1
|
Sun M, Fu L, Chen T, Dong N. Extracellular production of antifungal peptides from oxidative endotoxin-free E. coli and application. Appl Microbiol Biotechnol 2024; 108:56. [PMID: 38175241 DOI: 10.1007/s00253-023-12888-4] [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] [Received: 06/27/2023] [Revised: 10/15/2023] [Accepted: 10/20/2023] [Indexed: 01/05/2024]
Abstract
Antifungal peptides (AFPs) can be used as novel preservatives, but achieving large-scale production and application remains a long-term challenge. In this study, we developed a hybrid peptide MD (metchnikowin-drosomycin fusion) secreted into Escherichia coli supernatant, demonstrating strong inhibitory activity against Aspergillus flavus and Botrytis cinerea. The fusion tag did not impact its activity. Moreover, an endotoxin-free and oxidative leaky strain was developed by knocking out the trxB, gor, and lpp genes of endotoxin-free E. coli ClearColi-BL21(DE3). This strain facilitates the proper folding of multi-disulfide bond proteins and promotes the extracellular production of recombinant bioactive AFP MD, achieving efficient production of endotoxin-free MD. In addition, temperature control replaces chemical inducers to further reduce production costs and circumvent the toxicity of inducers. This extracellularly produced MD exhibited favorable effectiveness in inhibiting fruit mold growth, and its safety was preliminarily established by gavage testing in mice, suggesting that it can be developed into a green and sustainable fruit fungicide. In conclusion, this study provides novel approaches and systematic concepts for producing extracellularly active proteins or peptides with industrial significance. KEY POINTS: • First report of extracellular production of bioactive antifungal peptide in Escherichia coli. • The hybrid antifungal peptide MD showed strong inhibitory activity against Aspergillus flavus and Botrytis cinerea, and the activity was not affected by the fusion tag. • Endotoxin-free oxidative Escherichia coli suitable for the expression of multi-disulfide bond proteins was constructed.
Collapse
Affiliation(s)
- Mengning Sun
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Linglong Fu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Tong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100193, People's Republic of China
| | - Na Dong
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
| |
Collapse
|
2
|
Osgerby A, Overton TW. Approaches for high-throughput quantification of periplasmic recombinant proteins. N Biotechnol 2023; 77:149-160. [PMID: 37708933 DOI: 10.1016/j.nbt.2023.09.003] [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] [Received: 05/03/2023] [Revised: 09/01/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The Gram-negative periplasm is a convenient location for the accumulation of many recombinant proteins including biopharmaceutical products. It is the site of disulphide bond formation, required by some proteins (such as antibody fragments) for correct folding and function. It also permits simpler protein release and downstream processing than cytoplasmic accumulation. As such, targeting of recombinant proteins to the E. coli periplasm is a key strategy in biologic manufacture. However, expression and translocation of each recombinant protein requires optimisation including selection of the best signal peptide and growth and production conditions. Traditional methods require separation and analysis of protein compositions of periplasmic and cytoplasmic fractions, a time- and labour-intensive method that is difficult to parallelise. Therefore, approaches for high throughput quantification of periplasmic protein accumulation offer advantages in rapid process development.
Collapse
Affiliation(s)
- Alexander Osgerby
- School of Chemical Engineering and Institute of Microbiology and Infection, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Tim W Overton
- School of Chemical Engineering and Institute of Microbiology and Infection, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| |
Collapse
|
3
|
Arauzo‐Aguilera K, Saaranen MJ, Robinson C, Ruddock LW. Highly efficient export of a disulfide‐bonded protein to the periplasm and medium by the Tat pathway using CyDisCo in Escherichia coli. Microbiologyopen 2023; 12:e1350. [PMID: 37186227 PMCID: PMC9995818 DOI: 10.1002/mbo3.1350] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/24/2023] [Accepted: 02/24/2023] [Indexed: 03/11/2023] Open
Abstract
High‐value heterologous proteins produced in Escherichia coli that contain disulfide bonds are almost invariably targeted to the periplasm via the Sec pathway as it, among other advantages, enables disulfide bond formation and simplifies downstream processing. However, the Sec system cannot transport complex or rapidly folding proteins, as it only transports proteins in an unfolded state. The Tat system also transports proteins to the periplasm, and it has significant potential as an alternative means of recombinant protein production because it transports fully folded proteins. Most of the studies related to Tat secretion have used the well‐studied TorA signal peptide that is Tat‐specific, but this signal peptide also tends to induce degradation of the protein of interest, resulting in lower yields. This makes it difficult to use Tat in the industry. In this study, we show that a model disulfide bond‐containing protein, YebF, can be exported to the periplasm and media at a very high level by the Tat pathway in a manner almost completely dependent on cytoplasmic disulfide formation, by other two putative Tat SPs: those of MdoD and AmiC. In contrast, the TorA SP exports YebF at a low level.
Collapse
Affiliation(s)
| | - Mirva J. Saaranen
- Faculty of Biochemistry and Molecular MedicineUniversity of OuluOuluFinland
| | | | - Lloyd W. Ruddock
- Faculty of Biochemistry and Molecular MedicineUniversity of OuluOuluFinland
| |
Collapse
|
4
|
Yu X, Li S, Feng H, Liao X, Xing XH, Bai Z, Liu X, Zhang C. CRISPRi-microfluidics screening enables genome-scale target identification for high-titer protein production and secretion. Metab Eng 2023; 75:192-204. [PMID: 36572334 DOI: 10.1016/j.ymben.2022.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/25/2022]
Abstract
Genome-scale target identification promises to guide microbial cell factory engineering for higher-titer production of biomolecules such as recombinant proteins (r-protein), but challenges remain due to the need not only for comprehensive genotypic perturbation but also in conjunction with high-throughput phenotypic screening strategies. Here, we developed a CRISPRi-microfluidics screening platform to systematically identify crucial gene targets that can be engineered to enhance r-protein secretion in Corynebacterium glutamicum. We created a CRISPR interference (CRISPRi) library containing 46,549 single-guide RNAs, where we aimed to unbiasedly target all genes for repression. Meanwhile, we developed a highly efficient droplet-based microfluidics system integrating the FlAsH-tetracysteine assay that enables screening of millions of strains to identify potential knockdowns conducive to nanobody VHH secretion. Among our highest-ranking candidates are a slew of previously unknown targets involved in transmembrane transport, amino-acid metabolism and redox regulation. Guided by these findings, we eventually constructed a hyperproducer for multiple proteins via combinatorial engineering of redox-response transcription factors. As the near-universal applicability of CRISPRi technology and the FlAsH-based screening platform, this procedure might be expanded to include a varied variety of microbial species and recombinant proteins.
Collapse
Affiliation(s)
- Xinyu Yu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Shuang Li
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Huibao Feng
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xihao Liao
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xin-Hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, China
| | - Zhonghu Bai
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiuxia Liu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China.
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
5
|
Engineering Ag43 Signal Peptides with Bacterial Display and Selection. Methods Protoc 2022; 6:mps6010001. [PMID: 36648950 PMCID: PMC9844295 DOI: 10.3390/mps6010001] [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: 11/04/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/28/2022] Open
Abstract
Protein display, secretion, and export in prokaryotes are essential for utilizing microbial systems as engineered living materials, medicines, biocatalysts, and protein factories. To select for improved signal peptides for Escherichia coli protein display, we utilized error-prone polymerase chain reaction (epPCR) coupled with single-cell sorting and microplate titer to generate, select, and detect improved Ag43 signal peptides. Through just three rounds of mutagenesis and selection using green fluorescence from the 56 kDa sfGFP-beta-lactamase, we isolated clones that modestly increased surface display from 1.4- to 3-fold as detected by the microplate plate-reader and native SDS-PAGE assays. To establish that the functional protein was displayed extracellularly, we trypsinized the bacterial cells to release the surface displayed proteins for analysis. This workflow demonstrated a fast and high-throughput method leveraging epPCR and single-cell sorting to augment bacterial surface display rapidly that could be applied to other bacterial proteins.
Collapse
|
6
|
Fu L, Sun M, Wen W, Dong N, Li D. Extracellular production of Ulp1 403-621 in leaky E. coli and its application in antimicrobial peptide production. Appl Microbiol Biotechnol 2022; 106:7805-7817. [PMID: 36260100 DOI: 10.1007/s00253-022-12235-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/02/2022]
Abstract
Small ubiquitin-like modifier (SUMO) tag is widely used to promote soluble expression of exogenous proteins, which can then be cleaved by ubiquitin-like protease 1 (Ulp1) to obtain interested protein. But the application of Ulp1 in large-scale recombinant protein production is limited by complicated purification procedures and high cost. In this study, we describe an efficient and simple method of extracellular production of Ulp1403-621 using a leaky Escherichia coli BL21(DE3), engineered by deleting the peptidoglycan-associated outer membrane lipoprotein (pal) gene. Ulp1403-621 was successfully leaked into extracellular supernatant by the BL21(DE3)-Δpal strain after IPTG induction. The addition of 1% glycine increased the extracellular production of Ulp1403-621 approximately four fold. Moreover, extracellular Ulp1403-621 without purification had high activities for cleaving SUMO fusion proteins, and antimicrobial peptide pBD2 obtained after cleavage can inhibit the growth of Staphylococcus aureus. The specific activity of extracellular Ulp1403-621 containing 1 mM EDTA and 8 mM DTT reached 2.0 × 106 U/L. Another commonly used protease, human rhinovirus 3C protease, was also successfully secreted by leaky E. coli strains. In conclusion, extracellular production of tool enzymes is an attractive way for producing large-scale active recombinant proteins at a lower cost for pharmaceutical, industrial, and biotechnological applications. KEY POINTS: • First report of extracellular production of Ulp1403-621 in leaky Escherichia coli BL21(DE3) strain. • One percent glycine addition into cultivation medium increased the extracellular production of Ulp1403-621 approximately four fold. • The specific activity of extracellular Ulp1403-621 produced in this study reached 2.0 × 106 U/L.
Collapse
Affiliation(s)
- Linglong Fu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Mengning Sun
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Weizhang Wen
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Na Dong
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
| | - Defa Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
| |
Collapse
|
7
|
Development of a novel platform for recombinant protein production in Corynebacterium glutamicum on ethanol. Synth Syst Biotechnol 2022; 7:765-774. [PMID: 35387228 PMCID: PMC8942793 DOI: 10.1016/j.synbio.2022.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 03/04/2022] [Accepted: 03/15/2022] [Indexed: 02/03/2023] Open
Abstract
Corynebacterium glutamicum represents an emerging recombinant protein expression factory due to its ideal features for protein secretion, but its applicability is harmed by the lack of an autoinduction system with tight regulation and high yield. Here, we propose a new recombinant protein manufacturing platform that leverages ethanol as both a delayed carbon source and an inducer. First, we reanalysed the native inducible promoter PICL from the acetate uptake operon and found that its limited capacity is the result of the inadequate translation initial architecture. The two strategies of bicistronic design and ribozyme-based insulator can ensure the high activity of this promoter. Next, through transcriptional engineering that alters transcription factor binding sites (TFBSs) and the first transcribed sequence, the truncated promoter PA256 with a dramatically higher transcription level was generated. When producing the superfolder green fluorescent protein (sfGFP) under 1% ethanol conditions, PA256 exhibited substantially lower protein accumulation in prophase but an approximately 2.5-fold greater final yield than the strong promoter PH36. This superior expression mode was further validated using two secreted proteins, camelid antibody fragment (VHH) and endoxylanase (XynA). Furthermore, utilizing CRISPRi technology, ethanol utilization blocking strains were created, and PA256 was shown to be impaired in the phosphotransacetylase (PTA) knockdown strains, indicating that ethanol metabolism into the tricarboxylic acid cycle is required for PA256 upregulation. Finally, this platform was applied to produce the “de novo design” protein NEO-2/15, and by introducing the N-propeptide of CspB, NEO-2/15 was effectively secreted with the accumulation 281 mg/L obtained after 24 h of shake-flask fermentation. To the best of our knowledge, this is the first report of NEO-2/15 secretory overexpression.
Collapse
|
8
|
Pomorski A, Krężel A. Biarsenical fluorescent probes for multifunctional site-specific modification of proteins applicable in life sciences: an overview and future outlook. Metallomics 2021; 12:1179-1207. [PMID: 32658234 DOI: 10.1039/d0mt00093k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Fluorescent modification of proteins of interest (POI) in living cells is desired to study their behaviour and functions in their natural environment. In a perfect setting it should be easy to perform, inexpensive, efficient and site-selective. Although multiple chemical and biological methods have been developed, only a few of them are applicable for cellular studies thanks to their appropriate physical, chemical and biological characteristics. One such successful system is a tetracysteine tag/motif and its selective biarsenical binders (e.g. FlAsH and ReAsH). Since its discovery in 1998 by Tsien and co-workers, this method has been enhanced and revolutionized in terms of its efficiency, formed complex stability and breadth of application. Here, we overview the whole field of knowledge, while placing most emphasis on recent reports. We showcase the improvements of classical biarsenical probes with various optical properties as well as multifunctional molecules that add new characteristics to proteins. We also present the evolution of affinity tags and motifs of biarsenical probes demonstrating much more possibilities in cellular applications. We summarize protocols and reported observations so both beginners and advanced users of biarsenical probes can troubleshoot their experiments. We address the concerns regarding the safety of biarsenical probe application. We showcase examples in virology, studies on receptors or amyloid aggregation, where application of biarsenical probes allowed observations that previously were not possible. We provide a summary of current applications ranging from bioanalytical sciences to allosteric control of selected proteins. Finally, we present an outlook to encourage more researchers to use these magnificent probes.
Collapse
Affiliation(s)
- Adam Pomorski
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
| | | |
Collapse
|
9
|
Trehalose Degradation by Cellvibrio japonicus Exhibits No Functional Redundancy and Is Solely Dependent on the Tre37A Enzyme. Appl Environ Microbiol 2020; 86:AEM.01639-20. [PMID: 32917758 DOI: 10.1128/aem.01639-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
The α-diglucoside trehalose has historically been known as a component of the bacterial stress response, though it more recently has been studied for its relevance in human gut health and biotechnology development. The utilization of trehalose as a nutrient source by bacteria relies on carbohydrate-active enzymes, specifically those of the glycoside hydrolase family 37 (GH37), to degrade the disaccharide into substituent glucose moieties for entry into metabolism. Environmental bacteria using oligosaccharides for nutrients often possess multiple carbohydrate-active enzymes predicted to have the same biochemical activity and therefore are thought to be functionally redundant. In this study, we characterized trehalose degradation by the biotechnologically important saprophytic bacterium Cellvibrio japonicus This bacterium possesses two predicted α-α-trehalase genes, tre37A and tre37B, and our investigation using mutational analysis found that only the former is essential for trehalose utilization by C. japonicus Heterologous expression experiments found that only the expression of the C. japonicus tre37A gene in an Escherichia coli treA mutant strain allowed for full utilization of trehalose. Biochemical characterization of C. japonicus GH37 activity determined that the tre37A gene product is solely responsible for cleaving trehalose and is an acidic α-α-trehalase. Bioinformatic and mutational analyses indicate that Tre37A directly cleaves trehalose to glucose in the periplasm, as C. japonicus does not possess a phosphotransferase system. This study facilitates the development of a comprehensive metabolic model for α-linked disaccharides in C. japonicus and more broadly expands our understanding of the strategies that saprophytic bacteria employ to capture diverse carbohydrates from the environment.IMPORTANCE The metabolism of trehalose is becoming increasingly important due to the inclusion of this α-diglucoside in a number of foods and its prevalence in the environment. Bacteria able to utilize trehalose in the human gut possess a competitive advantage, as do saprophytic microbes in terrestrial environments. While the biochemical mechanism of trehalose degradation is well understood, what is less clear is how bacteria acquire this metabolite from the environment. The significance of this report is that by using the model saprophyte Cellvibrio japonicus, we were able to functionally characterize the two predicted trehalase enzymes that the bacterium possesses and determined that the two enzymes are not equivalent and are not functionally redundant. The results and approaches used to understand the complex physiology of α-diglucoside metabolism from this study can be applied broadly to other polysaccharide-degrading bacteria.
Collapse
|
10
|
Burdette LA, Leach SA, Wong HT, Tullman-Ercek D. Developing Gram-negative bacteria for the secretion of heterologous proteins. Microb Cell Fact 2018; 17:196. [PMID: 30572895 PMCID: PMC6302416 DOI: 10.1186/s12934-018-1041-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/08/2018] [Indexed: 11/10/2022] Open
Abstract
Gram-negative bacteria are attractive hosts for recombinant protein production because they are fast growing, easy to manipulate, and genetically stable in large cultures. However, the utility of these microbes would expand if they also could secrete the product at commercial scales. Secretion of biotechnologically relevant proteins into the extracellular medium increases product purity from cell culture, decreases downstream processing requirements, and reduces overall cost. Thus, researchers are devoting significant attention to engineering Gram-negative bacteria to secrete recombinant proteins to the extracellular medium. Secretion from these bacteria operates through highly specialized systems, which are able to translocate proteins from the cytosol to the extracellular medium in either one or two steps. Building on past successes, researchers continue to increase the secretion efficiency and titer through these systems in an effort to make them viable for industrial production. Efforts include modifying the secretion tags required for recombinant protein secretion, developing methods to screen or select rapidly for clones with higher titer or efficiency, and improving reliability and robustness of high titer secretion through genetic manipulations. An additional focus is the expression of secretion machineries from pathogenic bacteria in the "workhorse" of biotechnology, Escherichia coli, to reduce handling of pathogenic strains. This review will cover recent advances toward the development of high-expressing, high-secreting Gram-negative production strains.
Collapse
Affiliation(s)
- Lisa Ann Burdette
- Department of Chemical and Biomolecular Engineering, University of California-Berkeley, Berkeley, USA
- Present Address: Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208 USA
| | - Samuel Alexander Leach
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, USA
| | - Han Teng Wong
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, USA
- Present Address: Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208 USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, USA
| |
Collapse
|
11
|
Linkage-Specific Detection and Metabolism of Human Milk Oligosaccharides in Escherichia coli. Cell Chem Biol 2018; 25:1292-1303.e4. [PMID: 30017916 DOI: 10.1016/j.chembiol.2018.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 03/10/2018] [Accepted: 06/01/2018] [Indexed: 01/05/2023]
Abstract
Human milk oligosaccharides (HMOs) are important prebiotic complex carbohydrates with demonstrated beneficial effects on the microbiota of neonates. However, optimization of their biotechnological synthesis is limited by the relatively low throughput of monosaccharide and linkage analysis. To enable high-throughput screening of HMO structures, we constructed a whole-cell biosensor that uses heterologous expression of glycosidases to generate linkage-specific, quantitative fluorescent readout for a range of HMOs at detection limits down to 20 μM in approximately 6 hr. We also demonstrate the use of this system for orthogonal control of growth rate or protein expression of particular strains in mixed populations. This work enables rapid non-chromatographic linkage analysis and lays the groundwork for the application of directed evolution to biosynthesis of complex carbohydrates as well as the prebiotic manipulation of population dynamics in natural and engineered microbial communities.
Collapse
|
12
|
Gao W, Yin J, Bao L, Wang Q, Hou S, Yue Y, Yao W, Gao X. Engineering Extracellular Expression Systems in Escherichia coli Based on Transcriptome Analysis and Cell Growth State. ACS Synth Biol 2018; 7:1291-1302. [PMID: 29668266 DOI: 10.1021/acssynbio.7b00400] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Escherichia coli extracellular expression systems have a number of advantages over other systems, such as lower pyrogen levels and a simple purification process. Various approaches, such as the generation of leaky mutants via chromosomal engineering, have been explored for this expression system. However, extracellular protein yields in leaky mutants are relatively low compared to that in intracellular expression systems and therefore need to be improved. In this work, we describe the construction, characterization, and mechanism of enhanced extracellular expression in Escherichia coli. On the basis of the localizations, functions, and transcription levels of cell envelope proteins, we systematically elucidated the effects of multiple gene deletions on cell growth and extracellular expression using modified CRISPR/Cas9-based genome editing and a FlAsH labeling assay. High extracellular yields of heterologous proteins of different sizes were obtained by screening multiple gene mutations. The enhancement of extracellular secretion was associated with the derepression of translation and translocation. This work utilized universal methods in the design of extracellular expression systems for genes not directly associated with protein synthesis that were used to generate strains with higher protein expression capability. We anticipate that extracellular expression systems may help to shed light on the poorly understood aspects of these secretion processes as well as to further assist in the construction of engineered prokaryotic cells for efficient extracellular production of heterologous proteins.
Collapse
Affiliation(s)
- Wen Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Jun Yin
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Lichen Bao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Qun Wang
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Shan Hou
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Yali Yue
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Wenbing Yao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Xiangdong Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| |
Collapse
|
13
|
Natarajan A, Haitjema CH, Lee R, Boock JT, DeLisa MP. An Engineered Survival-Selection Assay for Extracellular Protein Expression Uncovers Hypersecretory Phenotypes in Escherichia coli. ACS Synth Biol 2017; 6:875-883. [PMID: 28182400 DOI: 10.1021/acssynbio.6b00366] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The extracellular expression of recombinant proteins using laboratory strains of Escherichia coli is now routinely achieved using naturally secreted substrates, such as YebF or the osmotically inducible protein Y (OsmY), as carrier molecules. However, secretion efficiency through these pathways needs to be improved for most synthetic biology and metabolic engineering applications. To address this challenge, we developed a generalizable survival-based selection strategy that effectively couples extracellular protein secretion to antibiotic resistance and enables facile isolation of rare mutants from very large populations (i.e., 1010-12 clones) based simply on cell growth. Using this strategy in the context of the YebF pathway, a comprehensive library of E. coli single-gene knockout mutants was screened and several gain-of-function mutations were isolated that increased the efficiency of extracellular expression without compromising the integrity of the outer membrane. We anticipate that this user-friendly strategy could be leveraged to better understand the YebF pathway and other secretory mechanisms-enabling the exploration of protein secretion in pathogenesis as well as the creation of designer E. coli strains with greatly expanded secretomes-all without the need for expensive exogenous reagents, assay instruments, or robotic automation.
Collapse
Affiliation(s)
- Aravind Natarajan
- Department
of Microbiology, Cornell University, Ithaca, New York 14853, United States
| | - Charles H. Haitjema
- Department
of Microbiology, Cornell University, Ithaca, New York 14853, United States
| | - Robert Lee
- School
of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Jason T. Boock
- School
of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Matthew P. DeLisa
- Department
of Microbiology, Cornell University, Ithaca, New York 14853, United States
- School
of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| |
Collapse
|
14
|
Schlegel S, Genevaux P, de Gier JW. Isolating Escherichia coli strains for recombinant protein production. Cell Mol Life Sci 2016; 74:891-908. [PMID: 27730255 PMCID: PMC5306230 DOI: 10.1007/s00018-016-2371-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/22/2016] [Accepted: 09/16/2016] [Indexed: 12/14/2022]
Abstract
Escherichia coli has been widely used for the production of recombinant proteins. To improve protein production yields in E. coli, directed engineering approaches have been commonly used. However, there are only few reported examples of the isolation of E. coli protein production strains using evolutionary approaches. Here, we first give an introduction to bacterial evolution and mutagenesis to set the stage for discussing how so far selection- and screening-based approaches have been used to isolate E. coli protein production strains. Finally, we discuss how evolutionary approaches may be used in the future to isolate E. coli strains with improved protein production characteristics.
Collapse
Affiliation(s)
- Susan Schlegel
- Department of Environmental Systems Science, ETH Zürich, 8092, Zürich, Switzerland
| | - Pierre Genevaux
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrheniusväg 16C, 106 91, Stockholm, Sweden.
| |
Collapse
|
15
|
Ollis AA, Chai Y, DeLisa MP. GlycoSNAP: A High-Throughput Screening Methodology for Engineering Designer Glycosylation Enzymes. Methods Mol Biol 2016; 1321:37-47. [PMID: 26082213 DOI: 10.1007/978-1-4939-2760-9_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The Campylobacter jejuni protein glycosylation locus (pgl) encodes enzymes for asparagine-linked (N-linked) glycosylation and serves as the prototype for N-glycosylation in bacteria. This pathway has been functionally transferred into Escherichia coli, thereby enabling efficient N-linked glycosylation of acceptor proteins with the C. jejuni heptasaccharide in this genetically tractable host. However, expansion of this bacterial system to encompass the vast biological diversity of potential glycans and target proteins often requires engineering of the non-native enzymes to isolate variants with optimal or altered functions. Here, we describe a genetic assay named glycoSNAP (glycosylation of secreted N-linked acceptor proteins) that facilitates engineering of glycosylation enzymes directly in E. coli. To date, this method has been successfully applied to screen (1) combinatorial libraries of bacterial oligosaccharyltransferases (OSTs) for relaxed substrate specificity and (2) acceptor site libraries to identify sequons recognized by natural OSTs as well as engineered variants.
Collapse
Affiliation(s)
- Anne A Ollis
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | | | | |
Collapse
|
16
|
Beyond the cytoplasm of Escherichia coli: localizing recombinant proteins where you want them. Methods Mol Biol 2015; 1258:79-97. [PMID: 25447860 DOI: 10.1007/978-1-4939-2205-5_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
Abstract
Recombinant protein expression in Escherichia coli represents a cornerstone of the biotechnology enterprise. While cytoplasmic expression in this host has received the most attention, achieving substantial yields of correctly folded proteins in this compartment can sometimes be met with difficulties. These issues can often be overcome by targeting protein expression to extracytoplasmic compartments (e.g., membrane, periplasm) or to the culture medium. This chapter discusses various strategies for exporting proteins out of the cytoplasm as well as tools for monitoring and optimizing these different export mechanisms.
Collapse
|
17
|
Yim SS, Bang HB, Kim YH, Lee YJ, Jeong GM, Jeong KJ. Rapid isolation of antibody from a synthetic human antibody library by repeated fluorescence-activated cell sorting (FACS). PLoS One 2014; 9:e108225. [PMID: 25303314 PMCID: PMC4193741 DOI: 10.1371/journal.pone.0108225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 08/27/2014] [Indexed: 11/19/2022] Open
Abstract
Antibodies and their derivatives are the most important agents in therapeutics and diagnostics. Even after the significant progress in the technology for antibody screening from huge libraries, it takes a long time to isolate an antibody, which prevents a prompt action against the spread of a disease. Here, we report a new strategy for isolating desired antibodies from a combinatorial library in one day by repeated fluorescence-activated cell sorting (FACS). First, we constructed a library of synthetic human antibody in which single-chain variable fragment (scFv) was expressed in the periplasm of Escherichia coli. After labeling the cells with fluorescent antigen probes, the highly fluorescent cells were sorted by using a high-speed cell sorter, and these cells were reused without regeneration in the next round of sorting. After repeating this sorting, the positive clones were completely enriched in several hours. Thus, we screened the library against three viral antigens, including the H1N1 influenza virus, Hepatitis B virus, and Foot-and-mouth disease virus. Finally, the potential antibody candidates, which show KD values between 10 and 100 nM against the target antigens, could be successfully isolated even though the library was relatively small (∼106). These results show that repeated FACS screening without regeneration of the sorted cells can be a powerful method when a rapid response to a spreading disease is required.
Collapse
Affiliation(s)
- Sung Sun Yim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) (BK21 plus program), Daejeon, Republic of Korea
| | - Hyun Bae Bang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) (BK21 plus program), Daejeon, Republic of Korea
| | - Young Hwan Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) (BK21 plus program), Daejeon, Republic of Korea
| | - Yong Jae Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) (BK21 plus program), Daejeon, Republic of Korea
| | - Gu Min Jeong
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) (BK21 plus program), Daejeon, Republic of Korea
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) (BK21 plus program), Daejeon, Republic of Korea
- Institute for the BioCentury, KAIST, Daejeon, Republic of Korea
- * E-mail:
| |
Collapse
|
18
|
Ollis AA, Zhang S, Fisher AC, DeLisa MP. Engineered oligosaccharyltransferases with greatly relaxed acceptor-site specificity. Nat Chem Biol 2014; 10:816-22. [PMID: 25129029 DOI: 10.1038/nchembio.1609] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/12/2014] [Indexed: 01/23/2023]
Abstract
The Campylobacter jejuni protein glycosylation locus (pgl) encodes machinery for asparagine-linked (N-linked) glycosylation and serves as the archetype for bacterial N-linked glycosylation. This machinery has been functionally transferred into Escherichia coli, enabling convenient mechanistic dissection of the N-linked glycosylation process in this genetically tractable host. Here we sought to identify sequence determinants in the oligosaccharyltransferase PglB that restrict its specificity to only those glycan acceptor sites containing a negatively charged residue at the -2 position relative to asparagine. This involved creation of a genetic assay, glycosylation of secreted N-linked acceptor proteins (glycoSNAP), that facilitates high-throughput screening of glycophenotypes in E. coli. Using this assay, we isolated several C. jejuni PglB variants that could glycosylate an array of noncanonical acceptor sequences, including one in a eukaryotic N-glycoprotein. These results underscore the utility of glycoSNAP for shedding light on poorly understood aspects of N-linked glycosylation and for engineering designer N-linked glycosylation biocatalysts.
Collapse
Affiliation(s)
- Anne A Ollis
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA
| | - Sheng Zhang
- Proteomics and Mass Spectrometry Core Facility, Cornell University, Ithaca, New York, USA
| | | | - Matthew P DeLisa
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA
| |
Collapse
|