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Silveira MAV, Batista Dos Santos SM, Okamoto DN, de Melo IS, Juliano MA, Ribeiro Chagas J, Vasconcellos SP. Atlantic Forest's and Caatinga's semiarid soils and their potential as a source for halothermotolerant actinomycetes and proteolytic enzymes. ENVIRONMENTAL TECHNOLOGY 2023; 44:1566-1578. [PMID: 34783646 DOI: 10.1080/09593330.2021.2008015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Actinomycetes are versatile about their metabolism, displaying high capacity to produce bioactive metabolites. Enzymes from actinomycetes represent new opportunities for industrial applications. However, proteases from actinomycetes are poorly described by literature. Thereby, to verify proteolytic potential of actinomycetes, the present study aimed the investigation of bacterial isolates from Caatinga and Atlantic Forest rhizosphere. Fluorescence resonance energy transfer (FRET) peptide libraries were adopted for the evaluations, since they are faster and more qualitative methods, if compared with others described by most reports. A total of 52 microorganisms were inoculated in different culture media (PMB, potato dextrose agar, brain heart infusion agar, Starch Casein Agar and Reasoner's 2A agar), temperatures (12, 20, 30, 37, 45 and 60°C), and saline conditions (0-4 M NaCl), during 7 days. The actinomycetes named as AC 01, 02 and 52 were selected and showed enzymatic abilities under the peptide probes Abz-KLRSSKQ-EDDnp and Abz-KLYSSKQ-EDDnp, achieving enhanced performance at 30 °C. Biochemical parameters were established, showing a predominance of alkaline proteases with activity under saline conditions. Secreted proteases hydrolysed preferentially polar uncharged residues (Y and N) and positively charged groups (R). Phenylmethylsulfonyl fluoride and ethylenediaminetetraacetic acid inhibited the proteins, a characteristic of serine (AC 01 e 02) and metalloproteases (AC 52). All selected strains belonged to Streptomyces genera. In summary, actinomycete strains with halophilic proteolytic abilities were selected, which improve possibilities for their use in detergent formulations, food processing, waste management and industrial bioconversion. It is important to highlight that this is the first report using FRET libraries for proteolytic screening from Caatinga and Atlantic Forest actinobacteria.
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Affiliation(s)
- Marghuel A Vieira Silveira
- Laboratory of Biochemistry, Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Saara M Batista Dos Santos
- Laboratory of Biochemistry and Enzymology, Institute of Pharmacology and Molecular Biology, Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil
| | - Débora Noma Okamoto
- Laboratory of Health and Environment Sciences, Department of Pharmaceutical Sciences, Universidade Federal de São Paulo, Diadema, Brazil
| | - Itamar Soares de Melo
- Laboratory of Environment Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, Jaguariúna, Brazil
| | - Maria A Juliano
- Laboratory of Biochemistry and Enzymology, Institute of Pharmacology and Molecular Biology, Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil
| | - Jair Ribeiro Chagas
- Laboratory of Biochemistry and Enzymology, Institute of Pharmacology and Molecular Biology, Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil
| | - Suzan P Vasconcellos
- Laboratory of Health and Environment Sciences, Department of Pharmaceutical Sciences, Universidade Federal de São Paulo, Diadema, Brazil
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2
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Lima LMS, Okamoto DN, Passarini MRZ, Gonçalves SS, Goldman GH, Silveira MAV, Ramos PL, Cruz JB, Juliano M, Marcondes MFM, Vasconcellos SP. Enzymatic diversity of filamentous fungi isolated from forest soil incremented by sugar cane solid waste. ENVIRONMENTAL TECHNOLOGY 2022; 43:3037-3046. [PMID: 33826477 DOI: 10.1080/09593330.2021.1914179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
Fungi are natural degraders of organic matter which can produce enzymes for many industrial and biotechnological applications. In this context, crude enzymatic extracts of fungal isolates were evaluated regarding their hydrolytic and ligninolytic abilities. The fungal strains were isolated from soil samples from Atlantic Rain Forest Park incremented with sugar cane biomass (filter cake), which allowed the selection of efficient lignocellulolytic enzymes. A total of 190 fungi were isolated and evaluated by endocellulase screenings. Thirteen fungi were selected about their hydrolytic and ligninolytic abilities. Among them, three isolates showed xylanolytic activity. Eleven of the isolates were selected by their cellulolytic abilities. Proteolytic enzymes were also detected for three fungi, allowing the classification as metalloprotease and serine protease. The isolates SPZPF3_47 (Mucor sp.), SPZPF1_129 (Byssochlamys nivea) and SPZPF1_141 (Paecilomyces saturatus) were selected for further investigation on their lignin peroxidase abilities. KM, Vmax and kcat apparent for lignin peroxidases were also determined. The strain of Mucor sp. (SPZPF3_47) was highlighted since this fungal genus was not well described about its isolation in the adopted conditions in our study, and showing ligninolytic abilities.
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Affiliation(s)
- Lidiane M S Lima
- Institute of Environmental, Chemical and Pharmaceutical Sciences, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Debora N Okamoto
- Institute of Environmental, Chemical and Pharmaceutical Sciences, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Michel R Z Passarini
- Latin American Institute of Life and Natural Sciences, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu, Brazil
| | - Sarah S Gonçalves
- Health Science Center, Universidade Federal do Espírito Santo, Espírito Santo, Brazil
| | - Gustavo H Goldman
- Faculty of Pharmaceutical Sciences of Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Marghuel A V Silveira
- Department of Biophysics, Paulista School of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - João B Cruz
- São Paulo Zoo Park Foundation, São Paulo, Brazil
| | - Maria Juliano
- Department of Biophysics, Paulista School of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Marcelo F M Marcondes
- Department of Biophysics, Paulista School of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Suzan P Vasconcellos
- Institute of Environmental, Chemical and Pharmaceutical Sciences, Universidade Federal de São Paulo, São Paulo, Brazil
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3
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Bąchor R. Peptidyl-Resin Substrates as a Tool in the Analysis of Caspase Activity. Molecules 2022; 27:molecules27134107. [PMID: 35807352 PMCID: PMC9268085 DOI: 10.3390/molecules27134107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
Caspases, proteolytic enzymes belonging to the group of cysteine proteases, play a crucial role in apoptosis. Understanding their activity and substrate specificity is extremely important. Fluorescence-based approaches, including fluorogenic substrates, are generally used to confirm cleavage preferences. Here we present a new method of substrate specificity and activity analysis based on the application of fix-charge tagged peptides located on the resin. The proteolysis of peptide bond on the resin, occurring even with low efficiency, results in the formation of N-terminal fragments of model peptide containing ionization enhancers in the form of quaternary ammonium groups, allowing for ultrasensitive and reliable analysis by LC-MS/MS. The possibility of application of the proposed solution was tested through the analysis of substrate specificity and activity of caspase 3 or 7. The obtained results confirm the known substrate specificity of executioner caspases. Our solution also allowed us to observe that caspases can hydrolyze peptides shorter than those presented to date in the scientific literature.
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Affiliation(s)
- Remigiusz Bąchor
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wrocław, Poland
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4
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Veni, Vidi, Vici: Immobilized Peptide-Based Conjugates as Tools for Capture, Analysis, and Transformation. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10010031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Analysis of peptide biomarkers of pathological states of the organism is often a serious challenge, due to a very complex composition of the cell and insufficient sensitivity of the current analytical methods (including mass spectrometry). One of the possible ways to overcome this problem is sample enrichment by capturing the selected components using a specific solid support. Another option is increasing the detectability of the desired compound by its selective tagging. Appropriately modified and immobilized peptides can be used for these purposes. In addition, they find application in studying the specificity and activity of proteolytic enzymes. Immobilized heterocyclic peptide conjugates may serve as metal ligands, to form complexes used as catalysts or analytical markers. In this review, we describe various applications of immobilized peptides, including selective capturing of cysteine-containing peptides, tagging of the carbonyl compounds to increase the sensitivity of their detection, enrichment of biological samples in deoxyfructosylated peptides, and fishing out of tyrosine–containing peptides by the formation of azo bond. Moreover, the use of the one-bead-one-compound peptide library for the analysis of substrate specificity and activity of caspases is described. Furthermore, the evolution of immobilization from the solid support used in peptide synthesis to nanocarriers is presented. Taken together, the examples presented here demonstrate immobilized peptides as a multifunctional tool, which can be successfully used to solve multiple analytical problems.
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Kasperkiewicz P. Peptidyl Activity-Based Probes for Imaging Serine Proteases. Front Chem 2021; 9:639410. [PMID: 33996745 PMCID: PMC8117214 DOI: 10.3389/fchem.2021.639410] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/15/2021] [Indexed: 01/12/2023] Open
Abstract
Proteases catalyze the hydrolysis of peptide bonds. Products of this breakdown mediate signaling in an enormous number of biological processes. Serine proteases constitute the most numerous group of proteases, accounting for 40%, and they are prevalent in many physiological functions, both normal and disease-related functions, making them one of the most important enzymes in humans. The activity of proteases is controlled at the expression level by posttranslational modifications and/or endogenous inhibitors. The study of serine proteases requires specific reagents not only for detecting their activity but also for their imaging. Such tools include inhibitors or substrate-related chemical molecules that allow the detection of proteolysis and visual observation of active enzymes, thus facilitating the characterization of the activity of proteases in the complex proteome. Peptidyl activity-based probes (ABPs) have been extensively studied recently, and this review describes the basic principles in the design of peptide-based imaging agents for serine proteases, provides examples of activity-based probe applications and critically discusses their strengths, weaknesses, challenges and limitations.
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Affiliation(s)
- Paulina Kasperkiewicz
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland
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Groborz K, Kołt S, Kasperkiewicz P, Drag M. Internally quenched fluorogenic substrates with unnatural amino acids for cathepsin G investigation. Biochimie 2019; 166:103-111. [PMID: 31103725 DOI: 10.1016/j.biochi.2019.05.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 05/14/2019] [Indexed: 02/01/2023]
Abstract
Cathepsin G is one of four members of the neutrophil serine protease family and constitutes an important biological target in various human inflammatory diseases, such as chronic obstructive pulmonary disease, acute respiratory distress syndrome and cystic fibrosis. Many studies have been focused on determining its biological roles, the latest ones concerning its involvement in acute myeloid leukemia, and as such, multiple chemical and biochemical tools were developed to investigate cathepsin G. Nevertheless, most of them lack selectivity or sensitivity and therefore cannot be used in complex systems. Here we present the development of an optimal cathepsin G Internally Quenched Fluorescence (IQF) substrate that incorporates unnatural amino acids causing the increase of its selectivity toward neutrophil elastase and potency in in vitro studies.
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Affiliation(s)
- Katarzyna Groborz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Sonia Kołt
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Paulina Kasperkiewicz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
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7
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Simon AH, Liebscher S, Aumüller TH, Treblow D, Bordusa F. Application of a Dual Internally Quenched Fluorogenic Substrate in Screening for D-Arginine Specific Proteases. Front Microbiol 2019; 10:711. [PMID: 31001242 PMCID: PMC6456654 DOI: 10.3389/fmicb.2019.00711] [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: 07/05/2018] [Accepted: 03/21/2019] [Indexed: 11/13/2022] Open
Abstract
The application of D-stereospecific proteases (DSPs) in resolution of racemic amino acids and in the semisynthesis of proteins has been a successful strategy. The main limitation for a broader application is, however, the accessibility of suitable DSPs covering multiple substrate specificities. To identify DSPs with novel primary substrate preferences, a fast specificity screening method using the easily accessible internally quenched fluorogenic substrate aminobenzoyl-D-arginyl-D-alanyl-p-nitroanilide was developed. By monitoring both UV/vis-absorbance and fluorescence signals at the same time it allows to detect two distinct D-amino acid substrate specificities simultaneously and separately with respect to the individual specificities. In order to identify novel DSP specificities for synthesis applications, DSPs specific for D-arginine were of special interest due to their potential ability as catalysts for substrate mimetics-mediated peptide and protein ligations. D-alanine in the substrate served as positive control and reference based on its known acceptance by numerous DSPs. In silico analysis suggested that DSPs are predominantly present in gram-positive microorganisms, therefore this study focused on the bacilli strains Bacillus thuringiensis and Bacillus subtilis as potential hosts of D-Arg-specific DSPs. While protease activities toward D-alanine were found in both organisms, a novel and so far unknown D-arginine specific DSP was detected within the culture supernatant of B. thuringiensis. Enrichment of this activity via cation exchange and size exclusion chromatography allowed isolation and further characterization of this novel enzyme consisting of a molecular mass of 37.7 kDa and an enzymatic activity of 8.3 U mg-1 for cleaving the D-Arg|D-Ala bond in the detecting substrate. Independent experiments also showed that the identified enzyme shows similarities to the class of penicillin binding proteins. In future applications this enzyme will be a promising starting point for the development of novel strategies for the semisynthesis of all-L-proteins.
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Affiliation(s)
- Andreas H Simon
- Institute of Biochemistry/Biotechnology, Charles Tanford Protein Centre, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Sandra Liebscher
- Institute of Biochemistry/Biotechnology, Charles Tanford Protein Centre, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Tobias H Aumüller
- Max Planck Research Unit for Enzymology of Protein Folding, Halle, Germany
| | - Dennis Treblow
- Institute of Biochemistry/Biotechnology, Charles Tanford Protein Centre, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Frank Bordusa
- Institute of Biochemistry/Biotechnology, Charles Tanford Protein Centre, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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8
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Lapek JD, Jiang Z, Wozniak JM, Arutyunova E, Wang SC, Lemieux MJ, Gonzalez DJ, O'Donoghue AJ. Quantitative Multiplex Substrate Profiling of Peptidases by Mass Spectrometry. Mol Cell Proteomics 2019; 18:968-981. [PMID: 30705125 DOI: 10.1074/mcp.tir118.001099] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/31/2018] [Indexed: 12/14/2022] Open
Abstract
Proteolysis is an integral component of life and has been implicated in many disease processes. To improve our understanding of peptidase function, it is imperative to develop tools to uncover substrate specificity and cleavage efficiency. Here, we combine the quantitative power of tandem mass tags (TMTs) with an established peptide cleavage assay to yield quantitative Multiplex Substrate Profiling by Mass Spectrometry (qMSP-MS). This assay was validated with papain, a well-characterized cysteine peptidase, to generate cleavage efficiency values for hydrolysis of 275 unique peptide bonds in parallel. To demonstrate the breath of this assay, we show that qMSP-MS can uncover the substrate specificity of minimally characterized intramembrane rhomboid peptidases, as well as define hundreds of proteolytic activities in complex biological samples, including secretions from lung cancer cell lines. Importantly, our qMSP-MS library uses synthetic peptides whose termini are unmodified, allowing us to characterize not only endo- but also exo-peptidase activity. Each cleaved peptide sequence can be ranked by turnover rate, and the amino acid sequence of the best substrates can be used for designing fluorescent reporter substrates. Discovery of peptide substrates that are selectively cleaved by peptidases which are active at the site of disease highlights the potential for qMSP-MS to guide the development of peptidase-activating drugs for cancer and infectious disease.
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Affiliation(s)
- John D Lapek
- From the ‡Department of Pharmacology, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; From the ‡Department of Pharmacology, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093
| | - Zhenze Jiang
- §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; ¶Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; From the ‡Department of Pharmacology, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093
| | - Jacob M Wozniak
- From the ‡Department of Pharmacology, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093
| | - Elena Arutyunova
- ‖Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Steven C Wang
- §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; **Division of Biological Sciences, University of California, San Diego, 9500, Gilman Drive, La Jolla, California 92093
| | - M Joanne Lemieux
- ‖Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - David J Gonzalez
- From the ‡Department of Pharmacology, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;.
| | - Anthony J O'Donoghue
- §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;.
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9
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Marem A, Okamoto DN, Oliveira LC, Ruiz DM, Paggi RA, Kondo MY, Gouvea IE, Juliano MA, de Castro RE, Juliano L, Icimoto MY. Functional roles of C-terminal extension (CTE) of salt-dependent peptidase activity of the Natrialba magadii extracellular protease (NEP). Int J Biol Macromol 2018. [DOI: 10.1016/j.ijbiomac.2018.03.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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10
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Sato D, Kondo T, Kato T. Dual emissive bispyrene peptide probes for highly sensitive measurements of trypsin activity and evaluation of trypsin inhibitors. Bioorg Med Chem 2018; 26:3468-3473. [DOI: 10.1016/j.bmc.2018.05.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/11/2018] [Accepted: 05/15/2018] [Indexed: 01/15/2023]
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11
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A Tropical Composting Operation Unit at São Paulo Zoo as a Source of Bacterial Proteolytic Enzymes. Appl Biochem Biotechnol 2018; 187:282-297. [PMID: 29936594 DOI: 10.1007/s12010-018-2810-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/05/2018] [Indexed: 01/08/2023]
Abstract
Composting operation systems are valuable sources of microorganisms and enzymes. This work reports the assessment of proteolytic enzymes from cultivable bacteria isolated from a composting facility of the São Paulo Zoo Park (SPZPF), São Paulo, Brazil. Three hundred bacterial isolates were obtained and identified based on 16S rRNA gene as belonging to 13 different genera. The most common genus among the isolates was Bacillus (67%); some of which show high proteolytic activity in their culture media. Biochemical assays of hydrolytic activities using FRET peptides as substrates allowed the characterization of a repertoire of serine proteases and metalloproteases with different molecular weights secreted by Bacillus strains isolated from composting. Furthermore, thermostable serine and metalloproteases were detected in the composting leachate, which might be of interest for industrial applications.
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12
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Wood SE, Sinsinbar G, Gudlur S, Nallani M, Huang CF, Liedberg B, Mrksich M. A Bottom-Up Proteomic Approach to Identify Substrate Specificity of Outer-Membrane Protease OmpT. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707535] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sarah E. Wood
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
| | - Gaurav Sinsinbar
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Sushanth Gudlur
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Madhavan Nallani
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Che-Fan Huang
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
| | - Bo Liedberg
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Milan Mrksich
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
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Wood SE, Sinsinbar G, Gudlur S, Nallani M, Huang CF, Liedberg B, Mrksich M. A Bottom-Up Proteomic Approach to Identify Substrate Specificity of Outer-Membrane Protease OmpT. Angew Chem Int Ed Engl 2017; 56:16531-16535. [DOI: 10.1002/anie.201707535] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/06/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Sarah E. Wood
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
| | - Gaurav Sinsinbar
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Sushanth Gudlur
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Madhavan Nallani
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Che-Fan Huang
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
| | - Bo Liedberg
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Milan Mrksich
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
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14
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Andrade SS, Sumikawa JT, Castro ED, Batista FP, Paredes-Gamero E, Oliveira LC, Guerra IM, Peres GB, Cavalheiro RP, Juliano L, Nazário AP, Facina G, Tsai SM, Oliva MLV, Girão MJBC. Interface between breast cancer cells and the tumor microenvironment using platelet-rich plasma to promote tumor angiogenesis - influence of platelets and fibrin bundles on the behavior of breast tumor cells. Oncotarget 2017; 8:16851-16874. [PMID: 28187434 PMCID: PMC5370006 DOI: 10.18632/oncotarget.15170] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/24/2017] [Indexed: 12/27/2022] Open
Abstract
Cancer progression is associated with an evolving tissue interface of direct epithelial-tumor microenvironment interactions. In biopsies of human breast tumors, extensive alterations in molecular pathways are correlated with cancer staging on both sides of the tumor-stroma interface. These interactions provide a pivotal paracrine signaling to induce malignant phenotype transition, the epithelial-mesenchymal transition (EMT). We explored how the direct contact between platelets-fibrin bundles primes metastasis using platelet-rich plasma (PRP) as a source of growth factors and mimics the provisional fibrin matrix between actively growing breast cancer cells and the tumor stroma. We have demonstrated PRP functions, modulating cell proliferation that is tumor-subtype and cancer cell-type-specific. Epithelial and stromal primary cells were prepared from breast cancer biopsies from 21 women with different cancer subtypes. Cells supplemented with PRP were immunoblotted with anti-phospho and total Src-Tyr-416, FAK-Try-925, E-cadherin, N-cadherin, TGF-β, Smad2, and Snail monoclonal antibodies. Breast tumor cells from luminal B and HER2 subtypes showed the most malignant profiles and the expression of thrombin and other classes of proteases at levels that were detectable through FRET peptide libraries. The angiogenesis process was investigated in the interface obtained between platelet-fibrin-breast tumor cells co-cultured with HUVEC cells. Luminal B and HER2 cells showed robust endothelial cell capillary-like tubes ex vivo. The studied interface contributes to the attachment of endothelial cells, provides a source of growth factors, and is a solid substrate. Thus, replacement of FBS supplementation with PRP supplementation represents an efficient and simple approach for mimicking the real multifactorial tumor microenvironment.
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Affiliation(s)
- Sheila Siqueira Andrade
- Department of Gynecology of The Federal University of São Paulo, Brazil
- Charitable Association of Blood Collection – COLSAN, São Paulo, SP, Brazil
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Piracicaba, SP, Brazil
| | | | | | | | | | | | | | | | | | - Luiz Juliano
- Department of Biophysics of The Federal University of São Paulo, Brazil
| | | | - Gil Facina
- Department of Gynecology of The Federal University of São Paulo, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Piracicaba, SP, Brazil
| | | | - Manoel João Batista Castello Girão
- Department of Gynecology of The Federal University of São Paulo, Brazil
- Charitable Association of Blood Collection – COLSAN, São Paulo, SP, Brazil
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Highly sensitive and adaptable fluorescence-quenched pair discloses the substrate specificity profiles in diverse protease families. Sci Rep 2017; 7:43135. [PMID: 28230157 PMCID: PMC5322338 DOI: 10.1038/srep43135] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/19/2017] [Indexed: 12/20/2022] Open
Abstract
Internally quenched fluorescent (IQF) peptide substrates originating from FRET (Förster Resonance Energy Transfer) are powerful tool for examining the activity and specificity of proteases, and a variety of donor/acceptor pairs are extensively used to design individual substrates and combinatorial libraries. We developed a highly sensitive and adaptable donor/acceptor pair that can be used to investigate the substrate specificity of cysteine proteases, serine proteases and metalloproteinases. This novel pair comprises 7-amino-4-carbamoylmethylcoumarin (ACC) as the fluorophore and 2,4-dinitrophenyl-lysine (Lys(DNP)) as the quencher. Using caspase-3, caspase-7, caspase-8, neutrophil elastase, legumain, and two matrix metalloproteinases (MMP2 and MMP9), we demonstrated that substrates containing ACC/Lys(DNP) exhibit 7 to 10 times higher sensitivity than conventional 7-methoxy-coumarin-4-yl acetic acid (MCA)/Lys(DNP) substrates; thus, substantially lower amounts of substrate and enzyme can be used for each assay. We therefore propose that the ACC/Lys(DNP) pair can be considered a novel and sensitive scaffold for designing substrates for any group of endopeptidases. We further demonstrate that IQF substrates containing unnatural amino acids can be used to investigate protease activities/specificities for peptides containing post-translationally modified amino acids. Finally, we used IQF substrates to re-investigate the P1-Asp characteristic of caspases, thus demonstrating that some human caspases can also hydrolyze substrates after glutamic acid.
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16
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da Cruz Ramos GF, Ramos PL, Passarini MRZ, Vieira Silveira MA, Okamoto DN, de Oliveira LCG, Zezzo LV, Marem A, Santos Rocha RC, da Cruz JB, Juliano L, de Vasconcellos SP. Cellulolytic and proteolytic ability of bacteria isolated from gastrointestinal tract and composting of a hippopotamus. AMB Express 2016; 6:17. [PMID: 26931430 PMCID: PMC4773312 DOI: 10.1186/s13568-016-0188-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 02/23/2016] [Indexed: 11/16/2022] Open
Abstract
The bioprospection for cellulase and protease producers is a promise strategy for the discovery of potential biocatalysts for use in hydrolysis of lignocellulosic materials as well as proteic residues. These enzymes can increment and turn viable the production of second generation ethanol from different and alternative sources. In this context, the goal of this study was the investigation of cellulolytic and proteolytic abilities of bacteria isolated from the gastrointestinal tract of a hippopotamus as well as from its composting process. It is important to highlight that hippopotamus gastrointestinal samples were a non-typical sources of efficient hydrolytic bacteria with potential for application in biotechnological industries, like biofuel production. Looking for this, a total of 159 bacteria were isolated, which were submitted to qualitative and quantitative enzymatic assays. Proteolytic analyzes were conducted through the evaluation of fluorescent probes. Qualitative assays for cellulolytic abilities revealed 70 positive hits. After quantitative analyzes, 44 % of these positive hits were selected, but five (5) strains showed cellulolytic activity up to 11,8 FPU/mL. Regarding to proteolytic activities, six (6) strains showed activity above 10 %, which overpassed results described in the literature. Molecular analyzes based on the identification of 16S rDNA, revealed that all the selected bacterial isolates were affiliated to Bacillus genus. In summary, these results strongly indicate that the isolated bacteria from a hippopotamus can be a potential source of interesting biocatalysts with cellulolytic and proteolytic activities, with relevance for industrial applications.
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Kondo MY, Gouvea IE, Okamoto DN, Santos JAN, Souccar C, Oda K, Juliano L, Juliano MA. Analysis of catalytic properties of tripeptidyl peptidase I (TTP-I), a serine carboxyl lysosomal protease, and its detection in tissue extracts using selective FRET peptide substrate. Peptides 2016; 76:80-6. [PMID: 26775801 DOI: 10.1016/j.peptides.2016.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/01/2016] [Accepted: 01/10/2016] [Indexed: 11/30/2022]
Abstract
Tripeptidyl peptidase I (TPP-I), also named ceroid lipofuscinosis 2 protease (CLN2p), is a serine carboxyl lysosomal protease involved in neurodegenerative diseases, and has both tripeptidyl amino- and endo- peptidase activities under different pH conditions. We developed fluorescence resonance energy transfer (FRET) peptides using tryptophan (W) as the fluorophore to study TPP-I hydrolytic properties based on previous detailed substrate specificity study (Tian Y. et al., J. Biol. Chem. 2006, 281:6559-72). Tripeptidyl amino peptidase activity is enhanced by the presence of amino acids in the prime side and the peptide NH2-RWFFIQ-EDDnp is so far the best substrate described for TPP-I. The hydrolytic parameters of this peptide and its analogues indicated that the S4 subsite of TPP-I is occluded and there is an electrostatic interaction of the positively charged substrate N-terminus amino group and a negative locus in the region of the enzyme active site. KCl activated TPP-I in contrast to the inhibition by Ca(2+) and NaCl. Solvent kinetic isotope effects (SKIEs) show the importance of the free N-terminus amino group of the substrates, whose absence results in a more complex solvent-dependent enzyme: substrate interaction and catalytic process. Like pure TPP-I, rat spleen and kidney homogenates cleaved NH2-RWFFIQ-EDDnp only at F-F bond and is not inhibited by pepstatin, E-64, EDTA or PMSF. The selectivity of NH2-RWFFIQ-EDDnp to TPP-I was also demonstrated by the 400 times higher k(cat)/K(M) compared to generally used substrate, NH2-AAF-MCA and by its resistance to hydrolysis by cathepsin D that is present in high levels in kidneys.
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Affiliation(s)
- Marcia Y Kondo
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Iuri E Gouvea
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Débora N Okamoto
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Jorge A N Santos
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Caden Souccar
- Department of Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Kohei Oda
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan
| | - Luiz Juliano
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Maria A Juliano
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil.
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18
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Oliveira JR, Bertolin TC, Andrade D, Oliveira LCG, Kondo MY, Santos JAN, Blaber M, Juliano L, Severino B, Caliendo G, Santagada V, Juliano MA. Specificity studies on Kallikrein-related peptidase 7 (KLK7) and effects of osmolytes and glycosaminoglycans on its peptidase activity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:73-83. [PMID: 25448018 DOI: 10.1016/j.bbapap.2014.10.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/20/2014] [Accepted: 10/21/2014] [Indexed: 11/29/2022]
Abstract
KLK7 substrate specificity was evaluated by families of fluorescence resonance energy transfer (FRET) peptides derived from Abz-KLFSSK-Q-EDDnp (Abz=ortho-aminobenzoic acid and Q-EDDnp=glutaminyl-N-[2,4-dinitrophenyl] ethylenediamine), by one bead-one peptide FRET peptide library in PEGA resin, and by the FRET peptide libraries Abz-GXX-Z-XX-Q-EDDnp (Z and X are fixed and random natural amino acids, respectively). KLK7 hydrolyzed preferentially F, Y or M, and its S1' and S2' subsites showed selectivity for hydrophilic amino acids, particularly R and K. This set of specificities was confirmed by the efficient kininogenase activity of KLK7 on Abz-MISLM(↓)KRPPGFSPF(↓)RSSRI-NH2 ((↓)indicates cleavage), hydrolysis of somatostatin and substance P and inhibition by kallistatin. The peptide Abz-NLY(↓)RVE-Q-EDDnp is the best synthetic substrate so far described for KLK7 [kcat/Km=455 (mMs)(-1)] that was designed from the KLK7 substrate specificity analysis. It is noteworthy that the NLYRVE sequence is present in human semaphorin 6B. KLK7 is activated by GAGs, inhibited by neutral salts, and activated by high concentration of kosmotropic salt. Pyroglutamic acid inhibited KLK7 (Ki=33mM) and is present in skin moisturizing factor (124mM). The KLK7 specificity described here and elsewhere reflects its participation in patho-physiological events in skin, the gastrointestinal tract and central nervous system, where KLK7 is significantly expressed.
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Affiliation(s)
- Juliana R Oliveira
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil
| | - Thiago C Bertolin
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil
| | - Douglas Andrade
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil
| | - Lilian C G Oliveira
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil
| | - Marcia Y Kondo
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil
| | - Jorge A N Santos
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil; Instituto Federal de Educação, Ciência e Tecnologia do Sul de Minas Gerais, Câmpus Inconfidentes, Brazil
| | - Michael Blaber
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA
| | - Luiz Juliano
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil
| | - Beatrice Severino
- Dipartimento di Farmacia, Università degli Studi di Napoli ‟Federico II", Via D. Montesano, 49, 80131, Napoli, Italy
| | - Giuseppe Caliendo
- Dipartimento di Farmacia, Università degli Studi di Napoli ‟Federico II", Via D. Montesano, 49, 80131, Napoli, Italy
| | - Vincenzo Santagada
- Dipartimento di Farmacia, Università degli Studi di Napoli ‟Federico II", Via D. Montesano, 49, 80131, Napoli, Italy
| | - Maria A Juliano
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil.
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19
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Oliveira LC, Okamoto DN, Oliveira JR, Kondo MY, Gouvea IE, Biteau N, Baltz T, Murakami MT, Juliano L, Juliano MA. Analysis of peptidase activities of a cathepsin B-like (TcoCBc1) from Trypanosoma congolense. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1260-7. [DOI: 10.1016/j.bbapap.2014.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 03/27/2014] [Accepted: 04/01/2014] [Indexed: 10/25/2022]
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20
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Kaman WE, Hays JP, Endtz HP, Bikker FJ. Bacterial proteases: targets for diagnostics and therapy. Eur J Clin Microbiol Infect Dis 2014; 33:1081-7. [PMID: 24535571 DOI: 10.1007/s10096-014-2075-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/30/2014] [Indexed: 02/02/2023]
Abstract
Proteases are essential for the proliferation and growth of bacteria, and are also known to contribute to bacterial virulence. This makes them interesting candidates as diagnostic and therapeutic targets for infectious diseases. In this review, the authors discuss the most recent developments and potential applications for bacterial proteases in the diagnosis and treatment of bacterial infections. Current and future bacterial protease targets are described and their limitations outlined.
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Affiliation(s)
- W E Kaman
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, 's-Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands,
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21
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The Aspergillus nidulans ATM kinase regulates mitochondrial function, glucose uptake and the carbon starvation response. G3-GENES GENOMES GENETICS 2014; 4:49-62. [PMID: 24192833 PMCID: PMC3887539 DOI: 10.1534/g3.113.008607] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mitochondria supply cellular energy and also perform a role in the adaptation to metabolic stress. In mammals, the ataxia-telangiectasia mutated (ATM) kinase acts as a redox sensor controlling mitochondrial function. Subsequently, transcriptomic and genetic studies were utilized to elucidate the role played by a fungal ATM homolog during carbon starvation. In Aspergillus nidulans, AtmA was shown to control mitochondrial function and glucose uptake. Carbon starvation responses that are regulated by target of rapamycin (TOR) were shown to be AtmA-dependent, including autophagy and hydrolytic enzyme secretion. AtmA also regulated a p53-like transcription factor, XprG, inhibiting starvation-induced XprG-dependent protease secretion and cell death. Thus, AtmA possibly represents a direct or indirect link between mitochondrial stress, metabolism, and growth through the influence of TOR and XprG function. The coordination of cell growth and division with nutrient availability is crucial for all microorganisms to successfully proliferate in a heterogeneous environment. Mitochondria supply cellular energy but also perform a role in the adaptation to metabolic stress and the cross-talk between prosurvival and prodeath pathways. The present study of Aspergillus nidulans demonstrated that AtmA also controlled mitochondrial mass, function, and oxidative phosphorylation, which directly or indirectly influenced glucose uptake. Carbon starvation responses, including autophagy, shifting metabolism to the glyoxylate cycle, and the secretion of carbon scavenging enzymes were AtmA-dependent. Transcriptomic profiling of the carbon starvation response demonstrated how TOR signaling and the retrograde response, which signals mitochondrial dysfunction, were directly or indirectly influenced by AtmA. The AtmA kinase was also shown to influence a p53-like transcription factor, inhibiting starvation-induced XprG-dependent protease secretion and cell death. Therefore, in response to metabolic stress, AtmA appears to perform a role in the regulation of TOR signaling, involving the retrograde and SnfA pathways. Thus, AtmA may represent a link between mitochondrial function and cell cycle or growth, possibly through the influence of the TOR and XprG function.
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22
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Okamoto DN, Kondo MY, Oliveira LCG, Honorato RV, Zanphorlin LM, Coronado MA, Araújo MS, da Motta G, Veronez CL, Andrade SS, Oliveira PSL, Arni RK, Cintra ACO, Sampaio SV, Juliano MA, Juliano L, Murakami MT, Gouvea IE. P-I class metalloproteinase from Bothrops moojeni venom is a post-proline cleaving peptidase with kininogenase activity: insights into substrate selectivity and kinetic behavior. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:545-52. [PMID: 24373874 DOI: 10.1016/j.bbapap.2013.12.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 12/17/2013] [Accepted: 12/19/2013] [Indexed: 11/29/2022]
Abstract
Snake venom metalloproteinases (SVMPs) belonging to P-I class are able to hydrolyze extracellular matrix proteins and coagulation factors triggering local and systemic reactions by multiple molecular mechanisms that are not fully understood. BmooMPα-I, a P-I class SMVP from Bothrops moojeni venom, was active upon neuro- and vaso-active peptides including angiotensin I, bradykinin, neurotensin, oxytocin and substance P. Interestingly, BmooMPα-I showed a strong bias towards hydrolysis after proline residues, which is unusual for most of characterized peptidases. Moreover, the enzyme showed kininogenase activity similar to that observed in plasma and cells by kallikrein. FRET peptide assays indicated a relative promiscuity at its S2-S'2 subsites, with proline determining the scissile bond. This unusual post-proline cleaving activity was confirmed by the efficient hydrolysis of the synthetic combinatorial library MCA-GXXPXXQ-EDDnp, described as resistant for canonical peptidases, only after Pro residues. Structural analysis of the tripeptide LPL complexed with BmooMPα-I, generated by molecular dynamics simulations, assisted in defining the subsites and provided the structural basis for subsite preferences such as the restriction of basic residues at the S2 subsite due to repulsive electrostatic effects and the steric impediment for large aliphatic or aromatic side chains at the S1 subsite. These new functional and structural findings provided a further understanding of the molecular mechanisms governing the physiological effects of this important class of enzymes in envenomation process.
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Affiliation(s)
- Débora N Okamoto
- Departamento de Biofísica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Marcia Y Kondo
- Departamento de Biofísica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Lilian C G Oliveira
- Departamento de Biofísica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Rodrigo V Honorato
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisas em Energia e Materiais, 13083-100 Campinas, SP, Brazil
| | - Leticia M Zanphorlin
- Departamento de Orgânica, Instituto de Química, UNICAMP, 13083-970 Campinas, Brazil
| | - Monika A Coronado
- Departamento de Física, IBILCE, UNESP, 15054-000 São José do Rio Preto, Brazil
| | - Mariana S Araújo
- Departamento de Bioquímica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Guacyara da Motta
- Departamento de Bioquímica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Camila L Veronez
- Departamento de Bioquímica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Sheila S Andrade
- Departamento de Ginecologia, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Paulo S L Oliveira
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisas em Energia e Materiais, 13083-100 Campinas, SP, Brazil
| | - Raghuvir K Arni
- Departamento de Física, IBILCE, UNESP, 15054-000 São José do Rio Preto, Brazil
| | - Adelia C O Cintra
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, 14040-903 Ribeirão Preto, SP, Brazil
| | - Suely V Sampaio
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, 14040-903 Ribeirão Preto, SP, Brazil
| | - Maria A Juliano
- Departamento de Biofísica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Luiz Juliano
- Departamento de Biofísica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Mário T Murakami
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisas em Energia e Materiais, 13083-100 Campinas, SP, Brazil.
| | - Iuri E Gouvea
- Departamento de Biofísica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil.
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Evaluation of a D-amino-acid-containing fluorescence resonance energy transfer peptide library for profiling prokaryotic proteases. Anal Biochem 2013; 441:38-43. [DOI: 10.1016/j.ab.2013.06.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 06/25/2013] [Accepted: 06/27/2013] [Indexed: 02/02/2023]
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24
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Moitinho-Silva L, Kondo MY, Oliveira LCG, Okamoto DN, Paes JA, Machado MFM, Veronez CL, Motta G, Andrade SS, Juliano MA, Ferreira HB, Juliano L, Gouvea IE. Mycoplasma hyopneumoniae in vitro peptidase activities: identification and cleavage of kallikrein-kinin system-like substrates. Vet Microbiol 2013; 163:264-73. [PMID: 23421966 DOI: 10.1016/j.vetmic.2013.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 01/15/2013] [Accepted: 01/17/2013] [Indexed: 01/24/2023]
Abstract
Bacterial proteases are important for metabolic processes and pathogenesis in host organisms. The bacterial swine pathogen Mycoplasma hyopneumoniae has 15 putative protease-encoding genes annotated, but none of them have been functionally characterized. To identify and characterize peptidases that could be relevant for infection of swine hosts, we investigated the peptidase activity present in the pathogenic 7448 strain of M. hyopneumoniae. Combinatorial libraries of fluorescence resonance energy transfer peptides, specific inhibitors and pH profiling were used to screen and characterize endopeptidase, aminopeptidase and carboxypeptidase activities in cell lysates. One metalloendopeptidase, one serine endopeptidase, and one aminopeptidase were detected. The detected metalloendopeptidase activity, prominent at neutral and basic pH ranges, was due to a thimet oligopeptidase family member (M3 family), likely an oligoendopeptidase F (PepF), which cleaved the peptide Abz-GFSPFRQ-EDDnp at the F-S bond. A chymotrypsin-like serine endopeptidase activity, possibly a subtilisin-like serine protease, was prominent at higher pH levels, and was characterized by its preference for a Phe residue at the P1 position of the substrate. The aminopeptidase P (APP) activity showed a similar profile to that of human membrane-bound APP. Genes coding for these three peptidases were identified and their transcription was confirmed in the 7448 strain. Furthermore, M. hyopneumoniae cell lysate peptidases showed effects on kallikrein-kinin system-like substrates, such as bradykinin-derived substrates and human high molecular weight kininogen. The M. hyopneumoniae peptidase activities, here characterized for the first time, may be important for bacterial survival strategies and thus represent possible targets for drug development against M. hyopneumoniae swine infections.
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Affiliation(s)
- Lucas Moitinho-Silva
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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25
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Le DV, Nguyen VT, Tang LJ, Jiang JH, Yu RQ, Wang YZ. Proteolysis-mediated protection of gold nanoparticles for sensitive activity assay of peptidases. Talanta 2013; 107:233-8. [PMID: 23598217 DOI: 10.1016/j.talanta.2013.01.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 01/08/2013] [Accepted: 01/09/2013] [Indexed: 11/28/2022]
Abstract
Rapid, sensitive and quantitative assays for peptide hydrolysis enzymes are of paramount importance for drug development and in the diagnosis of disease. Here, we proposed a novel biosensor for sensitive and selective active screening of peptidases. This strategy relies on the proteolysis-mediated protection of gold nanoparticles (AuNPs) that were decorated with biotin-labeled substrate peptides and can be aggregated by streptavidin. Enzyme-mediated protection of AuNPs offers this strategy high specificity, and the use of AuNPs additionally allows a visual and homogeneous assay format, thus permitting improved simplicity and throughput of the assays. As a model case, desirable selectivity and sensitivity in peptidase assay were achieved in the active assays of pancreatic elastase with a wide linear response range from 0.005 to 0.10 U/mL and a detection limit of 0.003 U/mL. The results indicated that this strategy can offer a simple, robust and convenient platform for visualized peptidase activity analysis and related biochemical studies with high sensitivity and selectivity.
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Affiliation(s)
- Dinh-Vu Le
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
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