1
|
Niu T, Cui Y, Shan X, Qin S, Zhou X, Wang R, Chang A, Ma N, Jing J, He J. Comparative transcriptomic analysis-based identification of the regulation of foreign proteins with different stabilities expressed in Pichia pastoris. Front Microbiol 2022; 13:1074398. [PMID: 36620045 PMCID: PMC9814716 DOI: 10.3389/fmicb.2022.1074398] [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: 10/19/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction The industrial yeast Pichia pastoris is widely used as a cell factory to produce proteins, chemicals and advanced biofuels. We have previously constructed P. pastoris strains that overexpress protein disulfide isomerase (PDI), which is a kind of molecular chaperone that can improve the expression of an exogenous protein when they are co-expressed. Chicken cystatin (cC) is a highly thermostable cysteine protease inhibitor and a homologous protein of human cystatin C (HCC). Wild-type cC and the two mutants, I66Q and ΔW (a truncated cC lacking the á-helix 2) represent proteins with different degrees of stability. Methods Wild-type cC, I66Q and ΔW were each overexpressed in P. pastoris without and with the coexpression of PDI and their extracellular levels were determined and compared. Transcriptomic profiling was performed to compare the changes in the main signaling pathways and cell components (other than endoplasmic reticulum quality control system represented by molecular chaperones) in P. pastoris in response to intracellular folding stress caused by the expression of exogenous proteins with different stabilities. Finally, hub genes hunting was also performed. Results and discussion The coexpression of PDI was able to increase the extracellular levels of both wild-type cC and the two mutants, indicating that overexpression of PDI could prevent the misfolding of unstable proteins or promote the degradation of the misfolded proteins to some extent. For P. pastoris cells that expressed the I66Q or ΔW mutant, GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses of the common DEGs in these cells revealed a significant upregulation of the genes involved in protein processing, but a significant downregulation of the genes enriched in the Ribosome, TCA and Glycolysis/Gluconeogenesis pathways. Hub genes hunting indicated that the most downregulated ribosome protein, C4QXU7 in this case, might be an important target protein that could be manipulated to increase the expression of foreign proteins, especially proteins with a certain degree of instability. Conclusion These findings should shed new light on our understanding of the regulatory mechanism in yeast cells that responds to intracellular folding stress, providing valuable information for the development of a convenient platform that could improve the efficiency of heterologous protein expression in P. pastoris.
Collapse
Affiliation(s)
- Tingting Niu
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Yi Cui
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Xu Shan
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Shuzhen Qin
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Xuejie Zhou
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Rui Wang
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Alan Chang
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, China
| | - Nan Ma
- China Academy of Transportation Sciences, Beijing, China,Nan Ma,
| | - Jingjing Jing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China,Jingjing Jing,
| | - Jianwei He
- School of Life Sciences, Liaoning University, Shenyang, China,*Correspondence: Jianwei He,
| |
Collapse
|
2
|
Taherian E, Mohammadi E, Jahanian-Najafabadi A, Moazen F, Akbari V. Cloning, Optimization of Periplasmic Expression and Purification of Recombinant Granulocyte Macrophage-Stimulating Factor in Escherichia coli BL21 (DE3). Adv Biomed Res 2019; 8:71. [PMID: 32002394 PMCID: PMC6952766 DOI: 10.4103/abr.abr_166_19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/18/2019] [Accepted: 09/28/2019] [Indexed: 12/17/2022] Open
Abstract
Background: Molgramostim, a nonglycosylated version of recombinant granulocyte-macrophage colony-stimulating factor (GM-CSF), can be produced in a high level by Escherichia coli. However, overexpression of GM-CSF in bacterial cells usually leads to formation of inclusion bodies and insoluble protein aggregates which are not biologically active. The aim of the present study was to improve the expression of soluble and biologically active GM-CSF in periplasmic space of E. coli BL21 (DE3). Materials and Methods: The codon-optimized GM-CSF gene was subcloned into pET-22b expression vector, in frame with the pelB secretion signal peptide for periplasmic secretion. Cultivation conditions including as isopropyl β-D-1-thiogalactopyranoside (IPTG) concentration, incubation temperature, and presence of sucrose were optimized to improve periplasmic expression of GM-CSF. The expressed protein was purified using Ni-NTA affinity column. Biological activity of GM-CSF on HL-60 cells was evaluated using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Results: The amount of soluble protein for periplasmic expression was more when compared with one of the cytoplasmic expressions. The optimum condition for periplasmic expression of GM-CSF was expression at 23°C, using 1 mM IPTG as inducer and in the presence of 0.4 M sucrose. The biological activity of purified GM-CSF on HL-60 cell line was assessed by MTT assay, and the specific activity of produced GM-CSF was determined as 1.2 × 104 IU/μg. Conclusion: The present work suggests that periplasmic expression and optimization of cultivation conditions could improve soluble expression of recombinant proteins by E. coli.
Collapse
Affiliation(s)
- Elham Taherian
- Department of Pharmaceutical Biotechnology, Isfahan Pharmaceutical Research Center, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elmira Mohammadi
- Department of Pharmaceutical Biotechnology, Isfahan Pharmaceutical Research Center, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ali Jahanian-Najafabadi
- Department of Pharmaceutical Biotechnology, Isfahan Pharmaceutical Research Center, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fatemeh Moazen
- Department of Pharmaceutical Biotechnology, Isfahan Pharmaceutical Research Center, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Vajihe Akbari
- Department of Pharmaceutical Biotechnology, Isfahan Pharmaceutical Research Center, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| |
Collapse
|
3
|
Zhang Y, Zhao J, He S, Cao X. Soluble Expression of Recombinant Human Cystatin C and Comparison of the Ni Column and Magnetic Bead Purification. Protein J 2019; 39:85-95. [PMID: 31625059 DOI: 10.1007/s10930-019-09873-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cystatin C, also known as γ-trace or post-γ-globulin, is a cysteine protease inhibitor from the cystatin superfamily. It is usually used as a marker of the glomerular filtration rate owing to its low molecular weight and constant secretion. The recently available methods for cystatin C preparation have low outputs. Hence, a productive preparation system is urgently required. In this study, a 6 × His-tag coupled with a thrombin cleavage site was fused to the C-terminus of cystatin C, and the protein was well expressed in Escherichia coli after optimization. Then, two different systems were used to obtain no-tag cystatin C: a traditional nickel (Ni)-column system and a subtly Ni magnetic bead system. The column system was more commonly used, and the magnetic bead system was more convenient. Cystatin C (purity > 97%) was successfully obtained, and the yields in both the systems were higher than those in previous studies. Further, the proper folding status and bioactivity of recombinant cystatin C were confirmed using the papain inhibition assay, dynamic light scattering, and circular dichroism spectroscopy.
Collapse
Affiliation(s)
- Yibin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Jian Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Shiyu He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xuni Cao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
| |
Collapse
|
4
|
Santos BD, Morones-Ramirez JR, Balderas-Renteria I, Casillas-Vega NG, Galbraith DW, Zarate X. Optimizing Periplasmic Expression in Escherichia coli for the Production of Recombinant Proteins Tagged with the Small Metal-Binding Protein SmbP. Mol Biotechnol 2019; 61:451-460. [PMID: 30997666 DOI: 10.1007/s12033-019-00176-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We have previously shown that the small metal-binding protein (SmbP) extracted from the gram-negative bacterium Nitrosomonas europaea can be employed as a fusion protein for the expression and purification of recombinant proteins in Escherichia coli. With the goal of increasing the amounts of SmbP-tagged proteins produced in the E. coli periplasm, we replaced the native SmbP signal peptide with three different signal sequences: two were from the proteins CusF and PelB, for transport via the Sec pathway, and one was the signal peptide from TorA, for transport via the Tat pathway. Expression of SmbP-tagged Red Fluorescent Protein (RFP) using these three alternative signal peptides individually showed a considerable increase in protein levels in the periplasm of E. coli as compared to its level using the SmbP signal sequence. Therefore, for routine periplasmic expression and purification of recombinant proteins in E. coli, we highly recommend the use of the fusion proteins PelB-SmbP or CusF-SmbP, since these signal sequences increase periplasmic production considerably as compared to the wild-type. Our work, finally, demonstrates that periplasmic expression for SmbP-tagged proteins is not limited to the Sec pathway, in that the TorA-SmbP construct can export reasonable quantities of folded proteins to the periplasm. Although the Sec route has been the most widely used, sometimes, depending on the nature of the protein of interest, for example, if it contains cofactors, it is more appropriate to consider using the Tat route over the Sec. SmbP therefore can be recommended in terms of its particular versatility when combined with signal peptides for the two different routes.
Collapse
Affiliation(s)
- Bryan D Santos
- Universidad Autonoma de Nuevo Leon, Facultad de Ciencias Quimicas, 66455, San Nicolas de los Garza, NL, Mexico
| | - Jose Ruben Morones-Ramirez
- Universidad Autonoma de Nuevo Leon, Facultad de Ciencias Quimicas, 66455, San Nicolas de los Garza, NL, Mexico
- Universidad Autonoma de Nuevo Leon, Centro de Investigacion en Biotecnologia y Nanotecnologia, Facultad de Ciencias Quimicas, Parque de Investigacion e Innovacion Tecnologica, 66629, Apodaca, NL, Mexico
| | - Isaias Balderas-Renteria
- Universidad Autonoma de Nuevo Leon, Facultad de Ciencias Quimicas, 66455, San Nicolas de los Garza, NL, Mexico
- Universidad Autonoma de Nuevo Leon, Centro de Investigacion en Biotecnologia y Nanotecnologia, Facultad de Ciencias Quimicas, Parque de Investigacion e Innovacion Tecnologica, 66629, Apodaca, NL, Mexico
| | - Nestor G Casillas-Vega
- Departamento de Patologia Clinica, Universidad Autonoma de Nuevo Leon, Hospital Universitario Dr. Jose Eleuterio Gonzalez, 64460, Monterrey, NL, Mexico
| | - David W Galbraith
- School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Xristo Zarate
- Universidad Autonoma de Nuevo Leon, Facultad de Ciencias Quimicas, 66455, San Nicolas de los Garza, NL, Mexico.
- Universidad Autonoma de Nuevo Leon, Centro de Investigacion en Biotecnologia y Nanotecnologia, Facultad de Ciencias Quimicas, Parque de Investigacion e Innovacion Tecnologica, 66629, Apodaca, NL, Mexico.
| |
Collapse
|
5
|
Faret M, de Morais SB, Zanchin NIT, de Souza TDACB. L-Asparaginase from Erwinia carotovora: insights about its stability and activity. Mol Biol Rep 2018; 46:1313-1316. [PMID: 30446961 DOI: 10.1007/s11033-018-4459-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/30/2018] [Indexed: 11/26/2022]
Abstract
Enzymatic prospection indicated that L-asparaginase from Erwinia carotovora (ECAR-LANS) posses low glutaminase activity and much effort has been made to produce therapeutic ECAR-LANS. However, its low stability precludes its use in therapy. Herein, biochemical and biophysical assays provided data highlighting the influence of solubilization and storage into ECAR-LANS structure, stability, and activity. Moreover, innovations in recombinant expression and purification guaranteed the purification of functional tetramers. According to solubilization condition, the L-asparaginase activity and temperature of melting ranged up to 25-32%, respectively. CD spectra indicate the tendency of ECAR-LANS to instability and the influence of β-structures in activity. These results provide relevant information to guide formulations with prolonged action in the bloodstream.
Collapse
Affiliation(s)
- Marcele Faret
- Instituto Carlos Chagas, ICC - FIOCRUZ/PR, Rua Algacyr Munhoz Mader, 3775, bloco C, Curitiba,, Paraná, 81350-010, Brazil
| | - Stephanie Bath de Morais
- Instituto Carlos Chagas, ICC - FIOCRUZ/PR, Rua Algacyr Munhoz Mader, 3775, bloco C, Curitiba,, Paraná, 81350-010, Brazil
| | - Nilson Ivo Tonin Zanchin
- Instituto Carlos Chagas, ICC - FIOCRUZ/PR, Rua Algacyr Munhoz Mader, 3775, bloco C, Curitiba,, Paraná, 81350-010, Brazil
| | | |
Collapse
|
6
|
Perlenfein TJ, Mehlhoff JD, Murphy RM. Insights into the mechanism of cystatin C oligomer and amyloid formation and its interaction with β-amyloid. J Biol Chem 2017; 292:11485-11498. [PMID: 28487367 DOI: 10.1074/jbc.m117.786558] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 04/21/2017] [Indexed: 01/12/2023] Open
Abstract
Cystatin C (CysC) is a versatile and ubiquitously-expressed member of the cysteine protease inhibitor family that is present at notably high concentrations in cerebrospinal fluid. Under mildly denaturing conditions, CysC forms inactive domain-swapped dimers. A destabilizing mutation, L68Q, increases the rate of domain-swapping and causes a fatal amyloid disease, hereditary cystatin C amyloid angiopathy. Wild-type (wt) CysC will also aggregate into amyloid fibrils under some conditions. Propagated domain-swapping has been proposed as the mechanism by which CysC fibrils grow. We present evidence that a CysC mutant, V57N, stabilized against domain-swapping, readily forms fibrils, contradicting the propagated domain-swapping hypothesis. Furthermore, in physiological buffer, wt CysC can form oligomers without undergoing domain-swapping. These non-swapped oligomers are identical in secondary structure to CysC monomers and completely retain protease inhibitory activity. However, unlike monomers or dimers, the oligomers bind fluorescent dyes that indicate they have characteristics of pre-amyloid aggregates. Although these oligomers appear to be a pre-amyloid assembly, they are slower than CysC monomers to form fibrils. Fibrillation of CysC therefore likely initiates from the monomer and does not require domain-swapping. The non-swapped oligomers likely represent a dead-end offshoot of the amyloid pathway and must dissociate to monomers prior to rearranging to amyloid fibrils. These prefibrillar CysC oligomers were potent inhibitors of aggregation of the Alzheimer's-related peptide, β-amyloid. This result illustrates an example where heterotypic interactions between pre-amyloid oligomers prevent the homotypic interactions that would lead to mature amyloid fibrils.
Collapse
Affiliation(s)
- Tyler J Perlenfein
- From the Department of Chemical and Biological Engineering, University of Wisconsin, Madison, Wisconsin 53706
| | - Jacob D Mehlhoff
- From the Department of Chemical and Biological Engineering, University of Wisconsin, Madison, Wisconsin 53706
| | - Regina M Murphy
- From the Department of Chemical and Biological Engineering, University of Wisconsin, Madison, Wisconsin 53706
| |
Collapse
|
7
|
Chen T, Xu W. A purification method for tag-free human cystatin C recombinant protein expressed in Escherichia coli. Prep Biochem Biotechnol 2017; 47:123-128. [PMID: 27143404 DOI: 10.1080/10826068.2016.1181087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To obtain recombinant cystatin C (CysC) protein, which can be used in immunological diagnostic kits, we focused on the preparation of tag-free CysC. The 6 × His-TF-CysC fusion protein was found to overexpress in soluble form in cells of BL21-Gold (DE3)/pCold TF-CysC, which had been induced with isopropyl-D-1-thiogalactopyranoside. Subsequently, we established a protein purification method for tag-free CysC using immobilized metal-affinity chromatography and size-exclusion chromatography. In this method, glutathione-S-transferase-human rhinovirus 3C proteases were used to remove the protein tags. High homogeneity of the purified CysC was determined by SDS-PAGE, while the purity of the tag-free CysC was ascertained to be above 95%. With a yield of 25 mg/L from bacterial culture, the biological activity of the tag-free CysC was evaluated as inhibitors like natural CysC. The performance of this purification method was successfully evaluated in the preparation of other low molecular weight heterologous proteins in Escherichia coli.
Collapse
Affiliation(s)
- Te Chen
- a Department of Laboratory Medicine , The First Affiliated Hospital of Chongqing Medical University , Chongqing , China
| | - Wenchun Xu
- b Laboratory of Medical Diagnostics (Ministry of Education of China) , Department of Key Laboratory Medicine, Chongqing Medical University , Chongqing , China
| |
Collapse
|
8
|
Chauhan S, Tomar RS. Efficient expression and purification of biologically active human cystatin proteins. Protein Expr Purif 2016; 118:10-7. [DOI: 10.1016/j.pep.2015.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/07/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022]
|
9
|
Perlenfein TJ, Murphy RM. Expression, purification, and characterization of human cystatin C monomers and oligomers. Protein Expr Purif 2015; 117:35-43. [PMID: 26409164 DOI: 10.1016/j.pep.2015.09.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/16/2015] [Accepted: 09/22/2015] [Indexed: 11/19/2022]
Abstract
Human cystatin C (cysC) is a soluble basic protein belonging to the cysteine protease inhibitor family. CysC is a potent inhibitor of cathepsins--proteolytic enzymes that degrade intracellular and endocytosed proteins, remodel extracellular matrix, and trigger apoptosis. Inhibition is via tight reversible binding involving the N-terminus as well as two β-hairpin loops of cysC. As a significant component of cerebrospinal fluid, cysC has numerous other functions, including support of neural stem cell growth and differentiation. Several studies suggest that cysC may bind to the Alzheimer-related protein beta-amyloid (Aβ), and inhibit its aggregation and toxicity. Because of an increasing recognition of its important biological roles, there is considerable interest in methods to produce full-length recombinant human cysC. Several researchers have reported success, but with processes that require multiple purification steps. Here we report successful production of human cysC using an intein-based expression system and a simple one-column purification scheme. The recombinant protein so obtained was natively folded and active as an enzyme inhibitor. Unexpectedly, even mild concentration by ultrafiltration caused significant oligomerization. The oligomers are noncovalent and retain the native secondary structure and inhibitory activity of the monomer. The oligomers, but not the monomers, were highly effective at inhibiting aggregation of Aβ. These results demonstrate the critical importance of careful physicochemical characterization of recombinant cysC protein prior to evaluation of its biological functions.
Collapse
Affiliation(s)
- Tyler J Perlenfein
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706, United States
| | - Regina M Murphy
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706, United States.
| |
Collapse
|