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Lam UTF, Nguyen TTT, Raechell R, Yang J, Singer H, Chen ES. A Normalization Protocol Reduces Edge Effect in High-Throughput Analyses of Hydroxyurea Hypersensitivity in Fission Yeast. Biomedicines 2023; 11:2829. [PMID: 37893202 PMCID: PMC10604075 DOI: 10.3390/biomedicines11102829] [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: 09/19/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Edge effect denotes better growth of microbial organisms situated at the edge of the solid agar media. Although the precise reason underlying edge effect is unresolved, it is generally attributed to greater nutrient availability with less competing neighbors at the edge. Nonetheless, edge effect constitutes an unavoidable confounding factor that results in misinterpretation of cell fitness, especially in high-throughput screening experiments widely employed for genome-wide investigation using microbial gene knockout or mutant libraries. Here, we visualize edge effect in high-throughput high-density pinning arrays and report a normalization approach based on colony growth rate to quantify drug (hydroxyurea)-hypersensitivity in fission yeast strains. This normalization procedure improved the accuracy of fitness measurement by compensating cell growth rate discrepancy at different locations on the plate and reducing false-positive and -negative frequencies. Our work thus provides a simple and coding-free solution for a struggling problem in robotics-based high-throughput screening experiments.
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Affiliation(s)
- Ulysses Tsz-Fung Lam
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
| | - Thi Thuy Trang Nguyen
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
| | - Raechell Raechell
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
| | - Jay Yang
- Singer Instruments, Roadwater, Watchet TA23 0RE, UK; (J.Y.); (H.S.)
| | - Harry Singer
- Singer Instruments, Roadwater, Watchet TA23 0RE, UK; (J.Y.); (H.S.)
| | - Ee Sin Chen
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
- NUS Center for Cancer Research, National University of Singapore, Singapore 117599, Singapore
- NUS Synthetic Biology for Clinical & Technological Innovation (SynCTI), Life Science Institute, National University of Singapore, Singapore 117456, Singapore
- National University Health System (NUHS), Singapore 119228, Singapore
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Kawarasaki Y, Kurose T, Ohashi S, Watabe R, Tanaka M, Ito K. High Cell-Density Expression System: Yeast Cells in a Phalanx Efficiently Produce a Certain Range of "Difficult-to-Express" Secretory Recombinant Proteins. Methods Mol Biol 2022; 2406:269-279. [PMID: 35089563 DOI: 10.1007/978-1-0716-1859-2_16] [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] [Indexed: 06/14/2023]
Abstract
Yeast's extracellular expression provides a cost-efficient means of producing recombinant proteins of academic or commercial interests. However, depending on the protein to be expressed, the production occasionally results in a poor yield, which is frequently accompanied with a deteriorated growth of the host. Here we describe our simple approach, high cell-density expression, to circumvent the cellular toxicity and achieve the production of a certain range of "difficult-to-express" secretory protein in preparative amount. The system features an ease of performing: (a) pre-cultivate yeast cells to the stationary phase in non-inducing condition, (b) suspend the cells to a small aliquot of inducing medium to form a high cell-density suspension or "a phalanx," then (c) give a sufficient aeration to the phalanx. Factors and pitfalls that affect the system's performance are also described.
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Affiliation(s)
- Yasuaki Kawarasaki
- Biomolecular Engineering Lab., Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan.
| | - Takeshi Kurose
- Biomolecular Engineering Lab., Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Sayaka Ohashi
- Biomolecular Engineering Lab., Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Runa Watabe
- Biomolecular Engineering Lab., Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Mizuki Tanaka
- Biomolecular Engineering Lab., Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Keisuke Ito
- Biomolecular Engineering Lab., Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
- Laboratory of Food Chemistry, Tokyo, Japan
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Parikh SB, Castilho Coelho N, Carvunis AR. LI Detector: a framework for sensitive colony-based screens regardless of the distribution of fitness effects. G3-GENES GENOMES GENETICS 2021; 11:6161305. [PMID: 33693606 PMCID: PMC8022918 DOI: 10.1093/g3journal/jkaa068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/15/2020] [Indexed: 11/13/2022]
Abstract
Microbial growth characteristics have long been used to investigate fundamental questions of biology. Colony-based high-throughput screens enable parallel fitness estimation of thousands of individual strains using colony growth as a proxy for fitness. However, fitness estimation is complicated by spatial biases affecting colony growth, including uneven nutrient distribution, agar surface irregularities, and batch effects. Analytical methods that have been developed to correct for these spatial biases rely on the following assumptions: (1) that fitness effects are normally distributed, and (2) that most genetic perturbations lead to minor changes in fitness. Although reasonable for many applications, these assumptions are not always warranted and can limit the ability to detect small fitness effects. Beneficial fitness effects, in particular, are notoriously difficult to detect under these assumptions. Here, we developed the linear interpolation-based detector (LI Detector) framework to enable sensitive colony-based screening without making prior assumptions about the underlying distribution of fitness effects. The LI Detector uses a grid of reference colonies to assign a relative fitness value to every colony on the plate. We show that the LI Detector is effective in correcting for spatial biases and equally sensitive toward increase and decrease in fitness. LI Detector offers a tunable system that allows the user to identify small fitness effects with unprecedented sensitivity and specificity. LI Detector can be utilized to develop and refine gene-gene and gene-environment interaction networks of colony-forming organisms, including yeast, by increasing the range of fitness effects that can be reliably detected.
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Affiliation(s)
- Saurin Bipin Parikh
- Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Nelson Castilho Coelho
- Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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Inokuma K, Bamba T, Ishii J, Ito Y, Hasunuma T, Kondo A. Enhanced cell-surface display and secretory production of cellulolytic enzymes withSaccharomyces cerevisiaeSed1 signal peptide. Biotechnol Bioeng 2016; 113:2358-66. [DOI: 10.1002/bit.26008] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Kentaro Inokuma
- Organization of Advanced Science and Technology; Kobe University; Kobe Japan
| | - Takahiro Bamba
- Department of Chemical Science and Engineering; Graduate School of Engineering; Kobe University; 1-1 Rokkodai, Nada Kobe 657-8501 Japan
| | - Jun Ishii
- Organization of Advanced Science and Technology; Kobe University; Kobe Japan
| | - Yoichiro Ito
- Department of Chemical Science and Engineering; Graduate School of Engineering; Kobe University; 1-1 Rokkodai, Nada Kobe 657-8501 Japan
| | - Tomohisa Hasunuma
- Organization of Advanced Science and Technology; Kobe University; Kobe Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering; Graduate School of Engineering; Kobe University; 1-1 Rokkodai, Nada Kobe 657-8501 Japan
- Biomass Engineering Program; RIKEN; 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama Kanagawa 230-0045 Japan
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Mori A, Hara S, Sugahara T, Kojima T, Iwasaki Y, Kawarasaki Y, Sahara T, Ohgiya S, Nakano H. Signal peptide optimization tool for the secretion of recombinant protein from Saccharomyces cerevisiae. J Biosci Bioeng 2015; 120:518-25. [PMID: 25912446 DOI: 10.1016/j.jbiosc.2015.03.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/01/2015] [Accepted: 03/03/2015] [Indexed: 11/27/2022]
Abstract
The secretion efficiency of foreign proteins in recombinant microbes is strongly dependent on the combination of the signal peptides (SPs) used and the target proteins; therefore, identifying the optimal SP sequence for each target protein is a crucial step in maximizing the efficiency of protein secretion in both prokaryotes and eukaryotes. In this study, we developed a novel method, named the SP optimization tool (SPOT), for the generation and rapid screening of a library of SP-target gene fusion constructs to identify the optimal SP for maximizing target protein secretion. In contrast to libraries generated in previous studies, SPOT fusion constructs are generated without adding the intervening sequences associated with restriction enzyme digestion sites. Therefore, no extra amino acids are inserted at the N-terminus of the target protein that might affect its function or conformational stability. As a model system, β-galactosidase (LacA) from Aspergillus oryzae was used as a target protein for secretion from Saccharomyces cerevisiae. In total, 60 SPs were selected from S. cerevisiae secretory proteins and utilized to generate the SP library. While many of the SP-LacA fusions were not secreted, several of the SPs, AGA2, CRH1, PLB1, and MF(alpha)1, were found to enhance LacA secretion compared to the WT sequence. Our results indicate that SPOT is a valuable method for optimizing the bioproduction of any target protein, and could be adapted to many host strains.
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Affiliation(s)
- Akihiro Mori
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Shoichi Hara
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Tomohiro Sugahara
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Takaaki Kojima
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yugo Iwasaki
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yasuaki Kawarasaki
- Biomolecular Engineering Laboratory, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Takehiko Sahara
- Bioproduction Research Institute (BPRI), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan
| | - Satoru Ohgiya
- Bioproduction Research Institute (BPRI), National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Hideo Nakano
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
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Kawarasaki Y, Kurose T, Ito K. High cell-density expression system: yeast cells in a phalanx efficiently produce a certain range of "difficult-to-express" secretory recombinant proteins. Methods Mol Biol 2014; 1258:169-78. [PMID: 25447864 DOI: 10.1007/978-1-4939-2205-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Yeast's extracellular expression provides a cost-efficient means of producing recombinant proteins of academic or commercial interests. However, depending on the protein to be expressed, the production occasionally results in a poor yield, which is frequently accompanied with a deteriorated growth of the host. Here we describe our simple approach, high cell-density expression, to circumvent the cellular toxicity and achieve in a production of a certain range of "difficult-to-express" secretory protein in preparative amount. The system features an ease of performing: (1) precultivate yeast cells to the stationary phase in non-inducing condition, (2) suspend the cells to a small aliquot of inducing medium to form a high cell-density suspension or "a phalanx," and then (3) give a sufficient aeration to the phalanx. Factors and pitfalls that affect the system's performance are also described.
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Affiliation(s)
- Yasuaki Kawarasaki
- Biomolecular Engineering Laboratory, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka, 422-8526, Japan,
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Kurose T, Saito Y, Kimata K, Nakagawa Y, Yano A, Ito K, Kawarasaki Y. Secretory expression of Lentinula edodes intracellular laccase by yeast high-cell-density system: Sub-milligram production of difficult-to-express secretory protein. J Biosci Bioeng 2014; 117:659-63. [DOI: 10.1016/j.jbiosc.2013.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 11/18/2013] [Accepted: 11/19/2013] [Indexed: 11/29/2022]
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Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev 2012; 76:331-82. [PMID: 22688816 DOI: 10.1128/mmbr.05021-11] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.
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Kimata K, Yamaguchi M, Saito Y, Hata H, Miyake K, Yamane T, Nakagawa Y, Yano A, Ito K, Kawarasaki Y. High cell-density expression system: A novel method for extracellular production of difficult-to-express proteins. J Biosci Bioeng 2012; 113:154-9. [DOI: 10.1016/j.jbiosc.2011.10.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 09/04/2011] [Accepted: 10/12/2011] [Indexed: 11/15/2022]
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Kojima T, Nagao N, Ando D, Ojima T, Kawarasaki Y, Kobayashi I, Nakajima M, Nakano H. Emulsion culture: A miniaturized library screening system based on micro-droplets in an emulsified medium. J Biosci Bioeng 2011; 112:299-303. [DOI: 10.1016/j.jbiosc.2011.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 05/06/2011] [Accepted: 05/31/2011] [Indexed: 10/18/2022]
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Jessulat M, Pitre S, Gui Y, Hooshyar M, Omidi K, Samanfar B, Tan LH, Alamgir M, Green J, Dehne F, Golshani A. Recent advances in protein-protein interaction prediction: experimental and computational methods. Expert Opin Drug Discov 2011; 6:921-35. [PMID: 22646215 DOI: 10.1517/17460441.2011.603722] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Proteins within the cell act as part of complex networks, which allow pathways and processes to function. Therefore, understanding how proteins interact is a significant area of current research. AREAS COVERED This review aims to present an overview of key experimental techniques (yeast two-hybrid, tandem affinity purification and protein microarrays) used to discover protein-protein interactions (PPIs), as well as to briefly discuss certain computational methods for predicting protein interactions based on gene localization, phylogenetic information, 3D structural modeling or primary protein sequence data. Due to the large-scale applicability of primary sequence-based methods, the authors have chosen to focus on this strategy for our review. There is an emphasis on a recent algorithm called Protein Interaction Prediction Engine (PIPE) that can predict global PPIs. The readers will discover recent advances both in the practical determination of protein interaction and the strategies that are available to attempt to anticipate interactions without the time and costs of experimental work. EXPERT OPINION Global PPI maps can help understand the biology of complex diseases and facilitate the identification of novel drug target sites. This study describes different techniques used for PPI prediction that we believe will significantly impact the development of the field in a new future. We expect to see a growing number of similar techniques capable of large-scale PPI predictions.
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Affiliation(s)
- Matthew Jessulat
- Carleton University , Department of Biology , 209 Nesbitt Building, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6 , Canada
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