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Omar A, Wali A, Arken A, Gao Y, Aisa HA, Yili A. Covalent binding of flavonoids with silk sericin hydrolysate: Anti‐inflammatory, antioxidant, and physicochemical properties of flavonoid–sericin hydrolysate conjugates. J Food Biochem 2022; 46:e14125. [DOI: 10.1111/jfbc.14125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/18/2022] [Accepted: 02/16/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Adil Omar
- Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences Beijing China
- University of the Chinese Academy of Sciences Beijing China
| | - Ahmidin Wali
- Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences Beijing China
| | - Amina Arken
- Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences Beijing China
- University of the Chinese Academy of Sciences Beijing China
| | - Yanhua Gao
- Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences Beijing China
| | - Haji Akber Aisa
- Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences Beijing China
| | - Abulimiti Yili
- Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences Beijing China
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Jamwal S, Ansari S, Malakar D, Kaushik JK, Kumar S, Mohanty AK. Production of biologically active recombinant buffalo leukemia inhibitory factor (BuLIF) in Escherichia Coli. J Genet Eng Biotechnol 2022; 20:47. [PMID: 35294648 PMCID: PMC8927517 DOI: 10.1186/s43141-022-00328-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 02/11/2022] [Indexed: 12/27/2022]
Abstract
Background Leukemia inhibitory factor (LIF) is a multifunctional cytokine which plays multiple roles in different biological processes such as implantation, bone remodeling, and hematopoiesis. The buESCs are difficult to culture due to lack of proper understanding of the culture conditions. LIF is one of the important factors which maintain the pluripotency in embryonic stem cells and commercial LIF from murine and human origin is used in the establishment of buffalo embryonic stem cells (buESCs). The LIF from a foreign origin is not able to maintain pluripotency and proliferation in buESCs for a long term which is contributed by difference in the binding sites on LIF; therefore, culture medium supplemented with buffalo-specific LIF may enhance the efficiency of buESCs by improving the environment of culture conditions. The high cost of LIF is another major drawback which restricts buESCs research, thus limits the scope of buffalo stem cell use. Various methods have been developed to produce human and murine LIF in prokaryotic system. However, Buffalo leukemia inhibitory factor (BuLIF) has not been yet produced in prokaryotic system. Here, we describe a simple strategy for the expression and purification of biologically active BuLIF in Escherichia coli (E. coli). Results The BuLIF cDNA from buffalo (Bubalus bubalis) was cloned into pET22b(+) and expressed in E. coli Lemo-21(DE3). The expression of BuLIF was directed into periplasmic space of E. coli which resulted in the formation of soluble recombinant protein. One step immobilized metal affinity chromatography (IMAC chromatography) was performed for purification of BuLIF with ≥ 95% of homogeneity. The recombinant protein was confirmed by western blot and identified by mass spectroscopy. The biological activity of recombinant BuLIF was determined on murine myeloid leukemic cells (M1 cells) by MTT proliferation assay. The addition of BuLIF increased the reduction of MTT by stimulated M1 cells in a dose-dependent manner. The BuLIF induced the formation of macrophage like structures from M1 cells where they engulfed fluorescent latex beads. The recombinant BuLIF successfully maintained pluripotency in buffalo embryonic stem cells (buESCs) and were positive for stem cells markers such as Oct-4, Sox-2, Nanog, and alkaline phosphatase activity. Conclusions The present study demonstrated a simple method for the production of bioactive BuLIF in E. coli through single step purification. BuLIF effectively maintained buffalo embryonic stem cells pluripotency. Thus, this purified BuLIF can be used in stem cell study, biomedical, and agricultural research. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00328-1.
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Affiliation(s)
- Shradha Jamwal
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, India
| | - Shama Ansari
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, India
| | - Dhruba Malakar
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, India
| | - Jai Kumar Kaushik
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, India
| | - Sudarshan Kumar
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, India.
| | - Ashok Kumar Mohanty
- Indian Council of Agricultural Research-Indian Veterinary Research Institute, Mukteshwar, India.
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Pei Q, Ni W, Yuan Y, Yuan J, Zhang X, Yao M. HSP70 Ameliorates Septic Lung Injury via Inhibition of Apoptosis by Interacting with KANK2. Biomolecules 2022; 12:410. [PMID: 35327602 PMCID: PMC8946178 DOI: 10.3390/biom12030410] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 02/27/2022] [Accepted: 03/04/2022] [Indexed: 02/04/2023] Open
Abstract
Acute lung injury is the most common type of organ damage with high incidence and mortality in sepsis, which is a poorly understood syndrome of disordered inflammation. The aims of this study are to explore whether heat shock protein 70 (HSP70), as a molecular chaperone, attenuates the septic lung injury, and to understand the underlying mechanisms. In our study, treatment with HSP70 ameliorated the survival rate, dysfunction of lung, inflammation, and apoptosis in cecal ligation and puncture (CLP)-treated mice as well as in LPS-treated human alveolar epithelial cells. Furthermore, HSP70 interacted with KANK2, leading to reversed cell viability and reduced apoptosis-inducing factor (AIF) and apoptosis. Additionally, knockdown of KANK2 in epithelial cells and deletion of hsp70.1 gene in CLP mice aggravated apoptosis and tissue damage, suggesting that interaction of KANK2 and HSP70 is critical for protecting lung injury induced by sepsis. HSP70 plays an important role in protection of acute lung injury caused by sepsis through interaction with KANK2 to reduce AIF release and apoptotic cell. HSP70 is a novel potential therapeutic approach for attenuation of septic lung injury.
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Affiliation(s)
- Qing Pei
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China;
| | - Wei Ni
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430000, China; (W.N.); (J.Y.)
| | - Yihang Yuan
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;
| | - Jing Yuan
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430000, China; (W.N.); (J.Y.)
| | - Xiong Zhang
- Department of Burn, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Min Yao
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China;
- Institute of Traumatic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 201999, China
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Man CH, Shimura Y, Suzuki I. Identification of Extracellular Proteases Induced by Nitrogen-Limited Conditions in the Thraustochytrids Schizochytrium aggregatum ATCC 28209. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:243-254. [PMID: 35262804 DOI: 10.1007/s10126-022-10103-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Thraustochytrids have attracted attention due to the high contents of useful lipids and growth rate. Genus Schizochytrium is commonly used for docosahexaenoic acid (DHA) production, while a strain, which produces a high amount of squalene, has been reported in the genus Aurantiochytrium. These organisms are heterotrophic, and Schizochytrium degrades the extracellular macromolecules, e.g., proteins and polysaccharides, as the nutrients. However, the extracellular lytic enzymes are not well-studied yet. Here, we investigated the induction of extracellular proteases of Schizochytrium aggregatum ATCC 28209. A casein-hydrolytic activity was induced in the nitrogen-limited conditions, and that was also detected by zymography after fractionation by non-heat denatured SDS-PAGE. The proteinous band corresponding to the protease activity was analyzed by MALDI-TOF mass spectrometry after digestion with trypsin. The molecular mass data of the protein fragments were compared to the protein database of S. aggregatum ATCC 28209 in the Joint Genome Institute, and we found that the molecular masses of the six peptides were matched with the prediction from the sequence of a protein, ID 63992, which was annotated as a peptidase S8 family protein. Interestingly, we found that a paralogous protein, ID 99856, was encoded by a gene flanking at the downstream of the gene for ID 63992, and the expression of both genes was similarly induced under the nitrogen-limited conditions. These findings may provide us a key to disclose the induction mechanisms of the extracellular lytic enzymes and the function of the proteolytic enzyme for the nutrition acquisition in thraustochytrids.
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Affiliation(s)
- Chun Hung Man
- Graduate School of Science and Technology, University of Tsukuba, 1-1-1, Tsukuba, Tennoudai, 305-8572, Japan
| | - Yohei Shimura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tsukuba, Tennoudai, 305-8572, Japan
- Algal Bio Co. Ltd, Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Iwane Suzuki
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tsukuba, Tennoudai, 305-8572, Japan.
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Unraveling the regulation of sugar beet pulp utilization in the industrially relevant fungus Aspergillus niger. iScience 2022; 25:104065. [PMID: 35359804 PMCID: PMC8961234 DOI: 10.1016/j.isci.2022.104065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/07/2022] [Accepted: 03/09/2022] [Indexed: 11/21/2022] Open
Abstract
Efficient utilization of agro-industrial waste, such as sugar beet pulp, is crucial for the bio-based economy. The fungus Aspergillus niger possesses a wide array of enzymes that degrade complex plant biomass substrates, and several regulators have been reported to play a role in their production. The role of the regulators GaaR, AraR, and RhaR in sugar beet pectin degradation has previously been reported. However, genetic regulation of the degradation of sugar beet pulp has not been assessed in detail. In this study, we generated a set of single and combinatorial deletion mutants targeting the pectinolytic regulators GaaR, AraR, RhaR, and GalX as well as the (hemi-)cellulolytic regulators XlnR and ClrB to address their relative contribution to the utilization of sugar beet pulp. We show that A. niger has a flexible regulatory network, adapting to the utilization of (hemi-)cellulose at early timepoints when pectin degradation is impaired. Major sugar beet pulp components are sequentially utilized by A. niger Contribution of major regulators toward sugar beet pulp utilization was compared Deletion of araR and clrB showed high impact on growth after 8 and 24 h, respectively
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Detection of Bacterial α-l-Fucosidases with an Ortho-Quinone Methide-Based Probe and Mapping of the Probe-Protein Adducts. Molecules 2022; 27:molecules27051615. [PMID: 35268716 PMCID: PMC8911971 DOI: 10.3390/molecules27051615] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 11/24/2022] Open
Abstract
Fucosidases are associated with several pathological conditions and play an important role in the health of the human gut. For example, fucosidases have been shown to be indicators and/or involved in hepatocellular carcinoma, breast cancer, and helicobacter pylori infections. A prerequisite for the detection and profiling of fucosidases is the formation of a specific covalent linkage between the enzyme of interest and the activity-based probe (ABP). The most commonly used fucosidase ABPs are limited to only one of the classes of fucosidases, the retaining fucosidases. New approaches are needed that allow for the detection of the second class of fucosidases, the inverting type. Here, we report an ortho-quinone methide-based probe with an azide mini-tag that selectively labels both retaining and inverting bacterial α-l-fucosidases. Mass spectrometry-based intact protein and sequence analysis of a probe-labeled bacterial fucosidase revealed almost exclusive single labeling at two specific tryptophan residues outside of the active site. Furthermore, the probe could detect and image extracellular fucosidase activity on the surface of live bacteria.
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Manna S, Biswas P, Haldar R, Naskar TK, Law S. Cord and peripheral blood erythrocyte analysis by scanning electron microscopy and flow cytometry. Int J Lab Hematol 2022; 44:679-687. [PMID: 35150189 DOI: 10.1111/ijlh.13810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Human umbilical cord blood is rich in hematopoietic cells. We aimed to focus on the morphological, biochemical, membrane protein profile and surface protein expression differences of erythrocytes, isolated from cord and adult peripheral blood using techniques such as high-resolution scanning electron microscopy (SEM), gel electrophoresis (SDS-PAGE) and flow cytometry. METHODS Adult peripheral blood was collected from consenting adults, and umbilical cord blood was procured from consenting mothers, post-delivery at Medical College, Kolkata. We emphasized on cord and adult peripheral blood erythrocytes' morphological variations using SEM images and protein expression by flow cytometric analysis. Some conventional biochemical analyses such as osmotic fragility of the cell membrane, haemoglobin co-oxidation study and lipid peroxidation assay were done for supporting evidence along with membrane protein content using gel electrophoresis. RESULTS Our SEM images indicated clear morphological variations in cord erythrocyte with a higher degree of cellular deformities and difference in membrane texture. Flow cytometric analysis of cord erythrocyte showed a significant difference in CD235a expression than adults. We observed an overexpression of GLUT1 and decreased expression of Band 3 in cord erythrocyte membrane. Our results also showed cord erythrocytes have low osmotic fragility, a slower rate of co-oxidation of cord haemoglobin and a lesser lipid peroxidation level than that of adults. CONCLUSION Cord blood erythrocytes have deeper indentations leading to higher flexibility, more oxygen-carrying capacity and less osmotic fragility in comparison with adult erythrocytes. The expression of CD235a and Band 4.5 (GLUT 1) was significantly higher in cord erythrocytes than peripheral adult erythrocytes.
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Affiliation(s)
- Sayak Manna
- Stem Cell Research and Application Unit, Department of Biochemistry and Medical Biotechnology, Calcutta School of Tropical Medicine, Kolkata, India
| | - Payel Biswas
- Biophysics and Electrophysiology Unit, Department of Physiology, University of Calcutta, Kolkata, India
| | - Rajen Haldar
- Biophysics and Electrophysiology Unit, Department of Physiology, University of Calcutta, Kolkata, India
| | - Tapan Kumar Naskar
- Department of Obstetrics and Gynaecology, Medical College Kolkata, Kolkata, India
| | - Sujata Law
- Stem Cell Research and Application Unit, Department of Biochemistry and Medical Biotechnology, Calcutta School of Tropical Medicine, Kolkata, India
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p38-MAPK recruits the proteolytic pathways in Caenorhabditis elegans during bacterial infection. Int J Biol Macromol 2022; 204:116-135. [PMID: 35124023 DOI: 10.1016/j.ijbiomac.2022.01.191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 11/21/2022]
Abstract
In eukaryotic organisms, cell-signalling completely relies on Post Translational Modifications (PTMs) that can function as regulatory switches. Phosphorylation is a fundamental and frequently occurring PTM in almost all eukaryotes. Herein, we have studied the importance of protein phosphorylation using classical proteomic techniques in C. elegans upon bacterial infection. The differentially regulated proteins during bacterial infection were excised from SDS-PAGE (One-Dimensional) gel (TiO2 column elutes) and subjected to MALDI-TOF-MS which ended up in identifying 220 proteins kinetically. KEGG pathway analysis of those proteins suggested that MAPK pathway was part of the innate immunity. Thus, we have characterized p38-MAPK (one of the crucial downstream MAPKs) using immunoblotting, subcellular fractionation, coimmunoprecipitation, LC-MS/MS, bioinformatics studies and qPCR. Meanwhile, KU25 strain (pmk-1 mutant) exhibited an earlier mortality during infection suggesting the crucial role of p38-MAPK during host-pathogen interaction. Interestingly, Reactome pathway analysis of p38 interactors (CoIP coupled to LC-MS/MS) revealed the involvement of various proteolytic pathway players (ubiquitination, SUMOylation and Neddylation) during bacterial infection. Further, the regulation of SUMOylation and Neddylation was identified and validated using immunoblotting and qPCR analyses, respectively. Concisely, our study indicated that bacterial infection triggers the MAPK cascade to elicit innate immunity which in turn recruits proteolytic pathways to counteract the invading pathogen.
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59
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Plant protein-based food packaging films; recent advances in fabrication, characterization, and applications. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.01.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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60
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Bommasamudram J, Muthu A, Devappa S. Effect of sub-lethal heat stress on viability of Lacticaseibacillus casei N in spray-dried powders. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Han H, Ke L, Wang H, Gao G, zhang Y, Rao P, Zhou J, Tirosh O, Schwartz B. Incidental Nanoparticles in Black Tea Infusion: Carriers of Bioactives Fortifying Protection on Intestinal Mucosal Cells Against Oxidative Stresses. FOOD BIOPHYS 2022. [DOI: 10.1007/s11483-021-09708-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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62
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Smith JP, Ralbovsky NM, Lauro ML, Hoyt E, Guetschow ED, Wang F, McIntosh JA, Liu Z, Mangion I, Variankaval N, Bu X. Quantitation and speciation of residual protein within active pharmaceutical ingredients using image analysis with SDS-PAGE. J Pharm Biomed Anal 2022; 207:114393. [PMID: 34607166 DOI: 10.1016/j.jpba.2021.114393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022]
Abstract
Recent advances in biocatalysis and directed enzyme evolution has led to a variety of enzymatically-driven, elegant processes for active pharmaceutical ingredient (API) production. For biocatalytic processes, quantitation of any residual protein within a given API is of great importance to ensure process robustness and quality, pure pharmaceutical products. Typical analytical methods for analyzing residual enzymes within an API, such as enzyme-linked immunosorbent assays (ELISA), colorimetric assays, and liquid chromatographic techniques, are limited for determining only the concentration of known proteins and require harsh solvents with high API levels for analysis. For the first time, total residual protein content in a small molecule API was quantitated using image analysis applied to SDS-PAGE. Herein, a proposed methodology for residual protein detection, quantitation, and size-based speciation is presented, in which an orthogonal technique is offered to traditional analysis methods, such as ELISA. Results indicate that our application of the analytical methodology is able to reliably quantitate both protein standards and the total residual protein present within a final API, with good agreement as compared to traditional ELISA results. Further, speciation of the residual protein within the API provides key information concerning the individual residual proteins present, including their molecular weight, which can lead to improved process development efforts for residual protein rejection and control. This analytical methodology thus offers an alternative tool for easily identifying, quantitating, and speciating residual protein content in the presence of small molecule APIs, with potential for wide applicability across industry for biocatalytic or directed enzyme evolution efforts within process development.
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Affiliation(s)
- Joseph P Smith
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, PA 19486, USA.
| | - Nicole M Ralbovsky
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, PA 19486, USA
| | - Mackenzie L Lauro
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, PA 19486, USA
| | - Erik Hoyt
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, PA 19486, USA
| | - Erik D Guetschow
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, PA 19486, USA
| | - Fengqiang Wang
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, PA 19486, USA
| | - John A McIntosh
- Process Research & Development, MRL, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Zhijian Liu
- Process Research & Development, MRL, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Ian Mangion
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, PA 19486, USA
| | - Narayan Variankaval
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, PA 19486, USA
| | - Xiaodong Bu
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, PA 19486, USA
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Kumar S, Bhardwaj VK, Guleria S, Purohit R, Kumar S. Improving the catalytic efficiency and dimeric stability of Cu,Zn superoxide dismutase by combining structure-guided consensus approach with site-directed mutagenesis. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148505. [PMID: 34626596 DOI: 10.1016/j.bbabio.2021.148505] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/26/2021] [Accepted: 09/30/2021] [Indexed: 01/05/2023]
Abstract
Superoxide dismutase (SOD) leads the front line of defense against injuries mediated by the reactive oxygen species (ROS). The SOD from a high-altitude plant Potentilla atrosanguinea is a unique thermostable enzyme. In this study, we applied a structure-guided consensus approach on Cu,Zn SOD from Potentilla atrosanguinea plant, to improve its enzymatic properties. The polar uncharged amino acid (threonine) at position 97 of wild-type (WT) SOD was selected as a target residue for substitution by aspartate (T97D) through site-directed mutagenesis. The WT and T97D were examined by a combinative approach consisting of robust computational and experimental tools. The in-silico analysis indicated improved dimeric stability in T97D as compared to the WT. The strong interactions between the monomers were related to improved dimerization and enhanced catalytic efficiency of T97D. These results were validated by in-vitro assays showing improved dimer stability and catalytic efficiency in T97D than WT. Moreover, the mutation also improved the thermostability of the enzyme. The combined structural and functional data described the basis for improved specific activity and thermostability. This study could expand the scope of interface residue to be explored as targets for designing of SODs with improved kinetics.
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Affiliation(s)
- Sachin Kumar
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Shweta Guleria
- Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India; Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
| | - Sanjay Kumar
- Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India.
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Orf GS, Gisriel CJ, Granstrom J, Baker PL, Redding KE. The PshX subunit of the photochemical reaction center from Heliobacterium modesticaldum acts as a low-energy antenna. PHOTOSYNTHESIS RESEARCH 2022; 151:11-30. [PMID: 34480322 DOI: 10.1007/s11120-021-00871-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
The anoxygenic phototrophic bacterium Heliobacterium modesticaldum contains a photochemical reaction center protein complex (called the HbRC) consisting of a homodimer of the PshA polypeptide and two copies of a newly discovered polypeptide called PshX, which is a single transmembrane helix that binds two bacteriochlorophyll g molecules. To assess the function of PshX, we produced a ∆pshX strain of Hbt. modesticaldum by leveraging the endogenous Hbt. modesticaldum Type I-A CRISPR-Cas system to aid in mutant selection. We optimized this system by separating the homologous recombination and CRISPR-based selection steps into two plasmid transformations, allowing for markerless gene replacement. Fluorescence and low-temperature absorbance of the purified HbRC from the wild-type and ∆pshX strains showed that the bacteriochlorophylls bound by PshX have the lowest site energies in the entire HbRC. This indicates that PshX acts as a low-energy antenna subunit, participating in entropy-assisted uphill energy transfer toward the P800 special bacteriochlorophyll g pair. We further discuss the role that PshX may play in stability of the HbRC, its conservation in other heliobacterial species, and the evolutionary pressure to produce and maintain single-TMH subunits in similar locations in other reaction centers.
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Affiliation(s)
- Gregory S Orf
- Center for Bioenergy and Photosynthesis, School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Park, IL, 60064, USA
| | - Christopher J Gisriel
- Center for Bioenergy and Photosynthesis, School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Jesse Granstrom
- Center for Bioenergy and Photosynthesis, School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Patricia L Baker
- Center for Bioenergy and Photosynthesis, School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Kevin E Redding
- Center for Bioenergy and Photosynthesis, School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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Hu Y, Li M, Liu Z, Song X, Qu Y, Qin Y. Carbon catabolite repression involves physical interaction of the transcription factor CRE1/CreA and the Tup1-Cyc8 complex in Penicillium oxalicum and Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:244. [PMID: 34952627 PMCID: PMC8710005 DOI: 10.1186/s13068-021-02092-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 12/04/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Cellulolytic enzyme production in filamentous fungi requires a release from carbon catabolite repression (CCR). The protein CRE1/CreA (CRE = catabolite responsive element) is a key transcription factor (TF) that is involved in CCR and represses cellulolytic gene expression. CRE1/CreA represents the functional equivalent of Mig1p, an important Saccharomyces cerevisiae TF in CCR that exerts its repressive effect by recruiting a corepressor complex Tup1p-Cyc8p. Although it is known from S. cerevisiae that CRE1/CreA might repress gene expression via interacting with the corepressor complex Tup1-Cyc8, this mechanism is unconfirmed in other filamentous fungi, since the physical interaction has not yet been verified in these organisms. The precise mechanism on how CRE1/CreA achieves transcriptional repression after DNA binding remains unknown. RESULTS The results from tandem affinity purification and bimolecular fluorescence complementation revealed a direct physical interaction between the TF CRE1/CreA and the complex Tup1-Cyc8 in the nucleus of cellulolytic fungus Trichoderma reesei and Penicillium oxalicum. Both fungi have the ability to secrete a complex arsenal of enzymes to synergistically degrade lignocellulosic materials. In P. oxalicum, the protein PoCyc8, a subunit of complex Tup1-Cyc8, interacts directly with TF PoCreA and histone H3 lysine 36 (H3K36) methyltransferase PoSet2 in the nucleus. The di-methylation level of H3K36 in the promoter of prominent cellulolytic genes (cellobiohydrolase-encoding gene Pocbh1/cel7A and endoglucanase-encoding gene Poegl1/cel7B) is positively correlated with the expression levels of TF PoCreA. Since the methylation of H3K36 was also demonstrated to be a repression marker of cellulolytic gene expression, it appears feasible that the cellulolytic genes are repressed via PoCreA-Tup1-Cyc8-Set2-mediated transcriptional repression. CONCLUSION This study verifies the long-standing conjecture that the TF CRE1/CreA represses gene expression by interacting with the corepressor complex Tup1-Cyc8 in filamentous fungi. A reasonable explanation is proposed that PoCreA represses gene expression by recruiting complex PoTup1-Cyc8. Histone methyltransferase Set2, which methylates H3K36, is also involved in the regulatory network by interacting with PoCyc8. The findings contribute to the understanding of CCR mechanism in filamentous fungi and could aid in biotechnologically relevant enzyme production.
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Affiliation(s)
- Yueyan Hu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-Based Medicine, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
| | - Mengxue Li
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
| | - Zhongjiao Liu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
| | - Xin Song
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
| | - Yinbo Qu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
| | - Yuqi Qin
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
- NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-Based Medicine, Shandong University, No. 72 Binhai Road, Qingdao, 266237 China
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Ravee R, Baharin A, Cho WT, Ting TY, Goh HH. Protease activity is maintained in Nepenthes ampullaria digestive fluids depleted of endogenous proteins with compositional changes. PHYSIOLOGIA PLANTARUM 2021; 173:1967-1978. [PMID: 34455610 DOI: 10.1111/ppl.13540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/22/2021] [Indexed: 06/13/2023]
Abstract
Nepenthes ampullaria is a unique carnivorous tropical pitcher plant with the detritivorous capability of sequestering nutrients from leaf litter apart from being insectivorous. The changes in the protein composition and protease activity of its pitcher fluids during the early opening of pitchers (D0 and D3C) were investigated via a proteomics approach and a controlled protein depletion experiment (D3L). A total of 193 proteins were identified. Common proteins such as pathogenesis-related protein, proteases (Nep [EC:3.4.23.12], SCP [EC:3.4.16.-]), peroxidase [EC:1.11.1.7], GDSL esterase/lipase [EC:3.1.1.-], and purple acid phosphatase [EC:3.1.3.2] were found in high abundance in the D0 pitchers and were replenished in D3L samples. This reflects their importance for biological processes upon pitcher opening. Meanwhile, prey-inducible chitinases [EC:3.2.1.14] were found in D0 but not in D3C and D3L samples, which suggests their degradation in the absence of prey. Protease activity assays demonstrated the replenishment of proteases in D3L with similar levels of proteolytic activities to that of D3C samples. This supports a feedback mechanism and signaling in the molecular regulation of endogenous protein secretion, turnover, and activity in Nepenthes pitcher fluids. Furthermore, we also discovered several new enzymes (XTH [EC:2.4.1.207], PAE [EC:3.1.1.98]) with possible functions in cell wall degradation that could contribute to the detritivory habit of N. ampullaria.
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Affiliation(s)
- Rishiesvari Ravee
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Anis Baharin
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Weng-Tim Cho
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Tiew-Yik Ting
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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García-Carnero LC, Salinas-Marín R, Lozoya-Pérez NE, Wrobel K, Wrobel K, Martínez-Duncker I, Niño-Vega GA, Mora-Montes HM. The Heat Shock Protein 60 and Pap1 Participate in the Sporothrixschenckii-Host Interaction. J Fungi (Basel) 2021; 7:jof7110960. [PMID: 34829247 PMCID: PMC8620177 DOI: 10.3390/jof7110960] [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: 10/20/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
Sporothrixschenckii is one of the etiological agents of sporotrichosis, a worldwide-distributed subcutaneous mycosis. Its cell wall contains a glycoconjugate composed of rhamnose, mannose, glucuronic acid, and proteins, named peptidorhamnomannan, which harbors important Sporothrix-specific immunogenic epitopes. Although the peptidorhamnomannan carbohydrate moiety has been extensively studied, thus far, little is known about the protein core. Here, using LC-MS/MS, we analyzed the S.schenckii peptidorhamnomannan peptide fraction and generated mass signals of 325 proteins, most of them likely to be moonlighting proteins. Among the identified proteins, chaperonin GroEL/Hsp60 and the uncharacterized protein Pap1 were selected for further analysis. Both proteins were heterologously expressed in bacteria, and they showed adhesive properties to the extracellular matrix proteins laminin, elastin, fibrinogen, and fibronectin, although Pap1 also was bound to type-I and type-II collagen. The inoculation of concentrations higher than 40 μg of these proteins, separately, increased immune effectors in the hemolymph of Galleriamellonella larvae and protected animals from an S.schenckii lethal challenge. These observations were confirmed when yeast-like cells, pre-incubated with anti-rHsp60 or anti-rPap1 antibodies were used to inoculate larvae. The animals inoculated with pretreated cells showed increased survival rates when compared to the control groups. In conclusion, we report that Hsp60 and Pap1 are part of the cell wall peptidorhamnomannan, can bind extracellular matrix components, and contribute to the S.schenckii virulence. To our knowledge, this is the first report about moonlighting protein in the S.schenckii cell wall with an important role during the pathogen-host interaction.
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Affiliation(s)
- Laura C. García-Carnero
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, C.P., Guanajuato 36050, Gto., Mexico; (L.C.G.-C.); (N.E.L.-P.); (G.A.N.-V.)
| | - Roberta Salinas-Marín
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mor., Mexico; (R.S.-M.); (I.M.-D.)
| | - Nancy E. Lozoya-Pérez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, C.P., Guanajuato 36050, Gto., Mexico; (L.C.G.-C.); (N.E.L.-P.); (G.A.N.-V.)
| | - Katarzyna Wrobel
- Departamento de Química, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, C.P., Guanajuato 36050, Gto., Mexico; (K.W.); (K.W.)
| | - Kazimierz Wrobel
- Departamento de Química, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, C.P., Guanajuato 36050, Gto., Mexico; (K.W.); (K.W.)
| | - Iván Martínez-Duncker
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mor., Mexico; (R.S.-M.); (I.M.-D.)
| | - Gustavo A. Niño-Vega
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, C.P., Guanajuato 36050, Gto., Mexico; (L.C.G.-C.); (N.E.L.-P.); (G.A.N.-V.)
| | - Héctor M. Mora-Montes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, C.P., Guanajuato 36050, Gto., Mexico; (L.C.G.-C.); (N.E.L.-P.); (G.A.N.-V.)
- Correspondence: ; Tel.: +52-473-7320006 (ext. 8193)
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Choi J, Shin JH, An HJ, Oh MJ, Kim SR. Analysis of secretome and N-glycosylation of Chlorella species. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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69
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Bonea D, Noureddine J, Gazzarrini S, Zhao R. Oxidative and salt stresses alter the 26S proteasome holoenzyme and associated protein profiles in Arabidopsis thaliana. BMC PLANT BIOLOGY 2021; 21:486. [PMID: 34696730 PMCID: PMC8543921 DOI: 10.1186/s12870-021-03234-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/29/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND The 26S proteasome, canonically composed of multi-subunit 19S regulatory (RP) and 20S core (CP) particles, is crucial for cellular proteostasis. Proteasomes are re-modeled, activated, or re-localized and this regulation is critical for plants in response to environmental stresses. The proteasome holoenzyme assembly and dissociation are therefore highly dynamic in vivo. However, the stoichiometric changes of the plant proteasomes and how proteasome associated chaperones vary under common abiotic stresses have not been systematically studied. RESULTS Here, we studied the impact of abiotic stresses on proteasome structure, activity, and interacting partners in Arabidopsis thaliana. We analyzed available RNA expression data and observed that expressions of proteasome coding genes varied substantially under stresses; however, the protein levels of a few key subunits did not change significantly within 24 h. Instead, a switch in the predominant proteasome complex, from 26S to 20S, occurs under oxidative or salt stress. Oxidative stress also reduced the cellular ATP content and the association of HSP70-family proteins to the 20S proteasome, but enhanced the activity of cellular free form CP. Salt stress, on the other hand, did not affect cellular ATP level, but caused subtle changes in proteasome subunit composition and impacted bindings of assembly chaperones. Analyses of an array of T-DNA insertional mutant lines highlighted important roles for several putative assembly chaperones in seedling establishment and stress sensitivity. We also observed that knockout of PBAC1, one of the α-ring assembly chaperones, resulted in reduced germination and tearing of the seed coat following sterilization. CONCLUSIONS Our study revealed an evolutionarily conserved mechanism of proteasome regulation during oxidative stress, involving dynamic regulation of the holoenzyme formation and associated regulatory proteins, and we also identified a novel role of the PBAC1 proteasome assembly chaperone in seed coat development.
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Affiliation(s)
- Diana Bonea
- Department of Biological Sciences, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4 Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5 Canada
| | - Jenan Noureddine
- Department of Biological Sciences, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4 Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5 Canada
| | - Sonia Gazzarrini
- Department of Biological Sciences, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4 Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5 Canada
| | - Rongmin Zhao
- Department of Biological Sciences, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4 Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5 Canada
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70
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Tsai W, Yin H, Lin Y, Liu H, Tseng C, Wen H. A rapid lateral flow assay using immunomagnetic nanoparticles for detecting mango allergen residues in processed foods. J Food Saf 2021. [DOI: 10.1111/jfs.12929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Wen‐Che Tsai
- Department of Food Science and Biotechnology National Chung Hsing University Taichung Taiwan
| | - Hsin‐Yi Yin
- Department of Food Science and Biotechnology National Chung Hsing University Taichung Taiwan
- Food and Animal Product Safety Inspection Center National Chung Hsing University Taichung Taiwan
| | - Ya‐Ting Lin
- Department of Food Science and Biotechnology National Chung Hsing University Taichung Taiwan
| | - Hung‐Jen Liu
- Institute of Molecular Biology National Chung Hsing University Taichung Taiwan
- The iEGG and Animal Biotechnology Center National Chung Hsing University Taichung Taiwan
- Rong Hsing Research Center for Translational Medicine National Chung Hsing University Taichung Taiwan
- PhD Program in Translational Medicine National Chung Hsing University Taichung Taiwan
| | - Cheng‐Yen Tseng
- Department of Applied Chemistry Chaoyang University of Technology Taichung Taiwan
| | - Hsiao‐Wei Wen
- Department of Food Science and Biotechnology National Chung Hsing University Taichung Taiwan
- Food and Animal Product Safety Inspection Center National Chung Hsing University Taichung Taiwan
- Graduate Institute of Food Safety National Chung Hsing University Taichung Taiwan
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71
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Movaghar Asareh S, Savei T, Arjmand S, Ranaei Siadat SO, Fatemi F, Pourmadadi M, Shabani Shayeh J. Expression of functional eGFP-fused antigen-binding fragment of ranibizumab in Pichia pastoris. BIOIMPACTS : BI 2021; 12:203-210. [PMID: 35677669 PMCID: PMC9124873 DOI: 10.34172/bi.2021.23219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 01/02/2021] [Accepted: 01/06/2021] [Indexed: 11/25/2022]
Abstract
Introduction: Ranibizumab is a mouse monoclonal antibody fragment antigen-binding (Fab) against human vascular endothelial growth factor-A (VEGF-A), inhibiting angiogenesis. This antibody is commercially produced in Escherichia coli host and used to treat wet age-related macular degeneration (AMD). Methods: In this study, the heavy and light chains of ranibizumab were expressed in Pichia pastoris. The expressed chains were incubated overnight at 4°C for interaction. The formation of an active structure was evaluated based on the interaction with substrate VEGF-A using an indirect ELISA, and an electrochemical setup. Furthermore, reconstruction of split enhanced green fluorescent protein (eGFP) reporter, chimerized at the C-terminus of the heavy and light chains, was used to characterize chains' interaction. Results: P. pastoris efficiently expressed designed constructs and secreted them into the culture medium. The anti-Fab antibody detected the constructed Fab structure in western blot analysis. Reconstruction of the split reporter confirmed the interaction between heavy and light chains. The designed ELISA and electrochemical setup results verified the binding activity of the recombinant Fab structure against VEGF-A. Conclusion: In this work, we indicated that the heavy and light chains of ranibizumab Fab fragments (with or without linkage to split parts of eGFP protein) were produced in P. pastoris. The fluorescence of reconstructed eGFP was detected after incubating the equal ratio of chimeric-heavy and light chains. Immunoassay and electrochemical tests verified the bioactivity of constructed Fab. The data suggested that P. pastoris could be considered a potential efficient eukaryotic host for ranibizumab production.
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Affiliation(s)
| | - Tahereh Savei
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Sareh Arjmand
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | | | - Fataneh Fatemi
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
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Lu Y, Huang Y, Li J, Huang J, Zhang L, Feng J, Li J, Xia Q, Zhao Q, Huang L, Jiang S, Su S. Eosinophil extracellular traps drive asthma progression through neuro-immune signals. Nat Cell Biol 2021; 23:1060-1072. [PMID: 34616019 DOI: 10.1038/s41556-021-00762-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 08/26/2021] [Indexed: 12/18/2022]
Abstract
Eosinophilic inflammation is a feature of allergic asthma. Despite mounting evidence showing that chromatin filaments released from neutrophils mediate various diseases, the understanding of extracellular DNA from eosinophils is limited. Here we show that eosinophil extracellular traps (EETs) in bronchoalveolar lavage fluid are associated with the severity of asthma in patients. Functionally, we find that EETs augment goblet-cell hyperplasia, mucus production, infiltration of inflammatory cells and expressions of type 2 cytokines in experimental non-infection-related asthma using both pharmaceutical and genetic approaches. Multiple clinically relevant allergens trigger EET formation at least partially via thymic stromal lymphopoietin in vivo. Mechanically, EETs activate pulmonary neuroendocrine cells via the CCDC25-ILK-PKCα-CRTC1 pathway, which is potentiated by eosinophil peroxidase. Subsequently, the pulmonary neuroendocrine cells amplify allergic immune responses via neuropeptides and neurotransmitters. Therapeutically, inhibition of CCDC25 alleviates allergic inflammation. Together, our findings demonstrate a previously unknown role of EETs in integrating immunological and neurological cues to drive asthma progression.
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Affiliation(s)
- Yiwen Lu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yijiao Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Department of Pulmonary and Critical Care Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jiang Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jingying Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Lizhi Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Department of Pulmonary and Critical Care Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jingwei Feng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jiaqian Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qidong Xia
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qiyi Zhao
- Department of Infectious Diseases, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Linjie Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Department of Pulmonary and Critical Care Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Institute of Pulmonary Diseases, Sun Yat-Sen University, Guangzhou, China
| | - Shanping Jiang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China. .,Department of Pulmonary and Critical Care Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China. .,Institute of Pulmonary Diseases, Sun Yat-Sen University, Guangzhou, China.
| | - Shicheng Su
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China. .,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China. .,Department of Infectious Diseases, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China. .,Department of Immunology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
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Moreira FTC, Correia BP, Sousa MP, Sales GF. Colorimetric cellulose-based test-strip for rapid detection of amyloid β-42. Mikrochim Acta 2021; 188:334. [PMID: 34498145 DOI: 10.1007/s00604-021-04996-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/13/2021] [Indexed: 11/30/2022]
Abstract
An innovative sensing assay is described for point-of-care (PoC) quantification of a biomarker of Alzheimer's disease, amyloid β-42 (Aβ-42). This device is based on a cellulose paper-dye test strip platform in which the corresponding detection layer is integrated by applying a molecularly imprinted polymer (MIP) to the cellulose paper surface. Briefly, the cellulose paper is chemically modified with a silane to subsequently apply the MIP detection layer. The imprinting process is confirmed by the parallel preparation of a control material, namely a non-imprinted polymer (NIP). The chemical changes of the surface were evaluated by Fourier transform infrared spectroscopy (FTIR), contact angle, and thermogravimetric analysis (TG). Proteins and peptides can be quantified by conventional staining methods. For this purpose, Coomassie blue (CB) was used as a staining dye for the detection and quantification of Aβ-42. Quantitative determination is made possible by taking a photograph and applying an appropriate mathematical treatment to the color coordinates provided by the ImageJ program. The MIP shows a linear range between 1.0 ng/mL and 10 μg/mL and a detection limit of 0.71 ng/mL. Overall, this cellulose-based assay is suitable for the detection of peptides or proteins in a sample by visual comparison of color change. The test strip provides a simple, instrument-free, and cost-effective method with high chemical stability, capable of detecting very small amounts of peptides or proteins in a sample, and can be used for the detection of any (bio)molecule of interest.
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Affiliation(s)
- Felismina T C Moreira
- BioMark@ISEP, School of Engineering, Polytechnic of Porto, R. Dr. António Bernardino de Almeida, 431, 4249-015, Porto, Portugal. .,CEB, Centre of Biological Engineering, Minho University, Braga, Portugal.
| | - Barbara P Correia
- BioMark@ISEP, School of Engineering, Polytechnic of Porto, R. Dr. António Bernardino de Almeida, 431, 4249-015, Porto, Portugal.,CEB, Centre of Biological Engineering, Minho University, Braga, Portugal
| | - Mariana P Sousa
- BioMark@ISEP, School of Engineering, Polytechnic of Porto, R. Dr. António Bernardino de Almeida, 431, 4249-015, Porto, Portugal.,CEB, Centre of Biological Engineering, Minho University, Braga, Portugal
| | - Goreti F Sales
- CEB, Centre of Biological Engineering, Minho University, Braga, Portugal.,BioMark@UC, Faculty of Sciences and Technology, University of Coimbra, R. Sílvio Lima, pólo II, 3030-790, Coimbra, Portugal
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Kassem S, van der Pan K, de Jager AL, Naber BAE, de Laat IF, Louis A, van Dongen JJM, Teodosio C, Díez P. Proteomics for Low Cell Numbers: How to Optimize the Sample Preparation Workflow for Mass Spectrometry Analysis. J Proteome Res 2021; 20:4217-4230. [PMID: 34328739 PMCID: PMC8419858 DOI: 10.1021/acs.jproteome.1c00321] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Indexed: 12/20/2022]
Abstract
Nowadays, massive genomics and transcriptomics data can be generated at the single-cell level. However, proteomics in this setting is still a big challenge. Despite the great improvements in sensitivity and performance of mass spectrometry instruments and the better knowledge on sample preparation processing, it is widely acknowledged that multistep proteomics workflows may lead to substantial sample loss, especially when working with paucicellular samples. Still, in clinical fields, frequently limited sample amounts are available for downstream analysis, thereby hampering comprehensive characterization at protein level. To aim at better protein and peptide recoveries, we compare existing and novel approaches in the multistep sample preparation protocols for mass spectrometry studies, from sample collection, cell lysis, protein quantification, and electrophoresis/staining to protein digestion, peptide recovery, and LC-MS/MS instruments. From this critical evaluation, we conclude that the recent innovations and technologies, together with high quality management of samples, make proteomics on paucicellular samples possible, which will have immediate impact for the proteomics community.
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Affiliation(s)
- Sara Kassem
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Kyra van der Pan
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Anniek L. de Jager
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Brigitta A. E. Naber
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Inge F. de Laat
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Alesha Louis
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Jacques J. M. van Dongen
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Cristina Teodosio
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Paula Díez
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
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75
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Motiei M, Mirahmadi-Zare SZ, Nasr-Esfahani MH. Chemical stabilization of γ-polyglutamate by chitosan and the effect of co-solvents on the stability. Biophys Chem 2021; 275:106605. [PMID: 33964508 DOI: 10.1016/j.bpc.2021.106605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 12/23/2022]
Abstract
In protein-based formulations, conformational distortions and attractive interactions may cause insoluble and undesired aggregates. In the case of ionic peptides, including cationic or anionic, commonly electrostatic interactions are the main factors that control structure assembling. In this study, it was proposed that grafting of chitosan (CS) to γ-polyglutamic acid (γ-PGA) might exhibit much strong inhibiting effect on the formation of protein aggregates due to multiple amino groups and hydrophilic properties. To guarantee stable and safe biopharmaceutical formulation, the potency of a variety of stabilizers including sugars (glucose, sucrose), polyols (sorbitol, glycerol), surfactant (Tween 20), salting-out salt (PBS), and also different pH values have been evaluated on stabilizing or destabilizing the native state of CS-g-PGA copolymer using FTIR, CD, DLS, and SDS-PAGE. The comparable analysis revealed that the stability of CS-g-PGA was strongly dependent on pH owing to the polyelectrolyte characteristics of the polymers. Altogether these results implied that CS at optimized conditions might be an important precursor for the pharmaceutical industry and function as a new polymer for aggregation suppression and protein stabilization.
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Affiliation(s)
- Marjan Motiei
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, 8159358686 Isfahan, Iran; Centre of Polymer Systems, Tomas Bata University in Zlín, Třída Tomáše Bati 5678, 76001 Zlín, Czech Republic
| | - Seyede Zohreh Mirahmadi-Zare
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, 8159358686 Isfahan, Iran.
| | - Mohammad Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, 8159358686 Isfahan, Iran
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76
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Martínez
Ceron MC, Ávila L, Giudicessi SL, Minoia JM, Fingermann M, Camperi SA, Albericio F, Cascone O. Fully Automated Screening of a Combinatorial Library to Avoid False Positives: Application to Tetanus Toxoid Ligand Identification. ACS OMEGA 2021; 6:18756-18762. [PMID: 34337215 PMCID: PMC8319927 DOI: 10.1021/acsomega.1c01814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 07/02/2021] [Indexed: 05/12/2023]
Abstract
Peptide ligands are widely used in protein purification by affinity chromatography. Here, we applied a fully automated two-stage library screening method that avoids false positive peptidyl-bead selection and applied it to tetanus toxoid purification. The first library screening was performed using only sulforhodamine (a fluorescent dye), and fluorescent beads were isolated automatically by flow cytometry and discarded. A second screening was then performed with the rest of the library, using the target protein (tetanus toxoid)-rhodamine conjugate. This time, fluorescent beads were isolated, and peptide sequences were identified by matrix-assisted laser desorption/ionization tandem mass spectrometry. Those appearing with greater frequency were synthesized and immobilized on agarose to evaluate a range of chromatographic purification conditions. The affinity matrix PTx1-agarose (Ac-Leu-Arg-Val-Tyr-His-Gly-Gly-Ala-Gly-Lys-agarose) showed the best performance when 20 mM sodium phosphate, 0.05% Tween 20, pH 5.9 as adsorption buffer and 100 mM Tris-HCl, 100 mM NaCl, pH 8.0 as elution buffer were used. A pure tetanus toxoid (Ttx) was loaded on a chromatographic column filled with the PTx1 matrix, and 96% adsorption was achieved, with a K d of 9.18 ± 0.07 nmol/L and a q m of 1.31 ± 0.029 μmol Ttx/mL matrix. Next, a Clostridium tetani culture supernatant treated with formaldehyde (to obtain the toxoid) was applied as a sample. The sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis showed a band, identified by electrospray ionization mass spectrometry as the Ttx, that appeared only in the elution fraction, where an S-layer protein was also detected.
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Affiliation(s)
- María C. Martínez
Ceron
- Facultad
de Farmacia y Bioquímica, Cátedra de Biotecnología, Universidad de Buenos Aires, Junín 956, 1113 Buenos Aires, Argentina
- Instituto
de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires (UBA) - Consejo Nacional de Investigaciones
Científicas y Técnicas (CONICET), Junín 956, 1113 Buenos
Aires, Argentina
- . Tel.: +54 11
5287-4671
| | - Lucía Ávila
- Instituto
Nacional de Producción de Biológicos, ANLIS “Dr.
Carlos G. Malbrán”, Av. Vélez Sársfield 563, 1282 Buenos Aires, Argentina
| | - Silvana L. Giudicessi
- Facultad
de Farmacia y Bioquímica, Cátedra de Biotecnología, Universidad de Buenos Aires, Junín 956, 1113 Buenos Aires, Argentina
- Instituto
de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires (UBA) - Consejo Nacional de Investigaciones
Científicas y Técnicas (CONICET), Junín 956, 1113 Buenos
Aires, Argentina
| | - Juan M. Minoia
- Facultad
de Farmacia y Bioquímica, Cátedra de Biotecnología, Universidad de Buenos Aires, Junín 956, 1113 Buenos Aires, Argentina
- Instituto
de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires (UBA) - Consejo Nacional de Investigaciones
Científicas y Técnicas (CONICET), Junín 956, 1113 Buenos
Aires, Argentina
| | - Matías Fingermann
- Instituto
Nacional de Producción de Biológicos, ANLIS “Dr.
Carlos G. Malbrán”, Av. Vélez Sársfield 563, 1282 Buenos Aires, Argentina
- CONICET, Godoy Cruz
2290, 1425 Buenos
Aires, Argentina
| | - Silvia A. Camperi
- Facultad
de Farmacia y Bioquímica, Cátedra de Biotecnología, Universidad de Buenos Aires, Junín 956, 1113 Buenos Aires, Argentina
- Instituto
de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires (UBA) - Consejo Nacional de Investigaciones
Científicas y Técnicas (CONICET), Junín 956, 1113 Buenos
Aires, Argentina
| | - Fernando Albericio
- Institute
for Advanced Chemistry of Catalonia (IQAC-CSIC), 08034 Barcelona, Spain
- CIBER-BBN,
Networking Centre on Bioengineering, Biomaterials and Nanomedicine,
Department of Organic Chemistry, University
of Barcelona, 08028 Barcelona, Spain
- School
of Chemistry & Physics, University of
Kwazulu-Natal, 4001 Durban, South Africa
| | - Osvaldo Cascone
- Facultad
de Farmacia y Bioquímica, Cátedra de Biotecnología, Universidad de Buenos Aires, Junín 956, 1113 Buenos Aires, Argentina
- Instituto
de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires (UBA) - Consejo Nacional de Investigaciones
Científicas y Técnicas (CONICET), Junín 956, 1113 Buenos
Aires, Argentina
- Instituto
Nacional de Producción de Biológicos, ANLIS “Dr.
Carlos G. Malbrán”, Av. Vélez Sársfield 563, 1282 Buenos Aires, Argentina
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77
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Cotabarren J, Ozón B, Claver S, Garcia-Pardo J, Obregón WD. Purification and Identification of Novel Antioxidant Peptides Isolated from Geoffroea decorticans Seeds with Anticoagulant Activity. Pharmaceutics 2021; 13:1153. [PMID: 34452114 PMCID: PMC8399481 DOI: 10.3390/pharmaceutics13081153] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/16/2021] [Accepted: 07/22/2021] [Indexed: 11/17/2022] Open
Abstract
Geoffroea decorticans is a xerophilous deciduous tree present in most arid forests of southern South America, which is commonly used in traditional medicine. The seeds of this tree have been previously investigated for their singular chemical composition, but their protein content has been poorly investigated. Herein, we report the isolation, purification, and characterization of a set of thermostable peptides derived from Geoffroea decorticans seeds (GdAPs) with strong antioxidant and anticoagulant activities. The most potent antioxidant peptides showed a half maximal inhibitory concentration (IC50) of 35.5 ± 0.3 µg/mL determined by 1,1-diphenyl-2-picrylhydrazyl (DPPH). They also caused a dose-dependent prolongation of the aPTT clotting time with an IC50 value of ~82 µg/mL. Interestingly, MALDI-TOF/MS analysis showed the presence of three major peptides with low molecular weights of 2257.199 Da, 2717.165 Da, and 5422.002 Da. The derived amino-acid sequence of GdAPs revealed their unique structural features, exhibiting homology with various proteins present in the genome of Arachis hypogaea. All in all, our data suggest a direct applicability of GdAPs for pharmaceutical purposes.
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Affiliation(s)
- Juliana Cotabarren
- Centro de Investigación de Proteínas Vegetales (CIPROVE), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de la Plata, Buenos Aires B1900, Argentina; (B.O.); (S.C.)
| | - Brenda Ozón
- Centro de Investigación de Proteínas Vegetales (CIPROVE), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de la Plata, Buenos Aires B1900, Argentina; (B.O.); (S.C.)
| | - Santiago Claver
- Centro de Investigación de Proteínas Vegetales (CIPROVE), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de la Plata, Buenos Aires B1900, Argentina; (B.O.); (S.C.)
| | - Javier Garcia-Pardo
- Institut de Biotecnologia i Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Walter David Obregón
- Centro de Investigación de Proteínas Vegetales (CIPROVE), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de la Plata, Buenos Aires B1900, Argentina; (B.O.); (S.C.)
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78
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Omar A, Gao Y, Wubulikasimu A, Arken A, Aisa HA, Yili A. Effects of trypsin-induced limited hydrolysis on the structural, functional, and bioactive properties of sericin. RSC Adv 2021; 11:25431-25440. [PMID: 35478883 PMCID: PMC9036984 DOI: 10.1039/d1ra03772b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/10/2021] [Indexed: 12/23/2022] Open
Abstract
The effects of trypsin-induced hydrolysis on the structural, functional, and antioxidant properties of sericin were studied. The structural properties of sericin and its hydrolysates were characterized by using SDS-PAGE, SEC-HPLC, surface hydrophobicity, and circular dichroism. Antioxidative properties were evaluated based on quenching capacity against hydroxyl, DPPH, and ABTS, and metal (Fe2+, Cu2+) chelating activity. The enzymatic hydrolysis raised the flexibility, changed emulsifying and foaming properties, and improved the solubility and antioxidant activity of sericin. Meanwhile, the hydrolysis led to a decline in gelation capacity, oil holding capacity, and water holding capacity. Sericin and its hydrolysates exhibited excellent function with regard to oil holding, emulsifying, and foaming. Sericin and its hydrolysates had clear effects on the growth of both Enterococcus faecalis and Lactobacillus bulgaricus strains. Sericin was hydrolyzed to a limited extent using trypsin, then the physicochemical, prebiotic, and antioxidative properties of the obtained hydrolysates were investigated.![]()
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Affiliation(s)
- Adil Omar
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences Beijing South Road 40-1 Urumqi 830011 China +86 991 3838957 +86 991 3835708.,University of the Chinese Academy of Sciences Beijing 100039 China
| | - Yanhua Gao
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences Beijing South Road 40-1 Urumqi 830011 China +86 991 3838957 +86 991 3835708
| | - Atikan Wubulikasimu
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences Beijing South Road 40-1 Urumqi 830011 China +86 991 3838957 +86 991 3835708.,University of the Chinese Academy of Sciences Beijing 100039 China
| | - Amina Arken
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences Beijing South Road 40-1 Urumqi 830011 China +86 991 3838957 +86 991 3835708.,University of the Chinese Academy of Sciences Beijing 100039 China
| | - Haji Akber Aisa
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences Beijing South Road 40-1 Urumqi 830011 China +86 991 3838957 +86 991 3835708
| | - Abulimiti Yili
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences Beijing South Road 40-1 Urumqi 830011 China +86 991 3838957 +86 991 3835708
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79
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Kun RS, Garrigues S, Di Falco M, Tsang A, de Vries RP. The chimeric GaaR-XlnR transcription factor induces pectinolytic activities in the presence of D-xylose in Aspergillus niger. Appl Microbiol Biotechnol 2021; 105:5553-5564. [PMID: 34236481 PMCID: PMC8285313 DOI: 10.1007/s00253-021-11428-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/10/2021] [Accepted: 06/12/2021] [Indexed: 01/03/2023]
Abstract
Abstract Aspergillus niger is a filamentous fungus well known for its ability to produce a wide variety of pectinolytic enzymes, which have many applications in the industry. The transcriptional activator GaaR is induced by 2-keto-3-deoxy-L-galactonate, a compound derived from D-galacturonic acid, and plays a major role in the regulation of pectinolytic genes. The requirement for inducer molecules can be a limiting factor for the production of enzymes. Therefore, the generation of chimeric transcription factors able to activate the expression of pectinolytic genes by using underutilized agricultural residues would be highly valuable for industrial applications. In this study, we used the CRISPR/Cas9 system to generate three chimeric GaaR-XlnR transcription factors expressed by the xlnR promoter by swapping the N-terminal region of the xylanolytic regulator XlnR to that of the GaaR in A. niger. As a test case, we constructed a PpgaX-hph reporter strain to evaluate the alteration of transcription factor specificity in the chimeric mutants. Our results showed that the chimeric GaaR-XlnR transcription factor was induced in the presence of D-xylose. Additionally, we generated a constitutively active GaaR-XlnR V756F version of the most efficient chimeric transcription factor to better assess its activity. Proteomics analysis confirmed the production of several pectinolytic enzymes by ΔgaaR mutants carrying the chimeric transcription factor. This correlates with the improved release of D-galacturonic acid from pectin by the GaaR-XlnR V756F mutant, as well as by the increased L-arabinose release from the pectin side chains by both chimeric mutants under inducing condition, which is required for efficient degradation of pectin. Key points • Chimeric transcription factors were generated by on-site mutations using CRISPR/Cas9. • PpgaX-hph reporter strain allowed for the screening of functional GaaR-XlnR mutants. • Chimeric GaaR-XlnR induced pectinolytic activities in the presence of D-xylose. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11428-2.
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Affiliation(s)
- Roland S Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
| | - Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
| | - Marcos Di Falco
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, H4B 1R6, Canada
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, H4B 1R6, Canada
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.
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80
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Dhar S, Bhattacharjee M, Baishya D, Acharjee S. Characterization of Seed Proteome Profile of Wild and Cultivated Chickpeas of India. Protein Pept Lett 2021; 28:323-332. [PMID: 32914710 DOI: 10.2174/0929866527666200910164118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/14/2020] [Accepted: 09/21/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Chickpea is a widely grown legume in India, Australia, Canada, and Mediterranean regions. Seeds of chickpea are good source of protein for both human and animals. Wild relatives of chickpea (Cicer arietinum) are the potential gene pool for crop improvement; however, very little information is available on the seed proteome of these wild chickpeas. OBJECTIVE We aimed to analyze the seed proteome profiles of three wild relatives of chickpea, Cicer bijugum, Cicer judaicum and Cicer microphyllum along with two cultivated varieties JG11 and DCP 92/3. METHODS Total seed proteins were extracted using various extraction buffers for 2-D gel electrophoresis. Protein separated in a 2-D gels were subjected to image analyses, differentially expressed proteins were extracted from the gels and identified by the MALDI TOF/TOF. Seed protease inhibitors were analysed biochemically. RESULTS We have standardized the 2-D gel electrophoresis method and separated seed proteins using the modified method. We identified a large number (400) of protein proteins which were differentially expressed in cultivated and wild type species of chickpea. A comparative analysis between C. bijugum and JG 11 revealed the presence of 9 over-expressed and 22 under-expressed proteins, while the comparison between C. bijugum with DCP 92/3 showed 8 over-expressed and 18 under-- expressed proteins. Similarly, comparative analysis between C. microphyllum with DCP 92/3 showed 8 over-expressed proteins along with 22 under-expressed proteins, while the comparative study of C. microphyllum with JG11 displayed 9 over-expressed and 24 under-expressed proteins. We also compared C. judaicum with DCP 92/3 which revealed 15 overexpressed and 11 under-expressed proteins. On the other hand, the comparative analysis of C. judaicum with JG11 showed 10 over-expressed proteins, while the numbers of under-expressed proteins were 14. Among the differentially expressed protein proteins, 19 proteins were analyzed by the MS/MS, and peptides were identified using the MASCOT search engine. In the wild relatives the differentially expressed proteins are phosphatidylinositol 4-phosphate 5- kinase, β-1-6 galactosyltransferase, RNA helicase, phenyl alanine ammonia lyase 2, flavone 3'-0-methyl transferase, Argonaute 2, Myb related protein, Tubulin beta-2 chain and others. The most important one was legumin having α- amylase inhibition activity which was up regulated in C. bijugum. We also studied the activity of protease inhibitor (trypsin and α- amylase inhibitors) in these seed lines which showed differential activity of protease inhibitors. The highest trypsin and α- amylase inhibition was observed in C. judaicum and C. bijugum, respectively. CONCLUSION The differentially expressed proteins of wild relatives of chickpea appeared to be involved in various metabolic pathways. The study provides us information about the differences in the seed proteome of these wild species and cultivated varieties for the first time.
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Affiliation(s)
- Santanu Dhar
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India
| | - Mamta Bhattacharjee
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India
| | - Debabrat Baishya
- Department of Bioengineering and Technology, Gauhati University, Guwahati 781014, India
| | - Sumita Acharjee
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India
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81
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Adigal SS, Rizvi A, Rayaroth NV, John RV, Barik A, Bhandari S, George SD, Lukose J, Kartha VB, Chidangil S. Human tear fluid analysis for clinical applications: progress and prospects. Expert Rev Mol Diagn 2021; 21:767-787. [PMID: 34115952 DOI: 10.1080/14737159.2021.1941879] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction: Human blood and saliva are increasingly under investigation for the detection of biomarkers for early diagnosis of non-communicable (e.g.cancers) and communicable diseases like COVID-19. Exploring the potential application of human tears, an easily accessible body fluid, for the diagnosis of various diseases is the need of the hour.Areas covered: This review deals with a comprehensive account of applications of tear analysis using different techniques, their comparison and overall progress achieved till now. The techniques used for tear fluid analysis are HPLC/UPLC/SDS-PAGE, CE, etc., together with ELISA, Mass Spectrometry, etc. But, with advances in instrumentation and data processing methods, it has become easy to couple the various separation methods with highly sensitive optical techniques for the analysis of body fluids.Expert opinion: Tear analysis can provide valuable information about the health condition of the eyes since it contains several molecular constituents, and their relative concentrations may alter under abnormal conditions. Tear analysis has the advantage that it is totally non-invasive. This study recommends tear fluid as a reliable clinical sample to be probed by highly sensitive optical techniques to diagnose different health conditions, with special emphasis on eye diseases.
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Affiliation(s)
- Sphurti S Adigal
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Alisha Rizvi
- Department of Ophthalmology, Kasthurba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Nidheesh V Rayaroth
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Reena V John
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Ajayakumar Barik
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sulatha Bhandari
- Department of Ophthalmology, Kasthurba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sajan D George
- Centre for Applied Nanotechnology, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Jijo Lukose
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Vasudevan B Kartha
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Santhosh Chidangil
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka, India
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82
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Roy NS, Ramekar RV, Kim NS. Sequence-Specific Amplified Polymorphism (SSAP) and Sequence Characterized Amplified Region (SCAR) Markers in Zea mays. Methods Mol Biol 2021; 2250:207-218. [PMID: 33900607 DOI: 10.1007/978-1-0716-1134-0_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Transposable elements (TEs) are mobile, recurring DNA sequences scattered throughout genome and have a large impact on genome structure and function. Several genetic marker techniques were developed to exploit their ubiquitous nature. Sequence-specific amplified polymorphism (SSAP) is a TE-based genetic marker system that has been used in various purposes such as measuring genetic relatedness between species, deciphering the population structures, molecular tagging for agronomic development in marker-assisted breeding (MAS). In addition to SSAP, sequence characterized amplified region (SCAR) from the SSAP markers provides an added advantage in identifying qualitative traits. Once developed SCAR markers are efficient, fast, and reliable method for genetic evaluations. These methods can be useful especially for the crops which have no genetic sequence information. With improved discriminatory ability they offer access to dynamic and polymorphic regions of genome. These techniques can be useful in breeding programs to improve or develop high yielding crops.
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Affiliation(s)
- Neha Samir Roy
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Rahul Vasudeo Ramekar
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Nam-Soo Kim
- Department of Molecular Bioscience, Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, South Korea.
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83
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Lim JY, Lee SS. Quartz crystal microbalance cardiac Troponin I immunosensors employing signal amplification with TiO 2 nanoparticle photocatalyst. Talanta 2021; 228:122233. [PMID: 33773737 DOI: 10.1016/j.talanta.2021.122233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 10/22/2022]
Abstract
A sensitive and highly reproducible cardiac troponin I (cTnI) immunoassay in human serum is a challenging research goal for researchers studying biosensors because cTnI can undergo proteolysis and various modifications in blood. Furthermore, the reproducible detection of cTnI at very low concentrations is also required for diagnosing acute myocardial infarction. Here, we present sensitive and highly reproducible quartz crystal microbalance (QCM) immunosensors for the detection of cTnI in human serum. The unique features of this study are the use of a pair of capture antibodies that bind to different epitopes of cTnI, and the use of a signal amplification technique that enlarged the size of the titanium dioxide nanoparticles using photocatalytic silver staining. Since QCM measures changes in the resonance frequency due to the changes in mass occurring on the sensor surface, it is possible to quantitatively analyze cTnI based on the enormous increase in mass using a sandwich immunoassay and subsequent signal amplification by silver staining. The detection limit of the cTnI immunoassay in human serum without photocatalytic silver staining was 307 pg/ml, but 18 pg/ml in photocatalytic silver staining-mediated signal amplification. Thus, amplifying the signal increased the sensitivity and reproducibility of the cTnI immunoassay in human serum.
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Affiliation(s)
- Ji Yoon Lim
- Department of Medical Science, Soonchunhyang University, Asan, 31538, Republic of Korea
| | - Soo Suk Lee
- Department of Medical Science, Soonchunhyang University, Asan, 31538, Republic of Korea; Department of Pharmaceutical Engineering, Soonchunhyang University, Asan, 31538, Republic of Korea.
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84
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Laurent E, Sieber A, Salzer B, Wachernig A, Seigner J, Lehner M, Geyeregger R, Kratzer B, Jäger U, Kunert R, Pickl WF, Traxlmayr MW. Directed Evolution of Stabilized Monomeric CD19 for Monovalent CAR Interaction Studies and Monitoring of CAR-T Cell Patients. ACS Synth Biol 2021; 10:1184-1198. [PMID: 33843201 PMCID: PMC8155657 DOI: 10.1021/acssynbio.1c00010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
CD19 is among the most relevant targets in cancer immunotherapy. However, its extracellular domain (ECD) is prone to aggregation and misfolding, representing a major obstacle for the development and analysis of CD19-targeted therapeutics. Here, we engineered stabilized CD19-ECD (termed SuperFolder) variants, which also showed improved expression rates and, in contrast to the wild type protein, they could be efficiently purified in their monomeric forms. Despite being considerably more stable, these engineered mutants largely preserved the wild type sequence (>98.8%). We demonstrate that the variant SF05 enabled the determination of the monovalent affinity between CD19 and a clinically approved FMC63-based CAR, as well as monitoring and phenotypic characterization of CD19-directed CAR-T cells in the blood of lymphoma patients. We anticipate that the SuperFolder mutants generated in this study will be highly valuable tools for a range of applications in basic immunology and CD19-targeted cancer immunotherapy.
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Affiliation(s)
- Elisabeth Laurent
- Department of Biotechnology and BOKU Core Facility Biomolecular and Cellular Analysis, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Anna Sieber
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Benjamin Salzer
- St. Anna Children’s Cancer Research Institute, Zimmermannplatz 10, 1090 Vienna, Austria
| | - Anna Wachernig
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Jacqueline Seigner
- Department of Chemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Manfred Lehner
- St. Anna Children’s Cancer Research Institute, Zimmermannplatz 10, 1090 Vienna, Austria
| | - René Geyeregger
- St. Anna Children’s Cancer Research Institute, Zimmermannplatz 10, 1090 Vienna, Austria
| | - Bernhard Kratzer
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Lazarettgasse 19, 1090 Vienna, Austria
| | - Ulrich Jäger
- Department of Internal Medicine, Division of Hematology and Hemostaseology, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Renate Kunert
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Winfried F. Pickl
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Lazarettgasse 19, 1090 Vienna, Austria
| | - Michael W. Traxlmayr
- Department of Chemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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85
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Arruebo-Rivera PL, Castillo-Alfonso F, Troya A, Cárdenas-Moreno Y, Pérez-Ramos P, González-Bacerio J, Seijas JMG, Del Monte-Martínez A. Modeling and Experimental Validation of Algorithms for Maximum Quantity of Protein to be Immobilized on Solid Supports by Electrostatic Adsorption in the Strategy of Rational Design of Immobilized Derivatives. Protein J 2021; 40:576-588. [PMID: 33973097 DOI: 10.1007/s10930-021-09992-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 11/29/2022]
Abstract
Protein immobilization by electrostatic adsorption to a support could represent a good option. On the other hand, lysozyme (EC 3.2.1.17) is a little and basic protein. The objective of this work was to test the functionality of the strategy of Rational Design of Immobilized Derivatives for the immobilization by electrostatic adsorption of egg white lysozyme on SP-Sepharose FastFlow support. The RDID1.0 software was used to predict the superficial lysozyme clusters, the electrostatic configuration probability for each cluster, and the theoretical and estimated maximum quantity of protein to be immobilized. In addition, immobilization was performed and the experimental parameter practical maximum quantity of protein to be immobilized and the enzymatic activity of the immobilized derivative were assessed. The estimated maximum quantity of protein to be immobilized (9.49 protein mg/support g) was close to the experimental practical maximum quantity of protein to be immobilized (14.73 ± 0.09 protein mg/support g). The enzymatic activity assay with the chitosan substrate showed the catalytic functionality of the lysozyme-SP-Sepharose immobilized derivative (35.85 ± 3.07 U/support g), which preserved 78% functional activity. The used algorithm to calculate the estimated maximum quantity of protein to be immobilized works for other proteins, porous solid supports and immobilization methods, and this parameter has a high predictive value, useful for obtaining optimum immobilized derivatives. The applied methodology is valid to predict the most probable protein-support configurations and their catalytic competences, which concur with the experimental results. The produced biocatalyst had a high retention of functional activity. This indicates its functionality in enzymatic bioconversion processes.
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Affiliation(s)
- Pedro L Arruebo-Rivera
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba
| | - Freddy Castillo-Alfonso
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba.,Posgrado en Ciencias Naturales E Ingeniería, Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Delegación Cuajimalpa, 05348, Mexico City, Mexico
| | - Amanda Troya
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba.,Instituto de Farmacia y Alimentos, Universidad de La Habana, San Lázaro y L, Vedado, 10400, Havana, Cuba
| | - Yosberto Cárdenas-Moreno
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba.,Departamento de Microbiología y Virología, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba
| | - Patricia Pérez-Ramos
- Instituto de Farmacia y Alimentos, Universidad de La Habana, San Lázaro y L, Vedado, 10400, Havana, Cuba
| | - Jorge González-Bacerio
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba.
| | - José M Guisán Seijas
- Departamento de Biocatálisis, Instituto de Catálisis y Petroleoquímica, Consejo Superior de Investigaciones Científicas (CSIC), Campus Cantoblanco, 28049, Madrid, Spain
| | - Alberto Del Monte-Martínez
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba.
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86
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Silver Staining of 2D Electrophoresis Gels. Methods Mol Biol 2021. [PMID: 33950484 DOI: 10.1007/978-1-0716-1024-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Silver staining is used to detect proteins after electrophoretic separation on polyacrylamide gels. It combines excellent sensitivity (in the low nanogram range) with the use of very simple and cheap equipment and chemicals. For its use in proteomics, two important additional features must be considered, compatibility with mass spectrometry and quantitative response. Both features are discussed in this chapter, and optimized silver staining protocols are proposed.
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87
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Moysa A, Steczkiewicz K, Niedzialek D, Hammerschmid D, Zhukova L, Sobott F, Dadlez M. A model of full-length RAGE in complex with S100B. Structure 2021; 29:989-1002.e6. [PMID: 33887170 DOI: 10.1016/j.str.2021.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/03/2021] [Accepted: 04/02/2021] [Indexed: 01/10/2023]
Abstract
The receptor for advanced glycation end products (RAGE) is an immunoglobulin-type multiligand transmembrane protein expressed in numerous cell types, including the central nervous system cells. RAGE interaction with S100B, released during brain tissue damage, leads to RAGE upregulation and initialization of a spiral proinflammatory associated with different neural disorders. Here, we present the structural characterization of the hetero-oligomeric complex of the full-length RAGE with S100B, obtained by a combination of mass spectrometry-based methods and molecular modeling. We predict that RAGE functions as a tightly packed tetramer exposing a positively charged surface formed by V domains for S100B binding. Based on HDX results we demonstrate an allosteric coupling of the distal extracellular V domains and the transmembrane region, indicating a possible mechanism of signal transmission by RAGE across the membrane. Our model provides an insight into RAGE-ligand interactions, providing a basis for the rational design of the therapeutic modifiers of its activity.
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Affiliation(s)
- Alexander Moysa
- Institute of Biochemistry and Biophysics, PAS, Pawinskiego 5a, 02-109 Warsaw, Poland.
| | - Kamil Steczkiewicz
- Institute of Biochemistry and Biophysics, PAS, Pawinskiego 5a, 02-109 Warsaw, Poland.
| | - Dorota Niedzialek
- Institute of Biochemistry and Biophysics, PAS, Pawinskiego 5a, 02-109 Warsaw, Poland
| | - Dietmar Hammerschmid
- Department of Chemistry, King's College London, 7 Trinity Street, SE1 1DB London, UK; Department of Chemistry, Biomolecular & Analytical Mass Spectrometry Group, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Lilia Zhukova
- Institute of Biochemistry and Biophysics, PAS, Pawinskiego 5a, 02-109 Warsaw, Poland
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, LS2 9JT Leeds, UK; Department of Chemistry, Biomolecular & Analytical Mass Spectrometry Group, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Michal Dadlez
- Institute of Biochemistry and Biophysics, PAS, Pawinskiego 5a, 02-109 Warsaw, Poland
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88
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Identification of conserved Mycoplasma agalactiae surface antigens by immunoproteomics. Vet Immunol Immunopathol 2021; 236:110239. [PMID: 33845295 DOI: 10.1016/j.vetimm.2021.110239] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/16/2021] [Accepted: 04/02/2021] [Indexed: 10/21/2022]
Abstract
Contagious agalactia represents one of the most relevant infectious diseases of dairy sheep, with Mycoplasma agalactiae being the primary etiological agent. The early, sensitive, and specific identification of infected animals, as well as the development of efficient prophylactic tools, remain challenging. Here, we present a comprehensive characterization of M. agalactiae antigens focusing on those shared among different isolates. Leveraging on previous proteomic data obtained on individual strains, we adopted a strategy entailing sample pooling to optimize the identification of conserved proteins that induce an immune response. The liposoluble proteins from previously characterized field isolates and the type strain PG2T were enriched by Triton X-114 fractionation, pooled, analysed by one-dimensional (1D) and two-dimensional (2D) electrophoresis, and subjected to western immunoblotting against sheep sera collected during natural infection with M. agalactiae. Immunodominant antigens were identified by Matrix-Assisted Laser Desorption-Time-Of-Flight-Mass Spectrometry (MALDI-TOF-MS). This combined immunoproteomic approach confirmed the role of several known immunogens, including P80, P48, and P40, and most variable surface proteins (Vpmas), and unveiled novel immunodominant, conserved antigens, including MAG_1000, MAG_2220, MAG_1980, phnD, MAG_4740, and MAG_2430. Genomic context, functional prediction, subcellular localization, and invariable expression of these proteins in all isolates suggest their possible involvement in bacterial pathogenicity and metabolism. Moreover, most of the identified antigens elicit a host humoral response since the early stages of infection, persisting for at least 270 days. The immunodominant, conserved antigen panel identified in this work supports the development of effective vaccines and diagnostic tools with higher sensitivity and specificity in all the natural infection stages.
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89
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Sarkar A, Monu, Kumar V, Malhotra R, Pandit H, Jones E, Ponchel F, Biswas S. Poor Clearance of Free Hemoglobin Due to Lower Active Haptoglobin Availability is Associated with Osteoarthritis Inflammation. J Inflamm Res 2021; 14:949-964. [PMID: 33776468 PMCID: PMC7987317 DOI: 10.2147/jir.s300801] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/22/2021] [Indexed: 12/02/2022] Open
Abstract
Introduction Circulating plasma proteins play an important role in various diseases, and analysis of the plasma proteome has led to the discovery of various disease biomarkers. Osteoarthritis (OA) is the most common chronic joint disease, mostly affecting people of older age. OA typically starts as a focal disease (in a single compartment, typically treated with unicompartmental knee replacement), and then progresses to the other compartments (if not treated in time, typically treated with total knee replacement). For this, identification of differential proteins was carried out in plasma samples of OA cases and compared with healthy controls. The aim of this study was to identify circulatory differentially expressed proteins (DEPs) in knee-OA patients undergoing total knee replacement or unicompartmental knee replacement compared to healthy controls and assess their role, in order to have better understanding of the etiology behind OA pathophysiology. Methods DEPs were identified with two-dimensional gel electrophoresis (2DE) and isobaric tags for relative and absolute quantification (iTRAQ), followed by liquid chromatography with tandem mass spectrometry. Validation of DEPs was carried out using Western blot and ELISA. Posttranslational modifications were checked after running native gel using purified protein from patients, followed by detection of autoantibodies. Results In total, 52 DEPs were identified, among which 45 were distinct DEPs. Haptoglobin (Hp) was identified as one of the most significantly upregulated proteins in OA (P=0.005) identified by both 2DE and iTRAQ. Decreased levels of Hp tetramers and increased levels of autoantibodies against Hpβ were observed in OA plasma. Conclusion Our data suggest that poor clearance of free hemoglobin and low levels of Hp tetramers may be associated with OA pathogenesis and inflammation.
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Affiliation(s)
- Ashish Sarkar
- Department of Integrative and Functional Biology, CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Monu
- Department of Integrative and Functional Biology, CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vijay Kumar
- All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Rajesh Malhotra
- All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Hemant Pandit
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - Elena Jones
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - Frederique Ponchel
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - Sagarika Biswas
- Department of Integrative and Functional Biology, CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110007, India
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90
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Buska-Mach K, Kedzierska AE, Lepczynski A, Herosimczyk A, Ozgo M, Karpinski P, Gomulkiewicz A, Lorek D, Slawek A, Dziegiel P, Chelmonska-Soyta A. Differential Signals From TNFα-Treated and Untreated Embryos in Uterine Tissues and Splenic CD4 + T Lymphocytes During Preimplantation Pregnancy in Mice. Front Vet Sci 2021; 8:641553. [PMID: 33763465 PMCID: PMC7982469 DOI: 10.3389/fvets.2021.641553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/12/2021] [Indexed: 11/13/2022] Open
Abstract
The main aim of this study was to examine if a female mouse body in preimplantation pregnancy can distinguish between embryos of normal and impaired biological quality in the local and peripheral compartments. Normal (control group) and TNFα (tumor necrosis factor-α)-treated embryos (experimental group) at the morula stage were non-surgically transferred into the uteri of CD-1 strain [Crl:CD1(Icr)] female murine recipients. Twenty-four hours after the embryo transfer, females were euthanised, and uteri and spleens were dissected. In uterine tissues (local compartment), we assessed the expression of 84 genes comprising nine signal transduction pathways, using a modified RT2 Profiler PCR Array. In the spleen (peripheral compartment), we determined the proteome of splenic CD4+ lymphocytes using 2D protein electrophoresis with subsequent protein identification by mass spectrometry. Sample clustering and differential gene expression analyses within individual signal transduction pathways revealed differential expression of genes in the uteri of females after transplantation of normal vs. TNFα-treated embryos. The most affected signal transduction cascade was the NFKB (Nuclear factor NF-kappa-B) pathway, where 87.5% of the examined genes were significantly differentially expressed. Proteomic analysis of splenic CD4+ T lymphocytes revealed significant differential expression of 8 out of 132 protein spots. Identified proteins were classified as proteins influenced by cell stress, proteins engaged in the regulation of cytoskeleton stabilization and cell motility, and proteins having immunomodulatory function. These results support the hypothesis that even before embryo implantation, the body of pregnant female mice can sense the biological quality of an embryo both at the local and peripheral level.
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Affiliation(s)
- Katarzyna Buska-Mach
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Anna Ewa Kedzierska
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Adam Lepczynski
- Department of Physiology, Cytobiology and Proteomics, West Pomeranian University of Technology, Szczecin, Poland
| | - Agnieszka Herosimczyk
- Department of Physiology, Cytobiology and Proteomics, West Pomeranian University of Technology, Szczecin, Poland
| | - Małgorzata Ozgo
- Department of Physiology, Cytobiology and Proteomics, West Pomeranian University of Technology, Szczecin, Poland
| | - Pawel Karpinski
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.,Department of Genetics, Wroclaw Medical University, Wrocław, Poland
| | - Agnieszka Gomulkiewicz
- Department of Human Morphology and Embryology, Wroclaw Medical University, Wrocław, Poland
| | - Daria Lorek
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Anna Slawek
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Piotr Dziegiel
- Department of Human Morphology and Embryology, Wroclaw Medical University, Wrocław, Poland
| | - Anna Chelmonska-Soyta
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.,The Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
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91
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Flores-Tornero M, Wang L, Potěšil D, Hafidh S, Vogler F, Zdráhal Z, Honys D, Sprunck S, Dresselhaus T. Comparative analyses of angiosperm secretomes identify apoplastic pollen tube functions and novel secreted peptides. PLANT REPRODUCTION 2021; 34:47-60. [PMID: 33258014 PMCID: PMC7902602 DOI: 10.1007/s00497-020-00399-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/10/2020] [Indexed: 05/14/2023]
Abstract
KEY MESSAGE Analyses of secretomes of in vitro grown pollen tubes from Amborella, maize and tobacco identified many components of processes associated with the cell wall, signaling and metabolism as well as novel small secreted peptides. Flowering plants (angiosperms) generate pollen grains that germinate on the stigma and produce tubes to transport their sperm cells cargo deep into the maternal reproductive tissues toward the ovules for a double fertilization process. During their journey, pollen tubes secrete many proteins (secreted proteome or secretome) required, for example, for communication with the maternal reproductive tissues, to build a solid own cell wall that withstands their high turgor pressure while softening simultaneously maternal cell wall tissue. The composition and species specificity or family specificity of the pollen tube secretome is poorly understood. Here, we provide a suitable method to obtain the pollen tube secretome from in vitro grown pollen tubes of the basal angiosperm Amborella trichopoda (Amborella) and the Poaceae model maize. The previously published secretome of tobacco pollen tubes was used as an example of eudicotyledonous plants in this comparative study. The secretome of the three species is each strongly different compared to the respective protein composition of pollen grains and tubes. In Amborella and maize, about 40% proteins are secreted by the conventional "classic" pathway and 30% by unconventional pathways. The latter pathway is expanded in tobacco. Proteins enriched in the secretome are especially involved in functions associated with the cell wall, cell surface, energy and lipid metabolism, proteolysis and redox processes. Expansins, pectin methylesterase inhibitors and RALFs are enriched in maize, while tobacco secretes many proteins involved, for example, in proteolysis and signaling. While the majority of proteins detected in the secretome occur also in pollen grains and pollen tubes, and correlate in the number of mapped peptides with relative gene expression levels, some novel secreted small proteins were identified. Moreover, the identification of secreted proteins containing pro-peptides indicates that these are processed in the apoplast. In conclusion, we provide a proteome resource from three distinct angiosperm clades that can be utilized among others to study the localization, abundance and processing of known secreted proteins and help to identify novel pollen tube secreted proteins for functional studies.
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Affiliation(s)
- María Flores-Tornero
- Cell Biology and Plant Biochemistry, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Lele Wang
- Cell Biology and Plant Biochemistry, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany ASCR, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Frank Vogler
- Cell Biology and Plant Biochemistry, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany ASCR, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany.
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92
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Dahlgren KK, Gates C, Lee T, Cameron JC. Proximity-based proteomics reveals the thylakoid lumen proteome in the cyanobacterium Synechococcus sp. PCC 7002. PHOTOSYNTHESIS RESEARCH 2021; 147:177-195. [PMID: 33280076 PMCID: PMC7880944 DOI: 10.1007/s11120-020-00806-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Cyanobacteria possess unique intracellular organization. Many proteomic studies have examined different features of cyanobacteria to learn about the intracellular structures and their respective functions. While these studies have made great progress in understanding cyanobacterial physiology, the conventional fractionation methods used to purify cellular structures have limitations; specifically, certain regions of cells cannot be purified with existing fractionation methods. Proximity-based proteomics techniques were developed to overcome the limitations of biochemical fractionation for proteomics. Proximity-based proteomics relies on spatiotemporal protein labeling followed by mass spectrometry of the labeled proteins to determine the proteome of the region of interest. We performed proximity-based proteomics in the cyanobacterium Synechococcus sp. PCC 7002 with the APEX2 enzyme, an engineered ascorbate peroxidase. We determined the proteome of the thylakoid lumen, a region of the cell that has remained challenging to study with existing methods, using a translational fusion between APEX2 and PsbU, a lumenal subunit of photosystem II. Our results demonstrate the power of APEX2 as a tool to study the cell biology of intracellular features and processes, including photosystem II assembly in cyanobacteria, with enhanced spatiotemporal resolution.
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Affiliation(s)
- Kelsey K Dahlgren
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
- Interdisciplinary Quantitative Biology Program (IQ Biology), BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Colin Gates
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Thomas Lee
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Jeffrey C Cameron
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA.
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA.
- National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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93
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Ke L, Xu W, Gao J, Gao G, Wang H, Zhou J, Liu J, Rao P, Xu Y. Isolation and characterization of thermo-tolerant polyphenol oxidases in a black tea infusion. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107465] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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94
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Abstract
Two-dimensional gel electrophoresis has been instrumental in the development of proteomics. Although it is no longer the exclusive scheme used for proteomics, its unique features make it a still highly valuable tool, especially when multiple quantitative comparisons of samples must be made, and even for large samples series. However, quantitative proteomics using two-dimensional gels is critically dependent on the performances of the protein detection methods used after the electrophoretic separations. This chapter therefore examines critically the various detection methods, (radioactivity, dyes, fluorescence, and silver) as well as the data analysis issues that must be taken into account when quantitative comparative analysis of two-dimensional gels is performed.
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95
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Comitini F, Agarbati A, Canonico L, Galli E, Ciani M. Purification and Characterization of WA18, a New Mycocin Produced by Wickerhamomyces anomalus Active in Wine Against Brettanomyces bruxellensis Spoilage Yeasts. Microorganisms 2020; 9:microorganisms9010056. [PMID: 33379214 PMCID: PMC7824415 DOI: 10.3390/microorganisms9010056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 01/02/2023] Open
Abstract
Wickerhamomyces anomalus strain 18, isolated from a natural underground cheese ripening pit, secretes a mycocin named WA18 that inhibits wine spoilage yeasts belonging to Brettanomyces bruxellensis species, with a broad-spectrum of activity. WA18 was purified, and the purified protein was digested with specific restriction enzymes (lysine K and arginine R cut sites). The LC-MS and LC-MS/MS analysis after enzymatic digestions revealed a molecular weight of 31 kDa. Bioinformatics processing and database research of digested pure killer protein showed 99% identity with a UDP-glycosyltransferase protein. Competitive inhibition assay of killer activity by cell-wall polysaccharides suggests that branched glucans represent the first receptor site of the toxin on the envelope of the sensitive target. The WA18 partially purified crude extract (PPCE) showed high stability of antimicrobial activity at the physicochemical conditions suitable for the winemaking process. Indeed, in wine WA18 was able to counteract B. bruxellensis and control the production of ethyl phenols. In addition, the strain WA18 was compatible with Saccharomyces cerevisiae in co-culture conditions with a potential application together with commercial starter cultures. These data suggest that WA18 mycocin is a promising biocontrol agent against spoilage yeasts in winemaking, particularly during wine storage.
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96
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Flores-Tornero M, Vogler F, Mutwil M, Potěšil D, Ihnatová I, Zdráhal Z, Sprunck S, Dresselhaus T. Transcriptomic and Proteomic Insights into Amborella trichopoda Male Gametophyte Functions. PLANT PHYSIOLOGY 2020; 184:1640-1657. [PMID: 32989009 PMCID: PMC7723084 DOI: 10.1104/pp.20.00837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/16/2020] [Indexed: 05/27/2023]
Abstract
Flowering plants (angiosperms) are characterized by pollen tubes (PTs; male gametophytes) carrying two immobile sperm cells that grow over long distances through the carpel toward the ovules, where double fertilization is executed. It is not understood how these reproductive structures evolved, which genes occur de novo in male gametophytes of angiosperms, and to which extent PT functions are conserved among angiosperms. To contribute to a deeper understanding of the evolution of gametophyte functions, we generated RNA sequencing data from seven reproductive and two vegetative control tissues of the basal angiosperm Amborella trichopoda and complemented these with proteomic data of pollen grains (PGs) and PTs. The eudicot model plant Arabidopsis (Arabidopsis thaliana) served as a reference organism for data analysis, as more than 200 genes have been associated with male gametophyte functions in this species. We describe methods to collect bicellular A. trichopoda PGs, to induce their germination in vitro, and to monitor PT growth and germ cell division. Transcriptomic and proteomic analyses indicate that A. trichopoda PGs are prepared for germination requiring lipids, energy, but likely also reactive oxygen species, while PTs are especially characterized by catabolic/biosynthetic and transport processes including cell wall biosynthesis and gene regulation. Notably, a number of pollen-specific genes were lacking in Arabidopsis, and the number of genes involved in pollen signaling is significantly reduced in A. trichopoda In conclusion, we provide insight into male gametophyte functions of the most basal angiosperm and establish a valuable resource for future studies on the evolution of flowering plants.
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Affiliation(s)
- María Flores-Tornero
- Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Frank Vogler
- Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Ivana Ihnatová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
- RECETOX, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
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97
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Takalloo Z, Ardakani ZA, Maroufi B, Shahangian SS, Sajedi RH. Stress-dependent conformational changes of artemin: Effects of heat and oxidant. PLoS One 2020; 15:e0242206. [PMID: 33196673 PMCID: PMC7668597 DOI: 10.1371/journal.pone.0242206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/28/2020] [Indexed: 11/24/2022] Open
Abstract
Artemin is an abundant thermostable protein in Artemia embryos and it is considered as a highly efficient molecular chaperone against extreme environmental stress conditions. The conformational dynamics of artemin have been suggested to play a critical role in its biological functions. In this study, we have investigated the conformational and functional changes of artemin under heat and oxidative stresses to identify the relationship between its structure and function. The tertiary and quaternary structures of artemin were evaluated by fluorescence measurements, protein cross-linking analysis, and dynamic light scattering. Based on the structural analysis, artemin showed irreversible substantial conformational lability in responses to heat and oxidant, which was mainly mediated through the hydrophobic interactions and dimerization of the chaperone. In addition, the chaperone-like activity of heated and oxidized artemin was examined using lysozyme refolding assay and the results showed that although both factors, i.e. heat and oxidant, at specific levels improved artemin potency, simultaneous incubation with both stressors significantly triggered the chaperone activation. Moreover, the heat-induced dimerization of artemin was found to be the most critical factor for its activation. It was suggested that oxidation presumably acts through stabilizing the dimer structures of artemin through formation of disulfide bridges between the subunits and strengthens its chaperoning efficacy. Accordingly, it is proposed that artemin probably exists in a monomer–oligomer equilibrium in Artemia cysts and environmental stresses and intracellular portion of protein substrates may shift the equilibrium towards the active dimer forms of the chaperone.
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Affiliation(s)
- Zeinab Takalloo
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zahra Afshar Ardakani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | | | - Reza H. Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- * E-mail:
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98
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Raber HF, Heerde T, El Din SN, Flaig C, Hilgers F, Bitzenhofer N, Jäger KE, Drepper T, Gottschalk KE, Bodenberger NE, Weil T, Kubiczek DH, Rosenau F. Azulitox—A Pseudomonas aeruginosa P28-Derived Cancer-Cell-Specific Protein Photosensitizer. Biomacromolecules 2020; 21:5067-5076. [DOI: 10.1021/acs.biomac.0c01216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Heinz Fabian Raber
- Institute for Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Thomas Heerde
- Institute for Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Suzanne Nour El Din
- Institute for Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Carolin Flaig
- Institute for Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Institute for Experimental Physics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426 Jülich, Germany
| | - Nora Bitzenhofer
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426 Jülich, Germany
| | - Karl-Erich Jäger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426 Jülich, Germany
- Institute of Bio- and Geosciences (IBG-1: Biotechnology) Forschungszentrum Jülich, Stetternicher Forst, 52426 Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426 Jülich, Germany
| | - Kay-Eberhard Gottschalk
- Institute for Experimental Physics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | | | - Tanja Weil
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128 Mainz, Germany
| | - Dennis Horst Kubiczek
- Institute for Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Frank Rosenau
- Institute for Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128 Mainz, Germany
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99
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Beasley KL, Cristy SA, Elmassry MM, Dzvova N, Colmer-Hamood JA, Hamood AN. During bacteremia, Pseudomonas aeruginosa PAO1 adapts by altering the expression of numerous virulence genes including those involved in quorum sensing. PLoS One 2020; 15:e0240351. [PMID: 33057423 PMCID: PMC7561203 DOI: 10.1371/journal.pone.0240351] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/24/2020] [Indexed: 12/17/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that produces numerous virulence factors and causes serious infections in trauma patients and patients with severe burns. We previously showed that the growth of P. aeruginosa in blood from severely burned or trauma patients altered the expression of numerous genes. However, the specific influence of whole blood from healthy volunteers on P. aeruginosa gene expression is not known. Transcriptome analysis of P. aeruginosa grown for 4 h in blood from healthy volunteers compared to that when grown in laboratory medium revealed that the expression of 1085 genes was significantly altered. Quorum sensing (QS), QS-related, and pyochelin synthesis genes were downregulated, while genes of the type III secretion system and those for pyoverdine synthesis were upregulated. The observed effect on the QS and QS-related genes was shown to reside within serum fraction: growth of PAO1 in the presence of 10% human serum from healthy volunteers significantly reduced the expression of QS and QS-regulated genes at 2 and 4 h of growth but significantly enhanced their expression at 8 h. Additionally, the production of QS-regulated virulence factors, including LasA and pyocyanin, was also influenced by the presence of human serum. Serum fractionation experiments revealed that part of the observed effect resides within the serum fraction containing <10-kDa proteins. Growth in serum reduced the production of many PAO1 outer membrane proteins but enhanced the production of others including OprF, a protein previously shown to play a role in the regulation of QS gene expression. These results suggest that factor(s) within human serum: 1) impact P. aeruginosa pathogenesis by influencing the expression of different genes; 2) differentially regulate the expression of QS and QS-related genes in a growth phase- or time-dependent mechanism; and 3) manipulate the production of P. aeruginosa outer membrane proteins.
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Affiliation(s)
- Kellsie L. Beasley
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, Texas, Untied States of America
| | - Shane A. Cristy
- Honors College, Texas Tech University, Lubbock, Texas, Untied States of America
| | - Moamen M. Elmassry
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, Untied States of America
| | - Nyaradzo Dzvova
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, Texas, Untied States of America
| | - Jane A. Colmer-Hamood
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, Texas, Untied States of America
- Department of Medical Education, Texas Tech University Health Sciences Center, Lubbock, Texas, Untied States of America
| | - Abdul N. Hamood
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, Texas, Untied States of America
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, Texas, Untied States of America
- * E-mail:
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100
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Platzer R, Rossboth BK, Schneider MC, Sevcsik E, Baumgart F, Stockinger H, Schütz GJ, Huppa JB, Brameshuber M. Unscrambling fluorophore blinking for comprehensive cluster detection via photoactivated localization microscopy. Nat Commun 2020; 11:4993. [PMID: 33020470 PMCID: PMC7536177 DOI: 10.1038/s41467-020-18726-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 09/10/2020] [Indexed: 12/22/2022] Open
Abstract
Determining nanoscale protein distribution via Photoactivated Localization Microscopy (PALM) mandates precise knowledge of the applied fluorophore's blinking properties to counteract overcounting artifacts that distort the resulting biomolecular distributions. Here, we present a readily applicable methodology to determine, optimize and quantitatively account for the blinking behavior of any PALM-compatible fluorophore. Using a custom-designed platform, we reveal complex blinking of two photoswitchable fluorescence proteins (PS-CFP2 and mEOS3.2) and two photoactivatable organic fluorophores (PA Janelia Fluor 549 and Abberior CAGE 635) with blinking cycles on time scales of several seconds. Incorporating such detailed information in our simulation-based analysis package allows for robust evaluation of molecular clustering based on individually recorded single molecule localization maps.
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Affiliation(s)
- René Platzer
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | | | - Eva Sevcsik
- Institute of Applied Physics, TU Wien, Vienna, Austria
| | | | - Hannes Stockinger
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Johannes B Huppa
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.
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