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McDonald RC, Schott MJ, Idowu TA, Lyons PJ. Biochemical and genetic analysis of Ecm14, a conserved fungal pseudopeptidase. BMC Mol Cell Biol 2020; 21:86. [PMID: 33256608 PMCID: PMC7706225 DOI: 10.1186/s12860-020-00330-w] [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: 08/14/2020] [Accepted: 11/18/2020] [Indexed: 01/28/2023] Open
Abstract
Background Like most major enzyme families, the M14 family of metallocarboxypeptidases (MCPs) contains a number of pseudoenzymes predicted to lack enzyme activity and with poorly characterized molecular function. The genome of the yeast Saccharomyces cerevisiae encodes one member of the M14 MCP family, a pseudoenzyme named Ecm14 proposed to function in the extracellular matrix. In order to better understand the function of such pseudoenzymes, we studied the structure and function of Ecm14 in S. cerevisiae. Results A phylogenetic analysis of Ecm14 in fungi found it to be conserved throughout the ascomycete phylum, with a group of related pseudoenzymes found in basidiomycetes. To investigate the structure and function of this conserved protein, His6-tagged Ecm14 was overexpressed in Sf9 cells and purified. The prodomain of Ecm14 was cleaved in vivo and in vitro by endopeptidases, suggesting an activation mechanism; however, no activity was detectable using standard carboxypeptidase substrates. In order to determine the function of Ecm14 using an unbiased screen, we undertook a synthetic lethal assay. Upon screening approximately 27,000 yeast colonies, twenty-two putative synthetic lethal clones were identified. Further analysis showed many to be synthetic lethal with auxotrophic marker genes and requiring multiple mutations, suggesting that there are few, if any, single S. cerevisiae genes that present synthetic lethal interactions with ecm14Δ. Conclusions We show in this study that Ecm14, although lacking detectable enzyme activity, is a conserved carboxypeptidase-like protein that is secreted from cells and is processed to a mature form by the action of an endopeptidase. Our study and datasets from other recent large-scale screens suggest a role for Ecm14 in processes such as vesicle-mediated transport and aggregate invasion, a fungal process that has been selected against in modern laboratory strains of S. cerevisiae. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-020-00330-w.
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Affiliation(s)
| | - Matthew J Schott
- Department of Biology, Andrews University, Berrien Springs, MI, USA
| | - Temitope A Idowu
- Department of Biology, Andrews University, Berrien Springs, MI, USA
| | - Peter J Lyons
- Department of Biology, Andrews University, Berrien Springs, MI, USA.
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García-León M, Cuyas L, El-Moneim DA, Rodriguez L, Belda-Palazón B, Sanchez-Quant E, Fernández Y, Roux B, Zamarreño ÁM, García-Mina JM, Nussaume L, Rodriguez PL, Paz-Ares J, Leonhardt N, Rubio V. Arabidopsis ALIX Regulates Stomatal Aperture and Turnover of Abscisic Acid Receptors. THE PLANT CELL 2019; 31:2411-2429. [PMID: 31363038 PMCID: PMC6790096 DOI: 10.1105/tpc.19.00399] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/03/2019] [Accepted: 07/26/2019] [Indexed: 05/03/2023]
Abstract
The plant endosomal trafficking pathway controls the abundance of membrane-associated soluble proteins, as shown for abscisic acid (ABA) receptors of the PYRABACTIN RESISTANCE1/PYR1-LIKE/REGULATORY COMPONENTS OF ABA RECEPTORS (PYR/PYL/RCAR) family. ABA receptor targeting for vacuolar degradation occurs through the late endosome route and depends on FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING1 (FYVE1) and VACUOLAR PROTEIN SORTING23A (VPS23A), components of the ENDOSOMAL SORTING COMPLEX REQUIRED FOR TRANSPORT-I (ESCRT-I) complexes. FYVE1 and VPS23A interact with ALG-2 INTERACTING PROTEIN-X (ALIX), an ESCRT-III-associated protein, although the functional relevance of such interactions and their consequences in cargo sorting are unknown. In this study we show that Arabidopsis (Arabidopsis thaliana) ALIX directly binds to ABA receptors in late endosomes, promoting their degradation. Impaired ALIX function leads to altered endosomal localization and increased accumulation of ABA receptors. In line with this activity, partial loss-of-function alix-1 mutants display ABA hypersensitivity during growth and stomatal closure, unveiling a role for the ESCRT machinery in the control of water loss through stomata. ABA-hypersensitive responses are suppressed in alix-1 plants impaired in PYR/PYL/RCAR activity, in accordance with ALIX affecting ABA responses primarily by controlling ABA receptor stability. ALIX-1 mutant protein displays reduced interaction with VPS23A and ABA receptors, providing a molecular basis for ABA hypersensitivity in alix-1 mutants. Our findings unveil a negative feedback mechanism triggered by ABA that acts via ALIX to control the accumulation of specific PYR/PYL/RCAR receptors.
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Affiliation(s)
| | - Laura Cuyas
- Centro Nacional de Biotecnología, 28049 Madrid, Spain
- Aix Marseille Université, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, BIAM, UMR7265, SAVE, Saint Paul-Lez-Durance, France
- Centre Mondial de l'Innovation, Groupe Roullier, Saint-Malo, France
| | - Diaa Abd El-Moneim
- Centro Nacional de Biotecnología, 28049 Madrid, Spain
- Department of Plant Production, Genetic Branch, Faculty of Environmental and Agricultural Sciences, Arish University, North Sinai, Egypt
| | - Lesia Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain
| | - Borja Belda-Palazón
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain
| | | | | | - Brice Roux
- Aix Marseille Université, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, BIAM, UMR7265, SAVE, Saint Paul-Lez-Durance, France
| | - Ángel María Zamarreño
- Department of Environmental Biology, Agricultural Chemistry and Biology Group-CMI Roullier, Faculty of Sciences, University of Navarra, 31008 Pamplona, Spain
| | - José María García-Mina
- Department of Environmental Biology, Agricultural Chemistry and Biology Group-CMI Roullier, Faculty of Sciences, University of Navarra, 31008 Pamplona, Spain
| | - Laurent Nussaume
- Aix Marseille Université, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, BIAM, UMR7265, SAVE, Saint Paul-Lez-Durance, France
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain
| | | | - Nathalie Leonhardt
- Aix Marseille Université, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, BIAM, UMR7265, SAVE, Saint Paul-Lez-Durance, France
| | - Vicente Rubio
- Centro Nacional de Biotecnología, 28049 Madrid, Spain
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Evaluation of rice tetraticopeptide domain-containing thioredoxin as a novel solubility-enhancing fusion tag in Escherichia coli. J Biosci Bioeng 2018; 125:160-167. [DOI: 10.1016/j.jbiosc.2017.08.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/18/2017] [Accepted: 08/24/2017] [Indexed: 02/06/2023]
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Kukk K, Samel N. Enhanced expression of human prostaglandin H synthase-2 in the yeast Pichia pastoris and removal of the C-terminal tag with bovine carboxypeptidase A. J Biotechnol 2016; 231:224-231. [PMID: 27316830 DOI: 10.1016/j.jbiotec.2016.06.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/09/2016] [Accepted: 06/13/2016] [Indexed: 11/19/2022]
Abstract
Vertebrate prostaglandin H synthases (PGHSs) are membrane-bound disulphide-containing hemoglycoproteins. Therefore, eukaryotic expression systems are required for the production of recombinant PGHSs. Recently we announced the expression of human PGHS-2 (hPGHS-2) in the yeast Pichia pastoris. Here we report improved production of hPGHS-2 in P. pastoris and a convenient method for the purification and de-tagging of the protein. An affinity tag comprised of a proline, a glycine and eight histidines was introduced into the C-terminal end of hPGHS-2. The tagged hPGHS-2 was expressed intracellularly in P. pastoris under the control of a constitutive or methanol-inducible promoter. Compared to constitutive expression, methanol-induced expression yielded approximately four times more protein. The analysis of high and low gene copy number recombinants revealed a positive correlation between the gene copy number and the expression level of hPGHS-2. The recombinant hPGHS-2 was purified using immobilised metal ion affinity chromatography. A novel elution method, treatment of the affinity resin with bovine carboxypeptidase A, was employed. The yield of pure de-tagged hPGHS-2 from 1l of yeast culture was approximately 3mg. The protein purification process with simultaneous removal of the C-terminal polyhistidine tag could be easily applied for the affinity purification of other proteins.
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Affiliation(s)
- Kaia Kukk
- Department of Chemistry, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Nigulas Samel
- Department of Chemistry, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
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Jung W, Campbell RL, Gwak Y, Kim JI, Davies PL, Jin E. New Cysteine-Rich Ice-Binding Protein Secreted from Antarctic Microalga, Chloromonas sp. PLoS One 2016; 11:e0154056. [PMID: 27097164 PMCID: PMC4838330 DOI: 10.1371/journal.pone.0154056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/07/2016] [Indexed: 11/18/2022] Open
Abstract
Many microorganisms in Antarctica survive in the cold environment there by producing ice-binding proteins (IBPs) to control the growth of ice around them. An IBP from the Antarctic freshwater microalga, Chloromonas sp., was identified and characterized. The length of the Chloromonas sp. IBP (ChloroIBP) gene was 3.2 kb with 12 exons, and the molecular weight of the protein deduced from the ChloroIBP cDNA was 34.0 kDa. Expression of the ChloroIBP gene was up- and down-regulated by freezing and warming conditions, respectively. Western blot analysis revealed that native ChloroIBP was secreted into the culture medium. This protein has fifteen cysteines and is extensively disulfide bonded as shown by in-gel mobility shifts between oxidizing and reducing conditions. The open-reading frame of ChloroIBP was cloned and over-expressed in Escherichia coli to investigate the IBP’s biochemical characteristics. Recombinant ChloroIBP produced as a fusion protein with thioredoxin was purified by affinity chromatography and formed single ice crystals of a dendritic shape with a thermal hysteresis activity of 0.4±0.02°C at a concentration of 5 mg/ml. In silico structural modeling indicated that the three-dimensional structure of ChloroIBP was that of a right-handed β-helix. Site-directed mutagenesis of ChloroIBP showed that a conserved region of six parallel T-X-T motifs on the β-2 face was the ice-binding region, as predicted from the model. In addition to disulfide bonding, hydrophobic interactions between inward-pointing residues on the β-1 and β-2 faces, in the region of ice-binding motifs, were crucial to maintaining the structural conformation of ice-binding site and the ice-binding activity of ChloroIBP.
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Affiliation(s)
- Woongsic Jung
- Department of Life Science, Hanyang University, Seoul, South Korea
| | - Robert L. Campbell
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Canada K7L-3N6
| | - Yunho Gwak
- Department of Life Science, Hanyang University, Seoul, South Korea
| | - Jong Im Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Peter L. Davies
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Canada K7L-3N6
- * E-mail: (PLD); (EJ)
| | - EonSeon Jin
- Department of Life Science, Hanyang University, Seoul, South Korea
- * E-mail: (PLD); (EJ)
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Raran-Kurussi S, Waugh DS. Unrelated solubility-enhancing fusion partners MBP and NusA utilize a similar mode of action. Biotechnol Bioeng 2014; 111:2407-11. [PMID: 24942647 DOI: 10.1002/bit.25317] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/06/2014] [Accepted: 06/13/2014] [Indexed: 11/10/2022]
Abstract
The tendency of recombinant proteins to accumulate in the form of insoluble aggregates in Escherichia coli is a major hindrance to their overproduction. One of the more effective approaches to circumvent this problem is to use translation fusion partners {solubility-enhancers (SEs)}. E. coli maltose-binding protein (MBP) and N-utilization substance A (NusA) are arguably the most effective solubilizing agents that have been discovered so far. Here, we show that although these two proteins are structurally, functionally, and physicochemically distinct, they influence the solubility and folding of their fusion partners in a very similar manner. These SEs act as "holdases" that prevent the aggregation of their fusion partners. Subsequent folding of the passenger proteins, when it occurs, is either spontaneous or chaperone-mediated.
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Affiliation(s)
- Sreejith Raran-Kurussi
- Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
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Tan Z, Li J, Wu M, Wang J. Enhancing the thermostability of a cold-active lipase from Penicillium cyclopium by in silico design of a disulfide bridge. Appl Biochem Biotechnol 2014; 173:1752-64. [PMID: 24867629 DOI: 10.1007/s12010-014-0962-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 05/14/2014] [Indexed: 11/29/2022]
Abstract
Cysteine mutants of a cold-active lipase (PcLipI) from Penicillium cyclopium were designed by the software Disulfide by Design Ver. 1.20 in an effort to improve enzyme thermostability by addition of a disulfide bridge. Those mutants predicted by molecular dynamics simulation to have better thermostability than the wild type were first expressed in Escherichia coli BL21(DE3) and then, for further investigation, in Pichia pastoris GS115. By replacing Val248 and Thr251 with cysteines to create a disulfide bridge, the recombinant lipases reE-PcLipV248C-T251C (expressed in E. coli) and reP-PcLipV248C-T251C (expressed in P. pastoris) were obtained. Both had enhanced thermostability with half-lives at 35 °C about 4.5- and 12.8-fold longer than that of the parent PcLipI expressed in E. coli and P. pastoris, respectively. The temperature optima of reE-PcLipV248C-T251C and reP-PcLipV248C-T251C were 35 and 30 °C, which were each 5 °C higher than those of the parent PcLipI expressed in E. coli and P. pastoris. The K ms of reE-PcLipV248C-T251C and reP-PcLipV248C-T251C toward tributyrin were 53.2 and 39.5 mM, while their V maxs were 1,460 and 3,800 U/mg, respectively. PcLipV248C-T251C had better thermostability and catalytic efficiency than the other mutants and the parent PcLipI.
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Affiliation(s)
- Zhongbiao Tan
- School of Biotechnology and Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China
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Sangawa T, Tabata S, Suzuki K, Saheki Y, Tanaka K, Takagi J. A multipurpose fusion tag derived from an unstructured and hyperacidic region of the amyloid precursor protein. Protein Sci 2013; 22:840-50. [PMID: 23526492 DOI: 10.1002/pro.2254] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/14/2013] [Accepted: 03/14/2013] [Indexed: 11/06/2022]
Abstract
Expression and purification of aggregation-prone and disulfide-containing proteins in Escherichia coli remains as a major hurdle for structural and functional analyses of high-value target proteins. Here, we present a novel gene-fusion strategy that greatly simplifies purification and refolding procedure at very low cost using a unique hyperacidic module derived from the human amyloid precursor protein. Fusion with this polypeptide (dubbed FATT for Flag-Acidic-Target Tag) results in near-complete soluble expression of variety of extracellular proteins, which can be directly refolded in the crude bacterial lysate and purified in one-step by anion exchange chromatography. Application of this system enabled preparation of functionally active extracellular enzymes and antibody fragments without the need for condition optimization.
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Affiliation(s)
- Takeshi Sangawa
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
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Raran-Kurussi S, Waugh DS. The ability to enhance the solubility of its fusion partners is an intrinsic property of maltose-binding protein but their folding is either spontaneous or chaperone-mediated. PLoS One 2012; 7:e49589. [PMID: 23166722 PMCID: PMC3500312 DOI: 10.1371/journal.pone.0049589] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Accepted: 10/11/2012] [Indexed: 11/19/2022] Open
Abstract
Escherichia coli maltose binding protein (MBP) is commonly used to promote the solubility of its fusion partners. To investigate the mechanism of solubility enhancement by MBP, we compared the properties of MBP fusion proteins refolded in vitro with those of the corresponding fusion proteins purified under native conditions. We fused five aggregation-prone passenger proteins to 3 different N-terminal tags: His6-MBP, His6-GST and His6. After purifying the 15 fusion proteins under denaturing conditions and refolding them by rapid dilution, we recovered far more of the soluble MBP fusion proteins than their GST- or His-tagged counterparts. Hence, we can reproduce the solubilizing activity of MBP in a simple in vitro system, indicating that no additional factors are required to mediate this effect. We assayed both the soluble fusion proteins and their TEV protease digestion products (i.e., with the N-terminal tag removed) for biological activity. Little or no activity was detected for some fusion proteins whereas others were quite active. When the MBP fusions proteins were purified from E. coli under native conditions they were all substantially active. These results indicate that the ability of MBP to promote the solubility of its fusion partners in vitro sometimes, but not always, results in their proper folding. We show that the folding of some passenger proteins is mediated by endogenous chaperones in vivo. Hence, MBP serves as a passive participant in the folding process; passenger proteins either fold spontaneously or with the assistance of chaperones.
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Affiliation(s)
- Sreejith Raran-Kurussi
- Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - David S. Waugh
- Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- * E-mail:
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de Marco A. Recent contributions in the field of the recombinant expression of disulfide bonded proteins in bacteria. Microb Cell Fact 2012; 11:129. [PMID: 22978724 PMCID: PMC3462667 DOI: 10.1186/1475-2859-11-129] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 09/13/2012] [Indexed: 12/03/2022] Open
Abstract
The production of heterologous disulfide bonded proteins in bacteria remains a biotechnological challenge. A rapid literature survey results in the identification of some interesting proposals, such as the option of producing functional proteins in the cytoplasm in the presence of sulfhydryl oxidases and isomerases. Furthermore, an ever-increasing number of applications refers to recombinant proteins displayed at the bacterial surface. Time will tell whether these developments will lead to universally accepted laboratory protocols.
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