Lifestyle Regulation. mSystems 2022; 7:e0151821. [PMID: 35311563 PMCID: PMC9040814 DOI: 10.1128/msystems.01518-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Shewanella spp. play important ecological and biogeochemical roles, due in part to their versatile metabolism and swift integration of stimuli. While Shewanella spp. are primarily considered environmental microbes, Shewanella algae is increasingly recognized as an occasional human pathogen. S. algae shares the broad metabolic and respiratory repertoire of Shewanella spp. and thrives in similar ecological niches. In S. algae, nitrate and dimethyl sulfoxide (DMSO) respiration promote biofilm formation strain specifically, with potential implication of taxis and cyclic diguanosine monophosphate (c-di-GMP) signaling. Signal transduction systems in S. algae have not been investigated. To fill these knowledge gaps, we provide here an inventory of the c-di-GMP turnover proteome and chemosensory networks of the type strain S. algae CECT 5071 and compare them with those of 41 whole-genome-sequenced clinical and environmental S. algae isolates. Besides comparative analysis of genetic content and identification of laterally transferred genes, the occurrence and topology of c-di-GMP turnover proteins and chemoreceptors were analyzed. We found S. algae strains to encode 61 to 67 c-di-GMP turnover proteins and 28 to 31 chemoreceptors, placing S. algae near the top in terms of these signaling capacities per Mbp of genome. Most c-di-GMP turnover proteins were predicted to be catalytically active; we describe in them six novel N-terminal sensory domains that appear to control their catalytic activity. Overall, our work defines the c-di-GMP and chemosensory signal transduction pathways in S. algae, contributing to a better understanding of its ecophysiology and establishing S. algae as an auspicious model for the analysis of metabolic and signaling pathways within the genus Shewanella. IMPORTANCEShewanella spp. are widespread aquatic bacteria that include the well-studied freshwater model strain Shewanella oneidensis MR-1. In contrast, the physiology of the marine and occasionally pathogenic species Shewanella algae is poorly understood. Chemosensory and c-di-GMP signal transduction systems integrate environmental stimuli to modulate gene expression, including the switch from a planktonic to sessile lifestyle and pathogenicity. Here, we systematically dissect the c-di-GMP proteome and chemosensory pathways of the type strain S. algae CECT 5071 and 41 additional S. algae isolates. We provide insights into the activity and function of these proteins, including a description of six novel sensory domains. Our work will enable future analyses of the complex, intertwined c-di-GMP metabolism and chemotaxis networks of S. algae and their ecophysiological role.
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Yang F, Jia G, Guo J, Liu Y, Wang C. Quantitative Chemoproteomic Profiling with Data-Independent Acquisition-Based Mass Spectrometry. J Am Chem Soc 2022; 144:901-911. [PMID: 34986311 DOI: 10.1021/jacs.1c11053] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Activity-based protein profiling (ABPP) has emerged as a powerful and versatile tool to enable annotation of protein functions and discovery of targets of bioactive ligands in complex biological systems. It utilizes chemical probes to covalently label functional sites in proteins so that they can be enriched for mass spectrometry (MS)-based quantitative proteomics analysis. However, the semistochastic nature of data-dependent acquisition and high cost associated with isotopically encoded quantification reagents compromise the power of ABPP in multidimensional analysis and high-throughput screening, when a large number of samples need to be quantified in parallel. Here, we combine the data-independent acquisition (DIA) MS with ABPP to develop an efficient label-free quantitative chemical proteomic method, DIA-ABPP, with good reproducibility and high accuracy for high-throughput quantification. We demonstrated the power of DIA-ABPP for comprehensive profiling of functional cysteineome in three distinct applications, including dose-dependent quantification of cysteines' sensitivity toward a reactive metabolite, screening of ligandable cysteines with a covalent fragment library, and profiling of cysteinome fluctuation in circadian clock cycles. DIA-ABPP will open new opportunities for in-depth and multidimensional profiling of functional proteomes and interactions with bioactive small molecules in complex biological systems.
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Affiliation(s)
- Fan Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Guogeng Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiuzhou Guo
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yuan Liu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chu Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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12
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Bioinformatic Analyses of Peroxiredoxins and RF-Prx: A Random Forest-Based Predictor and Classifier for Prxs. Methods Mol Biol 2022; 2499:155-176. [PMID: 35696080 PMCID: PMC9844236 DOI: 10.1007/978-1-0716-2317-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Peroxiredoxins (Prxs) are a protein superfamily, present in all organisms, that play a critical role in protecting cellular macromolecules from oxidative damage but also regulate intracellular and intercellular signaling processes involving redox-regulated proteins and pathways. Bioinformatic approaches using computational tools that focus on active site-proximal sequence fragments (known as active site signatures) and iterative clustering and searching methods (referred to as TuLIP and MISST) have recently enabled the recognition of over 38,000 peroxiredoxins, as well as their classification into six functionally relevant groups. With these data providing so many examples of Prxs in each class, machine learning approaches offer an opportunity to extract additional information about features characteristic of these protein groups.In this study, we developed a novel computational method named "RF-Prx" based on a random forest (RF) approach integrated with K-space amino acid pairs (KSAAP) to identify peroxiredoxins and classify them into one of six subgroups. Our process performed in a superior manner compared to other machine learning classifiers. Thus the RF approach integrated with K-space amino acid pairs enabled the detection of class-specific conserved sequences outside the known functional centers and with potential importance. For example, drugs designed to target Prx proteins would likely suffer from cross-reactivity among distinct Prxs if targeted to conserved active sites, but this may be avoidable if remote, class-specific regions could be targeted instead.
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Abstract
Significance: Unique to the branched-chain aminotransferase (BCAT) proteins is their redox-active CXXC motif. Subjected to post-translational modification by reactive oxygen species and reactive nitrogen species, these proteins have the potential to adopt numerous cellular roles, which may be fundamental to their role in oncogenesis and neurodegenerative diseases. An understanding of the interplay of the redox regulation of BCAT with important cell signaling mechanisms will identify new targets for future therapeutics. Recent Advances: The BCAT proteins have been assigned novel thiol oxidoreductase activity that can accelerate the refolding of proteins, in particular when S-glutathionylated, supporting a chaperone role for BCAT in protein folding. Other metabolic proteins were also shown to have peroxide-mediated redox associations with BCAT, indicating that the cellular function of BCAT is more diverse. Critical Issues: While the role of branched-chain amino acid metabolism and its metabolites has dominated aspects of cancer research, less is known about the role of BCAT. The importance of the CXXC motif in regulating the BCAT activity under hypoxic conditions, a characteristic of tumors, has not been addressed. Understanding how these proteins operate under various cellular redox conditions will become important, in particular with respect to their moonlighting roles. Future Directions: Advances in the quantification of thiols, their measurement, and the manipulation of metabolons that rely on redox-based interactions should accelerate the investigation of the cellular role of moonlighting proteins such as BCAT. Given the importance of cross talk between signaling pathways, research should focus more on these "housekeeping" proteins paying attention to their wider application. Antioxid. Redox Signal. 34, 1048-1067.
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Affiliation(s)
- Myra Elizabeth Conway
- Department of Applied Science, University of the West of England, Bristol, United Kingdom
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14
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Turnšek J, Brunson JK, Viedma MDPM, Deerinck TJ, Horák A, Oborník M, Bielinski VA, Allen AE. Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway. eLife 2021; 10:e52770. [PMID: 33591270 PMCID: PMC7972479 DOI: 10.7554/elife.52770] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Iron is a biochemically critical metal cofactor in enzymes involved in photosynthesis, cellular respiration, nitrate assimilation, nitrogen fixation, and reactive oxygen species defense. Marine microeukaryotes have evolved a phytotransferrin-based iron uptake system to cope with iron scarcity, a major factor limiting primary productivity in the global ocean. Diatom phytotransferrin is endocytosed; however, proteins downstream of this environmentally ubiquitous iron receptor are unknown. We applied engineered ascorbate peroxidase APEX2-based subcellular proteomics to catalog proximal proteins of phytotransferrin in the model marine diatom Phaeodactylum tricornutum. Proteins encoded by poorly characterized iron-sensitive genes were identified including three that are expressed from a chromosomal gene cluster. Two of them showed unambiguous colocalization with phytotransferrin adjacent to the chloroplast. Further phylogenetic, domain, and biochemical analyses suggest their involvement in intracellular iron processing. Proximity proteomics holds enormous potential to glean new insights into iron acquisition pathways and beyond in these evolutionarily, ecologically, and biotechnologically important microalgae.
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Affiliation(s)
- Jernej Turnšek
- Biological and Biomedical Sciences, The Graduate School of Arts and Sciences, Harvard UniversityCambridgeUnited States
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
- Wyss Institute for Biologically Inspired Engineering, Harvard UniversityBostonUnited States
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
- Center for Research in Biological Systems, University of California San DiegoLa JollaUnited States
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
| | - John K Brunson
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
| | | | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, University of California San DiegoLa JollaUnited States
| | - Aleš Horák
- Biology Centre CAS, Institute of ParasitologyČeské BudějoviceCzech Republic
- University of South Bohemia, Faculty of ScienceČeské BudějoviceCzech Republic
| | - Miroslav Oborník
- Biology Centre CAS, Institute of ParasitologyČeské BudějoviceCzech Republic
- University of South Bohemia, Faculty of ScienceČeské BudějoviceCzech Republic
| | - Vincent A Bielinski
- Synthetic Biology and Bioenergy, J. Craig Venter InstituteLa JollaUnited States
| | - Andrew Ellis Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
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15
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McNeill DR, Whitaker AM, Stark WJ, Illuzzi JL, McKinnon PJ, Freudenthal BD, Wilson DM. Functions of the major abasic endonuclease (APE1) in cell viability and genotoxin resistance. Mutagenesis 2021; 35:27-38. [PMID: 31816044 DOI: 10.1093/mutage/gez046] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/12/2019] [Indexed: 12/24/2022] Open
Abstract
DNA is susceptible to a range of chemical modifications, with one of the most frequent lesions being apurinic/apyrimidinic (AP) sites. AP sites arise due to damage-induced (e.g. alkylation) or spontaneous hydrolysis of the N-glycosidic bond that links the base to the sugar moiety of the phosphodiester backbone, or through the enzymatic activity of DNA glycosylases, which release inappropriate bases as part of the base excision repair (BER) response. Unrepaired AP sites, which lack instructional information, have the potential to cause mutagenesis or to arrest progressing DNA or RNA polymerases, potentially causing outcomes such as cellular transformation, senescence or death. The predominant enzyme in humans responsible for repairing AP lesions is AP endonuclease 1 (APE1). Besides being a powerful AP endonuclease, APE1 possesses additional DNA repair activities, such as 3'-5' exonuclease, 3'-phophodiesterase and nucleotide incision repair. In addition, APE1 has been shown to stimulate the DNA-binding activity of a number of transcription factors through its 'REF1' function, thereby regulating gene expression. In this article, we review the structural and biochemical features of this multifunctional protein, while reporting on new structures of the APE1 variants Cys65Ala and Lys98Ala. Using a functional complementation approach, we also describe the importance of the repair and REF1 activities in promoting cell survival, including the proposed passing-the-baton coordination in BER. Finally, results are presented indicating a critical role for APE1 nuclease activities in resistance to the genotoxins methyl methanesulphonate and bleomycin, supporting biologically important functions as an AP endonuclease and 3'-phosphodiesterase, respectively.
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Affiliation(s)
- Daniel R McNeill
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Amy M Whitaker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Wesley J Stark
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | | | - Peter J McKinnon
- Department of Genetics and Tumor Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - David M Wilson
- Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
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16
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Li S, Zhao Q, Zhang K, Sun W, Li J, Guo X, Yin J, Zhang J, Tang C. Selenium Deficiency-Induced Pancreatic Pathology Is Associated with Oxidative Stress and Energy Metabolism Disequilibrium. Biol Trace Elem Res 2021; 199:154-165. [PMID: 32314143 DOI: 10.1007/s12011-020-02140-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/30/2020] [Indexed: 12/16/2022]
Abstract
Selenium (Se) is an essential micronutrient that plays a crucial role in development and physiological processes. The present study aimed to investigate the effects of Se deficiency on pancreatic pathology and the potential mechanism in pigs. Twenty-four castrated male Yorkshire pigs were divided into two groups and fed a Se-deficient diet (0.007 mg Se/kg) or a Se-adequate diet (0.3 mg Se/kg) for 16 weeks. The serum concentrations of insulin and glucagon, Se concentration, histologic characteristics, apoptotic status, antioxidant activity, free radical content, and major metabolite concentrations were analyzed. The results showed that Se deficiency reduced the concentrations of insulin and glucagon in the serum and of Se in pancreas, decreased the number of islets and cells in the local islets, and induced pancreatic apoptosis. Se deficiency caused a redox imbalance, which led to an increase in the content of free radicals and decreased the activity of antioxidant enzymes. Of 147 targeted metabolites judged to be present in pancreas, only hypotaurine and D-glucuronic acid had differential concentrations with the false discovery rate < 0.05. Pathway analysis using metabolites with differential expression (unadjusted P < 0.05, fold change > 1.4 or < 0.67) found that 8 glycolytic metabolites were significantly increased by Se-deficient, whereas most of the tricarboxylic acid cycle and pentose phosphate pathway metabolites were not significantly changed. Our studies indicated that Se deficiency-induced pancreatic pathology was associated with oxidative stress and enhanced activity of glycolysis, which may provide gaining insight into the actions of Se as a diabetogenic factor.
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Affiliation(s)
- Shuang Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Scientific Observing and Experiment Station of Animal Genetic Resources and Nutrition in North China of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qingyu Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Scientific Observing and Experiment Station of Animal Genetic Resources and Nutrition in North China of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Kai Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Scientific Observing and Experiment Station of Animal Genetic Resources and Nutrition in North China of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wenjuan Sun
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Scientific Observing and Experiment Station of Animal Genetic Resources and Nutrition in North China of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jing Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Scientific Observing and Experiment Station of Animal Genetic Resources and Nutrition in North China of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaoqing Guo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Scientific Observing and Experiment Station of Animal Genetic Resources and Nutrition in North China of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jingdong Yin
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Junmin Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Scientific Observing and Experiment Station of Animal Genetic Resources and Nutrition in North China of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Chaohua Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- Scientific Observing and Experiment Station of Animal Genetic Resources and Nutrition in North China of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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17
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Abstract
Iodothyronine deiodinases (Dios) are important selenoproteins that control the concentration of the active thyroid hormone (TH) triiodothyronine through regioselective deiodination. The X-ray structure of a truncated monomer of Type III Dio (Dio3), which deiodinates TH inner rings through a selenocysteine (Sec) residue, revealed a thioredoxin-fold catalytic domain supplemented with an unstructured Ω-loop. Loop dynamics are driven by interactions of the conserved Trp207 with solvent in multi-microsecond molecular dynamics simulations of the Dio3 thioredoxin(Trx)-fold domain. Hydrogen bonding interactions of Glu200 with residues conserved across the Dio family anchor the loop’s N-terminus to the active site Ser-Cys-Thr-Sec sequence. A key long-lived loop conformation coincides with the opening of a cryptic pocket that accommodates thyroxine (T4) through an I⋯Se halogen bond to Sec170 and the amino acid group with a polar cleft. The Dio3-T4 complex is stabilized by an I⋯O halogen bond between an outer ring iodine and Asp211, consistent with Dio3 selectivity for inner ring deiodination. Non-conservation of residues, such as Asp211, in other Dio types in the flexible portion of the loop sequence suggests a mechanism for regioselectivity through Dio type-specific loop conformations. Cys168 is proposed to attack the selenenyl iodide intermediate to regenerate Dio3 based upon structural comparison with related Trx-fold proteins.
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18
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Maki JA, Cavallin JE, Lott KG, Saari TW, Ankley GT, Villeneuve DL. A method for CRISPR/Cas9 mutation of genes in fathead minnow (Pimephales promelas). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 222:105464. [PMID: 32160575 PMCID: PMC7280908 DOI: 10.1016/j.aquatox.2020.105464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/10/2020] [Accepted: 03/01/2020] [Indexed: 06/10/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 genome editing allows for the disruption or modification of genes in a multitude of model organisms. In the present study, we describe and employ the method for use in the fathead minnow (Pimephales promelas), in part, to assist in the development and validation of adverse outcome pathways (AOPs). The gene coding for an enzyme responsible for melanin production, tyrosinase (tyr), was the initial target chosen for development and assessment of the method since its disruption results in abnormal pigmentation, a phenotype obvious within 3-4 d after injection of fathead minnow embryos. Three tyrosinase-targeting guide strands were generated using the fathead minnow sequence in tandem with the CRISPOR guide strand selection tool. The strands targeted two areas: one stretch of sequence in a conserved region that demonstrated homology to EGF-like or laminin-like domains as determined by Protein Basic Local Alignment Search Tool in concert with the Conserved Domain Database, and a second area in the N-terminal region of the tyrosinase domain. To generate one cell embryos, in vitro fertilization was performed, allowing for microinjection of hundreds of developmentally-synchronized embryos with Cas9 proteins complexed to each of the three guide strands. Altered retinal pigmentation was observed in a portion of the tyr guide strand injected population within 3 d post fertilization (dpf). By 14 dpf, fish without skin and swim bladder pigmentation were observed. Among the three guide strands injected, the guide targeting the EGF/laminin-like domain was most effective in generating mutants. CRISPR greatly advances our ability to directly investigate gene function in fathead minnow, allowing for advanced approaches to AOP validation and development.
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Affiliation(s)
- Jennifer A Maki
- ORISE Research Participation Program, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, 6201 Congdon Blvd., Duluth, MN, 55804, USA; Department of Chemistry and Biochemistry, The College of St. Scholastica, 1200 Kenwood Ave., Duluth, MN, 55811, USA.
| | - Jenna E Cavallin
- Badger Technical Services, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, 6201 Congdon Blvd., Duluth, MN, 55804, USA
| | - Kevin G Lott
- Badger Technical Services, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, 6201 Congdon Blvd., Duluth, MN, 55804, USA
| | - Travis W Saari
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, 6201 Congdon Blvd., Duluth, MN, 55804, USA
| | - Gerald T Ankley
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, 6201 Congdon Blvd., Duluth, MN, 55804, USA
| | - Daniel L Villeneuve
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, 6201 Congdon Blvd., Duluth, MN, 55804, USA
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19
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Park KA, Yun N, Oh YJ. Anamorsin attenuates cupric chloride-induced dopaminergic neuronal cell death. Biochem Biophys Res Commun 2019; 520:99-106. [DOI: 10.1016/j.bbrc.2019.09.089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 09/21/2019] [Indexed: 12/11/2022]
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20
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Liu P, Chen Y, Shao Z, Chen J, Wu J, Guo Q, Shi J, Wang H, Chu X. AhlX, an N-acylhomoserine Lactonase with Unique Properties. Mar Drugs 2019; 17:md17070387. [PMID: 31261836 PMCID: PMC6669651 DOI: 10.3390/md17070387] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/12/2019] [Accepted: 06/25/2019] [Indexed: 11/16/2022] Open
Abstract
N-Acylhomoserine lactonase degrades the lactone ring of N-acylhomoserine lactones (AHLs) and has been widely suggested as a promising candidate for use in bacterial disease control. While a number of AHL lactonases have been characterized, none of them has been developed as a commercially available enzymatic product for in vitro AHL quenching due to their low stability. In this study, a highly stable AHL lactonase (AhlX) was identified and isolated from the marine bacterium Salinicola salaria MCCC1A01339. AhlX is encoded by a 768-bp gene and has a predicted molecular mass of 29 kDa. The enzyme retained approximately 97% activity after incubating at 25 °C for 12 days and ~100% activity after incubating at 60 °C for 2 h. Furthermore, AhlX exhibited a high salt tolerance, retaining approximately 60% of its activity observed in the presence of 25% NaCl. In addition, an AhlX powder made by an industrial spray-drying process attenuated Erwinia carotovora infection. These results suggest that AhlX has great potential for use as an in vitro preventive and therapeutic agent for bacterial diseases.
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Affiliation(s)
- Pengfu Liu
- Collaborative Innovation Center of Yangtze River DeltaRegion Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Pudong, Shanghai 201210, China.
| | - Yan Chen
- Collaborative Innovation Center of Yangtze River DeltaRegion Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, The Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China.
| | - Jianwei Chen
- Collaborative Innovation Center of Yangtze River DeltaRegion Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
| | - Jiequn Wu
- Collaborative Innovation Center of Yangtze River DeltaRegion Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
| | - Qian Guo
- Collaborative Innovation Center of Yangtze River DeltaRegion Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
| | - Jiping Shi
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Pudong, Shanghai 201210, China.
| | - Hong Wang
- Collaborative Innovation Center of Yangtze River DeltaRegion Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
| | - Xiaohe Chu
- Collaborative Innovation Center of Yangtze River DeltaRegion Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
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21
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Bayse CA, Pollard DB. Conformation dynamics of cyclic disulfides and selenosulfides in CXXC(U) (X = Gly, Ala) tetrapeptide redox motifs. J Pept Sci 2019; 25:e3160. [PMID: 30873692 DOI: 10.1002/psc.3160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/26/2019] [Accepted: 02/05/2019] [Indexed: 02/01/2023]
Abstract
Thioredoxin fold proteins often contain a Cys-(Xxx)n -Cys(Sec) or CXn C(U) motif, where the active cysteine (C) or selenocysteine (U) is bridged by X residues, which vary with protein function. The effect of the X residues on the conformation space of the oxidized disulfide and selenosulfide forms of the CXXC(U) motif has been investigated using molecular dynamics (MD) and density functional theory. Multi-microsecond-length MD simulations of the CGGC, CGAC, and CAGC cyclic peptides show that CGGC rings readily exchange between several conformations over the course of the simulation, but steric interactions with the methyl group of Ala limit the conformation space available to the cyclic peptide, especially for CGAC. The potential for the motif to be reduced, as measured by the energy of the lowest unoccupied molecular orbitals, is dependent upon the ring conformation. These results suggest that control of available conformations by the bridging residues and the protein tertiary structure may be important for defining the function of the CXXC motif. Theoretical 77 Se chemical shifts of the selenosulfide moiety are dependent upon the conformation and/or intramolecular Se···O interactions with the backbone carbonyl group of the C-terminal U residue.
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Affiliation(s)
- Craig A Bayse
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, 23529
| | - Deanna B Pollard
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, 23529
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22
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Mikheyeva IV, Thomas JM, Kolar SL, Corvaglia AR, Gaϊa N, Leo S, Francois P, Liu GY, Rawat M, Cheung AL. YpdA, a putative bacillithiol disulfide reductase, contributes to cellular redox homeostasis and virulence in Staphylococcus aureus. Mol Microbiol 2019; 111:1039-1056. [PMID: 30636083 DOI: 10.1111/mmi.14207] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/27/2018] [Indexed: 11/28/2022]
Abstract
The intracellular redox environment of Staphylococcus aureus is mainly buffered by bacillithiol (BSH), a low molecular weight thiol. The identity of enzymes responsible for the recycling of oxidized bacillithiol disulfide (BSSB) to the reduced form (BSH) remains elusive. We examined YpdA, a putative bacillithiol reductase, for its role in maintaining intracellular redox homeostasis. The ypdA mutant showed increased levels of BSSB and a lower bacillithiol redox ratio vs. the isogenic parent, indicating a higher level of oxidative stress within the bacterial cytosol. We showed that YpdA consumed NAD(P)H; and YpdA protein levels were augmented in response to stress. Wild type strains overexpressing YpdA showed increased tolerance to oxidants and electrophilic agents. Importantly, YpdA overexpression in the parental strain caused an increase in BSH levels accompanied by a decrease in BSSB concentration in the presence of stress, resulting in an increase in bacillithiol redox ratio vs. the vector control. Additionally, the ypdA mutant exhibited decreased survival in human neutrophils (PMNs) as compared with the parent, while YpdA overexpression protected the resulting strain from oxidative stress in vitro and from killing by human neutrophils ex vivo. Taken together, these data present a new role for YpdA in S. aureus physiology and virulence through the bacillithiol system.
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Affiliation(s)
- Irina V Mikheyeva
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jason M Thomas
- Biology Department, California State University, Fresno, Fresno, CA 93740, USA
| | - Stacey L Kolar
- Department of Pediatrics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Anna-Rita Corvaglia
- Genomic Research Laboratory, Service of Infectious Diseases, University Hospital of Geneva, 1205 Geneva 4, Switzerland
| | - Nadia Gaϊa
- Genomic Research Laboratory, Service of Infectious Diseases, University Hospital of Geneva, 1205 Geneva 4, Switzerland
| | - Stefano Leo
- Genomic Research Laboratory, Service of Infectious Diseases, University Hospital of Geneva, 1205 Geneva 4, Switzerland
| | - Patrice Francois
- Genomic Research Laboratory, Service of Infectious Diseases, University Hospital of Geneva, 1205 Geneva 4, Switzerland
| | - George Y Liu
- Department of Pediatrics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mamta Rawat
- Biology Department, California State University, Fresno, Fresno, CA 93740, USA
| | - Ambrose L Cheung
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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23
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Efficient oral vaccination by bioengineering virus-like particles with protozoan surface proteins. Nat Commun 2019; 10:361. [PMID: 30664644 PMCID: PMC6341118 DOI: 10.1038/s41467-018-08265-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/22/2018] [Indexed: 12/13/2022] Open
Abstract
Intestinal and free-living protozoa, such as Giardia lamblia, express a dense coat of variant-specific surface proteins (VSPs) on trophozoites that protects the parasite inside the host’s intestine. Here we show that VSPs not only are resistant to proteolytic digestion and extreme pH and temperatures but also stimulate host innate immune responses in a TLR-4 dependent manner. We show that these properties can be exploited to both protect and adjuvant vaccine antigens for oral administration. Chimeric Virus-like Particles (VLPs) decorated with VSPs and expressing model surface antigens, such as influenza virus hemagglutinin (HA) and neuraminidase (NA), are protected from degradation and activate antigen presenting cells in vitro. Orally administered VSP-pseudotyped VLPs, but not plain VLPs, generate robust immune responses that protect mice from influenza infection and HA-expressing tumors. This versatile vaccine platform has the attributes to meet the ultimate challenge of generating safe, stable and efficient oral vaccines. Giardia lamblia express a dense coat of variant-specific surface proteins (VSPs) on trophozoites that protects the parasite inside the host´s intestine. Here the authors show that stability and immunomodulatory properties of VSPs can be exploited to both protect and adjuvant vaccine antigens for oral administration.
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Kilgore HR, Raines RT. n→π* Interactions Modulate the Properties of Cysteine Residues and Disulfide Bonds in Proteins. J Am Chem Soc 2018; 140:17606-17611. [PMID: 30403347 DOI: 10.1021/jacs.8b09701] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Noncovalent interactions are ubiquitous in biology, taking on roles that include stabilizing the conformation of and assembling biomolecules, and providing an optimal environment for enzymatic catalysis. Here, we describe a noncovalent interaction that engages the sulfur atoms of cysteine residues and disulfide bonds in proteins-their donation of electron density into an antibonding orbital of proximal amide carbonyl groups. This n→ π* interaction tunes the reactivity of the CXXC motif, which is the critical feature of thioredoxin and other enzymes involved in redox homeostasis. In particular, an n→ π* interaction lowers the p Ka value of the N-terminal cysteine residue of the motif, which is the nucleophile that initiates catalysis. In addition, the interplay between disulfide n→ π* interactions and C5 hydrogen bonds leads to hyperstable β-strands. Finally, n→ π* interactions stabilize vicinal disulfide bonds, which are naturally diverse in function. These previously unappreciated n→ π* interactions are strong and underlie the ability of cysteine residues and disulfide bonds to engage in the structure and function of proteins.
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Affiliation(s)
- Henry R Kilgore
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Ronald T Raines
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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25
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Wang H, Chen X, Li C, Liu Y, Yang F, Wang C. Sequence-Based Prediction of Cysteine Reactivity Using Machine Learning. Biochemistry 2017; 57:451-460. [DOI: 10.1021/acs.biochem.7b00897] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Haobo Wang
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory for
Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xuemin Chen
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory for
Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Can Li
- Department
of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yuan Liu
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory for
Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
| | - Fan Yang
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory for
Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chu Wang
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory for
Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
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26
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Gyrdymova YV, Sudarikov DV, Shevchenko OG, Rubtsova SA, Slepukhin PA, Kutchin AV. Caryophyllane Thiols, Vinyl Thioethers, Di- and Bis-Sulfides: Antioxidant and Membrane Protective Activities. Chem Biodivers 2017; 14. [PMID: 28704572 DOI: 10.1002/cbdv.201700296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 07/10/2017] [Indexed: 11/11/2022]
Abstract
Caryophyllane thioterpenoids were synthesized in 23 - 81% yields. The antioxidant properties of the obtained compounds in various model systems were found. It was revealed that 4,5-epoxycaryophyll-9-ylmethanethiol has the greatest antioxidant activity. The isomerism of sesquiterpenic fragments was shown to have a significant effect on the biological activity of the compounds.
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Affiliation(s)
- Yulia V Gyrdymova
- Institute of Chemistry of the Komi Science Center, Ural Branch of the Russian Academy of Sciences, 48, Pervomaiskaya Ul., Syktyvkar, 167000, Russia
| | - Denis V Sudarikov
- Institute of Chemistry of the Komi Science Center, Ural Branch of the Russian Academy of Sciences, 48, Pervomaiskaya Ul., Syktyvkar, 167000, Russia
| | - Oksana G Shevchenko
- Institute of Biology of the Komi Science Center, Ural Branch of the Russian Academy of Sciences, 28, Kommunisticheskaya Ul., Syktyvkar, 167000, Russia
| | - Svetlana A Rubtsova
- Institute of Chemistry of the Komi Science Center, Ural Branch of the Russian Academy of Sciences, 48, Pervomaiskaya Ul., Syktyvkar, 167000, Russia
| | - Pavel A Slepukhin
- Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, 22, S Kovalevskaya Ul., Ekaterinburg, 620137, Russia
| | - Aleksandr V Kutchin
- Institute of Chemistry of the Komi Science Center, Ural Branch of the Russian Academy of Sciences, 48, Pervomaiskaya Ul., Syktyvkar, 167000, Russia
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27
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Jamithireddy AK, Samajdar RN, Gopal B, Bhattacharyya AJ. Determination of Redox Sensitivity in Structurally Similar Biological Redox Sensors. J Phys Chem B 2017; 121:7005-7015. [DOI: 10.1021/acs.jpcb.7b02081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Rudra N. Samajdar
- Solid
State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - B. Gopal
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Aninda J. Bhattacharyya
- Solid
State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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28
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Harper AF, Leuthaeuser JB, Babbitt PC, Morris JH, Ferrin TE, Poole LB, Fetrow JS. An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PLoS Comput Biol 2017; 13:e1005284. [PMID: 28187133 PMCID: PMC5302317 DOI: 10.1371/journal.pcbi.1005284] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 12/06/2016] [Indexed: 12/15/2022] Open
Abstract
Peroxiredoxins (Prxs or Prdxs) are a large protein superfamily of antioxidant enzymes that rapidly detoxify damaging peroxides and/or affect signal transduction and, thus, have roles in proliferation, differentiation, and apoptosis. Prx superfamily members are widespread across phylogeny and multiple methods have been developed to classify them. Here we present an updated atlas of the Prx superfamily identified using a novel method called MISST (Multi-level Iterative Sequence Searching Technique). MISST is an iterative search process developed to be both agglomerative, to add sequences containing similar functional site features, and divisive, to split groups when functional site features suggest distinct functionally-relevant clusters. Superfamily members need not be identified initially-MISST begins with a minimal representative set of known structures and searches GenBank iteratively. Further, the method's novelty lies in the manner in which isofunctional groups are selected; rather than use a single or shifting threshold to identify clusters, the groups are deemed isofunctional when they pass a self-identification criterion, such that the group identifies itself and nothing else in a search of GenBank. The method was preliminarily validated on the Prxs, as the Prxs presented challenges of both agglomeration and division. For example, previous sequence analysis clustered the Prx functional families Prx1 and Prx6 into one group. Subsequent expert analysis clearly identified Prx6 as a distinct functionally relevant group. The MISST process distinguishes these two closely related, though functionally distinct, families. Through MISST search iterations, over 38,000 Prx sequences were identified, which the method divided into six isofunctional clusters, consistent with previous expert analysis. The results represent the most complete computational functional analysis of proteins comprising the Prx superfamily. The feasibility of this novel method is demonstrated by the Prx superfamily results, laying the foundation for potential functionally relevant clustering of the universe of protein sequences.
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Affiliation(s)
- Angela F. Harper
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Janelle B. Leuthaeuser
- Department of Molecular Genetics and Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Patricia C. Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco School of Pharmacy, San Francisco, California, United States of America
| | - John H. Morris
- Department of Pharmaceutical Chemistry, University of California San Francisco School of Pharmacy, San Francisco, California, United States of America
| | - Thomas E. Ferrin
- Department of Pharmaceutical Chemistry, University of California San Francisco School of Pharmacy, San Francisco, California, United States of America
| | - Leslie B. Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Jacquelyn S. Fetrow
- Department of Chemistry, University of Richmond, Richmond, Virginia, United States of America
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29
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Dominiak A, Wilkaniec A, Wroczyński P, Adamczyk A. Selenium in the Therapy of Neurological Diseases. Where is it Going? Curr Neuropharmacol 2016; 14:282-99. [PMID: 26549649 PMCID: PMC4857624 DOI: 10.2174/1570159x14666151223100011] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 08/20/2015] [Accepted: 09/16/2015] [Indexed: 12/19/2022] Open
Abstract
Selenium (34Se), an antioxidant trace element, is an important regulator of brain function. These beneficial properties that Se possesses are attributed to its ability to be incorporated into selenoproteins as an amino acid. Several selenoproteins are expressed in the brain, in which some of them, e.g. glutathione peroxidases (GPxs), thioredoxin reductases (TrxRs) or selenoprotein P (SelP), are strongly involved in antioxidant defence and in maintaining intercellular reducing conditions. Since increased oxidative stress has been implicated in neurological disorders, including Parkinson’s disease, Alzheimer’s disease, stroke, epilepsy and others, a growing body of evidence suggests that Se depletion followed by decreased activity of Se-dependent enzymes may be important factors connected with those pathologies. Undoubtedly, the remarkable progress that has been made in understanding the biological function of Se in the brain has opened up new potential possibilities for the treatment of neurological diseases by using Se as a potential drug. However, further research in the search for optimal Se donors is necessary in order to achieve an effective and safe therapeutic income.
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Affiliation(s)
| | - Anna Wilkaniec
- Department of Cellular Signaling, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawińskiego 5 St., 02-106 Warsaw, Poland.
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30
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Tofanello A, Miranda ÉA, Dias IWR, Lanfredi AJC, Arantes JT, Juliano M, Nantes IL. pH-Dependent Synthesis of Anisotropic Gold Nanostructures by Bioinspired Cysteine-Containing Peptides. ACS OMEGA 2016; 1:424-434. [PMID: 31457138 PMCID: PMC6640750 DOI: 10.1021/acsomega.6b00140] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/06/2016] [Indexed: 05/28/2023]
Abstract
In the present study, alkaline peptides AAAXCX (X = lysine or arginine residues) were designed based on the conserved motif of the enzyme thioredoxin and used for the synthesis of gold nanoparticles (GNPs) in the pH range of 2-11. These peptides were compared with free cysteine, the counterpart acidic peptides AAAECE and γ-ECG (glutathione), and the neutral peptide AAAACA. The objective was to investigate the effect of the amino acids neighboring a cysteine residue on the pH-dependent synthesis of gold nanocrystals. Kohn-Sham density functional theory (KS-DFT) calculations indicated an increase in the reducing capacity of AAAKCK favored by the successive deprotonation of their ionizable groups at increasing pH values. Experimentally, it was observed that gold speciation and the peptide structure also have a strong influence on the synthesis and stabilization of GNPs. AAAKCK produced GNPs at room temperature, in the whole investigated pH range. By contrast, alkaline pH was the best condition for the synthesis of GNP assisted by the AAARCR peptide. The acidic peptides produced GNPs only in the presence of polyethylene glycol, and the synthesis using AAAECE and γ-ECG also required heating. The ionization state of AAAKCK had a strong influence on the preferential growth of the GNPs. Therefore, pH had a remarkable effect on the synthesis, kinetics, size, shape, and polydispersity of GNPs produced using AAAKCK. The AAAKCK peptide produced anisotropic decahedral and platelike nanocrystals at acidic pH values and spherical GNPs at alkaline pH values. Both alkaline peptides were also efficient capping agents for GNPs, but they produced a significant difference in the zeta potential, probably because of different orientations on the gold surface.
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Affiliation(s)
- Aryane Tofanello
- NanoBioMAv, Centro de Ciências Naturais e Humanas (CCNH) and Centro de Engenharia,
Modelagem e Ciências Sociais Aplicadas (CECS), Universidade Federal do ABC (UFABC), Avenida dos Estados 5001, Bairro Bangu, 09210-580 Santo André, São Paulo, Brazil
| | - Érica
G. A. Miranda
- NanoBioMAv, Centro de Ciências Naturais e Humanas (CCNH) and Centro de Engenharia,
Modelagem e Ciências Sociais Aplicadas (CECS), Universidade Federal do ABC (UFABC), Avenida dos Estados 5001, Bairro Bangu, 09210-580 Santo André, São Paulo, Brazil
| | - Igor W. R. Dias
- NanoBioMAv, Centro de Ciências Naturais e Humanas (CCNH) and Centro de Engenharia,
Modelagem e Ciências Sociais Aplicadas (CECS), Universidade Federal do ABC (UFABC), Avenida dos Estados 5001, Bairro Bangu, 09210-580 Santo André, São Paulo, Brazil
| | - Alexandre J. C. Lanfredi
- NanoBioMAv, Centro de Ciências Naturais e Humanas (CCNH) and Centro de Engenharia,
Modelagem e Ciências Sociais Aplicadas (CECS), Universidade Federal do ABC (UFABC), Avenida dos Estados 5001, Bairro Bangu, 09210-580 Santo André, São Paulo, Brazil
| | - Jeverson T. Arantes
- NanoBioMAv, Centro de Ciências Naturais e Humanas (CCNH) and Centro de Engenharia,
Modelagem e Ciências Sociais Aplicadas (CECS), Universidade Federal do ABC (UFABC), Avenida dos Estados 5001, Bairro Bangu, 09210-580 Santo André, São Paulo, Brazil
| | - Maria
A. Juliano
- Departamento
de Biologia Molecular, Universidade Federal
de São Paulo, Rua 3 de Maio 100, Vila Clementino, 04044-020 São Paulo, São Paulo, Brazil
| | - Iseli L. Nantes
- NanoBioMAv, Centro de Ciências Naturais e Humanas (CCNH) and Centro de Engenharia,
Modelagem e Ciências Sociais Aplicadas (CECS), Universidade Federal do ABC (UFABC), Avenida dos Estados 5001, Bairro Bangu, 09210-580 Santo André, São Paulo, Brazil
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31
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El Gamal A, Agarwal V, Rahman I, Moore BS. Enzymatic Reductive Dehalogenation Controls the Biosynthesis of Marine Bacterial Pyrroles. J Am Chem Soc 2016; 138:13167-13170. [PMID: 27676265 DOI: 10.1021/jacs.6b08512] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Enzymes capable of performing dehalogenating reactions have attracted tremendous contemporary attention due to their potential application in the bioremediation of anthropogenic polyhalogenated persistent organic pollutants. Nature, in particular the marine environment, is also a prolific source of polyhalogenated organic natural products. The study of the biosynthesis of these natural products has furnished a diverse array of halogenation biocatalysts, but thus far no examples of dehalogenating enzymes have been reported from a secondary metabolic pathway. Here we show that the penultimate step in the biosynthesis of the highly brominated marine bacterial product pentabromopseudilin is catalyzed by an unusual debrominase Bmp8 that utilizes a redox thiol mechanism to remove the C-2 bromine atom of 2,3,4,5-tetrabromopyrrole to facilitate oxidative coupling to 2,4-dibromophenol. To the best of our knowledge, Bmp8 is first example of a dehalogenating enzyme from the established genetic and biochemical context of a natural product biosynthetic pathway.
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Affiliation(s)
- Abrahim El Gamal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, Scripps Institution of Oceanography, University of California, San Diego , San Diego, California 92093, United States
| | - Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, Scripps Institution of Oceanography, University of California, San Diego , San Diego, California 92093, United States
| | - Imran Rahman
- Center for Oceans and Human Health, Scripps Institution of Oceanography, Scripps Institution of Oceanography, University of California, San Diego , San Diego, California 92093, United States
| | - Bradley S Moore
- Center for Oceans and Human Health, Scripps Institution of Oceanography, Scripps Institution of Oceanography, University of California, San Diego , San Diego, California 92093, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , San Diego, California 92093, United States
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32
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Nesmelov AA, Devatiyarov RM, Voronina TA, Kondratyeva SA, Cherkasov AV, Cornette R, Kikawada T, Shagimardanova EI. New Antioxidant Genes from an Anhydrobiotic Insect: Unique Structural Features in Functional Motifs of Thioredoxins. BIONANOSCIENCE 2016. [DOI: 10.1007/s12668-016-0278-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Bocian-Ostrzycka KM, Grzeszczuk MJ, Banaś AM, Jastrząb K, Pisarczyk K, Kolarzyk A, Łasica AM, Collet JF, Jagusztyn-Krynicka EK. Engineering of Helicobacter pylori Dimeric Oxidoreductase DsbK (HP0231). Front Microbiol 2016; 7:1158. [PMID: 27507968 PMCID: PMC4960241 DOI: 10.3389/fmicb.2016.01158] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/12/2016] [Indexed: 12/16/2022] Open
Abstract
The formation of disulfide bonds that are catalyzed by proteins of the Dsb (disulfide bond) family is crucial for the correct folding of many extracytoplasmic proteins. Thus, this formation plays an essential, pivotal role in the assembly of many virulence factors. The Helicobacter pylori disulfide bond-forming system is uncomplicated compared to the best-characterized Escherichia coli Dsb pathways. It possesses only two extracytoplasmic Dsb proteins named HP0377 and HP0231. As previously shown, HP0377 is a reductase involved in the process of cytochrome c maturation. Additionally, it also possesses disulfide isomerase activity. HP0231 was the first periplasmic dimeric oxidoreductase involved in disulfide generation to be described. Although HP0231 function is critical for oxidative protein folding, its structure resembles that of dimeric EcDsbG, which does not confer this activity. However, the HP0231 catalytic motifs (CXXC and the so-called cis-Pro loop) are identical to that of monomeric EcDsbA. To understand the functioning of HP0231, we decided to study the relations between its sequence, structure and activity through an extensive analysis of various HP0231 point mutants, using in vivo and in vitro strategies. Our work shows the crucial role of the cis-Pro loop, as changing valine to threonine in this motif completely abolishes the protein function in vivo. Functioning of HP0231 is conditioned by the combination of CXXC and the cis-Pro loop, as replacing the HP0231 CXXC motif by the motif from EcDsbG or EcDsbC results in bifunctional protein, at least in E. coli. We also showed that the dimerization domain of HP0231 ensures contact with its substrates. Moreover, the activity of this oxidase is independent on the structure of the catalytic domain. Finally, we showed that HP0231 chaperone activity is independent of its redox function.
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Affiliation(s)
- Katarzyna M Bocian-Ostrzycka
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Magdalena J Grzeszczuk
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Anna M Banaś
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Katarzyna Jastrząb
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Karolina Pisarczyk
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Anna Kolarzyk
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Anna M Łasica
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Jean-François Collet
- Walloon Excellence in Life Sciences and BiotechnologyBrussels, Belgium; de Duve Institute, Université Catholique de LouvainBrussels, Belgium
| | - Elżbieta K Jagusztyn-Krynicka
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
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34
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Mariotti M, Lobanov AV, Manta B, Santesmasses D, Bofill A, Guigó R, Gabaldón T, Gladyshev VN. Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems. Mol Biol Evol 2016; 33:2441-53. [PMID: 27413050 PMCID: PMC4989117 DOI: 10.1093/molbev/msw122] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Selenocysteine (Sec) is the 21st amino acid in the genetic code, inserted in response to UGA codons with the help of RNA structures, the SEC Insertion Sequence (SECIS) elements. The three domains of life feature distinct strategies for Sec insertion in proteins and its utilization. While bacteria and archaea possess similar sets of selenoproteins, Sec biosynthesis is more similar among archaea and eukaryotes. However, SECIS elements are completely different in the three domains of life. Here, we analyze the archaeon Lokiarchaeota that resolves the relationships among Sec insertion systems. This organism has selenoproteins representing five protein families, three of which have multiple Sec residues. Remarkably, these archaeal selenoprotein genes possess conserved RNA structures that strongly resemble the eukaryotic SECIS element, including key eukaryotic protein-binding sites. These structures also share similarity with the SECIS element in archaeal selenoprotein VhuD, suggesting a relation of direct descent. These results identify Lokiarchaeota as an intermediate form between the archaeal and eukaryotic Sec-encoding systems and clarify the evolution of the Sec insertion system.
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Affiliation(s)
- Marco Mariotti
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF); and Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Alexei V Lobanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Bruno Manta
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Didac Santesmasses
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF); and Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Andreu Bofill
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF); and Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Roderic Guigó
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF); and Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF); and Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
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35
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Saidijam M, Azizpour S, Patching SG. Amino acid composition analysis of human secondary transport proteins and implications for reliable membrane topology prediction. J Biomol Struct Dyn 2016; 35:929-949. [PMID: 27159787 DOI: 10.1080/07391102.2016.1167622] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Secondary transporters in humans are a large group of proteins that transport a wide range of ions, metals, organic and inorganic solutes involved in energy transduction, control of membrane potential and osmotic balance, metabolic processes and in the absorption or efflux of drugs and xenobiotics. They are also emerging as important targets for development of new drugs and as target sites for drug delivery to specific organs or tissues. We have performed amino acid composition (AAC) and phylogenetic analyses and membrane topology predictions for 336 human secondary transport proteins and used the results to confirm protein classification and to look for trends and correlations with structural domains and specific substrates and/or function. Some proteins showed statistically high contents of individual amino acids or of groups of amino acids with similar physicochemical properties. One recurring trend was a correlation between high contents of charged and/or polar residues with misleading results in predictions of membrane topology, which was especially prevalent in Mitochondrial Carrier family proteins. We demonstrate how charged or polar residues located in the middle of transmembrane helices can interfere with their identification by membrane topology tools resulting in missed helices in the prediction. Comparison of AAC in the human proteins with that in 235 secondary transport proteins from Escherichia coli revealed similar overall trends along with differences in average contents for some individual amino acids and groups of similar amino acids that are presumed to result from a greater number of functions and complexity in the higher organism.
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Affiliation(s)
- Massoud Saidijam
- a Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Sonia Azizpour
- a Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Simon G Patching
- b School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , UK
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36
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Huang JQ, Ren FZ, Jiang YY, Lei X. Characterization of Selenoprotein M and Its Response to Selenium Deficiency in Chicken Brain. Biol Trace Elem Res 2016; 170:449-58. [PMID: 26315306 DOI: 10.1007/s12011-015-0486-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 08/18/2015] [Indexed: 12/19/2022]
Abstract
Selenoprotein M (SelM) may function as thiol disulfide oxidoreductase that participates in the formation of disulfide bonds and can be implicated in calcium responses. SelM may have a functional role in catalyzing free radicals and has been associated with Alzheimer's disease (AD). However, studies of SelM in chicken remain very limited. In this study, two groups of day-old broiler chicks (n = 40/group) were fed a corn-soy basal diet (BD, 13 μg Se/kg) and BD supplemented with Se (as sodium selenite) at 0.3 mg/kg. The brain was collected at 14, 21, 28, and 42 days of age. We performed a sequence analysis and predicted the structure and function of SelM. We also investigated the effects of Se deficiency on the expression of Selt, Selw, and Selm and the Se status in the chicken brain. The results show that Se deficiency induced the lower (P < 0.05) Se content, glutathione peroxidase (GPx), and catalase (CAT) activities; increased (P < 0.05) malondialdehyde (MDA) content; and reduced (P < 0.05) the expression of Selm messenger RNA (mRNA) and protein abundance of SelM in the brain. However, there were no significant brain Selt and Selw mRNA levels by dietary Se deficiency in chicks. The different regulations of these three redox (Rdx) protein expressions by Se deficiency represent a novel finding of the present study. Our results demonstrated that SelM may have an important role in protecting against oxidative damage in the brain of chicken, which might shed light on the role of SelM in human neurodegenerative disease. More studies are needed to confirm our conclusion.
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Affiliation(s)
- Jia-Qiang Huang
- The Innovation Centre of Food Nutrition and Human Health (Beijing), College of Food Science and Nutritional Engineering, China Agricultural University, P.O. Box 287, No. 17 Qinghua East Road, Beijing, 100083, China
- Beijing Higher Institution Engineering Research Center of Animal Product, Beijing, 100083, China
| | - Fa-Zheng Ren
- The Innovation Centre of Food Nutrition and Human Health (Beijing), College of Food Science and Nutritional Engineering, China Agricultural University, P.O. Box 287, No. 17 Qinghua East Road, Beijing, 100083, China.
- Beijing Higher Institution Engineering Research Center of Animal Product, Beijing, 100083, China.
| | - Yun-Yun Jiang
- The Innovation Centre of Food Nutrition and Human Health (Beijing), College of Food Science and Nutritional Engineering, China Agricultural University, P.O. Box 287, No. 17 Qinghua East Road, Beijing, 100083, China
| | - XinGen Lei
- The Innovation Centre of Food Nutrition and Human Health (Beijing), College of Food Science and Nutritional Engineering, China Agricultural University, P.O. Box 287, No. 17 Qinghua East Road, Beijing, 100083, China
- Department of Animal Science, Cornell University, Ithaca, NY, 14853, USA
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Randall L, Manta B, Nelson KJ, Santos J, Poole LB, Denicola A. Structural changes upon peroxynitrite-mediated nitration of peroxiredoxin 2; nitrated Prx2 resembles its disulfide-oxidized form. Arch Biochem Biophys 2016; 590:101-108. [PMID: 26612102 PMCID: PMC9123601 DOI: 10.1016/j.abb.2015.11.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/15/2015] [Accepted: 11/16/2015] [Indexed: 12/12/2022]
Abstract
Peroxiredoxins are cys-based peroxidases that function in peroxide detoxification and H2O2-induced signaling. Human Prx2 is a typical 2-Cys Prx arranged as pentamers of head-to-tail homodimers. During the catalytic mechanism, the active-site cysteine (CP) cycles between reduced, sulfenic and disulfide state involving conformational as well as oligomeric changes. Several post-translational modifications were shown to affect Prx activity, in particular CP overoxidation which leads to inactivation. We have recently reported that nitration of Prx2, a post-translational modification on non-catalytic tyrosines, unexpectedly increases its peroxidase activity and resistance to overoxidation. To elucidate the cross-talk between this post-translational modification and the enzyme catalysis, we investigated the structural changes of Prx2 after nitration. Analytical ultracentrifugation, UV absorption, circular dichroism, steady-state and time-resolved fluorescence were used to connect catalytically relevant redox changes with tyrosine nitration. Our results show that the reduced nitrated Prx2 structurally resembles the disulfide-oxidized native form of the enzyme favoring a locally unfolded conformation that facilitates disulfide formation. These results provide structural basis for the kinetic analysis previously reported, the observed increase in activity and the resistance to overoxidation of the peroxynitrite-treated enzyme.
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Affiliation(s)
- Lía Randall
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Bruno Manta
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Uruguay; Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Kimberly J Nelson
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Javier Santos
- IQUIFIB (UBA-CONICET) and Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Leslie B Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Ana Denicola
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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Davey L, Cohen A, LeBlanc J, Halperin SA, Lee SF. The disulfide oxidoreductase SdbA is active in Streptococcus gordonii using a single C-terminal cysteine of the CXXC motif. Mol Microbiol 2015; 99:236-53. [PMID: 26395460 DOI: 10.1111/mmi.13227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2015] [Indexed: 12/31/2022]
Abstract
Recently, we identified a novel disulfide oxidoreductase, SdbA, in the oral bacterium Streptococcus gordonii. Disulfide oxidoreductases form disulfide bonds in nascent proteins using a CXXC catalytic motif. Typically, the N-terminal cysteine interacts with substrates, whereas the C-terminal cysteine is buried and only reacts with the first cysteine of the motif. In this study, we investigated the SdbA C(86) P(87) D(88) C(89) catalytic motif. In vitro, SdbA single cysteine variants at the N or C-terminal position (SdbAC86P and SdbAC89A ) were active but displayed different susceptibility to oxidation, and N-terminal cysteine was prone to sulfenylation. In S. gordonii, mutants with a single N-terminal cysteine were inactive and formed unstable disulfide adducts with other proteins. Activity was partially restored by inactivation of pyruvate oxidase, a hydrogen peroxide generator. Presence of the C-terminal cysteine alone (in the SdbAC86P variant) could complement the ΔsdbA mutant and restore disulfide bond formation in recombinant and natural protein substrates. These results provide evidence that certain disulfide oxidoreductases can catalyze disulfide bond formation using a single cysteine of the CXXC motif, including the buried C-terminal cysteine.
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Affiliation(s)
- Lauren Davey
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H 1X5, Canada.,Canadian Center for Vaccinology (CCfV), Dalhousie University and the Izaak Walton Killam (IWK) Health Centre, Halifax, NS, Canada
| | - Alejandro Cohen
- Proteomics and Mass Spectrometry Core Facility, Life Sciences Research Institute, Dalhousie University, Halifax, NS, Canada
| | - Jason LeBlanc
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H 1X5, Canada.,Department of Pathology, Dalhousie University, Halifax, NS, Canada.,Department of Pathology and Laboratory Medicine, Nova Scotia Health Authority (NSHA), Halifax, NS, Canada
| | - Scott A Halperin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H 1X5, Canada.,Canadian Center for Vaccinology (CCfV), Dalhousie University and the Izaak Walton Killam (IWK) Health Centre, Halifax, NS, Canada.,Department of Pediatrics, Faculty of Medicine, Dalhousie University and the IWK Health Centre, Halifax, NS, Canada
| | - Song F Lee
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H 1X5, Canada.,Canadian Center for Vaccinology (CCfV), Dalhousie University and the Izaak Walton Killam (IWK) Health Centre, Halifax, NS, Canada.,Department of Pediatrics, Faculty of Medicine, Dalhousie University and the IWK Health Centre, Halifax, NS, Canada.,Department of Applied Oral Sciences, Faculty of Dentistry, Dalhousie University, Halifax, NS, Canada
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Jiang YY, Huang JQ, Lin GC, Guo HY, Ren FZ, Zhang H. Characterization and Expression of Chicken Selenoprotein U. Biol Trace Elem Res 2015; 166:216-24. [PMID: 25876085 DOI: 10.1007/s12011-015-0257-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 01/27/2015] [Indexed: 12/15/2022]
Abstract
Selenoprotein U (SelU) may regulate a myriad of biological processes through its redox function. In chicks, neither the nucleotide sequence nor the amino acid sequence is known. The main objectives of this study were to clone and characterize the chicken Selu gene and investigate Selu messenger RNA (mRNA) and protein expression in chicken tissues. The coding sequence (CDS) of Selu contained 387 bases with a typical mammalian selenocysteine insertion sequence (SECIS) located in the 3'-untranslated region. The deduced amino acid sequence of chicken SelU contains 224 amino acids with UAA as the stop codon. Like all SelU genes identified in different species, chicken SelU contains one well-conserved selenocysteine (Sec) at the 85th position encoded by the UGA codon. The SECIS element was with the conserved denosine (--AAA--) rather than the motif cytidine (--CC--) motif. Moreover, the expression pattern of Selu mRNA in muscle, liver, kidney, heart, spleen, lung, testis, and brain was analyzed with real-time quantitative PCR in young male chickens fed a Se-deficient corn-soybean meal basal diet supplemented with 0.0 and 0.3 mg Se/kg in the form of sodium selenite. We found that the abundance of Selu mRNA in muscle, liver, kidney, heart, spleen, and lung was downregulated (P < 0.05) by Se deficiency. However, it was not affected by dietary Se concentrations in testis and brain. Furthermore, protein abundance of SelU in these seven tissues was consistent with the mRNA abundance. Hence, we suggest that Selu might play an important role in the biochemical function of Se in birds.
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Affiliation(s)
- Yun-Yun Jiang
- Beijing Laboratory of Food Quality and Safety, and Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
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The putative herpes simplex virus 1 chaperone protein UL32 modulates disulfide bond formation during infection. J Virol 2014; 89:443-53. [PMID: 25320327 DOI: 10.1128/jvi.01913-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED During DNA encapsidation, herpes simplex virus 1 (HSV-1) procapsids are converted to DNA-containing capsids by a process involving activation of the viral protease, expulsion of the scaffold proteins, and the uptake of viral DNA. Encapsidation requires six minor capsid proteins (UL6, UL15, UL17, UL25, UL28, and UL33) and one viral protein, UL32, not found to be associated with capsids. Although functions have been assigned to each of the minor capsid proteins, the role of UL32 in encapsidation has remained a mystery. Using an HSV-1 variant containing a functional hemagglutinin-tagged UL32, we demonstrated that UL32 was synthesized with true late kinetics and that it exhibited a previously unrecognized localization pattern. At 6 to 9 h postinfection (hpi), UL32 accumulated in viral replication compartments in the nucleus of the host cell, while at 24 hpi, it was additionally found in the cytoplasm. A newly generated UL32-null mutant was used to confirm that although B capsids containing wild-type levels of capsid proteins were synthesized, these procapsids were unable to initiate the encapsidation process. Furthermore, we showed that UL32 is redox sensitive and identified two highly conserved oxidoreductase-like C-X-X-C motifs that are essential for protein function. In addition, the disulfide bond profiles of the viral proteins UL6, UL25, and VP19C and the viral protease, VP24, were altered in the absence of UL32, suggesting that UL32 may act to modulate disulfide bond formation during procapsid assembly and maturation. IMPORTANCE Although functions have been assigned to six of the seven required packaging proteins of HSV, the role of UL32 in encapsidation has remained a mystery. UL32 is a cysteine-rich viral protein that contains C-X-X-C motifs reminiscent of those in proteins that participate in the regulation of disulfide bond formation. We have previously demonstrated that disulfide bonds are required for the formation and stability of the viral capsids and are also important for the formation and stability of the UL6 portal ring. In this report, we demonstrate that the disulfide bond profiles of the viral proteins UL6, UL25, and VP19C and the viral protease, VP24, are altered in cells infected with a newly isolated UL32-null mutant virus, suggesting that UL32 acts as a chaperone capable of modulating disulfide bond formation. Furthermore, these results suggest that proper regulation of disulfide bonds is essential for initiating encapsidation.
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Structure of the substrate-binding b' domain of the Protein Disulfide Isomerase-Like protein of the Testis. Sci Rep 2014; 4:4464. [PMID: 24662985 PMCID: PMC4894388 DOI: 10.1038/srep04464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/10/2014] [Indexed: 11/26/2022] Open
Abstract
Protein Disulfide Isomerase-Like protein of the Testis (PDILT) is a testis-specific member of the PDI family. PDILT displays similar domain architecture to PDIA1, the founding member of this protein family, but lacks catalytic cysteines needed for oxidoreduction reactions. This suggests special importance of chaperone activity of PDILT, but how it recognizes misfolded protein substrates is unknown. Here, we report the high-resolution crystal structure of the b′ domain of human PDILT. The structure reveals a conserved hydrophobic pocket, which is likely a principal substrate-binding site in PDILT. In the crystal, this pocket is occupied by side chains of tyrosine and tryptophan residues from another PDILT molecule, suggesting a preference for binding exposed aromatic residues in protein substrates. The lack of interaction of the b′ domain with the P-domains of calreticulin-3 and calmegin hints at a novel way of interaction between testis-specific lectin chaperones and PDILT. Further studies of this recently discovered PDI member would help to understand the important role that PDILT plays in the differentiation and maturation of spermatozoids.
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Botello-Morte L, Bes MT, Heras B, Fernández-Otal Á, Peleato ML, Fillat MF. Unraveling the redox properties of the global regulator FurA from Anabaena sp. PCC 7120: disulfide reductase activity based on its CXXC motifs. Antioxid Redox Signal 2014; 20:1396-406. [PMID: 24093463 PMCID: PMC3936511 DOI: 10.1089/ars.2013.5376] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
UNLABELLED Cyanobacterial FurA works as a global regulator linking iron homeostasis to photosynthetic metabolism and the responses to different environmental stresses. Additionally, FurA modulates several genes involved in redox homeostasis and fulfills the characteristics of a heme-sensor protein whose interaction with this cofactor negatively affects its DNA binding ability. FurA from Anabaena PCC 7120 contains five cysteine residues, four of them arranged in two redox CXXC motifs. AIMS Our goals were to analyze in depth the putative contribution of these CXXC motifs in the redox properties of FurA and to identify potential interacting partners of this regulator. RESULTS Insulin reduction assays unravel that FurA exhibits disulfide reductase activity. Simultaneous presence of both CXXC signatures greatly enhances the reduction rate, although the redox motif containing Cys(101) and Cys(104) seems a major contributor to this activity. Disulfide reductase activity was not detected in other ferric uptake regulator (Fur) proteins isolated from heterotrophic bacteria. In vivo, FurA presents different redox states involving intramolecular disulfide bonds when is partially oxidized. Redox potential values for CXXC motifs, -235 and -238 mV, are consistent with those reported for other proteins displaying disulfide reductase activity. Pull-down and two-hybrid assays unveil potential FurA interacting partners, namely phosphoribulokinase Alr4123, the hypothetical amidase-containing domain All1140 and the DNA-binding protein HU. INNOVATION A novel biochemical activity of cyanobacterial FurA based on its cysteine arrangements and the identification of novel interacting partners are reported. CONCLUSION The present study discloses a putative connection of FurA with the cyanobacterial redox-signaling pathway.
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Affiliation(s)
- Laura Botello-Morte
- 1 Department of Biochemistry and Molecular and Cell Biology, Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza , Zaragoza, Spain
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Chemes LB, Camporeale G, Sánchez IE, de Prat-Gay G, Alonso LG. Cysteine-rich positions outside the structural zinc motif of human papillomavirus E7 provide conformational modulation and suggest functional redox roles. Biochemistry 2014; 53:1680-96. [PMID: 24559112 DOI: 10.1021/bi401562e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The E7 protein from high-risk human papillomavirus is essential for cell transformation in cervical, oropharyngeal, and other HPV-related cancers, mainly through the inactivation of the retinoblastoma (Rb) tumor suppressor. Its high cysteine content (~7%) and the observation that HPV-transformed cells are under oxidative stress prompted us to investigate the redox properties of the HPV16 E7 protein under biologically compatible oxidative conditions. The seven cysteines in HPV16 E7 remain reduced in conditions resembling the basal reduced state of a cell. However, under oxidative stress, a stable disulfide bridge forms between cysteines 59 and 68. Residue 59 has a protective effect on the other cysteines, and its mutation leads to an overall increase in the oxidation propensity of E7, including cysteine 24 central to the Rb binding motif. Gluthationylation of Cys 24 abolishes Rb binding, which is reversibly recovered upon reduction. Cysteines 59 and 68 are located 18.6 Å apart, and the formation of the disulfide bridge leads to a large structural rearrangement while retaining strong Zn association. These conformational and covalent changes are fully reversible upon restoration of the reductive environment. In addition, this is the first evidence of an interaction between the N-terminal intrinsically disordered and the C-terminal globular domains, known to be highly and separately conserved among human papillomaviruses. The significant conservation of such noncanonical cysteines in HPV E7 proteins leads us to propose a functional redox activity. Such an activity adds to the previously discovered chaperone activity of E7 and supports the picture of a moonlighting pathological role of this paradigmatic viral oncoprotein.
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Affiliation(s)
- Lucía B Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
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Kendall JJ, Barrero-Tobon AM, Hendrixson DR, Kelly DJ. Hemerythrins in the microaerophilic bacterium Campylobacter jejuni help protect key iron-sulphur cluster enzymes from oxidative damage. Environ Microbiol 2013; 16:1105-21. [PMID: 24245612 PMCID: PMC4257069 DOI: 10.1111/1462-2920.12341] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 11/12/2013] [Indexed: 01/27/2023]
Abstract
Microaerophilic bacteria are adapted to low oxygen environments, but the mechanisms by which their growth in air is inhibited are not well understood. The citric acid cycle in the microaerophilic pathogen Campylobacter jejuni is potentially vulnerable, as it employs pyruvate and 2-oxoglutarate:acceptor oxidoreductases (Por and Oor), which contain labile (4Fe-4S) centres. Here, we show that both enzymes are rapidly inactivated after exposure of cells to a fully aerobic environment. We investigated the mechanisms that might protect enzyme activity and identify a role for the hemerythrin HerA (Cj0241). A herA mutant exhibits an aerobic growth defect and reduced Por and Oor activities after exposure to 21% (v/v) oxygen. Slow anaerobic recovery of these activities after oxygen damage was observed, but at similar rates in both wild-type and herA strains, suggesting the role of HerA is to prevent Fe-S cluster damage, rather than promote repair. Another hemerythrin (HerB; Cj1224) also plays a protective role. Purified HerA and HerB exhibited optical absorption, ligand binding and resonance Raman spectra typical of μ-oxo-bridged di-iron containing hemerythrins. We conclude that oxygen lability and poor repair of Por and Oor are major contributors to microaerophily in C. jejuni; hemerythrins help prevent enzyme damage microaerobically or during oxygen transients.
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Affiliation(s)
- John J Kendall
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
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Dufour V, Stahl M, Rosenfeld E, Stintzi A, Baysse C. Insights into the mode of action of benzyl isothiocyanate on Campylobacter jejuni. Appl Environ Microbiol 2013; 79:6958-68. [PMID: 24014524 PMCID: PMC3811535 DOI: 10.1128/aem.01967-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/28/2013] [Indexed: 12/24/2022] Open
Abstract
Campylobacter jejuni is a widespread pathogen responsible for most of the food-borne gastrointestinal diseases in Europe. The use of natural antimicrobial molecules is a promising alternative to antibiotic treatments for pathogen control in the food industry. Isothiocyanates are natural antimicrobial compounds, which also display anticancer activity. Several studies described the chemoprotective effect of isothiocyanates on eukaryotic cells, but the antimicrobial mechanism is still poorly understood. We investigated the early cellular response of C. jejuni to benzyl isothiocyanate by both transcriptomic and physiological approaches. The transcriptomic response of C. jejuni to benzyl isothiocyanate showed upregulation of heat shock response genes and an impact on energy metabolism. Oxygen consumption was progressively impaired by benzyl isothiocyanate treatment, as revealed by high-resolution respirometry, while the ATP content increased soon after benzyl isothiocyanate exposition, which suggests a shift in the energy metabolism balance. Finally, benzyl isothiocyanate induced intracellular protein aggregation. These results indicate that benzyl isothiocyanate affects C. jejuni by targeting proteins, resulting in the disruption of major metabolic processes and eventually leading to cell death.
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Affiliation(s)
- Virginie Dufour
- EA1254 Microbiologie et Risques Infectieux, University of Rennes 1, Rennes, France
| | - Martin Stahl
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | | | - Alain Stintzi
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Christine Baysse
- EA1254 Microbiologie et Risques Infectieux, University of Rennes 1, Rennes, France
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Analysis of Arabidopsis thioredoxin-h isotypes identifies discrete domains that confer specific structural and functional properties. Biochem J 2013; 456:13-24. [DOI: 10.1042/bj20130618] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In this study, we identified specific domains and amino acids responsible for the structural and functional properties of AtTrx-hs (Arabidopsis h-type thioredoxins). Specific domains and amino acids for the chaperone function of AtTrx-hs played a critical role in heat-shock-resistance in vivo.
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47
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Varlamova EG, Goltyaev MV, Novoselov SV, Novoselov VI, Fesenko EE. Characterization of several members of the thiol oxidoreductase family. Mol Biol 2013. [DOI: 10.1134/s0026893313040146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Hemmis CW, Schildbach JF. Thioredoxin-like proteins in F and other plasmid systems. Plasmid 2013; 70:168-89. [PMID: 23721857 DOI: 10.1016/j.plasmid.2013.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 05/12/2013] [Accepted: 05/13/2013] [Indexed: 11/29/2022]
Abstract
Bacterial conjugation is the process by which a conjugative plasmid transfers from donor to recipient bacterium. During this process, single-stranded plasmid DNA is actively and specifically transported from the cytoplasm of the donor, through a large membrane-spanning assembly known as the pore complex, and into the cytoplasm of the recipient. In Gram negative bacteria, construction of the pore requires localization of a subset of structural and catalytically active proteins to the bacterial periplasm. Unlike the cytoplasm, the periplasm contains proteins that promote disulfide bond formation within or between cysteine-containing proteins. To ensure proper protein folding and assembly, bacteria employ periplasmic redox systems for thiol oxidation, disulfide bond/sulfenic acid reduction, and disulfide bond isomerization. Recent data suggest that plasmid-based proteins belonging to the disulfide bond formation family play an integral role in the conjugative process by serving as mediators in folding and/or assembly of pore complex proteins. Here we report the identification of 165 thioredoxin-like family members across 89 different plasmid systems. Using phylogenetic analysis, all but nine family members were categorized into thioredoxin-like subfamilies. In addition, we discuss the diversity, conservation, and putative roles of thioredoxin-like proteins in plasmid systems, which include homologs of DsbA, DsbB, DsbC, DsbD, DsbG, and CcmG from Escherichia coli, TlpA from Bradyrhizobium japonicum, Com1 from Coxiella burnetii, as well as TrbB and TraF from plasmid F, and the absolute conservation of a disulfide isomerase in plasmids containing homologs of the transfer proteins TraH, TraN, and TraU.
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Affiliation(s)
- Casey W Hemmis
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
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Cui H, Wang Y, Wang Y, Qin S. Genome-wide analysis of putative peroxiredoxin in unicellular and filamentous cyanobacteria. BMC Evol Biol 2012; 12:220. [PMID: 23157370 PMCID: PMC3514251 DOI: 10.1186/1471-2148-12-220] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Accepted: 10/25/2012] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Cyanobacteria are photoautotrophic prokaryotes with wide variations in genome sizes and ecological habitats. Peroxiredoxin (PRX) is an important protein that plays essential roles in protecting own cells against reactive oxygen species (ROS). PRXs have been identified from mammals, fungi and higher plants. However, knowledge on cyanobacterial PRXs still remains obscure. With the availability of 37 sequenced cyanobacterial genomes, we performed a comprehensive comparative analysis of PRXs and explored their diversity, distribution, domain structure and evolution. RESULTS Overall 244 putative prx genes were identified, which were abundant in filamentous diazotrophic cyanobacteria, Acaryochloris marina MBIC 11017, and unicellular cyanobacteria inhabiting freshwater and hot-springs, while poor in all Prochlorococcus and marine Synechococcus strains. Among these putative genes, 25 open reading frames (ORFs) encoding hypothetical proteins were identified as prx gene family members and the others were already annotated as prx genes. All 244 putative PRXs were classified into five major subfamilies (1-Cys, 2-Cys, BCP, PRX5_like, and PRX-like) according to their domain structures. The catalytic motifs of the cyanobacterial PRXs were similar to those of eukaryotic PRXs and highly conserved in all but the PRX-like subfamily. Classical motif (CXXC) of thioredoxin was detected in protein sequences from the PRX-like subfamily. Phylogenetic tree constructed of catalytic domains coincided well with the domain structures of PRXs and the phylogenies based on 16s rRNA. CONCLUSIONS The distribution of genes encoding PRXs in different unicellular and filamentous cyanobacteria especially those sub-families like PRX-like or 1-Cys PRX correlate with the genome size, eco-physiology, and physiological properties of the organisms. Cyanobacterial and eukaryotic PRXs share similar conserved motifs, indicating that cyanobacteria adopt similar catalytic mechanisms as eukaryotes. All cyanobacterial PRX proteins share highly similar structures, implying that these genes may originate from a common ancestor. In this study, a general framework of the sequence-structure-function connections of the PRXs was revealed, which may facilitate functional investigations of PRXs in various organisms.
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Affiliation(s)
- Hongli Cui
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road, Yantai 264003, People’s Republic of China
- University of Chinese Academy of Sciences, Yuquan Road, Beijing 100049, People’s Republic of China
| | - Yipeng Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road, Yantai 264003, People’s Republic of China
| | - Yinchu Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road, Yantai 264003, People’s Republic of China
- University of Chinese Academy of Sciences, Yuquan Road, Beijing 100049, People’s Republic of China
| | - Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road, Yantai 264003, People’s Republic of China
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2-nitrobenzoate 2-nitroreductase (NbaA) switches its substrate specificity from 2-nitrobenzoic acid to 2,4-dinitrobenzoic acid under oxidizing conditions. J Bacteriol 2012; 195:180-92. [PMID: 23123905 DOI: 10.1128/jb.02016-12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
2-Nitrobenzoate 2-nitroreductase (NbaA) of Pseudomonas fluorescens strain KU-7 is a unique enzyme, transforming 2-nitrobenzoic acid (2-NBA) and 2,4-dinitrobenzoic acid (2,4-DNBA) to the 2-hydroxylamine compounds. Sequence comparison reveals that NbaA contains a conserved cysteine residue at position 141 and two variable regions at amino acids 65 to 74 and 193 to 216. The truncated mutant Δ65-74 exhibited markedly reduced activity toward 2,4-DNBA, but its 2-NBA reduction activity was unaffected; however, both activities were abolished in the Δ193-216 mutant, suggesting that these regions are necessary for the catalysis and specificity of NbaA. NbaA showed different lag times for the reduction of 2-NBA and 2,4-DNBA with NADPH, and the reduction of 2,4-DNBA, but not 2-NBA, failed in the presence of 1 mM dithiothreitol or under anaerobic conditions, indicating oxidative modification of the enzyme for 2,4-DNBA. The enzyme was irreversibly inhibited by 5,5'-dithio-bis-(2-nitrobenzoic acid) and ZnCl(2), which bind to reactive thiol/thiolate groups, and was eventually inactivated during the formation of higher-order oligomers at high pH, high temperature, or in the presence of H(2)O(2). SDS-PAGE and mass spectrometry revealed the formation of intermolecular disulfide bonds by involvement of the two cysteines at positions 141 and 194. Site-directed mutagenesis indicated that the cysteines at positions 39, 103, 141, and 194 played a role in changing the enzyme activity and specificity toward 2-NBA and 2,4-DNBA. This study suggests that oxidative modifications of NbaA are responsible for the differential specificity for the two substrates and further enzyme inactivation through the formation of disulfide bonds under oxidizing conditions.
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