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Xiong J, Luo M, Chen Y, Hu Q, Fang Y, Sun T, Hu G, Zhang CJ. Subtilisin-like proteases from Fusarium graminearum induce plant cell death and contribute to virulence. PLANT PHYSIOLOGY 2024; 195:1681-1693. [PMID: 38478507 DOI: 10.1093/plphys/kiae155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 02/20/2024] [Indexed: 06/02/2024]
Abstract
Fusarium head blight (FHB), caused by Fusarium graminearum, causes huge annual economic losses in cereal production. To successfully colonize host plants, pathogens secrete hundreds of effectors that interfere with plant immunity and facilitate infection. However, the roles of most secreted effectors of F. graminearum in pathogenesis remain unclear. We analyzed the secreted proteins of F. graminearum and identified 255 candidate effector proteins by liquid chromatography-mass spectrometry (LC-MS). Five subtilisin-like family proteases (FgSLPs) were identified that can induce cell death in Nicotiana benthamiana leaves. Further experiments showed that these FgSLPs induced cell death in cotton (Gossypium barbadense) and Arabidopsis (Arabidopsis thaliana). A signal peptide and light were not essential for the cell death-inducing activity of FgSLPs. The I9 inhibitor domain and the entire C-terminus of FgSLPs were indispensable for their self-processing and cell death-inducing activity. FgSLP-induced cell death occurred independent of the plant signal transduction components BRI-ASSOCIATED KINASE 1 (BAK1), SUPPRESSOR OF BIR1 1 (SOBIR1), ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1), and PHYTOALEXIN DEFICIENT 4 (PAD4). Reduced virulence was observed when FgSLP1 and FgSLP2 were simultaneously knocked out. This study reveals a class of secreted toxic proteins essential for F. graminearum virulence.
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Affiliation(s)
- Jiang Xiong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Mingyu Luo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yunshen Chen
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- School of Life Sciences, Henan University, Kaifeng 475004, China
- Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Qianyong Hu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ying Fang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tongjun Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Guanjing Hu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Cui-Jun Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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Ariyoshi R, Matsuzaki T, Sato R, Minamihata K, Hayashi K, Koga T, Orita K, Nishioka R, Wakabayashi R, Goto M, Kamiya N. Engineering the Propeptide of Microbial Transglutaminase Zymogen: Enabling Substrate-Dependent Activation for Bioconjugation Applications. Bioconjug Chem 2024; 35:340-350. [PMID: 38421254 DOI: 10.1021/acs.bioconjchem.3c00544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Microbial transglutaminase (MTG) from Streptomyces mobaraensis is a powerful biocatalytic glue for site-specific cross-linking of a range of biomolecules and synthetic molecules that have an MTG-reactive moiety. The preparation of active recombinant MTG requires post-translational proteolytic digestion of a propeptide that functions as an intramolecular chaperone to assist the correct folding of the MTG zymogen (MTGz) in the biosynthesis. Herein, we report engineered active zymogen of MTG (EzMTG) that is expressed in soluble form in the host Escherichia coli cytosol and exhibits cross-linking activity without limited proteolysis of the propeptide. We found that the saturation mutagenesis of residues K10 or Y12 in the propeptide domain generated several active MTGz mutants. In particular, the K10D/Y12G mutant exhibited catalytic activity comparable to that of mature MTG. However, the expression level was low, possibly because of decreased chaperone activity and/or the promiscuous substrate specificity of MTG, which is potentially harmful to the host cells. The K10R/Y12A mutant exhibited specific substrate-dependent reactivity toward peptidyl substrates. Quantitative analysis of the binding affinity of the mutated propeptides to the active site of MTG suggested an inverse relationship between the binding affinity and the catalytic activity of EzMTG. Our proof-of-concept study provides insights into the design of a new biocatalyst using the MTGz as a scaffold and a potential route to high-throughput screening of EzMTG mutants for bioconjugation applications.
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Affiliation(s)
- Ryutaro Ariyoshi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Takashi Matsuzaki
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Ryo Sato
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Kosuke Minamihata
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Kounosuke Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Taisei Koga
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Kensei Orita
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Riko Nishioka
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Rie Wakabayashi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
- Division of Biotechnology, Center for Future Chemistry, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
- Division of Biotechnology, Center for Future Chemistry, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
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Pei ZF, Zhu L, Nair SK. Core-dependent post-translational modifications guide the biosynthesis of a new class of hypermodified peptides. Nat Commun 2023; 14:7734. [PMID: 38007494 PMCID: PMC10676384 DOI: 10.1038/s41467-023-43604-5] [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: 08/21/2023] [Accepted: 11/14/2023] [Indexed: 11/27/2023] Open
Abstract
The ribosomally synthesized and post-translationally modified peptide (RiPPs) class of natural products has undergone significant expansion due to the rapid growth in genome sequencing data. Using a bioinformatics approach, we identify the dehydrazoles, a novel class of hypermodified RiPPs that contain both side chain dehydration of Ser residues, and backbone heterocyclization at Ser, Thr, and Cys residues to the corresponding azol(in)es. Structure elucidation of the hypermodified peptide carnazolamide, a representative class member, shows that 18 post-translational modifications are installed by just five enzymes. Complete biosynthetic reconstitution demonstrates that dehydration is carried out by an unusual DUF4135 dehydration domain fused to a zinc-independent cyclase domain (CcaM). We demonstrate that CcaM only modifies Ser residues that precede an azole in the core peptide. As heterocyclization removes the carbonyl following the Ser residue, CcaM likely catalyzes dehydration without generating an enolate intermediate. Additionally, CcaM does not require the leader peptide, and this core-dependence effectively sets the order for the biosynthetic reactions. Biophysical studies demonstrate direct binding of azoles to CcaM consistent with this azole moiety-dependent dehydration. Bioinformatic analysis reveals more than 50 related biosynthetic gene clusters that contain additional catalysts that may produce structurally diverse scaffolds.
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Affiliation(s)
- Zeng-Fei Pei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Lingyang Zhu
- School of Chemical Sciences, NMR Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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4
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Gedi V, Duarte F, Patel P, Bhattacharjee P, Tecza M, McGourty K, Hudson SP. Impact of Propeptide Cleavage on the Stability and Activity of a Streptococcal Immunomodulatory C5a Peptidase for Biopharmaceutical Development. Mol Pharm 2023; 20:4041-4049. [PMID: 37406301 PMCID: PMC10410607 DOI: 10.1021/acs.molpharmaceut.3c00207] [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: 03/06/2023] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023]
Abstract
Posttranslational modifications of proteins can impact their therapeutic efficacy, stability, and potential for pharmaceutical development. The Group AStreptococcus pyogenesC5a peptidase (ScpA) is a multi-domain protein composed of an N-terminal signal peptide, a catalytic domain (including propeptide), three fibronectin domains, and cell membrane-associated domains. It is one of several proteins produced by Group AS. pyogenesknown to cleave components of the human complement system. After signal peptide removal, ScpA undergoes autoproteolysis and cleaves its propeptide for full maturation. The exact location and mechanism of the propeptide cleavage, and the impact of this cleavage on stability and activity, are not clearly understood, and the exact primary sequence of the final enzyme is not known. A form of ScpA with no autoproteolysis fragments of propeptide present may be more desirable for pharmaceutical development from a regulatory and a biocompatibility in the body perspective. The current study describes an in-depth structural and functional characterization of propeptide truncated variants of ScpA expressed inEscherichia colicells. All three purified ScpA variants, ScpA, 79ΔPro, and 92ΔPro, starting with N32, D79, and A92 positions, respectively, showed similar activity against C5a, which suggests a propeptide-independent activity profile of ScpA. CE-SDS and MALDI top-down sequencing analyses highlight a time-dependent propeptide autoproteolysis of ScpA at 37 °C with a distinct end point at A92 and/or D93. In comparison, all three variants of ScpA exhibit similar stability, melting temperatures, and secondary structure orientation. In summary, this work not only highlights propeptide localization but also provides a strategy to recombinantly produce a final mature and active form of ScpA without any propeptide-related fragments.
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Affiliation(s)
- Vinayakumar Gedi
- Department
of Chemical Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Francisco Duarte
- Department
of Chemical Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Pratikkumar Patel
- Department
of Chemical Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Promita Bhattacharjee
- Department
of Chemical Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Malgorzata Tecza
- Department
of Chemical Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Kieran McGourty
- Department
of Chemical Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
- SSPC
SFI Research Centre for Pharmaceuticals, University of Limerick, Limerick V94 T9PX, Ireland
| | - Sarah P. Hudson
- Department
of Chemical Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
- SSPC
SFI Research Centre for Pharmaceuticals, University of Limerick, Limerick V94 T9PX, Ireland
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Sachan S, Moya CG, Voigt B, Köhn M, Balbach J. The pro-sequence of parathyroid hormone prevents premature amyloid fibril formation. FEBS Lett 2023; 597:995-1006. [PMID: 36700832 DOI: 10.1002/1873-3468.14587] [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: 12/22/2022] [Accepted: 01/16/2023] [Indexed: 01/27/2023]
Abstract
The parathyroid hormone (PTH) regulates the calcium and phosphate level in blood after secretion from parathyroid chief cells. The pre- and pro-sequences of precursor preproPTH get cleaved during PTH maturation. In secretory granules, PTH forms functional amyloids. Using thioflavin T fibrillation assays, circular dichroism, NMR spectroscopy, and cellular cAMP activation, we show that the pro-sequence prevents premature fibrillation by impairing primary nucleation because of Coulomb repulsion of positively charged residues. Under seeding or high salt conditions or in the presence of heparin at pH 5.5, proPTH fibril formation is delayed, but the monomer release properties are conserved. ProPTH can still activate in cellulo PTH receptor 1 but with impaired potency. These findings give some perspectives on medical applications of PTH in hormone therapy.
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Affiliation(s)
- Shubhra Sachan
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, Germany
| | - Celia González Moya
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, Germany
| | - Bruno Voigt
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, Germany
| | - Marcel Köhn
- Medical Faculty, Martin-Luther-University Halle-Wittenberg, Germany
| | - Jochen Balbach
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, Germany
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6
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Liu N, Li SB, Zheng YZ, Xu SY, Shen JS. Minimalistic Artificial Catalysts with Esterase-Like Activity from Multivalent Nanofibers Formed by the Self-Assembly of Dipeptides. ACS OMEGA 2023; 8:2491-2500. [PMID: 36687071 PMCID: PMC9851029 DOI: 10.1021/acsomega.2c06972] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Imitating and incorporating the multiple key structural features observed in natural enzymes into a minimalistic molecule to develop an artificial catalyst with outstanding catalytic efficiency is an attractive topic for chemists. Herein, we designed and synthesized one class of minimalistic dipeptide molecules containing a terminal -SH group and a terminal His-Phe dipeptide head linked by a hydrophobic alkyl chain with different lengths, marked as HS-C n+1-His-Phe (n = 4, 7, 11, 15, and 17; n + 1 represents the carbon atom number of the alkyl chain). The His (-imidazole), Phe (-CO2 -) moieties, the terminal -SH group, and a long hydrophobic alkyl chain were found to have important contributions to achieve high binding ability leading to outstanding absolute catalytic efficiency (k cat/K M) toward the hydrolysis reactions of carboxylic ester substrates.
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Affiliation(s)
- Ning Liu
- Xiamen
Key Laboratory of Optoelectronic Materials and Advanced Manufacturing,
College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Shuai-Bing Li
- Xiamen
Key Laboratory of Optoelectronic Materials and Advanced Manufacturing,
College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Yan-Zhen Zheng
- College
of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Su-Ying Xu
- State
Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory
of Environmentally Harmful Chemical Analysis, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jiang-Shan Shen
- Xiamen
Key Laboratory of Optoelectronic Materials and Advanced Manufacturing,
College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
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Chen X, Li X, Duan Y, Pei Z, Liu H, Yin W, Huang J, Luo C, Chen X, Li G, Xie K, Hsiang T, Zheng L. A secreted fungal subtilase interferes with rice immunity via degradation of SUPPRESSOR OF G2 ALLELE OF skp1. PLANT PHYSIOLOGY 2022; 190:1474-1489. [PMID: 35861434 PMCID: PMC9516721 DOI: 10.1093/plphys/kiac334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Serine protease subtilase, found widely in both eukaryotes and prokaryotes, participates in various biological processes. However, how fungal subtilase regulates plant immunity is a major concern. Here, we identified a secreted fungal subtilase, UvPr1a, from the rice false smut (RFS) fungus Ustilaginoidea virens. We characterized UvPr1a as a virulence effector localized to the plant cytoplasm that inhibits plant cell death induced by Bax. Heterologous expression of UvPr1a in rice (Oryza sativa) enhanced plant susceptibility to rice pathogens. UvPr1a interacted with the important rice protein SUPPRESSOR OF G2 ALLELE OF skp1 (OsSGT1), a positive regulator of innate immunity against multiple rice pathogens, degrading OsSGT1 in a protease activity-dependent manner. Furthermore, host-induced gene silencing of UvPr1a compromised disease resistance of rice plants. Our work reveals a previously uncharacterized fungal virulence strategy in which a fungal pathogen secretes a subtilase to interfere with rice immunity through degradation of OsSGT1, thereby promoting infection. These genetic resources provide tools for introducing RFS resistance and further our understanding of plant-pathogen interactions.
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Affiliation(s)
| | | | - Yuhang Duan
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhangxin Pei
- Wuhan Institute of Landscape Architecture, Wuhan 430081, China
| | - Hao Liu
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Weixiao Yin
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Junbin Huang
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaoxi Luo
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaolin Chen
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Guotian Li
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kabin Xie
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph N1G 2W1, Canada
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8
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The antifungal activity of a serine protease and the enzyme production of characteristics of Bacillus licheniformis TG116. Arch Microbiol 2022; 204:601. [PMID: 36057891 DOI: 10.1007/s00203-022-03216-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/02/2022]
Abstract
The growth of Phytophthora capsica, Rhizoctonia solani, Fusarium graminearum, Fusarium oxysporum and Botrytis cinerea were all inhibited by the fermentation supernatant of Bacillus licheniformis TG116, a biocontrol strain isolated from Typhonium giganteum Engl. previously with broad-spectrum resistance to plant pathogens. The fermentation supernatant of the TG116 has a great stability on temperature and UV, and shows the biological activity of protease and cellulase. The antifungal protease produced by B. licheniformis TG116 was purified to homogeneity by ammonium sulfate precipitation, DEAE Sepharose Fast Flow column chromatography and Sephadex G-50 column chromatography. The inhibition of protease by the three surfactants increased with increasing concentration inhibition. Among these surfactants, EDTA showed the strongest inhibition, with only 25% protein activity at a concentration of 1.1 mmol·L-1. Gene amplification verified the presence of a gene fragment of serine protease in the strain TG116. The antimicrobial substance isolated from the fermentation broth of TG116 is a serine protease component.
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9
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The role of pro-domains in human growth factors and cytokines. Biochem Soc Trans 2021; 49:1963-1973. [PMID: 34495310 PMCID: PMC8589418 DOI: 10.1042/bst20200663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 11/30/2022]
Abstract
Many growth factors and cytokines are produced as larger precursors, containing pro-domains, that require proteolytic processing to release the bioactive ligand. These pro-domains can be significantly larger than the mature domains and can play an active role in the regulation of the ligands. Mining the UniProt database, we identified almost one hundred human growth factors and cytokines with pro-domains. These are spread across several unrelated protein families and vary in both their size and composition. The precise role of each pro-domain varies significantly between the protein families. Typically they are critical for controlling bioactivity and protein localisation, and they facilitate diverse mechanisms of activation. Significant gaps in our understanding remain for pro-domain function — particularly their fate once the bioactive ligand has been released. Here we provide an overview of pro-domain roles in human growth factors and cytokines, their processing, regulation and activation, localisation as well as therapeutic potential.
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10
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Komarevtsev SK, Evseev PV, Shneider MM, Popova EA, Tupikin AE, Stepanenko VN, Kabilov MR, Shabunin SV, Osmolovskiy AA, Miroshnikov KA. Gene Analysis, Cloning, and Heterologous Expression of Protease from a Micromycete Aspergillus ochraceus Capable of Activating Protein C of Blood Plasma. Microorganisms 2021; 9:1936. [PMID: 34576831 PMCID: PMC8471544 DOI: 10.3390/microorganisms9091936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/05/2021] [Accepted: 09/08/2021] [Indexed: 12/16/2022] Open
Abstract
Micromycetes are known to secrete numerous enzymes of biotechnological and medical potential. Fibrinolytic protease-activator of protein C (PAPC) of blood plasma from micromycete Aspergillus ochraceus VKM-F4104D was obtained in recombinant form utilising the bacterial expression system. This enzyme, which belongs to the proteinase-K-like proteases, is similar to the proteases encoded in the genomes of Aspergillus fumigatus ATCC MYA-4609, A. oryzae ATCC 42149 and A. flavus 28. Mature PAPC-4104 is 282 amino acids long, preceded by the 101-amino acid propeptide necessary for proper folding and maturation. The recombinant protease was identical to the native enzyme from micromycete in terms of its biological properties, including an ability to hydrolyse substrates of activated protein C (pGlu-Pro-Arg-pNA) and factor Xa (Z-D-Arg-Gly-Arg-pNA) in conjugant reactions with human blood plasma. Therefore, recombinant PAPC-4104 can potentially be used in medicine, veterinary science, diagnostics, and other applications.
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Affiliation(s)
- Sergei K. Komarevtsev
- Biology Department, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.A.P.); (A.A.O.)
- All-Russian Scientific Research Veterinary Institute of Pathology, Pharmacology and Therapy, 394087 Voronezh, Russia; (S.V.S.); (K.A.M.)
| | - Peter V. Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (M.M.S.); (V.N.S.)
| | - Mikhail M. Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (M.M.S.); (V.N.S.)
| | - Elizaveta A. Popova
- Biology Department, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.A.P.); (A.A.O.)
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.E.T.); (M.R.K.)
| | - Vasiliy N. Stepanenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (M.M.S.); (V.N.S.)
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.E.T.); (M.R.K.)
| | - Sergei V. Shabunin
- All-Russian Scientific Research Veterinary Institute of Pathology, Pharmacology and Therapy, 394087 Voronezh, Russia; (S.V.S.); (K.A.M.)
| | - Alexander A. Osmolovskiy
- Biology Department, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.A.P.); (A.A.O.)
- All-Russian Scientific Research Veterinary Institute of Pathology, Pharmacology and Therapy, 394087 Voronezh, Russia; (S.V.S.); (K.A.M.)
| | - Konstantin A. Miroshnikov
- All-Russian Scientific Research Veterinary Institute of Pathology, Pharmacology and Therapy, 394087 Voronezh, Russia; (S.V.S.); (K.A.M.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (M.M.S.); (V.N.S.)
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11
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Recombinant Production and Characterization of an Extracellular Subtilisin-Like Serine Protease from Acinetobacter baumannii of Fermented Food Origin. Protein J 2021; 40:419-435. [PMID: 33870461 PMCID: PMC8053418 DOI: 10.1007/s10930-021-09986-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2021] [Indexed: 12/20/2022]
Abstract
Acinetobacter baumannii is a ubiquitous bacteria that is increasingly becoming a formidable nosocomial pathogen. Due to its clinical relevance, studies on the bacteria's secretory molecules especially extracellular proteases are of interest primarily in relation to the enzyme's role in virulence. Besides, favorable properties that extracellular proteases possess may be exploited for commercial use thus there is a need to investigate extracellular proteases from Acinetobacter baumannii to gain insights into their catalytic properties. In this study, an extracellular subtilisin-like serine protease from Acinetobacter baumannii designated as SPSFQ that was isolated from fermented food was recombinantly expressed and characterized. The mature catalytically active form of SPSFQ shared a high percentage sequence identity of 99% to extracellular proteases from clinical isolates of Acinetobacter baumannii and Klebsiella pneumoniae as well as a moderately high percentage identity to other bacterial proteases with known keratinolytic and collagenolytic activity. The homology model of mature SPSFQ revealed its structure is composed of 10 β-strands, 8 α-helices, and connecting loops resembling a typical architecture of subtilisin-like α/β motif. SPSFQ is catalytically active at an optimum temperature of 40 °C and pH 9. Its activity is stimulated in the presence of Ca2+ and severely inhibited in the presence of PMSF. SPSFQ also displayed the ability to degrade several tissue-associated protein substrates such as keratin, collagen, and fibrin. Accordingly, our study shed light on the catalytic properties of a previously uncharacterized extracellular serine protease from Acinetobacter baumannii that warrants further investigations into its potential role as a virulence factor in pathogenicity and commercial applications.
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Peng Z, Zhang J, Song Y, Guo R, Du G, Chen J. Engineered pro-peptide enhances the catalytic activity of keratinase to improve the conversion ability of feather waste. Biotechnol Bioeng 2021; 118:2559-2571. [PMID: 33788275 DOI: 10.1002/bit.27771] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/22/2021] [Accepted: 03/28/2021] [Indexed: 01/28/2023]
Abstract
Keratinase is an attractive industrial enzyme that can specifically catalyze keratin waste to obtain value-added products. A challenge to the application of keratinase is improving catalytic capacity to achieve efficient hydrolysis. In this study, we effectively expressed the keratinase gene from Bacillus licheniformis BBE11-1 in Bacillus subtilis WB600 based on pro-peptide engineering. Partial deletion of the pro-peptide sequence and the substitution of amino acid at the pro-peptide cleavage site (P1) suggested that the "chaperone effect" and "cleavage efficiency" of the pro-peptide determine the activity of the mature enzyme. Subsequently, seven target sites that can increase the activity of the mature enzyme by 16%-66% were obtained through the multiple sequence alignment of pro-peptides and site-directed mutation. We further performed combinatorial mutations at six sites based on the design principle of three-codon saturation mutations and obtained mutant 2-D12 (236.8 KU/mg) with a mature enzyme activity of 186% of the original (127.6 KU/mg). Finally, continuous fermentation was carried out in a 5-L bioreactor for 22 h, and the activity of the 2-D12 mature enzyme was increased to 391.6 KU/mg. Most importantly, 2-D12 could degrade more than 90% of feather waste into amino acids and peptides within 12 h with the aid of sulfite.
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Affiliation(s)
- Zheng Peng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yang Song
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Rong Guo
- Wuhan Institute of Industrial Control Technology Co., Ltd., Wuhan, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jian Chen
- School of Biotechnology, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
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13
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Guevara T, Rodriguez-Banqueri A, Ksiazek M, Potempa J, Gomis-Rüth FX. Structure-based mechanism of cysteine-switch latency and of catalysis by pappalysin-family metallopeptidases. IUCRJ 2020; 7:18-29. [PMID: 31949901 PMCID: PMC6949598 DOI: 10.1107/s2052252519013848] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/10/2019] [Indexed: 05/23/2023]
Abstract
Tannerella forsythia is an oral dysbiotic periodontopathogen involved in severe human periodontal disease. As part of its virulence factor armamentarium, at the site of colonization it secretes mirolysin, a metallopeptidase of the unicellular pappalysin family, as a zymogen that is proteolytically auto-activated extracellularly at the Ser54-Arg55 bond. Crystal structures of the catalytically impaired promirolysin point mutant E225A at 1.4 and 1.6 Å revealed that latency is exerted by an N-terminal 34-residue pro-segment that shields the front surface of the 274-residue catalytic domain, thus preventing substrate access. The catalytic domain conforms to the metzincin clan of metallopeptidases and contains a double calcium site, which acts as a calcium switch for activity. The pro-segment traverses the active-site cleft in the opposite direction to the substrate, which precludes its cleavage. It is anchored to the mature enzyme through residue Arg21, which intrudes into the specificity pocket in cleft sub-site S1'. Moreover, residue Cys23 within a conserved cysteine-glycine motif blocks the catalytic zinc ion by a cysteine-switch mechanism, first described for mammalian matrix metallopeptidases. In addition, a 1.5 Å structure was obtained for a complex of mature mirolysin and a tetradecapeptide, which filled the cleft from sub-site S1' to S6'. A citrate molecule in S1 completed a product-complex mimic that unveiled the mechanism of substrate binding and cleavage by mirolysin, the catalytic domain of which was already preformed in the zymogen. These results, including a preference for cleavage before basic residues, are likely to be valid for other unicellular pappalysins derived from archaea, bacteria, cyanobacteria, algae and fungi, including archetypal ulilysin from Methanosarcina acetivorans. They may further apply, at least in part, to the multi-domain orthologues of higher organisms.
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Affiliation(s)
- Tibisay Guevara
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Arturo Rodriguez-Banqueri
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Miroslaw Ksiazek
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, 501 South Preston Street, Louisville, KY 40202, USA
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, Kraków 30-387, Poland
| | - Jan Potempa
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, 501 South Preston Street, Louisville, KY 40202, USA
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, Kraków 30-387, Poland
| | - F. Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
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14
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Hou Y, Lu F, Tian J, Tian Y. Cloning, Heterologous Expression and Characterization of an Intracellular Serine Protease from Bacillus sp. LCB10. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819050168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Paulus JK, Van der Hoorn RAL. Do proteolytic cascades exist in plants? JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1997-2002. [PMID: 30668744 PMCID: PMC6460957 DOI: 10.1093/jxb/erz016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/15/2018] [Accepted: 01/08/2019] [Indexed: 05/10/2023]
Affiliation(s)
- Judith K Paulus
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford, UK
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16
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Lee J, Son A, Kim P, Kwon SB, Yu JE, Han G, Seong BL. RNA‐dependent chaperone (chaperna) as an engineered pro‐region for the folding of recombinant microbial transglutaminase. Biotechnol Bioeng 2019; 116:490-502. [DOI: 10.1002/bit.26879] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/15/2018] [Accepted: 11/22/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Jinhee Lee
- Department of Integrated OMICS for Biomedical Science, College of Life science and BiotechnologyYonsei UniversitySeoul Korea
| | - Ahyun Son
- Department of Integrated OMICS for Biomedical Science, College of Life science and BiotechnologyYonsei UniversitySeoul Korea
- Present affiliation: Department of Chemistry and BiochemistryKnoebel Institute for Healthy AgingUniversity of DenverDenver Colorado
| | - Paul Kim
- Department of Integrated OMICS for Biomedical Science, College of Life science and BiotechnologyYonsei UniversitySeoul Korea
| | - Soon Bin Kwon
- Department of BiotechnologyCollege of Life science and BiotechnologyYonsei UniversitySeoul Korea
| | - Ji Eun Yu
- Department of BiotechnologyCollege of Life science and BiotechnologyYonsei UniversitySeoul Korea
| | - Gyoonhee Han
- Department of Integrated OMICS for Biomedical Science, College of Life science and BiotechnologyYonsei UniversitySeoul Korea
- Department of BiotechnologyCollege of Life science and BiotechnologyYonsei UniversitySeoul Korea
| | - Baik L. Seong
- Department of BiotechnologyCollege of Life science and BiotechnologyYonsei UniversitySeoul Korea
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17
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Schulze Hüynck J, Kaschani F, van der Linde K, Ziemann S, Müller AN, Colby T, Kaiser M, Misas Villamil JC, Doehlemann G. Proteases Underground: Analysis of the Maize Root Apoplast Identifies Organ Specific Papain-Like Cysteine Protease Activity. FRONTIERS IN PLANT SCIENCE 2019; 10:473. [PMID: 31114592 PMCID: PMC6503450 DOI: 10.3389/fpls.2019.00473] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/28/2019] [Indexed: 05/14/2023]
Abstract
Plant proteases are key regulators of plant cell processes such as seed development, immune responses, senescence and programmed cell death (PCD). Apoplastic papain-like cysteine proteases (PL) are hubs in plant-microbe interactions and play an important role during abiotic stresses. The apoplast is a crucial interface for the interaction between plant and microbes. So far, apoplastic maize PL and their function have been mostly described for aerial parts. In this study, we focused on apoplastic PLCPs in the roots of maize plants. We have analyzed the phylogeny of maize PLCPs and investigated their protein abundance after salicylic acid (SA) treatment. Using activity-based protein profiling (ABPP) we have identified a novel root-specific PLCP belonging to the RD21-like subfamily, as well as three SA activated PLCPs. The root specific PLCP CP1C shares sequence and structural similarities to known CP1-like proteases. Biochemical analysis of recombinant CP1C revealed different substrate specificities and inhibitor affinities compared to the related proteases. This study characterized a root-specific PLCP and identifies differences between the SA-dependent activation of PLCPs in roots and leaves.
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Affiliation(s)
- Jan Schulze Hüynck
- Center of Excellence on Plant Sciences (CEPLAS), Botanical Institute, University of Cologne, Cologne, Germany
| | | | | | - Sebastian Ziemann
- Center of Excellence on Plant Sciences (CEPLAS), Botanical Institute, University of Cologne, Cologne, Germany
| | - André N. Müller
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Thomas Colby
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Markus Kaiser
- Institute of Chemical Biology, University of Duisburg-Essen, Essen, Germany
| | - Johana C. Misas Villamil
- Center of Excellence on Plant Sciences (CEPLAS), Botanical Institute, University of Cologne, Cologne, Germany
- *Correspondence: Johana C. Misas Villamil, Gunther Doehlemann,
| | - Gunther Doehlemann
- Center of Excellence on Plant Sciences (CEPLAS), Botanical Institute, University of Cologne, Cologne, Germany
- *Correspondence: Johana C. Misas Villamil, Gunther Doehlemann,
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18
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Bjerga GEK, Larsen Ø, Arsın H, Williamson A, García-Moyano A, Leiros I, Puntervoll P. Mutational analysis of the pro-peptide of a marine intracellular subtilisin protease supports its role in inhibition. Proteins 2018; 86:965-977. [PMID: 29907987 PMCID: PMC6220982 DOI: 10.1002/prot.25528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/09/2018] [Accepted: 05/16/2018] [Indexed: 11/06/2022]
Abstract
Intracellular subtilisin proteases (ISPs) have important roles in protein processing during the stationary phase in bacteria. Their unregulated protein degrading activity may have adverse effects inside a cell, but little is known about their regulatory mechanism. Until now, ISPs have mostly been described from Bacillus species, with structural data from a single homolog. Here, we study a marine ISP originating from a phylogenetically distinct genus, Planococcus sp. The enzyme was successfully overexpressed in E. coli, and is active in presence of calcium, which is thought to have a role in minor, but essential, structural rearrangements needed for catalytic activity. The ISP operates at alkaline pH and at moderate temperatures, and has a corresponding melting temperature around 60 °C. The high-resolution 3-dimensional structure reported here, represents an ISP with an intact catalytic triad albeit in a configuration with an inhibitory pro-peptide bound. The pro-peptide is removed in other homologs, but the removal of the pro-peptide from the Planococcus sp. AW02J18 ISP appears to be different, and possibly involves several steps. A first processing step is described here as the removal of 2 immediate N-terminal residues. Furthermore, the pro-peptide contains a conserved LIPY/F-motif, which was found to be involved in inhibition of the catalytic activity.
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Affiliation(s)
- Gro E K Bjerga
- Uni Research, Center for Applied Biotechnology, Thormøhlens gate 55, Bergen, 5006, Norway
| | - Øivind Larsen
- Uni Research, Center for Applied Biotechnology, Thormøhlens gate 55, Bergen, 5006, Norway
| | - Hasan Arsın
- Department of Biological Sciences, University of Bergen, Thormøhlens gate 53, Bergen, 5006, Norway
| | - Adele Williamson
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, Tromsø, 9037, Norway
| | - Antonio García-Moyano
- Uni Research, Center for Applied Biotechnology, Thormøhlens gate 55, Bergen, 5006, Norway
| | - Ingar Leiros
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, Tromsø, 9037, Norway
| | - Pål Puntervoll
- Uni Research, Center for Applied Biotechnology, Thormøhlens gate 55, Bergen, 5006, Norway
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19
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Arolas JL, Goulas T, Cuppari A, Gomis-Rüth FX. Multiple Architectures and Mechanisms of Latency in Metallopeptidase Zymogens. Chem Rev 2018; 118:5581-5597. [PMID: 29775286 DOI: 10.1021/acs.chemrev.8b00030] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Metallopeptidases cleave polypeptides bound in the active-site cleft of catalytic domains through a general base/acid mechanism. This involves a solvent molecule bound to a catalytic zinc and general regulation of the mechanism through zymogen-based latency. Sixty reported structures from 11 metallopeptidase families reveal that prosegments, mostly N-terminal of the catalytic domain, block the cleft regardless of their size. Prosegments may be peptides (5-14 residues), which are only structured within the zymogens, or large moieties (<227 residues) of one or two folded domains. While some prosegments globally shield the catalytic domain through a few contacts, others specifically run across the cleft in the same or opposite direction as a substrate, making numerous interactions. Some prosegments block the zinc by replacing the solvent with particular side chains, while others use terminal α-amino or carboxylate groups. Overall, metallopeptidase zymogens employ disparate mechanisms that diverge even within families, which supports that latency is less conserved than catalysis.
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Affiliation(s)
- Joan L Arolas
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
| | - Theodoros Goulas
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
| | - Anna Cuppari
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
| | - F Xavier Gomis-Rüth
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
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20
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Schaller A, Stintzi A, Rivas S, Serrano I, Chichkova NV, Vartapetian AB, Martínez D, Guiamét JJ, Sueldo DJ, van der Hoorn RAL, Ramírez V, Vera P. From structure to function - a family portrait of plant subtilases. THE NEW PHYTOLOGIST 2018; 218:901-915. [PMID: 28467631 DOI: 10.1111/nph.14582] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/13/2017] [Indexed: 05/20/2023]
Abstract
Contents Summary 901 I. Introduction 901 II. Biochemistry and structure of plant SBTs 902 III. Phylogeny of plant SBTs and family organization 903 IV. Physiological roles of plant SBTs 905 V. Conclusions and outlook 911 Acknowledgements 912 References 912 SUMMARY: Subtilases (SBTs) are serine peptidases that are found in all three domains of life. As compared with homologs in other Eucarya, plant SBTs are more closely related to archaeal and bacterial SBTs, with which they share many biochemical and structural features. However, in the course of evolution, functional diversification led to the acquisition of novel, plant-specific functions, resulting in the present-day complexity of the plant SBT family. SBTs are much more numerous in plants than in any other organism, and include enzymes involved in general proteolysis as well as highly specific processing proteases. Most SBTs are targeted to the cell wall, where they contribute to the control of growth and development by regulating the properties of the cell wall and the activity of extracellular signaling molecules. Plant SBTs affect all stages of the life cycle as they contribute to embryogenesis, seed development and germination, cuticle formation and epidermal patterning, vascular development, programmed cell death, organ abscission, senescence, and plant responses to their biotic and abiotic environments. In this article we provide a comprehensive picture of SBT structure and function in plants.
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Affiliation(s)
- Andreas Schaller
- Institute of Plant Physiology and Biotechnology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Annick Stintzi
- Institute of Plant Physiology and Biotechnology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Susana Rivas
- Laboratoire des Interactions Plantes-Microorganismes, LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, 31326, France
| | - Irene Serrano
- Laboratoire des Interactions Plantes-Microorganismes, LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, 31326, France
| | - Nina V Chichkova
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Andrey B Vartapetian
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Dana Martínez
- Instituto de Fisiología Vegetal, Universidad Nacional de La Plata, La Plata, 1900, Argentina
| | - Juan J Guiamét
- Instituto de Fisiología Vegetal, Universidad Nacional de La Plata, La Plata, 1900, Argentina
| | - Daniela J Sueldo
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Vicente Ramírez
- Institute for Plant Cell Biology and Biotechnology, Heinrich-Heine University, Düsseldorf, 40225, Germany
| | - Pablo Vera
- Institute for Plant Molecular and Cell Biology, Universidad Politécnica de Valencia-CSIC, Valencia, 46022, Spain
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21
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Figueiredo J, Sousa Silva M, Figueiredo A. Subtilisin-like proteases in plant defence: the past, the present and beyond. MOLECULAR PLANT PATHOLOGY 2018; 19:1017-1028. [PMID: 28524452 PMCID: PMC6638164 DOI: 10.1111/mpp.12567] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/19/2017] [Accepted: 05/13/2017] [Indexed: 05/13/2023]
Abstract
Subtilisin-like proteases (or subtilases) are a very diverse family of serine peptidases present in many organisms, but mostly in plants. With a broad spectrum of biological functions, ranging from protein turnover and plant development to interactions with the environment, subtilases have been gaining increasing attention with regard to their involvement in plant defence responses against the most diverse pathogens. Over the last 5 years, the number of published studies associating plant subtilases with pathogen resistance and plant immunity has increased tremendously. In addition, the observation of subtilases and serine protease inhibitors secreted by pathogens has also gained prominence. In this review, we focus on the active participation of subtilases in the interactions established by plants with the environment, highlighting their role in plant-pathogen communication.
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Affiliation(s)
- Joana Figueiredo
- Biosystems & Integrative Sciences Institute (BioISI)Faculdade de Ciências da Universidade de LisboaLisbon 1749‐016Portugal
- Laboratório de FTICR e Espectrometria de Massa EstruturalFaculdade de Ciências da Universidade de LisboaLisbon 1749‐016Portugal
- Centro de Química e BioquímicaFaculdade de Ciências da Universidade de LisboaLisbon 1749‐016Portugal
| | - Marta Sousa Silva
- Laboratório de FTICR e Espectrometria de Massa EstruturalFaculdade de Ciências da Universidade de LisboaLisbon 1749‐016Portugal
- Centro de Química e BioquímicaFaculdade de Ciências da Universidade de LisboaLisbon 1749‐016Portugal
| | - Andreia Figueiredo
- Biosystems & Integrative Sciences Institute (BioISI)Faculdade de Ciências da Universidade de LisboaLisbon 1749‐016Portugal
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Koneru L, Ksiazek M, Waligorska I, Straczek A, Lukasik M, Madej M, Thøgersen IB, Enghild JJ, Potempa J. Mirolysin, a LysargiNase from Tannerella forsythia, proteolytically inactivates the human cathelicidin, LL-37. Biol Chem 2017; 398:395-409. [PMID: 27997347 DOI: 10.1515/hsz-2016-0267] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 10/13/2016] [Indexed: 12/14/2022]
Abstract
Tannerella forsythia is a periodontal pathogen expressing six secretory proteolytic enzymes with a unique multidomain structure referred to as KLIKK proteases. Two of these proteases, karilysin and mirolysin, were previously shown to protect the bacterium against complement-mediated bactericidal activity. The latter metalloprotease, however, was not characterized at the protein level. Therefore, we purified recombinant mirolysin and subjected it to detailed biochemical characterization. Mirolysin was obtained as a 66 kDa zymogen, which autoproteolytically processed itself into a 31 kDa active form via truncations at both the N- and C-termini. Further autodegradation was prevented by calcium. Substrate specificity was determined by the S1' subsite of the substrate-binding pocket, which shows strong preference for Arg and Lys at the carbonyl side of a scissile peptide bond (P1' residue). The protease cleaved an array of host proteins, including human fibronectin, fibrinogen, complement proteins C3, C4, and C5, and the antimicrobial peptide, LL-37. Degradation of LL-37 abolished not only the bactericidal activity of the peptide, but also its ability to bind lipopolysaccharide (LPS), thus quenching the endotoxin proinflammatory activity. Taken together, these results indicate that, through cleavage of LL-37 and complement proteins, mirolysin might be involved in evasion of the host immune response.
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23
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Hohl M, Stintzi A, Schaller A. A novel subtilase inhibitor in plants shows structural and functional similarities to protease propeptides. J Biol Chem 2017; 292:6389-6401. [PMID: 28223360 DOI: 10.1074/jbc.m117.775445] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/13/2017] [Indexed: 12/24/2022] Open
Abstract
The propeptides of subtilisin-like serine proteinases (subtilases, SBTs) serve dual functions as intramolecular chaperones that are required for enzyme folding and as inhibitors of the mature proteases. SBT propeptides are homologous to the I9 family of protease inhibitors that have only been described in fungi. Here we report the identification and characterization of subtilisin propeptide-like inhibitor 1 (SPI-1) from Arabidopsis thaliana Sequence similarity and the shared β-α-β-β-α-β core structure identified SPI-1 as a member of the I9 inhibitor family and as the first independent I9 inhibitor in higher eukaryotes. SPI-1 was characterized as a high-affinity, tight-binding inhibitor of Arabidopsis subtilase SBT4.13 with Kd and Ki values in the picomolar range. SPI-1 acted as a stable inhibitor of SBT4.13 over the physiologically relevant range of pH, and its inhibitory profile included many other SBTs from plants but not bovine chymotrypsin or bacterial subtilisin A. Upon binding to SBT4.13, the C-terminal extension of SPI-1 was proteolytically cleaved. The last four amino acids at the newly formed C terminus of SPI-1 matched both the cleavage specificity of SBT4.13 and the consensus sequence of Arabidopsis SBTs at the junction of the propeptide with the catalytic domain. The data suggest that the C terminus of SPI-1 acts as a competitive inhibitor of target proteases as it remains bound to the active site in a product-like manner. SPI-1 thus resembles SBT propeptides with respect to its mode of protease inhibition. However, in contrast to SBT propeptides, SPI-1 could not substitute as a folding assistant for SBT4.13.
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Affiliation(s)
- Mathias Hohl
- From the Institute of Plant Physiology and Biotechnology, University of Hohenheim, D-70593 Stuttgart, Germany
| | - Annick Stintzi
- From the Institute of Plant Physiology and Biotechnology, University of Hohenheim, D-70593 Stuttgart, Germany
| | - Andreas Schaller
- From the Institute of Plant Physiology and Biotechnology, University of Hohenheim, D-70593 Stuttgart, Germany
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24
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Pomowski A, Usón I, Nowakowska Z, Veillard F, Sztukowska MN, Guevara T, Goulas T, Mizgalska D, Nowak M, Potempa B, Huntington JA, Potempa J, Gomis-Rüth FX. Structural insights unravel the zymogenic mechanism of the virulence factor gingipain K from Porphyromonas gingivalis, a causative agent of gum disease from the human oral microbiome. J Biol Chem 2017; 292:5724-5735. [PMID: 28196869 DOI: 10.1074/jbc.m117.776724] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/06/2017] [Indexed: 01/11/2023] Open
Abstract
Skewing of the human oral microbiome causes dysbiosis and preponderance of bacteria such as Porphyromonas gingivalis, the main etiological agent of periodontitis. P. gingivalis secretes proteolytic gingipains (Kgp and RgpA/B) as zymogens inhibited by a pro-domain that is removed during extracellular activation. Unraveling the molecular mechanism of Kgp zymogenicity is essential to design inhibitors blocking its activity. Here, we found that the isolated 209-residue Kgp pro-domain is a boomerang-shaped all-β protein similar to the RgpB pro-domain. Using composite structural information of Kgp and RgpB, we derived a plausible homology model and mechanism of Kgp-regulating zymogenicity. Accordingly, the pro-domain would laterally attach to the catalytic moiety in Kgp and block the active site through an exposed inhibitory loop. This loop features a lysine (Lys129) likely occupying the S1 specificity pocket and exerting latency. Lys129 mutation to glutamate or arginine led to misfolded protein that was degraded in vivo Mutation to alanine gave milder effects but still strongly diminished proteolytic activity, without affecting the subcellular location of the enzyme. Accordingly, the interactions of Lys129 within the S1 pocket are also essential for correct folding. Uniquely for gingipains, the isolated Kgp pro-domain dimerized through an interface, which partially overlapped with that between the catalytic moiety and the pro-domain within the zymogen, i.e. both complexes are mutually exclusive. Thus, pro-domain dimerization, together with partial rearrangement of the active site upon activation, explains the lack of inhibition of the pro-domain in trans. Our results reveal that the specific latency mechanism of Kgp differs from those of Rgps.
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Affiliation(s)
- Anja Pomowski
- From the Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
| | - Isabel Usón
- the Proteolysis Lab and Crystallographic Methods Lab, Structural Biology Unit, "María de Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Catalonia, Spain.,the Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Catalonia, Spain
| | - Zuzanna Nowakowska
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland, and
| | - Florian Veillard
- the Department of Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - Maryta N Sztukowska
- the Department of Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - Tibisay Guevara
- the Proteolysis Lab and Crystallographic Methods Lab, Structural Biology Unit, "María de Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Catalonia, Spain
| | - Theodoros Goulas
- the Proteolysis Lab and Crystallographic Methods Lab, Structural Biology Unit, "María de Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Catalonia, Spain
| | - Danuta Mizgalska
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland, and
| | - Magdalena Nowak
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland, and
| | - Barbara Potempa
- the Department of Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - James A Huntington
- From the Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
| | - Jan Potempa
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland, and .,the Department of Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - F Xavier Gomis-Rüth
- the Proteolysis Lab and Crystallographic Methods Lab, Structural Biology Unit, "María de Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Catalonia, Spain,
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25
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Garvie CW, Fraley CV, Elowe NH, Culyba EK, Lemke CT, Hubbard BK, Kaushik VK, Daniels DS. Point mutations at the catalytic site of PCSK9 inhibit folding, autoprocessing, and interaction with the LDL receptor. Protein Sci 2016; 25:2018-2027. [PMID: 27534510 DOI: 10.1002/pro.3019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/21/2016] [Accepted: 07/18/2016] [Indexed: 01/05/2023]
Abstract
Circulating low-density lipoprotein cholesterol (LDLc) is regulated by membrane-bound LDL receptor (LDLr). Upon LDLc and LDLr interaction the complex is internalized by the cell, leading to LDLc degradation and LDLr recycling back to the cell surface. The proprotein convertase subtilisin/kexin type 9 (PCSK9) protein regulates this cycling. PCSK9 is secreted from the cell and binds LDLr. When the complex is internalized, PCSK9 prevents LDLr from shuttling back to the surface and instead targets it for degradation. PCSK9 is a serine protease expressed as a zymogen that undergoes autoproteolysis, though the two resulting protein domains remain stably associated as a heterodimer. This PCSK9 autoprocessing is required for the protein to be secreted from the cell. To date, direct analysis of PCSK9 autoprocessing has proven challenging, as no catalytically active zymogen has been isolated. A PCSK9 loss-of-function point mutation (Q152H) that reduces LDLc levels two-fold was identified in a patient population. LDLc reduction was attributed to a lack of PCSK9(Q152H) autoprocessing preventing secretion of the protein. We have isolated a zymogen form of PCSK9, PCSK9(Q152H), and a related mutation (Q152N), that can undergo slow autoproteolysis. We show that the point mutation prevents the formation of the mature form of PCSK9 by hindering folding, reducing the rate of autoproteolysis, and destabilizing the heterodimeric form of the protein. In addition, we show that the zymogen form of PCSK9 adopts a structure that is distinct from the processed form and is unable to bind a mimetic peptide based on the EGF-A domain of the LDLr.
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Affiliation(s)
- Colin W Garvie
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142.
| | - Cara V Fraley
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142
| | - Nadine H Elowe
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142
| | - Elizabeth K Culyba
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142
| | - Christopher T Lemke
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142
| | - Brian K Hubbard
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142
| | - Virendar K Kaushik
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142
| | - Douglas S Daniels
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142.
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26
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The prosegment catalyzes native folding of Plasmodium falciparum plasmepsin II. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1356-62. [DOI: 10.1016/j.bbapap.2016.06.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 01/15/2023]
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27
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Meyer M, Leptihn S, Welz M, Schaller A. Functional Characterization of Propeptides in Plant Subtilases as Intramolecular Chaperones and Inhibitors of the Mature Protease. J Biol Chem 2016; 291:19449-61. [PMID: 27451395 DOI: 10.1074/jbc.m116.744151] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Indexed: 12/23/2022] Open
Abstract
Subtilisin-like serine proteases (SBTs) are extracellular proteases that depend on their propeptides for zymogen maturation and activation. The function of propeptides in plant SBTs is poorly understood and was analyzed here for the propeptide of tomato subtilase 3 (SBT3PP). SBT3PP was found to be required as an intramolecular chaperone for zymogen maturation and secretion of SBT3 in vivo Secretion was impaired in a propeptide-deletion mutant but could be restored by co-expression of the propeptide in trans SBT3 was inhibited by SBT3PP with a Kd of 74 nm for the enzyme-inhibitor complex. With a melting point of 87 °C, thermal stability of the complex was substantially increased as compared with the free protease suggesting that propeptide binding stabilizes the structure of SBT3. Even closely related propeptides from other plant SBTs could not substitute for SBT3PP as a folding assistant or autoinhibitor, revealing high specificity for the SBT3-SBT3PP interaction. Separation of the chaperone and inhibitor functions of SBT3PP in a domain-swap experiment indicated that they are mediated by different regions of the propeptide and, hence, different modes of interaction with SBT3. Release of active SBT3 from the autoinhibited complex relied on a pH-dependent cleavage of the propeptide at Asn-38 and Asp-54. The remarkable stability of the autoinhibited complex and pH dependence of the secondary cleavage provide means for stringent control of SBT3 activity, to ensure that the active enzyme is not released before it reaches the acidic environment of the trans-Golgi network or its final destination in the cell wall.
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Affiliation(s)
- Michael Meyer
- From the Institute of Plant Physiology and Biotechnology and
| | - Sebastian Leptihn
- the Department of Microbiology, University of Hohenheim, D-70593 Stuttgart, Germany
| | - Max Welz
- From the Institute of Plant Physiology and Biotechnology and
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28
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Foldase and inhibitor functionalities of the pepsinogen prosegment are encoded within discrete segments of the 44 residue domain. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1300-6. [PMID: 26003941 DOI: 10.1016/j.bbapap.2015.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 05/09/2015] [Accepted: 05/13/2015] [Indexed: 11/22/2022]
Abstract
Pepsin is initially produced as the zymogen pepsinogen, containing a 44 residue prosegment (PS) domain. When folded without the PS, pepsin forms a thermodynamically stable denatured state (refolded pepsin, Rp). To guide native folding, the PS binds to Rp, stabilizes the folding transition state, and binds tightly to native pepsin (Np), thereby driving the folding equilibrium to favor the native state. It is unknown whether these functionalities of the PS are encoded within the entire sequence or within discrete segments. PS residues 1p-29p correspond to a highly conserved region in pepsin-like aspartic proteases and we hypothesized that this segment is critical to PS-catalyzed folding. This notion was tested in the present study by characterizing the ability of various truncated PS peptides to bind Rp, catalyze folding from Rp to Np, and to inhibit Np. Four PS truncations were examined, corresponding to PS residues 1p-16p (PS1-16), 1p-29p (PS1-29), 17p-44p (PS17-44) and 30p-44p (PS30-44). The three PS functionalities could be ascribed primarily to discrete regions within the highly conserved motif: 1p-16p dictated Rp binding, 17p-29p dictated Np binding/inhibition, while the entire 1p-29p dictated transition state binding/catalyzing folding. Conversely, PS30-44 played no obvious role in PS-catalyzed folding; it is hypothesized that this more variable region may serve as a linker between PS1-29 and the mature domain. The high sequence conservation of PS1-29 and its role in catalyzing pepsin folding strongly suggest that there is a conserved PS-catalyzed folding mechanism shared by pepsin-like aspartic proteases with this motif.
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29
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Demidyuk IV, Shubin AV, Gasanov EV, Kostrov SV. Propeptides as modulators of functional activity of proteases. Biomol Concepts 2015; 1:305-22. [PMID: 25962005 DOI: 10.1515/bmc.2010.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Most proteases are synthesized in the cell as precursor-containing propeptides. These structural elements can determine the folding of the cognate protein, function as an inhibitor/activator peptide, mediate enzyme sorting, and mediate the protease interaction with other molecules and supramolecular structures. The data presented in this review demonstrate modulatory activity of propeptides irrespective of the specific mechanism of action. Changes in propeptide structure, sometimes minor, can crucially alter protein function in the living organism. Modulatory activity coupled with high variation allows us to consider propeptides as specific evolutionary modules that can transform biological properties of proteases without significant changes in the highly conserved catalytic domains. As the considered properties of propeptides are not unique to proteases, propeptide-mediated evolution seems to be a universal biological mechanism.
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30
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Ksiazek M, Mizgalska D, Eick S, Thøgersen IB, Enghild JJ, Potempa J. KLIKK proteases of Tannerella forsythia: putative virulence factors with a unique domain structure. Front Microbiol 2015; 6:312. [PMID: 25954253 PMCID: PMC4404884 DOI: 10.3389/fmicb.2015.00312] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 03/29/2015] [Indexed: 11/13/2022] Open
Abstract
Comparative genomics of virulent Tannerella forsythia ATCC 43037 and a close health-associated relative, Tannerella BU063, revealed, in the latter, the absence of an entire array of genes encoding putative secretory proteases that possess a nearly identical C-terminal domain (CTD) that ends with a -Lys-Leu-Ile-Lys-Lys motif. This observation suggests that these proteins, referred to as KLIKK proteases, may function as virulence factors. Re-sequencing of the loci of the KLIKK proteases found only six genes grouped in two clusters. All six genes were expressed by T. forsythia in routine culture conditions, although at different levels. More importantly, a transcript of each gene was detected in gingival crevicular fluid (GCF) from periodontitis sites infected with T. forsythia indicating that the proteases are expressed in vivo. In each protein, a protease domain was flanked by a unique N-terminal profragment and a C-terminal extension ending with the CTD. Partially purified recombinant proteases showed variable levels of proteolytic activity in zymography gels and toward protein substrates, including collagen, gelatin, elastin, and casein. Taken together, these results indicate that the pathogenic strain of T. forsythia secretes active proteases capable of degrading an array of host proteins, which likely represents an important pathogenic feature of this bacterium.
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Affiliation(s)
- Miroslaw Ksiazek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
| | - Danuta Mizgalska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
| | - Sigrum Eick
- Laboratory of Oral Microbiology, Department of Periodontology, University of Bern Bern, Switzerland
| | - Ida B Thøgersen
- Department of Molecular Biology and Genetics, Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University Aarhus, Denmark
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University Aarhus, Denmark
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland ; Department of Oral Immunology and Infectious Disease, University of Louisville School of Dentistry Louisville, KY, USA
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31
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Cloning, expression and in silico studies of a serine protease from a marine actinomycete (Nocardiopsis sp. NCIM 5124). Process Biochem 2015. [DOI: 10.1016/j.procbio.2014.12.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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32
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López-Pelegrín M, Ksiazek M, Karim AY, Guevara T, Arolas JL, Potempa J, Gomis-Rüth FX. A novel mechanism of latency in matrix metalloproteinases. J Biol Chem 2015; 290:4728-4740. [PMID: 25555916 DOI: 10.1074/jbc.m114.605956] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The matrix metalloproteinases (MMPs) are a family of secreted soluble or membrane-anchored multimodular peptidases regularly found in several paralogous copies in animals and plants, where they have multiple functions. The minimal consensus domain architecture comprises a signal peptide, a 60-90-residue globular prodomain with a conserved sequence motif including a cysteine engaged in "cysteine-switch" or "Velcro" mediated latency, and a catalytic domain. Karilysin, from the human periodontopathogen Tannerella forsythia, is the only bacterial MMP to have been characterized biochemically to date. It shares with eukaryotic forms the catalytic domain but none of the flanking domains. Instead of the consensus MMP prodomain, it features a 14-residue propeptide, the shortest reported for a metallopeptidase, which lacks cysteines. Here we determined the structure of a prokarilysin fragment encompassing the propeptide and the catalytic domain, and found that the former runs across the cleft in the opposite direction to a bound substrate and inhibits the latter through an "aspartate-switch" mechanism. This finding is reminiscent of latency maintenance in the otherwise unrelated astacin and fragilysin metallopeptidase families. In addition, in vivo and biochemical assays showed that the propeptide contributes to protein folding and stability. Our analysis of prokarilysin reveals a novel mechanism of latency and activation in MMPs. Finally, our findings support the view that the karilysin catalytic domain was co-opted by competent bacteria through horizontal gene transfer from a eukaryotic source, and later evolved in a specific bacterial environment.
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Affiliation(s)
- Mar López-Pelegrín
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Miroslaw Ksiazek
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Ul. Gronostajowa 7, 30-387 Kraków, Poland, and
| | - Abdulkarim Y Karim
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Ul. Gronostajowa 7, 30-387 Kraków, Poland, and
| | - Tibisay Guevara
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Joan L Arolas
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain,.
| | - Jan Potempa
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Ul. Gronostajowa 7, 30-387 Kraków, Poland, and; the Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202.
| | - F Xavier Gomis-Rüth
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain,.
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33
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Subbian E, Williamson DM, Shinde U. Protein Folding Mediated by an Intramolecular Chaperone: Energy Landscape for Unimolecular Pro-Subtilisin E Maturation. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/abb.2015.62008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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34
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Xiao H, Bryksa BC, Bhaumik P, Gustchina A, Kiso Y, Yao SQ, Wlodawer A, Yada RY. The zymogen of plasmepsin V from Plasmodium falciparum is enzymatically active. Mol Biochem Parasitol 2014; 197:56-63. [PMID: 25447707 PMCID: PMC6310130 DOI: 10.1016/j.molbiopara.2014.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 10/15/2014] [Accepted: 10/16/2014] [Indexed: 10/24/2022]
Abstract
Plasmepsin V, a membrane-bound aspartic protease present in Plasmodium falciparum, is involved in the export of malaria parasite effector proteins into host erythrocytes and therefore is a potential target for antimalarial drug development. The present study reports the bacterial recombinant expression and initial characterization of zymogenic and mature plasmepsin V. A 484-residue truncated form of proplasmepsin (Glu37-Asn521) was fused to a fragment of thioredoxin and expressed as inclusion bodies. Refolding conditions were optimized and zymogen was processed into a mature form via cleavage at the Asn80-Ala81 peptide bond. Mature plasmepsin V exhibited a pH optimum of 5.5-7.0 with Km and kcat of 4.6 μM and 0.24s(-1), respectively, at pH 6.0 using the substrate DABCYL-LNKRLLHETQ-E(EDANS). Furthermore, the prosegment of proplasmepsin V was shown to be nonessential for refolding and inhibition. Unexpectedly, unprocessed proplasmepsin V was enzymatically active with slightly reduced substrate affinity (∼ 2-fold), and similar pH optimum as well as turnover compared to the mature form. Both zymogenic and mature plasmepsin V were partially inhibited by pepstatin A as well as several KNI aspartic protease inhibitors while certain metals strongly inhibited activity. Overall, the present study provides the first report on the nonessentiality of the prosegment for plasmepsin V folding and activity, and therefore, subsequent characterization of its structure-function relationships of both zymogen and mature forms in the development of novel inhibitors with potential antimalarial activities is warranted.
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Affiliation(s)
- Huogen Xiao
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G2W1
| | - Brian C Bryksa
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G2W1
| | - Prasenjit Bhaumik
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Alla Gustchina
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Yoshiaki Kiso
- Laboratory of Peptide Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore 117543, Singapore
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Rickey Y Yada
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G2W1; Faculty of Land and Food Systems, University of British Columbia 248-2357 Main Mall Vancouver, BC V6T 1Z4.
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35
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Raran-Kurussi S, Waugh DS. Unrelated solubility-enhancing fusion partners MBP and NusA utilize a similar mode of action. Biotechnol Bioeng 2014; 111:2407-11. [PMID: 24942647 DOI: 10.1002/bit.25317] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/06/2014] [Accepted: 06/13/2014] [Indexed: 11/10/2022]
Abstract
The tendency of recombinant proteins to accumulate in the form of insoluble aggregates in Escherichia coli is a major hindrance to their overproduction. One of the more effective approaches to circumvent this problem is to use translation fusion partners {solubility-enhancers (SEs)}. E. coli maltose-binding protein (MBP) and N-utilization substance A (NusA) are arguably the most effective solubilizing agents that have been discovered so far. Here, we show that although these two proteins are structurally, functionally, and physicochemically distinct, they influence the solubility and folding of their fusion partners in a very similar manner. These SEs act as "holdases" that prevent the aggregation of their fusion partners. Subsequent folding of the passenger proteins, when it occurs, is either spontaneous or chaperone-mediated.
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Affiliation(s)
- Sreejith Raran-Kurussi
- Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
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36
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Dee DR, Horimoto Y, Yada RY. Conserved prosegment residues stabilize a late-stage folding transition state of pepsin independently of ground states. PLoS One 2014; 9:e101339. [PMID: 24983988 PMCID: PMC4077824 DOI: 10.1371/journal.pone.0101339] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 06/05/2014] [Indexed: 11/24/2022] Open
Abstract
The native folding of certain zymogen-derived enzymes is completely dependent upon a prosegment domain to stabilize the folding transition state, thereby catalyzing the folding reaction. Generally little is known about how the prosegment accomplishes this task. It was previously shown that the prosegment catalyzes a late-stage folding transition between a stable misfolded state and the native state of pepsin. In this study, the contributions of specific prosegment residues to catalyzing pepsin folding were investigated by introducing individual Ala substitutions and measuring the effects on the bimolecular folding reaction between the prosegment peptide and pepsin. The effects of mutations on the free energies of the individual misfolded and native ground states and the transition state were compared using measurements of prosegment-pepsin binding and folding kinetics. Five out of the seven prosegment residues examined yielded relatively large kinetic effects and minimal ground state perturbations upon mutation, findings which indicate that these residues form strengthened and/or non-native contacts in the transition state. These five residues are semi- to strictly conserved, while only a non-conserved residue had no kinetic effect. One conserved residue was shown to form native structure in the transition state. These results indicated that the prosegment, which is only 44 residues long, has evolved a high density of contacts that preferentially stabilize the folding transition state over the ground states. It is postulated that the prosegment forms extensive non-native contacts during the process of catalyzing correct inter- and intra-domain contacts during the final stages of folding. These results have implications for understanding the folding of multi-domain proteins and for the evolution of prosegment-catalyzed folding.
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Affiliation(s)
- Derek R. Dee
- Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Yasumi Horimoto
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Rickey Y. Yada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
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37
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Wang S, Horimoto Y, Dee DR, Yada RY. Understanding the mechanism of prosegment-catalyzed folding by solution NMR spectroscopy. J Biol Chem 2014; 289:697-707. [PMID: 24265313 DOI: 10.1074/jbc.m113.505891] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Multidomain protein folding is often more complex than a two-state process, which leads to the spontaneous folding of the native state. Pepsin, a zymogen-derived enzyme, without its prosegment (PS), is irreversibly denatured and folds to a thermodynamically stable, non-native conformation, termed refolded pepsin, which is separated from native pepsin by a large activation barrier. While it is known that PS binds refolded pepsin and catalyzes its conversion to the native form, little structural details are known regarding this conversion. In this study, solution NMR was used to elucidate the PS-catalyzed folding mechanism by examining the key equilibrium states, e.g. native and refolded pepsin, both in the free and PS-bound states, and pepsinogen, the zymogen form of pepsin. Refolded pepsin was found to be partially structured and lacked the correct domain-domain structure and active-site cleft formed in the native state. Analysis of chemical shift data revealed that upon PS binding refolded pepsin folds into a state more similar to that of pepsinogen than to native pepsin. Comparison of pepsin folding by wild-type and mutant PSs, including a double mutant PS, indicated that hydrophobic interactions between residues of prosegment and refolded pepsin lower the folding activation barrier. A mechanism is proposed for the binding of PS to refolded pepsin and how the formation of the native structure is mediated.
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38
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Uehara R, Angkawidjaja C, Koga Y, Kanaya S. Formation of the High-Affinity Calcium Binding Site in Pro-subtilisin E with the Insertion Sequence IS1 of Pro-Tk-subtilisin. Biochemistry 2013; 52:9080-8. [DOI: 10.1021/bi401342k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryo Uehara
- Department
of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Clement Angkawidjaja
- Department
of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- International
College, Osaka University, 1-30 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yuichi Koga
- Department
of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shigenori Kanaya
- Department
of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Yuzaki K, Sanda Y, You DJ, Uehara R, Koga Y, Kanaya S. Increase in activation rate of Pro-Tk-subtilisin by a single nonpolar-to-polar amino acid substitution at the hydrophobic core of the propeptide domain. Protein Sci 2013; 22:1711-21. [PMID: 24115021 DOI: 10.1002/pro.2371] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 09/03/2013] [Indexed: 11/07/2022]
Abstract
Tk-subtilisin (Gly70-Gly398) is a subtilisin homolog from Thermococcus kodakarensis. Active Tk-subtilisin is produced from its inactive precursor, Pro-Tk-subtilisin (Gly1-Gly398), by autoprocessing and degradation of the propeptide (Tk-propeptide, Gly1-Leu69). This activation process is extremely slow at moderate temperatures owing to high stability of Tk-propeptide. Tk-propeptide is stabilized by the hydrophobic core. To examine whether a single nonpolar-to-polar amino acid substitution at this core affects the activation rate of Pro-Tk-subtilisin, the Pro-Tk-subtilisin derivative with the Phe17 → His mutation (Pro-F17H), Tk-propeptide derivative with the same mutation (F17H-propeptide), and two active-site mutants of Pro-F17H (Pro-F17H/S324A and Pro-F17H/S324C) were constructed. The crystal structure of Pro-F17H/S324A was nearly identical to that of Pro-S324A, indicating that the mutation does not affect the structure of Pro-Tk-subtilisin. The refolding rate of Pro-F17H/S324A and autoprocessing rate of Pro-F17H/S324C were also nearly identical to those of their parent proteins (Pro-S324A and Pro-S324C). However, the activation rate of Pro-F17H greatly increased when compared with that of Pro-Tk-subtilisin, such that Pro-F17H is efficiently activated even at 40°C. The far-UV circular dichroism spectrum of F17H-propeptide did not exhibit a broad trough at 205-230 nm, which is observed in the spectrum of Tk-propeptide. F17H-propeptide is more susceptible to chymotryptic degradation than Tk-propeptide. These results suggest that F17H-propeptide is unfolded in an isolated form and is therefore rapidly degraded by Tk-subtilisin. Thus, destabilization of the hydrophobic core of Tk-propeptide by a nonpolar-to-polar amino acid substitution is an effective way to increase the activation rate of Pro-Tk-subtilisin.
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Affiliation(s)
- Kota Yuzaki
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
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40
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Mao YB, Xue XY, Tao XY, Yang CQ, Wang LJ, Chen XY. Cysteine protease enhances plant-mediated bollworm RNA interference. PLANT MOLECULAR BIOLOGY 2013; 83:119-29. [PMID: 23460027 PMCID: PMC3755213 DOI: 10.1007/s11103-013-0030-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 02/15/2013] [Indexed: 05/17/2023]
Abstract
Oral ingestion of plant-expressed double stranded RNA (dsRNA) triggers target gene suppression in insect. An important step of this process is the transmission of dsRNA from plant to midgut cells. Insect peritrophic matrix (PM) presents a barrier that prevents large molecules from entering midgut cells. Here, we show that uptake of plant cysteine proteases, such as GhCP1 from cotton (Gossypium hirsutum) and AtCP2 from Arabidopsis, by cotton bollworm (Helicoverpa armigera) larvae resulted in attenuating the PM. When GhCP1 or AtCP2 pre-fed larvae were transferred to gossypol-containing diet, the bollworm accumulated higher content of gossypol in midgut. Larvae previously ingested GhCP1 or AtCP2 were more susceptible to infection by Dendrolimus punctatus cytoplasmic polyhedrosis virus (DpCPV), a dsRNA virus. Furthermore, the pre-fed larvae exhibited enhanced RNAi effects after ingestion of the dsRNA-expressing plant. The bollworm P450 gene CYP6AE14 is involved in the larval tolerance to gossypol; cotton plants producing dsRNA of CYP6AE14 (dsCYP6AE14) were more resistant to bollworm feeding (Mao et al. in Transgenic Res 20:665-673, 2011). We found that cotton plants harboring both 35S:dsCYP6AE14 and 35S:GhCP1 were better protected from bollworm than either of the single-transgene lines. Our results demonstrate that plant cysteine proteases, which have the activity of increasing PM permeability, can be used to improve the plant-mediated RNAi against herbivorous insects.
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Affiliation(s)
- Ying-Bo Mao
- National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 People’s Republic of China
| | - Xue-Yi Xue
- National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 People’s Republic of China
| | - Xiao-Yuan Tao
- National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 People’s Republic of China
| | - Chang-Qing Yang
- National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 People’s Republic of China
| | - Ling-Jian Wang
- National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 People’s Republic of China
| | - Xiao-Ya Chen
- National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 People’s Republic of China
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41
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Proteolysin, a novel highly thermostable and cosolvent-compatible protease from the thermophilic bacterium Coprothermobacter proteolyticus. Appl Environ Microbiol 2013; 79:5625-32. [PMID: 23851086 DOI: 10.1128/aem.01479-13] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Through genome mining, we identified a gene encoding a putative serine protease of the thermitase subgroup of subtilases (EC 3.4.21.66) in the thermophilic bacterium Coprothermobacter proteolyticus. The gene was functionally expressed in Escherichia coli, and the enzyme, which we called proteolysin, was purified to near homogeneity from crude cell lysate by a single heat treatment step. Proteolysin has a broad pH tolerance and is active at temperatures of up to 80°C. In addition, the enzyme shows good activity and stability in the presence of organic solvents, detergents, and dithiothreitol, and it remains active in 6 M guanidinium hydrochloride. Based on its stability and activity profile, proteolysin can be an excellent candidate for applications where resistance to harsh process conditions is required.
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Veillard F, Sztukowska M, Mizgalska D, Ksiazek M, Houston J, Potempa B, Enghild JJ, Thogersen IB, Gomis-Rüth FX, Nguyen KA, Potempa J. Inhibition of gingipains by their profragments as the mechanism protecting Porphyromonas gingivalis against premature activation of secreted proteases. Biochim Biophys Acta Gen Subj 2013; 1830:4218-28. [PMID: 23583629 DOI: 10.1016/j.bbagen.2013.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 03/20/2013] [Accepted: 04/02/2013] [Indexed: 01/14/2023]
Abstract
BACKGROUND Arginine-specific (RgpB and RgpA) and lysine-specific (Kgp) gingipains are secretory cysteine proteinases of Porphyromonas gingivalis that act as important virulence factors for the organism. They are translated as zymogens with both N- and C-terminal extensions, which are proteolytically cleaved during secretion. In this report, we describe and characterize inhibition of the gingipains by their N-terminal prodomains to maintain latency during their export through the cellular compartments. METHODS Recombinant forms of various prodomains (PD) were analyzed for their interaction with mature gingipains. The kinetics of their inhibition of proteolytic activity along with the formation of stable inhibitory complexes with native gingipains was studied by gel filtration, native PAGE and substrate hydrolysis. RESULTS PDRgpB and PDRgpA formed tight complexes with arginine-specific gingipains (Ki in the range from 6.2nM to 0.85nM). In contrast, PDKgp showed no inhibitory activity. A conserved Arg-102 residue in PDRgpB and PDRgpA was recognized as the P1 residue. Mutation of Arg-102 to Lys reduced inhibitory potency of PDRgpB by one order of magnitude while its substitutions with Ala, Gln or Gly totally abolished the PD inhibitory activity. Covalent modification of the catalytic cysteine with tosyl-l-Lys-chloromethylketone (TLCK) or H-D-Phe-Arg-chloromethylketone did not affect formation of the stable complex. CONCLUSION Latency of arginine-specific progingipains is efficiently exerted by N-terminal prodomains thus protecting the periplasm from potentially damaging effect of prematurely activated gingipains. GENERAL SIGNIFICANCE Blocking progingipain activation may offer an attractive strategy to attenuate P. gingivalis pathogenicity.
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Affiliation(s)
- Florian Veillard
- University of Louisville School of Dentistry, Louisville, KY 40202, USA.
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de Diego I, Veillard FT, Guevara T, Potempa B, Sztukowska M, Potempa J, Gomis-Rüth FX. Porphyromonas gingivalis virulence factor gingipain RgpB shows a unique zymogenic mechanism for cysteine peptidases. J Biol Chem 2013; 288:14287-14296. [PMID: 23558682 DOI: 10.1074/jbc.m112.444927] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Zymogenicity is a regulatory mechanism that prevents inadequate catalytic activity in the wrong context. It plays a central role in maintaining microbial virulence factors in an inactive form inside the pathogen until secretion. Among these virulence factors is the cysteine peptidase gingipain B (RgpB), which is the major virulence factor secreted by the periodontopathogen Porphyromonas gingivalis that attacks host vasculature and defense proteins. The structure of the complex between soluble mature RgpB, consisting of a catalytic domain and an immunoglobulin superfamily domain, and its 205-residue N-terminal prodomain, the largest structurally characterized to date for a cysteine peptidase, reveals a novel fold for the prodomain that is distantly related to sugar-binding lectins. It attaches laterally to the catalytic domain through a large concave surface. The main determinant for latency is a surface "inhibitory loop," which approaches the active-site cleft of the enzyme on its non-primed side in a substrate-like manner. It inserts an arginine (Arg(126)) into the S1 pocket, thus matching the substrate specificity of the enzyme. Downstream of Arg(126), the polypeptide leaves the cleft, thereby preventing cleavage. Moreover, the carbonyl group of Arg(126) establishes a very strong hydrogen bond with the co-catalytic histidine, His(440), pulling it away from the catalytic cysteine, Cys(473), and toward Glu(381), which probably plays a role in orienting the side chain of His(440) during catalysis. The present results provide the structural determinants of zymogenic inhibition of RgpB by way of a novel inhibitory mechanism for peptidases in general and open the field for the design of novel inhibitory strategies in the treatment of human periodontal disease.
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Affiliation(s)
- Iñaki de Diego
- Proteolysis Laboratory, Molecular Biology Institute of Barcelona, Spanish Research Council (CSIC), Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Florian T Veillard
- University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - Tibisay Guevara
- Proteolysis Laboratory, Molecular Biology Institute of Barcelona, Spanish Research Council (CSIC), Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Barbara Potempa
- University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - Maryta Sztukowska
- University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - Jan Potempa
- University of Louisville School of Dentistry, Louisville, Kentucky 40202; Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland.
| | - F Xavier Gomis-Rüth
- Proteolysis Laboratory, Molecular Biology Institute of Barcelona, Spanish Research Council (CSIC), Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain.
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44
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Uehara R, Ueda Y, You D, Koga Y, Kanaya S. Accelerated maturation of Tk‐subtilisin by a
L
eu→
P
romutation at the
C
‐terminus of the propeptide, which reduces the binding of the propeptide to
T
k‐subtilisin. FEBS J 2013; 280:994-1006. [DOI: 10.1111/febs.12091] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/06/2012] [Accepted: 12/07/2012] [Indexed: 02/07/2023]
Affiliation(s)
- Ryo Uehara
- Department of Material and Life Science Graduate School of Engineering Osaka University Japan
| | - Yasunori Ueda
- Department of Material and Life Science Graduate School of Engineering Osaka University Japan
| | - Dong‐Ju You
- Department of Material and Life Science Graduate School of Engineering Osaka University Japan
| | - Yuichi Koga
- Department of Material and Life Science Graduate School of Engineering Osaka University Japan
| | - Shigenori Kanaya
- Department of Material and Life Science Graduate School of Engineering Osaka University Japan
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Houssen WE, Koehnke J, Zollman D, Vendome J, Raab A, Smith MCM, Naismith JH, Jaspars M. The Discovery of New Cyanobactins fromCyanothecePCC 7425 Defines a New Signature for Processing of Patellamides. Chembiochem 2012; 13:2683-9. [DOI: 10.1002/cbic.201200661] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Indexed: 11/07/2022]
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46
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He Y, Chen Y, Oganesyan N, Ruan B, O'Brochta D, Bryan PN, Orban J. Solution NMR structure of a sheddase inhibitor prodomain from the malarial parasite Plasmodium falciparum. Proteins 2012; 80:2810-7. [PMID: 23011838 DOI: 10.1002/prot.24187] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 09/06/2012] [Accepted: 09/19/2012] [Indexed: 11/10/2022]
Abstract
Plasmodium subtilisin 2 (Sub2) is a multidomain protein that plays an important role in malaria infection. Here, we describe the solution NMR structure of a conserved region of the inhibitory prodomain of Sub2 from Plasmodium falciparum, termed prosub2. Despite the absence of any detectable sequence homology, the protozoan prosub2 has structural similarity to bacterial and mammalian subtilisin-like prodomains. Comparison with the three-dimensional structures of these other prodomains suggests a likely binding interface with the catalytic domain of Sub2 and provides insights into the locations of primary and secondary processing sites in Plasmodium prodomains.
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Affiliation(s)
- Yanan He
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
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47
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Requirement of insertion sequence IS1 for thermal adaptation of Pro-Tk-subtilisin from hyperthermophilic archaeon. Extremophiles 2012; 16:841-51. [DOI: 10.1007/s00792-012-0479-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 08/27/2012] [Indexed: 10/27/2022]
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48
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49
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Gamble M, Künze G, Brancale A, Wilson KS, Jones DD. The role of substrate specificity and metal binding in defining the activity and structure of an intracellular subtilisin. FEBS Open Bio 2012; 2:209-15. [PMID: 23650602 PMCID: PMC3642151 DOI: 10.1016/j.fob.2012.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 07/02/2012] [Indexed: 11/25/2022] Open
Abstract
The dimeric intracellular subtilisin proteases (ISPs) found throughout Gram-positive bacteria are a structurally distinct class of the subtilase family. Unlike the vast majority of subtilisin-like proteases, the ISPs function exclusively within the cell, contributing the majority of observed cellular proteolytic activity. Given that they are active within the cell, little is known about substrate specificity and the role of stress signals such as divalent metal ions in modulating ISP function. We demonstrate that both play roles in defining the proteolytic activity of Bacillus clausii ISP and propose the molecular basis of their effects. Enzyme kinetics reveal that one particular synthetic tetrapeptide substrate, Phe-Ala-Ala-Phe-pNA, is hydrolysed with a catalytic efficiency ∼100-fold higher than any other tested. Heat-denatured whole proteins were found to be better substrates for ISP than the native forms. Substrate binding simulations suggest that the S1, S2 and S4 sites form defined binding pockets. The deep S1 cavity and wide S4 site are fully occupied by the hydrophobic aromatic side-chains of Phe. Divalent metal ions, probably Ca2+, are proposed to be important for ISP activity through structural changes. The presence of >0.01 mM EDTA inactivates ISP, with CD and SEC suggesting that the protein becomes less structured and potentially monomeric. Removal of Ca2+ at sites close to the dimer interface and the S1 pocket are thought to be responsible for the effect. These studies provide a new insight into the potential physiological function of ISPs, by reconciling substrate specificity and divalent metal binding to associate ISP with the unfolded protein response under stress conditions.
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Affiliation(s)
- Michael Gamble
- School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
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50
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Uehara R, Takeuchi Y, Tanaka SI, Takano K, Koga Y, Kanaya S. Requirement of Ca2+ Ions for the Hyperthermostability of Tk-Subtilisin from Thermococcus kodakarensis. Biochemistry 2012; 51:5369-78. [DOI: 10.1021/bi300427u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Ryo Uehara
- Department of Material and Life Science, Graduate School
of Engineering, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Yuki Takeuchi
- Department of Material and Life Science, Graduate School
of Engineering, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Shun-ichi Tanaka
- Department of Material and Life Science, Graduate School
of Engineering, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Kazufumi Takano
- Department of Material and Life Science, Graduate School
of Engineering, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Yuichi Koga
- Department of Material and Life Science, Graduate School
of Engineering, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Shigenori Kanaya
- Department of Material and Life Science, Graduate School
of Engineering, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
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