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Gonçalves AAM, Ribeiro AJ, Resende CAA, Couto CAP, Gandra IB, Dos Santos Barcelos IC, da Silva JO, Machado JM, Silva KA, Silva LS, Dos Santos M, da Silva Lopes L, de Faria MT, Pereira SP, Xavier SR, Aragão MM, Candida-Puma MA, de Oliveira ICM, Souza AA, Nogueira LM, da Paz MC, Coelho EAF, Giunchetti RC, de Freitas SM, Chávez-Fumagalli MA, Nagem RAP, Galdino AS. Recombinant multiepitope proteins expressed in Escherichia coli cells and their potential for immunodiagnosis. Microb Cell Fact 2024; 23:145. [PMID: 38778337 PMCID: PMC11110257 DOI: 10.1186/s12934-024-02418-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Recombinant multiepitope proteins (RMPs) are a promising alternative for application in diagnostic tests and, given their wide application in the most diverse diseases, this review article aims to survey the use of these antigens for diagnosis, as well as discuss the main points surrounding these antigens. RMPs usually consisting of linear, immunodominant, and phylogenetically conserved epitopes, has been applied in the experimental diagnosis of various human and animal diseases, such as leishmaniasis, brucellosis, cysticercosis, Chagas disease, hepatitis, leptospirosis, leprosy, filariasis, schistosomiasis, dengue, and COVID-19. The synthetic genes for these epitopes are joined to code a single RMP, either with spacers or fused, with different biochemical properties. The epitopes' high density within the RMPs contributes to a high degree of sensitivity and specificity. The RMPs can also sidestep the need for multiple peptide synthesis or multiple recombinant proteins, reducing costs and enhancing the standardization conditions for immunoassays. Methods such as bioinformatics and circular dichroism have been widely applied in the development of new RMPs, helping to guide their construction and better understand their structure. Several RMPs have been expressed, mainly using the Escherichia coli expression system, highlighting the importance of these cells in the biotechnological field. In fact, technological advances in this area, offering a wide range of different strains to be used, make these cells the most widely used expression platform. RMPs have been experimentally used to diagnose a broad range of illnesses in the laboratory, suggesting they could also be useful for accurate diagnoses commercially. On this point, the RMP method offers a tempting substitute for the production of promising antigens used to assemble commercial diagnostic kits.
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Affiliation(s)
- Ana Alice Maia Gonçalves
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Anna Julia Ribeiro
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Carlos Ananias Aparecido Resende
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Carolina Alves Petit Couto
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Isadora Braga Gandra
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Isabelle Caroline Dos Santos Barcelos
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Jonatas Oliveira da Silva
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Juliana Martins Machado
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Kamila Alves Silva
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Líria Souza Silva
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Michelli Dos Santos
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Lucas da Silva Lopes
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Mariana Teixeira de Faria
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Sabrina Paula Pereira
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Sandra Rodrigues Xavier
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Matheus Motta Aragão
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Mayron Antonio Candida-Puma
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa, 04000, Peru
| | | | - Amanda Araujo Souza
- Biophysics Laboratory, Institute of Biological Sciences, Department of Cell Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | - Lais Moreira Nogueira
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Mariana Campos da Paz
- Bioactives and Nanobiotechnology Laboratory, Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Eduardo Antônio Ferraz Coelho
- Postgraduate Program in Health Sciences, Infectious Diseases and Tropical Medicine, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, 30130-100, Brazil
| | - Rodolfo Cordeiro Giunchetti
- Laboratory of Biology of Cell Interactions, National Institute of Science and Technology on Tropical Diseases (INCT-DT), Department of Morphology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Sonia Maria de Freitas
- Biophysics Laboratory, Institute of Biological Sciences, Department of Cell Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa, 04000, Peru
| | - Ronaldo Alves Pinto Nagem
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Alexsandro Sobreira Galdino
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil.
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Khlebodarova TM, Bogacheva NV, Zadorozhny AV, Bryanskaya AV, Vasilieva AR, Chesnokov DO, Pavlova EI, Peltek SE. Komagataella phaffii as a Platform for Heterologous Expression of Enzymes Used for Industry. Microorganisms 2024; 12:346. [PMID: 38399750 PMCID: PMC10892927 DOI: 10.3390/microorganisms12020346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
In the 1980s, Escherichia coli was the preferred host for heterologous protein expression owing to its capacity for rapid growth in complex media; well-studied genetics; rapid and direct transformation with foreign DNA; and easily scalable fermentation. Despite the relative ease of use of E. coli for achieving the high expression of many recombinant proteins, for some proteins, e.g., membrane proteins or proteins of eukaryotic origin, this approach can be rather ineffective. Another microorganism long-used and popular as an expression system is baker's yeast, Saccharomyces cerevisiae. In spite of a number of obvious advantages of these yeasts as host cells, there are some limitations on their use as expression systems, for example, inefficient secretion, misfolding, hyperglycosylation, and aberrant proteolytic processing of proteins. Over the past decade, nontraditional yeast species have been adapted to the role of alternative hosts for the production of recombinant proteins, e.g., Komagataella phaffii, Yarrowia lipolytica, and Schizosaccharomyces pombe. These yeast species' several physiological characteristics (that are different from those of S. cerevisiae), such as faster growth on cheap carbon sources and higher secretion capacity, make them practical alternative hosts for biotechnological purposes. Currently, the K. phaffii-based expression system is one of the most popular for the production of heterologous proteins. Along with the low secretion of endogenous proteins, K. phaffii efficiently produces and secretes heterologous proteins in high yields, thereby reducing the cost of purifying the latter. This review will discuss practical approaches and technological solutions for the efficient expression of recombinant proteins in K. phaffii, mainly based on the example of enzymes used for the feed industry.
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Affiliation(s)
- Tamara M. Khlebodarova
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Natalia V. Bogacheva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Andrey V. Zadorozhny
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alla V. Bryanskaya
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Asya R. Vasilieva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Danil O. Chesnokov
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Elena I. Pavlova
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Sergey E. Peltek
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
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Nuta GC, Gilad Y, Goldberg N, Meril S, Bahlsen M, Carvalho S, Kozer N, Barr H, Fridmann Sirkis Y, Hercík K, Břehová P, Nencka R, Bialik S, Eisenstein M, Kimchi A. Identifying a selective inhibitor of autophagy that targets ATG12-ATG3 protein-protein interaction. Autophagy 2023; 19:2372-2385. [PMID: 37184247 PMCID: PMC10351452 DOI: 10.1080/15548627.2023.2178159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/24/2023] Open
Abstract
Macroautophagy/autophagy is a catabolic process by which cytosolic content is engulfed, degraded and recycled. It has been implicated as a critical pathway in advanced stages of cancer, as it maintains tumor cell homeostasis and continuous growth by nourishing hypoxic or nutrient-starved tumors. Autophagy also supports alternative cellular trafficking pathways, providing a mechanism of non-canonical secretion of inflammatory cytokines. This opens a significant therapeutic opportunity for using autophagy inhibitors in cancer and acute inflammatory responses. Here we developed a high throughput compound screen to identify inhibitors of protein-protein interaction (PPI) in autophagy, based on the protein-fragment complementation assay (PCA). We chose to target the ATG12-ATG3 PPI, as this interaction is indispensable for autophagosome formation, and the analyzed structure of the interaction interface predicts that it may be amenable to inhibition by small molecules. We screened 41,161 compounds yielding 17 compounds that effectively inhibit the ATG12-ATG3 interaction in the PCA platform, and which were subsequently filtered by their ability to inhibit autophagosome formation in viable cells. We describe a lead compound (#189) that inhibited GFP-fused MAP1LC3B/LC3B (microtubule associated protein 1 light chain 3 beta) puncta formation in cells with IC50 value corresponding to 9.3 μM. This compound displayed a selective inhibitory effect on the growth of autophagy addicted tumor cells and inhibited secretion of IL1B/IL-1β (interleukin 1 beta) by macrophage-like cells. Compound 189 has the potential to be developed into a therapeutic drug and its discovery documents the power of targeting PPIs for acquiring specific and selective compound inhibitors of autophagy.Abbreviations: ANOVA: analysis of variance; ATG: autophagy related; CQ: chloroquine; GFP: green fluorescent protein; GLuc: Gaussia Luciferase; HEK: human embryonic kidney; IL1B: interleukin 1 beta; LPS: lipopolysaccharide; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; PCA: protein-fragment complementation assay; PDAC: pancreatic ductal adenocarcinoma; PMA: phorbol 12-myristate 13-acetate; PPI: protein-protein interaction. VCL: vinculin.
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Affiliation(s)
- Gal Chaim Nuta
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yuval Gilad
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Nadav Goldberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sara Meril
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Marcela Bahlsen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Silvia Carvalho
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot, Israel
| | - Noga Kozer
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot, Israel
| | - Haim Barr
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot, Israel
| | - Yael Fridmann Sirkis
- Department of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Kamil Hercík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Petra Břehová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Shani Bialik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Miriam Eisenstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Kimchi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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Pham PN, Zahradník J, Kolářová L, Schneider B, Fuertes G. Regulation of IL-24/IL-20R2 complex formation using photocaged tyrosines and UV light. Front Mol Biosci 2023; 10:1214235. [PMID: 37484532 PMCID: PMC10361524 DOI: 10.3389/fmolb.2023.1214235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023] Open
Abstract
Human interleukin 24 (IL-24) is a multifunctional cytokine that represents an important target for autoimmune diseases and cancer. Since the biological functions of IL-24 depend on interactions with membrane receptors, on-demand regulation of the affinity between IL-24 and its cognate partners offers exciting possibilities in basic research and may have applications in therapy. As a proof-of-concept, we developed a strategy based on recombinant soluble protein variants and genetic code expansion technology to photocontrol the binding between IL-24 and one of its receptors, IL-20R2. Screening of non-canonical ortho-nitrobenzyl-tyrosine (NBY) residues introduced at several positions in both partners was done by a combination of biophysical and cell signaling assays. We identified one position for installing NBY, tyrosine70 of IL-20R2, which results in clear impairment of heterocomplex assembly in the dark. Irradiation with 365-nm light leads to decaging and reconstitutes the native tyrosine of the receptor that can then associate with IL-24. Photocaged IL-20R2 may be useful for the spatiotemporal control of the JAK/STAT phosphorylation cascade.
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Affiliation(s)
- Phuong Ngoc Pham
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
- Faculty of Science, Charles University, Prague, Czechia
| | - Jiří Zahradník
- First Faculty of Medicine, BIOCEV Center, Charles University, Prague, Czechia
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lucie Kolářová
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Bohdan Schneider
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Gustavo Fuertes
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
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Gong C, Xu D, Sun D, Kang J, Wang W, Xu JR, Zhang X. FgSnt1 of the Set3 HDAC complex plays a key role in mediating the regulation of histone acetylation by the cAMP-PKA pathway in Fusarium graminearum. PLoS Genet 2022; 18:e1010510. [PMID: 36477146 PMCID: PMC9728937 DOI: 10.1371/journal.pgen.1010510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/01/2022] [Indexed: 12/13/2022] Open
Abstract
The cAMP-PKA pathway is critical for regulating growth, differentiation, and pathogenesis in fungal pathogens. In Fusarium graminearum, mutants deleted of PKR regulatory-subunit of PKA had severe defects but often produced spontaneous suppressors. In this study eleven pkr suppressors were found to have mutations in FgSNT1, a component of the Set3C histone deacetylase (HDAC) complex, that result in the truncation of its C-terminal region. Targeted deletion of the C-terminal 98 aa (CT98) in FgSNT1 suppressed the defects of pkr in growth and H4 acetylation. CT98 truncation also increased the interaction of FgSnt1 with Hdf1, a major HDAC in the Set3 complex. The pkr mutant had no detectable expression of the Cpk1 catalytic subunit and PKA activities, which was not suppressed by mutations in FgSNT1. Cpk1 directly interacted with the N-terminal region of FgSnt1 and phosphorylated it at S443, a conserved PKA-phosphorylation site. CT98 of FgSnt1 carrying the S443D mutation interacted with its own N-terminal region. Expression of FgSNT1S443D rescued the defects of pkr in growth and H4 acetylation. Therefore, phosphorylation at S443 and suppressor mutations may relieve self-inhibitory binding of FgSnt1 and increase its interaction with Hdf1 and H4 acetylation, indicating a key role of FgSnt1 in crosstalk between cAMP signaling and Set3 complex.
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Affiliation(s)
- Chen Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Daiying Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Daiyuan Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Jiangang Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Wei Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail: (J-RX); (XZ)
| | - Xue Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
- * E-mail: (J-RX); (XZ)
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Gołębiowski A, Pomastowski P, Rafińska K, Zuvela P, Wong MW, Pryshchepa O, Madajski P, Buszewski B. Functionalization of Alpha-Lactalbumin by Zinc Ions. ACS OMEGA 2022; 7:38459-38474. [PMID: 36340177 PMCID: PMC9631873 DOI: 10.1021/acsomega.2c03674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Alpha-lactalbumin (α-LA) and binding of zinc cations to protein were studied. Molecular characteristics of protein was determined by MALDI-TOF/MS and electrophoresis SDS-PAGE, and also, for complexes, it was determined by spectroscopic techniques (ATR-FT-IR and Raman) and microscopic techniques (SEM along with an EDX detector and also TEM). The pH dependence of zeta potential of α-LA was determined in saline solution. The zinc binding to the protein mechanism was investigated; zinc binding to protein kinetics, the molecular modeling by the DFT method, and electron microscopy (SEM and TEM) for microstructure observation were performed. The experiments performed indicate a quick binding process (equilibrium takes place after 2 min of incubation) which occurs onto the surface of α-LA. Zinc cations change the conformation of the protein and create spherical particles from the morphological point of view. DFT studies indicate the participation of acidic functional groups of the protein (aspartic acid and glutamic acid residues), and these have a decisive influence on the interaction with zinc cations. Application studies of general toxicity and cytotoxicity and bioavailability were conducted.
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Affiliation(s)
- Adrian Gołębiowski
- Centre
for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, 4 Wileńska Street, 87-100 Torun, Poland
- Department
of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, 7 Gagarina Street, 87-100 Torun, Poland
| | - Paweł Pomastowski
- Centre
for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, 4 Wileńska Street, 87-100 Torun, Poland
| | - Katarzyna Rafińska
- Department
of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, 7 Gagarina Street, 87-100 Torun, Poland
| | - Petar Zuvela
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore, Singapore
| | - Ming Wah Wong
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore, Singapore
| | - Oleksandra Pryshchepa
- Centre
for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, 4 Wileńska Street, 87-100 Torun, Poland
- Department
of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, 7 Gagarina Street, 87-100 Torun, Poland
| | - Piotr Madajski
- Department
of Chemistry of Materials Adsorption and Catalysis, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Bogusław Buszewski
- Centre
for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, 4 Wileńska Street, 87-100 Torun, Poland
- Department
of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, 7 Gagarina Street, 87-100 Torun, Poland
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Zhang W, Zhao Y, Hu L, Guan C, Xun M, Wu F, Lei Y. Establishment of purification method for prokaryotic expression of Serpin gene for Dermatophagoides farinae. Protein Expr Purif 2022; 195-196:106080. [PMID: 35304262 DOI: 10.1016/j.pep.2022.106080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 11/17/2022]
Abstract
This study aimed to develop an effective method for the expression and purification of the Dermatophagoides farinae serpin protein and to establish an experimental foundation for elucidating its role in the temperature stress response. The total RNA of D. farinae was extracted, and specific primers were designed for serpin amplification. Serpin was joined with pET32a vector and transformed into BL21 (DE3) cells. Expression of recombinant proteins was induced. Proteins were extracted by enzymatic lysis or enzymatic lysis combined with ultrasonication. Recombinant proteins were purified by Ni-NTA method. SDS-PAGE was conducted to evaluate protein expression, extraction, and purification efficiency. Agarose gel electrophoresis and sequencing analysis showed that the amplified serpin open reading frame was 1284 bp, encoding a hydrophilic and stable protein with a relative molecular weight of 48.30 kD. SDS-PAGE demonstrated that there was a specific band at 55-70 kD, which was consistent with the predicted size of the recombinant pET32a-Serpin protein. Enzymatic lysis combined with 30% ultrasonic power promoted the release of soluble protein more effectively than enzymatic lysis alone. 16 °C for 4 h was optimal for inducing expression. The optimal imidazole concentrations for washing non-His-tagged protein and eluting His-tagged protein were determined to be 20 mM and 200 mM, respectively. In this study, A prokaryotic expression and purification system for the D. farinae serpin protein was successfully established, providing a technical reference for functional gene research in mites at the protein level.
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Affiliation(s)
- Wanyu Zhang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yae Zhao
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Li Hu
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Chenglin Guan
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Meng Xun
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Feng Wu
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yanjun Lei
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, China
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8
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Scott KA, Williams SA, Santangelo TJ. Thermococcus kodakarensis provides a versatile hyperthermophilic archaeal platform for protein expression. Methods Enzymol 2021; 659:243-273. [PMID: 34752288 PMCID: PMC8878339 DOI: 10.1016/bs.mie.2021.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Hyperthermophiles, typically defined as organisms with growth optima ≥80°C, are dominated by the Archaea. Proteins that support life at the extremes of temperatures often retain substantial biotechnological and commercial value, but the recombinant expression of individual hyperthermophilic proteins is commonly complicated in non-native mesophilic hosts due to differences in codon bias, intracellular solutes and the requirement for accessory factors that aid in folding or deposition of metal centers within archaeal proteins. The development of versatile protein expression and facilitated protein purification systems in the model, genetically tractable, hyperthermophilic marine archaeon Thermococcus kodakarensis provides an attractive platform for protein expression within the hyperthermophiles. The assortment of T. kodakarensis genetic backgrounds and compatible selection markers allow iterative genetic manipulations that facilitate protein overexpression and expedite protein purifications. Expression vectors that stably replicate both in T. kodakarensis and Escherichia coli have been validated and permit high-level ectopic gene expression from a variety of controlled and constitutive promoters. Biologically relevant protein associations can be maintained during protein purifications to identify native protein partnerships and define protein interaction networks. T. kodakarensis thus provides a versatile platform for the expression and purification of thermostable proteins.
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Affiliation(s)
- Kristin A Scott
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, United States
| | - Sere A Williams
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, United States
| | - Thomas J Santangelo
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, United States; Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States.
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9
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Peleg Y, Vincentelli R, Collins BM, Chen KE, Livingstone EK, Weeratunga S, Leneva N, Guo Q, Remans K, Perez K, Bjerga GEK, Larsen Ø, Vaněk O, Skořepa O, Jacquemin S, Poterszman A, Kjær S, Christodoulou E, Albeck S, Dym O, Ainbinder E, Unger T, Schuetz A, Matthes S, Bader M, de Marco A, Storici P, Semrau MS, Stolt-Bergner P, Aigner C, Suppmann S, Goldenzweig A, Fleishman SJ. Community-Wide Experimental Evaluation of the PROSS Stability-Design Method. J Mol Biol 2021; 433:166964. [PMID: 33781758 DOI: 10.1016/j.jmb.2021.166964] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/08/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
Recent years have seen a dramatic improvement in protein-design methodology. Nevertheless, most methods demand expert intervention, limiting their widespread adoption. By contrast, the PROSS algorithm for improving protein stability and heterologous expression levels has been successfully applied to a range of challenging enzymes and binding proteins. Here, we benchmark the application of PROSS as a stand-alone tool for protein scientists with no or limited experience in modeling. Twelve laboratories from the Protein Production and Purification Partnership in Europe (P4EU) challenged the PROSS algorithm with 14 unrelated protein targets without support from the PROSS developers. For each target, up to six designs were evaluated for expression levels and in some cases, for thermal stability and activity. In nine targets, designs exhibited increased heterologous expression levels either in prokaryotic and/or eukaryotic expression systems under experimental conditions that were tailored for each target protein. Furthermore, we observed increased thermal stability in nine of ten tested targets. In two prime examples, the human Stem Cell Factor (hSCF) and human Cadherin-Like Domain (CLD12) from the RET receptor, the wild type proteins were not expressible as soluble proteins in E. coli, yet the PROSS designs exhibited high expression levels in E. coli and HEK293 cells, respectively, and improved thermal stability. We conclude that PROSS may improve stability and expressibility in diverse cases, and that improvement typically requires target-specific expression conditions. This study demonstrates the strengths of community-wide efforts to probe the generality of new methods and recommends areas for future research to advance practically useful algorithms for protein science.
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Affiliation(s)
- Yoav Peleg
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Renaud Vincentelli
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Brett M Collins
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Kai-En Chen
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Emma K Livingstone
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Saroja Weeratunga
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Natalya Leneva
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Qian Guo
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Kim Remans
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Kathryn Perez
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gro E K Bjerga
- NORCE Norwegian Research Centre, Postboks 22 Nygårdstangen, 5038 Bergen, Norway
| | - Øivind Larsen
- NORCE Norwegian Research Centre, Postboks 22 Nygårdstangen, 5038 Bergen, Norway
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Ondřej Skořepa
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Sophie Jacquemin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, France
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Evangelos Christodoulou
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Shira Albeck
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orly Dym
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elena Ainbinder
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tamar Unger
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anja Schuetz
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Susann Matthes
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Michael Bader
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany; University of Lübeck, Institute for Biology, Ratzeburger Allee 160, 23562 Lübeck, Germany; Charité University Medicine, Charitéplatz 1, 10117 Berlin, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Slovenia
| | - Paola Storici
- Elettra Sincrotrone Trieste - SS 14 - km 163, 5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Marta S Semrau
- Elettra Sincrotrone Trieste - SS 14 - km 163, 5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Peggy Stolt-Bergner
- Vienna Biocenter Core Facilities GmbH, Dr. Bohr-gasse 3, 1030 Vienna, Austria
| | - Christian Aigner
- Vienna Biocenter Core Facilities GmbH, Dr. Bohr-gasse 3, 1030 Vienna, Austria
| | - Sabine Suppmann
- Max-Planck Institute of Biochemistry, Biochemistry Core Facility, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Adi Goldenzweig
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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10
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Duman-Özdamar ZE, Binay B. Production of Industrial Enzymes via Pichia pastoris as a Cell Factory in Bioreactor: Current Status and Future Aspects. Protein J 2021; 40:367-376. [DOI: 10.1007/s10930-021-09968-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2021] [Indexed: 02/06/2023]
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An orphan protein of Fusarium graminearum modulates host immunity by mediating proteasomal degradation of TaSnRK1α. Nat Commun 2020; 11:4382. [PMID: 32873802 PMCID: PMC7462860 DOI: 10.1038/s41467-020-18240-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 08/06/2020] [Indexed: 02/06/2023] Open
Abstract
Fusarium graminearum is a causal agent of Fusarium head blight (FHB) and a deoxynivalenol (DON) producer. In this study, OSP24 is identified as an important virulence factor in systematic characterization of the 50 orphan secreted protein (OSP) genes of F. graminearum. Although dispensable for growth and initial penetration, OSP24 is important for infectious growth in wheat rachis tissues. OSP24 is specifically expressed during pathogenesis and its transient expression suppresses BAX- or INF1-induced cell death. Osp24 is translocated into plant cells and two of its 8 cysteine-residues are required for its function. Wheat SNF1-related kinase TaSnRK1α is identified as an Osp24-interacting protein and shows to be important for FHB resistance in TaSnRK1α-overexpressing or silencing transgenic plants. Osp24 accelerates the degradation of TaSnRK1α by facilitating its association with the ubiquitin-26S proteasome. Interestingly, TaSnRK1α also interacts with TaFROG, an orphan wheat protein induced by DON. TaFROG competes against Osp24 for binding with the same region of TaSnRKα and protects it from degradation. Overexpression of TaFROG stabilizes TaSnRK1α and increases FHB resistance. Taken together, Osp24 functions as a cytoplasmic effector by competing against TaFROG for binding with TaSnRK1α, demonstrating the counteracting roles of orphan proteins of both host and fungal pathogens during their interactions. Fusarium graminearum is a major fungal pathogen of cereals. Here the authors show that F. graminearum secretes an effector, Osp24, that induces degradation of the wheat TaSnRK1α kinase to promote disease while an orphan wheat protein, TaFROG1, can compete with Osp24 for binding to TaSnRK1α and protect it from degradation
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12
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Affiliation(s)
- Paul D. Riggs
- New England Biolabs, Inc., Research; Ipswich Massachusetts
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13
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Peleg Y, Prabahar V, Bednarczyk D, Unger T. Harnessing the Profinity eXact™ System for Expression and Purification of Heterologous Proteins in E. coli. Methods Mol Biol 2017; 1586:33-43. [PMID: 28470597 DOI: 10.1007/978-1-4939-6887-9_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Highly purified recombinant proteins in large quantities are valuable material for biochemical and structural studies. To achieve this goal, versatile tools were developed to increase the expression of the recombinant proteins and to facilitate the purification process. Fusion tags are commonly used for enhancing expression and solubility and some can be used in the purification process. However, these tags may need to be removed by treatment with specific proteases in order to obtain the tag-free protein. The Profinity eXact™ system provides an alternative system for a fusion tag, enhancing expression and purification in one-step. Here we describe a set of new vectors in which the Profinity eXact™ tag, in addition to a 6× His-tag, with or without additional expression-enhancing sequences, could be used in the Profinity eXact™ system. We show that the solubility enhancing tags (Trx, GST, GB1) increase the yield of the purified tested protein compared to the vector containing only a His-tag upstream of the Profinity eXact™ fusion tag.
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Affiliation(s)
- Yoav Peleg
- The Israel Structural Proteomics Center (ISPC), Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Vadivel Prabahar
- Migal-Galilee Research Institute, S. Industrial Zone, Kiryat Shmona, Israel
| | - Dominika Bednarczyk
- Department of Bimolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Tamar Unger
- The Israel Structural Proteomics Center (ISPC), Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel.
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14
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Huang X, Li Z, Du C, Wang J, Li S. Improved Expression and Characterization of a Multidomain Xylanase from Thermoanaerobacterium aotearoense SCUT27 in Bacillus subtilis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:6430-9. [PMID: 26132889 DOI: 10.1021/acs.jafc.5b01259] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
A xylanase gene was cloned and characterized from Thermoanerobacterium aotearoense SCUT27, which was attested to consist of a signal peptide, one glycoside hydrolase family 10 domain, four carbohydrate binding modules, and three surface layer homology domains. The change of expression host from Escherichia coli to Bacillus subtilis resulted in a 4.1-fold increase of specific activity for the truncated XynAΔSLH. Five different versions of secretion signals in B. subtilis indicated that it was preferably routed via a Sec-dependent pathway. Purified XynAΔSLH showed a high activity of 379.8 U/mg on beechwood xylan. XynAΔSLH was optimally active at 80 °C, pH 6.5. Thin layer chromatography results showed that xylobiose and the presumed methylglucuronoxylotriose (MeGlcAXyl3) were the main products liberated from beechwood xylan catalyzed by the recombinant xylanase. All of the results suggest that XynAΔSLH is a suitable candidate for generating xylooligosaccharides from cellulosic materials for industrial uses.
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Affiliation(s)
- Xiongliang Huang
- †Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Zhe Li
- †Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Chenyu Du
- §School of Applied Sciences, The University of Huddersfield, Queensgate, Huddersfield, United Kingdom
| | - Jufang Wang
- †Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Shuang Li
- †Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
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15
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Zimhony O, Schwarz A, Raitses-Gurevich M, Peleg Y, Dym O, Albeck S, Burstein Y, Shakked Z. AcpM, the meromycolate extension acyl carrier protein of Mycobacterium tuberculosis, is activated by the 4'-phosphopantetheinyl transferase PptT, a potential target of the multistep mycolic acid biosynthesis. Biochemistry 2015; 54:2360-71. [PMID: 25785780 DOI: 10.1021/bi501444e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Modification of acyl carrier proteins (ACP) or domains by the covalent binding of a 4'-phosphopantetheine (4'-PP) moiety is a fundamental condition for activation of fatty acid synthases (FASes) and polyketide synthases (PKSes). Binding of 4'-PP is mediated by 4' phosphopantetheinyl transfersases (PPTases). Mycobacterium tuberculosis (Mtb) possesses two essential PPTases: acyl carrier protein synthase (Mtb AcpS), which activates the multidomain fatty acid synthase I (FAS I), and Mtb PptT, an Sfp-type broad spectrum PPTase that activates PKSes. To date, it has not been determined which of the two Mtb PPTases, AcpS or PptT, activates the meromycolate extension ACP, Mtb AcpM, en route to the production of mycolic acids, the main components of the mycobacterial cell wall. In this study, we tested the enzymatic activation of a highly purified Mtb apo-AcpM to Mtb holo-AcpM by either Mtb PptT or Mtb AcpS. By using SDS-PAGE band shift assay and mass spectrometry analysis, we found that Mtb PptT is the PPTase that activates Mtb AcpM. We measured the catalytic activity of Mtb PptT toward CoA, using an activation assay of a blue pigment synthase, BpsA (a nonribosomal peptide synthase, NRPS). BpsA activation by Mtb PptT was inhibited by Mtb apo-AcpM through competition for CoA, in accord with Mtb AcpM activation. A structural model of the putative interaction between Mtb PptT and Mtb AcpM suggests that both hydrophobic and electrostatic interactions stabilize this complex. To conclude, activation of Mtb AcpM by Mtb PptT reveals a potential target of the multistep mycolic acid biosynthesis.
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Affiliation(s)
- Oren Zimhony
- †Kaplan Medical Center, Affiliated to the School of Medicine, Hebrew University of Jerusalem and Hadassah Medical Center, POB1 Rehovot 76100, Israel
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16
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Fatty acid synthase is preferentially degraded by autophagy upon nitrogen starvation in yeast. Proc Natl Acad Sci U S A 2015; 112:1434-9. [PMID: 25605918 DOI: 10.1073/pnas.1409476112] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Autophagy, an evolutionarily conserved intracellular catabolic process, leads to the degradation of cytosolic proteins and organelles in the vacuole/lysosome. Different forms of selective autophagy have recently been described. Starvation-induced protein degradation, however, is considered to be nonselective. Here we describe a novel interaction between autophagy-related protein 8 (Atg8) and fatty acid synthase (FAS), a pivotal enzymatic complex responsible for the entire synthesis of C16- and C18-fatty acids in yeast. We show that although FAS possesses housekeeping functions, under starvation conditions it is delivered to the vacuole for degradation by autophagy in a Vac8- and Atg24-dependent manner. We also provide evidence that FAS degradation is essential for survival under nitrogen deprivation. Our results imply that during nitrogen starvation specific proteins are preferentially recruited into autophagosomes.
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17
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Erijman A, Shifman JM, Peleg Y. A single-tube assembly of DNA using the transfer-PCR (TPCR) platform. Methods Mol Biol 2014; 1116:89-101. [PMID: 24395359 DOI: 10.1007/978-1-62703-764-8_7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
DNA cloning is a basic methodology employed for multiple applications in all life-science disciplines. In order to facilitate DNA cloning we developed Transfer-PCR (TPCR), a novel approach that integrates in a single tube, PCR amplification of the target DNA from an origin vector and its subsequent integration into the destination vector. TPCR can be applied for incorporation of DNA fragments into any desired position within a circular plasmid without the need for purification of the intermediate PCR product and without the use of any commercial kit. TPCR reaction is most efficient within a narrow range of primer concentrations. Adaptation of the TPCR should facilitate, simplify, and significantly reduce time and costs for DNA assembly, as well as protein engineering studies. In the current publication we describe a detailed protocol for implementation of the TPCR method for DNA assembly.
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Affiliation(s)
- Ariel Erijman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
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18
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Peleg Y, Unger T. Application of the Restriction-Free (RF) cloning for multicomponents assembly. Methods Mol Biol 2014; 1116:73-87. [PMID: 24395358 DOI: 10.1007/978-1-62703-764-8_6] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Molecular manipulations, including DNA cloning and mutagenesis, are currently employed on a routine basis in all life science disciplines. Over the last decade new methodologies have emerged that expanded and facilitated the applications for DNA cloning. The classical Ligation-Dependent Cloning (LDC) is gradually replaced by Ligation-Independent Cloning (LIC) techniques. The Restriction-Free (RF) cloning was originally developed for introduction of a foreign DNA into a plasmid at any desired position. The RF methodology is based on generation of a PCR product, which serves as a set of mega-primers for subsequent incorporation into any desired position within a circular plasmid. We have expanded the applications of the RF methodology for multiple simultaneous alterations of a target DNA and for multicomponents assembly. In the current manuscript we describe a step-by-step protocol for application of the RF methodology for simultaneous multiple DNA fragments assembly in tandem and at distinct positions within an expression vector.
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Affiliation(s)
- Yoav Peleg
- Israel Structural Proteomics Center (ISPC), Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
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19
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Screening libraries for improved solubility: using E. coli dihydrofolate reductase as a reporter. Methods Mol Biol 2013. [PMID: 23423901 DOI: 10.1007/978-1-62703-293-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Low protein solubility is a problem in many areas of protein science. Although chemical methods have been developed to solubilize proteins these are not always effective and add to the cost of producing the protein. One way of overcoming these difficulties is to evolve the protein to be more soluble. A major hurdle in this process is the ability to select mutant proteins with enhanced solubility from a large library of randomly mutated proteins. In this article, we describe such a method. The method relies on the fact that increasing the expression of dihydrofolate reductase (DHFR) makes Escherichia coli resistant to Trimethoprim (TMP). Proteins fused to DHFR will produce chimeras with altered levels of resistance to TMP. This variation in TMP resistance can be used to identify mutant proteins with enhanced solubility.
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