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Polenkowski M, Burbano de Lara S, Allister AB, Nguyen TNQ, Tamura T, Tran DDH. Identification of Novel Micropeptides Derived from Hepatocellular Carcinoma-Specific Long Noncoding RNA. Int J Mol Sci 2021; 23:ijms23010058. [PMID: 35008483 PMCID: PMC8744898 DOI: 10.3390/ijms23010058] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022] Open
Abstract
Identification of cancer-specific target molecules and biomarkers may be useful in the development of novel treatment and immunotherapeutic strategies. We have recently demonstrated that the expression of long noncoding (lnc) RNAs can be cancer-type specific due to abnormal chromatin remodeling and alternative splicing. Furthermore, we identified and determined that the functional small protein C20orf204-189AA encoded by long intergenic noncoding RNA Linc00176 that is expressed predominantly in hepatocellular carcinoma (HCC), enhances transcription of ribosomal RNAs and supports growth of HCC. In this study we combined RNA-sequencing and polysome profiling to identify novel micropeptides that originate from HCC-specific lncRNAs. We identified nine lncRNAs that are expressed exclusively in HCC cells but not in the liver or other normal tissues. Here, DNase-sequencing data revealed that the altered chromatin structure plays a key role in the HCC-specific expression of lncRNAs. Three out of nine HCC-specific lncRNAs contain at least one open reading frame (ORF) longer than 50 amino acid (aa) and enriched in the polysome fraction, suggesting that they are translated. We generated a peptide specific antibody to characterize one candidate, NONHSAT013026.2/Linc013026. We show that Linc013026 encodes a 68 amino acid micropeptide that is mainly localized at the perinuclear region. Linc013026-68AA is expressed in a subset of HCC cells and plays a role in cell proliferation, suggesting that Linc013026-68AA may be used as a HCC-specific target molecule. Our finding also sheds light on the role of the previously ignored ’dark proteome’, that originates from noncoding regions in the maintenance of cancer.
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Affiliation(s)
- Mareike Polenkowski
- Institut fuer Zellbiochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30623 Hannover, Germany; (M.P.); (S.B.d.L.); (A.B.A.); (T.N.Q.N.)
| | - Sebastian Burbano de Lara
- Institut fuer Zellbiochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30623 Hannover, Germany; (M.P.); (S.B.d.L.); (A.B.A.); (T.N.Q.N.)
- Systems Biology of Signal Transduction B200, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Aldrige Bernardus Allister
- Institut fuer Zellbiochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30623 Hannover, Germany; (M.P.); (S.B.d.L.); (A.B.A.); (T.N.Q.N.)
| | - Thi Nhu Quynh Nguyen
- Institut fuer Zellbiochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30623 Hannover, Germany; (M.P.); (S.B.d.L.); (A.B.A.); (T.N.Q.N.)
| | - Teruko Tamura
- Institut fuer Zellbiochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30623 Hannover, Germany; (M.P.); (S.B.d.L.); (A.B.A.); (T.N.Q.N.)
| | - Doan Duy Hai Tran
- Institut fuer Zellbiochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30623 Hannover, Germany; (M.P.); (S.B.d.L.); (A.B.A.); (T.N.Q.N.)
- Correspondence: ; Tel.: +49-511-532-2857
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Febbraio F, Ionata E, Marcolongo L. Forty years of study on the thermostable β-glycosidase from S. solfataricus: Production, biochemical characterization and biotechnological applications. Biotechnol Appl Biochem 2020; 67:602-618. [PMID: 32621790 DOI: 10.1002/bab.1982] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The aim of this paper is to make the point on the fortieth years study on the β-glycosidase from Sulfolobus solfataricus. This enzyme represents one of the thermophilic biocatalysts, which is more extensively studied as witnessed by the numerous literature reports available since 1980. Comprehensive biochemical studies highlighted its broad substrate specificity for β-d-galacto-, gluco-, and fuco-sides and also showed its remarkable exo-glucosidase and transglycosidase activities. The enzyme demonstrated to be active and stable over a wide range of temperature and pHs, withstanding to several drastic conditions comprising solvents and detergents. Over the years, a great deal of studies were focused on its homotetrameric tridimensional structure, elucidating several structural features involved in the enzyme stability, such as ion pairs and post-translational modifications. Several β-glycosidase mutants were produced in the years in order to understand its peculiar behavior in extreme conditions and/or to improve its functional properties. The β-glycosidase overproduction was also afforded reporting numerous studies dealing with its production in the mesophilic host Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris, and Lactococcus lactis. Relevant applications in food, beverages, bioenergy, pharmaceuticals, and nutraceutical fields of this enzyme, both in free and immobilized forms, highlighted its biotechnological relevance.
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Affiliation(s)
- Ferdinando Febbraio
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Naples, Italy
| | - Elena Ionata
- Research Institute on Terrestrial Ecosystems, National Research Council (CNR), Naples, 80131, Italy
| | - Loredana Marcolongo
- Research Institute on Terrestrial Ecosystems, National Research Council (CNR), Naples, 80131, Italy
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Ouimet P, Kienzle L, Lubosny M, Burzyński A, Angers A, Breton S. The ORF in the control region of the female-transmitted Mytilus mtDNA codes for a protein. Gene 2020; 725:144161. [DOI: 10.1016/j.gene.2019.144161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/02/2019] [Accepted: 10/07/2019] [Indexed: 01/14/2023]
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Šnajder M, Carrillo Rincón AF, Magdevska V, Bahun M, Kranjc L, Paš M, Juntes P, Petković H, Poklar Ulrih N. Extracellular production of the engineered thermostable protease pernisine from Aeropyrum pernix K1 in Streptomyces rimosus. Microb Cell Fact 2019; 18:196. [PMID: 31699090 PMCID: PMC6839199 DOI: 10.1186/s12934-019-1245-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/27/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The thermostable serine protease pernisine originates from the hyperthermophilic Archaeaon Aeropyrum pernix and has valuable industrial applications. Due to its properties, A. pernix cannot be cultivated in standard industrial fermentation facilities. Furthermore, pernisine is a demanding target for heterologous expression in mesophilic heterologous hosts due to the relatively complex processing step involved in its activation. RESULTS We achieved production of active extracellular pernisine in a Streptomyces rimosus host through heterologous expression of the codon-optimised gene by applying step-by-step protein engineering approaches. To ensure secretion of fully active enzyme, the srT signal sequence from the S. rimosus protease was fused to pernisine. To promote correct processing and folding of pernisine, the srT functional cleavage site motif was fused directly to the core pernisine sequence, this way omitting the proregion. Comparative biochemical analysis of the wild-type and recombinant pernisine confirmed that the enzyme produced by S. rimosus retained all of the desired properties of native pernisine. Importantly, the recombinant pernisine also degraded cellular and infectious bovine prion proteins, which is one of the particular applications of this protease. CONCLUSION Functional pernisine that retains all of the advantageous properties of the native enzyme from the thermophilic host was successfully produced in a S. rimosus heterologous host. Importantly, we achieved extracellular production of active pernisine, which significantly simplifies further downstream procedures and also omits the need for any pre-processing step for its activation. We demonstrate that S. rimosus can be used as an attractive host for industrial production of recombinant proteins that originate from thermophilic organisms.
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Affiliation(s)
- Marko Šnajder
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia.,Labena Ltd., Ljubljana, Slovenia
| | | | - Vasilka Magdevska
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia.,AciesBio Ltd., Ljubljana, Slovenia
| | - Miha Bahun
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Luka Kranjc
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Maja Paš
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Polona Juntes
- Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Hrvoje Petković
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia.
| | - Nataša Poklar Ulrih
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia. .,The Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia.
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Rodríguez-Decuadro S, Dans PD, Borba MA, Benko-Iseppon AM, Cecchetto G. Gene isolation and structural characterization of a legume tree defensin with a broad spectrum of antimicrobial activity. PLANTA 2019; 250:1757-1772. [PMID: 31428874 DOI: 10.1007/s00425-019-03260-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
The recombinant EcgDf1 defensin has an antimicrobial effect against both plant and human pathogens. In silico analyses predict that EcgDf1 is prone to form dimers capable of interacting with the membranes of microorganisms. Plant defensins comprise a large family of antimicrobial peptides (AMP) with a wide range of biological functions. They are cysteine-rich molecules, highly sequence diverse but with a conserved and stable structure. In this work, a defensin gene (EcgDf1) was isolated from Erythrina crista-galli, a legume tree native from South America. The predicted peptide presents eight cysteines, with a γ-core motif GXCX3-9C and six cysteines distributed like the typical defensin αβ motif. The mature EcgDf1 coding sequence was heterologously expressed in Escherichia coli strains and purified by affinity chromatography. Possible dimer and oligomers of EcgDf1 were visible in SDS electrophoresis. Moreover, its 3D structure, determined by homology modeling, docking, and molecular dynamics simulations, was found to be compatible with the formation of homodimers between the β3 and β1-loop-α1, leaving the β2-loop-β3 free to interact with lipid membranes. The purified recombinant peptide inhibited the growth of several critical plant and human pathogens, like the opportunistic fungi Candida albicans and Aspergillus niger and the plant pathogens Clavibacter michiganensis ssp. michiganensis, Penicillium expansum, Botrytis cinerea, and Alternaria alternata. EcgDf1 is a promising candidate for the development of antimicrobial products for use in agriculture and medicine.
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Affiliation(s)
- Susana Rodríguez-Decuadro
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Garzón 780, 12900, Montevideo, Uruguay
| | - Pablo D Dans
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain
- Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - María Alejandra Borba
- Instituto de Química Biológica, Facultad de Ciencias-Facultad de Química, Universidad de la República, General Flores 2124, 11800, Montevideo, Uruguay
| | - Ana Maria Benko-Iseppon
- Universidade Federal de Pernambuco, Centro de Biociências, Av. Prof. Moraes Rego, 1235, Recife, PE, CEP 50.670-420, Brazil
| | - Gianna Cecchetto
- Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, 11800, Montevideo, Uruguay.
- Instituto de Química Biológica, Facultad de Ciencias-Facultad de Química, Universidad de la República, General Flores 2124, 11800, Montevideo, Uruguay.
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Non-Conventional Metal Ion Cofactor Requirement of Dinoflagellate Alkaline Phosphatase and Translational Regulation by Phosphorus Limitation. Microorganisms 2019; 7:microorganisms7080232. [PMID: 31374942 PMCID: PMC6723241 DOI: 10.3390/microorganisms7080232] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/15/2019] [Accepted: 07/30/2019] [Indexed: 12/30/2022] Open
Abstract
Alkaline phosphatase (AP) enables marine phytoplankton to utilize dissolved organic phosphorus (DOP) when dissolved inorganic phosphate (DIP) is depleted in the ocean. Dinoflagellate AP (Dino-AP) represents a newly classified atypical type of AP, PhoAaty. Despite While being a conventional AP, PhoAEC is known to recruit Zn2+ and Mg2+ in the active center, and the cofactors required by PhoAaty have been contended and remain unclear. In this study, we investigated the metal ion requirement of AP in five dinoflagellate species. After AP activity was eliminated by using EDTA to chelate metal ions, the enzymatic activity could be recovered by the supplementation of Ca2+, Mg2+ and Mn2+ in all cases but not by that of Zn2+. Furthermore, the same analysis conducted on the purified recombinant ACAAP (AP of Amphidinium carterae) verified that the enzyme could be activated by Ca2+, Mg2+, and Mn2+ but not Zn2+. We further developed an antiserum against ACAAP, and a western blot analysis using this antibody showed a remarkable up-regulation of ACAAP under a phosphate limitation, consistent with elevated AP activity. The unconventional metal cofactor requirement of Dino-AP may be an adaptation to trace metal limitations in the ocean, which warrants further research to understand the niche differentiation between dinoflagellates and other phytoplankton that use Zn–Mg AP in utilizing DOP.
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Huda N, Hossain M, Bhuyan AK. Complete observation of all structural, conformational, and fibrillation transitions of monomeric globular proteins at submicellar sodium dodecyl sulfate concentrations. Biopolymers 2019; 110:e23255. [PMID: 30633322 DOI: 10.1002/bip.23255] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/18/2018] [Accepted: 12/21/2018] [Indexed: 11/06/2022]
Abstract
Although considerable information is available regarding protein-sodium dodecyl sulfate (SDS) interactions, it is still unclear as to how much SDS is needed to denature proteins. The role of protein charge and micellar surfactant concentration on amyloid fibrillation is also unclear. This study reports on equilibrium measurements of SDS interaction with six model proteins and analyzes the results to obtain a general understanding of conformational breakdown, reorganization and restructuring of secondary structure, and entry into the amyloid fibrillar state. Significantly, all of these responses are entirely resolved at much lower than the critical micellar concentration (CMC) of SDS. Electrostatic interaction of the dodecyl sulfate anion (DS- ) with positive surface potential on the protein can completely unfold both secondary and tertiary structures, which is followed by protein chain restructuration to α-helices. All SDS-denatured proteins contain more α-helices than the corresponding native state. SDS interaction stochastically drives proteins to the aggregated fibrillar state.
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Affiliation(s)
- Noorul Huda
- School of Chemistry, University of Hyderabad, Hyderabad, India
| | - Mujahid Hossain
- School of Chemistry, University of Hyderabad, Hyderabad, India
| | - Abani K Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad, India
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Ionata E, Marcolongo L, La Cara F, Cetrangolo GP, Febbraio F. Improvement of functional properties of a thermostable β-glycosidase for milk lactose hydrolysis. Biopolymers 2018; 109:e23118. [DOI: 10.1002/bip.23118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/14/2018] [Accepted: 03/16/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Elena Ionata
- Institute of Agro-Environmental and Forest Biology-Consiglio Nazionale delle Ricerche (CNR), via P. Castellino 111; Naples 80131 Italy
| | - Loredana Marcolongo
- Institute of Agro-Environmental and Forest Biology-Consiglio Nazionale delle Ricerche (CNR), via P. Castellino 111; Naples 80131 Italy
| | - Francesco La Cara
- Institute of Agro-Environmental and Forest Biology-Consiglio Nazionale delle Ricerche (CNR), via P. Castellino 111; Naples 80131 Italy
| | - Giovanni P. Cetrangolo
- Institute of Protein Biochemistry-Consiglio Nazionale delle Ricerche (CNR), via P. Castellino 111; Naples 80131 Italy
| | - Ferdinando Febbraio
- Institute of Protein Biochemistry-Consiglio Nazionale delle Ricerche (CNR), via P. Castellino 111; Naples 80131 Italy
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Uddin MS, Naider F, Becker JM. Dynamic roles for the N-terminus of the yeast G protein-coupled receptor Ste2p. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2058-2067. [PMID: 28754538 DOI: 10.1016/j.bbamem.2017.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/13/2017] [Accepted: 07/24/2017] [Indexed: 12/11/2022]
Abstract
The Saccharomyces cerevisiae α-factor receptor Ste2p has been used extensively as a model to understand the molecular mechanism of signal transduction by G protein-coupled receptors (GPCRs). Single and double cysteine mutants of Ste2p were created and served as surrogates to detect intramolecular interactions and dimerization of Ste2p using disulfide cross-linking methodology. When a mutation was introduced into the phylogenetically conserved tyrosine residue at position 26 (Y26C) in the N-terminus of Ste2p, dimerization was increased greatly. The amount of dimer formed by this Y26C mutant was greatly reduced by ligand binding even though the ligand binding site is far removed from the N-terminus; the lowering of the dimer formation was consistent with a conformational change in the N-terminus of the receptor upon activation. Dimerization was decreased by double mutations Y26C/V109C or Y26C/T114C indicating that Y26 is in close proximity to V109 and T114 of extracellular loop 1 in native Ste2p. Combined with earlier studies, these results indicate previously unrecognized roles for the N-terminus of Ste2p, and perhaps of GPCRs in general, and reveal a specific N-terminus residue or region, that is involved in GPCR signaling, intrareceptor interactions, and receptor dimerization.
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Affiliation(s)
- M Seraj Uddin
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Fred Naider
- Department of Chemistry and Macromolecular Assemblies Institute, College of Staten Island, CUNY, New York, New York 10314, United States; Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States
| | - Jeffrey M Becker
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States.
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Velásquez AC, Nomura K, Cooper MD, Herrin BR, He SY. Leucine-rich-repeat-containing variable lymphocyte receptors as modules to target plant-expressed proteins. PLANT METHODS 2017; 13:29. [PMID: 28428809 PMCID: PMC5395774 DOI: 10.1186/s13007-017-0180-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 04/09/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The ability to target and manipulate protein-based cellular processes would accelerate plant research; yet, the technology to specifically and selectively target plant-expressed proteins is still in its infancy. Leucine-rich repeats (LRRs) are ubiquitously present protein domains involved in mediating protein-protein interactions. LRRs confer the binding specificity to the highly diverse variable lymphocyte receptor (VLR) antibodies (including VLRA, VLRB and VLRC types) that jawless vertebrates make as the functional equivalents of jawed vertebrate immunoglobulin-based antibodies. RESULTS In this study, VLRBs targeting an effector protein from a plant pathogen, HopM1, were developed by immunizing lampreys and using yeast surface display to select for high-affinity VLRBs. HopM1-specific VLRBs (VLRM1) were expressed in planta in the cytosol, the trans-Golgi network, and the apoplast. Expression of VLRM1 was higher when the protein localized to an oxidizing environment that would favor disulfide bridge formation (when VLRM1 was not localized to the cytoplasm), as disulfide bonds are necessary for proper VLR folding. VLRM1 specifically interacted in planta with HopM1 but not with an unrelated bacterial effector protein while HopM1 failed to interact with a non-specific VLRB. CONCLUSIONS In the future, VLRs may be used as flexible modules to bind proteins or carbohydrates of interest in planta, with broad possibilities for their use by binding directly to their targets and inhibiting their action, or by creating chimeric proteins with new specificities in which endogenous LRR domains are replaced by those present in VLRs.
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Affiliation(s)
- André C. Velásquez
- DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
| | - Kinya Nomura
- DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
| | - Max D. Cooper
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322 USA
| | - Brantley R. Herrin
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322 USA
| | - Sheng Yang He
- DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824 USA
- Howard Hughes Medical Institute, Gordon and Betty Moore Foundation, Michigan State University, East Lansing, MI 48824 USA
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Tantong S, Pringsulaka O, Weerawanich K, Meeprasert A, Rungrotmongkol T, Sarnthima R, Roytrakul S, Sirikantaramas S. Two novel antimicrobial defensins from rice identified by gene coexpression network analyses. Peptides 2016; 84:7-16. [PMID: 27527801 DOI: 10.1016/j.peptides.2016.07.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 07/22/2016] [Accepted: 07/23/2016] [Indexed: 11/26/2022]
Abstract
Defensins form an antimicrobial peptides (AMP) family, and have been widely studied in various plants because of their considerable inhibitory functions. However, their roles in rice (Oryza sativa L.) have not been characterized, even though rice is one of the most important staple crops that is susceptible to damaging infections. Additionally, a previous study identified 598 rice genes encoding cysteine-rich peptides, suggesting there are several uncharacterized AMPs in rice. We performed in silico gene expression and coexpression network analyses of all genes encoding defensin and defensin-like peptides, and determined that OsDEF7 and OsDEF8 are coexpressed with pathogen-responsive genes. Recombinant OsDEF7 and OsDEF8 could form homodimers. They inhibited the growth of the bacteria Xanthomonas oryzae pv. oryzae, X. oryzae pv. oryzicola, and Erwinia carotovora subsp. atroseptica with minimum inhibitory concentration (MIC) ranging from 0.6 to 63μg/mL. However, these OsDEFs are weakly active against the phytopathogenic fungi Helminthosporium oryzae and Fusarium oxysporum f.sp. cubense. This study describes a useful method for identifying potential plant AMPs with biological activities.
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Affiliation(s)
- Supaluk Tantong
- Biotechnology Program, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Onanong Pringsulaka
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand.
| | - Kamonwan Weerawanich
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Arthitaya Meeprasert
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Thanyada Rungrotmongkol
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Rakrudee Sarnthima
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand.
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Klong Luang, Pathumthani, 12120, Thailand.
| | - Supaart Sirikantaramas
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Omics Sciences and Bioinformatics Center, Chulalongkorn University, Bangkok 10330, Thailand.
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Striz AC, Tuma PL. The GTP-bound and Sumoylated Form of the rab17 Small Molecular Weight GTPase Selectively Binds Syntaxin 2 in Polarized Hepatic WIF-B Cells. J Biol Chem 2016; 291:9721-32. [PMID: 26957544 DOI: 10.1074/jbc.m116.723353] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Indexed: 12/29/2022] Open
Abstract
A major focus for our laboratory is identifying the molecules and mechanisms that regulate polarized apical protein sorting in hepatocytes, the major epithelial cells of the liver. These trafficking pathways are regulated, in part, by small molecular weight rab GTPases. We chose to investigate rab17, whose expression is restricted to polarized epithelial cells, is enriched in liver, and has been implicated in regulating basolateral to apical transcytosis. To initiate our studies, we generated three recombinant adenoviruses expressing wild type, constitutively active (GTP bound), or dominant-negative (GDP bound) rab17. Immunoblotting revealed rab17 immunoreactive species at 25 kDa (the predicted rab17 molecular mass) and 40 kDa. We determined that mono-sumoylation of the 25-kDa rab17 is responsible for the shift in molecular mass, and that rab17 prenylation is required for sumoylation. We further determined that sumoylation selectively promotes interactions with syntaxin 2 (but not syntaxins 3 or 4) and that these interactions are nucleotide dependent. Furthermore, a K68R-mutated rab17 led to the redistribution of syntaxin 2 and 5' nucleotidase from the apical membrane to subapical puncta, whereas multidrug resistance protein 2 distributions were not changed. Together these data are consistent with the proposed role of rab17 in vesicle fusion with the apical plasma membrane and further implicate sumoylation as an important mediator of protein-protein interactions. The selectivity in syntaxin binding and apical protein redistribution further suggests that rab17 and syntaxin 2 mediate fusion of transcytotic vesicles at the apical surface.
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Affiliation(s)
- Anneliese C Striz
- From the Department of Biology, The Catholic University of America, Washington, D. C. 20064
| | - Pamela L Tuma
- From the Department of Biology, The Catholic University of America, Washington, D. C. 20064
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Factors Affecting Inducible Expression of Outer Membrane Protein A (OmpA) of Shigella dysenteriae Type-1 in Lactococcus lactis Using Nisin Inducible Controlled Expression (NICE). Indian J Microbiol 2015; 56:80-7. [PMID: 26843700 DOI: 10.1007/s12088-015-0556-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 10/19/2015] [Indexed: 02/01/2023] Open
Abstract
Potential use of Lactococcus lactis (L. lactis) as a heterologous protein expression host as well as for delivery of multiple therapeutic proteins has been investigated extensively using Nisin Inducible Controlled Expression (NICE) system. Optimum inducible expression of heterologous protein by NICE system in L. lactis depends on multiple factors. To study the unexplored role of factors affecting heterologous protein expression in L. lactis using NICE, the present study outlines the optimization of various key parameters such as inducer concentration, host's proteases and precipitating agent using Outer membrane protein A (OmpA). For efficient expression and secretion of OmpA, pSEC:OmpA vector was successfully constructed. To circumvent the troubles encountered during detection of expressed OmpA, the precipitating agent was switched from TCA to methanol. Nevertheless, detection was achieved accompanied by degraded protein products. Speculating the accountability of observed degradation at higher inducer concentration, different nisin concentrations were evaluated. Lower nisin concentrations were found desirable for optimum expression of OmpA. Consistently observed degradation was eliminated by incorporation of protease inhibitor cocktail which inhibits intracellular proteases and expression in VEL1153 (NZ9000 ΔhtrA) strain which inhibits extracellular protease leading to optimum expression of OmpA. Versatility and complexity of NICE system in L. lactis requires fine-tuning of target protein specific parameters for optimum expression.
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Rivera-Najera LY, Saab-Rincón G, Battaglia M, Amero C, Pulido NO, García-Hernández E, Solórzano RM, Reyes JL, Covarrubias AA. A group 6 late embryogenesis abundant protein from common bean is a disordered protein with extended helical structure and oligomer-forming properties. J Biol Chem 2014; 289:31995-32009. [PMID: 25271167 DOI: 10.1074/jbc.m114.583369] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Late embryogenesis-abundant proteins accumulate to high levels in dry seeds. Some of them also accumulate in response to water deficit in vegetative tissues, which leads to a remarkable association between their presence and low water availability conditions. A major sub-group of these proteins, also known as typical LEA proteins, shows high hydrophilicity and a high percentage of glycine and other small amino acid residues, distinctive physicochemical properties that predict a high content of structural disorder. Although all typical LEA proteins share these characteristics, seven groups can be distinguished by sequence similarity, indicating structural and functional diversity among them. Some of these groups have been extensively studied; however, others require a more detailed analysis to advance in their functional understanding. In this work, we report the structural characterization of a group 6 LEA protein from a common bean (Phaseolus vulgaris L.) (PvLEA6) by circular dichroism and nuclear magnetic resonance showing that it is a disordered protein in aqueous solution. Using the same techniques, we show that despite its unstructured nature, the addition of trifluoroethanol exhibited an intrinsic potential in this protein to gain helicity. This property was also promoted by high osmotic potentials or molecular crowding. Furthermore, we demonstrate that PvLEA6 protein is able to form soluble homo-oligomeric complexes that also show high levels of structural disorder. The association between PvLEA6 monomers to form dimers was shown to occur in plant cells by bimolecular fluorescence complementation, pointing to the in vivo functional relevance of this association.
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Affiliation(s)
- Lucero Y Rivera-Najera
- Departamentos de Biología Molecular de Plantas and Universidad Nacional Autónoma de México, Apdo. Postal 510-3, 62250 Cuernavaca, Mor
| | - Gloria Saab-Rincón
- Departamentos de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, 62250 Cuernavaca, Mor
| | - Marina Battaglia
- Departamentos de Biología Molecular de Plantas and Universidad Nacional Autónoma de México, Apdo. Postal 510-3, 62250 Cuernavaca, Mor
| | - Carlos Amero
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad No. 1001, Col Chamilpa, 62209 Cuernavaca, Morelos, and
| | - Nancy O Pulido
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México 04510, D. F. México
| | - Enrique García-Hernández
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México 04510, D. F. México
| | - Rosa M Solórzano
- Departamentos de Biología Molecular de Plantas and Universidad Nacional Autónoma de México, Apdo. Postal 510-3, 62250 Cuernavaca, Mor
| | - José L Reyes
- Departamentos de Biología Molecular de Plantas and Universidad Nacional Autónoma de México, Apdo. Postal 510-3, 62250 Cuernavaca, Mor
| | - Alejandra A Covarrubias
- Departamentos de Biología Molecular de Plantas and Universidad Nacional Autónoma de México, Apdo. Postal 510-3, 62250 Cuernavaca, Mor..
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Shibasaki H, Uchimura K, Miura T, Kobayashi T, Usami R, Horikoshi K. Highly thermostable and surfactant-activated chitinase from a subseafloor bacterium, Laceyella putida. Appl Microbiol Biotechnol 2014; 98:7845-53. [DOI: 10.1007/s00253-014-5692-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 03/13/2014] [Accepted: 03/14/2014] [Indexed: 10/25/2022]
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An intermolecular disulfide bond is required for thermostability and thermoactivity of β-glycosidase from Thermococcus kodakarensis KOD1. Appl Microbiol Biotechnol 2014; 98:7825-36. [PMID: 24728717 DOI: 10.1007/s00253-014-5731-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/26/2014] [Accepted: 03/27/2014] [Indexed: 12/24/2022]
Abstract
Scientists are interested in understanding the molecular origin of protein thermostability and thermoactivity for possible biotechnological applications. The enzymes from extremophilic organisms have been of particular interest in the last two decades. β-glycosidase, Tkβgly is a hyperthermophilic enzyme from Thermococcus kodakarensis KOD1. Tkβgly contains two conserved cysteine residues, C88 and C376. The protein tertiary structure obtained through homology modeling suggests that the C88 residue is located on the surface whereas C376 is inside the protein. To study the role of these cysteine residues, we substituted C88 and C376 with serine residues through site-directed mutagenesis. The wild-type and C376S protein existed in dimeric form and C88S in monomeric form, in an SDS-PAGE gel under non-reducing conditions. Optimal temperature experiments revealed that the wild-type was active at 100 °C whereas the C88S mutant exhibited optimal activity at 70 °C. The half-life of the enzyme at 70 °C was drastically reduced from 266 h to less than 1 h. Although C88 was not present in the active site region, the kcat/Km of C88S was reduced by 2-fold. Based on the structural model and biochemical properties, we propose that C88 is crucial in maintaining the thermostability and thermoactivity of the Tkβgly enzyme.
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Amara I, Zaidi I, Masmoudi K, Ludevid MD, Pagès M, Goday A, Brini F. Insights into Late Embryogenesis Abundant (LEA) Proteins in Plants: From Structure to the Functions. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ajps.2014.522360] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Gonçalves KM, Barbosa LR, Lima LMT, Cortines JR, Kalume DE, Leal IC, Mariz e Miranda LS, de Souza RO, Cordeiro Y. Conformational dissection of Thermomyces lanuginosus lipase in solution. Biophys Chem 2014; 185:88-97. [DOI: 10.1016/j.bpc.2013.12.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/02/2013] [Accepted: 12/04/2013] [Indexed: 01/05/2023]
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19
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Acrylamide concentration determines the direction and magnitude of helical membrane protein gel shifts. Proc Natl Acad Sci U S A 2013; 110:15668-73. [PMID: 24019476 DOI: 10.1073/pnas.1311305110] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
SDS/PAGE is universally used in biochemistry, cell biology, and immunology to resolve minute protein amounts readily from tissue and cell extracts. Although molecular weights of water-soluble proteins are reliably determined from their SDS/PAGE mobility, most helical membrane proteins, which comprise 20-30% of the human genome and the majority of drug targets, migrate to positions that have for decades been unpredictably slower or faster than their actual formula weight, often confounding their identification. Using de novo designed transmembrane-mimetic polypeptides that match the composition of helical membrane-spanning sequences, we quantitate anomalous SDS/PAGE fractionation of helical membrane proteins by comparing the relative mobilities of these polypeptides with typical water-soluble reference proteins on Laemmli gels. We find that both the net charge and effective molecular size of the migrating particles of transmembrane-mimetic species exceed those of the corresponding reference proteins and that gel acrylamide concentration dictates the impact of these two factors on the direction and magnitude of anomalous migration. Algorithms we derived from these data compensate for this differential effect of acrylamide concentration on the SDS/PAGE mobility of a variety of natural membrane proteins. Our results provide a unique means to predict anomalous migration of membrane proteins, thereby facilitating straightforward determination of their molecular weights via SDS/PAGE.
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20
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Lalioti VS, Vergarajauregui S, Villasante A, Pulido D, Sandoval IV. C6orf89 encodes three distinct HDAC enhancers that function in the nucleolus, the golgi and the midbody. J Cell Physiol 2013; 228:1907-21. [PMID: 23460338 DOI: 10.1002/jcp.24355] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 02/12/2013] [Indexed: 11/06/2022]
Abstract
We report here that C6orf89, which encodes a protein that interacts with bombesin receptor subtype-3 and accelerates cell cycle progression and wound repair in human bronchial epithelial cells (Liu et al., 2011, PLoS ONE 6: e23072), encodes one soluble and two type II membrane proteins that function as histone deacetylases (HDAC) enhancers. Soluble 34/64sp is selectively targeted to the nucleolus and is retained in nucleolar organiser regions (NORs) in mitotic cells. Nucleolar 34/64sp is integrated into the ribosomal gene transcription machinery, colocalises and coimmunoprecipitates with the Pol I transcription factor UBF, and undergoes a dramatic relocalisation to the nucleolus upon the arrest of rDNA transcription, protein synthesis and PI3K/mTORC2 signalling. Membrane 42/116mp localises to the Golgi and the midbody, and its controlled ectopic expression provokes the disruption of the Golgi cisternae and hinders the separation of daughter cells and the completion of mitosis. The latter effect is also produced by the microinjection of an affinity-purified amfion antibody. The identification of C60rf89 as a gene that encodes three distinct proteins with the capacity to enhance the activity of histone deacetylases (HDACs) in the nucleolus, the Golgi and the midbody provides new information regarding the components of the acetylome and their capacity to interact with different functional groups in the cell.
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Affiliation(s)
- Vasiliki S Lalioti
- Centro de Biología Molecular Severo Ochoa, CSIC, Universidad Autónoma de Madrid, Departamento Biología Celular e Inmunología, Cantoblanco, Madrid, Spain.
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21
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Cao H, Chapital DC, Howard OD, Deterding LJ, Mason CB, Shockey JM, Klasson KT. Expression and purification of recombinant tung tree diacylglycerol acyltransferase 2. Appl Microbiol Biotechnol 2012; 96:711-27. [PMID: 22270236 PMCID: PMC11338361 DOI: 10.1007/s00253-012-3869-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 12/19/2011] [Accepted: 12/23/2011] [Indexed: 12/11/2022]
Abstract
Diacylglycerol acyltransferases (DGATs) esterify sn-1,2-diacylglycerol with a long-chain fatty acyl-CoA, the last and rate-limiting step of triacylglycerol (TAG) biosynthesis in eukaryotic organisms. At least 74 DGAT2 sequences from 61 organisms have been identified, but the expression of any DGAT2 as a partial or full-length protein in Escherichia coli had not been reported. The main objective of this study was to express and purify recombinant DGAT2 (rDGAT2) from E. coli for antigen production with a minor objective to compare rDGAT2 expression in yeast. A plasmid was engineered to express tung tree DGAT2 fused to maltose binding protein and poly-histidine (His) affinity tags. Immunoblotting showed that rDGAT2 was detected in the soluble, insoluble, and membrane fractions. The rDGAT2 in the soluble fraction was partially purified by amylose resin, nickel-nitrilotriacetic agarose (Ni-NTA) beads, and tandem affinity chromatography. Multiple proteins co-purified with rDGAT2. Size exclusion chromatography estimated the size of the rDGAT2-enriched fraction to be approximately eight times the monomer size. Affinity-purified rDGAT2 fractions had a yellow tint and contained fatty acids. The rDGAT2 in the insoluble fraction was partially solubilized by seven detergents with SDS being the most effective. Recombinant DGAT2 was purified to near homogeneity by SDS solubilization and Ni-NTA affinity chromatography. Mass spectrometry identified rDGAT2 as a component in the bands corresponding to the monomer and dimer forms as observed by SDS-PAGE. Protein bands with monomer and dimer sizes were also observed in the microsomal membranes of Saccharomyces cerevisiae expressing hemagglutinin-tagged DGAT2. Nonradioactive assay showed TAG synthesis activity of DGAT2 from yeast but not E. coli. The results suggest that rDGAT2 is present as monomer and dimer forms on SDS-PAGE, associated with other proteins, lipids, and membranes, and that post-translational modification of rDGAT2 may be required for its enzymatic activity and/or the E. coli protein is misfolded.
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Affiliation(s)
- Heping Cao
- Commodity Utilization Research Unit, Southern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA.
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22
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Fengler VHI, Boritsch EC, Tutz S, Seper A, Ebner H, Roier S, Schild S, Reidl J. Disulfide bond formation and ToxR activity in Vibrio cholerae. PLoS One 2012; 7:e47756. [PMID: 23144706 PMCID: PMC3483227 DOI: 10.1371/journal.pone.0047756] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 09/20/2012] [Indexed: 11/19/2022] Open
Abstract
Virulence factor production in Vibrio cholerae is complex, with ToxRS being an important part of the regulatory cascade. Additionally, ToxR is the transcriptional regulator for the genes encoding the major outer membrane porins OmpU and OmpT. ToxR is a transmembrane protein and contains two cysteine residues in the periplasmic domain. This study addresses the influence of the thiol-disulfide oxidoreductase system DsbAB, ToxR cysteine residues and ToxR/ToxS interaction on ToxR activity. The results show that porin production correlates with ToxR intrachain disulfide bond formation, which depends on DsbAB. In contrast, formation of ToxR intrachain or interchain disulfide bonds is dispensable for virulence factor production and in vivo colonization. This study further reveals that in the absence of ToxS, ToxR interchain disulfide bond formation is facilitated, whereat cysteinyl dependent homo- and oligomerization of ToxR is suppressed if ToxS is coexpressed. In summary, new insights into gene regulation by ToxR are presented, demonstrating a mechanism by which ToxR activity is linked to a DsbAB dependent intrachain disulfide bond formation.
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Affiliation(s)
| | | | | | | | | | | | | | - Joachim Reidl
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse, Graz, Austria
- * E-mail:
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Kado Y, Inoue T, Ishikawa K. Structure of hyperthermophilic β-glucosidase from Pyrococcus furiosus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1473-9. [PMID: 22139147 PMCID: PMC3232120 DOI: 10.1107/s1744309111035238] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 08/29/2011] [Indexed: 04/20/2023]
Abstract
Recombinant hyperthermophilic β-glucosidase from P. furiosus was crystallized. The crystal structure was solved to a resolution of 2.35 Å. Three categories of cellulases, endoglucanases, cellobiohydrolases and β-glucosidases, are commonly used in the process of cellulose saccharification. In particular, the activity and characteristics of hyperthermophilic β-glucosidase make it promising in industrial applications of biomass. In this paper, the crystal structure of the hyperthermophilic β-glucosidase from Pyrococcus furiosus (BGLPf) was determined at 2.35 Å resolution in a new crystal form. The structure showed that there is one tetramer in the asymmetric unit and that the dimeric molecule exhibits a structure that is stable towards sodium dodecyl sulfate (SDS). The dimeric molecule migrated in reducing SDS polyacrylamide gel electrophoresis (SDS–PAGE) buffer even after boiling at 368 K. Energy calculations demonstrated that one of the two dimer interfaces acquired the largest solvation free energy. Structural comparison and sequence alignment with mesophilic β-glucosidase A from Clostridium cellulovorans (BGLACc) revealed that the elongation at the C-terminal end forms a hydrophobic patch at the dimer interface that might contribute to hyperthermostability.
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Affiliation(s)
- Yuji Kado
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Osaka, Japan
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24
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Structural and functional insights into Aeropyrum pernix OppA, a member of a novel archaeal OppA subfamily. J Bacteriol 2010; 193:620-30. [PMID: 21097609 DOI: 10.1128/jb.00899-10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study we gain insight into the structural and functional characterization of the Aeropyrum pernix oligopeptide-binding protein (OppA(Ap)) previously identified from the extracellular medium of an Aeropyrum pernix cell culture at late stationary phase. OppA(Ap) showed an N-terminal Q32 in a pyroglutamate form and C-terminal processing at the level of a threonine-rich region probably involved in protein membrane anchoring. Moreover, the OppA(Ap) protein released into the medium was identified as a "nicked" form composed of two tightly associated fragments detachable only under strong denaturing conditions. The cleavage site E569-G570 seems be located on an exposed surface loop that is highly conserved in several three-dimensional (3D) structures of dipeptide/oligopeptide-binding proteins from different sources. Structural and biochemical properties of the nicked protein were virtually indistinguishable from those of the intact form. Indeed, studies of the entire bacterially expressed OppA(Ap) protein owning the same N and C termini of the nicked form supported these findings. Moreover, in the middle exponential growth phase, OppA(Ap) was found as an intact cell membrane-associated protein. Interestingly, the native exoprotein OppA(Ap) was copurified with a hexapeptide (EKFKIV) showing both lysines methylated and possibly originating from an A. pernix endogenous stress-induced lipoprotein. Therefore, the involvement of OppA(Ap) in the recycling of endogenous proteins was suggested to be a potential physiological function. Finally, a new OppA from Sulfolobus solfataricus, SSO1288, was purified and preliminarily characterized, allowing the identification of a common structural/genetic organization shared by all "true" archaeal OppA proteins of the dipeptide/oligopeptide class.
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Kenanova VE, Olafsen T, Salazar FB, Williams LE, Knowles S, Wu AM. Tuning the serum persistence of human serum albumin domain III:diabody fusion proteins. Protein Eng Des Sel 2010; 23:789-98. [PMID: 20802234 DOI: 10.1093/protein/gzq054] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The long circulation persistence of human serum albumin (HSA) is enabled by its domain III (DIII) interaction with the neonatal Fc receptor (FcRn). A protein scaffold based on HSA DIII was designed. To modify the serum half life of the scaffold, residues H535, H510, and H464 were individually mutated to alanine. HSA DIII wild type (WT) and variants were fused to the anti-carcinoembryonic antigen (CEA) T84.66 diabody (Db), radiolabeled with (124)I and injected into xenografted athymic mice for serial PET/CT imaging. All proteins targeted the CEA-positive tumor. The mean residence times (MRT) of the proteins, calculated by quantifying blood activity from the PET images, were: Db-DIII WT (56.7 h), H535A (25 h), H510A (20 h), H464A (17 h), compared with Db (2.9 h). Biodistribution confirmed the order of blood clearance from slow to fast: Db-DIII WT > H535A > H510A > H464A > Db with 4.0, 2.0, 1.8, 1.6 and 0.08 %ID/g of remaining blood activity at 51 h, respectively. This study demonstrates that attenuating the DIII-FcRn interaction provides a way of controlling the pharmacokinetics of the entire Db-DIII fusion protein without compromising tumor targeting. H464 appears to be most crucial for FcRn binding (greatest reduction in MRT), followed by H510 and H535. By mutating the DIII scaffold, we can dial serum kinetics for imaging or therapy applications.
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Affiliation(s)
- Vania E Kenanova
- Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, California Nanosystems Institute, University of California, Los Angeles, 570 Westwood Plaza, CA 90095-1770, USA
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A highly selective oligopeptide binding protein from the archaeon Sulfolobus solfataricus. J Bacteriol 2010; 192:3123-31. [PMID: 20382765 DOI: 10.1128/jb.01414-09] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SSO1273 of Sulfolobus solfataricus was identified as a cell surface-bound protein by a proteomics approach. Sequence inspection of the genome revealed that the open reading frame of sso1273 is associated in an operon-like structure with genes encoding all the remaining components of a canonical protein-dependent ATP-binding cassette (ABC) transporter. sso1273 gene expression and SSO1273 protein accumulation on the cell surface were demonstrated to be strongly induced by the addition of a peptide mixture (tryptone) to the culture medium. The native protein was obtained in multimeric form, mostly hexameric, under the purification conditions used, and it was characterized as an oligopeptide binding protein, named S. solfataricus OppA (OppA(Ss)). OppaA(Ss) possesses typical sequence patterns required for glycosylphosphatidylinositol lipid anchoring, resulting in an N-linked glycoprotein with carbohydrate moieties likely composed of high mannose and/or hybrid complex carbohydrates. OppA(Ss) specifically binds oligopeptides and shows a marked selectivity for the amino acid composition of substrates when assayed in complex peptide mixtures. Moreover, a truncated version of OppA(Ss), produced in recombinant form and including the putative binding domain, showed a low but significant oligopeptide binding activity.
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Regulated oligomerisation and molecular interactions of the early gametocyte protein Pfg27 in Plasmodium falciparum sexual differentiation. Int J Parasitol 2009; 40:663-73. [PMID: 19968995 DOI: 10.1016/j.ijpara.2009.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 10/12/2009] [Accepted: 11/02/2009] [Indexed: 11/22/2022]
Abstract
Gametocytes of the protozoan Plasmodium falciparum ensure malaria parasite transmission from humans to the insect vectors. In their development, they produce the abundant specific protein Pfg27, the function and in vivo molecular interactions of which are unknown. Here we reveal a previously unreported localisation of Pfg27 in the gametocyte nucleus by immunoelectron microscopy and studies with HaloTag and Green Fluorescent Protein fusions, and identify a network of interactions established by the protein during gametocyte development. We report the ability of endogenous Pfg27 to form oligomeric complexes that are affected by phosphorylation of the protein, possibly through the identified phosphorylation sites, Ser32 and Thr208. We show that Pfg27 binds RNA molecules through specific residues and that the protein interacts with parasite RNA-binding proteins such as EF1alpha and PfH45. We propose a structural model for Pfg27 oligomerisation, based on the sequence and structural conservation here recognised between Pfg27 and sterile alpha motif. This study provides a molecular basis for Pfg27 to establish an interaction network with RNA and RNA-binding proteins and to govern its dynamic oligomerisation in developing gametocytes.
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Mamat U, Schmidt H, Munoz E, Lindner B, Fukase K, Hanuszkiewicz A, Wu J, Meredith TC, Woodard RW, Hilgenfeld R, Mesters JR, Holst O. WaaA of the hyperthermophilic bacterium Aquifex aeolicus is a monofunctional 3-deoxy-D-manno-oct-2-ulosonic acid transferase involved in lipopolysaccharide biosynthesis. J Biol Chem 2009; 284:22248-22262. [PMID: 19546212 DOI: 10.1074/jbc.m109.033308] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The hyperthermophile Aquifex aeolicus belongs to the deepest branch in the bacterial genealogy. Although it has long been recognized that this unique Gram-negative bacterium carries genes for different steps of lipopolysaccharide (LPS) formation, data on the LPS itself or detailed knowledge of the LPS pathway beyond the first committed steps of lipid A and 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) synthesis are still lacking. We now report the functional characterization of the thermostable Kdo transferase WaaA from A. aeolicus and provide evidence that the enzyme is monofunctional. Compositional analysis and mass spectrometry of purified A. aeolicus LPS, showing the incorporation of a single Kdo residue as an integral component of the LPS, implicated a monofunctional Kdo transferase in LPS biosynthesis of A. aeolicus. Further, heterologous expression of the A. aeolicus waaA gene in a newly constructed Escherichia coli DeltawaaA suppressor strain resulted in synthesis of lipid IVA precursors substituted with one Kdo sugar. When highly purified WaaA of A. aeolicus was subjected to in vitro assays using mass spectrometry for detection of the reaction products, the enzyme was found to catalyze the transfer of only a single Kdo residue from CMP-Kdo to differently modified lipid A acceptors. The Kdo transferase was capable of utilizing a broad spectrum of acceptor substrates, whereas surface plasmon resonance studies indicated a high selectivity for the donor substrate.
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Affiliation(s)
- Uwe Mamat
- Divisions of Structural Biochemistry, D-23845 Borstel, Germany
| | - Helgo Schmidt
- Divisions of Structural Biochemistry, D-23845 Borstel, Germany; Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, D-23538 Lübeck, Germany
| | - Eva Munoz
- the Institutes of Chemistry, D-23538 Lübeck, Germany
| | - Buko Lindner
- Immunochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, D-23845 Borstel, Germany
| | - Koichi Fukase
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | | | - Jing Wu
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Timothy C Meredith
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Ronald W Woodard
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Rolf Hilgenfeld
- Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, D-23538 Lübeck, Germany
| | - Jeroen R Mesters
- Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, D-23538 Lübeck, Germany
| | - Otto Holst
- Divisions of Structural Biochemistry, D-23845 Borstel, Germany
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Karst JC, Foucher AE, Campbell TL, Di Guilmi AM, Stroebel D, Mangat CS, Brown ED, Jault JM. The ATPase activity of an 'essential' Bacillus subtilis enzyme, YdiB, is required for its cellular function and is modulated by oligomerization. MICROBIOLOGY-SGM 2009; 155:944-956. [PMID: 19246765 DOI: 10.1099/mic.0.021543-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Characterization of 'unknown' proteins is one of the challenges of the post-genomic era. Here, we report a study of Bacillus subtilis YdiB, which belongs to an uncharted class of bacterial P-loop ATPases. Precise deletion of the ydiB gene yielded a mutant with much reduced growth rate compared to the wild-type strain. In vitro, purified YdiB was in equilibrium among different forms, monomers, dimers and oligomers, and this equilibrium was strongly affected by salts; high concentrations of NaCl favoured the monomeric over the oligomeric form of the enzyme. Interestingly, the ATPase activity of the monomer was about three times higher than that of the oligomer, and the monomer showed a K(m) of about 60 microM for ATP and a V(max) of about 10 nmol min(-1) (mg protein)(-1) (k(cat) approximately 10 h(-1)). This low ATPase activity was shown to be specific to YdiB because mutation of an invariant lysine residue in the P-loop motif (K41A) strongly attenuated this rate. This mutant was unable to restore a normal growth phenotype when introduced into a conditional knockout strain for ydiB, showing that the ATPase activity of YdiB is required for the in vivo function of the protein. Oligomerization was also observed with the purified YjeE from Escherichia coli, a YdiB orthologue, suggesting that this property is shared by all members of this family of ATPases. Importantly, dimers of YdiB were also observed in a B. subtilis extract, or when stabilized by formaldehyde cross-linking for YjeE from E. coli, suggesting that oligomerization might regulate the function of this new class of proteins in vivo.
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Affiliation(s)
- Johanna C Karst
- Institut de Biologie Structurale, UMR 5075 Université Joseph Fourier/CEA/CNRS, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - Anne-Emmanuelle Foucher
- Institut de Biologie Structurale, UMR 5075 Université Joseph Fourier/CEA/CNRS, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - Tracey L Campbell
- Antimicrobial Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8N 3Z5, Canada
| | - Anne-Marie Di Guilmi
- Institut de Biologie Structurale, UMR 5075 Université Joseph Fourier/CEA/CNRS, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - David Stroebel
- Institut de Biologie Structurale, UMR 5075 Université Joseph Fourier/CEA/CNRS, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - Chand S Mangat
- Antimicrobial Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8N 3Z5, Canada
| | - Eric D Brown
- Antimicrobial Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8N 3Z5, Canada
| | - Jean-Michel Jault
- Institut de Biologie Structurale, UMR 5075 Université Joseph Fourier/CEA/CNRS, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
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30
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Leshchiner AD, Minina EA, Rakitina DV, Vishnichenko VK, Solovyev AG, Morozov SY, Kalinina NO. Oligomerization of the potato virus X 25-kD movement protein. BIOCHEMISTRY (MOSCOW) 2008; 73:50-5. [PMID: 18294129 DOI: 10.1134/s0006297908010070] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A 25-kD movement protein (25K protein) encoded by the first gene of the potexvirus Potato virus X triple gene block of transport genes is essential for the viral movement in infected plants. The 25K protein belongs to superfamily 1 of NTPase/helicases and exhibits in vitro RNA helicase, Mg2+-dependent NTPase, and RNA-binding activities. In the present work, the ability of 25K protein for homologous interactions was studied using the yeast two-hybrid system, protein chemical cross-linking in the presence of glutaraldehyde, far-Western blotting, and ultracentrifugation in sucrose density gradients. The 25K protein was shown to form homodimers and homooligomers. Sites of homologous protein-protein interactions were found in both the N- and C-terminal portions of the protein.
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Affiliation(s)
- A D Leshchiner
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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31
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Overexpression, physicochemical characterization, and modeling of a hyperthermophilic pyrococcus furiosus type 2 IPP isomerase. Proteins 2007; 71:1699-707. [DOI: 10.1002/prot.21863] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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32
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Leshchiner AD, Solovyev AG, Morozov SY, Kalinina NO. A minimal region in the NTPase/helicase domain of the TGBp1 plant virus movement protein is responsible for ATPase activity and cooperative RNA binding. J Gen Virol 2006; 87:3087-3095. [PMID: 16963768 DOI: 10.1099/vir.0.81971-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The TGBp1 protein, encoded in the genomes of a number of plant virus genera as the first gene of the 'triple gene block', possesses an NTPase/helicase domain characterized by seven conserved sequence motifs. It has been shown that the TGBp1 NTPase/helicase domain exhibits NTPase, RNA helicase and RNA-binding activities. In this paper, we have analysed a series of deletion and point mutants in the TGBp1 proteins encoded by Potato virus X (PVX, genus Potexvirus) and Poa semilatent virus (PSLV, genus Hordeivirus) to map functional regions responsible for their biochemical activities in vitro. It was found that, in both PVX and PSLV, the N-terminal part of the TGBp1 NTPase/helicase domain comprising conserved motifs I, Ia and II was sufficient for ATP hydrolysis, RNA binding and homologous protein-protein interactions. Point mutations in a single conserved basic amino acid residue upstream of motif I had little effect on the activities of C-terminally truncated mutants of both TGBp1 proteins. However, when introduced into the full-length NTPase/helicase domains, these mutations caused a substantial decrease in the ATPase activity of the protein, suggesting that the conserved basic amino acid residue upstream of motif I was required to maintain a reaction-competent conformation of the TGBp1 ATPase active site.
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Affiliation(s)
- Anna D Leshchiner
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia
| | - Andrey G Solovyev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia
| | - Sergey Yu Morozov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia
| | - Natalia O Kalinina
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia
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33
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Palmieri G, Casbarra A, Fiume I, Catara G, Capasso A, Marino G, Onesti S, Rossi M. Identification of the first archaeal oligopeptide-binding protein from the hyperthermophile Aeropyrum pernix. Extremophiles 2006; 10:393-402. [PMID: 16636888 DOI: 10.1007/s00792-006-0508-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Accepted: 01/04/2006] [Indexed: 10/24/2022]
Abstract
The archaeon Aeropyrum pernix grows optimally at 90 degrees C and derives energy primarily from aerobic degradation of complex proteinaceous substrates. The ability of these nutrients to sustain growth is generally associated with the presence of oligopeptide transport systems, such as the well-known protein-dependent ATP-binding cassette (ABC) transporters. This study is concerned with the isolation and characterisation of the first archaeal oligopeptide-binding protein (OppA(Ap)) from the extracellular medium of A. pernix. The protein shows a pI of 3.9 and a molecular mass of about 90 kDa under native conditions. By using a proteomic approach, the OppA(Ap)-encoding gene was identified (APE1583) and about 55% of the protein amino-acid sequence was validated. The extracellular purified protein was able to efficiently bind oligopeptide substrates such as Xenopsin. The amount of a liganded peptide to OppA(Ap) was about 70% at 90 degrees C using a 1/100 (w/w) OppA(Ap)/substrate ratio. Sequence comparisons showed a weak but significant similarity of OppA(Ap) with bacterial oligopeptide binding proteins. Furthermore, APE1583 neighbouring genes encode for the cognate components of an ABC transport system, suggesting that these ORFs are organised in an operon-like structure, with OppA(Ap )as the extracellular component for the uptake of oligopeptides.
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Affiliation(s)
- Gianna Palmieri
- IBP-Consiglio Nazionale delle Ricerche, 80131 Naples, Italy.
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34
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Soufi A, Smith C, Clarke AR, Gaston K, Jayaraman PS. Oligomerisation of the developmental regulator proline rich homeodomain (PRH/Hex) is mediated by a novel proline-rich dimerisation domain. J Mol Biol 2006; 358:943-62. [PMID: 16540119 DOI: 10.1016/j.jmb.2006.02.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2005] [Revised: 02/02/2006] [Accepted: 02/02/2006] [Indexed: 11/22/2022]
Abstract
Homeodomain proteins regulate multiple developmental pathways by altering gene expression temporally and in a tissue-specific fashion. The Proline Rich Homeodomain protein (PRH/Hex) is a transcription factor and an essential regulator of embryonic development and haematopoiesis. Recent discoveries have implicated self-association as an important feature of transcription factor function. Here, we show using a variety of techniques including gel-filtration, analytical ultracentrifugation, electron microscopy and in vitro cross-linking, that purified recombinant PRH is oligomeric and we use in vivo cross-linking to confirm that this protein exists as oligomers in cells. This is the first demonstration that a homeodomain protein can oligomerise in vivo. Consistent with these findings we show that a fraction of endogenous and exogenous PRH appears as discrete foci within the nucleus and at the nuclear periphery. The N-terminal domain of PRH is involved in the regulation of cell proliferation and transcriptional repression and can make multiple protein-protein interactions. We show that this region of PRH contains a novel proline-rich dimerisation domain that mediates oligomerisation. We propose a model that explains how PRH forms oligomers and we discuss how these oligomers might control transcription.
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Affiliation(s)
- Abdenour Soufi
- Department of Biochemistry, University of Bristol, University Walk, Bristol BS81TD, UK
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35
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Ausili A, Di Lauro B, Cobucci-Ponzano B, Bertoli E, Scirè A, Rossi M, Tanfani F, Moracci M. Two-dimensional IR correlation spectroscopy of mutants of the beta-glycosidase from the hyperthermophilic archaeon Sulfolobus solfataricus identifies the mechanism of quaternary structure stabilization and unravels the sequence of thermal unfolding events. Biochem J 2005; 384:69-78. [PMID: 15283674 PMCID: PMC1134089 DOI: 10.1042/bj20040646] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Beta-glycosidase from the hyperthermophilic archaeon Sulfolobus solfataricus is a homotetramer with a higher number of ion pairs compared with mesophilic glycoside hydrolases. The ion pairs are arranged in large networks located mainly at the tetrameric interface of the molecule. In the present study, the structure and thermal stability of the wild-type beta-glycosidase and of three mutants in residues R488 and H489 involved in the C-terminal ionic network were examined by FTIR (Fourier-transform IR) spectroscopy. The FTIR data revealed small differences in the secondary structure of the proteins and showed a lower thermostability of the mutant proteins with respect to the wild-type. Generalized 2D-IR (two-dimensional IR correlation spectroscopy) at different temperatures showed different sequences of thermal unfolding events in the mutants with respect to the wild-type, indicating that punctual mutations affect the unfolding and aggregation process of the protein. A detailed 2D-IR analysis of synchronous maps of the proteins allowed us to identify the temperatures at which the ionic network that stabilizes the quaternary structure of the native and mutant enzymes at the C-terminal breaks down. This evidence gives support to the current theories on the mechanism of ion-pair stabilization in proteins from hyperthermophilic organisms.
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Affiliation(s)
- Alessio Ausili
- *Institute of Biochemistry, Faculty of Sciences, Università Politecnica delle Marche, Via Ranieri, 60131 Ancona, Italy
| | - Barbara Di Lauro
- †Institute of Protein Biochemistry, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | | | - Enrico Bertoli
- *Institute of Biochemistry, Faculty of Sciences, Università Politecnica delle Marche, Via Ranieri, 60131 Ancona, Italy
- ‡Faculty of Medicine, Università Politecnica delle Marche, Via Ranieri, 60131 Ancona, Italy
| | - Andrea Scirè
- *Institute of Biochemistry, Faculty of Sciences, Università Politecnica delle Marche, Via Ranieri, 60131 Ancona, Italy
| | - Mosè Rossi
- †Institute of Protein Biochemistry, CNR, Via P. Castellino 111, 80131 Naples, Italy
- §Department of Biological Chemistry, University of Naples “Federico II”, Via Mezzocannone 16, 80134 Naples, Italy
| | - Fabio Tanfani
- *Institute of Biochemistry, Faculty of Sciences, Università Politecnica delle Marche, Via Ranieri, 60131 Ancona, Italy
- To whom correspondence should be addressed (email )
| | - Marco Moracci
- †Institute of Protein Biochemistry, CNR, Via P. Castellino 111, 80131 Naples, Italy
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36
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Hancock SM, Corbett K, Fordham-Skelton AP, Gatehouse JA, Davis BG. Developing Promiscuous Glycosidases for Glycoside Synthesis: Residues W433 and E432 in Sulfolobus solfataricus β-Glycosidase are Important Glucoside- and Galactoside-Specificity Determinants. Chembiochem 2005; 6:866-75. [PMID: 15846595 DOI: 10.1002/cbic.200400341] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Two residues that have been implicated in determining the substrate specificity of the thermophilic beta-glycosidase from the archaeon Sulfolobus solfataricus (SsbetaG), a member of the glycosyl hydrolase family 1, have been mutated by site-directed mutagenesis so as to create more versatile catalysts for carbohydrate chemistry. The wild-type and mutated sequences were expressed in E. coli with a His(7)-tag to allow one-step chromatographic purification. The E432C and W433C mutations removed key interactions with the OH-4 and OH-3 of the sugar substrates, thus reducing the discrimination of glucose, galactose and fucose with respect to other glycosides. This resulted in two glycosidases with greatly broadened substrate specificities. Observed changes include a 24-fold increase in Man:Gal activity and an 18-fold increase in GalA:Gal activity. This promiscuous substrate tolerance was further illustrated by the parallel synthesis of a beta-glycoside library of glucose, galactose, xylose and mannose in one pot at 50 degrees C, in organic solvent. The synthetic potential of the catalysts was further evaluated through alkyl glycoside transglycosylation yields, including the first examples of synthesis of beta-mannosides and beta-xylosides with SsbetaG.
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Affiliation(s)
- Susan M Hancock
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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37
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Schofield LR, Patchett ML, Parker EJ. Expression, purification, and characterization of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Pyrococcus furiosus. Protein Expr Purif 2004; 34:17-27. [PMID: 14766297 DOI: 10.1016/j.pep.2003.11.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2003] [Revised: 11/06/2003] [Indexed: 11/25/2022]
Abstract
The enzyme 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyzes the condensation reaction between phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P). DAH7PS from the hyperthermophile Pyrococcus furiosus has been expressed in Escherichia coli. The expressed protein was insoluble but was partially solubilized as a dimer by the inclusion of 200 mM KCl in the cell lysis buffer. An effective two step purification procedure has been developed. The first step resulted in a high degree of purification and involved lysis by sonication at approximately 40 degrees C followed by a heat treatment at 70 degrees C. A continuous assay measuring the loss of PEP at 232 nm at elevated temperatures was also developed. Temperature, pH, and divalent metal ions all had an effect on the extinction coefficient of PEP. Purified recombinant P. furiosus DAH7PS is a dimer with a subunit Mr of 29,226 (determined by ESMS), shows resistance to denaturation by SDS, has activity over a broad pH range, and has an activation energy of 88 kJmol-1. The kinetic parameters are Km (PEP) 120 microM, Km (E4P) 28 microM, and kcat 1.5s-1, at 60 degrees C and pH 6.8. DAH7PS is not inhibited by phenylalanine, tyrosine, or tryptophan. EDTA inactivates the enzyme and enzyme activity is restored by a wide range of divalent metal ions including (in order of decreasing effectiveness): Zn2+, Cd2+, Mn2+, Co2+, Ni2+, Ca2+, Hg2+, and Cu2+. This detailed characterization of the DAH7PS from P. furiosus raises the possibility that the subfamily Ibeta DAH7PS enzymes are metal ion dependent, contrary to previous predictions.
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Affiliation(s)
- Linley R Schofield
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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38
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Febbraio F, Andolfo A, Tanfani F, Briante R, Gentile F, Formisano S, Vaccaro C, Scirè A, Bertoli E, Pucci P, Nucci R. Thermal stability and aggregation of sulfolobus solfataricus beta-glycosidase are dependent upon the N-epsilon-methylation of specific lysyl residues: critical role of in vivo post-translational modifications. J Biol Chem 2003; 279:10185-94. [PMID: 14660666 DOI: 10.1074/jbc.m308520200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Methylation in vivo is a post-translational modification observed in several organisms belonging to eucarya, bacteria, and archaea. Although important implications of this modification have been demonstrated in several eucaryotes, its biological role in hyperthermophilic archaea is far from being understood. The aim of this work is to clarify some effects of methylation on the properties of beta-glycosidase from Sulfolobus solfataricus, by a structural comparison between the native, methylated protein and its unmethylated counterpart, recombinantly expressed in Escherichia coli. Analysis by Fourier transform infrared spectroscopy indicated similar secondary structure contents for the two forms of the protein. However, the study of temperature perturbation by Fourier transform infrared spectroscopy and turbidimetry evidenced denaturation and aggregation events more pronounced in recombinant than in native beta-glycosidase. Red Nile fluorescence analysis revealed significant differences of surface hydrophobicity between the two forms of the protein. Unlike the native enzyme, which dissociated into SDS-resistant dimers upon exposure to the detergent, the recombinant enzyme partially dissociated into monomers. By electrospray mapping, the methylation sites of the native protein were identified. A computational analysis of beta-glycosidase three-dimensional structure and comparisons with other proteins from S. solfataricus revealed analogies in the localization of methylation sites in terms of secondary structural elements and overall topology. These observations suggest a role for the methylation of lysyl residues, located in selected domains, in the thermal stabilization of beta-glycosidase from S. solfataricus.
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MESH Headings
- Amino Acids/chemistry
- Coloring Agents/pharmacology
- Detergents/pharmacology
- Dimerization
- Electrophoresis, Polyacrylamide Gel
- Escherichia coli/metabolism
- Glucosidases/chemistry
- Hydrogen Bonding
- Hydrogen-Ion Concentration
- Hydrolysis
- Lysine/chemistry
- Mass Spectrometry
- Methylation
- Models, Chemical
- Models, Molecular
- Oxazines/pharmacology
- Protein Binding
- Protein Conformation
- Protein Denaturation
- Protein Processing, Post-Translational
- Protein Structure, Secondary
- Recombinant Proteins/chemistry
- Software
- Spectrometry, Fluorescence
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Spectrophotometry, Infrared
- Spectroscopy, Fourier Transform Infrared
- Sulfolobus/enzymology
- Temperature
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39
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Tendulkar AV, Wangikar PP, Sohoni MA, Samant VV, Mone CY. Parameterization and Classification of the Protein Universe via Geometric Techniques. J Mol Biol 2003; 334:157-72. [PMID: 14596807 DOI: 10.1016/j.jmb.2003.09.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a scheme for the classification of 3487 non-redundant protein structures into 1207 non-hierarchical clusters by using recurring structural patterns of three to six amino acids as keys of classification. This results in several signature patterns, which seem to decide membership of a protein in a functional category. The patterns provide clues to the key residues involved in functional sites as well as in protein-protein interaction. The discovered patterns include a "glutamate double bridge" of superoxide dismutase, the functional interface of the serine protease and inhibitor, interface of homo/hetero dimers, and functional sites of several enzyme families. We use geometric invariants to decide superimposability of structural patterns. This allows the parameterization of patterns and discovery of recurring patterns via clustering. The geometric invariant-based approach eliminates the computationally explosive step of pair-wise comparison of structures. The results provide a vast resource for the biologists for experimental validation of the proposed functional sites, and for the design of synthetic enzymes, inhibitors and drugs.
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Affiliation(s)
- Ashish V Tendulkar
- Kanwal Rekhi School of Information Technology, Indian Institute of Technology, Bombay, Powai, Mumbai 400 076, India
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40
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Rachow A, Gauss-Müller V, Probst C. Homogeneous hepatitis A virus particles. Proteolytic release of the assembly signal 2A from procapsids by factor Xa. J Biol Chem 2003; 278:29744-51. [PMID: 12782637 DOI: 10.1074/jbc.m300454200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Among the picornaviridae, hepatitis A virus (HAV) is unique in that its assembly is driven by domain 2A of P1-2A, the precursor of the structural proteins (Probst, C., Jecht, M., and Gauss-Müller, V. (1999) J. Biol. Chem. 274, 4527-4531). Whereas infected individuals excrete in stool mature HAV capsids with VP1 as the major structural protein, its C-terminal extended form VP1-2A is the main component of immature procapsids produced in HAV-infected cells in culture. Obviously, a postassembly proteolytic step is required to remove the primary assembly signal 2A from VP1-2A of procapsids. Mutants of VP1-2A were expressed in COS7 cells to determine the cleavage site in VP1-2A and to test for the cleavage potential of viral and host proteinases (factor Xa and thrombin). Site-specific in vitro cleavage by factor Xa and thrombin occurred in procapsids that contained VP1-2A with engineered cognate cleavage sites for these proteinases. Interestingly, factor Xa but not thrombin liberated mature VP1 also from native procapsids in an assembly-dependent manner. The data show that domain 2A, which is required for pentamerization of its precursor polypeptides and thus for the primary step of HAV assembly, is removed from the surface of immature procapsid by a host proteinase. Moreover, our data open a novel avenue to produce homogeneous HAV particles from recombinant intermediates by in vitro treatment with exogenously added proteases such as factor Xa or thrombin.
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Affiliation(s)
- Andrea Rachow
- Institute of Medical Molecular Biology, University of Luebeck, 23538 Luebeck, Germany
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41
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Taliansky M, Roberts IM, Kalinina N, Ryabov EV, Raj SK, Robinson DJ, Oparka KJ. An umbraviral protein, involved in long-distance RNA movement, binds viral RNA and forms unique, protective ribonucleoprotein complexes. J Virol 2003; 77:3031-40. [PMID: 12584328 PMCID: PMC149777 DOI: 10.1128/jvi.77.5.3031-3040.2003] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2002] [Accepted: 12/05/2002] [Indexed: 11/20/2022] Open
Abstract
Umbraviruses are different from most other viruses in that they do not encode a conventional capsid protein (CP); therefore, no recognizable virus particles are formed in infected plants. Their lack of a CP is compensated for by the ORF3 protein, which fulfils functions that are provided by the CPs of other viruses, such as protection and long-distance movement of viral RNA. When the Groundnut rosette virus (GRV) ORF3 protein was expressed from Tobacco mosaic virus (TMV) in place of the TMV CP [TMV(ORF3)], in infected cells it interacted with the TMV RNA to form filamentous ribonucleoprotein (RNP) particles that had elements of helical structure but were not as uniform as classical virions. These RNP particles were observed in amorphous inclusions in the cytoplasm, where they were embedded within an electron-dense matrix material. The inclusions were detected in all types of cells and were abundant in phloem-associated cells, in particular companion cells and immature sieve elements. RNP-containing complexes similar in appearance to the inclusions were isolated from plants infected with TMV(ORF3) or with GRV itself. In vitro, the ORF3 protein formed oligomers and bound RNA in a manner consistent with its role in the formation of RNP complexes. It is suggested that the cytoplasmic RNP complexes formed by the ORF3 protein serve to protect viral RNA and may be the form in which it moves through the phloem. Thus, the RNP particles detected here represent a novel structure which may be used by umbraviruses as an alternative to classical virions.
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Affiliation(s)
- Michael Taliansky
- Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom.
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