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Strawn G, Wong RWK, Young BP, Davey M, Nislow C, Conibear E, Loewen CJR, Mayor T. Genome-wide screen identifies new set of genes for improved heterologous laccase expression in Saccharomyces cerevisiae. Microb Cell Fact 2024; 23:36. [PMID: 38287338 PMCID: PMC10823697 DOI: 10.1186/s12934-024-02298-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/04/2024] [Indexed: 01/31/2024] Open
Abstract
The yeast Saccharomyces cerevisiae is widely used as a host cell for recombinant protein production due to its fast growth, cost-effective culturing, and ability to secrete large and complex proteins. However, one major drawback is the relatively low yield of produced proteins compared to other host systems. To address this issue, we developed an overlay assay to screen the yeast knockout collection and identify mutants that enhance recombinant protein production, specifically focusing on the secretion of the Trametes trogii fungal laccase enzyme. Gene ontology analysis of these mutants revealed an enrichment of processes including vacuolar targeting, vesicle trafficking, proteolysis, and glycolipid metabolism. We confirmed that a significant portion of these mutants also showed increased activity of the secreted laccase when grown in liquid culture. Notably, we found that the combination of deletions of OCA6, a tyrosine phosphatase gene, along with PMT1 or PMT2, two genes encoding ER membrane protein-O-mannosyltransferases involved in ER quality control, and SKI3, which encode for a component of the SKI complex responsible for mRNA degradation, further increased secreted laccase activity. Conversely, we also identified over 200 gene deletions that resulted in decreased secreted laccase activity, including many genes that encode for mitochondrial proteins and components of the ER-associated degradation pathway. Intriguingly, the deletion of the ER DNAJ co-chaperone gene SCJ1 led to almost no secreted laccase activity. When we expressed SCJ1 from a low-copy plasmid, laccase secretion was restored. However, overexpression of SCJ1 had a detrimental effect, indicating that precise dosing of key chaperone proteins is crucial for optimal recombinant protein expression. This study offers potential strategies for enhancing the overall yield of recombinant proteins and provides new avenues for further research in optimizing protein production systems.
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Affiliation(s)
- Garrett Strawn
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Ryan W K Wong
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Barry P Young
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Christopher J R Loewen
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Thibault Mayor
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
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2
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Flagg MP, Lam B, Lam DK, Le TM, Kao A, Slaiwa YI, Hampton RY. Exploring the "misfolding problem" by systematic discovery and analysis of functional-but-degraded proteins. Mol Biol Cell 2023; 34:ar125. [PMID: 37729018 PMCID: PMC10848938 DOI: 10.1091/mbc.e23-06-0248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023] Open
Abstract
In both health and disease, the ubiquitin-proteasome system (UPS) degrades point mutants that retain partial function but have decreased stability compared with their wild-type counterparts. This class of UPS substrate includes routine translational errors and numerous human disease alleles, such as the most common cause of cystic fibrosis, ΔF508-CFTR. Yet, there is no systematic way to discover novel examples of these "minimally misfolded" substrates. To address that shortcoming, we designed a genetic screen to isolate functional-but-degraded point mutants, and we used the screen to study soluble, monomeric proteins with known structures. These simple parent proteins yielded diverse substrates, allowing us to investigate the structural features, cytotoxicity, and small-molecule regulation of minimal misfolding. Our screen can support numerous lines of inquiry, and it provides broad access to a class of poorly understood but biomedically critical quality-control substrates.
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Affiliation(s)
- Matthew P. Flagg
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Breanna Lam
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Darren K. Lam
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Tiffany M. Le
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Andy Kao
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Yousif I. Slaiwa
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Randolph Y. Hampton
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
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3
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Lauer S, Luo J, Lazar-Stefanita L, Zhang W, McCulloch LH, Fanfani V, Lobzaev E, Haase MA, Easo N, Zhao Y, Yu F, Cai J, Bader JS, Stracquadanio G, Boeke JD. Context-dependent neocentromere activity in synthetic yeast chromosome VIII. CELL GENOMICS 2023; 3:100437. [PMID: 38020969 PMCID: PMC10667555 DOI: 10.1016/j.xgen.2023.100437] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 07/20/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023]
Abstract
Pioneering advances in genome engineering, and specifically in genome writing, have revolutionized the field of synthetic biology, propelling us toward the creation of synthetic genomes. The Sc2.0 project aims to build the first fully synthetic eukaryotic organism by assembling the genome of Saccharomyces cerevisiae. With the completion of synthetic chromosome VIII (synVIII) described here, this goal is within reach. In addition to writing the yeast genome, we sought to manipulate an essential functional element: the point centromere. By relocating the native centromere sequence to various positions along chromosome VIII, we discovered that the minimal 118-bp CEN8 sequence is insufficient for conferring chromosomal stability at ectopic locations. Expanding the transplanted sequence to include a small segment (∼500 bp) of the CDEIII-proximal pericentromere improved chromosome stability, demonstrating that minimal centromeres display context-dependent functionality.
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Affiliation(s)
- Stephanie Lauer
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Jingchuan Luo
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Luciana Lazar-Stefanita
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Laura H. McCulloch
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Viola Fanfani
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Evgenii Lobzaev
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- School of Informatics, The University of Edinburgh, Edinburgh, UK
| | - Max A.B. Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Nicole Easo
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Yu Zhao
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Fangzhou Yu
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Jitong Cai
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Joel S. Bader
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | - Jef D. Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
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Nejatfard A, Wauer N, Bhaduri S, Conn A, Gourkanti S, Singh N, Kuo T, Kandel R, Amaro RE, Neal SE. Derlin rhomboid pseudoproteases employ substrate engagement and lipid distortion to enable the retrotranslocation of ERAD membrane substrates. Cell Rep 2021; 37:109840. [PMID: 34686332 PMCID: PMC8641752 DOI: 10.1016/j.celrep.2021.109840] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/19/2021] [Accepted: 09/27/2021] [Indexed: 01/13/2023] Open
Abstract
Nearly one-third of proteins are initially targeted to the endoplasmic reticulum (ER) membrane, where they are correctly folded and then delivered to their final cellular destinations. To prevent the accumulation of misfolded membrane proteins, ER-associated degradation (ERAD) moves these clients from the ER membrane to the cytosol, a process known as retrotranslocation. Our recent work in Saccharomyces cerevisiae reveals a derlin rhomboid pseudoprotease, Dfm1, is involved in the retrotranslocation of ubiquitinated ERAD membrane substrates. In this study, we identify conserved residues of Dfm1 that are critical for retrotranslocation. We find several retrotranslocation-deficient Loop 1 mutants that display impaired binding to membrane substrates. Furthermore, Dfm1 possesses lipid thinning function to facilitate in the removal of ER membrane substrates, and this feature is conserved in its human homolog, Derlin-1, further implicating that derlin-mediated retrotranslocation is a well-conserved process.
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Affiliation(s)
- Anahita Nejatfard
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicholas Wauer
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Satarupa Bhaduri
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Adam Conn
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Saroj Gourkanti
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Narinderbir Singh
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Tiffany Kuo
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Rachel Kandel
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Sonya E Neal
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA.
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5
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Holland CL, Sanderson BA, Titus JK, Weis MF, Riojas AM, Malczewskyj E, Wasko BM, Lewis LK. Suppression of telomere capping defects of Saccharomyces cerevisiae yku70 and yku80 mutants by telomerase. G3-GENES GENOMES GENETICS 2021; 11:6395363. [PMID: 34718547 PMCID: PMC8664480 DOI: 10.1093/g3journal/jkab359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/27/2021] [Indexed: 11/18/2022]
Abstract
The Ku complex performs multiple functions inside eukaryotic cells, including protection of chromosomal DNA ends from degradation and fusion events, recruitment of telomerase, and repair of double-strand breaks (DSBs). Inactivation of Ku complex genes YKU70 or YKU80 in cells of the yeast Saccharomyces cerevisiae gives rise to mutants that exhibit shortened telomeres and temperature-sensitive growth. In this study, we have investigated the mechanism by which overexpression of telomerase suppresses the temperature sensitivity of yku mutants. Viability of yku cells was restored by overexpression of the Est2 reverse transcriptase and TLC1 RNA template subunits of telomerase, but not the Est1 or Est3 proteins. Overexpression of other telomerase- and telomere-associated proteins (Cdc13, Stn1, Ten1, Rif1, Rif2, Sir3, and Sir4) did not suppress the growth defects of yku70 cells. Mechanistic features of suppression were assessed using several TLC1 RNA deletion derivatives and Est2 enzyme mutants. Supraphysiological levels of three catalytically inactive reverse transcriptase mutants (Est2-D530A, Est2-D670A, and Est2-D671A) suppressed the loss of viability as efficiently as the wild-type Est2 protein, without inducing cell senescence. Roles of proteins regulating telomere length were also determined. The results support a model in which chromosomes in yku mutants are stabilized via a replication-independent mechanism involving structural reinforcement of protective telomere cap structures.
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Affiliation(s)
- Cory L Holland
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Brian A Sanderson
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - James K Titus
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Monica F Weis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Angelica M Riojas
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Eric Malczewskyj
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Brian M Wasko
- Department of Biology and Biotechnology, University of Houston-Clear Lake, Houston, TX, 77058, USA
| | - L Kevin Lewis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
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6
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Bhaduri S, Neal SE. Assays for studying normal versus suppressive ERAD-associated retrotranslocation pathways in yeast. STAR Protoc 2021; 2:100640. [PMID: 34278330 PMCID: PMC8271171 DOI: 10.1016/j.xpro.2021.100640] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In S. cerevisiae, we identified rhomboid pseudoprotease Dfm1 as the major mediator for removing or retrotranslocating misfolded membrane substrates from the ER (endoplasmic reticulum). Long-standing challenges with rapid suppression of dfm1-null cells have limited the biochemical study of Dfm1's role in ER protein quality control. Here, we provide a protocol for the generation and handling of dfm1-null cells and procedures for studying normal vs. suppressive alternative retrotranslocation pathways. Our methods can be utilized to study other components involved in retrotranslocation. For complete information on the generation and use of this protocol, please refer to Neal et al. (2017, 2018); Neal et al. (2019); Neal et al. (2020).
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Affiliation(s)
- Satarupa Bhaduri
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Sonya E. Neal
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
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Neal S, Syau D, Nejatfard A, Nadeau S, Hampton RY. HRD Complex Self-Remodeling Enables a Novel Route of Membrane Protein Retrotranslocation. iScience 2020; 23:101493. [PMID: 32891886 PMCID: PMC7481253 DOI: 10.1016/j.isci.2020.101493] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/09/2020] [Accepted: 08/19/2020] [Indexed: 12/17/2022] Open
Abstract
ER-associated degradation (ERAD) targets misfolded ER proteins for degradation. Retrotranslocation, a key feature of ERAD, entails removal of ubiquitinated substrates into the cytosol for proteasomal destruction. Recently, it has been shown that the Hrd1 E3 ligase forms a retrotranslocation channel for luminal (ERAD-L) substrates. Conversely, our studies found that integral membrane (ERAD-M) substrates exit the ER through a distinct pathway mediated by the Dfm1 rhomboid protein. Those studies also revealed a second, Hrd1-dependent pathway of ERAD-M retrotranslocation can arise in dfm1Δ null. Here we show that, in the dfm1Δ null, the HRD complex undergoes remodeling to a form that mediates ERAD-M retrotranslocation. Specifically, Hrd1's normally present stochiometric partner Hrd3 is efficiently removed during suppressive remodeling, allowing Hrd1 to function in this novel capacity. Neither Hrd1 autoubiquitination nor its cytosolic domain is required for suppressive ERAD-M retrotranslocation. Thus, the HRD complex displays remarkable functional flexibility in response to ER stress.
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Affiliation(s)
- Sonya Neal
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA.
| | - Della Syau
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Anahita Nejatfard
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Samantha Nadeau
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Randolph Y Hampton
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
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