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Lin Q, Jiang Z, Zhong B, Chen JQ, Lv ZB, Nie ZM. Unveiling the impact of cryptic plasmids curing on Escherichia coli Nissle 1917: massive increase in Ag43c expression. AMB Express 2024; 14:48. [PMID: 38678482 PMCID: PMC11056357 DOI: 10.1186/s13568-024-01681-9] [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: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 05/01/2024] Open
Abstract
Escherichia coli Nissle 1917 (EcN) is an important chassis strain widely used for the development of live biotherapeutic products (LBPs). EcN strain naturally harbors two cryptic plasmids with unknown function. During the development of LBPs using EcN strain, the cryptic plasmids were cured usually to avoid plasmid incompatibility or alleviate metabolic burdens associated with these cryptic plasmids. While the cryptic plasmids curing in EcN may appear to be a routine procedure, the comprehensive impact of cryptic plasmids curing on the EcN strain remains incompletely understood. In the present study, the effects of cryptic plasmids curing on EcN were investigated using transcriptome sequencing. The results revealed that only a small number of genes showed significant changes in mRNA levels after cryptic plasmid curing (4 upregulated and 6 downregulated genes), primarily involved in amino acid metabolism. Furthermore, the flu gene showed the most significant different expression, encoding Antigen 43 (Ag43) protein, a Cah family adhesin. Mass spectrometry analysis further confirmed the significant increase in Ag43 expression. Ag43 is commonly present in Escherichia coli and mediates the bacterial autoaggregation. However, despite the upregulation of Ag43 expression, no Ag43-mediated cell self-sedimentation was observed in the cured EcN strain. These findings contribute to making informed decisions regarding the curing of the cryptic plasmids when Escherichia coli Nissle 1917 is used as the chassis strain.
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Affiliation(s)
- Qi Lin
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
- Center for Bioreactor and Protein Drug Research, Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd, Shaoxing, 312075, China
| | - Zhuo Jiang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Bo Zhong
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jian-Qing Chen
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
- Center for Bioreactor and Protein Drug Research, Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd, Shaoxing, 312075, China
| | - Zheng-Bing Lv
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
- Center for Bioreactor and Protein Drug Research, Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd, Shaoxing, 312075, China
| | - Zuo-Ming Nie
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
- Center for Bioreactor and Protein Drug Research, Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd, Shaoxing, 312075, China.
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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.
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Yang SC, Ting WW, Ng IS. Effective whole cell biotransformation of arginine to a four-carbon diamine putrescine using engineered Escherichia coli. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Lopes AMM, Martins M, Goldbeck R. Heterologous Expression of Lignocellulose-Modifying Enzymes in Microorganisms: Current Status. Mol Biotechnol 2021; 63:184-199. [PMID: 33484441 DOI: 10.1007/s12033-020-00288-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2020] [Indexed: 02/06/2023]
Abstract
Heterologous expression of the carbohydrate-active enzymes in microorganisms is a promising approach to produce bio-based compounds, such as fuels, nutraceuticals and other value-added products from sustainable lignocellulosic sources. Several microorganisms, including Saccharomyces cerevisiae, Escherichia coli, and the filamentous fungi Aspergillus nidulans, have unique characteristics desirable for a biorefinery production approach like well-known genetic tools, thermotolerance, high fermentative capacity and product tolerance, and high amount of recombinant enzyme secretion. These microbial factories are already stablished in the heterologous production of the carbohydrate-active enzymes to produce, among others, ethanol, xylooligosaccharides and the valuable coniferol. A complete biocatalyst able to heterologous express the CAZymes of glycoside hydrolases, carbohydrate esterases and auxiliary activities families could release these compounds faster, with higher yield and specificity. Recent advances in the synthetic biology tools could expand the number and diversity of enzymes integrated in these microorganisms, and also modify those already integrated. This review outlines the heterologous expression of carbohydrate-active enzymes in microorganisms, as well as recent updates in synthetic biology.
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Affiliation(s)
- Alberto Moura Mendes Lopes
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Rua Monteiro Lobato no 80, Cidade Universitária, Campinas, São Paulo, 13083-862, Brazil
| | - Manoela Martins
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Rua Monteiro Lobato no 80, Cidade Universitária, Campinas, São Paulo, 13083-862, Brazil
| | - Rosana Goldbeck
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Rua Monteiro Lobato no 80, Cidade Universitária, Campinas, São Paulo, 13083-862, Brazil.
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Dvořák P, Bayer EA, de Lorenzo V. Surface Display of Designer Protein Scaffolds on Genome-Reduced Strains of Pseudomonas putida. ACS Synth Biol 2020; 9:2749-2764. [PMID: 32877604 DOI: 10.1021/acssynbio.0c00276] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The bacterium Pseudomonas putida KT2440 is gaining considerable interest as a microbial platform for biotechnological valorization of polymeric organic materials, such as lignocellulosic residues or plastics. However, P. putida on its own cannot make much use of such complex substrates, mainly because it lacks an efficient extracellular depolymerizing apparatus. We seek to address this limitation by adopting a recombinant cellulosome strategy for this host. In this work, we report an essential step in this endeavor-a display of designer enzyme-anchoring protein "scaffoldins", encompassing cohesin binding domains from divergent cellulolytic bacterial species on the P. putida surface. Two P. putida chassis strains, EM42 and EM371, with streamlined genomes and differences in the composition of the outer membrane were employed in this study. Scaffoldin variants were optimally delivered to their surface with one of four tested autotransporter systems (Ag43 from Escherichia coli), and the efficient display was confirmed by extracellular attachment of chimeric β-glucosidase and fluorescent proteins. Our results not only highlight the value of cell surface engineering for presentation of recombinant proteins on the envelope of Gram-negative bacteria but also pave the way toward designer cellulosome strategies tailored for P. putida.
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Affiliation(s)
- Pavel Dvořák
- Department of Experimental Biology (Section of Microbiology), Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología CNB-CSIC, Cantoblanco, Darwin 3, 28049 Madrid, Spain
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Jing K, Guo Y, Ng IS. Antigen-43-mediated surface display revealed in Escherichia coli by different fusion sites and proteins. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0248-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Surface Display of Small Affinity Proteins on Synechocystis sp. Strain PCC 6803 Mediated by Fusion to the Major Type IV Pilin PilA1. J Bacteriol 2018; 200:JB.00270-18. [PMID: 29844032 DOI: 10.1128/jb.00270-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 05/22/2018] [Indexed: 11/20/2022] Open
Abstract
Functional surface display of small affinity proteins, namely, affibodies (6.5 kDa), was evaluated for the model cyanobacterium Synechocystis sp. strain PCC 6803 through anchoring to native surface structures. These structures included confirmed or putative subunits of the type IV pili, the S-layer protein, and the heterologous Escherichia coli autotransporter antigen 43 system. The most stable display system was determined to be through C-terminal fusion to PilA1, the major type IV pilus subunit in Synechocystis, in a strain unable to retract these pili (ΔpilT1). Type IV pilus synthesis was upheld, albeit reduced, when fusion proteins were incorporated. However, pilus-mediated functions, such as motility and transformational competency, were negatively affected. Display of affibodies on Synechocystis and the complementary anti-idiotypic affibodies on E. coli or Staphylococcus carnosus was able to mediate interspecies cell-cell binding by affibody complex formation. The same strategy, however, was not able to drive cell-cell binding and aggregation of Synechocystis-only mixtures. Successful affibody tagging of the putative minor pilin PilA4 showed that it locates to the type IV pili in Synechocystis and that its extracellular availability depends on PilA1. In addition, affibody tagging of the S-layer protein indicated that the domains responsible for the anchoring and secretion of this protein are located at the N and C termini, respectively. This study can serve as a basis for future surface display of proteins on Synechocystis for biotechnological applications.IMPORTANCE Cyanobacteria are gaining interest for their potential as autotrophic cell factories. Development of efficient surface display strategies could improve their suitability for large-scale applications by providing options for designed microbial consortia, cell immobilization, and biomass harvesting. Here, surface display of small affinity proteins was realized by fusing them to the major subunit of the native type IV pili in Synechocystis sp. strain PCC 6803. The display of complementary affinity proteins allowed specific cell-cell binding between Synechocystis and Escherichia coli or Staphylococcus carnosus Additionally, successful tagging of the putative pilin PilA4 helped determine its localization to the type IV pili. Analogous tagging of the S-layer protein shed light on the regions involved in its secretion and surface anchoring.
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Refactoring the upper sugar metabolism of Pseudomonas putida for co-utilization of cellobiose, xylose, and glucose. Metab Eng 2018; 48:94-108. [DOI: 10.1016/j.ymben.2018.05.019] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/15/2018] [Accepted: 05/31/2018] [Indexed: 01/02/2023]
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Yan X, Zhu L, Yu Y, Xu Q, Huang H, Jiang L. In-Situ Biocatalytic Production of Trehalose with Autoinduction Expression of Trehalose Synthase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:1444-1451. [PMID: 29338242 DOI: 10.1021/acs.jafc.7b06031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We developed an in-situ biocatalytic process that couples autoinduction expression of trehalose synthase (TreS) and whole-cell catalysis for trehalose production. With lactose as the autoinducer, the activity of recombinant TreS in recombinant Escherichia coli was optimized through a visualization method, which resulted in a maximum value of 12 033 ± 730 U/mL in pH-stat fed-batch fermentation mode. Meanwhile, the permeability of the autoinduced E. coli increased significantly, which makes it possible to be directly used as a whole-cell biocatalyst for trehalose production, whereby the byproduct glucose can also act as an extra carbon source. In this case, the final yield of trehalose was improved to 90.5 ± 5.7% and remained as high as 83.2 ± 5.0% at the 10th batch, which is the highest value achieved using recombinant TreS. Finally, an integrated strategy for trehalose production was established, and its advantages compared to the traditional mode have been summarized.
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Affiliation(s)
- Xincheng Yan
- College of Food Science and Light Industry, ‡College of Biotechnology and Pharmaceutical Engineering, §College of Chemical and Molecular Engineering, and ⊥College of Pharmaceutical Sciences, Nanjing Tech University , Nanjing 210009, China
| | - Liying Zhu
- College of Food Science and Light Industry, ‡College of Biotechnology and Pharmaceutical Engineering, §College of Chemical and Molecular Engineering, and ⊥College of Pharmaceutical Sciences, Nanjing Tech University , Nanjing 210009, China
| | - Yadong Yu
- College of Food Science and Light Industry, ‡College of Biotechnology and Pharmaceutical Engineering, §College of Chemical and Molecular Engineering, and ⊥College of Pharmaceutical Sciences, Nanjing Tech University , Nanjing 210009, China
| | - Qing Xu
- College of Food Science and Light Industry, ‡College of Biotechnology and Pharmaceutical Engineering, §College of Chemical and Molecular Engineering, and ⊥College of Pharmaceutical Sciences, Nanjing Tech University , Nanjing 210009, China
| | - He Huang
- College of Food Science and Light Industry, ‡College of Biotechnology and Pharmaceutical Engineering, §College of Chemical and Molecular Engineering, and ⊥College of Pharmaceutical Sciences, Nanjing Tech University , Nanjing 210009, China
| | - Ling Jiang
- College of Food Science and Light Industry, ‡College of Biotechnology and Pharmaceutical Engineering, §College of Chemical and Molecular Engineering, and ⊥College of Pharmaceutical Sciences, Nanjing Tech University , Nanjing 210009, China
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Solution for promoting egl 3 gene of Trichoderma reesei high-efficiency secretory expression in Escherichia coli and Lactococcus lactis. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.07.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Loaces I, Bottini G, Moyna G, Fabiano E, Martínez A, Noya F. EndoG: A novel multifunctional halotolerant glucanase and xylanase isolated from cow rumen. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Loaces I, Amarelle V, Muñoz-Gutierrez I, Fabiano E, Martinez A, Noya F. Improved ethanol production from biomass by a rumen metagenomic DNA fragment expressed in Escherichia coli MS04 during fermentation. Appl Microbiol Biotechnol 2015; 99:9049-60. [DOI: 10.1007/s00253-015-6801-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 06/21/2015] [Accepted: 06/24/2015] [Indexed: 10/23/2022]
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