1
|
Noskova Y, Son O, Tekutyeva L, Balabanova L. Purification and Characterization of a DegP-Type Protease from the Marine Bacterium Cobetia amphilecti KMM 296. Microorganisms 2023; 11:1852. [PMID: 37513024 PMCID: PMC10383082 DOI: 10.3390/microorganisms11071852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
A new member of the DegP-type periplasmic serine endoproteases of the S1C family from the marine bacterium Cobetia amphilecti KMM 296 (CamSP) was expressed in Escherichia coli cells. The calculated molecular weight, number of amino acids, and isoelectric point (pI) of the mature protein CamSP are 69.957 kDa, 666, and 4.84, respectively. The proteolytic activity of the purified recombinant protease CamSP was 2369.4 and 1550.9 U/mg with the use of 1% bovine serum albumin (BSA) and casein as the substrates, respectively. The enzyme CamSP exhibited maximum activity at pH 6.0-6.2, while it was stable over a wide pH range from 5.8 to 8.5. The optimal temperature for the CamSP protease activity was 50 °C. The enzyme required NaCl or KCl at concentrations of 0.3 and 0.5 M, respectively, for its maximum activity. The Michaelis constant (Km) and Vmax for BSA were determined to be 41.7 µg/mL and 0.036 µg/mL min-1, respectively. The metal ions Zn2+, Cu2+, Mn2+, Li2+, Mg2+, and Ca2+ slightly activated CamSP, while the addition of CoCl2 to the incubation mixture resulted in a twofold increase in its protease activity. Ethanol, isopropanol, glycerol, and Triton-X-100 increased the activity of CamSP from two- to four-times. The protease CamSP effectively degraded the wheat flour proteins but had no proteolytic activity towards soybean, corn, and the synthetic substrates, α-benzoyl-Arg-p-nitroanilide (BAPNA) and N-Succinyl-L-alanyl-L-alanyl-L-prolyl-L-phenylalanine 4-nitroanilide (SAPNA).
Collapse
Affiliation(s)
- Yulia Noskova
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia
| | - Oksana Son
- Advanced Engineering School, Institute of Biotechnology, Bioengineering and Food Systems, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia
| | - Liudmila Tekutyeva
- Advanced Engineering School, Institute of Biotechnology, Bioengineering and Food Systems, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia
| | - Larissa Balabanova
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia
- Advanced Engineering School, Institute of Biotechnology, Bioengineering and Food Systems, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia
| |
Collapse
|
2
|
Patipong T, Kageyama H, Waditee-Sirisattha R. Insights into the phylogeny and transcriptional response of serine proteases in a halotolerant cyanobacterium Halothece sp. PCC7418. PLANT SIGNALING & BEHAVIOR 2021; 16:1913556. [PMID: 34184613 PMCID: PMC8281059 DOI: 10.1080/15592324.2021.1913556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 06/13/2023]
Abstract
Serine proteases are a class of versatile proteolytic enzymes. They are necessary for protein catabolism, intracellular amino acid turnover, and regulation of proteins involved in diverse molecular and cellular processes across taxa. In this study, bioinformatic analyses revealed a significantly large number of serine proteases in the halotolerant cyanobacterium Halothece sp. PCC7418 (hereafter referred to as Halothece 7418) compared to the model freshwater cyanobacterium Synechococcus elongatus PCC7942 (hereafter referred to as S. elongatus 7942). The cyanobacterial serine proteases are likely derived from different linages since no conserved motifs were detected. The presence of highly diverse serine proteases in Halothece 7418 implicated an evolutionary-mediated modification of several proteases, which may play numerous physiological roles. We also examined the gene expression patterns of 34 serine protease encoding genes in Halothece 7418 exposed to salt stress. Our results revealed that several serine protease genes were drastically up-regulated under salt with high concentration but remained unchanged under salt with low concentration. All four clp genes (H1996, H1997, H0950, and H3375) and H3553 gene (which encodes a putative HtrA protease) were significantly induced upon salt stress. These responses support the roles of the housekeeping pathways in both the degradation of damaged proteins induced by salt stress and regulation of proteins involved in the molecular recovery from salt stress. Since serine proteases share several biochemical features and physiological functions, the results from this study provide an insight into diversification of serine proteases in cyanobacteria. Further, these results will increase our understanding of several mechanisms at the subcellular level.
Collapse
Affiliation(s)
- Tanutcha Patipong
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Pathumwan, Thailand
| | - Hakuto Kageyama
- Graduate School of Environmental and Human Sciences, Meijo University, Nagoya, Japan
- Department of Chemistry, Faculty of Science and Technology, Meijo University, Nagoya, Japan
| | | |
Collapse
|
3
|
Sun B, Lv J, Chen J, Liu Z, Zhou Y, Liu L, Jin Y, Wang F. Size-Selective VAILase Proteolysis Provides Dynamic Insights into Protein Structures. Anal Chem 2021; 93:10653-10660. [PMID: 34291915 DOI: 10.1021/acs.analchem.1c02042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Monitoring the dynamic alterations of protein structures within an aqueous solution remains enormously challenging. In this study, we describe a size-selective VAILase proteolysis (SVP)-mass spectrometry (MS) strategy to probe the protein structure changes without strict control of the proteolysis kinetics. The unique conformation selectivity of SVP depends on the uniform nano-sized entrance pores of the VAILase hexameric cage as well as the six inherent molecular rulers in the VAILase-substrate recognition and cleavage. The dynamic insights into subtle conformation alterations of both myoglobin unfolding transition and Aurora kinase A-inhibitor binding are successfully captured using the SVP strategy, which matches well with the results in the molecular dynamics simulation. Our work provides a new paradigm of size-selective native proteolysis for exploring the aqueous protein structure-function relationships.
Collapse
Affiliation(s)
- Binwen Sun
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji Lv
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jin Chen
- Clinical Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362000, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Ye Zhou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lin Liu
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China
| | - Yan Jin
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
4
|
Santos M, Pereira SB, Flores C, Príncipe C, Couto N, Karunakaran E, Cravo SM, Oliveira P, Tamagnini P. Absence of KpsM (Slr0977) Impairs the Secretion of Extracellular Polymeric Substances (EPS) and Impacts Carbon Fluxes in Synechocystis sp. PCC 6803. mSphere 2021; 6:e00003-21. [PMID: 33504656 PMCID: PMC7885315 DOI: 10.1128/msphere.00003-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 12/02/2022] Open
Abstract
Many cyanobacteria produce extracellular polymeric substances (EPS), composed mainly of heteropolysaccharides, that play a variety of physiological roles, being crucial for cell protection, motility, and biofilm formation. However, due to their complexity, the EPS biosynthetic pathways as well as their assembly and export mechanisms are still far from being fully understood. Here, we show that the absence of a putative EPS-related protein, KpsM (Slr0977), has a pleiotropic effect on Synechocystis sp. strain PCC 6803 physiology, with a strong impact on the export of EPS and carbon fluxes. The kpsM mutant exhibits a significant reduction of released polysaccharides and a smaller decrease of capsular polysaccharides, but it accumulates more polyhydroxybutyrate (PHB) than the wild type. In addition, this strain shows a light/cell density-dependent clumping phenotype and exhibits an altered protein secretion capacity. Furthermore, the most important structural component of pili, the protein PilA, was found to have a modified glycosylation pattern in the mutant compared to the wild type. Proteomic and transcriptomic analyses revealed significant changes in the mechanisms of energy production and conversion, namely, photosynthesis, oxidative phosphorylation, and carbon metabolism, in response to the inactivation of slr0977 Overall, this work shows for the first time that cells with impaired EPS secretion undergo transcriptomic and proteomic adjustments, highlighting the importance of EPS as a major carbon sink in cyanobacteria. The accumulation of PHB in cells of the mutant, without affecting significantly its fitness/growth rate, points to its possible use as a chassis for the production of compounds of interest.IMPORTANCE Most cyanobacteria produce extracellular polymeric substances (EPS) that fulfill different biological roles depending on the strain/environmental conditions. The interest in the cyanobacterial EPS synthesis/export pathways has been increasing, not only to optimize EPS production but also to efficiently redirect carbon flux toward the production of other compounds, allowing the implementation of industrial systems based on cyanobacterial cell factories. Here, we show that a Synechocystis kpsM (slr0977) mutant secretes less EPS than the wild type, accumulating more carbon intracellularly, as polyhydroxybutyrate. Further characterization showed a light/cell density-dependent clumping phenotype, altered protein secretion, and modified glycosylation of PilA. The proteome and transcriptome of the mutant revealed significant changes, namely, in photosynthesis and carbon metabolism. Altogether, this work provides a comprehensive overview of the impact of kpsM disruption on Synechocystis physiology, highlighting the importance of EPS as a carbon sink and showing how cells adapt when their secretion is impaired, and the redirection of the carbon fluxes.
Collapse
Affiliation(s)
- Marina Santos
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
- Programa Doutoral em Biologia Molecular e Celular (MCbiology), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Sara B Pereira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
| | - Carlos Flores
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
| | - Catarina Príncipe
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Narciso Couto
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Esther Karunakaran
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Sara M Cravo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Matosinhos, Portugal
- Laboratório de Química Orgânica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Paulo Oliveira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Paula Tamagnini
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| |
Collapse
|
5
|
Zarzecka U, Grinzato A, Kandiah E, Cysewski D, Berto P, Skorko-Glonek J, Zanotti G, Backert S. Functional analysis and cryo-electron microscopy of Campylobacterjejuni serine protease HtrA. Gut Microbes 2020; 12:1-16. [PMID: 32960677 PMCID: PMC7524362 DOI: 10.1080/19490976.2020.1810532] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Campylobacter jejuni is a predominant zoonotic pathogen causing gastroenteritis and other diseases in humans. An important bacterial virulence factor is the secreted serine protease HtrA (HtrA Cj ), which targets tight and adherens junctional proteins in the gut epithelium. Here we have investigated the function and structure of HtrA Cj using biochemical assays and cryo-electron microscopy. Mass spectrometry analysis identified differences and similarities in the cleavage site specificity for HtrA Cj by comparison to the HtrA counterparts from Helicobacter pylori and Escherichia coli. We defined the architecture of HtrA Cj at 5.8 Å resolution as a dodecamer, built of four trimers. The contacts between the trimers are quite loose, a fact that explains the flexibility and mobility of the dodecameric assembly. This flexibility has also been studied through molecular dynamics simulation, which revealed opening of the dodecamer to expose the proteolytically active site of the protease. Moreover, we examined the rearrangements at the level of oligomerization in the presence or absence of substrate using size exclusion chromatography, which revealed hexamers, dodecamers and larger oligomeric forms, as well as remarkable stability of higher oligomeric forms (> 12-mers) compared to previously tested homologs from other bacteria. Extremely dynamic decay of the higher oligomeric forms into lower forms was observed after full cleavage of the substrate by the proteolytically active variant of HtrA Cj . Together, this is the first report on the in-depth functional and structural analysis of HtrA Cj , which may allow the construction of therapeutically relevant HtrA Cj inhibitors in the near future.
Collapse
Affiliation(s)
- Urszula Zarzecka
- Division of Microbiology, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany,Department of General and Medical Biochemistry, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | | | | | - Dominik Cysewski
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Science, Warsaw, Poland
| | - Paola Berto
- Department of Biomedical Sciences, University of Padua, Padova, Italy
| | - Joanna Skorko-Glonek
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Giuseppe Zanotti
- Department of Biomedical Sciences, University of Padua, Padova, Italy,Giuseppe Zanotti Department of Biomedical Sciences, University of Padua, Padova, Italy
| | - Steffen Backert
- Division of Microbiology, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany,CONTACT Steffen Backert Division of Microbiology, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| |
Collapse
|
6
|
The evolutionarily conserved HtrA is associated with stress tolerance and protein homeostasis in the halotolerant cyanobacterium Halothece sp. PCC7418. Extremophiles 2020; 24:377-389. [PMID: 32146515 DOI: 10.1007/s00792-020-01162-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 02/21/2020] [Indexed: 12/22/2022]
Abstract
The HtrA protein family represents an important class of serine proteases that are widely distributed across taxa. These evolutionarily conserved proteins are crucial for survival and function as monitors of protein synthesis during various stresses. Here, we performed gene expression analysis of the entire set of putative serine protease genes in Halothece sp. PCC7418 under salt stress conditions. The gene-encoding HtrA2 (H3553) was highly upregulated. This gene was cloned and functionally characterized, and its sub-cellular localization was determined. The recombinant H3553 protein (rH3553) displayed a pH optimum of 8.0, remained stable at 45 °C, and its proteolytic activity was not affected by salts. H3553 completely degraded the unfolded model protein, β-casein. In contrast, the folded model substrates (lysozyme or BSA) were not degraded by rH3553. Denaturation of BSA at a high temperature significantly increased its degradation by rH3553. H3553 was detected in the soluble protein fraction as well as the plasma membrane and thylakoid membrane fractions. Interestingly, the majority of H3553 was present in the plasma membrane under salt and heat stress conditions. Thus, H3553 resides in multiple sub-cellular locations and its localization drastically changes after exposure to stresses. Taken together, H3553 underpins protein quality-control process and is involved in the response and adaptation to salinity and heat stresses.
Collapse
|
7
|
Sun B, Liu Z, Fang Z, Dong W, Yu Y, Ye M, Liu L, Wang H, Wang F. Probing the Proteomics Dark Regions by VAILase Cleavage at Aliphatic Amino Acids. Anal Chem 2020; 92:2770-2777. [PMID: 31903742 DOI: 10.1021/acs.analchem.9b05048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteomics emerges from the protein identification to protein functional elucidation, which depends to a large extent on the characterization of protein sequences. However, a large part of proteome sequences remains unannotated due to the limitation in proteolytic digestion by golden standard protease trypsin. Herein, we demonstrated that a cyanobacterial protease VAILase could specifically cleave at the short-chain aliphatic amino acids valine, alanine, leucine, isoleucine and threonine with cleavage specificity about 92% in total for proteomic analysis. The unique features of VAILase cleavage facilitate the characterization of most proteins and exhibit high complementarity to trypsin, and 22% of the covered sequences by VAILase are unique. VAILase can greatly improve the coverages of sequences with abundant aliphatic residues that are usually dark regions in conventional proteomic analysis, such as the transmembrane regions within anion exchanger 1 and photosystem II.
Collapse
Affiliation(s)
- Binwen Sun
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , 116023 , China.,University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , 116023 , China
| | - Zheng Fang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , 116023 , China.,University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Wei Dong
- CAS Key Laboratory of Photobiology , Institute of Botany, Chinese Academy of Sciences , Beijing , 100049 , China
| | - Yang Yu
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun , 130022 , China.,University of Science and Technology of China , Hefei , 230026 , China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , 116023 , China
| | - Lin Liu
- CAS Key Laboratory of Photobiology , Institute of Botany, Chinese Academy of Sciences , Beijing , 100049 , China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun , 130022 , China.,University of Science and Technology of China , Hefei , 230026 , China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , 116023 , China.,University of Chinese Academy of Sciences , Beijing , 100049 , China
| |
Collapse
|
8
|
Zarzecka U, Modrak-Wójcik A, Figaj D, Apanowicz M, Lesner A, Bzowska A, Lipinska B, Zawilak-Pawlik A, Backert S, Skorko-Glonek J. Properties of the HtrA Protease From Bacterium Helicobacter pylori Whose Activity Is Indispensable for Growth Under Stress Conditions. Front Microbiol 2019; 10:961. [PMID: 31130939 PMCID: PMC6509562 DOI: 10.3389/fmicb.2019.00961] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/16/2019] [Indexed: 12/22/2022] Open
Abstract
The protease high temperature requirement A from the gastric pathogen Helicobacter pylori (HtrAHp) belongs to the well conserved family of serine proteases. HtrAHp is an important secreted virulence factor involved in the disruption of tight and adherens junctions during infection. Very little is known about the function of HtrAHp in the H. pylori cell physiology due to the lack of htrA knockout strains. Here, using a newly constructed ΔhtrA mutant strain, we found that bacteria deprived of HtrAHp showed increased sensitivity to certain types of stress, including elevated temperature, pH and osmotic shock, as well as treatment with puromycin. These data indicate that HtrAHp plays a protective role in the H. pylori cell, presumably associated with maintenance of important periplasmic and outer membrane proteins. Purified HtrAHp was shown to be very tolerant to a wide range of temperature and pH values. Remarkably, the protein exhibited a very high thermal stability with the melting point (Tm) values of above 85°C. Moreover, HtrAHp showed the capability to regain its active structure following treatment under denaturing conditions. Taken together, our work demonstrates that HtrAHp is well adapted to operate under harsh conditions as an exported virulence factor, but also inside the bacterial cell as an important component of the protein quality control system in the stressed cellular envelope.
Collapse
Affiliation(s)
- Urszula Zarzecka
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdańsk, Gdańsk, Poland.,Division of Microbiology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Anna Modrak-Wójcik
- Division of Biophysics, Faculty of Physics, Institute of Experimental Physics, University of Warsaw, Warsaw, Poland
| | - Donata Figaj
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Malgorzata Apanowicz
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Adam Lesner
- Department of Environmental Technology, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Agnieszka Bzowska
- Division of Biophysics, Faculty of Physics, Institute of Experimental Physics, University of Warsaw, Warsaw, Poland
| | - Barbara Lipinska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Anna Zawilak-Pawlik
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Steffen Backert
- Division of Microbiology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Joanna Skorko-Glonek
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| |
Collapse
|
9
|
Zarzecka U, Modrak-Wojcik A, Bayassi M, Szewczyk M, Gieldon A, Lesner A, Koper T, Bzowska A, Sanguinetti M, Backert S, Lipinska B, Skorko-Glonek J. Biochemical properties of the HtrA homolog from bacterium Stenotrophomonas maltophilia. Int J Biol Macromol 2017; 109:992-1005. [PMID: 29155201 DOI: 10.1016/j.ijbiomac.2017.11.086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/12/2017] [Accepted: 11/13/2017] [Indexed: 11/29/2022]
Abstract
The HtrA proteins due to their proteolytic, and in many cases chaperone activity, efficiently counteract consequences of stressful conditions. In the environmental bacterium and nosocomial pathogen Stenotrophomonas maltophilia HtrA (HtrASm) is induced as a part of adaptive response to host temperature (37°C). We examined the biochemical properties of HtrASm and compared them with those of model HtrAEc from Escherichia coli. We found that HtrASm is a protease and chaperone that operates over a wide range of pH and is highly active at temperatures between 35 and 37°C. The temperature-sensitive activity corresponded well with the lower thermal stability of the protein and weaker stability of the oligomer. Interestingly, the enzyme shows slightly different substrate cleavage specificity when compared to other bacterial HtrAs. A computational model of the three-dimensional structure of HtrASm indicates differences in the S1 substrate specificity pocket and suggests weaker inter-trimer interactions when compared to HtrAEc. The observed features of HtrASm suggest that this protein may play a protective role under stressful conditions acting both as a protease and a chaperone. The optimal temperatures for the protein activity may reflect the evolutionary adaptation of S. maltophilia to life in soil or aqueous environments, where the temperatures are usually much below 37°C.
Collapse
Affiliation(s)
- Urszula Zarzecka
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Gdansk 80-308, Poland
| | - Anna Modrak-Wojcik
- Department of Biophysics, Institute of Experimental Physics, University of Warsaw, Warsaw 02-089, Poland
| | - Martyna Bayassi
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Gdansk 80-308, Poland
| | - Maciej Szewczyk
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Gdansk 80-308, Poland
| | - Artur Gieldon
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Gdansk 80-952, Poland
| | - Adam Lesner
- Department of Molecular Biochemistry, Faculty of Chemistry, University of Gdansk, Gdansk 80-952, Poland
| | - Tomasz Koper
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Gdansk 80-308, Poland
| | - Agnieszka Bzowska
- Department of Biophysics, Institute of Experimental Physics, University of Warsaw, Warsaw 02-089, Poland
| | - Maurizio Sanguinetti
- Institute of Microbiology, Catholic University of the Sacred Heart, Rome 00168, Italy
| | - Steffen Backert
- Division of Microbiology, Department of Biology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen 91058, Germany
| | - Barbara Lipinska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Gdansk 80-308, Poland
| | - Joanna Skorko-Glonek
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Gdansk 80-308, Poland.
| |
Collapse
|
10
|
The HhoA protease from Synechocystis sp. PCC 6803 – Novel insights into structure and activity regulation. J Struct Biol 2017; 198:147-153. [DOI: 10.1016/j.jsb.2016.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 11/18/2022]
|
11
|
Zhu F, Yang X, Wu Y, Wang Y, Tang XF, Tang B. Release of an HtrA-Like Protease from the Cell Surface of Thermophilic Brevibacillus sp. WF146 via Substrate-Induced Autoprocessing of the N-terminal Membrane Anchor. Front Microbiol 2017; 8:481. [PMID: 28377763 PMCID: PMC5359297 DOI: 10.3389/fmicb.2017.00481] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 03/08/2017] [Indexed: 01/07/2023] Open
Abstract
High-temperature requirement A (HtrA)-like proteases participate in protein quality control in prokaryotes and eukaryotes by degrading damaged proteins; however, little is known about HtrAs produced by thermophiles. HtrAw is an HtrA-like protease of thermophilic Brevibacillus sp. WF146. The intact form of HtrAw (iHtrAw) consisting of a transmembrane segment-containing N-terminal domain, a trypsin-like protease domain, and a C-terminal PDZ domain was produced in Escherichia coli. Purified iHtrAw itself is unable to cleave the N-terminal domain, but requires protein substrates to autoprocess the N-terminal domain intermolecularly, yielding a short form (sHtrAw). Mutation at the substrate-binding site in the PDZ domain affects the conversion of iHtrAw to sHtrAw. Deletion analysis revealed that the N-terminal domain is not necessary for enzyme folding, activity, and thermostability. Compared with other known HtrAs, HtrAw contains an additional Ca2+-binding Dx[DN]xDG motif important for enzyme stability and/or activity. When produced in an htrA/htrB double deletion mutant of Bacillus subtilis, iHtrAw localized predominantly to the cell pellet, and the amount of sHtrAw in the culture supernatant increased at elevated temperatures. Moreover, HtrAw increased the heat resistance of the B. subtilis mutant. In strain WF146, HtrAw exists in both a cell-associated intact form and a cell-free short form; an increase in growth temperature enhanced HtrAw production and the amount of cell-free short form. Release of the short form of HtrAw from the membrane may have the advantage of allowing the enzyme to freely access and degrade damaged proteins surrounding the bacterium living at high temperatures.
Collapse
Affiliation(s)
- Fengtao Zhu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University Wuhan, China
| | - Xing Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University Wuhan, China
| | - Yan Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University Wuhan, China
| | - Yasi Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University Wuhan, China
| | - Xiao-Feng Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan UniversityWuhan, China; Hubei Provincial Cooperative Innovation Center of Industrial FermentationWuhan, China
| | - Bing Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan UniversityWuhan, China; Hubei Provincial Cooperative Innovation Center of Industrial FermentationWuhan, China
| |
Collapse
|
12
|
Dong W, Wang J, Niu G, Zhao S, Liu L. Crystal structure of the zinc-bound HhoA protease from Synechocystis sp. PCC 6803. FEBS Lett 2016; 590:3435-3442. [PMID: 27616292 DOI: 10.1002/1873-3468.12416] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/04/2016] [Accepted: 09/05/2016] [Indexed: 11/05/2022]
Abstract
The high temperature requirement A (HtrA) proteases are oligomeric serine proteases essential for protein quality control. HtrA homolog A (HhoA) from the photosynthetic cyanobacterium Synechocystis sp. PCC 6803 assembles into a proteolytically active hexamer. Herein, we present the crystal structure of the hexameric HhoA in complex with the copurified peptide. Our data indicate the presence of three methionines in close proximity to the peptide-binding site of the PDZ domain. Unexpectedly, we observed that a zinc ion is accommodated within the central channel formed by a HhoA trimer. However, neither calcium nor magnesium showed affinity for HhoA. The role of the zinc ion in HhoA was tested in an in vitro proteolytic assay against the nonspecific substrate β-casein and was found to be inhibitory. Our findings provide insights into the regulation of HhoA by a redox-related mechanism involving methionine residues and by zinc ion-binding within the central channel.
Collapse
Affiliation(s)
- Wei Dong
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jia Wang
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guoqi Niu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Shun Zhao
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Lin Liu
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
13
|
HtrA Is Important for Stress Resistance and Virulence in Haemophilus parasuis. Infect Immun 2016; 84:2209-2219. [PMID: 27217419 PMCID: PMC4962635 DOI: 10.1128/iai.00147-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/12/2016] [Indexed: 02/06/2023] Open
Abstract
Haemophilus parasuis is an opportunistic pathogen that causes Glässer's disease in swine, with polyserositis, meningitis, and arthritis. The high-temperature requirement A (HtrA)-like protease, which is involved in protein quality control, has been reported to be a virulence factor in many pathogens. In this study, we showed that HtrA of H. parasuis (HpHtrA) exhibited both chaperone and protease activities. Finally, nickel import ATP-binding protein (NikE), periplasmic dipeptide transport protein (DppA), and outer membrane protein A (OmpA) were identified as proteolytic substrates for HpHtrA. The protease activity reached its maximum at 40°C in a time-dependent manner. Disruption of the htrA gene from strain SC1401 affected tolerance to temperature stress and resistance to complement-mediated killing. Furthermore, increased autoagglutination and biofilm formation were detected in the htrA mutant. In addition, the htrA mutant was significantly attenuated in virulence in the murine model of infection. Together, these data demonstrate that HpHtrA plays an important role in the virulence of H. parasuis.
Collapse
|
14
|
Schmidt TP, Goetz C, Huemer M, Schneider G, Wessler S. Calcium binding protects E-cadherin from cleavage by Helicobacter pylori HtrA. Gut Pathog 2016; 8:29. [PMID: 27274359 PMCID: PMC4895972 DOI: 10.1186/s13099-016-0112-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/30/2016] [Indexed: 02/07/2023] Open
Abstract
Background The cell adhesion and tumor suppressor protein E-cadherin is an important factor in the establishment and maintenance of epithelial integrity. E-cadherin is a single transmembrane protein, which consists of an intracellular domain (IC), a transmembrane domain (TD), and five extracellular domains (EC). EC domains form homophilic interactions in cis and trans that require calcium binding to the linker region between the EC domains. In our previous studies, we identified the serine protease high temperature requirement A (HtrA) from the human pathogen and class-I carcinogen Helicobacter pylori (H. pylori) as a bacterial E-cadherin-cleaving protease that targets the linker region of the EC domains, thereby disrupting gastric epithelial integrity. However, it remains unclear how calcium binding to the E-cadherin linker regions affects HtrA-mediated cleavage. Results Investigating the influence of calcium on the HtrA-mediated cleavage of recombinant E-cadherin (rCdh1) in vitro, we tested different concentrations of calcium ions and the calcium chelator ethylenediaminetetraacetic acid (EDTA). Calcium efficiently reduced HtrA-mediated E-cadherin fragmentation. Conversely, the addition of EDTA strongly increased cleavage, resulting in a ladder of defined E-cadherin fragments. However, calcium ions did not affect HtrA oligomerization and protease activity as monitored by degradation of the universal protease substrate casein. Finally, addition of ethyleneglycol-bis-tetraacetic acid (EGTA) slightly enhanced E-cadherin cleavage during H. pylori infection of gastric epithelial cells. Conclusions Our results suggest that calcium blocks HtrA-mediated cleavage by interfering with the accessibility of calcium-binding regions between the individual EC domains, which have been identified as cleavage sites of HtrA. Electronic supplementary material The online version of this article (doi:10.1186/s13099-016-0112-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Thomas P Schmidt
- Cancer Cluster Salzburg, Department of Molecular Biology, Division of Microbiology, Paris-Lodron University, Salzburg, Austria
| | - Camilla Goetz
- Cancer Cluster Salzburg, Department of Molecular Biology, Division of Microbiology, Paris-Lodron University, Salzburg, Austria
| | - Markus Huemer
- Cancer Cluster Salzburg, Department of Molecular Biology, Division of Microbiology, Paris-Lodron University, Salzburg, Austria
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Silja Wessler
- Cancer Cluster Salzburg, Department of Molecular Biology, Division of Microbiology, Paris-Lodron University, Salzburg, Austria
| |
Collapse
|
15
|
Cheregi O, Wagner R, Funk C. Insights into the Cyanobacterial Deg/HtrA Proteases. FRONTIERS IN PLANT SCIENCE 2016; 7:694. [PMID: 27252714 PMCID: PMC4877387 DOI: 10.3389/fpls.2016.00694] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/05/2016] [Indexed: 06/05/2023]
Abstract
Proteins are the main machinery for all living processes in a cell; they provide structural elements, regulate biochemical reactions as enzymes, and are the interface to the outside as receptors and transporters. Like any other machinery proteins have to be assembled correctly and need maintenance after damage, e.g., caused by changes in environmental conditions, genetic mutations, and limitations in the availability of cofactors. Proteases and chaperones help in repair, assembly, and folding of damaged and misfolded protein complexes cost-effective, with low energy investment compared with neo-synthesis. Despite their importance for viability, the specific biological role of most proteases in vivo is largely unknown. Deg/HtrA proteases, a family of serine-type ATP-independent proteases, have been shown in higher plants to be involved in the degradation of the Photosystem II reaction center protein D1. The objective of this review is to highlight the structure and function of their cyanobacterial orthologs. Homology modeling was used to find specific features of the SynDeg/HtrA proteases of Synechocystis sp. PCC 6803. Based on the available data concerning their location and their physiological substrates we conclude that these Deg proteases not only have important housekeeping and chaperone functions within the cell, but also are needed for remodeling the cell exterior.
Collapse
|
16
|
Inactivation of the Deg protease family in the cyanobacterium Synechocystis sp. PCC 6803 has impact on the outer cell layers. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 152:383-94. [DOI: 10.1016/j.jphotobiol.2015.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/12/2015] [Accepted: 05/15/2015] [Indexed: 12/13/2022]
|
17
|
Purification, biochemical characterization and structural modeling of a potential htrA-like serine protease from Bacillus subtilis DR8806. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.02.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
18
|
Proteomic approaches to identify substrates of the three Deg/HtrA proteases of the cyanobacterium Synechocystis sp. PCC 6803. Biochem J 2015; 468:373-84. [PMID: 25877158 DOI: 10.1042/bj20150097] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 04/16/2015] [Indexed: 12/21/2022]
Abstract
The family of Deg/HtrA proteases plays an important role in quality control of cellular proteins in a wide range of organisms. In the genome of the cyanobacterium Synechocystis sp. PCC 6803, a model organism for photosynthetic research and renewable energy products, three Deg proteases are encoded, termed HhoA, HhoB and HtrA. In the present study, we compared wild-type (WT) Synechocystis cells with the single insertion mutants ΔhhoA, ΔhhoB and ΔhtrA. Protein expression of the remaining Deg/HtrA proteases was strongly affected in the single insertion mutants. Detailed proteomic studies using DIGE (difference gel electrophoresis) and N-terminal COFRADIC (N-terminal combined fractional diagonal chromatography) revealed that inactivation of a single Deg protease has similar impact on the proteomes of the three mutants; differences to WT were observed in enzymes involved in the major metabolic pathways. Changes in the amount of phosphate permease system Pst-1 were observed only in the insertion mutant ΔhhoB. N-terminal COFRADIC analyses on cell lysates of ΔhhoB confirmed changed amounts of many cell envelope proteins, including the phosphate permease systems, compared with WT. In vitro COFRADIC studies were performed to identify the specificity profiles of the recombinant proteases rHhoA, rHhoB or rHtrA added to the Synechocystis WT proteome. The combined in vivo and in vitro N-terminal COFRADIC datasets propose RbcS as a natural substrate for HhoA, PsbO for HhoB and HtrA and Pbp8 for HtrA. We therefore suggest that each Synechocystis Deg protease protects the cell through different, but connected mechanisms.
Collapse
|
19
|
Tanz SK, Castleden I, Hooper CM, Small I, Millar AH. Using the SUBcellular database for Arabidopsis proteins to localize the Deg protease family. FRONTIERS IN PLANT SCIENCE 2014; 5:396. [PMID: 25161662 PMCID: PMC4130198 DOI: 10.3389/fpls.2014.00396] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/24/2014] [Indexed: 05/20/2023]
Abstract
Sub-functionalization during the expansion of gene families in eukaryotes has occurred in part through specific subcellular localization of different family members. To better understand this process in plants, compiled records of large-scale proteomic and fluorescent protein localization datasets can be explored and bioinformatic predictions for protein localization can be used to predict the gaps in experimental data. This process can be followed by targeted experiments to test predictions. The SUBA3 database is a free web-service at http://suba.plantenergy.uwa.edu.au that helps users to explore reported experimental data and predictions concerning proteins encoded by gene families and to define the experiments required to locate these homologous sets of proteins. Here we show how SUBA3 can be used to explore the subcellular location of the Deg protease family of ATP-independent serine endopeptidases (Deg1-Deg16). Combined data integration and new experiments refined location information for Deg1 and Deg9, confirmed Deg2, Deg5, and Deg8 in plastids and Deg 15 in peroxisomes and provide substantial experimental evidence for mitochondrial localized Deg proteases. Two of these, Deg3 and Deg10, additionally localized to the plastid, revealing novel dual-targeted Deg proteases in the plastid and the mitochondrion. SUBA3 is continually updated to ensure that researchers can use the latest published data when planning the experimental steps remaining to localize gene family functions.
Collapse
Affiliation(s)
- Sandra K. Tanz
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western AustraliaPerth, WA, Australia
- *Correspondence: Sandra K. Tanz, The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, M316, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia e-mail:
| | - Ian Castleden
- Centre of Excellence in Computational Systems Biology, The University of Western AustraliaPerth, WA, Australia
| | - Cornelia M. Hooper
- Centre of Excellence in Computational Systems Biology, The University of Western AustraliaPerth, WA, Australia
| | - Ian Small
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western AustraliaPerth, WA, Australia
- Centre of Excellence in Computational Systems Biology, The University of Western AustraliaPerth, WA, Australia
| | - A. Harvey Millar
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western AustraliaPerth, WA, Australia
- Centre of Excellence in Computational Systems Biology, The University of Western AustraliaPerth, WA, Australia
- Centre for Comparative Analysis on Biomolecular Networks, The University of Western AustraliaPerth, WA, Australia
| |
Collapse
|
20
|
Miranda H, Cheregi O, Netotea S, Hvidsten TR, Moritz T, Funk C. Co-expression analysis, proteomic and metabolomic study on the impact of a Deg/HtrA protease triple mutant in Synechocystis sp. PCC 6803 exposed to temperature and high light stress. J Proteomics 2013; 78:294-311. [DOI: 10.1016/j.jprot.2012.09.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/14/2012] [Accepted: 09/30/2012] [Indexed: 11/26/2022]
|
21
|
Cassone M, Gagne AL, Spruce LA, Seeholzer SH, Sebert ME. The HtrA protease from Streptococcus pneumoniae digests both denatured proteins and the competence-stimulating peptide. J Biol Chem 2012; 287:38449-59. [PMID: 23012372 DOI: 10.1074/jbc.m112.391482] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The HtrA protease of Streptococcus pneumoniae functions both in a general stress response role and as an error sensor that specifically represses genetic competence when the overall level of biosynthetic errors in cellular proteins is low. However, the mechanism through which HtrA inhibits development of competence has been unknown. We found that HtrA digested the pneumococcal competence-stimulating peptide (CSP) and constituted the primary extracytoplasmic CSP-degrading activity in cultures of S. pneumoniae. Mass spectrometry demonstrated that cleavage predominantly followed residue Phe-8 of the CSP-1 isoform of the peptide within its central hydrophobic patch, and in competition assays, both CSP-1 and CSP-2 interacted with HtrA with similar efficiencies. More generally, analysis of β-casein digestion and of digestion within HtrA itself revealed a preference for substrates with non-polar residues at the P1 site. Consistent with a specificity for exposed hydrophobic residues, competition from native BSA only weakly inhibited digestion of CSP, but denaturation converted BSA into a strong competitive inhibitor of such proteolysis. Together these findings support a model in which digestion of CSP by HtrA is reduced in the presence of other unfolded proteins that serve as alternative targets for degradation. Such competition may provide a mechanism by which HtrA functions in a quality control capacity to monitor the frequency of biosynthetic errors that result in protein misfolding.
Collapse
Affiliation(s)
- Marco Cassone
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | | | | | | | | |
Collapse
|
22
|
Degradation of PsbO by the Deg protease HhoA Is thioredoxin dependent. PLoS One 2012; 7:e45713. [PMID: 23029195 PMCID: PMC3446894 DOI: 10.1371/journal.pone.0045713] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 08/24/2012] [Indexed: 02/02/2023] Open
Abstract
The widely distributed members of the Deg/HtrA protease family play an important role in the proteolysis of misfolded and damaged proteins. Here we show that the Deg protease rHhoA is able to degrade PsbO, the extrinsic protein of the Photosystem II (PSII) oxygen-evolving complex in Synechocystis sp. PCC 6803 and in spinach. PsbO is known to be stable in its oxidized form, but after reduction by thioredoxin it became a substrate for recombinant HhoA (rHhoA). rHhoA cleaved reduced eukaryotic (specifically, spinach) PsbO at defined sites and created distinct PsbO fragments that were not further degraded. As for the corresponding prokaryotic substrate (reduced PsbO of Synechocystis sp. PCC 6803), no PsbO fragments were observed. Assembly to PSII protected PsbO from degradation. For Synechocystis sp. PCC 6803, our results show that HhoA, HhoB, and HtrA are localized in the periplasma and/or at the thylakoid membrane. In agreement with the idea that PsbO could be a physiological substrate for Deg proteases, part of the cellular fraction of the three Deg proteases of Synechocystis sp. PCC 6803 (HhoA, HhoB, and HtrA) was detected in the PSII-enriched membrane fraction.
Collapse
|
23
|
Abstract
Yca1, the only metacaspase in Saccharomyces cerevisiae, is thought to be a clan CD cysteine protease that includes the caspase subfamily. Although yeast is a single cell eukaryote, it can undergo a cell death process reminiscent of apoptosis. Yca1 has been reported to play an important role in the regulation of such apoptotic process. However, the structure and functional mechanism of Yca1 remain largely enigmatic. In this study, we report the crystal structure of the Yca1 metacaspase at 1.7 Å resolution, confirming a caspase-like fold. In sharp contrast to canonical caspases, however, Yca1 exists as a monomer both in solution and in the crystals. Canonical caspase contains six β-strands, with strand β6 pairing up with β6 of another caspase molecule to form a homodimerization interface. In Yca1, an extra pair of antiparallel β-strands forms a continuous β-sheet with the six caspase-common β-strands, blocking potential dimerization. Yca1 was reported to undergo autocatalytic processing in yeast; overexpression in bacteria also led to autoprocessing of Yca1 into two fragments. Unexpectedly, we found that both the autocatalytic processing and the proteolytic activity of Yca1 are greatly facilitated by the presence of calcium (Ca(2+)), but not other divalent cations. Our structural and biochemical characterization identifies Yca1 as a Ca(2+)-activated cysteine protease that may cleave specific substrates during stress response in yeast.
Collapse
Affiliation(s)
- Ada Hang-Heng Wong
- Ministry of Education Protein Science Laboratory, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | | | | |
Collapse
|
24
|
Hoy B, Brandstetter H, Wessler S. The stability and activity of recombinant Helicobacter pylori HtrA under stress conditions. J Basic Microbiol 2012; 53:402-9. [PMID: 22736569 DOI: 10.1002/jobm.201200074] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 02/21/2012] [Indexed: 01/26/2023]
Abstract
The bifunctional protein HtrA displays chaperone and protease activities, enabling bacteria to cope with environmental stress conditions such as heat shock or extreme pH by orchestrating protein folding or degradation. Recently, we added a novel aspect to HtrA functions by identifying HtrA of the human pathogen and class I carcinogen Helicobacter pylori (Hp) as a secreted virulence factor that cleaves the cell adhesion molecule and tumor suppressor E-cadherin. In this study, we analyzed the structural integrity and activity of oligomeric HtrA from Hp under stress conditions. Examining different parameters, HtrA oligomers were investigated by casein zymography and HtrA activity was further analyzed in in vitro cleavage assays using E-cadherin as a substrate. HtrA showed temperature-dependent disintegration of oligomers. Denaturing agents targeting hydrogen bonds within HtrA destabilized HtrA oligomers while reducing agents disrupting disulfide bonds had no effect. Optimal proteolytic activity was dependent on a neutral pH; however, addition of mono- and divalent salts or reducing agents did not interfere with proteolytic activity. These data indicate the HtrA is active under stress conditions which might support Hp colonizing in the gastric environment.
Collapse
Affiliation(s)
- Benjamin Hoy
- Division of Microbiology, Paris-Lodron University, Salzburg, Austria
| | | | | |
Collapse
|
25
|
Schuhmann H, Huesgen PF, Adamska I. The family of Deg/HtrA proteases in plants. BMC PLANT BIOLOGY 2012; 12:52. [PMID: 22520048 PMCID: PMC3473262 DOI: 10.1186/1471-2229-12-52] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 03/21/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND The Deg/HtrA family of ATP-independent serine endopeptidases is present in nearly all organisms from bacteria to human and vascular plants. In recent years, multiple deg/htrA protease genes were identified in various plant genomes. During genome annotations most proteases were named according to the order of discovery, hence the same names were sometimes given to different types of Deg/HtrA enzymes in different plant species. This can easily lead to false inference of individual protease functions based solely on a shared name. Therefore, the existing names and classification of these proteolytic enzymes does not meet our current needs and a phylogeny-based standardized nomenclature is required. RESULTS Using phylogenetic and domain arrangement analysis, we improved the nomenclature of the Deg/HtrA protease family, standardized protease names based on their well-established nomenclature in Arabidopsis thaliana, and clarified the evolutionary relationship between orthologous enzymes from various photosynthetic organisms across several divergent systematic groups, including dicots, a monocot, a moss and a green alga. Furthermore, we identified a "core set" of eight proteases shared by all organisms examined here that might provide all the proteolytic potential of Deg/HtrA proteases necessary for a hypothetical plant cell. CONCLUSIONS In our proposed nomenclature, the evolutionarily closest orthologs have the same protease name, simplifying scientific communication when comparing different plant species and allowing for more reliable inference of protease functions. Further, we proposed that the high number of Deg/HtrA proteases in plants is mainly due to gene duplications unique to the respective organism.
Collapse
Affiliation(s)
- Holger Schuhmann
- Department of Plant Physiology and Biochemistry, University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
- School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Pitter F Huesgen
- Department of Plant Physiology and Biochemistry, University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Iwona Adamska
- Department of Plant Physiology and Biochemistry, University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
| |
Collapse
|