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Bueno JGR, Borelli G, Corrêa TLR, Fiamenghi MB, José J, de Carvalho M, de Oliveira LC, Pereira GAG, dos Santos LV. Novel xylose transporter Cs4130 expands the sugar uptake repertoire in recombinant Saccharomyces cerevisiae strains at high xylose concentrations. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:145. [PMID: 32818042 PMCID: PMC7427733 DOI: 10.1186/s13068-020-01782-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/04/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND The need to restructure the world's energy matrix based on fossil fuels and mitigate greenhouse gas emissions stimulated the development of new biobased technologies for renewable energy. One promising and cleaner alternative is the use of second-generation (2G) fuels, produced from lignocellulosic biomass sugars. A major challenge on 2G technologies establishment is the inefficient assimilation of the five-carbon sugar xylose by engineered Saccharomyces cerevisiae strains, increasing fermentation time. The uptake of xylose across the plasma membrane is a critical limiting step and the budding yeast S. cerevisiae is not designed with a broad transport system and regulatory mechanisms to assimilate xylose in a wide range of concentrations present in 2G processes. RESULTS Assessing diverse microbiomes such as the digestive tract of plague insects and several decayed lignocellulosic biomasses, we isolated several yeast species capable of using xylose. Comparative fermentations selected the yeast Candida sojae as a potential source of high-affinity transporters. Comparative genomic analysis elects four potential xylose transporters whose properties were evaluated in the transporter null EBY.VW4000 strain carrying the xylose-utilizing pathway integrated into the genome. While the traditional xylose transporter Gxf1 allows an improved growth at lower concentrations (10 g/L), strains containing Cs3894 and Cs4130 show opposite responses with superior xylose uptake at higher concentrations (up to 50 g/L). Docking and normal mode analysis of Cs4130 and Gxf1 variants pointed out important residues related to xylose transport, identifying key differences regarding substrate translocation comparing both transporters. CONCLUSIONS Considering that xylose concentrations in second-generation hydrolysates can reach high values in several designed processes, Cs4130 is a promising novel candidate for xylose uptake. Here, we demonstrate a novel eukaryotic molecular transporter protein that improves growth at high xylose concentrations and can be used as a promising target towards engineering efficient pentose utilization in yeast.
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Affiliation(s)
- João Gabriel Ribeiro Bueno
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo 13083-100 Brazil
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Guilherme Borelli
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Thamy Lívia Ribeiro Corrêa
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo 13083-100 Brazil
| | - Mateus Bernabe Fiamenghi
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Juliana José
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Murilo de Carvalho
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Leandro Cristante de Oliveira
- Department of Physics-Institute of Biosciences, Humanities and Exact Sciences, UNESP, São Paulo State University, São José do Rio Preto, São Paulo 15054-000 Brazil
| | - Gonçalo A. G. Pereira
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Leandro Vieira dos Santos
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo 13083-100 Brazil
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
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Celińska E, Nicaud JM. Filamentous fungi-like secretory pathway strayed in a yeast system: peculiarities of Yarrowia lipolytica secretory pathway underlying its extraordinary performance. Appl Microbiol Biotechnol 2018; 103:39-52. [PMID: 30353423 PMCID: PMC6311201 DOI: 10.1007/s00253-018-9450-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 12/22/2022]
Abstract
Microbial production of secretory proteins constitutes one of the key branches of current industrial biotechnology, earning billion dollar (USD) revenues each year. That industrial branch strongly relies on fluent operation of the secretory machinery within a microbial cell. The secretory machinery, directing the nascent polypeptide to its final destination, constitutes a highly complex system located across the eukaryotic cell. Numerous molecular identities of diverse structure and function not only build the advanced network assisting folding, maturation and secretion of polypeptides but also serve as sensors and effectors of quality control points. All these events must be harmoniously orchestrated to enable fluent processing of the protein traffic. Availability of these elements is considered to be the limiting factor determining capacity of protein traffic, which is of crucial importance upon biotechnological production of secretory proteins. The main purpose of this work is to review and discuss findings concerning secretory machinery operating in a non-conventional yeast species, Yarrowia lipolytica, and to highlight peculiarities of this system prompting its use as the production host. The reviewed literature supports the thesis that secretory machinery in Y. lipolytica is characterized by significantly higher complexity than a canonical yeast protein secretion pathway, making it more similar to filamentous fungi-like systems in this regard.
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Affiliation(s)
- Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland.
| | - Jean-Marc Nicaud
- INRA-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Micalis Institute, Domaine de Vilvert, 78352, Jouy-en-Josas, France
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Li C, Lin Y, Zheng X, Pang N, Liao X, Liu X, Huang Y, Liang S. Combined strategies for improving expression of Citrobacter amalonaticus phytase in Pichia pastoris. BMC Biotechnol 2015; 15:88. [PMID: 26410558 PMCID: PMC4584009 DOI: 10.1186/s12896-015-0204-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phytase is used as an animal feed additive that degrades phytic acid and reduces feeding costs and pollution caused by fecal excretion of phosphorus. Some phytases have been expressed in Pichia pastoris, among which the phytase from Citrobacter amalonaticus CGMCC 1696 had high specific activity (3548 U/mg). Improvement of the phytase expression level will contribute to facilitate its industrial applications. METHODS To improve the phytase expression, we use modification of P AOX1 and the α-factor signal peptide, increasing the gene copy number, and overexpressing HAC1 (i) to enhance folding and secretion of the protein in the endoplasmic reticulum. The genetic stability and fermentation in 10-L scaled-up fed-batch fermenter was performed to prepare for the industrial production. RESULTS The phytase gene from C. amalonaticus CGMCC 1696 was cloned under the control of the AOX1 promoter (P AOX1 ) and expressed in P. pastoris. The phytase activity achieved was 414 U/mL. Modifications of P AOX1 and the α-factor signal peptide increased the phytase yield by 35 and 12%, respectively. Next, on increasing the copy number of the Phy gene to six, the phytase yield was 141% higher than in the strain containing only a single gene copy. Furthermore, on overexpression of HAC1 (i) (i indicating induced), a gene encoding Hac1p that regulates the unfolded protein response, the phytase yield achieved was 0.75 g/L with an activity of 2119 U/mL, 412% higher than for the original strain. The plasmids in this high-phytase expression strain were stable during incubation at 30 °C in Yeast Extract Peptone Dextrose (YPD) Medium. In a 10-L scaled-up fed-batch fermenter, the phytase yield achieved was 9.58 g/L with an activity of 35,032 U/mL. DISCUSSION The production of a secreted protein will reach its limit at a specific gene copy number where further increases in transcription and translation due to the higher abundance of gene copies will not enhance the secretion process any further. Enhancement of protein folding in the ER can alleviate bottlenecks in the folding and secretion pathways during the overexpression of heterologous proteins in P. pastoris. CONCLUSIONS Using modification of P AOX1 and the α-factor signal peptide, increasing the gene copy number, and overexpressing HAC1 (i) to enhance folding and secretion of the protein in the endoplasmic reticulum, we have successfully increased the phytase yield 412% relative to the original strain. In a 10-L fed-batch fermenter, the phytase yield achieved was 9.58 g/L with an activity of 35,032 U/mL. Large-scale production of phytase can be applied towards different biocatalytic and feed additive applications.
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Affiliation(s)
- Cheng Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, P. R. China. .,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, P. R. China.
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, P. R. China. .,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, P. R. China.
| | - Xueyun Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, P. R. China. .,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, P. R. China.
| | - Nuo Pang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, P. R. China. .,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, P. R. China.
| | - Xihao Liao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, P. R. China. .,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, P. R. China.
| | - Xiaoxiao Liu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, P. R. China. .,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, P. R. China.
| | - Yuanyuan Huang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, P. R. China. .,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, P. R. China.
| | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, P. R. China. .,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, P. R. China.
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Improving the Secretory Production of the Heterologous Protein in Pichia pastoris by Focusing on Protein Folding. Appl Biochem Biotechnol 2014; 175:535-48. [DOI: 10.1007/s12010-014-1292-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 10/09/2014] [Indexed: 01/07/2023]
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Du Z, Treiber D, McCoy RE, Miller AK, Han M, He F, Domnitz S, Heath C, Reddy P. Non-invasive UPR monitoring system and its applications in CHO production cultures. Biotechnol Bioeng 2013; 110:2184-94. [DOI: 10.1002/bit.24877] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 02/15/2013] [Indexed: 02/04/2023]
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De Wilde K, De Buck S, Vanneste K, Depicker A. Recombinant antibody production in Arabidopsis seeds triggers an unfolded protein response. PLANT PHYSIOLOGY 2013; 161:1021-33. [PMID: 23188806 PMCID: PMC3561000 DOI: 10.1104/pp.112.209718] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 11/26/2012] [Indexed: 05/07/2023]
Abstract
Among the many plant-based production systems that are being tested for molecular farming, seeds are very attractive, as they provide a stable environment in which the accumulating recombinant proteins can be stored. However, it is not known exactly how high production levels of recombinant antibodies influence the endogenous transcriptome and proteome of the developing seed. To address this question, we studied the transcriptomic status in developing Arabidopsis (Arabidopsis thaliana) seeds 13 d post anthesis of three transgenic lines, producing varying levels of recombinant VHH or single-chain Fv antibody fragments fused to the human immunoglobulin G1-derived Fc fragment under the control of the β-PHASEOLIN seed-specific promoter. Using genome-wide Tiling arrays, we demonstrated that only a small proportion of the transcriptome was significantly changed in each of the lines compared with the wild type. Strikingly, in all three lines, we found a large overlap of up-regulated genes corresponding to protein folding, glycosylation/modification, translocation, vesicle transport, and protein degradation, suggestive of a state of cellular stress called the unfolded protein response. Moreover, the gene up-regulation amplitude was similar in all three lines. We hypothesize that the production of recombinant antibodies in the endoplasmic reticulum triggers endoplasmic reticulum stress, causing a disturbance of the normal cellular homeostasis.
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Affiliation(s)
- Kirsten De Wilde
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.); and Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.)
| | - Sylvie De Buck
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.); and Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.)
| | - Kevin Vanneste
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.); and Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.)
| | - Ann Depicker
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.); and Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.)
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Abstract
Recombinant antibody fragments, for example, the classic monovalent single-chain antibody (scFv), are emerging as credible alternatives to monoclonal antibody (mAb) products. scFv fragments maintain a diverse range of potential applications in biotechnology and can be implemented as powerful therapeutic and diagnostic agents. As such, a variety of hosts have been used to produce antibody fragments resulting in varying degrees of success. Yeast, Saccharomyces cerevisiae, is an attractive host due to quality control mechanisms of the secretory pathway that ensure secreted proteins are properly folded. However, the expression of a recombinant protein in yeast is not trivial; neither are the quality control mechanisms the cell initiates to respond to overwhelming stress, such as an increased protein load, simplistic. The endoplasmic reticulum (ER) is a dynamic organelle, capable of sensing and adjusting its folding capacity in response to increased demand. When protein abundance or terminally misfolded proteins overwhelm the ER's capacity, the unfolded protein response (UPR) is activated. In the guidelines presented here, we discuss varying aspects of quality control, its modulation, and ways to design appropriate constructs for yeast recombinant protein expression. Furthermore, we have provided protocols and methods to monitor intracellular protein expression and trafficking as well as evaluation of the UPR, with essential controls. The latter part of this chapter will review considerations for the experimental design of microarray and quantitative polymerase chain reaction (q-PCR) techniques while suggesting appropriate means of data analysis.
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Wang F, Agnello G, Sotolongo N, Segatori L. Ca2+ homeostasis modulation enhances the amenability of L444P glucosylcerebrosidase to proteostasis regulation in patient-derived fibroblasts. ACS Chem Biol 2011; 6:158-68. [PMID: 21043486 DOI: 10.1021/cb100321m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Gaucher's disease is caused by deficiency of lysosomal glucocerebrosidase (GC) activity and accumulation of GC substrate, glucosylceramide. A number of point mutations in GC encoding gene have been reported to destabilize the enzyme native structure, resulting in protein misfolding and degradation. Particularly, the L444P GC variant, often associated with neuropathic manifestations of the disease, is severely destabilized and immediately degraded, resulting in complete loss of enzymatic activity. In addition, glucosylceramide accumulation causes Ca(2+) efflux from the endoplasmic reticulum (ER) through ryanodine receptors (RyRs) in the neurons of Gaucher's disease patients. We hypothesized that excessive [Ca(2+)](ER) efflux impairs ER folding and studied how modulation of [Ca(2+)](ER) affects folding of L444P GC in patient-derived fibroblasts. We report that RyRs blockers mediated [Ca(2+)] modulation, recreating a "wild type-like" folding environment in the ER, more amenable to rescuing the folding of mutated L444P GC through proteostasis regulation. Treating patient-derived fibroblasts with a RyRs blocker and a proteostasis modulator, MG-132, results in enhanced folding, trafficking, and activity of the severely destabilized L444P GC variant. Global gene expression profiling and mechanistic studies were conducted to investigate the folding quality control expression pattern conducive to native folding of mutated L444P GC and revealed that the ER-lumenal BiP/GRP78 plays a key role in the biogenesis of this GC variant.
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Affiliation(s)
- Fan Wang
- Department of Chemical and Biomolecular Engineering and ‡Department of Biochemistry and Cell Biology, Rice University, CHBE-MS 362, 6100 Main St., Houston, Texas 77005, United States
| | - Giulia Agnello
- Department of Chemical and Biomolecular Engineering and ‡Department of Biochemistry and Cell Biology, Rice University, CHBE-MS 362, 6100 Main St., Houston, Texas 77005, United States
| | - Natasha Sotolongo
- Department of Chemical and Biomolecular Engineering and ‡Department of Biochemistry and Cell Biology, Rice University, CHBE-MS 362, 6100 Main St., Houston, Texas 77005, United States
| | - Laura Segatori
- Department of Chemical and Biomolecular Engineering and ‡Department of Biochemistry and Cell Biology, Rice University, CHBE-MS 362, 6100 Main St., Houston, Texas 77005, United States
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