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Ohyama T, Osawa T, Sekine SI, Ishii Y. NMR Studies of Genomic RNA in 3' Untranslated Region Unveil Pseudoknot Structure that Initiates Viral RNA Replication in SARS-CoV-2. JACS AU 2024; 4:1323-1333. [PMID: 38665648 PMCID: PMC11041675 DOI: 10.1021/jacsau.3c00641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/20/2024] [Accepted: 03/08/2024] [Indexed: 04/28/2024]
Abstract
In the 3' untranslated region of the SARS-CoV-2 virus RNA genome, genomic RNA replication is initiated in the highly conserved region called 3'PK, containing three stem structures (P1pk, P2, and P5). According to one proposed mechanism, P1pk and distal P2 stems switch their structure to a pseudoknot through base-pairing, thereby initiating transcription by recruiting RNA-dependent RNA polymerase complexed with nonstructural proteins (nsp)7 and nsp8. However, experimental evidence of pseudoknot formation or structural switching is unavailable. Using SARS-CoV-2 3'PK fragments, we show that 3'PK adopted stem-loop and pseudoknot forms in a mutually exclusive manner. When P1pk and P2 formed a pseudoknot, the P5 stem, which includes a sequence at the 3' end, exited from the stem-loop structure and opened up. Interaction with the nsp7/nsp8 complex destabilized the stem-loop form but did not alter the pseudoknot form. These results suggest that the interaction between the pseudoknot and nsp7/nsp8 complex transformed the 3' end of viral genomic RNA into single-stranded RNA ready for synthesis, presenting the unique pseudoknot structure as a potential pharmacological target.
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Affiliation(s)
- Takako Ohyama
- Laboratory for Advanced NMR Application and
Development, Center for Biosystems Dynamics Research, RIKEN,
1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa,
Japan
- School of Life Science and Technology,
Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku,
Yokohama 226-8503, Kanagawa, Japan
| | - Takuo Osawa
- Laboratory for Transcription Structural Biology,
Center for Biosystems Dynamics Research, RIKEN, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
| | - Shun-ichi Sekine
- Laboratory for Transcription Structural Biology,
Center for Biosystems Dynamics Research, RIKEN, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
| | - Yoshitaka Ishii
- Laboratory for Advanced NMR Application and
Development, Center for Biosystems Dynamics Research, RIKEN,
1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa,
Japan
- School of Life Science and Technology,
Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku,
Yokohama 226-8503, Kanagawa, Japan
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2
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Tomioka Y, Akuta T, Tokunaga M, Arakawa T. Different behavior of Ferguson plot between agarose and polyacrylamide gels. Biophys Chem 2024; 307:107200. [PMID: 38367540 DOI: 10.1016/j.bpc.2024.107200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/04/2024] [Accepted: 02/12/2024] [Indexed: 02/19/2024]
Abstract
In this study, we conducted Ferguson plot analyses using both agarose and polyacrylamide gels in native electrophoresis and SDS-PAGE. The results revealed intriguing differences in the behavior of bovine serum albumin (BSA) and other model proteins. Specifically, BSA exhibited Ferguson plot slopes that were dependent on the oligomer size in agarose native gel electrophoresis, while such size-dependent behavior was not observed in native-PAGE or SDS-PAGE. These findings suggest that Ferguson plot analysis is a suitable approach when using agarose gel under the electrophoretic conditions employed in this study. Furthermore, our investigation extended to model proteins with acidic isoelectric points and larger molecular weights, namely Ferritin and caseinolytic peptidase B (ClpB). Notably, these proteins displayed distinct Ferguson plot slopes when subjected to agarose gel electrophoresis. Intriguingly, when polyacrylamide gel was employed, ClpB exhibited multiple bands, each with its unique Ferguson plot slope, deviating from the expected behavior based on molecular size. This divergence in Ferguson plot characteristics between agarose and polyacrylamide gels points to an interesting and complex interplay between protein properties and gel electrophoresis conditions.
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Affiliation(s)
- Yui Tomioka
- Product Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki 318-0004, Japan.
| | - Teruo Akuta
- Product Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki 318-0004, Japan.
| | - Masao Tokunaga
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima-shi 890-0065, Japan
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Rd, San Diego, CA 92130, USA.
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3
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Park SC, Lim HS, Mun SE, Jung YJ, Yoon AM, Son H, Kim CM, Choo YK, Lee JR. Potent Antifungal Functions of a Living Modified Organism Protein, CP4-EPSPS, against Pathogenic Fungal Cells. Molecules 2023; 28:molecules28114289. [PMID: 37298765 DOI: 10.3390/molecules28114289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Various proteins introduced into living modified organism (LMO) crops function in plant defense mechanisms against target insect pests or herbicides. This study analyzed the antifungal effects of an introduced LMO protein, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) from Agrobacterium sp. strain CP4 (CP4-EPSPS). Pure recombinant CP4-EPSPS protein, expressed in Escherichia coli, inhibited the growth of human and plant fungal pathogens (Candida albicans, C. tropicalis, C. krusei, Colletotrichum gloeosporioides, Fusarium solani, F. graminearum, and Trichoderma virens), at minimum inhibitory concentrations (MICs) that ranged from 62.5 to 250 µg/mL. It inhibited fungal spore germination as well as cell proliferation on C. gloeosporioides. Rhodamine-labeled CP4-EPSPS accumulated on the fungal cell wall and within intracellular cytosol. In addition, the protein induced uptake of SYTOX Green into cells, but not into intracellular mitochondrial reactive oxygen species (ROS), indicating that its antifungal action was due to inducing the permeability of the fungal cell wall. Its antifungal action showed cell surface damage, as observed from fungal cell morphology. This study provided information on the effects of the LMO protein, EPSPS, on fungal growth.
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Affiliation(s)
- Seong-Cheol Park
- Department of Chemical Engineering, Sunchon National University, Suncheon 38286, Republic of Korea
| | - Hye Song Lim
- LMO Team, National Institute of Ecology (NIE), Seocheon 33657, Republic of Korea
- Department of Horticulture Industry, Wonkwang University, Iksan 54538, Republic of Korea
| | - Seong-Eun Mun
- Department of Biological Science, College of Natural Science, Wonkwang University, Iksan 54538, Republic of Korea
| | - Young Jun Jung
- LMO Team, National Institute of Ecology (NIE), Seocheon 33657, Republic of Korea
| | - A-Mi Yoon
- LMO Team, National Institute of Ecology (NIE), Seocheon 33657, Republic of Korea
- Division of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Hyosuk Son
- Department of Exhibition and Education, National Marine Biodiversity Institute of Korea, Seocheon 33662, Republic of Korea
| | - Chul Min Kim
- Department of Horticulture Industry, Wonkwang University, Iksan 54538, Republic of Korea
| | - Young-Kug Choo
- Department of Biological Science, College of Natural Science, Wonkwang University, Iksan 54538, Republic of Korea
| | - Jung Ro Lee
- LMO Team, National Institute of Ecology (NIE), Seocheon 33657, Republic of Korea
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4
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Russell BL, Ntwasa M. Expression, purification, and characterisation of the p53 binding domain of Retinoblastoma binding protein 6 (RBBP6). PLoS One 2023; 18:e0277478. [PMID: 36763571 PMCID: PMC9916574 DOI: 10.1371/journal.pone.0277478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 10/28/2022] [Indexed: 02/11/2023] Open
Abstract
RBBP6 is a 250 kDa eukaryotic protein known to be a negative regulator of p53 and essential for embryonic development. Furthermore, RBBP6 is a critical element in carcinogenesis and has been identified as a potential biomarker for certain cancers. RBBP6's ability to interact with p53 and cause its degradation makes it a potential drug target in cancer therapy. Therefore, a better understating of the p53 binding domain of RBBP6 is needed. This study presents a three-part purification protocol for the polyhistidine-tagged p53 binding domain of RBBP6, expressed in Escherichia coli bacterial cells. The purified recombinant domain was shown to have structure and is functional as it could bind endogenous p53. We characterized it using clear native PAGE and far-UV CD and found that it exists in a single form, most likely monomer. We predict that its secondary structure is predominantly random coil with 19% alpha-helices, 9% beta-strand and 14% turns. When we exposed the recombinant domain to increasing temperature or known denaturants, our investigation suggested that the domain undergoes relatively small structural changes, especially with increased temperature. Moreover, we notice a high percentage recovery after returning the domain close to starting conditions. The outcome of this study is a pure, stable, and functional recombinant RBBP6-p53BD that is primarily intrinsically disordered.
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Affiliation(s)
- Bonnie L. Russell
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Florida, Roodepoort, South Africa
- Innovation Hub, Buboo (Pty) Ltd, Pretoria, South Africa
| | - Monde Ntwasa
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Florida, Roodepoort, South Africa
- * E-mail:
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5
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Cockburn DW, Wilkens C, Svensson B. Affinity Electrophoresis for Analysis of Catalytic Module-Carbohydrate Interactions. Methods Mol Biol 2023; 2657:91-101. [PMID: 37149524 DOI: 10.1007/978-1-0716-3151-5_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Affinity electrophoresis has long been used to study the interaction between proteins and large soluble ligands. The technique has been found to have great utility for the examination of polysaccharide binding by proteins, particularly carbohydrate-binding modules (CBMs). In recent years carbohydrate surface binding sites of proteins, mostly enzymes, have also been investigated by this method. Here we describe a protocol for identifying binding interactions between enzyme catalytic modules and a variety of carbohydrate ligands.
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Affiliation(s)
- Darrell W Cockburn
- Department of Food Science, The Pennsylvania State University, University Park, PA, USA.
| | - Casper Wilkens
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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Recombinant Cathepsin L of Tribolium castaneum and Its Potential in the Hydrolysis of Immunogenic Gliadin Peptides. Int J Mol Sci 2022; 23:ijms23137001. [PMID: 35806001 PMCID: PMC9266932 DOI: 10.3390/ijms23137001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 02/04/2023] Open
Abstract
Wheat gliadins contain a large amount of glutamine- and proline-rich peptides which are not hydrolyzed by human digestive peptidases and can cause autoimmune celiac disease and other forms of gluten intolerance in predisposed people. Peptidases that efficiently cleave such immunogenic peptides can be used in enzyme therapy. The stored product insect pest Tribolium castaneum efficiently hydrolyzes gliadins. The main digestive peptidase of T. castaneum is cathepsin L, which is from the papain C1 family with post-glutamine cleavage activity. We describe the isolation and characterization of T. castaneum recombinant procathepsin L (rpTcCathL1, NP_001164001), which was expressed in Pichia pastoris cells. The activation of the proenzyme was conducted by autocatalytic processing. The effects of pH and proenzyme concentration in the reaction mixture on the processing were studied. The mature enzyme retained high activity in the pH range from 5.0 to 9.0 and displayed high pH-stability from 4.0 to 8.0 at 20 °C. The enzyme was characterized according to electrophoretic mobility under native conditions, activity and stability at various pH values, a sensitivity to various inhibitors, and substrate specificity, and its hydrolytic effect on 8-, 10-, 26-, and 33-mer immunogenic gliadins peptides was demonstrated. Our results show that rTcCathL1 is an effective peptidase that can be used to develop a drug for the enzyme therapy of various types of gluten intolerance.
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7
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Arakawa T, Nakagawa M, Tomioka Y, Sakuma C, Li C, Sato T, Sato R, Shibata T, Kurosawa Y, Akuta T. Gel-electrophoresis based method for biomolecular interaction. Methods Cell Biol 2022; 169:67-95. [PMID: 35623712 DOI: 10.1016/bs.mcb.2021.12.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Electrophoresis is one of the most important analytical technologies for characterization of macromolecules and their interactions. Among them, native gel electrophoresis is used to analyze the macromolecules in the native structure. It differs in principle and information from those obtained by sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) or blue native polyacrylamide gel electrophoresis (BN-PAGE). SDS-PAGE is carried out in the presence of strong denaturant, SDS, while BN-PAGE is done in the presence of negatively charged dye, e.g., Coomassie brilliant blue, G-250. Here, we describe native gel electrophoresis using agarose gel and a buffer at pH 6.1 composed of histidine and 2-(N-morpholino) ethanesulfonic acid. First, a protocol for vertical and horizontal formats of agarose native gel electrophoresis is described followed by different staining procedures. Then, various examples obtained using the developed procedure will be shown to demonstrate how the technology can be applied to specific cases and the advantages or caveats of the present technology.
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Affiliation(s)
- Tsutomu Arakawa
- Alliance Protein Laboratories, San Diego, CA, United States.
| | - Masataka Nakagawa
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, Japan
| | - Yui Tomioka
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, Japan
| | - Chiaki Sakuma
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, Japan
| | - Cynthia Li
- HTL Biosolutions Inc., Camarillo, CA, United States
| | - Tomomi Sato
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, Japan
| | - Ryo Sato
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, Japan
| | - Takashi Shibata
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, Japan
| | - Yasunori Kurosawa
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, Japan; Abwiz Bio Inc., San Diego, CA, United States
| | - Teruo Akuta
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, Japan.
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8
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A New Method to Characterize Conformation-Specific Antibody by a Combination of Agarose Native Gel Electrophoresis and Contact Blotting. Antibodies (Basel) 2022; 11:antib11020036. [PMID: 35645209 PMCID: PMC9149980 DOI: 10.3390/antib11020036] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
In this study, we review the agarose native gel electrophoresis that separates proteins and macromolecular complexes in their native state and transfer of the separated proteins from the agarose gel to membranes by contact blotting which retains the native state of these structures. Green fluorescent protein showed functional state both on agarose gel and blotted membrane. Based on the combined procedures, we discovered conformation-specific monoclonal antibodies against PLXDC2 and SARS-CoV-2 spike protein.
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9
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Naturally occurring deamidated triosephosphate isomerase is a promising target for cell-selective therapy in cancer. Sci Rep 2022; 12:4028. [PMID: 35256749 PMCID: PMC8901631 DOI: 10.1038/s41598-022-08051-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/28/2022] [Indexed: 11/08/2022] Open
Abstract
Human triosephosphate isomerase (HsTIM) is a central glycolytic enzyme and is overexpressed in cancer cells with accelerated glycolysis. Triple-negative breast cancer is highly dependent on glycolysis and is typically treated with a combination of surgery, radiation therapy, and chemotherapy. Deamidated HsTIM was recently proposed as a druggable target. Although thiol-reactive drugs affect cell growth in deamidated HsTIM-complemented cells, the role of this protein as a selective target has not been demonstrated. To delve into the usefulness of deamidated HsTIM as a selective target, we assessed its natural accumulation in breast cancer cells. We found that deamidated HsTIM accumulates in breast cancer cells but not in noncancerous cells. The cancer cells are selectively programmed to undergo cell death with thiol-reactive drugs that induced the production of methylglyoxal (MGO) and advanced glycation-end products (AGEs). In vivo, a thiol-reactive drug effectively inhibits the growth of xenograft tumors with an underlying mechanism involving deamidated HsTIM. Our findings demonstrate the usefulness of deamidated HsTIM as target to develop new therapeutic strategies for the treatment of cancers and other pathologies in which this post translationally modified protein accumulates.
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Biochemical and subcellular characterization of a squid hnRNPA/B-like protein 2 in osmotic stress activated cells reflects molecular properties conserved in this protein family. Mol Biol Rep 2022; 49:4257-4268. [PMID: 35192131 DOI: 10.1007/s11033-022-07260-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 02/10/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND We have identified endogenous p65 to be an SDS-stable dimer protein composed of ~ 37 kDa hnRNPA/B-like subunits. We have investigated molecular properties involved in the stability of dimeric form, and their regulation in the transition between monomeric and dimeric forms of hnRNPA/B-like protein 2. We also investigated a cellular property conserved between squid hnRNPA/B-like protein 2 and human hnRNPA1 protein in a neuronal context. METHODS AND RESULTS Here we show biochemical properties of a recombinant hnRNPA/B-like protein 2 (rP2) in vitro experiments, as one of p65 subunit. We found that interaction between rP2 and RNA molecules interfered with the dynamics of rP2 dimers formation, involved in disulfide bonds and/or postranslational alterations in distinct stage of SDS-stable dimers formation. In addition, we have performed immunofluorescence in SH-SY5Y cells and observed that the pEGFP-P2 fusion protein was expressed in the nucleus, similar to what is observed for human hnRNPA1 protein. CONCLUSION Our results reinforce the idea that p65 is an SDS-stable dimer. Thus, a deeper understanding between monomeric and dimeric transition dynamic is critical into evolution of several neurodegenerative disease.
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Dvoryakova EA, Vinokurov KS, Tereshchenkova VF, Dunaevsky YE, Belozersky MA, Oppert B, Filippova IY, Elpidina EN. Primary digestive cathepsins L of Tribolium castaneum larvae: Proteomic identification, properties, comparison with human lysosomal cathepsin L. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 140:103679. [PMID: 34763092 DOI: 10.1016/j.ibmb.2021.103679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
We previously described the most highly expressed enzymes from the gut of the red flour beetle, Tribolium castaneum, as cathepsins L. In the present study, two C1 family-specific cysteine cathepsin L enzymes from the larval midgut were isolated and identified using MALDI-TOF MS analysis. The isolated T. castaneum cathepsins were characterized according to their specificity against chromogenic and fluorogenic peptide substrates, and the most efficiently hydrolyzed substrate was Z-FR-pNA with Arg in the P1 subsite. The specificity of insect digestive cathepsins was compared with human lysosomal cathepsin L, the well-studied peptidase of the C1 family cathepsins. T. castaneum digestive cathepsins efficiently hydrolyzed substrates with small and uncharged amino acid residues at P1 (Ala, Gln) more than human cathepsin L. In particular, these insect digestive cathepsins cleaved with higher efficiency the analogs of immunogenic peptides of gliadins, which contribute to autoimmune celiac disease in susceptible people, and thus insect enzymes may be useful in enzymatic treatments for this disease. A bioinformatic study supported by the proteomic analysis of the primary structures of the isolated cathepsins was used to compare tertiary models. The phylogenetic analysis of coleopteran and human cathepsins from the L subfamily indicated that insect digestive cathepsins grouped separately from lysosomal cathepsins.
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Affiliation(s)
- E A Dvoryakova
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - K S Vinokurov
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Czech Republic, Branišovská 1160/31, České Budějovice, 370 05, Czech Republic
| | - V F Tereshchenkova
- Department of Chemistry, Moscow State University, Moscow, 119991, Russia
| | - Y E Dunaevsky
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - M A Belozersky
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - B Oppert
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, Manhattan, KS, 66502, USA.
| | - I Y Filippova
- Department of Chemistry, Moscow State University, Moscow, 119991, Russia
| | - E N Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
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12
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Okumura K, Maruyama Y, Takase R, Mikami B, Murata K, Hashimoto W. The role of calcium binding to the EF-hand-like motif in bacterial solute-binding protein for alginate import. Biosci Biotechnol Biochem 2021; 85:2410-2419. [PMID: 34610097 DOI: 10.1093/bbb/zbab170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/23/2021] [Indexed: 11/14/2022]
Abstract
Gram-negative Sphingomonas sp. A1 incorporates acidic polysaccharide alginate into the cytoplasm via a cell-surface alginate-binding protein (AlgQ2)-dependent ATP-binding cassette transporter (AlgM1M2SS). We investigated the function of calcium bound to the EF-hand-like motif in AlgQ2 by introducing mutations at the calcium-binding site. The X-ray crystallography of the AlgQ2 mutant (D179A/E180A) demonstrated the absence of calcium binding and significant disorder of the EF-hand-like motif. Distinct from the wild-type AlgQ2, the mutant was quite unstable at temperature of strain A1 growth, although unsaturated alginate oligosaccharides stabilized the mutant by formation of substrate/protein complex. In the assay of ATPase and alginate transport by AlgM1M2SS reconstructed in the liposome, the wild-type and mutant AlgQ2 induced AlgM1M2SS ATPase activity in the presence of unsaturated alginate tetrasaccharide. These results indicate that the calcium bound to EF-hand-like motif stabilizes the substrate-unbound AlgQ2 but is not required for the complexation of substrate-bound AlgQ2 and AlgM1M2SS.
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Affiliation(s)
- Kenji Okumura
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Yukie Maruyama
- Laboratory of Food Microbiology, Department of Life Science, Faculty of Science and Engineering, Setsunan University, Neyagawa, Osaka, Japan
| | - Ryuichi Takase
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Bunzo Mikami
- Laboratory of Metabolic Sciences of Forest Plants and Microorganisms, Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, Japan
| | - Kousaku Murata
- Laboratory of Food Microbiology, Department of Life Science, Faculty of Science and Engineering, Setsunan University, Neyagawa, Osaka, Japan
| | - Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
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13
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Weismiller HA, Holub TJ, Krzesinski BJ, Margittai M. A thiol-based intramolecular redox switch in four-repeat tau controls fibril assembly and disassembly. J Biol Chem 2021; 297:101021. [PMID: 34339733 PMCID: PMC8387771 DOI: 10.1016/j.jbc.2021.101021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/17/2021] [Accepted: 07/28/2021] [Indexed: 02/06/2023] Open
Abstract
Oxidative stress has been implicated in the pathogenesis and progression of several tauopathies, including Alzheimer's disease. The deposition of fibrillar inclusions made of tau protein is one of the pathological hallmarks of these disorders. Although it is becoming increasingly evident that the specific fibril structure may vary from one tauopathy to another and it is recognized that different types of isoforms (three-repeat and four-repeat tau) can be selectively deposited, little is known about the role oxidation may play in aggregation. Four-repeat tau contains two cysteines that can form an intramolecular disulfide bond, resulting in a structurally restrained compact monomer. There is discrepancy as to whether this monomer can aggregate or not. Using isolated four-repeat tau monomers (htau40) with intramolecular disulfide bonds, we demonstrate that these proteins form fibrils. The fibrils are less stable than fibrils formed under reducing conditions but are highly effective in seeding oxidized tau monomers. Conversely, a strong seeding barrier prevents incorporation of reduced tau monomers, tau mimics in which the cysteines have been replaced by alanines or serines, and three-repeat tau (htau23), a single-cysteine isoform. The barrier also holds true when seed and monomer types are reversed, indicating that oxidized and reduced tau are incompatible with each other. Surprisingly, fibrils composed of compact tau disaggregate upon reduction, highlighting the importance of the intramolecular disulfide bond for fibril stability. The findings uncover a novel binary redox switch that controls the aggregation and disaggregation of these fibrils and extend the conformational spectrum of tau aggregates.
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Affiliation(s)
- Hilary A Weismiller
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - Tyler J Holub
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - Brad J Krzesinski
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - Martin Margittai
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA.
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Sopoušek J, Věžník J, Houser J, Skládal P, Lacina K. Crucial factors governing the electrochemical impedance on protein-modified surfaces. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138616] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Park SC, Pyun JW, Jeong YJ, Park SH, Kim S, Kim YH, Lee JR, Kim CY, Jeong JC. Overexpression of VlPRX21 and VlPRX35 genes in Arabidopsis plants leads to bioconversion of trans-resveratrol to δ-viniferin. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:556-563. [PMID: 33773231 DOI: 10.1016/j.plaphy.2021.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Stilbenes, including resveratrol and viniferins, a small family of polyphenols, are considered the most important phytoalexin group in Vitis species. In a previous study, we found that co-treatment of methyl jasmonate (MJ) and stevioside (STE) resulted in enhanced extracellular production of viniferins in grapevine cell suspension cultures. Thus, to further understand the mechanisms of viniferin production in grapevine cell cultures, we performed transcriptome analysis and isolated seven candidates of grapevine peroxidase genes (VlAPX6, VlGPX5, VlPRX13, VlPRX21, VlPRX35, VlPRX40, and VlPRX50). Bioconversion of trans-resveratrol to δ-viniferin was examined using crude protein extracts isolated from agroinfiltration-based transient expression of VlPRXs in Nicotiana benthamiana. In addition, we found that crude protein extracts from VlPRX21-, VlPRX35-, and VlPRX40-overexpressing (OX) transgenic Arabidopsis plants led to the conversion of trans-resveratrol to δ-viniferin. We found that in vitro experiments with crude protein extracts from VlPRX21-OX and VlPRX35-OX Arabidopsis plants catalyzed the dimerization of trans-resveratrol to δ-viniferin. Our results suggest that VlPRX21 and VlPRX35 encode functional grapevine class III peroxidases and catalyze the oxidative dimerization of trans-resveratrol to form δ-viniferin in grapevine.
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Affiliation(s)
- Sung-Chul Park
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea
| | - Jang Won Pyun
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea; Department of Pharmaceutical Engineering, Daegu Haany University, Daegu, 38610, Republic of Korea
| | - Yu Jeong Jeong
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea
| | - Su Hyun Park
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea; Department of Plant Biotechnology, College of Agriculture and Life Science, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Soyoung Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea; Department of Plant Biotechnology, College of Agriculture and Life Science, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Yun-Hee Kim
- Department of Biology Education, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Jong Rok Lee
- Department of Pharmaceutical Engineering, Daegu Haany University, Daegu, 38610, Republic of Korea
| | - Cha Young Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea.
| | - Jae Cheol Jeong
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea.
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The crystal structure of a 250-kDa heterotetrameric particle explains inhibition of sheddase meprin β by endogenous fetuin-B. Proc Natl Acad Sci U S A 2021; 118:2023839118. [PMID: 33782129 DOI: 10.1073/pnas.2023839118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Meprin β (Mβ) is a multidomain type-I membrane metallopeptidase that sheds membrane-anchored substrates, releasing their soluble forms. Fetuin-B (FB) is its only known endogenous protein inhibitor. Herein, we analyzed the interaction between the ectodomain of Mβ (MβΔC) and FB, which stabilizes the enzyme and inhibits it with subnanomolar affinity. The MβΔC:FB crystal structure reveals a ∼250-kDa, ∼160-Å polyglycosylated heterotetrameric particle with a remarkable glycan structure. Two FB moieties insert like wedges through a "CPDCP trunk" and two hairpins into the respective peptidase catalytic domains, blocking the catalytic zinc ions through an "aspartate switch" mechanism. Uniquely, the active site clefts are obstructed from subsites S4 to S10', but S1 and S1' are spared, which prevents cleavage. Modeling of full-length Mβ reveals an EGF-like domain between MβΔC and the transmembrane segment that likely serves as a hinge to transit between membrane-distal and membrane-proximal conformations for inhibition and catalysis, respectively.
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Filippova IY, Dvoryakova EA, Sokolenko NI, Simonyan TR, Tereshchenkova VF, Zhiganov NI, Dunaevsky YE, Belozersky MA, Oppert B, Elpidina EN. New Glutamine-Containing Substrates for the Assay of Cysteine Peptidases From the C1 Papain Family. Front Mol Biosci 2020; 7:578758. [PMID: 33195423 PMCID: PMC7643032 DOI: 10.3389/fmolb.2020.578758] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/07/2020] [Indexed: 01/06/2023] Open
Abstract
New substrates with glutamine in the P1-position are introduced for the assay of peptidases from the C1 papain family, with a general formula of Glp-Phe-Gln-X, where Glp is pyroglutamyl and X is pNA (p-nitroanilide) or AMC (4-amino-7-methylcoumaride). The substrates have a simple structure, and C1 cysteine peptidases of various origins cleave them with high efficiency. The main advantage of the substrates is their selectivity for cysteine peptidases of the C1 family. Peptidases of other clans, including serine trypsin-like peptidases, do not cleave glutamine-containing substrates. We demonstrate that using Glp-Phe-Gln-pNA in combination with a commercially available substrate, Z-Arg-Arg-pNA, provided differential determination of cathepsins L and B. In terms of specific activity and kinetic parameters, the proposed substrates offer improvement over the previously described alanine-containing prototypes. The efficiency and selectivity of the substrates was demonstrated by the example of chromatographic and electrophoretic analysis of a multi-enzyme digestive complex of stored product pests from the Tenebrionidae family.
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Affiliation(s)
- Irina Y Filippova
- Division of Natural Compounds, Department of Chemistry, Moscow State University, Moscow, Russia
| | - Elena A Dvoryakova
- Department of Plant Proteins, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Nikolay I Sokolenko
- Laboratory of Protein Chemistry, Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | - Tatiana R Simonyan
- Division of Natural Compounds, Department of Chemistry, Moscow State University, Moscow, Russia
| | | | - Nikita I Zhiganov
- Division of Entomology, Faculty of Biology, Moscow State University, Moscow, Russia
| | - Yakov E Dunaevsky
- Department of Plant Proteins, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Mikhail A Belozersky
- Department of Plant Proteins, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Brenda Oppert
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, Manhattan, KS, United States
| | - Elena N Elpidina
- Department of Plant Proteins, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
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18
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Juhász T, Kardos J, Dürvanger Z, Harmat V, Liliom K. Comparison of ligand binding and conformational stability of human calmodulin with its homolog from the malaria parasite Plasmodium falciparum. FASEB Bioadv 2020; 2:489-505. [PMID: 32821880 PMCID: PMC7429351 DOI: 10.1096/fba.2020-00013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 03/24/2020] [Accepted: 06/16/2020] [Indexed: 11/11/2022] Open
Abstract
Calmodulin (CaM), the key calcium sensor of eukaryotic cells regulating a great number of target proteins, belongs to the most conserved proteins. We compared function and properties of CaMs from two evolutionarily distant species, the human (Homo sapiens) representing vertebrates, and the malaria parasite Plasmodium falciparum (Pf). The biophysical characterization revealed higher stability of Pf CaM attributed to the more stable C-terminal domain in both Ca2+ free and saturated states. In vitro binding and functional assays demonstrated that human and Pf CaM exhibit similar biochemical features involving small molecule inhibitor binding and target enzyme activation as illustrated by comparable affinities differing only within a factor of three. It has been reported that CaM antagonists proved to be antimalarials, so Pf CaM could be a potential target to combat malaria parasites. Indeed, we observed that phenotypically active compounds from the Malaria Box could show inhibitory action on Pf CaM, among them the most potent exhibited comparable inhibition to known antagonists of vertebrate CaM. However, based on the minor binding differences in Pf CaM to human CaM, we conclude that CaM is an unsuited target for human intervention against malaria, due to the likely interference with the host protein.
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Affiliation(s)
- Tünde Juhász
- Institute of Materials and Environmental ChemistryResearch Centre for Natural SciencesBudapestHungary
| | - József Kardos
- Department of BiochemistryInstitute of BiologyELTE Eötvös Loránd UniversityBudapestHungary
| | - Zsolt Dürvanger
- Laboratory of Structural Chemistry and BiologyInstitute of ChemistryEötvös Loránd UniversityBudapestHungary
| | - Veronika Harmat
- Laboratory of Structural Chemistry and BiologyInstitute of ChemistryEötvös Loránd UniversityBudapestHungary
- MTA‐ELTE Protein Modelling Research GroupBudapestHungary
| | - Károly Liliom
- Department of Biophysics and Radiation BiologyFaculty of MedicineSemmelweis UniversityBudapestHungary
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19
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Butz ZJ, Borgognoni K, Nemeth R, Nilsson ZN, Ackerson CJ. Metalloid Reductase Activity Modified by a Fused Se 0 Binding Peptide. ACS Chem Biol 2020; 15:1987-1995. [PMID: 32568515 DOI: 10.1021/acschembio.0c00387] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A selenium nanoparticle binding peptide was isolated from a phage display library and genetically fused to a metalloid reductase that reduces selenite (SeO32-) to a Se0 nanoparticle (SeNP) form. The fusion of the Se binding peptide to the metalloid reductase regulates the size of the resulting SeNP to ∼35 nm average diameter, where without the peptide, SeNPs grow to micron sized polydisperse precipitates. The SeNP product remains associated with the enzyme/peptide fusion. The Se binding peptide fusion to the enzyme increases the enzyme's SeO32- reductase activity. Size control of particles was diminished if the Se binding peptide was only added exogenously to the reaction mixture. The enzyme-peptide construct shows preference for binding smaller SeNPs. The peptide-SeNP interaction is attributed to His based ligation that results in a peptide conformational change on the basis of Raman spectroscopy.
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Affiliation(s)
- Zachary J. Butz
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Kanda Borgognoni
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Richard Nemeth
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Zach N. Nilsson
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Christopher J. Ackerson
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
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20
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Yeast Mitochondrial Translation Initiation Factor 3 Interacts with Pet111p to Promote COX2 mRNA Translation. Int J Mol Sci 2020; 21:ijms21103414. [PMID: 32408541 PMCID: PMC7279496 DOI: 10.3390/ijms21103414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial genomes code for several core components of respiratory chain complexes. Thus, mitochondrial translation is of great importance for the organelle as well as for the whole cell. In yeast, mitochondrial translation initiation factor 3, Aim23p, is not essential for the organellar protein synthesis; however, its absence leads to a significant quantitative imbalance of the mitochondrial translation products. This fact points to a possible specific action of Aim23p on the biosynthesis of some mitochondrial protein species. In this work, we examined such peculiar effects of Aim23p in relation to yeast mitochondrial COX2 mRNA translation. We show that Aim23p is indispensable to this process. According to our data, this is mediated by Aimp23p interaction with the known specific factor of the COX2 mRNA translation, Pet111p. If there is no Aim23p in the yeast cells, an increased amount of Pet111p ensures proper COX2 mRNA translation. Our results demonstrate the additional non-canonical function of initiation factor 3 in yeast mitochondrial translation.
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21
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Li C, Akuta T, Nakagawa M, Sato T, Shibata T, Maruyama T, Okumura C, Kurosawa Y, Arakawa T. Agarose native gel electrophoresis for characterization of antibodies. Int J Biol Macromol 2020; 151:885-890. [DOI: 10.1016/j.ijbiomac.2020.02.185] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/14/2020] [Accepted: 02/16/2020] [Indexed: 12/21/2022]
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Native aggregation is a common feature among triosephosphate isomerases of different species. Sci Rep 2020; 10:1338. [PMID: 31992784 PMCID: PMC6987189 DOI: 10.1038/s41598-020-58272-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 01/13/2020] [Indexed: 12/16/2022] Open
Abstract
Triosephosphate isomerase (TIM) is an enzyme of the glycolysis pathway which exists in almost all types of cells. Its structure is the prototype of a motif called TIM-barrel or (α/β)8 barrel, which is the most common fold of all known enzyme structures. The simplest form in which TIM is catalytically active is a homodimer, in many species of bacteria and eukaryotes, or a homotetramer in some archaea. Here we show that the purified homodimeric TIMs from nine different species of eukaryotes and one of an extremophile bacterium spontaneously form higher order aggregates that can range from 3 to 21 dimers per macromolecular complex. We analysed these aggregates with clear native electrophoresis with normal and inverse polarity, blue native polyacrylamide gel electrophoresis, liquid chromatography, dynamic light scattering, thermal shift assay and transmission electron and fluorescence microscopies, we also performed bioinformatic analysis of the sequences of all enzymes to identify and predict regions that are prone to aggregation. Additionally, the capacity of TIM from Trypanosoma brucei to form fibrillar aggregates was characterized. Our results indicate that all the TIMs we studied are capable of forming oligomers of different sizes. This is significant because aggregation of TIM may be important in some of its non-catalytic moonlighting functions, like being a potent food allergen, or in its role associated with Alzheimer’s disease.
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Tereshchenkova VF, Klyachko EV, Benevolensky SV, Belozersky MA, Dunaevsky YE, Filippova IY, Elpidina EN. Preparation and Purification of Recombinant Dipeptidyl Peptidase 4 from Tenebrio molitor. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819030141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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24
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Korotych O, Mondal J, Gattás-Asfura KM, Hendricks J, Bruce BD. Evaluation of commercially available styrene-co-maleic acid polymers for the extraction of membrane proteins from spinach chloroplast thylakoids. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2018.10.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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25
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Park SC, Kim IR, Hwang JE, Kim JY, Jung YJ, Choi W, Lee Y, Jang MK, Lee JR. Functional Mechanisms Underlying the Antimicrobial Activity of the Oryza sativa Trx-like Protein. Int J Mol Sci 2019; 20:ijms20061413. [PMID: 30897830 PMCID: PMC6471494 DOI: 10.3390/ijms20061413] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/13/2019] [Accepted: 03/19/2019] [Indexed: 12/14/2022] Open
Abstract
Plants are constantly subjected to a variety of environmental stresses and have evolved regulatory responses to overcome unfavorable conditions that might reduce or adversely change a plant’s growth or development. Among these, the regulated production of reactive oxygen species (ROS) as a signaling molecule occurs during plant development and pathogen defense. This study demonstrates the possible antifungal activity of Oryza sativa Tetratricopeptide Domain-containing thioredoxin (OsTDX) protein against various fungal pathogens. The transcription of OsTDX was induced by various environmental stresses known to elicit the generation of ROS in plant cells. OsTDX protein showed potent antifungal activity, with minimum inhibitory concentrations (MICs) against yeast and filamentous fungi ranging between 1.56 and 6.25 and 50 and 100 µg/mL, respectively. The uptake of SYTOX-Green into fungal cells and efflux of calcein from artificial fungus-like liposomes suggest that its killing mechanism involves membrane permeabilization and damage. In addition, irregular blebs and holes apparent on the surfaces of OsTDX-treated fungal cells indicate the membranolytic action of this protein. Our results suggest that the OsTDX protein represents a potentially useful lead for the development of pathogen-resistant plants.
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Affiliation(s)
- Seong-Cheol Park
- Department of Polymer Science and Engineering, Sunchon National University, Suncheon 57922, Korea.
| | - Il Ryong Kim
- National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon-gun 33657, Korea.
- Division of Applied Life Science (BK21+ Program) and PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Jung Eun Hwang
- National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon-gun 33657, Korea.
| | - Jin-Young Kim
- Department of Polymer Science and Engineering, Sunchon National University, Suncheon 57922, Korea.
| | - Young Jun Jung
- National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon-gun 33657, Korea.
| | - Wonkyun Choi
- National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon-gun 33657, Korea.
| | - Yongjae Lee
- Department of Nutrition and Food Science, Texas A&M University, College Station, TX 77843, USA.
| | - Mi-Kyeong Jang
- Department of Polymer Science and Engineering, Sunchon National University, Suncheon 57922, Korea.
- The Research Institute for Sanitation and Environment of Coastal Areas, Sunchon National University, Suncheon 57922, Korea.
| | - Jung Ro Lee
- National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon-gun 33657, Korea.
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Elpidina EN, Semashko TA, Smirnova YA, Dvoryakova EA, Dunaevsky YE, Belozersky MA, Serebryakova MV, Klyachko EV, Abd El-Latif AO, Oppert B, Filippova IY. Direct detection of cysteine peptidases for MALDI-TOF MS analysis using fluorogenic substrates. Anal Biochem 2018; 567:45-50. [PMID: 30528915 DOI: 10.1016/j.ab.2018.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/19/2018] [Accepted: 12/03/2018] [Indexed: 01/12/2023]
Abstract
A method is described for the direct detection of unstable cysteine peptidase activity in polyacrylamide gels after native electrophoresis using new selective fluorogenic peptide substrates, pyroglutamyl-phenylalanyl-alanyl-4-amino-7-methylcoumaride (Glp-Phe-Ala-AMC) and pyroglutamyl-phenylalanyl-alanyl-4-amino-7-trifluoromethyl-coumaride (Glp-Phe-Ala-AFC). The detection limit of the model enzyme papain was 17 pmol (0.29 μg) for Glp-Phe-Ala-AMC and 43 pmol (0.74 μg) for Glp-Phe-Ala-AFC, with increased sensitivity and selectivity compared to the traditional method of protein determination with Coomassie G-250 staining or detection of activity using chromogenic substrates. Using this method, we easily identified the target digestive peptidases of Tenebrio molitor larvae by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) analysis. The method offers simplicity, high sensitivity, and selectivity compared to traditional methods for improved identification of unstable cysteine peptidases in multi-component biological samples.
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Affiliation(s)
- Elena N Elpidina
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Tatiana A Semashko
- Department of Chemistry, Moscow State University, Moscow, 119991, Russia
| | - Yulia A Smirnova
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Elena A Dvoryakova
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Yakov E Dunaevsky
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Mikhail A Belozersky
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Marina V Serebryakova
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Elena V Klyachko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Ashraf O Abd El-Latif
- Department of Plant Protection, Faculty of Agriculture, Sohag University, Sohag, Egypt
| | - Brenda Oppert
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, Manhattan, KS, 66502, USA.
| | - Irina Y Filippova
- Department of Chemistry, Moscow State University, Moscow, 119991, Russia
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Thomas CM, Timson DJ. Calmodulins from Schistosoma mansoni: Biochemical analysis and interaction with IQ-motifs from voltage-gated calcium channels. Cell Calcium 2018; 74:1-13. [DOI: 10.1016/j.ceca.2018.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/08/2018] [Accepted: 05/16/2018] [Indexed: 01/27/2023]
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28
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Park SC, Kim IR, Kim JY, Lee Y, Kim EJ, Jung JH, Jung YJ, Jang MK, Lee JR. Molecular mechanism of Arabidopsis thaliana profilins as antifungal proteins. Biochim Biophys Acta Gen Subj 2018; 1862:2545-2554. [PMID: 30056100 DOI: 10.1016/j.bbagen.2018.07.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 07/18/2018] [Accepted: 07/24/2018] [Indexed: 12/23/2022]
Abstract
BACKGROUND It remains an open question whether plant phloem sap proteins are functionally involved in plant defense mechanisms. METHODS The antifungal effects of two profilin proteins from Arabidopsis thaliana, AtPFN1 and AtPFN2, were tested against 11 molds and 4 yeast fungal strains. Fluorescence profiling, biophysical, and biochemical analyses were employed to investigate their antifungal mechanism. RESULTS Recombinant AtPFN1 and AtPFN2 proteins, expressed in Escherichia coli, inhibited the cell growth of various pathogenic fungal strains at concentrations ranging from 10 to 160 μg/mL. The proteins showed significant intracellular accumulation and cell-binding affinity for fungal cells. Interestingly, the AtPFN proteins could penetrate the fungal cell wall and membrane and act as inhibitors of fungal growth via generation of cellular reactive oxygen species and mitochondrial superoxide. This triggered the AtPFN variant-induced cell apoptosis, resulting in morphological changes in the cells. CONCLUSION PFNs may play a critical role as antifungal proteins in the Arabidopsis defense system against fungal pathogen attacks. GENERAL SIGNIFICANCE The present study indicates that two profilin proteins, AtPFN1 and AtPFN2, can act as natural antimicrobial agents in the plant defense system.
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Affiliation(s)
- Seong-Cheol Park
- Department of Polymer Science and Engineering, Sunchon National University, Suncheon, Jeonnam 57922, Republic of Korea
| | - Il Ryong Kim
- National Institute of Ecology (NIE), Seocheon, Choongnam 33657, Republic of Korea; Division of Applied Life Science and PMBBRC, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Jin-Young Kim
- Department of Polymer Science and Engineering, Sunchon National University, Suncheon, Jeonnam 57922, Republic of Korea
| | - Yongjae Lee
- Department of Nutrition and Food Science, Texas A&M University, College Station, TX 77843, USA; Goseong Agricultural Development/Technology Center, Goseong-gun, Gyeongsangnam-do 52930, Republic of Korea
| | - Eun-Ji Kim
- Department of Polymer Science and Engineering, Sunchon National University, Suncheon, Jeonnam 57922, Republic of Korea
| | - Ji Hyun Jung
- Division of Applied Life Science and PMBBRC, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Department of Nutrition and Food Science, Texas A&M University, College Station, TX 77843, USA
| | - Young Jun Jung
- National Institute of Ecology (NIE), Seocheon, Choongnam 33657, Republic of Korea
| | - Mi-Kyeong Jang
- Department of Polymer Science and Engineering, Sunchon National University, Suncheon, Jeonnam 57922, Republic of Korea.
| | - Jung Ro Lee
- National Institute of Ecology (NIE), Seocheon, Choongnam 33657, Republic of Korea.
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29
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Onopiuk A, Półtorak A, Wierzbicka A. The impact of muscle and aging time on meat tenderness in the carcasses of Limousin × Holstein-Friesian crossbred bulls. J FOOD PROCESS PRES 2018. [DOI: 10.1111/jfpp.13619] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Anna Onopiuk
- Department of Technique and Food Development; Faculty of Human Nutrition and Consumer Sciences, Warsaw University of Life Sciences; Warsaw 02-776 Poland
| | - Andrzej Półtorak
- Department of Technique and Food Development; Faculty of Human Nutrition and Consumer Sciences, Warsaw University of Life Sciences; Warsaw 02-776 Poland
| | - Agnieszka Wierzbicka
- Department of Technique and Food Development; Faculty of Human Nutrition and Consumer Sciences, Warsaw University of Life Sciences; Warsaw 02-776 Poland
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de la Cruz S, Madrid R, García-García A, Alcocer M, Martín R, González I, García T. Identification and characterisation of the proteins bound by specific phage-displayed recombinant antibodies (scFv) obtained against Brazil nut and almond extracts. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:1685-1695. [PMID: 28846130 DOI: 10.1002/jsfa.8640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 02/08/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Almonds and Brazil nuts are widely consumed allergenic nuts whose presence must be declared according to food labelling regulations. Their detection in food products has been recently achieved by ELISA methods with recombinant antibodies (scFv) isolated against complete Brazil nut and almond protein extracts. The screening of phage-scFv libraries against complete protein extracts confers a series of advantages over the use of purified proteins, as recombinant proteins might alter their native folding. However, using this strategy, the nature of the target detected by phage-displayed antibodies remains unknown, and requires further research to identify whether they are nut allergens or other molecules present in the extract, but not related to their allergenic potential. RESULTS Electrophoretic, chromatographic, immunological and spectrometric techniques revealed that the Brazil nut (BE95) and almond (PD1F6 and PD2C9) specific phage-scFvs detected conformational epitopes of the Brazil nut and almond 11S globulins, recognised by WHO/IUIS as Ber e 2 and Pru du 6 major allergens. Circular dichroism data indicated that severe heat treatment would entail loss of epitope structure, disabling scFv for target detection. CONCLUSIONS The presence of important Brazil nut and almond allergens (Ber e 2 and Pru du 6) in foodstuffs can be determined by using phage-display antibodies BE95, PD1F6 and PD2C9 as affinity probes in ELISA. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Silvia de la Cruz
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Raquel Madrid
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Aina García-García
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Marcos Alcocer
- Department of Nutritional Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Rosario Martín
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Isabel González
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Teresa García
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
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Zhang Z, Li X, Cui L, Meng S, Ye N, Peng X. Catalytic and functional aspects of different isozymes of glycolate oxidase in rice. BMC PLANT BIOLOGY 2017; 17:135. [PMID: 28789632 PMCID: PMC5549332 DOI: 10.1186/s12870-017-1084-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/23/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Glycolate oxidase (GLO) is a key enzyme for photorespiration in plants. There are four GLO genes encoding and forming different isozymes in rice, but their functional differences are not well understood. In this study, enzymatic and physiological characteristics of the GLO isozymes were comparatively analyzed. RESULTS When expressed heterologously in yeast, GLO1, GLO4 and GLO1 + 4 showed the highest activities and lowest K m for glycolate as substrate, whereas GLO3 displayed high activities and affinities for both glycolate and L-lactate, and GLO5 was catalytically inactive with all substrates tested. To further reveal the physiological role of each GLO isozyme in plants, various GLO genetically modified rice lines were generated and functionally analyzed. GLO activity was significantly increased both in GLO1 and GLO4 overexpression lines. Nevertheless, when either GLO1 or GLO4 was knocked out, the activity was suppressed much more significantly in GLO1 knockout lines than in GLO4 knockout lines, and both knockout mutants exhibited obvious dwarfism phenotypes. Among GLO3 and GLO5 overexpression lines and RNAi lines, only GLO3 overexpression lines showed significantly increased L-lactate-oxidizing activity but no other noticeable phenotype changes. CONCLUSIONS These results indicate that rice GLO isozymes have distinct enzymatic characteristics, and they may have different physiological functions in rice.
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Affiliation(s)
- Zhisheng Zhang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Xiangyang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Lili Cui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Shuan Meng
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Nenghui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Xinxiang Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
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Pope TR. THE INFLUENCE OF DISPERSAL PATTERNS AND MATING SYSTEM ON GENETIC DIFFERENTIATION WITHIN AND BETWEEN POPULATIONS OF THE RED HOWLER MONKEY (ALOUATTA SENICULUS). Evolution 2017; 46:1112-1128. [PMID: 28564408 DOI: 10.1111/j.1558-5646.1992.tb00623.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/1989] [Accepted: 10/25/1991] [Indexed: 11/28/2022]
Abstract
The relationship between social structure and partitioning of genetic variance was examined in two red howler monkey populations (W and G) in Venezuela, one of which (G) was undergoing rapid growth through colonization by new troops. Rates and patterns of gene flow had been determined through radiotelemetry and direct observation data on solitary migrants, and 10 years of troop censusing. Standard electrophoresis techniques were used to examine 29 loci in blood samples taken from 137 of the study animals. Analysis of genetic variance demonstrated: (1) a significantly high level of genetic variation among troops within populations (FST = 0.225 for W and 0.142 for G), and (2) a significant excess of heterozygosity within troops relative to expected (FIS = -0.136 for W and -0.064 for G), despite relatively high levels of observed and inferred inbreeding in W. Differences between the populations in FST values conformed to those predicted based on differences in colonization rate. Comparison of partitioning of genetic variance among different genealogical subsets of troops demonstrated that the pattern of genetic differentiation observed among troops within populations was promoted by an essentially single-male harem breeding structure, a very low rate of random exchange of breeding males among troops, and a high degree of relatedness among troop females. Between-troop genetic differentiation (FST ) was thereby increased relative to that expected from other types of social organization, while the correlation between uniting gametes within troops (FIS ) was decreased. Genetic differentiation between populations (2%) corresponded to that predicted from migration rates. Such a mosaic of genetic variation, combined with differences in reproductive success observed among troops and a high troop failure rate, create conditions in which interdemic selection could result in more rapid spread of advantageous gene combinations than would be expected in a panmictic population, particularly in a colonizing situation in which the founder population is small.
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Affiliation(s)
- Theresa R Pope
- Department of Wildlife and Range Sciences, 118 Newins Ziegler, University of Florida, Gainesville, FL, 32611, USA
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Abstract
Affinity electrophoresis has long been used to study the interaction between proteins and large soluble ligands. The technique has been found to have great utility for the examination of polysaccharide binding by proteins, particularly carbohydrate binding modules (CBMs). In recent years, carbohydrate surface binding sites of proteins mostly enzymes have also been investigated by this method. Here, we describe a protocol for identifying binding interactions between enzyme catalytic modules and a variety of carbohydrate ligands.
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Uram Ł, Szuster M, Misiorek M, Filipowicz A, Wołowiec S, Wałajtys-Rode E. The effect of G3 PAMAM dendrimer conjugated with B-group vitamins on cell morphology, motility and ATP level in normal and cancer cells. Eur J Pharm Sci 2017; 102:275-283. [PMID: 28323116 DOI: 10.1016/j.ejps.2017.03.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 10/20/2022]
Abstract
In a search for the safe vitamin carrier the PAMAM G3 dendrimer covalently substituted with 9 and 10 molecules of vitamin B7 (biotin) and B6 (pyridoxal), respectively (BC-PAMAM) was investigated. Dendrimer substitution with B-group vitamins significantly alters its biological properties as compared to native form. Observed effects on investigated cell parameters including morphology, adhesion, migration and ATP level were different for normal human fibroblasts (BJ) and squamous cell carcinoma (SCC-15) cell lines. BC-PAMAM revealed significantly less pronounced effects on investigated parameters, particularly at higher concentrations (5-50μM), which is relevant with its lower positive surface charge, as compared with native form. The bioconjugate, up to 50μM concentration, appeared to be a safe vitamin carrier to normal fibroblasts, without significant effect on their adhesion, shape and migration as well as on intracellular ATP level. In SCC-15 cells BC-PAMAM, at low concentrations (0.1-0.5μM), altered the cell shape and increase adhesion, whereas at higher concentrations opposite effects were seen. Measurements of cellular level of ATP showed that higher resistance of cancer cells to toxic effects of native PAMAM dendrimers may be due to higher energy supply of cancer cells.
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Affiliation(s)
- Łukasz Uram
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave, 35-959 Rzeszów, Poland.
| | - Magdalena Szuster
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave, 35-959 Rzeszów, Poland
| | - Maria Misiorek
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave, 35-959 Rzeszów, Poland
| | - Aleksandra Filipowicz
- Faculty of Medical Sciences, Rzeszów University of Information Technology and Management, 2 Sucharskiego Str, 35-225 Rzeszów, Poland
| | - Stanisław Wołowiec
- Centre for Innovative Research in Medical and Natural Sciences, Faculty of Medicine, University of Rzeszów, Warzywna 1a, 35-310 Rzeszów, Poland
| | - Elżbieta Wałajtys-Rode
- Department of Drug Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology,75 Koszykowa Str,00-664 Warsaw, Poland
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Tereshchenkova VF, Goptar IA, Kulemzina IA, Zhuzhikov DP, Serebryakova MV, Belozersky MA, Dunaevsky YE, Oppert B, Filippova IY, Elpidina EN. Dipeptidyl peptidase 4 - An important digestive peptidase in Tenebrio molitor larvae. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 76:38-48. [PMID: 27395781 DOI: 10.1016/j.ibmb.2016.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 06/28/2016] [Accepted: 07/05/2016] [Indexed: 06/06/2023]
Abstract
Dipeptidyl peptidase 4 (DPP 4) is a proline specific serine peptidase that plays an important role in different regulatory processes in mammals. In this report, we isolated and characterized a unique secreted digestive DPP 4 from the anterior midgut of a stored product pest, Tenebrio molitor larvae (TmDPP 4), with a biological function different than that of the well-studied mammalian DPP 4. The sequence of the purified enzyme was confirmed by mass-spectrometry, and was identical to the translated RNA sequence found in a gut EST database. The purified peptidase was characterized according to its localization in the midgut, and substrate specificity and inhibitor sensitivity were compared with those of human recombinant DPP 4 (rhDPP 4). The T. molitor enzyme was localized mainly in the anterior midgut of the larvae, and 81% of the activity was found in the fraction of soluble gut contents, while human DPP 4 is a membrane enzyme. TmDPP 4 was stable in the pH range 5.0-9.0, with an optimum activity at pH 7.9, similar to human DPP 4. Only specific inhibitors of serine peptidases, diisopropyl fluorophosphate and phenylmethylsulfonyl fluoride, suppressed TmDPP 4 activity, and the specific dipeptidyl peptidase inhibitor vildagliptin was most potent. The highest rate of TmDPP 4 hydrolysis was found for the synthetic substrate Arg-Pro-pNA, while Ala-Pro-pNA was a better substrate for rhDPP 4. Related to its function in the insect midgut, TmDPP 4 efficiently hydrolyzed the wheat storage proteins gliadins, which are major dietary proteins of T. molitor.
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Affiliation(s)
| | - Irina A Goptar
- Chemical Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Irina A Kulemzina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitry P Zhuzhikov
- Biological Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Marina V Serebryakova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Mikhail A Belozersky
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Yakov E Dunaevsky
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Brenda Oppert
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, USA.
| | - Irina Yu Filippova
- Chemical Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Elena N Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
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German DP, Foti DM, Heras J, Amerkhanian H, Lockwood BL. Elevated Gene Copy Number Does Not Always Explain Elevated Amylase Activities in Fishes. Physiol Biochem Zool 2016; 89:277-93. [PMID: 27327179 DOI: 10.1086/687288] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Amylase activity variation in the guts of several model organisms appears to be explained by amylase gene copy number variation. We tested the hypothesis that amylase gene copy number is always elevated in animals with high amylolytic activity. We therefore sequenced the amylase genes and examined amylase gene copy number in prickleback fishes (family Stichaeidae) with different diets including two species of convergently evolved herbivores with the elevated amylase activity phenotype. We found elevated amylase gene copy number (six haploid copies) with sequence variation among copies in one herbivore (Cebidichthys violaceus) and modest gene copy number (two to three haploid copies) with little sequence variation in the remaining taxa, which included herbivores, omnivores, and a carnivore. Few functional differences in amylase biochemistry were observed, and previous investigations showed similar digestibility among the convergently evolved herbivores with differing amylase genetics. Hence, the phenotype of elevated amylase activity can be achieved by different mechanisms (i.e., elevated expression of fewer genes, increased gene copy number, or expression of more efficient amylase proteins) with similar results. Phylogenetic and comparative genomic analyses of available fish amylase genes show mostly lineage-specific duplication events leading to gene copy number variation, although a whole-genome duplication event or chromosomal translocation may have produced multiple amylase copies in the Ostariophysi, again showing multiple routes to the same result.
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Dubuke ML, Maniatis S, Shaffer SA, Munson M. The Exocyst Subunit Sec6 Interacts with Assembled Exocytic SNARE Complexes. J Biol Chem 2015; 290:28245-28256. [PMID: 26446795 DOI: 10.1074/jbc.m115.673806] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Indexed: 11/06/2022] Open
Abstract
In eukaryotic cells, membrane-bound vesicles carry cargo between intracellular compartments, to and from the cell surface, and into the extracellular environment. Many conserved families of proteins are required for properly localized vesicle fusion, including the multisubunit tethering complexes and the SNARE complexes. These protein complexes work together to promote proper vesicle fusion in intracellular trafficking pathways. However, the mechanism by which the exocyst, the exocytosis-specific multisubunit tethering complex, interacts with the exocytic SNAREs to mediate vesicle targeting and fusion is currently unknown. We have demonstrated previously that the Saccharomyces cerevisiae exocyst subunit Sec6 directly bound the plasma membrane SNARE protein Sec9 in vitro and that Sec6 inhibited the assembly of the binary Sso1-Sec9 SNARE complex. Therefore, we hypothesized that the interaction between Sec6 and Sec9 prevented the assembly of premature SNARE complexes at sites of exocytosis. To map the determinants of this interaction, we used cross-linking and mass spectrometry analyses to identify residues required for binding. Mutation of residues identified by this approach resulted in a growth defect when introduced into yeast. Contrary to our previous hypothesis, we discovered that Sec6 does not change the rate of SNARE assembly but, rather, binds both the binary Sec9-Sso1 and ternary Sec9-Sso1-Snc2 SNARE complexes. Together, these results suggest a new model in which Sec6 promotes SNARE complex assembly, similar to the role proposed for other tether subunit-SNARE interactions.
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Affiliation(s)
- Michelle L Dubuke
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Stephanie Maniatis
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605; Proteomics and Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, Massachusetts 01545
| | - Scott A Shaffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605; Proteomics and Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, Massachusetts 01545
| | - Mary Munson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605.
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Lico DTP, Lopes GS, Brusco J, Rosa JC, Gould RM, De Giorgis JA, Larson RE. A novel SDS-stable dimer of a heterogeneous nuclear ribonucleoprotein at presynaptic terminals of squid neurons. Neuroscience 2015; 300:381-92. [PMID: 26012490 DOI: 10.1016/j.neuroscience.2015.05.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/05/2015] [Accepted: 05/16/2015] [Indexed: 01/27/2023]
Abstract
The presence of mRNAs in synaptic terminals and their regulated translation are important factors in neuronal communication and plasticity. Heterogeneous nuclear ribonucleoprotein (hnRNP) complexes are involved in the translocation, stability, and subcellular localization of mRNA and the regulation of its translation. Defects in these processes and mutations in components of the hnRNP complexes have been related to the formation of cytoplasmic inclusion bodies and neurodegenerative diseases. Despite much data on mRNA localization and evidence for protein synthesis, as well as the presence of translation machinery, in axons and presynaptic terminals, the identity of RNA-binding proteins involved in RNA transport and function in presynaptic regions is lacking. We previously characterized a strongly basic RNA-binding protein (p65), member of the hnRNPA/B subfamily, in squid presynaptic terminals. Intriguingly, in sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), p65 migrated as a 65-kDa protein, whereas members of the hnRNPA/B family typically have molecular masses ranging from 35 to 42kDa. In this report we present further biochemical and molecular characterization that shows endogenous p65 to be an SDS-stable dimer composed of ∼37-kDa hnRNPA/B-like subunits. We cloned and expressed a recombinant protein corresponding to squid hnRNPA/B-like protein and showed its propensity to aggregate and form SDS-stable dimers in vitro. Our data suggest that this unique hnRNPA/B-like protein co-localizes with synaptic vesicle protein 2 and RNA-binding protein ELAV and thus may serve as a link between local mRNA processing and presynaptic function and regulation.
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Affiliation(s)
- D T P Lico
- Department of Cellular & Molecular Biology, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil; Marine Biological Laboratory, Woods Hole, MA 02543, United States.
| | - G S Lopes
- Department of Cellular & Molecular Biology, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil; Marine Biological Laboratory, Woods Hole, MA 02543, United States.
| | - J Brusco
- Department of Cellular & Molecular Biology, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil; Marine Biological Laboratory, Woods Hole, MA 02543, United States.
| | - J C Rosa
- Department of Cellular & Molecular Biology, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil.
| | - R M Gould
- Program in Sensory Physiology and Behavior, Marine Biological Laboratory, Woods Hole, MA 02543, United States.
| | - J A De Giorgis
- Biology Department, Providence College, Providence, RI 02918, United States; National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, United States; Marine Biological Laboratory, Woods Hole, MA 02543, United States.
| | - R E Larson
- Department of Cellular & Molecular Biology, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil; Marine Biological Laboratory, Woods Hole, MA 02543, United States.
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de la Mora-de la Mora I, Torres-Larios A, Enríquez-Flores S, Méndez ST, Castillo-Villanueva A, Gómez-Manzo S, López-Velázquez G, Marcial-Quino J, Torres-Arroyo A, García-Torres I, Reyes-Vivas H, Oria-Hernández J. Structural effects of protein aging: terminal marking by deamidation in human triosephosphate isomerase. PLoS One 2015; 10:e0123379. [PMID: 25884638 PMCID: PMC4401446 DOI: 10.1371/journal.pone.0123379] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/17/2015] [Indexed: 12/04/2022] Open
Abstract
Deamidation, the loss of the ammonium group of asparagine and glutamine to form aspartic and glutamic acid, is one of the most commonly occurring post-translational modifications in proteins. Since deamidation rates are encoded in the protein structure, it has been proposed that they can serve as molecular clocks for the timing of biological processes such as protein turnover, development and aging. Despite the importance of this process, there is a lack of detailed structural information explaining the effects of deamidation on the structure of proteins. Here, we studied the effects of deamidation on human triosephosphate isomerase (HsTIM), an enzyme for which deamidation of N15 and N71 has been long recognized as the signal for terminal marking of the protein. Deamidation was mimicked by site directed mutagenesis; thus, three mutants of HsTIM (N15D, N71D and N15D/N71D) were characterized. The results show that the N71D mutant resembles, structurally and functionally, the wild type enzyme. In contrast, the N15D mutant displays all the detrimental effects related to deamidation. The N15D/N71D mutant shows only minor additional effects when compared with the N15D mutation, supporting that deamidation of N71 induces negligible effects. The crystal structures show that, in contrast to the N71D mutant, where minimal alterations are observed, the N15D mutation forms new interactions that perturb the structure of loop 1 and loop 3, both critical components of the catalytic site and the interface of HsTIM. Based on a phylogenetic analysis of TIM sequences, we propose the conservation of this mechanism for mammalian TIMs.
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Affiliation(s)
| | - Alfredo Torres-Larios
- Departamento de Bioquímica Y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, D.F., México
| | - Sergio Enríquez-Flores
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
| | - Sara-Teresa Méndez
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
| | - Adriana Castillo-Villanueva
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
| | - Gabriel López-Velázquez
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
| | - Jaime Marcial-Quino
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
| | - Angélica Torres-Arroyo
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
| | - Itzhel García-Torres
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
| | - Horacio Reyes-Vivas
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
- * E-mail: (JOH); (HRV)
| | - Jesús Oria-Hernández
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
- * E-mail: (JOH); (HRV)
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Schultz I, Vollmers F, Lühmann T, Rybak JC, Wittmann R, Stank K, Steckel H, Kardziev B, Schmidt M, Högger P, Meinel L. Pulmonary Insulin-like Growth Factor I Delivery from Trehalose and Silk-Fibroin Microparticles. ACS Biomater Sci Eng 2015. [DOI: 10.1021/ab500101c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Isabel Schultz
- Institute
for Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, DE-97074 Wuerzburg, Germany
| | - Frederic Vollmers
- Institute
for Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, DE-97074 Wuerzburg, Germany
| | - Tessa Lühmann
- Institute
for Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, DE-97074 Wuerzburg, Germany
| | - Jens-Christoph Rybak
- Institute
for Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, DE-97074 Wuerzburg, Germany
| | - Ronja Wittmann
- Institute
for Pharmacy, University of Kiel, Grasweg 9a, DE-24118 Kiel, Germany
| | - Katharina Stank
- Institute
for Pharmacy, University of Kiel, Grasweg 9a, DE-24118 Kiel, Germany
| | - Hartwig Steckel
- Institute
for Pharmacy, University of Kiel, Grasweg 9a, DE-24118 Kiel, Germany
| | | | - Michael Schmidt
- Medical
Clinic and Polyclinic I, University of Wuerzburg, DE-97080, Germany
| | - Petra Högger
- Institute
for Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, DE-97074 Wuerzburg, Germany
| | - Lorenz Meinel
- Institute
for Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, DE-97074 Wuerzburg, Germany
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Thomas CM, Fitzsimmons CM, Dunne DW, Timson DJ. Comparative biochemical analysis of three members of the Schistosoma mansoni TAL family: Differences in ion and drug binding properties. Biochimie 2015; 108:40-7. [PMID: 25447146 PMCID: PMC4300400 DOI: 10.1016/j.biochi.2014.10.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 10/21/2014] [Indexed: 01/03/2023]
Abstract
The tegumental allergen-like (TAL) proteins from Schistosoma mansoni are part of a family of calcium binding proteins found only in parasitic flatworms. These proteins have attracted interest as potential drug or vaccine targets, yet comparatively little is known about their biochemistry. Here, we compared the biochemical properties of three members of this family: SmTAL1 (Sm22.6), SmTAL2 (Sm21.7) and SmTAL3 (Sm20.8). Molecular modelling suggested that, despite similarities in domain organisation, there are differences in the three proteins' structures. SmTAL1 was predicted to have two functional calcium binding sites and SmTAL2 was predicted to have one. Despite the presence of two EF-hand-like structures in SmTAL3, neither was predicted to be functional. These predictions were confirmed by native gel electrophoresis, intrinsic fluorescence and differential scanning fluorimetry: both SmTAL1 and SmTAL2 are able to bind calcium ions reversibly, but SmTAL3 is not. SmTAL1 is also able to interact with manganese, strontium, iron(II) and nickel ions. SmTAL2 has a different ion binding profile interacting with cadmium, manganese, magnesium, strontium and barium ions in addition to calcium. All three proteins form dimers and, in contrast to some Fasciola hepatica proteins from the same family; dimerization is not affected by calcium ions. SmTAL1 interacts with the anti-schistosomal drug praziquantel and the calmodulin antagonists trifluoperazine, chlorpromazine and W7. SmTAL2 interacts only with W7. SmTAL3 interacts with the aforementioned calmodulin antagonists and thiamylal, but not praziquantel. Overall, these data suggest that the proteins have different biochemical properties and thus, most likely, different in vivo functions.
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Affiliation(s)
- Charlotte M Thomas
- School of Biological Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK; Institute for Global Food Security, Queen's University Belfast, 18-30 Malone Road, Belfast, BT9 5BN, UK
| | | | - David W Dunne
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - David J Timson
- School of Biological Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK; Institute for Global Food Security, Queen's University Belfast, 18-30 Malone Road, Belfast, BT9 5BN, UK.
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Biochemical characterization of a nitrogen-type phosphotransferase system reveals that enzyme EI(Ntr) integrates carbon and nitrogen signaling in Sinorhizobium meliloti. J Bacteriol 2014; 196:1901-7. [PMID: 24633875 DOI: 10.1128/jb.01489-14] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In Sinorhizobium meliloti, catabolite repression is influenced by a noncanonical nitrogen-type phosphotransferase system (PTS(Ntr)). In this PTS(Ntr), the protein HPr is phosphorylated on histidine-22 by the enzyme EI(Ntr) and the flux of phosphate through this residue onto downstream proteins leads to an increase in succinate-mediated catabolite repression (SMCR). In order to explore the molecular determinants of HPr phosphorylation by EI(Ntr), both proteins were purified and the activity of EI(Ntr) was measured. Experimentally determined kinetic parameters of EI(Ntr) activity were significantly slower than those determined for the carbohydrate-type EI in Escherichia coli. Enzymatic assays showed that glutamine, a signal of nitrogen availability in many Gram-negative bacteria, strongly inhibits EI(Ntr). Binding experiments using the isolated GAF domain of EI(Ntr) (EIGAF) showed that it is the domain responsible for detection of glutamine. EI(Ntr) activity was not affected by α-ketoglutarate, and no binding between the EIGAF and α-ketoglutarate could be detected. These data suggest that in S. melilloti, EI(Ntr) phosphorylation of HPr is regulated by signals from both carbon metabolism (phosphoenolpyruvate) and nitrogen metabolism (glutamine).
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Abstract
Most biophysical experiments require protein samples of high quality and accurately determined concentration. This chapter attempts to compile basic information on the most common methods to assess the purity, dispersity, and stability of protein samples. It also reminds of methods to measure protein concentration and of their limits. The idea is to make aware and remind of the range of methods available and of commonly overlooked pitfalls. The aim is to enable experimenters to fully characterize their preparations of soluble or membrane proteins and gain reliable and reproducible results from their experimental work.
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Affiliation(s)
- Tina Daviter
- ISMB Biophysics Centre, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, UK
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De La Mora-De La Mora I, Torres-Larios A, Mendoza-Hernández G, Enriquez-Flores S, Castillo-Villanueva A, Mendez ST, Garcia-Torres I, Torres-Arroyo A, Gómez-Manzo S, Marcial-Quino J, Oria-Hernández J, López-Velázquez G, Reyes-Vivas H. The E104D mutation increases the susceptibility of human triosephosphate isomerase to proteolysis. Asymmetric cleavage of the two monomers of the homodimeric enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2702-11. [PMID: 24056040 DOI: 10.1016/j.bbapap.2013.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 08/26/2013] [Accepted: 08/27/2013] [Indexed: 11/27/2022]
Abstract
The deficiency of human triosephosphate isomerase (HsTIM) generates neurological alterations, cardiomyopathy and premature death. The mutation E104D is the most frequent cause of the disease. Although the wild type and mutant exhibit similar kinetic parameters, it has been shown that the E104D substitution induces perturbation of an interfacial water network that, in turn, reduces the association constant between subunits promoting enzyme inactivation. To gain further insight into the effects of the mutation on the structure, stability and function of the enzyme, we measured the sensitivity of recombinant E104D mutant and wild type HsTIM to limited proteolysis. The mutation increases the susceptibility to proteolysis as consequence of the loss of rigidity of its overall 3-D structure. Unexpectedly, it was observed that proteolysis of wild type HsTIM generated two different stable nicked dimers. One was formed in relatively short times of incubation with proteinase K; as shown by spectrometric and crystallographic data, it corresponded to a dimer containing a nicked monomer and an intact monomer. The formation of the other nicked species requires relatively long incubation times with proteinase K and corresponds to a dimer with two clipped subunits. The first species retains 50% of the original activity, whereas the second species is inactive. Collectively, we found that the E104D mutant is highly susceptible to proteolysis, which in all likelihood contributes to the pathogenesis of enzymopathy. In addition, the proteolysis data on wild type HsTIM illustrate an asymmetric conduct of the two monomers.
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In vitro-binding of the natural siderophore enantiomers pyochelin and enantiopyochelin to their AraC-type regulators PchR in Pseudomonas. Biometals 2013; 26:1067-73. [DOI: 10.1007/s10534-013-9676-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 09/08/2013] [Indexed: 11/30/2022]
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Goptar IA, Shagin DA, Shagina IA, Mudrik ES, Smirnova YA, Zhuzhikov DP, Belozersky MA, Dunaevsky YE, Oppert B, Filippova IY, Elpidina EN. A digestive prolyl carboxypeptidase in Tenebrio molitor larvae. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 43:501-509. [PMID: 23499933 DOI: 10.1016/j.ibmb.2013.02.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 02/27/2013] [Accepted: 02/28/2013] [Indexed: 06/01/2023]
Abstract
Prolyl carboxypeptidase (PRCP) is a lysosomal proline specific serine peptidase that also plays a vital role in the regulation of physiological processes in mammals. In this report, we isolate and characterize the first PRCP in an insect. PRCP was purified from the anterior midgut of larvae of a stored product pest, Tenebrio molitor, using a three-step chromatography strategy, and it was determined that the purified enzyme was a dimer. The cDNA of PRCP was cloned and sequenced, and the predicted protein was identical to the proteomic sequences of the purified enzyme. The substrate specificity and kinetic parameters of the enzyme were determined. The T. molitor PRCP participates in the hydrolysis of the insect's major dietary proteins, gliadins, and is the first PRCP to be ascribed a digestive function. Our collective data suggest that the evolutionary enrichment of the digestive peptidase complex in insects with an area of acidic to neutral pH in the midgut is a result of the incorporation of lysosomal peptidases, including PRCP.
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Affiliation(s)
- Irina A Goptar
- Chemical Faculty, Moscow State University, Moscow 119991, Russia
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Tanio M, Nishimura K. Intramolecular allosteric interaction in the phospholipase C-δ1 pleckstrin homology domain. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1034-43. [DOI: 10.1016/j.bbapap.2013.01.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/21/2013] [Accepted: 01/29/2013] [Indexed: 11/30/2022]
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A preparation of cow's late colostrum fraction containing αs1-casein promoted the proliferation of cultured rat intestinal IEC-6 epithelial cells. Biosci Biotechnol Biochem 2013; 77:992-7. [PMID: 23649260 DOI: 10.1271/bbb.120942] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Colostrum is a complex mixture of bioactives that promotes neonate growth. Recently, we have found by in vivo study that skimmed, sterilized, and concentrated bovine late colostrum (SCBLC), obtained from a Holstein herd on days 6-7 after parturition, had an ability to maintain intestinal integrity. In the present study we investigated effects of SCBLC on rat intestinal IEC-6 cell proliferation in vitro. A fraction containing αs1-casein was found to have a robust stimulation effect as compared to other protein fractions from SCBLC and even the αs1-casein fraction from milk from other Holstein herds. Furthermore, the SCBLC αs1-casein molecule demonstrated not only slightly slower mobility on both SDS- and native-PAGE than other bovine milk αs1-caseins, but also a peculiar conformation reminiscent of moltenglobule in the circular dichroism spectrum. These findings may be of relevant to the competence of SCBLC to preserve intestinal integrity.
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Identification of novel signalling roles and targets for G(α) and G(βγ) downstream of the insulin-like growth factor 1 receptor in vascular smooth muscle cells. Biochem J 2013. [PMID: 23186281 DOI: 10.1042/bj20112158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Vascular dysfunction is the underlying cause of nearly 80% of heart disease cases, and its initiation and progression can be exacerbated by circulating factors, such as IGF-1 (insulin-like growth factor 1). IGF-1, which is highly homologous with insulin, elicits a response via a classical tyrosine kinase receptor, the IGF-1R (IGF-1 receptor). However, it has been suggested that the IGF-1R may also be coupled to a heterotrimeric G-protein and can thus modulate cellular processes via this alternate pathway. The objective of the present study was to investigate the structural aspects of IGF-1R coupling to a heterotrimeric G-protein in VSMCs [vascular SMCs (smooth muscle cells)], as well as examine the contribution of this pathway to cellular responses that are related to vascular disease. We found that the intracellular subunit of the IGF-1R precipitates with two G-protein subunits. The G(βγ)-mediated pathway contributes to both proliferation and migration. We also show that IGF-1 specifically activates G(αi) and can directly interact with both G(αi1) and G(αi2). A phospho-screen using a novel specific G(αi)-peptide inhibitor reveals a number of potential downstream effectors of this pathway, although our results show that it is not essential for SMC proliferation or migration.
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Crowe A, James MJ, Lee VMY, Smith AB, Trojanowski JQ, Ballatore C, Brunden KR. Aminothienopyridazines and methylene blue affect Tau fibrillization via cysteine oxidation. J Biol Chem 2013; 288:11024-37. [PMID: 23443659 DOI: 10.1074/jbc.m112.436006] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Alzheimer disease and several other neurodegenerative disorders are characterized by the accumulation of intraneuronal fibrils comprised of the protein Tau. Tau is normally a soluble protein that stabilizes microtubules, with splice isoforms that contain either three (3-R) or four (4-R) microtubule binding repeats. The formation of Tau fibrils is thought to result in neuronal damage, and inhibitors of Tau fibrillization may hold promise as therapeutic agents. The process of Tau fibrillization can be replicated in vitro, and a number of small molecules have been identified that inhibit Tau fibril formation. However, little is known about how these molecules affect Tau fibrillization. Here, we examined the mechanism by which the previously described aminothieno pyridazine (ATPZ) series of compounds inhibit Tau fibrillization. Active ATPZs were found to promote the oxidation of the two cysteine residues within 4-R Tau by a redox cycling mechanism, resulting in the formation of a disulfide-containing compact monomer that was refractory to fibrillization. Moreover, the ATPZs facilitated intermolecular disulfide formation between 3-R Tau monomers, leading to dimers that were capable of fibrillization. The ATPZs also caused cysteine oxidation in molecules unrelated to Tau. Interestingly, methylene blue, an inhibitor of Tau fibrillization under evaluation in Alzheimer disease clinical trials, caused a similar oxidation of cysteines in Tau and other molecules. These findings reveal that the ATPZs and methylene blue act by a mechanism that may affect their viability as potential therapeutic agents.
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Affiliation(s)
- Alex Crowe
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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